Pablo's Origins Blog

DNA

2010-02-27T06:03:00.000-08:00

Let’s talk about DNA. The genetic code is the blueprint used to build our bodies and that of every living being. At the very beginning of the 20th century, it was already known to scientist that the code was in genes, which in turn resided in chromosomes. In this series of articles I want to get through the incredible history and see how this most interesting of molecules works.

Discovering the Genetic Code: We today know that chromosomes are made of DNA, but how that became a known fact? We must begin by going back to the earlier part of the 20th century, to the work of an English physician named Frederick Griffith. This experiment that I am about to describe really provided the first insight into the chemical nature of genetic information.
Proteins Vs. DNA: In the early part of the 20th century, when Griffith published his work, there was generally an assumption that the genetic material must be a protein. Why did they think that? They thought it because pretty much everything that happens in the cell is done by a protein. It makes sense that if you got something complex and important that is being done in the cell, like providing information, it is probably going to be a protein.
The Code is in DNA: In the early 1950’s, Hershey and Chase took a novel approach in trying to found out what the genetic material might be made of, by looking at how a particular kind of virus worked.

How it Works

The Building Blocks: The building blocks of nucleic acids are called nucleotides. There are only four types of nucleotides. This is one of the reasons why nucleic acids seem relatively simple compared to proteins. Each nucleotide has a sugar that forms a ring.
The DNA Structure: After the work of Hershey and Chase, biologists in the early 1950’s became convinced that DNA was what they needed to look at to understand the genetic code. They actually had no idea how DNA could possibly act as a mechanism for genetic inheritance.
Watson and Crick’s Double Helix: James Watson was a young American, who had just completed his PhD. He was interested in protein structure. He moved to Cambridge, England, and began working with Francis Crick, who was a physicist familiar with x-ray crystallography and how to interpret it. The story goes that Watson happened to visit London for a seminar, and saw the x-ray diffraction patterns that Rosalind Franklin had obtained from Maurice Wilkins’ purified DNA. Watson made some notes, rushed back to Cambridge and told Crick what he had seen.

Understanding Replication

Theories of Replication: The first alternative suggested that the DNA double helix must remain completely intact when it is replicated. That is, the two strands do not separate. The entire molecule is somehow used as a template for making more DNA. A second alternative suggested that the original DNA molecule becomes completely broken down during replication, with the newly copied DNA assembled by some unknown mechanism. In other words, the DNA double helix would actually be irrelevant. The mechanism that Watson and Crick proposed became known as the semi-conservative model of DNA replication. This was called semi-conservative because it predicts that during replication, the double helix unzips and the new daughter helixes would both have one strand of the old helix.
Watson and Crick had it right: Watson and Crick’s semi-conservative model contrasted with a couple of other possibilities for how DNA could possibly replicate. There is the conservative model, which suggests that both strands in the original DNA double helix stay together during replication. Then there is the dispersive model, which suggests that both strands are not only separated, but even broken up into smaller pieces during replication. Deciding which of these models was the correct one seemed to be pretty easy, because they make very different predictions. It was not obvious how to prove it in the laboratory, however.
The Process of Replication: In 1957, Arthur Kornberg made a really interesting discovery. He showed that DNA can be replicated outside of a cell, in a laboratory test tube. Kornberg wasn’t much interested in which model of replication was right. Instead, he was interested in specifically how replication occurred. Watson and Crick had suggested that the replication of DNA may not actually require an enzyme. If you could somehow unzip DNA, they thought that new DNA might just self-assemble, because the complimentary base-pairing would bring in all the appropriate nucleotides. Kornberg thought, though, that there must be some enzyme involved. He set out to figure out what that enzyme was.

Fossils

2010-02-26T05:24:00.000-08:00

Ancient microbial fossils are exceptionally rare. Those fragile fragmentary clues may help us bridge the vast gulf between life and non-life. Ancient rocks may reveal key steps in the origin of life. It is true that they are difficult to find, but it’s well worth the effort, because Earth’s earliest fossils provide us with unique information about life’s beginnings. For one thing they provide evidence regarding the size and shape of ancient life. In addition, they reveal a lot about the timing of life’s origin.

In thinking about life’s origins is critical to know roughly when it happened, and how quickly. After all, if life arose relatively quickly, then the process may be relatively easy. A fast emergence of life supports the idea that life is common in the universe. Our best guesses about the timing of life’s origin is in the form of a bracket in time. Fossil evidence suggests that 3.5 billion years ago life had established a firm foothold on Earth. Some geologists claim that Earth was a living planet perhaps 3.85 billion years ago. We don’t know exactly when life arose. In any case, life’s emergence was rapid, at least on a geological time scale.

Paleontologists devote their lives to looking for fragmentary signs of life in rocks. Paleontologists, perhaps more than scientists in any other discipline, can generate attention and appear on headlines. The media loves to relate stories about discoveries in ancient rocks. We’ve read stories about the discovery of history’s biggest sharp, or the most massive dinosaur, or the oldest human skull. These stories inspire the public imagination.

Famous paleontologist William Schopf announced in 1993 the discovery of Earth’s oldest fossils. Schopf claimed to have identified actual single cells of several different species. These cells may have been preserved for 3.4 billion years in rocks from Western Australia. What’s even more surprising is that these cells occurred in filament-like chains strongly reminiscent of those formed by modern microbes that are photosynthetic. These modern photosynthetic cells have the advanced chemical capability to harvest sunlight. Schopf hinted that these species might have also been chemically advanced.

For one thing, this 1993 discovery wasn’t really all that new. Ancient microbes in rocks from the same region of Australia and of similar age have been known since the late 1970’s. What’s more, Schopf had published a report on these several years earlier. It’s not at all clear why the 1993 paper attracted so much publicity compared to the earlier papers.

I should also state that many scientists think that the study of these ancient rocks tell us absolutely nothing about the origins of life. According to these scientists, these remains represent organisms that were already so advanced, that we can’t deduce anything about the transition from non-life to life.

Schopf’s claim was extraordinary, and scientists consequently demanded extraordinary evidence. In this case, however, the geological community was ready to accept Schopf’s claim. He had spent decades establishing a reputation as one of the world’s leading experts in finding and describing ancient fossils.

What Schopf’s new finding in Australia surely accomplished was to push back the record for the world’s oldest life by a few hundred million years. These ancient rocks reveal a host of tiny spheres, discs, rods and chains that appear to be just like modern bacteria. The discovery of unambiguous microfossils in several ancient rocks led to the first prominent publication on these supposed microbes, and they are now found on most biology textbooks.

Evidences of Life on Mars - Part 2

2010-02-25T05:36:00.000-08:00

So, what was the basis of McKay’s claim? Did they find convincing evidences of life on Mars? In their Science paper, McKay and his eight coworkers pointed to four types of data. Given their extraordinary claims, they were on scientific trial by the rest of the scientific community. Let’s go to the points they made:

1. The meteorite was found to contain organic molecules, including carbon-based compounds called polycyclic aromatic hydrocarbons (PAH). PAH’s commonly form when once living cells are subjected to high temperature. They are not proof of life by any means, but carbon is the key element of life as we know it. The presence of PAH’s distinguished this meteorite from the other Martian meteorites and had an extraordinary significance.

2. The meteorite had microscopic globules of carbonate minerals, similar to those found on walls of caves on Earth. Such carbonates are often deposited through the action of liquid water. Liquid water is the medium for all cells and a necessary condition for life as we know it.

3. The NASA team used an electron microscope to discover and characterize two iron-bearing minerals. Of particular interest were the chains of crystals. The perfect shape of these alien crystals and their unusual chemical purity seemed unlike anything ever seen, except in a few remarkable types of bacteria. They claimed that no known inorganic process could have produced such an ordered crystal array.

4. The meteorite holds tiny sausage shaped objects reminiscent of some species of bacteria. They’re much smaller than any Earthly microbes. These forms were found to be the most convincing evidence by the public. They actually look like fossils. Hundreds of newspapers and magazines reproduced the NASA images with the captions “Martian microbes”.

The main text of the six-page article on Science by McKay and his colleagues conveyed a sober discussion of their findings. They acknowledged that no single line of evidence was enough to trumpet the discovery of alien life. The concluding sentence shifted tone, however: “Although there are alternative explanations for each of these phenomena taken individually, when they are considered collectively in view of their special association, we conclude that they are evidence for primitive life on early Mars.”

To paraphrase the late Carl Sagan: “Extraordinary claims require extraordinary evidence.”

Controversy exploded. Experts aggressively challenged every one of the key points. Opinions ranged from cautious skepticism to outright contempt. Let’s looks at each of the NASA team’s supposed evidences of life on Mars:

Point number 1: the PAH’s. It turns out that PAH’s and other carbon molecules litter the cosmos, notably in the interstellar dust that forms comets and asteroids. These are actually the raw materials that formed Mars. Furthermore, such molecules would have been synthesized in abundance by natural chemical processes at or near the primitive surface of Mars. What’s more, PAH’s are among the most common constituents of pollution on Earth. Analyze the so-called pristine ice from Antarctica and you’ll find PAH’s. That’s why many scientists have concluded that the meteorite could have become contaminated while sitting on the ice.

Even if the PAH’s are from the Martian rock, there is no reason to conclude that these molecules represent remains of living cells.

Point 2: the carbonate globules. Mineralogists quickly pointed out that the carbonate minerals could have formed in many ways other than by circulating water. Carbonates can form in the reactions of rocks with carbon dioxide, which is the most common atmosphere gas on Mars. They can even crystallize directly by mineral processes. Indeed, a number of researches reanalyzed the minerals and found evidence that they formed at temperatures well above the boiling point of water, but that result is still a matter of debate.

Point 3: the chains of crystals. The chain-like arrays of exceptionally pure crystals are unusual indeed, but most observers feel that they are insufficient by themselves to prove the existence of Martian life.

Point 4: those fossil shapes that look like microbes. Many biologists attacked this claim because the fossils are too small, an order of magnitude smaller than any known Earthly bacteria. In fact, they are so small that they can contain no more than a few hundred biomolecules. That’s not nearly enough to support the chemical complexity of any known living cell. There is no reason to characterize these elongated shapes are fossils, since inorganic processes are known to produce similar structures.

The evidences of life on Mars became even less credible when scientists began examining other meteorites, Martian and otherwise. Surprisingly, all meteorites revealed sings of life. It was Earth’s life. Meteorites fall to the Earth’s surface, where microbes are everywhere. Bacteria inevitably contaminate any rock on the surface. Almost every meteorite ever found has been on a contaminated ground for periods ranging from several days to many thousands of years. Once found, most meteorites are usually handled and breathed on, and so exposed to more contamination.

Even meteorites collected in the pristine ice have been exposed to air for centuries. In a matter of months, microbes are able to migrate deep into a meteorite’s interior. Given such a contaminated Earth environment, how can anyone ever be sure that the Allan Hills supposed microbes are evidences of life on Mars?

Right from the start, one of the most vocal critics of the Martian claim was UCLA paleontologist Jay William Schopf. He is a leading expert of microfossils and an authority on Earth’s most ancient fossil life for at least 40 years. He was outraged. It was surprising that Schopf was invited by NASA to participate as an objective dissenting voice at the well publicized press conference in 1996 in which the discovery was announced. Schopf described the event in his popular book “Cradle of Life” (not the famous videogame).

He said he didn’t want to publicly humiliate the NASA crowd, so he was somewhat restrained in that public forum. He tried to be reasonable, even gentle. He underscored his criticism of the NASA work in an addendum to his book.

The majority of scientists at this point are unconvinced by the evidences of life on Mars found in the Allan Hills meteorite. Everyone, however, is wildly enthusiastic by getting more data.

The hunt for life on Mars features conflicts between our vivid imagination and the cold hard scientific facts.

Evidences of Life on Mars

2010-02-18T05:01:00.000-08:00

Here I want to talk about the possible evidences of life on Mars. Rocks from space constantly bombard our planet. A few of these visitors make it through the atmosphere without burning up, which are called meteorites. Of the thousands of meteorites that have been collected on the Earth surface, only a precious 2 dozen or so are known to have come from Mars. These chunks of rocks don’t look rare or valuable, but in the 1980’s, clever chemists deduced the origin of these rocks by analyzing their composition.

You might wonder how a chunk of Mars can find its way to Earth. The impact of giant asteroids on Mars is inevitable. Any such collision is going to throw rocks away from the planet and into an orbit around the sun. The sun and Jupiter would sweep most of those rocks because they are the two most massive objects in our solar system, and hence have the strongest gravitational pull. Eventually, however, after millions of years of collisions, a tiny fraction of Mars would inevitably find its way to Earth.

One in every thousand or so meteorites that hit Earth comes from the red planet. It is amazing to think that a piece of Mars has been transferred to us. Just imagine the implications if that piece of rock holds Martian microbes and that they could stand the long journey through space. Many scientists think some microbes could. If so, Earth could have been infected by Martian life.

Indeed, Mars was probably habitable hundreds of millions of years earlier than Earth. If life emerged on Mars first, and it was transferred to Earth, then that might be how life began here. We all may be Martians.

This idea sounds odd but highly respected scientists are given this proposal very serious thought.

The great majority of Martian meteorites that fall to Earth are never found. About three quarters of all meteorites land on the ocean and fall to the bottom. Even the ones that fall on land look so much like ordinary Earth rocks that you could kick one aside without noticing. So, we need to find a place where meteorites stand out as alien objects. For that there is no better place than a flat white sheet of ice.

The deserts of Antarctica are the world’s most productive grounds for meteorites. In these clean regions, dark colored meteorites stand out starkly. Scientists can collects hundreds of meteorites in one short season.

With the discovery of Martian meteorites, scientists could for the first time investigate actual pieces of another planet, and actually find evidences of life on Mars. Conventional wisdom would suggest that such meteorites should be utterly devoid of life.

One Mars meteorite, however, proves to be strikingly different from the others. This meteorite was collected in 1984. It has the scientific designation ALH84001. This meteorite is much older than the other Mars rocks: at least 4 billion years old. It also holds minerals that suggest the possibility of ancient interactions with liquid water. A team of biologists, planetary scientists and meteorite experts, led by NASA’s geologist David McKay, subjected pieces of that four pound rock to a battery of rigorous tests.

They probed the mineral with x-rays, lasers, gamma-rays, beams of electrons. No one in the NASA team ever expected to find evidences of life on Mars in the meteorite. All they really hoped for was a hint of freely flowing water. Yet, gradually, as more and more data piled up, David McKay and his colleagues began to see anomalies that could not easily be explained by normal mineral processes. They were, however, plausible evidences of life on Mars.

The group came to believe that this meteorite indeed had convincing evidences of life on Mars. After a lot of internal debate and cautious evaluation of the data, in 1996, they decided to go public. The NASA wrote up the results and sent the paper to the premier journal Science. It was accepted in short order and scheduled for publication in mid August.

NASA called a hasted news conference several days earlier. Naturally, with a discovery of this magnitude, the highest levels of government, including the White House, were alerted. It turns out that President Clinton’s chief political advisor learned the story and then bragged about the NASA discovery to a prostitute. The prostitute had been selling his secrets to a weekly tabloid, so by early August, NASA’s news was out.

In August 7, McKay’s team publicly claimed the discovery of tiny elongated objects that were once living Martian microbes. Headlines of newspapers screamed “Evidence of Life on Mars!!” The tabloid Weekly World News showed a large photo of an insect with the headline “New Photo of the Life on Mars NASA didn’t want the world to see”.

Meanwhile, Science published the NASA’s team results. This discovery was a huge deal for NASA. They were flooded by news conferences, scientific meetings, etc. President Clinton even got into the act by holding a national press conference during he reflected on the glory of NASA’s triumph.

So, what was the basis of McKay’s claim? Did they find convincing evidences of life on Mars? We’ll analyze their claims in my next post.

Is There Life on Mars?

2010-02-09T05:01:00.000-08:00

Is there life on Mars? Few questions, scientific or otherwise, fire the public imagination as much as this one. From H.G. Wells to David Bowie, speculations about Martian life have been a pervasive part of popular culture. There is a good reason for this intense interest: Mars is our planetary next-door neighbor, is the most exciting and accessible field on which to look for alien life. Mars, like Earth, formed about 4.5 billion years ago. A flood of new data from NASA reveals that Mars, like Earth, once had an abundance of surface water, especially during the planet’s first billion years.

Mars once had lakes, underwater volcanic systems and a benign temperature and atmosphere that might have allowed the spark of life. Indeed, Mars was probably habitable long before Earth. Mars still has water beneath its cold dry surface. It’s possible that Martian microbial life still survives in protected pockets underground.

In spite of these fascinating possibilities, today scientists tend to be weary when asked “is there life on mars?” This question has a long history of fraud, a history that underscores the profound difficulty of recognizing life on the base of limited data.

The first serious proposals regarding life on Mars were fueled by telescope observations of the red planet’s surface. The Italian astronomer Giovanni Schiaparelli (1835-1910) first reported what appeared to be faint straight line markings on the Martian surface in 1887. He called these features “canali”, which is the Italian word for channels. This is a neutral word with no suggestion of their origin and said nothing regarding the question “is there life on mars”.

As it turned out, the canali were just optical illusions. The human brain tends to connect the dots between dark patched on a light background. Ironically, Schiaparelli’s descriptions were mistranslated into English as canals. That designation fired the imagination of the wealthy American astronomer Percival Lowell (1855-1916). He was born and educated in Boston. In 1894, he used part of the family fortune to build and operate the Lowell Observatory, principally to try to find life on mars.

By 1895, he reported his first observations of a network of canals on the red planet, what he interpreted as evidence of an advanced civilization. Three years later, he founded a journal that promoted the idea of an ancient intelligent civilization on the red planet. Such speculation inspired the imagination of science fiction writers. H.G. Wells’ novel “The War of the Worlds” was published in the year 1898.

Nevertheless, the scientific community was not convinced. In fact, claims like those of Lowell hardened the scientific community for generations against any proposals regarding life elsewhere in the universe.

NASA’s early Missions: Is There Life on Mars?

Fast forward to the 1960’s, NASA began its widely successful effort to probe nearby planets with robotic missions. Efforts such as the Mariner and Viking missions had a variety of goals: geology, geophysics, mineralogy and more. The search for life, however, was always a prime objective. Beginning in 1965 and continuing through the early 1970’s, NASA’s four Mariner spacecrafts flew close to Mars and produced thousands of remarkable images of a hostile, dry and desolate world. The surface of Mars was full of craters and immense volcanoes, much bigger than any volcanoes on Earth. They found no canals and no cities. Not even a hint of life-sustaining water was found.

Then, in 1976, the first of NASA’s Viking missions carried an array of experiments to the Martian surface. One key objective of this mission was to look for organic compounds in the search for evidence of cellular activity. The result of these experiments confounded the scientists. On the one hand, an experiment specifically designed to look for microbial activity yielded a positive signal. The so called “labeled release experiment” involved scooping up a small amount of Martian soil, exposing it to a nutrient rich solution that had been labeled with radioactive carbon atoms, and then watch for the release of radioactive carbon dioxide. That’s a sign of life.

Sure enough, the experiment produced a big radioactive signal. The nutrients had reacted vigorously with the soil, releasing radioactive carbon dioxide in what appeared to be a metabolic reaction. A second experiment designed to identify carbon-based molecules in the soil seemed to contradict the labeled release results. Viking’s organic analyzer found nothing at all, not even a trace of carbon-based molecules. This result was a mystery, because Mars, like Earth, is subjected to a steady rain of microscopic organic-rich particles from space. There should be at least a little carbon on the Martian surface, yet the experiment showed nothing.

That result seemed to rule out any possibility of living cells. How could there be microbes and no carbon? These ambiguous results have led to years of controversy. The majority of scientists say that the lack of organic molecules proves that there is no life on Mars. They explained the strong labeled release as a result of chemicals on the soil. According to this view, potent chemicals reacted with the nutrients and caused the release of radioactive carbon dioxide.

Others, however, are equally convinced that Viking did find life. According to them, the organic analyzer wasn’t sensitive enough.

The bottom line is that Viking didn’t answer the question “is there life on Mars?”. We have to go back and do more experiments. NASA is taking a very cautious and measured approach to avoid any more ambiguous results. I will talk about new evidences for life on Mars and recent efforts by NASA in my future articles. Stay tuned.

Origin of Life

2010-02-04T05:12:00.000-08:00

The first chapter of Genesis contains the Christian account of the origin of life. It tells of God creating the heaven and the Earth, plants and animals, and then man in God’s image. All in six days. The Bible doesn’t state when this creation occurred, but most early Christians probably assumed that this did not occur too long ago. In the 1600’s, the Anglican bishop James Ussher fixed the date of creation at 4004 B.C.E. This is the established biblical view that continues to the present.

Physicists tell us, however, that the universe began between 10 and 20 billion years ago, at a moment in time they call the Big Bang. As soon as there were rocks to record the existence of life, we find evidence that life is there. How did this diversity of life appeared on Earth in a very short time span (from a geological point of view)? This is the materialist view that I try to explain in this series of articles on the origin of life.

• In the Beginning: The early planet Earth was a really miserable place. The way that the planet was formed, with ever larger and larger chunks of material slamming into it, created an enormous amount of heat. When the planet first formed it was melted. It was no place where one could ever conceive the origin of life. Less than a billion years later, however, the fossil record clearly shows that life was there.

• Miller’s Experiment: In 1953, Stanley Miller conducted his famous (or infamous) experiment. For decades, scientists had speculated whether the complex organic compounds characteristic of living things could have somehow been generated spontaneously on the early Earth. Spontaneous generation of organic compounds can’t happen today. This is because organic compounds are too fragile.

• Polymerization: The significance of Miller’s experiment was simply to show that non-biological processes could result in the formation of organic molecules, including amino-acids and nucleotides. These molecules that Miller got, however, were still relatively simple. They thus only represented a first small step.

• Primitive Cells: We know that the organic molecules that make us up are not just a jumble of things floating around in a primordial soup, they are highly ordered. They come in highly ordered packages. There are many such packages in living systems, but the most fundamental one is what we call the cell. All living things are made of units called cells. Minimally, for something to be living, requires a barrier between the living part and the non-living part. That barrier is what would define the cell.

• The Genetic Code: How does a living system reproduce? What minimally do we need to get reproduction? How reproduction arose is an especially tricky problem. It is the problem that is most debated today in the area of the origin of life.

Examples of Natural Selection - Part 2

2010-02-03T05:16:00.000-08:00

Here I will show you more examples of natural selection. Darwin’s thinking about natural selection and evolution was profoundly influenced by his observations of island organisms. Among them was a remarkable group of birds that he observed in the Galapagos Islands, collectively now known as Darwin’s finches. One of the best studied examples of natural selection occurring in the wild comes from the work of Peter and Rosemary Grant. They’ve been studying one species of Darwin’s finches for over three decades now.

The different species of finches were all very similar in their size, shape and color, but they differed specially in the size and shape of their beaks. This is consistent with the idea that natural selection has adapted the beaks of these different species to be specialized for eating different kinds of foods. There is also considerable variation within species in the size and shape of individuals’ beaks. If natural selection is responsible for the evolution of beak shape in this group of birds, then we should also be able to detect differences in the survivorship and reproductive success of individuals within a species.

It might seem impossible to think that we can detect this kind of differential reproductive success occurring in a natural population of birds, but this is exactly what the work of the Grants have revealed.

The Grants have focused much of their work on one population of a single species of Darwin’s finches, of the so-called medium-ground finch. The population of this finch is ideal for this kinds of long-term study because it occurs in a relatively small island, and the population size never gets above a thousand individuals. This makes it possible to capture, mark and measure almost every bird in the population.

Like many of the Darwin’s finches, the medium-ground finch’s diet consists primarily of seeds, which they crack open with its beaks. The Grants and many of their students have shown that both within this particular species as well across different species, the size of the beak actually corresponds to the size and the hardness of the seeds that they usually eat.

Within the population of the medium-ground finch, there is considerable variation in beak size. Most individuals have sort of average size beaks. Some birds in the population have beaks with depths as large as 13 or 14 millimeters. Other individuals have beaks with depths that are small as only 6 or 7 millimeters.

The evidence pointed to the possibility that natural selection may be occurring on beak shape as an adaptation for feeding. How could the Grants actually test this? This is where a bit of serendipity and bad weather came into play. In 1977, after the Grants had been studying this population for a number of years, there was a severe drought in Galapagos, brought on by an El Niño weather pattern. This drought had a profound effect on the population. Over 80% of the population died, leaving less than 200 birds as survivors.

The reason for this decrease in population size clearly was because the finches didn’t have enough food to eat. Specifically, the drought caused many of the plants that produce the seeds they normally eat to cease flowering. The plants didn’t produce seeds and the finches simply didn’t have enough to eat. Many emaciated dead birds were found.

The Grants’ most important observation, however, was that the individuals who survived the drought differed from those who didn’t survive. Specifically, they differed in the size of their beaks. The individuals who made it had larger beaks than the individuals who didn’t make it. Why should this be?

This was because the types of seed produced also were affected by the drought. One kind of plant proved to be drought-resistant, and thus did flowered and produced some seeds. This plant produced very large and hard seeds. So, the food that was available was larger seeds that only the birds with larger beaks were able to eat efficiently.

Following this drought in 1977, the distribution of beak size in this population of finches shifted dramatically. The average individual after 1977 had a much larger beak than the average individual before the drought. In other words, the selection brought on by this drought had changed the populations mean characteristics, and caused evolution to occur.

The 1977 drought wasn’t actually a unique event. The Galapagos are subject to periodic droughts. The Grants observed that following a drought, the population mean beak size would shift to larger sizes. Following a wet year, however, when a lot of small soft seeds were produces, the population would have its mean beak size actually shift back down. So, selection is pushing the characteristics of this population in a way that is predicted by the particular adaptation of beak size to the type of food. I think that this is one of the most compelling and complete examples of natural selection at work.

Return from Examples of Natural Selection to Darwin's Theory of Evolution

Examples of Natural Selection

2010-02-03T04:46:00.000-08:00

Here I want to show you some examples of natural selection to make it clearer how it works in nature. We call natural selection a theory, but it is a testable theory and has been tested many times. Darwin, when he proposed it, could only turn to examples of artificial selection, the breeding of domesticated plants and animals, where the selective agent was the breeder, not the environment. Since Darwin’s time, however, natural selection has been demonstrated to occur in many cases. There are well documented examples both in wild populations and in laboratory populations.

The Peppered Moths

This is a famous, or infamous, example of natural selection. It involves a small moth living in England, the English peppered moth. This example is notable not only because it offers definitive proof for natural selection occurring, but because it was the first widely publicized example of natural selection occurring in a wild population. It also provides a good example for illustrating some of the key tenets of natural selection.

Butterfly collectors are numerous among natural historians. For literally hundreds of years, professional and amateur naturalists have collected hundreds of thousands of specimens of butterflies and moths from all over the world. As a result, the natural history museums of the world are stuffed with collections that illustrate various patters of variation in the phenotypes of butterflies and moths.

In the case of the peppered moth, there is an extensive museum collection that portraits a hundred and fifty years or more of the history of this moth in England. If you look to the collection of the species that were made near Manchester you’ll notice an interesting thing. Moths that were collected before the 1850’s were mostly light colored. They had light colored wings. There are a few examples that you find in these older collections of dark forms, but most of the moths were light colored.

By contrast, if you look at specimens that were collected a half-century later, around 1900, about 98% of the moths collected are uniformly dark colored. There are only a few light colored individuals represented. The typical wing color phenotype in the population of this moth found around Manchester shifted dramatically from mostly light individuals to mostly dark individuals over a fifty year period.

It is well established that wing color is a heritable trait in butterflies and moths. Therefore, the historical change in wing color observed in this population may be consistent with the hypothesis that the shift represents and evolutionary change. Interestingly, this transformation occurred during Darwin’s lifetime, but he never knew about it.

If this change in wing color is an evolutionary transformation, we would expect that natural selection must be acting on these individuals because of their wing colors. How might natural selection act in this way?

It was in the mid 1950’s when an English physician named Bernard Kettlewell proposed the following idea. He noticed that the change in moth coloration correlated with the onset of the industrial revolution in England. This was a time when coal burning around industrial centers like Manchester produced enormous amount of soot.

The peppered moth is a night-flying moth, and it usually spends the whole day resting on tree trunks. Normally, in the English countryside, these tree trunks that the moth would settle on are covered with light-colored lichens. What Kettlewell suggested was that the tree trunks around Manchester, because they became covered with soot (and they did), had become considerably darker.

What’s natural selection doing here? Kettlewell argued that visual predators, such as birds, were hunting these moths during the day. Moths were light-colored, he argued, because when they rested on light-colored lichens they couldn’t be seen. When the trees became soot-covered, the light colored individuals stood out and were easily found by predators. On the other hand, those few dark colored individuals that occurred would do much better, because their dark coloration would fit it with the now dark background.

Kettlewell tried to test his hypothesis the following way. He took an equal number of dark colored and light colored moths, and released them into two kinds of woods. First he would release an equal number of light and dark colored moths into woods that were darkened with soot. Then he would ask which of the moths got eaten more. When he did this, he found out that the light-colored moths were the ones that were getting eaten.

If you took the same number of light and dark colored moths and put them instead in a forest that was more distant from Manchester, where the trunks were still light colored, he got the opposite effect. In this case, the dark colored moths would stand out and the birds would eat them more.

The results of Kettlewell’s experiment are consistent with the idea that natural selection, caused by visual predators hunting these animals, is acting on wing color, such as over time, the darker individuals were favored. In this way, dark coloration spread through the population.

The case of the peppered moth is a famous example of natural selection because it was considered to be the first demonstrated example of natural selection occurring in a wild population. I must tell you, however, that this example is a bit infamous nowadays. In recent years it had been suggested that Kettlewell might not had done this experiment as neatly as he could. Specifically, it appears that Kettlewell didn’t just release these moths, he actually attached them to the tree trunks. This is problematic, because the moths weren’t choosing where to land, Kettlewell did. So, a number of people had argued that this was a very poorly-conducted experiment.

Certainly, his experiment isn’t conclusive evidence, but I still think that this is a useful example of natural selection that helps to illustrate some important points about it.

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What is Natural Selection

2010-02-03T04:37:00.000-08:00

What is natural selection? Darwin’s main contribution was not to establish that evolution occurs, although he helped in that regard. His great achievement was his theory of natural selection. In a nutshell, Darwin’s theory runs as follows:

• There is heritable variation in a population.

• More individuals are born in a population than can survive.

• Individuals that do survive and reproduce are not a random subset of the population. These individuals possess traits that somehow make them better at surviving and reproducing in a particular environment.

• The heritable adaptive traits would become increasingly represented in a population over time, and thus shape the phenotypic characteristics of that population.

There are a couple of additional points. Natural selection can only act on existing heritable variation. If there is no variation for a particular trait, then selection simply cannot do anything with it. This is why the generation of variation in the context of mutation and genetic recombination is so central to our understanding of evolution.

Another important point is that although natural selection acts on individuals, its evolutionary consequences occur in populations. Individuals do not evolve. Evolution is measured as change in the average characteristics of individuals within a population. I think this, in a nutshell, answers the question.

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Darwin and Evolution - Part 2

2010-02-02T05:04:00.000-08:00

Let's continue here what we left in our left article about Darwin and evolution. It was his opportunity to serve as the naturalist on the Beagle that provided Darwin with his first insights into how evolution might work. In fact, it was this voyage that changed his worldview and convinced him that evolution occurred. Darwin began to observe and document the kinds of evidence for evolutionary change that I mentioned in my previous post: geological change, homologies among species, relationships between fossil forms and living forms.

Particularly illuminating to Darwin were groups of animals and plants occurring on islands. He would find that if you went to a group of islands, you will often find, on different islands, species that were similar enough to obviously be related to each other, and yet different enough to be considered other species. Furthermore, these species occurring on islands would often resemble a species occurring on the mainland.

Darwin’s Finches

The most celebrated example of this phenomenon is a closely related group birds species, now collectively known as Darwin’s finches, that are found on the Galapagos Islands, about 700 kilometers off the coast of Peru. Each island has a different species that appears to be uniquely suited for that habitat. These are really representative of Darwin and evolution itself.

In particular, these species differed largely in the size and shape of their beaks. They used their beaks in different ways to feed on different kinds of material. For example, there are some species with very large beaks that appear to be suitable for crushing large and hard seeds. Other species have smaller beaks that are more suitable for handling smaller seeds. The size and shape of the different beaks did correspond to what Darwin observed about their feeding ecology.

Darwin wondered how is it possible that there are different species on islands that were similar and yet clearly different, and that the differences related so clearly to the environment in which those species lived. This pattern made perfect sense to Darwin if the various species were all descended from the same common ancestor. This was presumably and ancestor that had come from the mainland. Eventually, all of the island species had gradually evolved and diversified in a way that matched the habitats in which they live. Darwin called this pattern “descent with modification”.

Working on the Species Problem

Darwin spent five years traveling around the world, collecting animals and plants and making observations. He returned from his trip in 1836, loaded with specimens and notebooks of his observations. He spent more than 20 years working on what he called the “species problem”. During the time that he was working on this problem, he spent most of his time in England. He nonetheless continued to amass evidence by talking to naturalists who were collecting plants and animals from other parts of the world, and specially by looking at the effects of domestication on species.

These observations convinced him not only that evolution occurred, but also suggested a particular mechanism by which evolution could occur. Darwin proposed this mechanism, the theory of natural selection, as early as 1844. He wrote a paper, but he never published it. He was urged by friends and colleagues to publish it, even by his wife, but Darwin preferred to perfect his ideas. He didn’t want to propose this idea until he had amassed so much evidence that the idea could simply not be refuted. So, he spent another ten or more years revising his ideas, collecting more specimens, evaluating more data.

The Publication of the Origin

Darwin hand was forced, however, in 1858, when he received a manuscript from Alfred Russell Wallace, a well-known naturalist. Wallace’s manuscript essentially presented the same idea of natural selection that Darwin had been working on for 20 years. Wallace asked Darwin to submit this manuscript he sent for publication.

I could not imagine what Darwin felt at that moment. He wrote to his friend Charles Lyell asking him for advice about what to do. Lyell arranged for Wallace’s paper, and an excerpted synopsis of Darwin’s 1844 manuscript to be published simultaneously, giving credit for the discovery of the theory of natural selection to both men.

Darwin then quickly finished the book-length version of his ideas, which was published the following year, 1859, with the title: “On the Origin of Species by Means of Natural Selection”.

What’s in On the Origin of Species

The essential observations behind the theory of natural selection are very straightforward. Darwin was struck by three things. First, he was struck by how much variation he observed among individuals of the same species. All individuals of the same species look alike, but no two were exactly alike. Darwin also recognized that some of this individual variation is passed on from parents to offspring. He observed that traits are heritable. Darwin didn’t know the mechanism responsible for this, but he argued that a mechanism must exist. We today know that DNA is the molecule that holds information in living things, how it is replicated, and all the stuff that makes it much clearer to us.

Darwin’s next important observation was that most species produced more offspring than ever survive. In this, Darwin was influenced by the writings of Thomas Malthus, who was an economist. Malthus wrote an essay arguing that much of human suffering was inevitable as the result of the fact that human population would always grow faster than the available resources needed to support it. In other words, the size of the human population is limited by competition. Darwin saw that this was true in animals and plants as well.

These observations led Darwin to the following conclusions. First, given that more individuals are born in a population that can ever live, there must be competition for limited resources, so that only some of those individuals are going to survive and eventually reproduce. Second, because individuals in a population differ in their characteristics, not all individuals are expected to be successful in this competition. Individuals with the more favorable variations would be more likely to survive and reproduce. Therefore, these naturally selected individuals, as Darwin called them, would contribute more offspring to later generations.

Finally, if the traits that contributed to the success of the parents are heritable, then over time, there would be more individuals possessing those traits. We call traits that evolved this way “adaptations”. Over time, natural selection is thought to cause populations to change their characteristics in such a way that would increase adaptation to the prevailing environment.

The first edition of Darwin’s book was published in 1859. All 1000 copies were sold on the first day. People knew this idea was coming and were eager to digest it. Despite the original controversy that it caused, Darwin’s work established the fact that evolution occurred. Darwin came to be considered one of the most famous and celebrated scientists of his day.

By the end of the century, pretty much every biologist accepted the idea that evolution occurs.

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Darwin and Evolution

2010-02-02T05:03:00.000-08:00

The words Darwin and evolution are nowadays associated in our minds. Nowadays,also, biologists take for granted that evolution occurred, but that wasn’t the case 150 years ago, when Charles Darwin introduced his ideas. As a boy, young Charles developed a keen passion for nature. He was the kind of kid who loved to walk in the woods, collect bugs, go hunting and fishing. He generally spent time learning about different kinds of plants and animals.

When he was only 16, he was sent to medical school. He found it “distasteful” and soon left the university without a degree. It wouldn’t do for a young man of Darwin’s social status to not study for some career. So, Darwin enrolled in Cambridge University to study theology, with the goal of entering the clergy. The fact that Darwin went to complete a bachelor’s degree in theology may sound a little surprising to us, but it isn’t really. The study of natural history in the early 1800’s was a monopoly of the clergy. Biology was done in what was called natural theology, describing nature in order to more fully appreciate the glory of God. Some of the most important natural historians of the time were clergymen. Mendel himself was a monk.

This seemed to Darwin to be a good way to pursue his true passions. Darwin excelled at his studies. After graduating he was offered a unique opportunity, he was asked to serve as the official naturalist on a five-year long voyage around the world on the Beagle. Darwin’s job was twofold; first, he was to provide interesting conversation to the ship’s captain for five years. Second, and more importantly, he was to acquire and catalog plant and animal specimens from every place the ship visited. This voyage changed forever the history of Darwin and evolution.

When Darwin started his voyage around the world, a long held view in science, and one that Darwin himself almost certainly subscribed to, was that all organisms were formed by a special creation, much as it is described in the book of Genesis. More importantly, it was generally held that species remained immutable throughout all time. This view isn’t just a Christian idea, some Greek philosophers talked about evolution, but Plato and Aristotle argued that species must be immutable. The idea that species living today were completely unchanged throughout time had been a dominant view in western culture for several thousand years.

Early Evidence for Evolution

Early in the 1800’s, there were a few scientific findings that began to suggest this view of immutability of species was not entirely correct. There were three general kinds of evidence that were challenging to the idea of immutable creation. The first sort of evidence came from the field of geology. Creationist views of the world argued that the Earth was relatively young. Archbishop Ussher calculated that the Earth was created in 4004. Geologists who studied landforms, however, saw evidence that convinced them that the Earth had to be a lot older than this. Many people today still challenge these well established views, as well as Darwin and evolution, arguing that Ussher's date was right.

Geological analysis showed that the Earth might be millions of years older. Second, geologists saw that landscape features had obviously undergone many radical transformations. You only have to drive along an interstate highway to see the folding in the rocks. Third, geologists began to realize that physical forces at work in nature today could explain the transformations in landforms that must have occurred in the distant past. For example, they saw how erosion, if given enough time, could lead to landscape transformation, such as the creation of a canyon.

These ideas were developed completely by the leading geologist of Darwin’s day, Charles Lyell, who in the 1820’s formally developed the idea of geological gradualism. The theory of gradualism argued that large-scale changes in the geological features of the Earth could be explained by the gradual accumulation of many small changes over a very long period of time. Charles Lyell theory and his book had a profound influence on Darwin and evolution.

The word evolution simply means change. What geology did was to show that the physical world, at least, could have changed over a long period of time.

Homologues and Vestigial Structures

Another kind of evidence that began challenging the immutability of biological species came from the work of comparative anatomists. At the time, biology was largely a descriptive enterprise, involving the collection, dissection and description of different kinds of plants and animals. In the process of doing this kind of description, anatomists noticed that very different-looking animals shared some of the same basic parts. For example, if you look at the forelimbs of different kinds of mammals, it is easy to see that each animal has one with a quite different shape, but they nonetheless share components. Despite their differences in shape and function, if you dissect these forelimbs, you can see that they include similar arrangements of bones, tendons, muscles and so forth.

These structures are different in each species, but they share sufficient similarities to appear as though they had been modified from some original common form. We refer to anatomical features having these kinds of similarities as homologues structures. These kinds of homologues structures could be best explained if living forms were not static, but instead had been transformed from some common form that was shared. That is, they are best explained by darwin and evolution.

An even more problematic case for immutability was the appearance of structures that had no apparent function at all, the so called vestigial organs or structures. An example of this might be the tiny pelvic bones that are still found in whales. If species were the result of a single perfect creation event, then why should such structures exist at all? A simpler explanation would be that species had changed over time in such a way that previously useful structures had lost their usefulness.

What About the Fossil Record?

Another sort of evidence that species were not immutable came from the branch of science we call paleontology today. Paleontologists are people who study fossils. In the early 1800’s, paleontologists began to describe fossils of species that were no longer living on the present day Earth. The existence of these fossils made it obvious that species weren’t constant.

There was another observation from the field of paleontology that was hard to explain away. It was obvious that some fossil species were similar enough in their anatomy to be related to living species, while at the same time differed enough to clearly have to be classified as a different species. It was possible to find series of fossil species occurring at different times in the fossil record which seemed to be connected, from one ancient form that looked one way, to one that existed today, with a number of intermediates in between. This was called the Law of Succession, and was consistent with the ideas of darwin and evolution.

These kinds of observations, coming from geology, comparative anatomy and paleontology were much discussed in the early part of the 19th century. Some scientists were beginning to suspect and even suggest in writing that species were not immutable. The idea that evolution might occur was beginning to be accepted. What was not at all clear was how evolution could occur. What would be a mechanism that could account for the evolutionary transformation of species?

Darwin’s main contribution, as it turns out, was not to suggest that evolution occurs, this was already out there. His real contribution was to understand the mechanism by which evolution could occur, which was embodied in his theory of natural selection. We'll see his theory in more detail in the next part of this article: Darwin and Evolution, Part 2.

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Darwin’s Theory of Evolution

2010-02-01T04:49:00.000-08:00

Nowadays, biologists take for granted that evolution occurred, but that wasn’t the case 150 years ago, when Darwin’s theory of evolution was introduced. Evolution is a simple and obvious idea if you think about it, but we needed Darwin to discover it. This series of articles covers much about Darwin’s life and work.

What Was There Before Darwin: We are particularly interested in our own origin. All cultures have their creation myths. Since the Greeks started doing science, however, some men tried to give a rational explanation to the origin of life’s diversity. Let’s review what they had to say.
De Maillet's Theory of Evolution: Among the earliest people to suggest that life had developed from simple to complex forms was Benoît de Maillet, who lived from 1656 to 1738. He realized his ideas were over the top for his day, so, he didn’t just come right out and declared the evolution of life to be his view.
Darwin and Evolution: As a boy, young Charles developed a keen passion for nature. He was the kind of kid who loved to walk in the woods, collect bugs, go hunting and fishing. He generally spent time learning about different kinds of plants and animals. When Darwin started his voyage around the world, a long held view in science, and one that Darwin himself almost certainly subscribed to, was that all organisms were formed by a special creation, much as it is described in the book of Genesis.
What is Natural Selection: Darwin’s main contribution was not to establish that evolution occurs, although he helped in that regard. His great achievement was his theory of natural selection. We call natural selection a theory, but it is a testable theory and has been tested many times.

Examples of Natural Selection: Some examples of natural selection to make it clearer how it works in nature.

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What is Life, Part III

2010-01-27T04:14:00.000-08:00

Even armed with NASA’s pragmatic definition of life, it is almost impossible to know what Earth’s very first life form was like. One very real possibility is that planet Earth’s earliest life may have been vastly different from anything we know today. Many experts suspect that the first living entity was not a single isolated cell, because even the simplest modern cells incorporate bewildering chemical complexity.

Most researchers assume that the first life form did not use DNA, given its exceedingly intricate mechanism. It may not even use proteins, which today act as the chemical work horses of cellular life. Naturally, experts propose different ideas regarding Earth’s first life form. Geologists propose that the Earth’s earliest living entity which fits NASA’s definition was an extremely thin molecular coding on a rock. It is easy to imagine the simple behavior of such flat life. It would have just spread across minerals in a layer of only a few billionths of a meter thick. Flat life would have exploited energy-rich mineral surfaces, and slowly spread outwards, from rock to rock.

Whatever that life form looked like, it must have arisen from chemical reactions among the oceans, the atmosphere and rocks.

Our Tendency to Dichotomize

The French anthropologist Claude Lévi-Strauss investigated the mythologies of many cultures. In the process, he recognized deep human tendency to reduce all sorts of complex situations to oversimplified dichotomies. We tend to divide people into friend and enemy. We divide the afterlife into heaven and hell. We divide actions into good and evil. We all know that most situations are much more subtle and complex.

The long history of sciences reveals that scientists are in no way immune to the trap of this kind of oversimplification. In the 18th century, for example, one group of naturalists called the “neptunists”, favored a watery origin for rocks. They fought many battles with the “plutonitsts”, who favored heat to describe the origin of rocks. It turns out that both were right. Rock sometimes form by the action of water, and sometimes by the action of heat, and sometimes even by a combination of both.

A similar contentious and misleading dichotomy raged between 18th century geologists was the one between catastrofists and uniformitarians. Catastrofists espoused the view that brief and cataclysmic events like earthquakes and floods dominated the geological history of Earth. Uniformitarians countered that geological processes are for the most part gradual and ongoing. Again, both groups were correct. Geological changes occur gradually over millions of years, but discrete catastrophic events, like the impact of big asteroids, also influence Earth’s history.

Similarly, there was a time when sharp distinctions were seen between plants and animals, and between single celled and multicellular organisms. Now, those sharp distinctions have become blurred.

I believe that any attempt to formulate an absolute definition of life, one that tries to differentiate between “life” and “non-life”, must represent a similar false dichotomy. Here’s why. It is obvious that the first living cell did not just appear fully formed with all its chemical complexity and genetic machinery. Rather, life must have arisen through a stepwise sequence of emergent events. I see life’s origin as a process of increasing chemical complexity.

What now looks to us as a divide between non-living matter and living cells tends to obscure the fact that the chemical evolution of life occurred in a stepwise sequence. Most of that history is lost, because when modern cells emerged, they quickly consumed all traces of the earlier stages of chemical evolution. They ate the evidence.

Our challenge is to use every available clue to establish a progressive hierarchy of emergent steps, leading from a prebiotic Earth rich in organic molecules to clusters of molecules, to self-replicating molecular systems, to encapsulation and membranes, to cellular life.

This view of life as a stepwise sequence of emergent events also informs the central question “what is life”. Any attempt to define the exact point in which a system of gradually increasing complexity becomes alive is intrinsically arbitrary. Where you or anyone tries to draw such a line is a question more of perceived value than of science. For example, if you value the intrinsic isolation of each living thing, then, for you, life’s origin probably would correspond to the stage when encapsulated cell membranes appeared. Perhaps you most value life’s ability to reproduce. If so, self-replication would be the demarcation point for life.

Many scientists today place special value on information as the key to life. They argue that life began with a genetic mechanism to pass information from one generation to the next. In this context, the question “what is life” becomes fundamentally a semantic question. It’s a subjective matter of taxonomy, rather than any absolute divide. Nature supports a rich variety of complex emergent chemical systems. Scientists are learning to craft a wide variety of those systems in the laboratory as well, but no matter how curious or noble the behavior of these systems may be, none of them comes with a label “life” or “non-life”.

Don’t get me wrong, labels are extremely important. They are vital for effective communication. However, I think that defining life is not helpful because there is so much we don’t know. Early attempts to classify animals purely by their color or shape ultimately failed. Similarly, early efforts to classify chemical elements according to their physical state (solid, liquid or gas) were unhelpful in elaborating a chemical theory.

We are in no position to define life. We don’t know if life’s biochemistry is highly constrained, or if there are many chemical solutions to life. It is much better at this point to keep an open mind and just describe the chemical characteristics of whatever we find.

What is Life, Part II

2010-01-26T04:03:00.000-08:00

So, here we continue with the “what is life” issue. A general definition that’s able to distinguish all imaginable living objects from the diversity of non-living objects remains elusive. Even today, we know relatively little about the cellular life on Earth. It’s been said that a shovel full of soil would contain hundreds of microbial species that are unknown to science. That’s not to mention the vast range of plausible non-cellular life forms that might be discovered elsewhere in the universe.

I have to conclude that endorsing any sweeping definition of life based on so little knowledge is like trying to define music after listening to a single Elvis Presley song.

Top-Down and Bottom-Up

So, what do we do? As you can imagine, scientists crave a definition of life. Such a definition remains elusive, but they adopted two complimentary approaches in their efforts to distinguish that which is alive from that which is not. On the one hand, many scientists have adopted the top-down approach. Top-down refers to the effort to scrutinize all modern living organisms and fossil entities to identify the most primitive forms that are or were alive. It turns out that primitive microbes and ancient fossils have the potential to provide relevant clues about life’s early chemistry.

I must say that I find this top-down strategy inherently limited. At least so far, all known life forms are based on biochemical sophisticated cells containing complex molecules, including DNA and proteins. Any definition of life based on top-down research is limited to what appears to be modern biochemistry.

By contrast, a small but determinate army of investigators adopt the so-called bottom-up approach. The principal objective of bottom-up researchers is to device laboratory experiments to mimic the emergent chemical process of environments in the ancient Earth. Ultimately, the bottom-up goal is to synthesize a self-reproducing chemical system in the laboratory. That’s an effort that might help clarify the ancient transition from non-life to life.

You might think that all bottom-up researchers hold a common view of what would constitute the first synthetic life form, but research actually leads to an amusing range of diverging opinions regarding what’s alive. Each scientist has a tendency to define life primarily in terms of his or her own chosen chemical or biological specialty. One notable group focuses on the origin of cell membranes. To them, life began when the first encapsulating membrane appeared.

Other well respected research teams study the emergence of metabolic cycles. Those are the process by which cells gather and use atoms and energy. Naturally, for them, the origin of life coincided with the origin of metabolism. Lots of other groups investigate the origin of primordial RNA, which many experts consider to be the first genetic material. For them, the origin of RNA is equivalent to the origin of life.

There are many other workers who focus on viruses, minerals or even artificial intelligence; and each researcher advocates his own definition of what constitutes life.

NASA’a Definition

Into this mix, quite a few philosophers, theologians and science fiction writers have injected a variety of more abstract views and speculations on the possible phenomena that might said to be alive. The possibilities seem endless: counscious clouds in space, high temperature silicate minerals, a self aware internet. Such proposals sound at times farfetched, but there is so much we don’t know.

Consequently, the scientific community, with the support of NASA and other governmental agencies, holds regular meetings to explore the definition of life. After all, if one of NASA’s primary missions is to look for life on other worlds, then we’d better have a clear definition for planning future missions. It’s amazing how the “what is life” question sparks passionate arguments.

Gerald Joyce, a biologist working at the Scripps Research Institute, developed a widely accepted definition for life, at least in the context of NASA’s space exploration. He concluded that “life is a self-sustained chemical system capable of undergoing Darwinian evolution”.

According to this opinion, life incorporates three distinctive characteristics. First, all life forms must be chemical systems. That means that computer programs or robots are not alive. The second characteristic is that life grows and sustains itself by gathering energy and atoms from its surroundings. That’s the essence of metabolism. Finally, all living entities must display some sort of variation. According to the concepts of Darwinian evolution, natural selection of more fit individuals inevitably leads to evolution and the emergence of more complex entities. A system that does not have the potential to evolve does not fit this definition of life.

There’s still so much we don’t know, but this NASA inspired definition is probably as general, useful and concise as anyone is likely to come up with, at least until we discover more about what’s actually out there.

What is Life

2010-01-25T04:16:00.000-08:00

We usually think that life is easy to recognize, that it would be obvious if something is alive or not. It turns out that is not that easy. The question “what is life” is asked in very different contexts by different groups of people. For centuries, theologians have hotly debated life’s definition and relation to the beginning of human life. Does life start at the moment of conception? Or does it begin when the brain’s first response, or with the heart’s first beat? In some theological doctrines, life commences not with a physical process, but rather at the unknowable supposed instant known as “ensoulment”.

At the other end of our human journey, doctors, lawyers and politicians require a definition of life in order to deal ethically with patients with brain death. As we saw with the contentious case of Terri Schiavo (the woman who spent more than a decade in comma), lots of people have intense and emotional views on this issue.

In sharp contrast with these ethically difficult and emotionally charged issues, are the more abstract ongoing scientific efforts to define life. A must read book on the origin of life is Noam Lahav’s “Biogenesis”, which was published in 1999. Lahav’s works in the Hebrew University at Jerusalem, and he has been involved in origins research for almost 40 years. His book is filled with insights, as well as countless technical details. As part of his text, he prepared an appendix with lots of different scientific definitions of life, which are written by over 48 different authorities.

These definitions span 150 years period, from the mid 18th century to the late 20th century. It’s worthwhile thinking about a few of those:

- Alexander Oparin: he reflects the view of many authorities. Life can be defined by a combination of traits. He says: “Life may be recognized only in bodies which have particularly special characteristics. These characteristics are peculiar to living things, and are not seen in the world of the dead.” What are these characteristics? In the first place, there is a definite structure or organization. Then there is the ability of organisms to metabolize, reproduce others like themselves and the response to stimulation. The problem is that Oparin’s characteristics are not unique to life. Many non-living systems have definite structure and organization (think about your car or your PC). Oparin says that organisms obtain energy from their surroundings to grow and reproduce, but fire does that also. Many natural non-living systems, such as flowing water or drifting clouds, respond to stimulation.

- John Desmond Bernal: an influential 20th century biological theorist, who provides a longer list of characteristics. He says: “Life is a partial, continuous, progressive, multi-form, and conditionally interactive self-realization of the potentialities of atomic electron states”. I don’t know about you, but that definition seems to be hopelessly fussy and unhelpful in distinguishing life from non-life.

- Stuart Kauffman offered a more promising definition of life in 1993. He claimed: “Life is an expected collectively self-organized property of catalytic polymers”. Embedded in this statement are a couple of key ideas. Kauffman said that life is self-organized. That is, life is a collective emergent phenomenon. He also states that life relies on chemicals to promote the production of more copies of themselves. In Kauffman’s view, life might be a relatively simple collection of self-replicating chemicals. That includes much more primitive entities than modern cellular life.

- John Maynard Smith proposed a short and persuasive definition of life in 1975. He describes life as “any population of entities which have the properties of multiplication, heredity and variation”. Here Smith introduces two key ideas and thus comes closer to a useful set of criteria. First, all life possesses information that’s passed from one generation to the next. That key idea of heredity may not be unique to life, but it is certainly one of life’s most important characteristics. Second, life displays variations. In life, heredity isn’t perfect like a Xerox copy. Variation, in turn, leads to evolution by natural selection.

Lahav goes on and on citing definitions of life, and remarkably, no two definitions are the same. I think you can see this lack of agreement might represent a problem for those of us who search for signs of living organisms in other worlds, as well as for anyone interested in the origin of life. After all, how can you be sure that you discovered life, or that you figured out the process of life origin, when you can’t come close to defining what exactly life is? In spite of generations of work by hundreds of thousands of biologists, we still have no universally accepted definition.

To be continued…

Spontaneous Generation

2010-01-18T04:57:00.000-08:00

What is spontaneous generation? Why did people accept it? Let’s look back at old Greece. By the 4th century B.C., a significant debate regarding the nature of matter arose between the school of Democritus and Aristotle. Democritus argued for a world of atoms: tiny particles that combine to form the variety of matter in our world. In his view, life arose spontaneously through the combination of atoms of soil and fire. Aristotle opposed this atomic hypothesis with its supposed chance mixing of elements. Nevertheless, he too embraced the spontaneous and naturalistic generation of life on Earth. At the core of this belief was the doctrine of vitalism: the idea that every organism is imbued with a life force different from the forces that act on inanimate matter. That’s the way things remained for almost 2000 years.

In the 17th century, the theory of life’s spontaneous generation was accepted knowledge. In fact, the only real challenge to the Aristotelian view came from a few theologians who argued that all living things were formed by God during the first days of creation. A famous quotation by Jan Baptiste van Helmont(1577-1644) exemplify the common views at the time: “If you press a piece of underwear soiled with sweat together with some wheat in an open mouth jar, after about 21 days the odor changes and the ferment, coming out of the underwear and penetrating through the husks of the wheat, changes the wheat into mice." Van Helmont was describing the spontaneous generation recipe for mice.

Redi’s Experiment

The first experiment to challenge this conventional wisdom was performed by the Italian physician Francesco Redi (1626-1697). Redi tackled the problem of preserving raw meat, which deteriorates rapidly on air. In the first part of his experiment, he used open containers. If you let flies land on the meat, then maggots would invariably appear a few days later. In the second part of the experiment, he covered the containers to protect them from the flies. In that case, no maggots grew. He described all these studies in his influential book “Experiments on the Generation of Insects”. Redi’s discovery that maggots only appear in meat contacted by flies let him to conclude that flies, not spontaneous generation, cause maggots.

Redi’s experiment was brilliantly conceived and executed, and it provides us with one of the earliest examples of the scientific method. Even so, Redi accepted the idea that microscopic organisms arise spontaneously all around us all the time.

For the better part of the next two centuries, well until the 19th century, the doctrine of vitalism was widely accepted. Many naturalists felt that this “life force” was not only different from the well studied forces of the non-living world, but also that it was inherently unknowable. The influential philosopher Immanuel Kant (1724-1804) wrote: “It is absurd for men to hope that another Newton will arise in the future who shall make comprehensible by us the production of a blade of grass according to natural laws which no design has ordered”. In other words, the origin of life is an ongoing supernatural phenomenon.

Why People Believed It

Why so many people accepted this idea of spontaneous generation? Think for a moment about your own experience and you’ll get a feeling for why this idea isn’t such a strange point of view. Worm-like maggots form in meat and every spring new leaves appear and flowers blossom in season of renewal. It is not surprising that many people accepted unquestioningly that life arises trough spontaneous generation.

This view continued well into the 19th century, when there were an increasing number of respected deniers of it. One important factor in the spontaneous generation controversy was the 17th century invention of the microscope and the surprising discovery that microscopic life is everywhere. Microorganisms, however, fail to resolve the controversy. After all, anyone who favors spontaneous generation could say that microbes are just one more manifestation of the life force.

As anyone who does experiments would tell, the interpretation of data is seldom unambiguous. This fact of scientific life was highlighted by a marvelous 18th century exchange. Lazzaro Spallanzani, who was opposed to spontaneous generation, explored the subject by comparing flasks filled with nutrient rich water. He boiled flasks that were sealed, and he observed that those flasks remained sterile indefinitely as long as they remained seal. However, when he boiled unsealed flasks, they rapidly took on a cloudy appearance due to the growth of microbes. Spallanzani concluded that ubiquitous microscopic life forms must have contaminated all of his unsealed flasks.

Spallanzani’s conclusions were challenged by Englishman John Needham. Needham agreed that boiling kills microbes, but he found that microbes soon reappear in abundance when the flask is cooled. That was a result that led him to a very different conclusion. He claimed that this new population of cells arose by spontaneous generation.

Naturally, Spallanzani countered that Needham’s new microbes came from the air contamination. To prove his point, he undertook a new set of experiments in which he pumped air out of his flasks, and then boiled the water. No microbes appeared in these trials. Needham countered with a new argument: It was a property of the air, not the water, that must carry the life force.

Today, we’re likely to react to this historical incident with a rather biased worldview. It seems obvious to us that Spallanzani’s conclusions about microbial contamination were correct. It seems just as obvious that Needham’s support of spontaneous generation was misguided. But put yourself in the place of an impartial observer of the time. You wouldn’t be that familiar with the nature of bacteria, nor with their ability to replicate rapidly. Faced with these conflicting claims you would have had a hard time choosing between invisible microbes on the one hand, an invisible life force on the other. Indeed, both arguments were internally consistent, so doubts remained.

Pasteur Takes Care of the Issue

By the 19th century, experiments had clearly disproved spontaneous generation of larger organisms, such as mice and flies. The origin of microbes was still a matter of much debate. It was the great French chemist Louis Pasteur (1822-1885) who resolved the issue once and for all. Pasteur was a giant of experimental research and he contributed many fundamental ideas to biology.

In the 1850’s and 1860’s, Pasteur helped to abolish belief in vitalism and the theory of spontaneous generation with a brilliant series of experiments on sterilized solutions. Like others, he prepared a nutrient rich sugar solution and poured it into several beakers. As with previous researches, one set of beakers was tightly sealed to prevent any contact with ambient air. Pasteur’s innovation was to prepare other beakers that were left open to the air but with a narrow twisted neck. Thus, the sugar solution was in contact with the ambient air, but microbes were unable to traverse that long glass passage.

Pasteur also ran a serious of controlled experiments by leaving beakers wide open or contaminating them with ordinary dust. Over the course of several years, she showed that boiled water, if isolated from air microbes, remains sterile indefinitely. His conclusion: only microbial contamination causes new growth; cells do not arise by spontaneous generation.

This unambiguous result had more than purely intellectual appeal. His discoveries and subsequent perfection of techniques to sterilize sealed containers of food and beverage proved to have a tremendous practical use. This helped to reduce the incidence of infectious diseases.

In the course of this elegant work, Pasteur also contributed in a significant way to the study of life’s origins. By experimentally verifying the dictum that no cellular life can occur without prior cellular life, he pushed back life’s origins to an inconceivable remote time and place. If life does not arise spontaneously, then where and when did it come from? How could anyone make useful observations and make experiments to study an event so ancient and inaccessible?

Mitochondrial DNA

2010-01-06T05:21:00.000-08:00

In women there is a DNA sequence that is passed on just through them. This is the sequence called mitochondrial DNA. The fact that is passed only by mothers to their sons and daughters has to do with the mechanics of fertilization. The sperm is extremely small compared to the egg. The sperm has its DNA concentrated in a very small area, the head. That’s indeed the only part of the sperm that gets into the egg. Included in the parts that don’t get into the egg is an organelle called mitochondria, which has a very small amount of DNA.

A molecular clock looks at differences between DNA sequences or proteins between two organisms, and then calculates back to their last common ancestor. If we have 20 differences between them, and their last common ancestor lived 20 million years ago (according to fossil evidence), one difference per million years is piling up. These differences are caused by non-selected mutations that are simply piling up over time. Then, considering a constant rate of mutations, if we have two organisms that have only 5 differences between them, we can infer that their common ancestor lived 5 million years ago.

If we want to make this argument for human genetics we have to use DNA sequences that are not subject to natural selection. If they are selected they would not be piling up over time. The sequences we can use in humans for looking at evolutionary clocks are sequences on the Y chromosome that is passed through males, and the mitochondrial DNA that is passed only through females. Both of these DNA sequences are not subject to selection.

First, let’s look at the Y chromosome sequence. On the Y chromosome are regions that are non-selected and mutate at a constant rate. The Y chromosome has very few functional genes, the most notable of which is that one that determines maleness. If we look at these DNA sequences, my brothers and I probably have identical sequences. Our last common ancestor is our father. We didn’t give our DNA much time to change; we just got it from our father.

My first cousins and I have a common grandfather, so maybe there might be a change. My third cousins might have slight differences, because we have a common ancestor longer time ago. And so on, to the most diverse humans.

A survey of Y chromosome sequences in different men from all over the world was conducted, and the group with most diversity, who obviously had a common ancestor the longest time ago, was from Africa. That says that humans’ last common ancestor for this particular sequence lived in Africa. How long ago? We can calculate the rate at which it changes. The Y chromosome “Adam” lived, according to Spencer Wells, 60000 years ago.

This is not necessarily the first man, but the one who’s Y chromosome was passed on uninterrupted to the current Africans.

Mitochondrial Eve

The small sequence of DNA in the mitochondria is not subject to natural selection and is passed only from mother to offspring. With mitochondrial DNA we can do the same analysis as with the Y chromosome in males. We can look at sequences of DNA, compare Africans to Africans, Asians to Asians, and so on. Using this method, we find that the greater diversity in mitochondrial DNA is found in Africans. The mitochondrial “Eve”, who’s DNA has been passed uninterrupted all the way to us lived about 150000 years ago. Wait a minute; she didn’t live at the same time as Y chromosome Adam. That’s just because of who passed on what. If a woman doesn’t reproduce, her sequence doesn’t get passed on.

We don’t have the first man or the first woman, but this is an interesting calculation. Maybe it is a pointer to where we originated.

A History Of Life, Part IV

2009-12-22T05:40:00.000-08:00

The evolution of eukaryotic cells is thought to have occurred 1.5 billion years ago or so. This led to an enormous diversification and innovation. The pace of evolutionary change quickened. Eukaryotic cells diversified into a broad range of single-celled organisms. Most strikingly, some lineages of eukaryotic cells gave rise to true multicellular organisms. The evidence for when multicellular organisms first appeared is conflicting. If we look at the molecular phylogenetic studies, they suggest that the first multicellular organism must have lived as long as 1.5 billion years ago. The oldest fossil that we could argue as truly multicellular, however, is about 1.2 billion years old. More convincing fossils don’t appear until as recently as 600 million years ago.

When multicellularity arose isn’t clear, but its significance is much clearer. It enormously expanded the potential for evolutionary diversification that organisms could explore. It did so for a number of reasons. First, a single organism could now be composed of many cells, each of which could specialize for a single function. In other words, selection could act in different ways on different cells so that they could become more specialized. Cells could do just one thing very well within the amalgamation of cells in the organism.

The evolution of multicellularity also allowed organisms to become larger, much larger. Through the first couple of billion years of evolutionary history there are few if any organisms that you can see without a microscope. Once multicellularity evolved, organisms could become very large. In doing so not only could they become large complex things like blue whales, but more significantly and fundamentally, they could create an internal environment. This environment within the amalgamation of cells was much more favorable than the harsh external environment that they otherwise would live in. This allowed the specialization of cells on the outside of the organism to deal with harsh environments.

Perhaps the most significant consequence of multicellularity was that certain cells within an organism’s body had to become specialized for sexual reproduction. With single-celled organisms all we need is mitotic division. The evolution of specialized reproductive cells was something that had to happen, though, when we have a number of cells with different specialized functions. Some of these cells had to be sequestered and saved specifically for the task of making more individuals. Also, a different kind of division process must have evolved. This is the process of meiosis, which creates enormous potential for genetic diversity through recombination.

With the advent of sexual reproduction and the genetic variation that is a consequence of it, there was an enormous opportunity for evolutionary change.

If we reduce the entire history of the planet Earth to the scale of a single calendar month, the appearance of multicellular organisms would occur somewhere around the 24th day. Most of the month has already passed by the time has made it past single cells. From this point on, however, things accelerated very rapidly. Life increasingly became adapted and diversified into the untold forms that we see today.

There’s so much we can talk about in this regard, but I’ll leave that for another time.

A History Of Life, Part III

2009-12-21T05:11:00.000-08:00

Not so long after photosynthesis and cellular respiration evolved, organisms started to eat each other. Single cells don’t have mouths, so the only way that one cell might eat another is by physically engulfing it. As prokaryotes diversified and competition for limited resources increased, it made sense that some cells would want to start eating each other this way, because to do so would be a very efficient way to obtain a big package of organic molecules all at once. Odd as it seems, the evolution of eukaryotic cells may be largely the consequence of cells trying to eat each other and getting indigestion.

This idea is known as the endosymbiotic theory of eukaryotic evolution, and was first proposed by Lynn Margulis. The endosymbiotic theory suggests that at least two of the most important organelles found in eukaryotic cells originated when one prokaryote engulfed another, and instead of ingesting it, it developed a symbiotic relationship with it. The Greek root symbio means “living together”. Endo is “inside”.

To get to endosymbiosis, probably the first thing that had to happen was that the cell membrane of the original eukaryotic cells had to evolve to become more flexible. Once a cell has a flexible membrane, it would be able to fold its membrane around and engulf another cell. It would also be able to do other things, like invaginate itself so that it could make internal compartments. For example, an enfolding of a cell membrane is thought to have given rise to the nucleus of modern cells, by providing an internal compartment in which the DNA of the cell could be protected from other biochemical activities of the cell.

It’s not clearly exactly how the origin of the nucleus is related to the evolution of the eukaryotic genomes, but there is no doubt that the existence of the nucleus in modern cells is essential for the way in they manage their DNA.

A Win-Win Situation

Once cells had developed a flexible membrane, larger cells began to engulf smaller cells as a way to obtain resources. Lynn Margulis contended that it is possible that a small prokaryote occasionally became engulfed but failed to be broken down. The smaller engulfed cell would now be trapped inside the larger cell. Of course, this arrangement could only be maintained over time if both cells benefitted in some way from the arrangement. In other words, this arrangement had to be adaptive in some way to both cells.

The advantage to the cell that had been engulfed seems obvious. It is now living inside of a very nutrient-rich environment, much more so than the outside. What could be the advantage to the large cell, serving as a host to the smaller cell? Margulis argued that there would be an advantage if the cell that was engulfed happened to have a more adaptive set of methabolic pathways. There are two such pathways that had evolved: photosynthesis and cellular respiration.

Specifically, Margulis suggested that the evolutionary origin of the organelles called mitochondria, which are specialized for energy processing, occurred when a cell capable of cellular respiration became endosymbiotic with a larger cell that lacked these pathways. Cellular respiration is much more efficient in the way it extracts energy from the breakdown of organic molecules. These proto-mitochondria would benefit by having a buffer from the rest of the world and a constant supply of nutrients. In return, the engulfing cell gained energy that was produced by the engulfed cell.

Similarly, Margulis suggested that chloroplasts, which are organelles specialized in photosynthesis, originated when an early eukaryotic cell engulfed a smaller photosynthetic cyanobacteria. As natural selection acted to make the host cell and its endosymbionts more dependent, this confederation of cells would eventually be integrated into a single organism. This single organism was a eukaryotic cell.

The Evidence

Margulis was greeted with skepticism when presented her theory. Over the decades that followed, however, a growing body of evidence has accumulated to suggest that she had it exactly right. Something like this happened about 1.5 billion years ago. Much of the original evidence was circumstantial. For example, if you look at the structure of mitochondria or chloroplasts, you see that they have not one membrane surrounding them, but two of them. This is what you would predict if a cell had been engulfed and maintained its own membrane.

There’s also the interesting fact that mitochondria and chloroplasts have their own genomes. It turns out that they not only have their own genomes, but they replicate by cell division themselves. This means that when a eukaryotic cell divides, in advance of that, the mitochondria and the chloroplast themselves have to divide. When the eukaryotic cell divides, there’s enough chloroplast and mitochondria to go around. The eukaryotic cell itself does not replicate mitochondria and chloroplast, they replicate themselves.

The most interesting piece of evidence, though, has come from phylogenetic studies of the mitochondrial and chloroplast gene sequences. If you look at the structure of the gene sequences found in these organelles, you find that they resemble their presumed ancestors: cyanobacteria.

Another interesting thing is that they have evolved together with the eukaryotic cell. Although they carry their own genes, they don’t carry enough genes to live entirely on their own. The genetic function of a mitochondria is in part due to genes that it bears in its own genome, and in part to genes that are found in the eukaryotic cell’s genome found in the nucleus.

The last interesting twist in our understanding of the evolution of eukaryotic cells is to ask: Who were the progenitors? It turns out that genetic evidence suggests that the archaea, not the bacteria, gave rise to the engulfing cell that became the eukaryotic cell. The organelles that were engulfed, however, were bacteria. What that means is that after the initial division of life into two major lineages, the archaea and bacteria, there was a reintegration of those cells to form this chimera as an innovative complex cell. To be continued…

A History Of Life, Part II

2009-12-20T05:40:00.000-08:00

During the early period in the history of life, an enormous number of different kinds of biochemical pathways evolved. These are what we today would call metabolic pathways. There had to be developed biochemical pathways to obtain energy, process food, build macromolecules and carry out the functioning of the cell. It’s clear that some of the biochemical pathways, which are still central to the functioning of the cells today, arose very early.

As prokaryotes multiplied and diversified, competition for limited resources must have led to the evolution of increasingly diverse ways to acquire materials from the outside. So, the early evolutionary history of prokaryotes is really the evolution of a variety of metabolic pathways, which in turn is really the evolution of proteins. All of these metabolic functions are mediated by protein enzymes, which are what are catalyzing the biochemical reactions.

This kind of evolution isn’t something we can observe in the fossil record, but it is something we can deduce from the analysis of the structure of macromolecules and the DNA that codes for them.

It’s clear that nearly all of the metabolic processes that we find in modern cells today evolved in prokaryotes before eukaryotes even appeared on the scene.

The evolution of one biochemical process in particular had an overwhelming effect in the subsequent history of all life on Earth. Because early prokaryotes must had been competing for organic resources that would provide energy, the evolution of a process that could tap into a new boundless source of energy would had been a tremendously successful adaptation. One such source of energy is sunlight.

The Miracle and Curse of Photosynthesis

Photosynthesis is a biochemical process by which the energy of sunlight can be captured and used to build sugars, which in turn store that energy for the cell. Photosynthesis also arose very early in the evolutionary history of prokaryotes. Because of the obvious selective advantage of this trait, those organisms that possessed it soon became a dominant force on the planet.

There are several different kinds of photosynthetic pathways existing in prokaryotes today. The most efficient kind of photosynthesis, which is found in modern plants and cyanobacteria, has an interesting property: its efficiency is coupled with the fact that it generates oxygen as a waste product. This means that beginning with the evolution of photosynthetic pathways, oxygen began to be produced in abundant quantities.

The fossil record and other evidence suggest that cyanobacteria probably appeared around or before 1.7 billion years ago. Beginning about that time, generation of oxygen increased as this photosynthetic adaptation increased. So, the entire atmosphere of the planet Earth transformed from one which had no oxygen in it to one that is composed of about 20% oxygen. What’s the significance of this? Oxygen is a highly reactive molecule that interacts with organic molecules breaking them down. The presence of oxygen proved to be an environmental disaster of global proportions for most of the organisms that lived before oxygen appeared, because they simply could not live and function in an oxygen-rich environment.

This was the key to how organic molecules could evolve in the first place, as you may remember from my articles on the origin of life. The theory that Miller tested in his famous experiment assumed that the atmosphere had to not have oxygen for life to arise. When oxygen appeared on the scene, that kind of spontaneous synthesis of organic molecules could no longer occur. Furthermore, those organisms that had evolved in a non-oxygen environment now had a very hard time.

The biochemical and physical adaptations of organisms that had accumulated up to that time couldn’t cope with the oxygen revolution, but a few kinds of organisms did evolve some mechanisms that allowed them not only to cope with it, but in fact to take advantage of it. Specifically, some organisms developed a completely different process for methabolizing energy. This is a process we call cellular respiration.

The methabolic pathways of cellular respiration actually take advantage of the presence of oxygen to enormously increase the efficiency with which energy can be extracted from organic molecules. The evolution of photosynthetic pathways radically and permanently changed the Earth’s atmosphere and the biological inhabitants living on it. In the long run, also, it made certain changes that were key milestones in the history of life. Notably, it increased the amount of energy that can be produced by cells in two ways. Cells had found a new fuel, the sunlight, and a better way to burn the old kind of fuel with cellular respiration.

This increase in the amount of energy available permitted cells and organisms to become ever larger and complex. Another positive consequence of the accumulation of oxygen was the development of a layer of ozone gas in the upper atmosphere of the Earth. Ozone absorbs the radiation that hits the planet, and in so doing it made it possible for organisms to inhabit environments that previously were unavailable to them, most notably leaving the water and entering a land environment. To be continued…

A History Of Life, Part I

2009-12-19T05:28:00.000-08:00

“All living things have much in common, in their chemical composition, their germinal vesicles, their cellular structure, and their laws of growth and reproduction. (...) Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from one primordial form, into which life was first breathed.”
Charles Darwin, On the Origin of Species

Darwin’s view of descent by modification led him to the conclusion that there existed sometime in the very remote past an organism that is literally the universal common ancestor of us all. I’ve already written some articles about how life could have arisen from non-living matter, you may be interested in reading some of them. At some point in the remote past, life was somehow “breathed” into a primordial form. An entity appeared we’ll all agree was living. Once this entity had gained a foothold on life, it became the common ancestor to everything that has ever lived on the planet.

Exactly when this organism arose is uncertain, but we know a few things. We know that it has to be around 3.9 billion years ago, when the surface of the Earth was no longer been bombarded, and the crust of the planet had cooled sufficiently for liquid water to appear. Also, it had to be sometime before 3.5 billion years ago, which is the date of the oldest fossil cells that had been found so far. These oldest fossils are found in rocks in Western Australia. They’re actually quite advanced in their appearance, resembling certain kinds of modern bacteria, so most biologists assume that cells must have appeared even earlier than this.

Let’s review the characteristics of this first living thing. This organism was certainly a single cell. It had to have a membrane that created a compartment separating it from the rest of the world, allowing the accumulation of specialized organic molecules within. Among the organic compounds that made up this first organism there must had been complex polymers capable of catalyzing biochemical reactions, the kinds of reaction that would be necessary for this primitive cell to process materials, grow and divide.

The most specialized of these biological polymers must have been some kind of molecule that could not only catalyze reactions, but also serve as a template for making more of itself. In the earliest cells, this information probably was in some form of RNA. Later, some kind of genetic system was established in an RNA world. DNA then took over the role of storing and transmitting genetic information, while proteins took over the role of the functional molecule responsible for everything else the cell might do.

Without doubt, at this early period in time, the major effect of natural selection on this primitive organism was to refine its genetic system and to ensure that the different kinds of molecules within it would cooperate. There had to be some selection so that these different kinds of molecules (lipids, proteins, nucleic acids and sugars) would be able to specialize to do their own jobs in coordination with each other.

A Prokaryote World

By the time we get to the oldest fossils, evolution had established a recognizable cell, which is not too different from what might be a typical bacteria we find today. There’s a rich fossil record that continues from that period up to the present day. This fossil record makes a couple of things clear. First of all, it shows that when life did emerge, it emerged very rapidly and quickly filled the planet.

It also shows that only prokaryotic cells existed for about 1.5 billion years, until about 2 billion years ago. In other words, the more complex eukaryotic cells didn’t exist for quite some time. The early evolution of life was all in the context of prokaryotic cells. The fact that prokaryotic cells ruled the Earth for 1.5 billion years might sound boring, but it’s nothing of the sort. There were at least two major and exciting evolutionary events that occurred during this period.

The first was that the prokaryotes themselves split into two major lineages. We call these the bacteria and the archaea. The differences between bacteria and archaea are relatively subtle in the modern world. There are biochemical differences in their internal composition and other things. In fact, there are enormously more bacteria in the world today than there are archaea. The archaea largely have been relegated to very extreme environments. These are the ones that we find in extremely saline water, for example.

In a sense, archaea are not necessarily an important form of life to understand today, but they are very important for understanding the origin of eukaryotic cells, as we’ll see later.

Applications of Genetic Engineering

2009-12-18T05:17:00.000-08:00

The applications of genetic engineering are increasing rapidly. In its broader definition, genetic engineering simply means the manipulation of organisms to make useful products. This is something humans had been doing since the beginnings of recorded history. Selective breeding of domestic plants and animals is a kind of biotechnology. It is though a very slow kind of biotechnology. What’s different about modern genetic engineering is that we can modify organisms much more rapidly and radically.

The first commercial use of genetic engineering is a relatively simple one. This is to manufacture particular kinds of proteins in abundance that would otherwise be tedious and costly to produce. Consider the protein insulin. This is a hormone that is involved in the regulation of blood sugar. People who suffer from diabetes are unable to produce enough insulin. Diabetes can be treated, however, by injections of insulin. The question is where to get the insulin.

A while ago, the only source of insulin would be from farm animals, such as cows and pigs. The organs of these animals would be harvested and they would provide insulin. That was, though, a tedious and costly process. Furthermore, the insulin of these animals, although very similar to human insulin, wasn’t identical to it. It didn’t always work in certain individuals.

With the advent of modern biotechnology, however, it becomes a relatively simple matter to insert the human insulin gene into the genome of an e. coli bacteria. In fact, now almost all insulin used in medical treatment is manufactured by genetically modified bacteria. It has a much lower cost and a higher level of purity.

There are dozens and dozens of other medically important proteins manufactured in the same way, and hundreds are in commercial development.

The bacteria we genetically modified essentially turned into a chemical manufacturing plant. Here we are more interested in the protein produced by the bacteria than in the organism itself. We might also genetically engineer organisms because we’re interested in the organisms themselves. Many examples of this come from crop plants that had been modified.

In the United States, close to 3 dozen transgenic crops are now in common commercial use. What kinds of gene might we want to insert into a crop species? We might want to insert genes that improve resistance to insects, for example. We might insert genes that cause increased growth, or that improve the nutritional value of the plant.

As you’re probably aware, there are many people who are strongly opposed to genetically modifying crop organisms. Why are they? Opponents worry about a number of issues. For example, if we modify a plant to include a pesticide, how do we know that pesticide produced by the plant won’t get into the environment? How do we know that the modified species won’t escape from cultivation and become some kind of super competitor with wild forms?

These concerns are valid, but at the same time genetic engineering proceeds, and I’m sure our scientists will continue to develop it further.

Genetic Engineering, Part II

2009-12-18T05:06:00.000-08:00

After the discovery of methods for making recombinant DNA, the second major advance that led to the current revolution in genetic engineering was to develop the ability to introduce DNA from one organism into another, creating what we call transgenic organisms. This may sound like a difficult thing to do, like creating a genetic Frankenstein monster. It isn’t so, however.

To understand this we need some background in a process called conjugation. Conjugation occurs when one bacterial cell forms a physical connection to other bacteria cell, and then transfers a small piece of DNA called a plasmid. Some biologists say it is something like sex between bacteria. Using recombinant DNA technology to modify the DNA in a bacterial plasmid, say by inserting a gene from another organism, we can use conjugation to transfer it into other bacterial cell.

Let’s say we want to insert a gene from a firefly into a bacterial cell. Let’s say we want to insert the gene for the enzyme luciferase, which is the enzyme responsible for making the firefly’s tail light up. Why would we want to do this? Well, for a couple of reasons maybe. We might want to insert a gene into the bacteria so we can make a lot of copies of that gene, which we would need to do if we wanted to study the structure of that gene. Alternatively, we might do that because we want to make a lot of copies of the protein produced by that gene, and it is a lot easier to make a lot of the protein using bacteria as opposed to raising fireflies.

To do this we need to get the firefly’s luciferase gene into e. coli bacteria using a restriction enzyme that would clip out the gene from the firefly’s genome, and also make a single cut in a bacterial plasmid piece of DNA. If we can find the right restriction enzyme to do this, and it is very likely we can because these restriction enzymes recognize so many kinds of sites, we can use the enzyme to cut bacterial plasmids and the firefly’s genome. Then we recombine the gene from the firefly with the plasmid using the sticky ends of both.

Once again, to get this process to work, there are more details we need to pay attention to. For example, we need to make sure that we’re actually putting in the right piece of DNA from the firefly. We also need to figure out ways to identify the particular bacteria that had taken up the recombinant plasmid. There is a wide array of techniques used in this area.

Other methods to make transgenic organisms involve genetically engineering small chromosomes that not only have the regions of DNA we’re interested in, but also all of the other regulatory DNA and other factors that are associated with normal chromosomes. These chromosomes can be replicated and function like normal chromosomes in the cell. For example, there has been great success in creating an artificial yeast chromosome. Yeasts are very simple eukaryotes. So, we can put artificial chromosomes with whatever genes we want into yeast cells very conveniently. There has been in fact considerable success in making a functional artificial human chromosome.

The technical challenges associated creating a transgenic organism do become increasingly difficult the more complex the host organism we want to manipulate. However, it won’t be very long before it comes routine to insert foreign DNA into any kind of cell.

Genetic Engineering, Part I

2009-12-17T04:55:00.000-08:00

It seems like barely a day goes by without a news story having to do with manipulating genes, moving genes from one organism to another or the impact of these kinds of genetic manipulations. The key points of genetic engineering are quite simple and stem from the description of the DNA double helix that was proposed by Watson and Crick. Advances in genetic engineering have much to do with learning how to apply what was learned long ago.

So, genetic engineering consists basically in cutting and pasting DNA. How can you cut and paste a molecule of DNA? The technical term for this is to "make recombinant DNA". “Recombinant DNA” refers to the combination of DNA from two different sources. Our ability to create recombinant DNA in the lab is based on a fortuitous discovery having to do with how bacteria defend themselves from being attacked by viruses. Many kinds of viruses specialize in attacking bacterial cells, and they are called bacteriophages. They attach to the outside of the cell and inject their DNA into it. Then, the virus’ genetic material takes control of the cellular machinery of the bacteria, turning it into a factory for making more copies of the virus.

This is very bad news for the bacteria, so you can imagine that natural selection would favor the evolution of mechanisms that defend the bacteria against viral attack. One such mechanism, discovered in the late 1960’s, involves enzymes produced by the bacteria, called “restriction endonucleases”, or simply restriction enzymes. They cleave the double helix of the DNA molecule, breaking it into two pieces. In so doing, they render the DNA non-functional. The viral DNA that’s injected into the bacterial cell is chopped up before it can take control of the bacteria. This is an effective defense, but there is in fact a problem here. If restriction enzymes produced by the bacteria can cut up a molecule of DNA, what’s to stop these enzymes from attacking the bacteria’s own DNA?

Part of the answer to this question is exactly what made restriction enzymes so useful to molecular biologists. Restriction enzymes don’t cut the DNA double helix in random places, but only at a precise point defined by a particular sequence of bases. These sites are called “recognition sites”, or “restriction sites”.

Restriction Sites

Restriction sites are typically only a few nucleotides long, about four or six bases long. Another interesting characteristic of these sites is that the two complimentary strands of DNA usually are palindromic. In language, a palindrome refers to a set of letters that are spelled the same way backwards or forwards. For example, the word “dad” is a palindrome, as is the sentence “Madam I’m Adam”. In DNA, a palindrome occurs when the two strands of the double helix have the same sequence of bases in reverse direction with respect to each other.

So, if the sequence of one strand is GAATTC, then the complimentary sequence on the opposite strand would be CTTAAG. It is indeed like this because of the complimentary rules that Watson and Crick discovered so long ago.

How does the fact that these restriction enzymes only cut DNA at specific palindromic sequences help prevent the enzymes from chopping the bacteria’s own DNA? This actually doesn’t help the bacteria directly, because given that these sequences are so short, it’s very likely that somewhere in the bacteria’s own DNA that sequence would occur. However, what the bacteria can do is to selectively protect the restriction sites found in its own genome by slightly modifying the bases.

Specifically, what happens is that so-called methyl groups are added to some of the bases occurring at the restriction sites of the bacteria’s own DNA. This “methylation” prevents the enzyme from identifying that area as a restriction site, and thus protects the bacteria’s own DNA.

So, how does this help us make recombinant DNA? The answer to this question relies on one more fact we have to learn about restriction enzymes. Not only does the restriction enzyme recognize particular sequences of nucleotides, it also cuts the DNA strands very precisely between just two particular nucleotides in the sequence. Because the restriction site is palindromic, the exact place where the cut is made on each of the complimentary strands of the double helix would be offset from each other by a few bases.

If the restriction site sequence of one strand of DNA is GAATTC, then we know that the sequence on the opposite complimentary strand would be CTTAAG. A restriction enzyme recognizing this site might cut the DNA exclusively between the G and A nucleotides. In this case, after the double strand is cut, each cut piece would now have a short section of single stranded DNA.

The exposed bases on these single stranded bases of the cut DNA molecule are called sticky ends. They are called sticky ends because they would line up, form complimentary base pairs, and essentially stick to any other single stranded sequence of bases having the complimentary sequence. Here’s the key point, the sticky ends from any fragment of DNA that had been cut using the same restriction enzyme would always be complimentary to each other by definition. This means that if you cut two different DNA double helixes with the same restriction enzyme, even DNA from completely different species, when you mix all of those fragments of DNA, they would come back together because of the base pairing.

Pasting the DNA

Then, you add to the mixture the enzyme DNA ligase. This enzyme sticks together the newly joined DNA helixes by building back the strong chemical bonds that the restriction enzyme had broken.

Once you’ve used DNA ligase to put the sticky ends back together permanently, you now have a piece of recombinant DNA that is made of two different original molecules.

There are hundreds of different kinds of restriction enzymes that had been isolated from a variety of bacteria. Each different kind recognizes a different DNA sequence. So, they cleave DNA at a different point along the overall length of the molecule. By using different restriction enzymes, you can cut molecules of DNA in different places, and then paste them back together in different arrangements. Actually in practice there are many other details that you have to consider to make this process work. In theory, at least, our ability to cut and paste DNA boils down to the use of enzymes normally used by bacteria to defend themselves against viruses.

Basics of Genetics

2009-12-15T04:37:00.000-08:00

In trying to solve the puzzling results he found in his experiment, Mendel developed a hypothesis that explains what genes do on chromosomes when they are transmitted, even though he had no idea what genes or chromosomes were. We can divide Mendel’s hypothesis into four related ideas. First, Mendel argued that the different versions of what he called “heritable factors” must be responsible for producing the different traits. A “heritable factor” was responsible for the purple flower, and a different one was responsible for white flowers. What Mendel called heritable factors are what we now call genes. The different versions of the genes are what we call alleles. For example, the gene responsible for flower color in peas has two alleles, one for purple flowers and the other for white flowers.

Mendel’s second idea was to conclude that each individual had not one but two different particles for each character. In other words, each individual has two alleles for each gene. Mendel made this conclusion knowing nothing about chromosomes, but microbiologists confirmed this by showing that each offspring has two copies of every gene.

Mendel’s third suggestion was that one allele of the two that an individual possesses might actually be dominant over the other one. In other words, one allele is expressed even if the other allele is present. We say that one allele would be dominant, and the one that is not expressed we call recessive.

Let’s go back to Mendel’s experiment to clarify this. He started with true breeding lines of purple and white flowers. He argued that these true breeding lines, that produce only one or the other flower color, must always have two of the same kind of allele. The purple flower plant has two purple alleles and the white plant has two white alleles.

The offspring of this cross must receive one allele from each parent, and thus have one purple allele from one parent and one allele from the other parent. Because all of the offspring in the F1 generation had purple flowers, Mendel argued that the purple form must be dominant over the recessive white form.

Mendel’s forth idea was that when a parent produces gametes in preparation for sexual reproduction; each gamete only gets one of the two alleles that that parent possesses for a particular gene. If we are talking about flower color, if a parent possesses two of the same kind of allele, when it produces gametes, all of the gametes would have only that kind of allele. For example, purple plants from Mendel’s parental generation would only make gametes that have purple flower alleles. The same would be true of the parental white plants.

Here’s the kicker. When we have individuals that have two different kinds of alleles, for example individuals in the F1 generation, can produce two kinds of alleles. They have both a purple allele and a white allele, so they can produce gametes that have either purple or white alleles. In fact, they do so in a 50:50 ratio. It is equally likely that their gametes would have one or the other allele.

The original parental plants Mendel started had two alleles for the same color. We call individuals that posses two of the same kind of allele “homozygous”. The parental plants were homozygous. By contrast, when an individual possesses two different kinds of alleles for the same gene, we say that it is heterozygous. Individuals in the F1 generation were heterozygous.

We give some labels to the alleles. We’re going to give the purple flower allele the capital letter P, and the white flower allele the lowercase p. Giving the uppercase and the lowercase versions of the same letter is one common way that geneticists designate different alleles for a gene.

Because the original in Mendel’s cross were homozygous, they could produce only one kind of gamete. We’ve already said why their offspring should have all purple flowers. If the purple allele is dominant to the white allele, the F1 offspring all have one big P and one little p. Because they all have a big P, which is dominant, they’ll all be purple, regardless of the fact that they have the little p too.

Now I want to introduce two new terms: phenotype and genotype. An organism’s phenotype refers to what it looks like. It refers to the traits that organism expresses. For example, we would say of a purple plant that it has the purple phenotype. The genotype of an organism represents its genetic makeup. The genetic makeup of an organism clearly would have something to do with the traits that the organism expresses. It is important to keep in mind, though, that a given phenotype might be produced by different genotypes.

Let’s go back to our pea plants. Because the purple allele is dominant over the white allele, there are two possible genotypes that could give rise to the purple flower phenotype. Individuals having two big P alleles clearly would have the purple phenotype. So would individuals having one P and one p allele. Both the PP and the Pp genotypes yield the purple flower phenotype. That’s because the purple allele is dominant over the white allele.

On the other hand, the only way we could get the white flower phenotype is if we have a genotype that has both p alleles. This helps us explain the surprising findings from Mendel’s first cross. The white flower phenotype had disappeared completely in the F1 generation, but not the white allele, which was hidden in the heterozygous genotypes of those individuals.

Let’s look at what Mendel found when he crossed these heterozygous F1 individuals together. He found that the offspring in the F2 generation produced both purple and white phenotypes in the ratio 3:1. To understand that 3:1 ratio, let’s consider again the kinds of gametes and the proportions of gametes that those F1 individuals could produce. Because these individuals were all heterozygous, they could produce two kinds of gametes, either a purple allele or a white one. Indeed, each individual would produce equal numbers of both types of gametes.

This makes an intuitive sense. This is very like flipping coins. We’ve got two possibilities; we could come up with a heads or a tails. The key question to ask is what proportion of individuals in the F2 generation would have the possible genotypes that could be formed by joining the gametes that the F1 individuals produced.

An easy way to think about this is to use a convention that we call a Punnett square. Along the top of the square we have one column that has big P on top of it and one column that has little p. Along the side, we have one big P and one little p.

The point of making this grid is that it helps us think about how these different gametes can combine to form genotypes in the offspring. If you fill out the grid by connecting the two alleles possible for each cell, you’ll see that you’ll get three different genotypes. We have PP, Pp and pp individuals. What you also see is that both PP and Pp have the dominant allele, which is the represented in the phenotype. Looking at this you’ll expect to see three purple individuals for every one individual.

With this we can explain why Mendel found a 3:1 ratio in his experiment in the F2 generation. Mendel’s brilliant insight was to put all of this together without knowing anything about genes or the physical basis of chromosomes.

We now refer to this key idea of the existence of two different alleles in each individual as “Mendel’s Law of Segregation”. This law is significant for a number of reasons. First, it completely refuted the blending hypothesis and demonstrated that heritable factors must be particulate. Second, what Mendel did was to provide a framework for looking at more complicated patterns of how traits are transmitted between parents and offspring, which allow us a more complete understanding of the genetic basis of inheritance.

Mendel: The Father of Genetics

2009-12-14T05:19:00.000-08:00

Mendel grew up on a small farm in Austria, so he got an intuitive understanding of plant and animal breeding. Mendel wasn’t an ordinary monk. In the 1850’s, his order sent him to study at the University of Vienna, one of the leading universities of Europe. He was taught by many outstanding scientists there, most notably the physicist Christian Doppler. When he returned to the monastery, he began to study heredity in garden peas.

At the time of Mendel’s work, chromosomes hadn’t been described, let alone mitosis and meiosis. Nothing was known about the physical basis of inheritance. It was obvious, though, as it had been for many thousands of years, that offspring tend to resemble their parents. It also was obvious that different combinations of traits in parents would appear to be mixed in different ways in their offspring, sometimes surprisingly so.

At that time, the dominant theory about how inheritance worked suggested that some material from the two parents was blended together when offspring were produced. You can think of this like mixing paint. What scientists thought was that when offspring were produced, paint from the two parental buckets would simply be poured together into the offspring’s bucket, and the result would be some mixture of the two. If for example an animal with light colored fur mated with a dark colored one, the result would be an intermediate color. Indeed, sometimes that is observed.

The blending hypothesis didn’t account for many other observations made by plant and animal breeders, though. Specifically, the blending hypothesis predicts that over time, all variation within a species should vanish. Think of blending buckets of paint. If we start with a whole bunch of colors in different buckets, and as those buckets are mixed together, over time we’ll just have buckets with the same color.

In the real world, however, plant and animal breeders realized that even when individuals in a population mated randomly for a very long period of time, there always remained variation among individuals. Also, sometimes traits would appear in offspring that weren’t present in either of the parents.

These were the problems Mendel was trying to address when he began his work on pea plants. To understand Mendel’s work, let’s see the very first experiment he did: the monohybrid cross.

Mendel’s most famous experiment involved looking at the inheritance of flower colors. In these pea plants, flower colors occur in only one of two forms: purple or white. We call this kind of character a “dichotomous character”. It’s one thing or the other. Pea plants have many such dichotomous characters, not only flower color, but also seed color, the shape of the seed and the height of the plant.

Mendel understood that the existence of this kind of dichotomous traits couldn’t be reconciled easily with the blending hypothesis, so he decided to investigate how these traits were transmitted across generations.

Mendel began his first experiment with parents that came from what we call true breeding lines. These were pea plants that would produce only one form of the trait. For example, one plant that produced only white flowers, or only purple flowers. He then crossed a white flower plant with a purple flower plant. This is called a monohybrid cross because he is hybridizing two varieties that differ in only a single character.

When Mendel performed this cross, he found a very surprising result. Remember, one parent was purple and the other white. When he crossed them, all of the offspring were purple.

We started with a parental generation, one purple and one white. The offspring of this parental generation are called the F1 generation. The result that Mendel got was surprising because it completely contradicted the blending hypothesis. The blending hypothesis predicted that he’ll get an intermediate color, like a light purple. But no, all of the offspring were purple flowered. The white flower color seemed to be completely lost.

Even more surprising was what happened when he crossed these F1 individuals. What he found in the so called F2 generation was that the white flower color reemerged. He would have some purple flower individuals and some with white flower individuals. Furthermore, these individuals would always occur in approximately the same ratio. There always would be about 3 purple individuals for every one white individual.

Mendel did this kind of cross with a number of other dichotomous traits, like seed color and seed shape, and he always got the same result. One trait would disappear in the F1. Then it would reappear in the F2 in the ratio of 3 to 1. What could account for this pattern of inheritance? How could you have one trait lost completely and then have it again?

In trying to solve this puzzle, Mendel developed a hypothesis that explains what genes do on chromosomes when they are transmitted, even though he had no idea what genes or chromosomes were. In so doing, he essentially established modern genetics. In the next article we’ll see the hypothesis Mendel developed to explain the surprising and exciting results he got.

Pea Images Source: Wikimedia Commons. Here and here.

Origins of Creationism

2009-12-11T05:08:00.000-08:00

During the 1800’s, in response to evidence of vast geological epochs, most theologians equated the days of creation in the Genesis account with geological ages. They accepted the idea that the Earth was very old. William Jennings Bryan still held these views in the 1920’s when he led the anti-evolution crusade.

During the early 1900’s, evangelicals in America often reconciled science and scripture by positing that the Genesis of account wasn’t really complete. They posited that there could be a gap between “In the beginning…” and the rest of the account. This would allow for unnumbered geological ages and a vaster array of fossils. That was a widely held belief among conservative Christians early in the 1900’s.

Prior to 1960, in fact, the leading advocates of a literalistic reading of Genesis tended to be in small Protestant sects, like the Seventh-Day Adventist Church. Indeed, the most visible proponent of young-earth creationism was a Seventh-Day Adventist science teacher named George McCready Price. He argued for a recent six-day creation, with Noah’s flood shaping the Earth’s features and laying down its fossils. His teachings were limited mostly to Seventh-Day Adventist Churches and colleges. This view of a young-Earth would utterly split religion from mainstream science. That is what has been happening during the last 40 years.

Creation Science

How this belief did became a main conservative Christian belief in America? Central in this story is a Baptist engineering professor named Henry Morris, who revived “Noah’s flood geology” in 1961, and began spreading it widely among conservative Protestants. He used the name “scientific creationism” or “creation science”.

Henry Morris was a very intelligent young man, I must admit. He became convinced that the entire bible must be literally true, or none of it can be trusted. Genesis had to be believed equally with the Gospel accounts. Believing this, he focused his career on the study of hydraulic engineering, to learn how catastrophic water action could impact geological features. Working with theologian John Whitcomb, Morris published the book The Genesis Flood. This book presented “scientific arguments” for creation within a biblical chronology. It attributed the fossil record and most geologic features to a single worldwide flood.

This book, as one could expect, was virtually ignored by the scientific community. During the 1960’s and 1970’s, however, it gained an enormous following within conservative protestant circles. Morris followed this book with a string of books, articles, tapes and lectures. He compounded his efforts with an institutional development. Henry Morris founded the Institute for Creation Research, or ICR, which has widely promoted “scientific creationism” through books, pamphlets, films, lectures and debates. ICR biology textbooks dominate the Christian school market.

During the mid 1970’s, the ICR prepared a creationist textbook stripped of any reference to a creator for the public school market. It was this textbook which began to be adopted by conservative school boards around the country, and drew the attention of secular scientists to these developments. This restarted the battle over biology education in public schools.

The battle for the teaching of scientific creationism in public schools began with the legal argument that it was as scientific as evolutionary science. The struggle ended, though, with the judicial conclusion that creation science was simply religious dogma. Morris and his followers freely admitted that teaching creation promotes belief in a creator. Indeed, he never tried to cover that. He claimed, however, that the promotion of this belief in a creator was simply an incidental result of teaching scientific evidence supporting the abrupt non-evolutionary appearance of the universe, life and species.

Morris claimed that teaching evolution promotes a philosophical viewpoint, citing the examples of Huxley or George Gaylord Simpson. Assuming this position, both evolutionary science and creation science, according to Morris, could be given balanced treatment in public school biology without violating the Constitution. He said that creationism isn’t more religious than evolution.

This argument had wide appeal. Public opinion surveys persistently found that Americans were evenly split over the questions of origins. About half believed that humans were created recently, as the Bible says; and half believed humans evolved. Americans broadly supported the idea of teaching both views in public schools. Three States adopted so-called “balanced treatment laws”. This is when there was a tremendous reaction by the other side.

Science groups, mainstream religious organizations and civil liberties groups challenged these new policies and laws in court. They argued they violated the separation of Church and State. One by one, each one of these laws was declared unconstitutional. In 1987, the United States Supreme Court ruled against the Louisiana balanced treatment act. No law is needed to teach scientific evidence for or against evolution.

These rulings ended the teaching of scientific creationism in public schools, but the battle sensitized school officials to the issue. The excluding of creation science from public schools further fed the Christian academy and homeschooling movements, where parents could control the type of biology was taught.

The battle continues to this day, and there aren’t signs of an ending.

The Real Causes of Creationism

2009-12-10T05:10:00.000-08:00

By 1959, the Neo-Darwinian synthesis had gained near universal acceptance among biologists. Scientists finally understood how evolution worked. To reverse the effects of the anti-evolution crusade, the Federal Government began funding a new series of high school biology textbooks that emphasized Neo-Darwinian evolution. Up to this time, as a lingering effect of the anti-evolution crusade, most of the textbooks had simply ignored the subject of origins.

Neo-Darwinists such as Julian Huxley and George Gaylord Simpson popularized the expansion of this new biological synthesis into a broad all-encompassing humanistic worldview. They saw science as the only source for truth, and evolution as an ethical principle within science. They urged all humanity to take hold of the evolutionary process and shape it for the good of society.

For Huxley, evolution was a progressive force, generating forms ever more able to transcend their environment. He takes this as an ethical goal for life, and for humans in particular. He would call his system a humanistic religion. He was in an influential position, not only was he a noted scientist, but after World War II, he had been appointed the founding director of UNESCO. He used UNESCO as a world platform to promote his humanistic religious views.

George Gaylord Simpson saw evolution producing beings of ever greater awareness. For him the goal was knowledge, which humans could use for the general good. We have to note that at this time evolution had ultimately triumphed and was almost universally accepted as truth. In their triumphalism, evolutionists in America ignored societal shifts that by 1959 had closed large segments of American population towards the theory of evolution.

Darwinism’s public revival in the media, often proposed by people who wanted to carry it beyond biology into an entire worldview, coupled with the reappearance of Darwinism in textbooks; triggered a strong and enduring reaction among American conservative Christians.

Let’s do a quick review of the religious history of America. Largely invisible to America’s cultural elite, theologically conservative strands of American Protestantism had not withered like they expected, but they had actually increased in size and influence. A variety of factors contributed to this. Literalistic protestant sects existed largely on the fringes of American society until 1920. There were mainline denominations like the Methodists, the Lutherans and the Episcopalians, which dominated protestant religion. The literalistic sects were on the fringes, they weren’t mainstream. They had untrained ministers who were “called” to ministry, who never were taught the modern ideas of biblical interpretation and evolutionary views of religion.

What happened since 1920 is that these small literalistic denominations grew larger and larger. As the clergy of America’s mainline protestant denominations became more liberal, many conservatives moved to denominations more committed to biblical inerrancy.

And Then There Was the South

The South was the only region of the country where conservatives dominated the mainline denominations. During the 20th century there had been a growth in the importance of the South. The South gained economic, cultural and political importance thanks probably to air conditioning, as more people could live there and the economy could thrive. As people moved to the South, they moved to these more conservative Churches, and southern ways spread nationally.

These Churches developed their own colleges, schools, publishing houses, journals and evangelist associations that would reach out other denominations. Before that, most of these structures (colleges, schools, etc…), were denominational. Now they became inter-denominational, but with a conservative bent. This opened the inter-denominational network where biblical inerrancy was central.

On the other side, the secularization of western society virtually emptied European Churches. Hardly anyone in Western Europe went to Church anymore. This affected the vitality of American liberal Protestantism, and strengthened American conservatism.

The Splitting Apart of Science and Religion

Another important point is that most scientists pulled out of the Church. Early in the 20th century most scientists would go to Church, and they would encourage the Church to engage science. Now, the liberal Churches didn’t have any scientist members who encouraged them to engage science, so they pulled out of the battle with conservatives.

Darwinism remained an anathema to conservative Protestants, but they largely kept their objections within their own subculture until the 1960’s. The appearance of these federally funded evolutionary biology textbooks ignited protests from the parents and Churches. When they saw these textbooks coming to the school, they were living in a subculture where evolution was ignored. Suddenly, their children were coming home with textbooks with heavily evolutionary content. This generated ignited reactions.

Citing the likes of Huxley and Simpson, conservatives denounced scientists who were trying to push their science beyond biology into how we should live. By the mid 1960’s, fundamentalists were protesting the teaching of evolution in public schools and demanding that equal time be given to their viewpoints.

These developments had created a new situation. Religion and science had split apart. On the side of science, the materialism of the Neo-Darwinian synthesis was simply less amicable to reconciliation with religion than earlier theories. Further, scientists cared less about reconciling science and religion. In the early 1900’s, scientists tried to work out a reconciliation. By the late 1900’s, scientists didn’t even care about religion. On the science side, there has been a shift towards ignoring the topic.

On the religion side, there was also a greater deviation. The expansion of conservative Churches, coupled with the erosion of liberal Churches, has shifted the center of American Protestantism toward biblical literalism. Conservatives showed less interest in reconciling modern science with scriptural interpretation.

So, this is the historical background on which the modern creationist movement emerged. It is interesting to note the historical causes, and we can understand why it appeared in America, and at this time.

The Scopes Trial, Part II

2009-12-09T05:42:00.000-08:00

The initial attention attracted by the new Tennessee statute expanded into media frenzy, when six weeks after the statute became law, John Scopes was indicted for violating it. From its bizarre beginnings to its inconclusive ends, the Scopes trial was never a normal criminal prosecution.

Soon after Tennessee enacted the anti-evolution statute, the ACLU, from New York, offered to defend any Tennessee school teacher willing to challenge this law’s constitutionality in court. Dayton, a small town in East Tennessee, was in an economic crisis because its main industries had closed recently. Its civic leaders invited a local science teacher named John Scopes to accept the ACLU challenge as a means to publicize their town. Scopes agreed to the scheme even though he was not a biology teacher, and he had never violated the statute.

Scopes’ indictment made front page news around the world. He was never arrested. Indeed, he was never even threatened with jail. He was assured his job back the following year, because he was invited to challenge the law by the President of the school board himself. He actually spent most of the time from the indictment to the actual trial making media appearances and traveling.

Both sides in the larger controversy saw the pending trial as an opportunity to make their case to the general public. Both Bryan and the ACLU lawyers recognized this as an opportunity to make their case. It became a show trial and in the actual trial John Scopes actually disappeared. He never testified or major appearance.

On the defense side, was America’s most famous trial lawyer, noted religious skeptic, who was known for talking and writing about the dangers of religion, Clarence Darrow. He volunteered his services to lead a team of crack ACLU lawyers to defend Scopes. It was the only time in Clarence Darrow’s entire career that he volunteered his legal services. His goal was to debunk religious law-making and to promote individual liberty.

On the other side, Jennings Bryan, who was a lawyer but hadn’t practiced law in over 30 years, volunteered too. He volunteered to make the case against the teaching of evolution. He knew that the law, and not John Scopes, was on trial.

The media promoted this heavyweight bout as “The Trial of the Century”. It was just a simple misdemeanor trial with a potential fine of 500$!! However, Scopes wasn’t really on trial, the teaching of evolution and academic freedom was on trial. It was the first broadcasted trial in American history. It was covered by over 200 reporters. It was said at the end that more words had been telegraphed from the United States to England about this trial than any event that had previously occurred in American history.

The trial itself was anticlimactic, as each side made their very familiar arguments. These had been circling around for five years. Neither side disputed that Scopes had violated the law. When the judge refused to strike the statute as unconstitutional, Clarence Darrow asked the jury to convict Scopes so that they could appeal the judges of a higher court. If Scopes wasn’t convicted there couldn’t be an appeal and they couldn’t challenge the law.

They convicted Scopes and he was fined the minimum amount of 100$, which was paid on his behalf by one of the reporters. The trial’s most memorable event occurred near its end, when Clarence Darrow invited William Jennings Bryan to take the stand as a witness in defense of the anti-evolution statute. Bryan agreed to do so. Darrow asked questions about biblical literalism, such as: Was Jonas inside the whale for three days? Was Eve made with Adam’s rib? These questions made Bryan and the biblical account look foolish.

Following the trial, Scopes accepted a scholarship to study Geology at the University of Chicago, and became a petroleum engineer in Venezuela, and later managed an oil refinery. Bryan died in Dayton, less than a week after the trial, maybe because of the stress of the trial. His crusade, however, continued. Scopes’ conviction went on to appeal into Tennessee’s Supreme Court and it was overturned on a technicality.

The anti-evolution statute was declared constitutional, which foreclose any further appeal to the United States Supreme Court. Other States imposed similar laws. Indeed, if you look at the textbooks of the time, the theory of evolution is virtually non-existent. This is really an interesting case of willful ignorance, which repeated itself later in our history.

The Scopes Trial, Part I

2009-12-09T05:39:00.000-08:00

Leading scientists and political figures, who were deeply religious themselves, got involved in the debate over the teaching of evolution, and took it to the public. In 1924, William Jennings Bryan transformed this religious dispute into a major political crusade. At age 62, William Jennings Bryan was a living legend, and America’s most famous orator. He had been nominated for President by the Democratic Party at age 36, the youngest presidential nominee of any political party ever. He was nominated again two times after that.

Following his narrow defeats, he remained in the public eye as a speaker and writer for progressive political causes. He served as Woodrow Wilson’s Secretary of State, until he resigned that post in protest over Wilson entering World War I. Bryan was almost a pacifist.

His progressive politics and his antimilitarism always had a moralistic religious basis. By the 1920’s, he led the fundamentalists forces within the mainline Presbyterian Church. In 1921, Bryan heard of an attempt by Kentucky Baptists to politicize the anti-evolution movement by seeking to outlaw the teaching of Darwinism in public schools.

As a political progressive, Bryan instinctively welcomed legislative ways to deal with social problems. As a political conservative, Bryan deplored Darwinism as corrosive of religion. As a leftist, he opposed militarism, imperialism and laissez-faire capitalism. As a populist, he was suspicious of the leading institutions, such as science, and believed that people has a right to control public education. He saw this Kentucky proposal as a solution to what he perceived to be an important social problem.

In 1922, Bryan went to Kentucky to support the Baptist proposal of outlawing the teaching of evolution. He then carried his crusade for such laws nationwide. Kentucky turned to be a narrow defeat, the proposal lost by one vote in the legislature. After that, Bryan took the crusade around the country. He spoke in State after State. In this way, these issues started coming up and being debated in State legislatures.

If you look at his speeches, you can see that Bryan objected only to the Darwinian theory of human evolution. He actually viewed the days of creation as vast geological ages. He acknowledged that “lower forms of animals”, as he called them, may have evolved over time. His concern was always with people. In this particular case, he was concerned with the belief that a brute ancestry for humans might undercut human morality and religious faith. It was important for him to believe that humans are special and divinely created.

The crusade went on for several years, and after many losses and a few partial victories, in 1925, Tennessee became the first State to outlaw the teaching of human evolution in public schools. Under the new Tennessee law, teaching evolution was a misdemeanor punished by a maximum fine of 500$. The law exceeded Bryan’s proposal, because it covered all theories of human evolution, and not just Darwinism. Bryan didn’t want to impose a criminal penalty, neither.

This was a national event. This was in the front-page news around the country. Religious conservatives backed it, but most people, such as President Calvin Coolidge and Herbert Hoover, denounced it. No one expected, however, that any teacher would ever be prosecuted under this law.

The Anti-evolution Crusade

2009-12-08T06:42:00.000-08:00

Evolutionary science produced a popular backslash in America during the 1920’s. This was known as America’s anti-evolution crusade. Conservative Christians had never liked the Darwinian theory of human evolution, but their concern became a crusade during the 1920’s. Several factors contributed to the timing of America’s anti-evolution crusade. Why so many years after the publication of Origin of Species? Why in the 1920’s and not the 1860’s?

There are several factors that contributed to this. The first of these is that protestant fundamentalism increased within the mainline religious denominations during the years leading up to 1920. The term fundamentalism, which is now so common, was indeed originally coined only around 1920 to characterize a group of religious believers within the mainline protestant denominations.

In the late 1800’s, with the rise of religious liberalism within the different denominations, notions of higher criticism of the Bible appeared. They treated the Bible as a written work by people. While everyone within these denominations considered the Bible a special work, liberals viewed it as a work that reflected the evolution of the Hebrew view of God. You have the early books of the Bible that reflect how early Hebrew people viewed God. Then they developed and you have the prophetic books. Then the New Testament presents a fuller view of God. This was really an evolutionary view of religion.

It was against this that conservatives within the Church fought back. They held a very high view of scripture. They consider the entire scripture to be the word of God. The liberals would say this too, but they meant that it was inspired in a special way. Conservatives saw this evolutionary view of religion as a modern heresy.

It was the conservative-modernist controversy what was tearing apart the mainline religious denominations: the Methodists, Episcopal, Presbyterians and Baptists. It came to the point where the fundamentalists within those different denominations had more in common with each other than they did with the liberals within their own denominations. American Protestantism was splitting open.

Further, there were other factors that influenced the explosion of the crusade. After the eclipse of Darwinism, Darwin’s natural selection was beginning to revive within evolutionary science with the advent of Mendelian genetics. Pure classic Darwinism was more hostile to religious views than Lamarckianism.

Further, compulsory high-school education was just beginning to take effect around the country. This was pushing evolutionary teaching into the face of more parents. Before that, people mostly only went to elementary school, where evolution isn’t taught. Evolution is taught in high-school. With children forced to go to school, more parents who were suspicious of evolution for religious reasons were reacting.

Also, evolutionary thinking at this time was associated in the public mind with German militarism (World War I was just finished), laissez-faire capitalism and eugenics. This gave people a negative view of evolution. Finally, the 1920’s was a period of heightened social stress, as reform competed with reaction for America’s future.

With this background, around 1920, several fundamentalist leaders began targeting the theory of evolution for public condemnation. New anti-evolution fundamentalist institutions that attracted widespread following across denominations were formed.

Mainline protestant denominations became embroiled in bitter disputes over the teaching of evolution within Church Colleges and from the pulpit. Conservatives demanded orthodoxy with respect to the special creation of humans in God’s image. On the other side, the liberals defended modern science and an evolutionary view of religious understanding. In the end, in most of the denominations, the liberals won.

I think these factors help to explain the timing and explosion of the anti-evolution crusade. Next time I’ll talk about the decisive event of this war, the Trial of the Century, the well-known Scopes Trial.

Eugenics

2009-12-07T05:48:00.000-08:00

Shortly after Darwin published his Origin of Species, his cousin Francis Galton conceived the idea of applying its teachings to human development. Galton’s own description of his ideas could be summarized with the following fragment: “qualities gained by good nourishment and education never descend by inheritance, but perish with the individual; while his inborn qualities are transmitted. (…) It is therefore a waste of labor to improve a poor stock by careful feeding. (…) The question then was forced upon me: could not the race of man be similarly improved? Could not the undesirable be gotten rid of, and the desirables multiplied? The answer to this question was a decided yes. Fit humans produce fit offspring, unfit humans produce unfit offspring. As a thinking species, humans can use this to accelerate the evolutionary process through the selective breeding of humans”. This is what is now called eugenics.

Galton defended his theory with social surveys and polls that showed that ability and success run in families, while inability and failure run in other families. Of course this could just as easily be explained by the environments of those families. Galton, however, didn’t see this that way.

He linked intelligence, beauty and health with ability, and they all should be together. Ignorance, ugliness and sickness he connected with inability. In fact, he once published in a popular British journal a “beauty-map” of England. He showed where the most beautiful women of England are found so that male seeking to eugenically mate would know where to go. These beautiful women would also be the most intelligent and able.

In 1883, Galton actually coined the term eugenics. He had been writing about it for a decade before that. He used the word eugenics to designate policies and programs designed to encourage more children from the fit, and less children from the unfit.

Eugenics was sort of a cult idea for half a generation, but it gained widespread interest after the rediscovery of Mendelian genetics. Mendel made it all seem more credible. Genetics appeared to offer a physical basis for Galton’s theories. Many experts saw such traits as mental illness, retardation, epilepsy, physical defects and criminality as the products of hereditary factors. If you want to get rid of criminals, just get rid of the gene that causes criminality.

The IQ Test

This was a time when science was held in high esteem. Biology was rising in authority and credibility, and genetics seemed to offer new solutions. Here, eugenics appeared to offer a scientific methodology for the social sciences. The IQ was invented at this time as an objective measure of intelligence. They came with the idea that you could quantify intelligence through IQ tests. The IQ test was actually brought to America to be used to differentiate people by eugenicists. They considered it a good parameter for determining who should breed and who should be discouraged from breeding.

Sociologists conducted public health surveys, compiled families’ pedigrees to show hereditary basis for crime, poverty and low IQ. Since they were looking for that, they found plenty of evidence. Who they picked and how they picked seemed to support their ideas.

Although eugenics never really gained broad popular appeal among the masses in America, many scientific, professional and philanthropic organizations promoted its acceptance actively. These efforts greatly influenced public policies throughout the United States in Europe during the first third of the 20th century.

Great Leaders Who Advocated Eugenics?… How Dare You…

People don’t talk about this anymore, as it isn't politically correct, but many “great leaders” advocated eugenics. Winston Churchill was a prime proponent of eugenics in England. Teddy Roosevelt, Calvin Coolidge and other presidents during this period were strong proponents of eugenic policies. They openly worried that the professional classes were not reproducing in sufficient numbers. Progressive sociologist, and good friend of Teddy Roosevelt, Edward Alsworth Ross, called it race suicide. Race suicide was going on because the able women were not producing enough kids. Professional classes were going to be swamped by the inferior products of their own race, that is, the worker classes.

There were efforts to taught students the value of eugenic mating. You could go back to biology and civics textbooks of the time and you’ll see eugenic mating advice, and the importance of having large families. Organizations would hold “fitter family” contests, much like “best sheep” contests.

Eugenic fitness was proposed as a prerequisite for marriage. Many States adopted laws requiring eugenic tests before a person could get married. Some churches, such as the Episcopal Church, actively proposed that only eugenically fit people could be married. Some countries adopted tax and employment policies to encourage its able citizens to have children.

Negative Eugenics

Until now, we’ve talked about positive eugenics. Let’s go now to the dark side of eugenics. Negative eugenics is the one that seeks less children from the unfit. Every single American State, and most western countries, adopted policies of sexually segregating certain dysgenic classes, typically the mentally retarded. 35 American States, and many European countries, instituted compulsory programs of sexual sterilization for the mentally ill and retarded, for criminals and epileptics.

From 1900 to 1960, some 60000 Americans were sterilized under compulsory State programs, and many more were sterilized under voluntary programs (parents took their children to be sterilized because of some supposed eugenic defect). Such programs were even upheld as constitutional by the United States Supreme Court in 1927, in the case involving Carrie Buck, who was sterilized against her will under evidence that both her mother and grandmother had been mentally retarded.

The Supreme Court unanimously declared this sacrifice was appropriate for society because, as Oliver Wendell Holmes put it, “three generations of imbeciles are enough”.

Nazi Germany and the Decline of Eugenics

Germany’s programs adopted during the Weimar Republic period were later extended under the Nazi era to include Jews, Gypsies and other “disfavored” groups. Nazi Germany then moved from eugenic sterilization to euthanasia. It is interesting to note that German geneticists and biologists joined the Nazi party at a much higher rate than other professional groups. Except for the Catholic Church, opposition to eugenics was disorganized and ineffective until the 1930’s, when Nazi practices discredited it a lot. Then, gradually, social scientists and geneticists began to turn form these ideas.

By the end of World War 2, social Darwinism and eugenics was morally bankrupt. This I consider to be an amazing “moral evolution”. For a half century, “scientifically” informed governments treated their unfortunate citizens eugenically. This is a great example of how far human arrogance can go.

Racism and Darwinism

2009-12-07T04:23:00.000-08:00

In my last article I wrote about social Darwinism, and specially remarked the historical background in which it originated. We’ve said that social Darwinism is simply a label for a group of utilitarian philosophies that attribute human progress to competition among individuals. For many late 19th century Europeans and Americans, the most important area of competition was not within a society, as I said in my last article, but the competition between races and nations. Social Darwinism was invoked to justify Western imperialism, colonialism, militarism and scientific racism. This was just the time when Europe was pushing out and colonizing Africa and Asia, and many justified their actions using social Darwinism.

Of course racism predated Darwinism. Racism has been with humans since the beginning of time. Biological evolution, however, appeared to justify racism. They called it scientific racism now. Many racist biologists of the time considered that the more civilized races were simply further along in evolutionary development from the less civilized ones. The cultural development of Western Europe expressed a basic biological difference over the aborigines of Australia, or the people of Africa. The cause of European superiority was considered biological.

Darwinists, including Darwin, saw a single line of human development, and inevitably viewed Northwestern Europeans as further along in that development. They explained this by saying that Europe has a harsher environment, and that forced humans to develop their brains further.

Darwin and Spencer believed that racial struggle contributed to human evolution by superior races replacing inferior ones. Indeed, Darwin’s book is titled: “On the Origin of Species, or the preservation of favored races in the struggle for life”. No one could read that title without thinking of human races.

It is really amazing that many Americans of European origin believed that Native Americans and African Americans would simply die out in the United States. They thought the European races would just naturally survive and dominate.

Beginning in the late 1800’s, Germany’s leading biologist, Ernst Haeckel, argued that nations and races advance through competition. And as an ardent nationalist, he advocated a strong united Germany that should dominate the world. Haeckel’s social Darwinism contributed to German militarism that led to World War I. Studies and interviews conducted in Germany during World War I, show that military leaders justified their actions on Darwinian terms, borrowed directly from the writings of people like Haeckel.

Germany’s defeat in that war deeply embittered Haeckel and his followers. Convinced of the biological superiority of the German people, though, some of Haeckel’s followers contributed to the rise of Nazism. It also contributed, rather sadly, to Hitler’s policies of racial purity. I think that we don’t need to go into that here; we all know what it is about. What I take from this, though, is that we should leave the job of selecting to nature, she knows better.

Social Darwinism

2009-12-06T07:24:00.000-08:00

The term “social Darwinism” was coined by its critics. It gained currency even by its proponents, though, during the Victorian Era, as a phrase to identify various utilitarian philosophies and policies that attributed human progress to competition among individuals. Valuing competition as a great good fit the spirit of the day, and it predated Darwinian biology.

In the late 1700’s, Adam Smith argued that economic progress depended on individual initiative. Not governmental regulation, not social networks, but individual initiative. His faith in the natural harmony of human interactions gave him hope that all people would benefit from laissez-faire capitalism (unregulated capitalism).

By 1800, Thomas Malthus noted that due to natural limits on resources, there would be losers as well as winners in any social competition. This separated him from Adam Smith, but yet he embraced the idea that the struggle for existence fosters the general good by weeding out the week. As painful as this might be to some, in the long run, it was for the best. Malthus’s thinking inspired Darwin to conceive natural selection as the engine for biological evolution.

Even before Darwin published his ideas, though, Herbert Spencer popularized the Malthusian view of individual and group competition. He is the one who coined the term survival of the fittest, which was later so much associated with Darwinian thinking. He held the struggle for survival as the only sure foundation for human progress.

With the advent of Darwinism in biology, Spencer’s views on social development became known as social Darwinism, rather than “social spencerianism”, even though Darwin did not publicly endorse the ideas. This is probably because biology carries so much credibility. Tying one’s ideas to biology rather than just social sciences gives them more credibility.

Social Darwinism encouraged laissez-faire capitalism and discourages helping the “weak”. This was in an era of industrialization and urbanization. In this period, Western Europe and the United States were being transformed from an agricultural land to urbanized areas where most people were thrown together in cities. This created the world we find in Dickens’ novels, where homelessness abounded and there weren’t social networks that took care of the mentally or physically disabled.

Was government going to move in and fill the social gaps left by urbanization? Were taxes going to be raised to provide welfare and social support networks? These were important questions in Western Europe and the United States in the late 1800’s. This is where Spencer ideas had an impact.

Spencer maintained that government should never interfere in domestic, economic or social affairs. He maintained also that public health and welfare programs, over the long run, simply harmed people. How could they harm people? They harm people by taxing and holding back the rich, the able, the hard-working; and allowing the “weak” to survive and multiply without improvement. Nature eliminates efficiency, and any interference in this process was doomed to failure.

Industrialists like Andrew Carnegie, John D. Rockefeller and James Jerome Hill, publicly justified their cutthroat business practices in social Darwinist terms. Sure there are some losers in these practices, but there are also winners. We happened to be the winners, and that’s because we’re the most fit. Ultimately, it is not to our benefit, but to the benefit of society.

Biologists who espoused Darwinism did not necessarily accepted social Darwinism. A great example is Alfred Russell Wallace. He was a prime advocate of socialism, and was the most visible opponent of social Darwinism. He argued that humans could guide their own evolution, and were not bound by the biological processes. At the time, however, he was swimming upstream. Social Darwinists continually used biological Darwinism to justify their views, and to give them weight and authority.

Genetic Mutations, Part III: Information

2009-12-04T04:48:00.000-08:00

Any change in DNA, whether is brought on by copy error or damage, we can call a mutation. In some cases, such as when mutations arise from mismatch errors, the change may be relatively small. We call those kinds of changes point-mutations. Mutations may also involve other relatively small, but potentially serious consequences, such as the insertion or deletion of a base-pair along the string of DNA.

Damage to DNA can actually cause much larger-scale changes. If the damage causes the DNA double helix to break entirely, then entire segments of the chromosome can be lost. We call those chromosomal deletions. Thousand of base-pairs can just be eliminated. Or, those segments that are broken out of the DNA molecule might get flipped around and put in reverse. We call those “inversions”. Or, those segments might actually be pulled out and moved to other part of the chromosome. We call those “translocation”. They might actually be pulled out and inserted in a number of different places. Those are “duplications”.

What are the consequences of these kinds of mutations? We talked briefly about the negative consequences that can happen if a critical gene in a cell is damaged. Not all mutations, however, have this kind of negative consequence. In fact, some may even have positive consequences, at least over the long run.

Mutations and Functionality of Proteins

The genetic code is redundant. That means that different combinations of bases code for the same amino-acid. For example, codons CCA and CCG both code for proline. If the A is somehow mutated and becomes a G, it doesn’t matter, we still have a code for proline. We call these kinds of mutations “silent mutations”. Unless we look at the DNA sequence itself, we would never know it is there.

If CCA, which codes for proline, is changed to UCA, which codes for serine, then we would have a change that affects the amino-acid sequence. Even a change in amino-acid sequence, however, may not be discernable. It may even have a slightly positive effect. The difference is hard to predict in advance, and it all depends on which amino-acid is substituted for the other, and how that substitution affects the shape, and therefore, the function of the protein.

It’s possible to have one amino-acid substituted for another and finding no noticeable change in the way the protein folds up. It’s also possible that an amino-acid substitution does cause a radical change in protein shape. These kinds of changes are what would lead to serious effects. For example, these are the kinds of change that may cause a cancer. If the amino-acid substituted happens to be a particularly critical one, the whole protein can be screwed up.

Interestingly, there is a third alternative. That is that the change of one amino-acid actually makes the protein work a little better. It is conceivable that a slight shape change would make it more functional. In this case, a mutation would have a positive effect.

Over the long run, mutations are important, because they change genetic information among individuals in populations. In that way, mutations add genetic variation, which is the stuff that natural selection works on. I have to point out, though, that the only mutations that matter are those that can be passed to offspring. Up to this point we were talking only about the cell. If a mutation occurs in a single celled organism, when it reproduces the mutations would be passed on to the offspring. For single celled organisms, any mutation is going to be passed on.

Mutations in Multicellular Organisms

If I have a mutation occurring in my skin cells, my future children don’t have to worry about that. Those mutations will die when I do. Those skin cells have no way of passing that genetic information on to my offspring. Instead, in multicellular organisms, such as ourselves, there are small groups of cells whose sole function is to produce reproductive cells. We call those germ cells. Only mutations occurring in germ cells can be passed on to subsequent generations.

I think that we this series of articles on mutations we’ve clarified the subject a little. Because of the ongoing debate over “information” in organisms, and how it is created in order for evolution to work, I think it is really important to share my little knowledge about the subject. In later articles I want to talk about other mechanisms of evolutionary change, like sexual reproduction and genetic drift. Be sure to check them out, and spread the word out, everyone needs to know this stuff. It's really eye-opening.

The Genetic Code, Part I

2009-12-03T04:51:00.001-08:00

You may be familiar with the cryptic code puzzles that appear on the comic sections of newspapers. They involve some famous or amusing quote that has all of the letters in it substituted for other letters. For example, all the A’s may be substituted with W’s, all the V’s with P’s, etc. The substitutions are always consistent, and the puzzle is solved simply by figuring out the correspondence of letters. This code is very simple, because it just involves finding the equivalents of single symbols, which are both in the same alphabet. Unfortunately, the code needed to direct protein synthesis has to be more complex than that.

The first reason our code needs to be more complex is that DNA and proteins are very different kinds of molecules. Even if we could imagine a code that establishes a relationship between the bases in the nucleic acid and amino-acids, how could this correspondence work on a molecular level? Is there some molecular mechanism that could predict an interaction between a particular amino-acid, and one or more particular nucleic acid bases?

The fact that proteins and nucleic acids have different biochemical properties suggests that a direct molecular correspondence is unlikely to occur. What we need is to have nucleic acids and proteins communicated through a translator, who speaks the language of both. Francis Crick was the first to propose this solution.

Crick suggested that there must be a molecule with two functionally different ends. On the one end there must be a mechanism for attaching a specific amino-acid, and at the other end, there must be a mechanism for interacting with a specific sequence of nucleotide bases. Crick was correct indeed. There are such molecules. These are small, highly specialized, strings of RNA, called “transfer RNA” (tRNA).

Three-Letters Words

The second reason the genetic code needs to be more complex than newspaper puzzles is that there are 20 kinds of amino-acids, but only four kinds of bases in nucleic acids. We have A, G, T and C, and that’s it. If we had a simple substitution that was one for one, we could only have a code that was specific for four different amino-acids. We have 20 of them to account for, however.

What that suggests is that sequences of more than one nucleotide must be used to code for a single amino-acid. This would be like having the bases of a nucleic acid combined together to form code-words, where each base is a single letter. How many letters long must each word be?

Imagine that we had code-words that were made up of two letters each. That would not be sufficient to code for all the amino-acids. This is simple math. If we have four things, and we combine these four things in pairs, then we can make 4 squared combinations. That’s sixteen combinations. However, if we make combinations of three things, we would have 4 cubed combinations, that’s 64, more than enough. Actually, a three letter code suggests that the code has some sort of redundancy.

The logic in support for having a three letter code seems pretty obvious, but it simply suggests a testable hypothesis which then had to be demonstrated. Once again, it was Francis Crick along with colleagues who demonstrated experimentally that the genetic code must involve sequences of three bases. Crick used a technique in which they could cause a very particular kind of mutation in the DNA of a virus. This involved the elimination of just one base-pair from a DNA double helix. Alternatively, the mutation involved the addition of just one base-pair. If they applied this treatment in the appropriate fashion, they could be assured that either one base pair, or one was added.

Consider the simple sentence: “Old men are fun”, but without the spacing. Consider it as a string of characters. That sentence is composed of four words, each specified by three letters. If we delete the first letter, and try to read it, we’ve got: “ldmenarefun”. If we deleted two letters, we’d have: “dmenarefun”. Neither of these strings of characters makes any sense because we have shifted the place we start reading by one or two positions. The resulting remainder of the string becomes nonsensical.

Now, if we delete three letters, the words make sense again: “menarefun”. It’s not the same sentence as we’ve started with, but that’s not the point. The point is that the words in that sentence, comprised of three letters, only make sense if we take out three letters. We could do the opposite. If we add three letters, part of the string would make sense.

Crick used the same kind of logic, deleting or adding just one base-pair from a viral DNA, to show that there must a three letter code. If they induced one mutation in a gene, then all of the amino-acids coded by that gene would get changed. If they eliminated two base-pairs, they’d have the same results. If they deleted three base-pairs, however, they found that the remaining portion of that gen would make sense, in the sense that most amino-acid sequences would be intact.

It was pretty clear that the genetic code had to be made of three bases each. Many experiments since that have used a variety of techniques to verify the existence of this three letter code. The three-base sequences that serve as fundamental units for the code have come to be known as codons. Each codon corresponds to a unique amino-acid.

The next step was to establish what the correspondence is between particular codons and particular amino-acids. I will leave that for next time.

Genetic Mutations, Part II: Induced Mutations

2009-12-02T04:42:00.000-08:00

It’s not just replication which is responsible for genetic mutations. Other things can happen to DNA as well. DNA does very important things, but one of the things that it isn’t good at is staying intact. DNA is not known for being a durable molecule. It is pretty fragile overall. DNA is constantly in danger of being broken or modified by a variety of physical and chemical agents.

For example, radiation is absorbed by nucleotides, which can break the molecules apart. If this happens, the bases themselves might be damaged, rendering it non-functional. Or, one or more base-pairs might be deleted. Or, they might even be added. Or both strands of the double helix might simply break, causing the entire molecule to split in two.

Many kinds of chemicals would interact with bonds in DNA and break them. For example, chemicals found in tobacco smoke are well-known to be highly reactive with DNA. So-called free radicals, which are produced normally by our own metabolism, also interact with DNA and can potentially damage it.

DNA is under constant assault. Even if replication goes well, once DNA is put together, there are many factors which are assaulting it and potentially damaging it. By one estimate, the DNA in a single human cell may be damaged a thousand times a day. A thousand times a day, something happens to your DNA. As you might imagine, there is molecular machinery that is devoted to detecting and correcting all sorts of errors that creep into DNA.

Most of these repair mechanisms share something in common. They depend on complimentary base-pairing to correct mistakes when they find them. When a mistake is detected, they cut out one or the other of the single strands of the double helix.

In spite of this molecular effort, some damage does remain unrepaired, and there can be consequences. A very high percentage of cancers are caused by genetic errors brought on by exposure to various DNA damaging agents. We call them carcinogens. Usually these cancers are caused by damage to certain classes of genes (antioncogenes or tumor suppressor genes). These genes code for proteins that are involved in regulating the way that cells normally divide and reproduce. They essentially act as ON or OFF switches for cell division. When these genes are damaged, they no longer function appropriately, and the cell begins to divide in an uncontrolled fashion. This is a common defining feature of cancers.

In my next article I will talk about the types of mutations that occur, and their specific consequences.

Genetic Mutations, Part I

2009-12-01T04:10:00.000-08:00

Mutations are often described by people as something going “wrong”, or something “bad”. Wrong is relative. From our perspective they are bad. They cause diseases and kill a lot of people. They are, however, responsible for creating the genetic variation on which natural selection works. Who are we to judge the process by which we came into being? How we dare label it “wrong”? The best thing we can do is to be part of it. Go with the flow. Try to understand it, at least. Be an admirer. Here I will try to enlighten this subject, so much debated, and not so much understood.

I have been writing a lot about DNA replication lately. We saw how many enzymes work together in what can be seen as an elegant and orchestrated ballet. As elegant as this process may be, though, replication doesn’t always work exactly right. Sometimes, the wrong base gets inserted in a sequence. DNA may also be damaged in a variety of ways, leading to what are essentially mistakes in the sequence of bases.

The cell puts a lot of effort into avoiding and correcting errors. Errors, however, are unavoidable. Often, when errors do occur, they have serious negative consequences for the individuals in which they occur. Over the long run, however, such errors also provide a source of genetic variation, which is the substrate on which evolution by natural selection acts.

We’ve seen in other article that DNA polymerase depends on complimentary base-pairing to accomplish the task of accurately synthesizing a new DNA molecule. It is the base-pairing that determines which nucleotide is going to be added next to a growing polymer of DNA. DNA polymerase, however, sometimes adds the incorrect base.

When the copying process ends, the number of mistakes in the DNA sequence is amazingly low. It is only about one mistake in every billion bases. On the other hand, if you count how many mistakes are actually made by DNA polymerase during the copying process itself, the number would be much larger: about one in every 10000.

The difference between the final product and the mistakes that are actually made during the copying process is due to the fact that there is an extensive amount of molecular machinery devoted to proofreading and repairing DNA in cells.

Who is to Blame?

I said that DNA polymerase was making mistakes. I should apologize. We can’t blame DNA polymerase. It is not really making the mistakes. The proper alignment of new bases with old bases during replication depends on the bases themselves. Ultimately, they line up because of the hydrogen bonding interactions that are responsible for the base-pairing rules. All that DNA polymerase does is to find what the next base is, and add it to the growing strand. It does that job right. If it happens to find the wrong base, it just adds it anyway. We call that “mismatch error”.

When a mismatch occurs, it means that after the DNA strand is synthesized, it will have somewhere in the sequence a non-complimentary base pair. For example, we may have an A paired with a C.

DNA polymerase itself does look out for these mistakes. DNA polymerase does what we call proofreading repair. We could think of DNA polymerase as walking down the template strand of DNA, it adds a base, but then it looks back over its shoulder and it checks: is it the right base? If it finds that it added the wrong base, it would cut the base out. It will wait for another base to come in and then synthesize.

This proofreading corrects a number of the errors that are introduced. It brings down the number of errors to as low as 1 in ten million. One in ten million seems pretty good. I wish I could make only one mistake in ten million tries, but it is actually still quite a high rate given the size of the task at hand. For example, the amount of DNA found in a human cell is about 3.2 billion base-pairs. If we have a rate of about 1 in ten million, that means every time the DNA in a human cell is replicated, there would be about 300 mistakes. When you consider the fact that over the lifetime of a human there are billions and billions of cell-divisions, the number of mistakes would become astronomical and unworkable. So, this mismatch repair done by DNA polymerase itself really doesn’t take it as far as we need.

Quality Control

Fortunately, there is another backup mechanism for correcting mismatches. There is an ensemble of enzymes that we call (with a touch of originality) “mismatch repair enzymes”. They work together to detect and correct mismatches that are found in newly synthesized DNA. Think as these mismatch repair enzymes as quality control officers. They are constantly inspecting the DNA that has been synthesized, and checking for incorrect base-pairings. If these enzymes do detect a mismatch, they cut out the incorrect nucleotide. They may even remove a section of nucleotides around this incorrect nucleotide, leaving a gap. Once that gat is created, new nucleotides would come in and base-pair with the template strand. DNA polymerase would come back and finish the job.

So, we have a lot of molecular machinery that is involved in finding mismatches and repairing them when they occur. In spite of all of this, some errors do get through. At the end of the day, when the entire mismatch repairing is completed, there is still one in a billion mistakes. This is pretty good. That might me on average three mistakes if an entire set of human DNA is replicated. Over the long time, however, they do add up. We will see the consequences of these mistakes in my next article. Stay tuned.

DNA Replication, Part III: How It Is Done

2009-11-30T05:07:00.000-08:00

In 1957, Arthur Kornberg made a really interesting discovery. He showed that DNA can be replicated outside of a cell, in a laboratory test tube. Kornberg wasn’t much interested in which model of replication was right. Instead, he was interested in specifically how replication occurred. Watson and Crick had suggested that the replication of DNA may not actually require an enzyme. If you could somehow unzip DNA, they thought that new DNA might just self-assemble, because the complimentary base-pairing would bring in all the appropriate nucleotides. Kornberg thought, though, that there must be some enzyme involved. He set out to figure out what that enzyme was.

What Kornberg did was some old-fashioned tedious work. He thought that there must be some enzyme, so he started looking at all the candidate proteins in bacteria cells, and seeing if any of these synthesize DNA. He would essentially create culture media where he would put three things: some single-stranded DNA that should serve as a template for making new DNA, some of the nucleotides that the DNA had to be made of, and some candidate enzymes from bacteria cells. He then would see if DNA is synthesized. He did this over and over, with all sorts of candidate enzymes.

He did find one, actually. He found an enzyme that he named DNA polymerase. When he put this enzyme into the mix, he would get the synthesis of a new complimentary strand on the old existing strand that he added.

This was really an important discovery. This really opened up the modern era of molecular biology. The discovery of DNA polymerase kick started a 50-year long (and still continuing today) study of how DNA replicates, and specifically how DNA polymerase does its job. This is often how science works. There is an initial discovery, and then generations of scientists come along and fill in the details.

The Mechanisms of Replication

What I want to do now is to step through the mechanisms we think are responsible for replicating DNA. The first thing we know that has to happen is that the two sides of the DNA double strand have to be separated. They are separated by an enzyme called helicase. You might by now note a pattern of how scientists name enzymes. They always end with “ase”, and their name tells you exactly what they do.

Once helicases have done its job, there are other sets of proteins that come along. These are generically called single-strand binding proteins. These proteins come and sit on the now open DNA and hold it open. This is like putting a chock in there, so that the thing can’t zip back.

Now is the turn of the major player, the enzyme Kornberg found, DNA polymerase. What this enzyme does, as it names implies, is to polymerize the new nucleotides on the growing new strand of DNA, as it is being complimentarily matched to the older template strand. The nucleotide monomers that are added on to the growing strand are in a slightly different form.

The bases that are being added on by DNA polymerase are not being chosen by DNA polymerase itself. Instead, they are being lined up through the complimentary base-pairing that’s inherent to the nucleotides. A with T, C with G. All DNA polymerase does is to go to the next nucleotide, and build a strong chemical bond between the growing strand and the next nucleotide that’s going to be added. It just finds what’s there, and what’s there is there because of the complimentary base-pairing of that nucleotide with the corresponding one on the old template strand.

Complimentary base-pairing is really the key to DNA replication. All else are just details. We could talk about all these details, but we’ve already seen the key issues. At the end we see that Watson and Crick not only had it right, but almost 50 years later, we’ve seen exactly how that mechanism works. Our understanding of these mechanisms of DNA replication has been central to sequencing human DNA and manipulating it to our whims. Also, it helps us understand one of the essential processes of life, which is reproduction, and, by extension, the evolution of life.

DNA Replication, Part II

2009-11-29T11:05:00.000-08:00

Watson and Crick’s semi-conservative model contrasted with a couple of other possibilities for how DNA could possibly replicate. There is the conservative model, which suggests that both strands in the original DNA double helix stay together during replication. Then there is the dispersive model, which suggests that both strands are not only separated, but even broken up into smaller pieces during replication. Deciding which of these models was the correct one seemed to be pretty easy, because they make very different predictions. It was not obvious how to prove it in the laboratory, however.

The prediction of Watson and Crick’s semi-conservative hypothesis is that each of the two daughter double helixes, after one round of replication, should be made up of one old strand and one new strand. The conservative model predicts that after replication, one of the double helixes that result would be entirely old. The daughter helixes would be entirely new. Finally, the dispersive model predicts that both the daughter and parental helixes would be made up of just a mixture of old and new DNA.

This sounds simple, but the difficulty was figuring how to actually test that. We need some way to be able to determine what’s old and what’s new DNA after replication. It took several years before anybody figured out how to do this.

Meselson-Stahl Experiment

This brings us to a pair of researchers, Matthew Meselson and Franklin Stahl. In 1957, a few years after Watson and Crick’s work, they came up with a novel method for distinguishing new and old DNA during replication. Let me explain how they did that.

First, they grew bacteria in two different kinds of culture media. One of these culture media had normal nitrogen in it (N14). The other media had a heavier isotope of nitrogen in it (N15). This isotope of nitrogen is not radioactive, it’s just a little bit heavier. Not much heavier, just a little bit.

The point of culturing bacteria in these two different media is that the nitrogen in those media would be taken up and incorporated into any new biological molecules that were being synthesized. Specifically, the nitrogen would be taken up and incorporated into any new DNA that was being synthesized.

If you culture bacteria for some period of time, what would be many generations, then you can assume that all of the nitrogen that is incorporated in that DNA would either have N14 or N15 depending on the culture media in which you are growing it. In this way, Meselson and Stahl could essentially label old and new DNA by how heavy (dense, really) that DNA was.

As you can imagine, the density difference between DNA that had been made with N15, as compared to DNA that was made with N14, is really small. The really clever part was figuring out how to very accurately measure the densities of these kinds of DNA.

The Clever Part

To do this, Meselson and Stahl devised a new kind of procedure called “density gradient centrifugation”. This density gradient centrifugation allowed them literally to sort out DNA according to how dense it was.

The idea behind this is actually similar to the reason why swimmers don’t sink in the Great Salt Lake. If the density of a liquid and an object in it are more or less the same, then the object would neither sink nor float, it would just sort of stay where you put it. So, if you add a lot of salt to water, actually it becomes of the same density as our own tissues, and you don’t sink in it, you just sort of stay there.

It is more interesting, though, if you have a gradient of densities. In other words, if you have some range from high to low densities in some liquid mediums, then objects of slightly different densities would sort themselves out. The objects would end up at that gradient at exactly where their own density matches the density of that point in the density gradient.

That’s the idea that Meselson and Stahl had. How do you create a density gradient? After trying a number of different kinds of solutions, they found a compound called Caesium Chloride. This is a salt that when it is put into a solution has approximately the same density as DNA. What they then did was take a tube of caesium chloride solution and centrifuge it. If you centrifuge a tube, what happens is that the heavier stuff goes to the end of the tube, and the lighter stuff stays at the top.

What Meselson and Stahl had to do with this experiment was centrifuge the ceasium chloride solution enormously quickly. They actually spun it around so fast that they created a 100000 g-forces. This is really fast, so it is called ultra-centrifugation. They did it for a number of days. At the end, they would get as a density gradient of the caesium chloride along the tube. Remember, caesium chloride is about the same density as DNA.

That means that if you then take some DNA and put it in that tube and spin it around, the DNA would ordinarily just be dispersed in that tube because is more or less the same density as the ceasium chloride. As the density of ceasium chloride develops, however, the DNA would all coalesce in a single band. That band would be in a position along the length of the tube that corresponds exactly to the density of DNA at that point in the tube.

This method was so sensitive, that Meselson and Stahl determined that they could tell the difference between N15 and N14 DNA.

Watson and Crick Had it Right

So, that’s the technique. Armed with this technique, Meselson and Stahl then did the following experiment, which should be sort of obvious bases on what we talked about. They took a culture of N15 bacteria and transferred them to a culture flask that had N14. Now, those bacteria, when they started to replicate their DNA, would start incorporating the lighter nitrogen. Any new DNA produced by those bacteria would be lighter than the old DNA that they had.

They waited for about 20 minutes, which is long enough for just one round of DNA replication. Then they took the bacteria out, extracted the DNA from them and used their density centrifugation method to determine what the densities of the DNA in the sample was.

The conservative model predicts that at this point there should be two separate sets of DNA. There should be lighter DNA and heavier DNA. The new DNA is going to be lighter and the old DNA is going to be heavier. This is because, according to this model, the parent strand stays intact. After one replication, you should have some DNA that is heavy, and some DNA that is all light.

This is not the result they observed. What they saw was just one intermediate band. So, they could rule out the conservative model directly. They couldn’t rule out the dispersive model, thought. After just one round of replication, both the dispersive and semi-conservative models made the same prediction. Each daughter double helix should be composed of half old(heavy) DNA and half new(light) DNA. All of the DNA in the sample, after one replication, should be at some intermediate weight. This is what they saw. The dispersive hypothesis made exactly the same prediction.

If you wait for two replications, however, all of a sudden you get a distinct difference in the predictions made by the semi-conservative and dispersive models. After two replications (about 40 minutes), the dispersive model would still predict there would be only one band, all of new and old DNA is all mixed up. Therefore, all of the DNA would be about the same density. The thing that should change is the position of that band along the gradient.

What Meselson and Stahl saw was the creation of two bands after two rounds of replication, which confirmed the prediction of the semi-conservative model.

Well, it took some years to prove it, but Watson and Crick had it right.

DNA Replication, Part I

2009-11-29T05:34:00.000-08:00

Lately I’ve been writing a lot about DNA, its history and structure. I think this is really important, I would say key, to understanding what is life about, and how it evolves. Here I’ll continue with this business. Here I want to look at the proposal Watson and Crick had for how the double helix might be replicated because of the complimentary base-pairing they discovered. This would be a series on DNA replication, which I think is one of the most fascinating and complex processes in the universe.

Watson and Crick suggested that the DNA molecule must unzip, and then, each half of the molecule could serve as a template for a newly formed half. This is a good hypothesis, but was it correct? As Watson and Crick proposed that, there were two alternative hypotheses on the scene.

The Alternative Hypotheses

The first alternative suggested that the DNA double helix must remain completely intact when it is replicated. That is, the two strands do not separate. The entire molecule is somehow used as a template for making more DNA. This alternative was called the conservative hypothesis of replication. The original DNA double helix molecule remained completely intact and conserved. The idea was that there must be some intermediate molecule that got information from the structure of the helix and used it to build a completely different helix.

A second alternative suggested that the original DNA molecule becomes completely broken down during replication, with the newly copied DNA assembled by some unknown mechanism. In other words, the DNA double helix would actually be irrelevant. This alternative was called the dispersive model. It was called dispersive obviously because the DNA in the original helix just becomes dispersed and incorporated in the new copies that were being created.

Based on what was known about molecular biology and DNA in the 1950’s, both of these hypotheses were reasonable. Neither offered a solution to the problem of duplicating the exact order of nucleotides, however. This order is the information that we are seeking. Based on what we know today, both of these alternatives seem unlikely. They’re value then was to serve as alternative hypotheses against which to test specific predictions made by the Watson and Crick model.

The mechanism that Watson and Crick proposed became known as the semi-conservative model of DNA replication. This was called semi-conservative because it predicts that during replication, the double helix unzips and the new daughter helixes would both have one strand of the old helix. We begin with one helix, it separates somehow, and the resulting daughter helixes that are formed maintain the original halves of that parent helix. Upon this old half, new halves are formed to create the new double helixes.

This hypothesis led to a specific prediction. The prediction was that if you could know which was old and new DNA after replication would occur, all the old DNA that was in the original parental double helix, would now be dispersed between the two daughter helixes equally. The daughter helixes would all be composed of one half of old DNA, and one half of new DNA.

Let’s contrast that to the prediction we might have if we look at the other two models. Let’s think about the conservative model first. That model suggests that the DNA helix just remains intact once you’ve got it. After replication, that model would suggest that the two daughter helixes would separately made up of, on the one hand all old DNA, and on the other hand, all new DNA. The old DNA in the original parent is still in the original parent, and the daughter DNA helix is completely new.

The dispersive model made yet another prediction. That prediction was that the old DNA that was found in the original parental helix would just randomly scattered across the two daughter helixes.

We have three specific and different predictions that could be used to distinguish between these three models of replication. The trick is figuring out how to know what’s old and new DNA. Actually, it was several years after Watson and Crick’s original proposal that anybody could figure out how to experimentally test it.

The way to test the hypothesis was pretty obvious conceptually. Let’s ask ourselves, after replication, what happens to the material in the original parent’s helix? We have very distinct predictions. The problem was figuring out how to know where old and new DNA was. This is often it is in science. An idea comes forward, people understand what they have to do, but the critical experiment isn’t actually done until somebody comes along and says not what’s the experiment, but how you can actually do it. This may take years, as it did in this case.

Eventually, researchers figured out an extremely clever way to know what the difference is between old and new DNA. I will talk about this interesting and brilliant experiment in my next article.

The DNA Structure, Part II

2009-11-27T04:58:00.000-08:00

James Watson was a young American, who had just completed his PhD. He was interested in protein structure. He moved to Cambridge, England, and began working with Francis Crick, who was a physicist familiar with x-ray crystallography and how to interpret it. The story goes that Watson happened to visit London for a seminar, and saw the x-ray diffraction patterns that Rosalind Franklin had obtained from Maurice Wilkins’ purified DNA. Watson made some notes, rushed back to Cambridge and told Crick what he had seen.

Using Franklin’s data, Watson and Crick were able to deduce a number of key structural elements about how DNA must be shaped. These are things they figured out by looking at those dots on the x-ray crystallograph. First, they learned that the molecule had to form some kind of helix. It had to have a kind of spiral structure, similar to the alpha helix that is characteristic of many parts of proteins. Second, they figured out that the width of this helix was about two nanometers. The interesting thing about this is that, this width was twice the width of what you would have expected if there was only a single helix. That gave them the idea that there had to be more than one helix. A double helix, perhaps.

Another thing they learned was what the regular spacing of the repeated patterning along the length of the molecule is. They saw that there was a repeating pattern at about 0.3 nanometers. This corresponded to the size of one nucleotide. Then there was a larger repeating pattern that was ten times that size. From this they inferred that the number of nucleotides that would occur when the spiral went around just once and returned to the same point in the spiral had to be about ten nucleotides.

That isn’t a lot of information. If I gave you that information you couldn’t tell me the structure of DNA. What Watson and Crick did was to use that data and set out to figure out the structure of DNA the old-fashioned way. They made physical models of the molecule with metal rods. They made large-scale models of DNA several feet tall.

They built many models and asked each time: when we have this model, does it all fit together? They tried over and over again. Eventually they came up with a model that fit. The trickiest part of the modeling was to figure out how the nitrogenous bases fit into the picture. Remember, a polymer of DNA is a repeating pattern of sugars and phosphates, with different nitrogenous bases hanging off the side (the guanines, the adenines and so forth). Where did they fit? If you had two, or even more molecules of DNA that were spiraling together, where do the nitrogenous bases go?

Well, after a couple of failed attempts putting the nitrogenous bases on the outside, Watson and Crick realized they had to go on the inside. Why they might want to put them on the outside? It is the nitrogenous bases that vary along the length of the molecule. It is the variation of the different kinds of nucleotides that must somehow involve the code. If we’re going to get access to that code, we’ve got to make what’s different about that code available to the outside world. They couldn’t get the backbones to work together in any way that made sense with the nitrogenous bases on the outside.

If they turned those nitrogenous bases in, and had the nitrogenous bases connecting with each other, forming kind of stairs, with the backbones of these molecules forming the stringers that are holding the steps; the molecule began to fit together. This actually made sense, because these nitrogenous bases are chemical repelled by water. They want to be on the inside of the molecule because of that.

There was one interesting additional problem. This is actually the most interesting part of the story. That is, how did the bases fit together? If the put the nitrogenous bases on the inside, they could get a double helical structure that began to fit the data, but there was still a problem remaining, there are two kinds of bases, the pyrimidines and the purines, and they are of different sizes. Purines have two rings, and pyrimidines only have one.

If you just try to put these stair steps across the two sides of the double helix, you’ll have some steps that are wider, and some that are narrower. For example, if you got two purines together, you’ll have a relatively narrow step. The outside of this spiral would be going in and out, which is not structurally stable. That’s were Chargaff's rule came in. They realized the implications of Chargaff's rule, which says that the amount of the base adenine (A), always equals the amount of thymine (T). Similarly, the amount of guanine (G), always equals the amount of cytosine (C). This suggested that it may be that one always pairs up with the other when they are matching together on the inside of the helix.

It turns out that when they looked at how these kinds of nitrogenous bases would match up, they found that those peculiar combinations (A and T, C and G) would always maximize that potential weak bonding that occurs between the bases. With this, they actually solved two problems. They figured out how you can have a regular distance along the whole length of the staircase. Also, they figured out what could hold the staircase together. If you always match A with T and G with C, the bonding that holds two sides together is maximized.

In April, 1953, which is only a year after people became convinced that DNA was the information molecule, Watson and Crick published a one-page paper in the journal Nature, which described the double helix. They described the molecular structure and how they thought it would all fit together. The real significance of this work was not simply to describe the 3D structure of DNA, but to show how that 3D structure might actually say something about replication.

Watson and Crick’s paper ends with the following sentence: “It had not escaped our attention that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”

The fact that A and T, G and C were always paired together, meant that if you took the two sides of the molecule apart, you would always know what the other side has to be. That’s called complementary base-pairing. It was this fact that suggested that mechanism by which DNA was replicated. I’m very excited about this subject, but I will leave it to another article.

The DNA Structure, Part I

2009-11-26T05:33:00.000-08:00

After the work of Hershey and Chase, biologists in the early 1950’s became convinced that DNA was what they needed to look at to understand the genetic code. They actually had no idea how DNA could possibly act as a mechanism for genetic inheritance. Let’s step back and remind ourselves of what this molecule has to accomplish. It needs to do two things. First, it needs to have some way of providing a code that can store information about proteins.

The linear structure of DNA, with variable bases along the chain was consistent with the idea that could provide such a code. Proteins also are linear chains. So, you can imagine that there could be some sort of mapping of the pattern of one molecule in the pattern of the other. It wasn’t clear what this mapping could be, but they thought they could figure that out. I will talk about that code in another article.

Second, the molecule had to be able to replicate. If we are going to transmit genetic information, from one generation to the next, it won’t work unless we make duplicate copies of the code, so we can handle one copy of the blueprint to the offspring. The real problem was that it wasn’t clear how DNA could be replicated. The linear structure of DNA offer some hope for a code, but it didn’t offer a clue about how replication might occur.

This is where the race, literally a race, for discovering the three-dimensional structure of DNA began. Scientists were convinced they needed to know the three dimensional structure of DNA to understand replication. It was this impetus that led to the discovery of the now famous DNA double-helix, by Watson and Crick. This was arguably the most important finding in biology in the 20th century.

Why biologists should be interested in the three-dimensional structure of DNA? Biochemists had begun to understand, in the 1950’s, that the function of proteins could be understood by figuring out something about their structure. So, it was hoped that some aspect of the function of DNA, specifically how it was replicated, could be understood by deducing its structure.

What kind of evidence could you use to deduce the three-dimensional structure? The first kind of evidence came from a procedure known as x-ray crystallography. The positions of atoms in a crystal can be inferred from the pattern that they create when you shoot a beam of x-rays through that substance. The x-rays would bend around those atoms, and then, when you look at the pattern on the other side, you see lines and dots in particular orientations and spacing. From them, if you’re familiar with the procedure and very clever, you’ll able to deduce something about the relative positions and orientations of the atoms that make up that structure.

If you shoot an x-ray through a relatively simple crystal, you’ll get a very regular pattern. If you shoot an x-ray through a more complex material, like an organic molecule, you’ll get a much more complex pattern. It is pretty difficult to pull information form that pattern, and infer something about the way the molecule must be structured.

You may be asking, what are we talking about here, crystals or organic molecules? Well, even the most complex organic molecules, in the hands of a good biochemist, can be crystallized. In fact, that’s where the story starts. Maurice Wilkins, a biochemist working at King’s College in London, was able to produce a remarkably pure crystal of DNA. Working with Wilkins was a woman named Rosalind Franklin. She was an expert x-ray crystallographer. She took Wilkins’ purified DNA crystal and was able to get what was to that point the most clear and accurate x-ray crystallograph of DNA that had yet been obtained.

As I said, these patterns are quite hard to interpret. Nowadays we can use computers and algorithms to deduce the structure of proteins from this kind of data, but back then was pretty much painstaking hand calculation and educated guesswork. As it turns out, Wilkins and Franklin puzzled over their x-ray crystallograph trying to deduce something about the structure of DNA. They didn’t quite figure it out. By the time, another person arrived on the scene, James Watson.

Before I introduce Watson, I want to introduce another kind of clue. There was a scientist working at Columbia University named Erwin Chargaff, who discovered a peculiar thing about DNA. He found that if you took the DNA from any organism, and decomposed it into its component nucleotides, you always found a quite interesting relationship. You always found that the amount of the base adenine (A), always equals the amount of thymine (T). Similarly, the amount of guanine (G), always equals the amount of cytosine (C). So, if you take apart the DNA of any organism, you always will find that the amount of A equals the amount T, and the amount of G equals the amount of C.

This was a very curious relationship that became known as Chargaff’s rule. Next time we’re going to talk about James Watson and his codiscovery of the double-helix with Francis Crick.

The Building Blocks of DNA: What Is DNA Made Of?

2009-11-25T04:51:00.000-08:00

The building blocks of nucleic acids are called nucleotides. There are only four types of nucleotides. This is one of the reasons why nucleic acids seem relatively simple compared to proteins. Each nucleotide has a sugar that forms a ring. Bonded to one part of this sugar is something called a phosphate group. This phosphate group is just a phosphorus atom with a bunch of oxygen around it. Bonded to another part of the sugar is a nitrogenous base. It is the nitrogenous base that differs from nucleotide to nucleotide. There are four different kinds of nitrogenous bases.

Organic chemists like to number carbons. They actually love carbons because organic chemistry is all about carbons, so they don’t even write them down when they are drawing structures of molecules. If there is a line between two elements, you must assume that there is a carbon there. Instead of writing them, they number the carbons in the sugar around the ring counter-clockwise from one to six. Like this:

There are four kinds of nitrogenous bases. These can be classed into two different groups which differ in size. The pyrimidines have a single six-element ring that’s made of carbons and nitrogens. There are two kinds of pyrimidines, we call them cytosine and thymine. The details aren’t important but these are two kinds of pyrimidines. Here we have drawings of them in order: cytosine and thymine.

The purines, the second kind of nitrogenous bases, are bigger. They are composed of two rings. In addition to the six-element ring that the pyrimidines are made of there is an additional five-element ring that is attached on the side. There are two kinds of purines: adenine and guanine.

We usually refer to the different nucleotides that we find in nucleic acids by the single letter which designates the type of base that it has. We have:

A: adenine.
G: guanine.
C: cytosine.
T: thymine.

Next time we’ll begin to see how this relatively simple polymer, with phosphates and sugars, could serve as a code.

A History Of DNA, Part III: The Code is in DNA

2009-11-24T13:33:00.000-08:00

In my last post we saw how Avery and his colleagues demonstrated (but not conclusively to the scientific community) that the molecule which holds the genetic material in living things is DNA. Now I want to look at a very interesting experiment that really changed the minds of biologist in the matter. In the early 1950’s, Hershey and Chase took a novel approach in trying to found out what the genetic material might be made of, by looking at how a particular kind of virus worked.

Let me give you some background. Viruses are not true cells. They are made of an outer coat of protein with an inner core of nucleic acid. Viruses are made of just two things. The way a virus makes its living is by attaching to a cell, say a bacteria cell, injecting something into that cell and taking over the machinery of the cell. Here is a great introduction to viruses by Salman Khan(Sal), I really recomend you to watch it to understand viruses better.

Hershey and Chase were working with a particular kind of virus, called the T2 phage. This is a bacteria-eating virus, which makes its living by taking over a bacteria and using the protein-synthesizing machinery of the bacteria to make more viruses. Viruses can’t replicate themselves, they have to take over another cell. Clearly, then, what a virus must be doing, is injecting some information. It’s the information that would cause the cell to be taken over. What Hershey and Chase set out to do was to ask, what is it that these T2 viruses are actually putting inside the bacteria? There were only two candidates, proteins and nucleic acids.

The trick was to figure out how to determine which part was being injected. It is a very simple experiment to propose conceptually, but like many experiments in science, the devil is in the details. Hershey and Chase developed a very clever way to figure that out. They did this by radioactively labeling the proteins and the DNA that the virus was made of. In proteins, sulfur is a fairly common element. There is a radioactive form of sulfur (S-35). So, they could grow some T2 viruses in a medium that had a lot of this radioactive sulfur in it. What would happen is that as the viruses reproduce, they would incorporate sulfur into their protein codes. That meant that you could ask not where did the protein go, but where did the radioactivity go.

Alternatively, they could label the DNA. They could grow the same kind of virus in a medium that had radioactive phosphorus (P-32). Phosphorus is not found in proteins, but it is a major chemical constituent of DNA.

So, they grew viruses in a medium that either had radioactive sulfur or radioactive phosphorus. This resulted in some viruses having their proteins radioactively labeled, and others their DNA radioactively labeled.

In separate experiments, they added either the radioactively labeled sulfur viruses (with the radioactive protein), or the radioactively labeled phosphorus viruses (with the radioactively labeled DNA). In both cases they would give these viruses just a couple of minutes. Enough time for them to attach to bacteria and inject whatever they are injecting. Then they would stop the whole process. They were given enough time to inject but not enough time to take over the cell and cause it to build more viruses.

They gave the viruses just 20 minutes, and then they would put the solution in a blender. Then they put this solution in a centrifuge, which spins it around. Because of the action of the centrifuge, the heavier stuff would go down to the bottom of the tube. This would be the relatively large bacterial cell bodies. The lighter stuff, which would be the outer coats of the tiny viruses, would remain up in the solution. If you centrifuge them just right, you’ll get a little lump of stuff at the bottom of the tube, that’s going to be all the bacteria. Then you’ll have the rest of the fluid in the tube, which would include the viral coats.

They then would ask, where is the radioactivity? Is the radioactivity at the bottom, or at the rest of the fluid? What they found was that if they radioactively labeled the sulfur, marking the proteins, the radioactivity was found in the fluid, where the viral coats were. If you radioactively labeled the DNA with phosphorus, the radioactivity was found at the bottom, where the bacteria were. This was a very simple result but took the world by storm, because it showed incontrovertibly that what these viruses were injecting in the bacteria (and happened to be the genetic material), was DNA.

Hershey and Chase published these results in 1952, and it really caused a lot of interest. Biologists began to take a closer look at nucleic acids. That is what I want to do in my next post, look at the structure of DNA.

A History Of DNA, Part II: Proteins Vs. DNA

2009-11-24T04:33:00.000-08:00

In the early part of the 20th century, when Griffith published his work, there was generally an assumption that the genetic material must be a protein. Why did they think that? They thought it because pretty much everything that happens in the cell is done by a protein. It makes sense that if you got something complex and important that is being done in the cell, like providing information, it is probably going to be a protein.

By weight, if you analyze the content of a typical chromosome, there is five to ten times more protein than there is DNA. Another thing that was going against DNA is that if you look at what nucleic acids (DNA and RNA) are made of, they are a string of subunits (called nucleotides). Proteins are made of 20 different kinds of amino-acids. Nucleic acids, on the other hand, are made up of only four different kinds of nucleotides.

Another thing they knew about nucleic acids was that they are actually structurally quite boring. Proteins have a complex structure that determines their function. Nucleic acids seemed to be strings that laid there. They didn’t have these complex structures. So, the sequence of the building blocks of nucleic acids seemed rather simple (with only four elements), the structure of nucleic acids seemed kind of simple and not very useful. Everybody assumed that it must be proteins that were somehow holding the code.

There was, however, one nagging piece of evidence that argued against proteins. If you heat proteins up, they break down. They break down because those chemical interactions that hold proteins together start to break apart. The protein loses its configuration and changes its shape. The problem here is that when Griffith had heated up those S strain bacteria to kill them, he probably denatured a lot of the proteins. So, there was some evidence that it might not be proteins, but nonetheless most biochemist thought that they should be looking at proteins in the early part of the 20th century.

How did scientists try to solve this problem? Back then, they did biochemical procedures that would selectively break down particular kinds of molecules. This kind of work was done in the early 1940’s, by three researchers at the Rockefeller Institute; Oswald Avery, Colin MacLeod, and Maclyn McCarty. These guys were biochemists who had being developing relatively sophisticated techniques at that time for selectively breaking down different classes of biological molecules. We have four major classes of molecules: proteins, nucleic acids, carbohydrates and lipids.

If you could take a beaker of transforming principle from experiments similar to Griffith’s, and selectively break down each of these classes of biological molecules, then you could ask which molecule, when it is broken down, causes the transforming principle to no longer work. You have some S strain and R strain bacteria, you extract some substance which you would call transforming principle, and then you treat that solution to selectively knock out the proteins, or the nucleic acids, or the other molecules. Then you ask, which one when it is broken down ends up the transforming principle to no longer transform?

They did that, and this is what they found. They could break the carbohydrates, no problem. They could break down the lipids, no problem, still got transformation. They could break down the proteins, and there was no problem. If they broke down the nucleic acids, however, the transforming stopped. They concluded from that, that the transforming principle Griffith discovered must be some kind of nucleic acid.

To me that is pretty good evidence, but interestingly, in the 1940’s, that result wasn’t widely accepted. This was for a couple of reasons. First of all, there was growing interest in protein biochemistry, and a lot of people were still focusing on the importance of proteins. There was a bias against believing it could possibly not be proteins that hold the code. The other reason that people were critical is that they biochemical techniques that these researchers were using were relatively novel. There was some argument that maybe they may not had destroyed all of the class of molecules they thought they had destroyed.

So, there was no way for Avery and his colleagues to prove otherwise at the time and the issue stood. This is where the work of two other researchers came in about a decade later: Alfred Hershey and Martha Chase. In my post I will talk about their clever experiment that shaped modern biochemistry.

A History Of DNA, Part I: Before the Discovery

2009-11-23T04:42:00.000-08:00

Proteins are the biological molecules that make things work in living systems. We could say that they are involved in every process in the cell. They are controllers of biochemical reactions, structural elements that hold parts of the cell together, motors that make things move, signals, and so forth. The function of a protein depends almost entirely on its shape. Its three dimensional shape determines its physical and chemical properties, which in turn allow the protein to serve its unique function. The three dimensional shape of a protein, in turn, depends almost entirely on the linear sequence of the building blocks of life, the amino-acids.

There are 20 kinds of amino-acids. An average protein might have a few hundred amino-acids. So, proteins are the work horses, and their function is determined by its chemical sequence of amino-acids. Now, how do we get a protein of a particular sequence built? To answer this question we need to address two things. First, what is the blueprint that is used to build proteins? Second, how does that molecule actually work?

It is the first question that I want to talk about today. Before we can understand how the code works, we need to understand what the code is made of. I think that we all know the answer today: DNA. Interestingly, though, that was one of the questions that defined molecular biology in the 20th century.

At the very beginning of the 20th century, it was already known to scientist that the code was in genes, which in turn resided in chromosomes. This was known from the work of early cell biologists, Walter Sutton and Theodor Boveri being the most important, who discovered that the particular movement of chromosomes that occurs when cells divide corresponded to patterns of transmission of traits between parents and their offspring. These patters of trait transmission had actually been discovered earlier by the Austrian monk Gregor Mendel.

Cell biologists knew about Mendel’s work, how chromosomes moved, and they developed what now is called the chromosomal theory of inheritance. This theory basically says that the way chromosomes move is somehow related to the way that inheritance occurs, therefore, chromosomes are related to information in cells.

We today know that chromosomes are made of DNA, but how that became a known fact? We must begin by going back to the earlier part of the 20th century, to the work of an English physician named Frederick Griffith. This experiment that I am about to describe really provided the first insight into the chemical nature of genetic information.

Griffith’s Experiment

Griffith was a physician and he wasn’t interested in the molecular basis of inheritance. Instead, he was working on a much more applied problem. He was studying Streptococcus pneumoniae, which is a bacteria that causes pneumonia in humans. What Griffith wanted to do was to develop a vaccine against this particular organism, because the pneumonia caused by it often proved fatal. This was before the advent of antibiotics, of course.

As often it is the case for disease-causing bacteria, there were different strains that varied in their virulence. They varied in how likely they were to induce the disease and cause death. Griffith was working with two strains of Streptococcus pneumoniae. He was working with what we call the S strain on the one hand. This was a very virulent strain. It is called S because if you grow it in a colony, it actually looks kind of shiny and smooth. He had another strain, which he called the R strain, which was non-virulent. If you got the R strain, you might be a little sick but you wouldn’t die. It is called the R strain because the bacteria look kind of rough on the surface.

The important thing to note is that these strains did breed true. In other words, as they reproduced, their offspring had the same properties. S strain bacteria gave rise to more S strain bacteria and so on. It is inferred from that, that the difference between the S strain and the R strain bacteria somehow must be genetically encoded.

What did Griffith do? Griffith was using the approach pioneered by Louis Pasteur, which was to take the organism that you want to develop a vaccine for and kill it. This organism could no longer harm you, but nonetheless, would perhaps induce some sort of immune response if injected in a subject. The idea was to take S strain bacteria, kill them by heating them up, and then take these dead S strain bacteria and inject them into a laboratory mouse, and see if that mouse develops immunity. The mouse wouldn’t die if you injected dead S strain bacteria, but the parts of the bacteria that are injected might nonetheless induce an immune response.

This is a great idea, but it didn’t work. It often doesn’t work. There wasn’t enough left of these dead S strain bacteria to induce an immune response. If you injected these in a mouse, and then injected live S strain bacteria, the mouse would die.

Another common technique that was used then and now to develop vaccines was to eject not only the dead offending organism, but some related organism that was less virulent. In this case, we are talking about the R strain bacteria. The idea is that the live R strain bacteria, because they are alive, would induce the organism to develop a full immune response. That development of a full immune response would somehow pickup some immunity to the dead S strain bacteria. This is a common technique and it often works.

What Griffith did then? He killed some S strain bacteria and injected them in with living R strain bacteria. What he hoped would happen is that the mouse would develop immunity to the S strain, but what happened instead was unexpected, and unfortunate for the mouse, the mouse died. This is a surprising result. What’s being injected into the mouse are dead S strain bacteria, that wouldn’t kill the mouse; and live R strain bacteria, that wouldn’t kill the mouse neither. Nothing was injected in the mouse that should kill it, and yet the mouse died.

What Griffith found out when he dissected the poor dead mouse was that inside it were living S strain bacteria. He injected dead S strain, and when he took the mouse apart, he found living S strain. What Griffith concluded from this work, and correctly, was that somehow the living R strain bacteria had taken up something from the dead S strain bacteria, and incorporated it into them. That somehow transformed the R strain into the S strain.

Griffith later showed that he didn’t need the mouse. You can do this in a beaker. If you put dead S strain and live R strain bacteria in a beaker, some of the live R strain would become transformed into live S strain.

What’s really interesting from this experiment, in my opinion, is that the material that they incorporated must somehow be genetic material. It must somehow have information in it. How else could the R strain bacteria now become virulent like an S strain bacteria? The difference between S and R had to have something to do with genetically transmitted information. What Griffith did was he left it there. It was only 1929 when he was doing this work. He said that he had discovered what he called the transforming principle.

Our interest in this, and of scientist interested in genetics, is that somehow this transforming stuff must involve genetic material. In my next post we will see how this experiment helped in discovering that DNA is the molecule that holds genetic material in living things.

Christians Juggling Biology and Theology Before Darwin

2009-11-15T05:35:00.001-08:00

The great French naturalist Georges Cuvier, more than anyone else, founded modern biology during the early 1800’s. He had a very long carrier in France. He held very important positions and was highly regarded worldwide. He was part of the reaction against atheistic speculations that emerged in the 18th century. He based his work, rather than on speculation, on empirical research. With his research, Cuvier thought he found plenty of evidence against evolution.

In his early work, he focused on the internal structure of various species, rather than on their external structure. He carefully studied how species are designed internally. From this work, Cuvier concluded that there are only a few basic patterns of animal organization. The various species that we see out there are simply variations on these basic designed types.

Looking at individual species, he saw that bodily interactions within each species are so delicate that any significant change in them would render the individual incapable of survival. Organisms are so neatly balanced that if anything changes in it, the organism would collapse.

From his viewpoint, the origin of new species through evolution was simply impossible. It is not surprising that this view fit with Cuvier’s basic Christian convictions. In his case, however, they were fundamentally based on his scientific research.

He became Chief of the French Museum of Natural History during the Napoleonic era. There, Cuvier moved from individual research to overseeing an entire laboratory. He oversaw the first comprehensive collections of fossils and biological specimens. Napoleon was conquering much of the world, and he wanted to bring trophies back to Paris. At this time, science was a vehicle of showing success and power. Fossils and mummies were the trophies, and Cuvier was in charge of overseeing a lot of them.

From his research with these fossils and his studies with biological specimens, he found that there were no significant changes in living organisms over time. The fossils seemed to be unchanged from the earliest time. He maintained that the basic types work and they couldn’t be changed.

Cuvier also was the man to establish that certain fossils, such as the mastodon from America, represented extinct species. This doesn’t directly agree with the Bible. With this, he showed his openness to new evidence (something which many Christians today should try to imitate).

When he looked closer he found sharp breaks in the fossil record, with each break containing a distinctive array of fossil types. He was the one who originated the idea of different geological epochs. Before Cuvier, the past was just the same as the present. He broke it into periods: the Paleozoic, where you find mostly marine invertebrates; the Mesozoic, were giant reptiles appeared; and then the Cenozoic, the age of birds and mammals.

He saw that each epoch had its own types of species, then there were breaks and new types laid on top of it. This suggested to Cuvier that there were great catastrophic extinctions in the past. By some vast environmental catastrophes, probably worldwide floods (he never suggested Noah’s flood being one of them). When his followers could not find any source for the repopulation of regions after the catastrophes, they concluded that God or some vital force in nature must had recreated life modeled on the few basic viable types after each catastrophe.

Fully developed by the mid 1800’s, this theory held that the Earth had gone through a series of massive floods or ice ages. This was followed by the creation of new life. This theory vastly elongated the biblical chronology. Many of Cuvier’s followers, who were Christians, tried to reconcile it with the account of creation found in the book of Genesis, by arguing that the days mentioned in Genesis were geological ages. This is the day-age view of creation.

After each massive catastrophe, God would recreate life. The intelligent design of each species, and the ongoing need for the intervention of a superior intelligence, proved, to these Christians, God’s existence and his intervention throughout history. Cuvier’s science was employed to prove Christian theology. This is where biology stood in Darwin’s youth. This is the biology that Darwin learnt when he went to Cambridge.

De Maillet's Theory of Evolution

2009-11-13T05:22:00.000-08:00

Among the earliest people to suggest that life had developed from simple to complex forms was Benoît de Maillet, who lived from 1656 to 1738. He realized his ideas were over the top for his day, so, he didn’t just come right out and declared the evolution of life to be his view. He used instead an old tactic that others had tried before him, to put the ideas out there, but put them out in a form that permits you to say “I’m not saying I believe this, I’m just reporting what others have said”. In this case, de Maillet placed evolutionary ideas into the mouth of an Indian philosopher.

How did de Maillet concluded that the Earth had being evolving in the first place? The answer to that is pretty interesting. He came from a good family in France and ended up as an ambassador to Egypt at the beginning of the 18th century. He went above and beyond the normal practice of making acquaintance of the region. De Maillet traveled widely in the Mediterranean. He was enormously curious about lots of things. For example, he wanted to know about the features of the Earth’s surfaces in the regions he visited.

I think he got some of this natural curiosity from his upbringing. His grandfather seemed to have been a similar kind of person. The family home was near the sea shore, and his grandfather had a theory about the sea that he passed down to his grandson. He thought he observed that the water level of the sea was dropping. De Maillet’s grandfather convinced his grandson of this. When he found himself in Egypt and other places around the Mediterranean, de Maillet began collecting his own information.

He mastered Arabic and read the histories of Arabic writers. When he traveled around he became familiar with historical landmarks, including the historical records that went with them. He deliberately exposed himself to this foreign Near Eastern culture, whose understanding of the history of the Earth was very different from that of Christian France. He became more open to the possibility that history had been going on a lot longer than what he learned as a youth.

When he examined sights from ancient Carthage he determined that the sea level had indeed been higher back when Carthage was an active port. His calculations suggested a rate of drop of three feet in a thousand years. He assumed this rate was and had been constant for a long time. He then turned to the implications of this idea.

De Maillet expanded his new system to include the entire history of the Earth. He was a follower of Rene Descartes, who had used the collisions of matter to explain how everything worked in nature. De Maillet utilized such mechanical interactions together with his own observations to create a non-Christian cosmogony.

The Publication of the Telliamed

De Maillet knew his manuscript tested the limits of acceptability, so he tried to deflect criticism by attributing the views expressed in the book to a pagan foreigner. The title of the work was the foreigner’s name (which was his own name spelled backwards, how original): “Telliamed. Conversations of an Indian philosopher with a French missionary on the diminution of the sea, the formation of the Earth, the origin of man.”

From the alleged Indian understanding of the Earth’s past, the French missionary learned that the Earth was originally covered by water, whose currents carved out the mountains beneath its surface. The depths of the primitive seas gradually decreased, exposing the highest mountains. As the process of diminution continued, more dry land emerged. As the French missionary pondered these ideas, he brought them to their logical conclusion: “This emergence led to the growth of grass and plants on the rocks. The vegetation, in turn, led to the creation of animals. And finally, the animals led to the creation of man, as the last work of the hands of God”.

Telliamed himself did not invoke the direct act of God to explain the appearance of life. He didn’t give details, but he maintained that various forms of aquatic animals had changed during the time the sea was gradually dropping in accordance with natural process. Flying fish grew little wings and became birds. Other fish grew feet and walked on land.

Clearly, such processes had taken a great deal of time, far longer than 6000 years. Using, the rate of diminution of three feet every thousand years, de Maillet concluded that over 2 billion years had passed since the primitive waters had begun to drop. Humans themselves were over 500000 years old.

The public immediately saw through de Maillet technique of camouflaging his ideas in a pagan philosophy. The reaction, I’m sure you’re not surprised, was outrage. Even Voltaire thought de Maillet had gone too far. The years after Telliamed appeared, Voltaire noted that there was no support for such an outrageous notion.

Retribution came down on this heretical work from far more official sources than Voltaire. De Maillet, who was long dead, was safe, but his book was roundly denounced. I find the story of De Maillet very interesting and enlightening. It shows us how difficult it was, and it is still today, to put forth ideas contrary to popular belief.

Return from De Maillet's Theory of Evolution to Darwin's Theory of Evolution

Theories of Origins Before Darwin

2009-11-11T05:43:00.000-08:00

What were the theories of origins before Darwin? What was there before Darwin? What did people think about the origin of life and the different species on Earty? One thing characterizes people, as Descartes would say, they think. As thinking creatures, we have always wondered about how the universe and things in it originated. We are particularly interested in our own origin.

The first chapter of Genesis contains the Christian creation account. It tells of God creating the heaven and the Earth, plants and animals, and then man in God’s image. All in six days. The Bible doesn’t state when this creation occurred, but most early Christians probably assumed that this did not occur too long ago. In the 1600’s, the Anglican bishop James Ussher fixed the date of creation at 4004 B.C.E. This is the established biblical view that continues to the present.

The Early Scientific Accounts of Origins

Over the past 2000 years, this creationist account did not exist alone within the western tradition. Religious accounts of origins, at least for the past 2000 years, have competed with scientific accounts of origins. Science began with the Greeks, about 600 B.C.E. At this time we find the firsts scientific explanations for natural phenomena.

Although many Greeks retained religious theories about nature founded on revelation or mythical stories, some philosophers proposed materialistic explanations founded on reason. What do I mean by materialistic? This means that they explained natural phenomena without recourse to God or the supernatural. These philosophers said that natural phenomena can be explained as the result of physical matter moving in accord with natural law, with God, at most, as the remote creator of the primordial matter and the laws of motion. We find this sort of account in Plato, for whom God created the primordial matter and its laws, and then left it operate.

Biological origins posed a particular puzzle for Greeks who tried to devise purely materialistic explanations for natural phenomena. Biological organisms, people specially, seemed much more intricate and intelligently designed than just rocks or mountains. They seemed created, and creation implies a creator.

So, to explain the origin of biological organisms, early natural philosophers, like Anaximander and the so-called atomists, proposed crude theories of evolution. They are not very detailed, but they had the idea that there was some sort of spontaneous generation of life and somehow species could evolve over time. They weren’t worked out very well.

Aristotle critiqued these ideas. Aristotle himself was an atheist, and first and foremost, a biologist. He was a very avid observer of life, particularly of fishes. Based on his close study of animals, Aristotle defined a species as a breeding group. A group of particular animals or plants that can breed, and produce offspring that eventually could reproduce. He concluded that species were fixed.

Rejecting both creation and evolution, Aristotle simply saw the species as eternal. They always existed. Later Christian philosophers tried to integrate Genesis with Aristotle. They typically viewed each species as created by God in the beginning, but then, using Aristotelian authority, asserted that these species remained fixed for all time in a perfect (albeit fallen) creation.

This was the dominant view for a millennium in the West. It began to break down, though, when religious authority began to break down.

Deist and Atheist Accounts

The breakdown of religious authority finally occurred during the Enlightenment, in the 1700’s. Notions of evolution began creeping back in. This happened particularly in France, where natural philosophers again struggled to devise purely materialistic explanations for life. Seeking to push God back to the beginning, deists proposed a variety of ideas. They proposed that the solar system was created not by God, but rather a comet once hit the sun and knocked off a bunch of matter, which separated, each piece becoming a planet.

They also proposed ideas for the origin of species. They said that the tremendous array of species evolved from a few common ancestral types. Some of the French natural philosophers were even more atheistical. Denis Diderot, for example, a committed materialist, proposed that all living forms developed by random chance mutations from spontaneously generated organisms.

Probably the most influential natural philosopher from this period was the astronomer Pierre Laplace, who proposed a purely materialistic explanation for the origin of the solar system. He said that the solar system was once a big rotating gas nebula, and as it rotated, centrifugal and centripetal forces would pull in matter to the center, which became the sun, but as it pulled in, it left little blobs of material that collapsed into the different planets. This was called the nebular hypothesis.

When Laplace described his theory to Napoleon, he was asked “how does God fit into it?”, Laplace famously responded “I have no need for God in my hypothesis”.

All the ideas that we’ve gone over were highly speculative and were driven more from philosophy than empirical scientific research. There were a few discoveries at the time, though, that reinforced these ideas.

For example, Abraham Trembley detected that polyps, which are very simple sea creatures, could regenerate. By cutting them into pieces they regenerated the whole. They could be flipped inside out and still operate. People saw this as “almost spontaneous generation”. Philosophers took this as scientific evidence for their speculations.

Overall, however, the empirical research during this period cut the other way. Even if these ideas were speculated about, when people actually did the experimental and observational work in nature, most of them opposed the evolutionary ideas. The generation after the Enlightenment reacted against the speculative nature of evolutionary ideas. They returned to creationism, although not the creationism of the Bible, but a creationism based on scientific evidence. I will discuss this in my next post, when we see how Georges Cuvier founded modern biology.

Return From Theories of Origins Before Darwin To Darwin's Theory of Evolution

The Truth About Ussher's Chronology

2009-11-10T05:50:00.000-08:00

James Ussher was an Irishman born near the end of the 16th century. Elizabeth was on Britain’s throne and remained there until Usher was 22. By that time, he had accomplished a great deal. He was very gifted with languages. Young James went off to Dublin to enter Trinity College when he was only 13. He was ordained a priest at the age of 20. He became a professor at Trinity when he was only 26. When he was 44, he became Archbishop of Armagh. That made him the head of the Anglo-Irish Church, a protestant leader in a predominantly Catholic land.

Ussher’s skills and his references were scholarly. He held an administrative position as Archbishop, but his heart laid elsewhere. In fact, he was criticized as an administrator because his inclination was to debate, not to simply deal with opposition by politics of intolerant decree.

It was during the final period of his life that he wrote the work for which he is now famous, the "Annals of the Old Testament, deduced from the first origins of the world". This work appeared right at mid-century in 1650. It’s common to say that Ussher reached his famous date of 4004 B.C.E. by simply calculating back from the time of Jesus by adding up years involved in the lineages of Christ given in the Bible, and going all the way back to Adam. It was much more complicated than that.

There is complete information given in the Old Testament to make an accurate calculation up to the time of Solomon, but after that, ambiguities begin to creep in. For approximately the last 400 years before the birth of Jesus, the Bible gives no help at all. What Ussher did was what to correlate information from this period with known dates from the histories of other cultures, specifically the Chaldean and Persian cultures. This required an incredible expertise in biblical history, secular history and language abilities. The bulk of the knowledge he applied was non-biblical. Ussher had one of the best minds of his time.

The late Stephen Jay Gould, noted paleontologist and Darwinian evolutionist, once wrote a wonderful explanation of how Ussher came to his conclusions (it is available here), including how he came to the precise date he gave for the creation: October 23, at noon.

Gould’s point in taking up the subject was to criticize those who dismiss Ussher’s work as the application of dogma to a scientific subject. They are not only ignorant, but they miss the point entirely. Gould said “I close with a final plea for judging people by their own criteria, not by later standards that they couldn't possibly know or assess”.

He was delighted with Ussher’s explanation of how he determined his result. Not only by the plain use of Holy Scripture, by also by light of reason well directed. Because of his erudition, Ussher’s calculation became accepted in the Western Christian tradition for a long time.

King James commissioned a translation of the Bible in the first decade of the 17th century. It became the authorized version in English and continues to exist to this day. By a half-century after Ussher’s death, his calculation of 4004 B.C.E. for the date of creation was inserted into the column of annotations that stood between the double columns of text. It lasted there until the second half of the 20th century.

The Origin of Life, Part IV: Genetic Code

2009-11-10T05:11:00.000-08:00

Ok. We’ve shown that it is possible for cell-like structures to spontaneously generate in certain conditions. How do we get from protobionts to all the enormously complicated and diverse stuff that we see today? We don’t know the answer to that question and we probably never will. We do know, however, part of the answer. Part of the answer has to do with reproduction.

How does a living system reproduce? What minimally do we need to get reproduction? How reproduction arose is an especially tricky problem. It is the problem that is most debated today in the area of the origin of life.

To understand what is needed for reproduction, let’s imagine we’re back in time. Let’s imagine we have some proto-cells that are functioning. Let’s say that by chance, one of these protobionts just happens to come up with some unique new trait. This trait could be anything. For example, it could be a new kind of molecule that makes this cell more durable. It could be a new kind of molecule that increases its ability to take up material from the outside.

This protobiont is different from the rest. It is somehow more efficient, better at doing its job. The problem is that we have only one of them. That individual won’t last forever. Even if it does, there will only be one of them. This issue leads us to reproduction. This problem would be solved if our protobiont could reproduce itself in a way that would pass that useful trait on to its progeny. How does it do that? Well, cells split into two. We have one cell, it grows a little larger and splits into two. In essence, that’s reproduction. This is not enough, however.

The Genetic Code and the Problem of Replication

If the trait we are talking about is a molecule, which of the daughter cells gets the molecule? Even if there is a lot of these molecules and each daughter cell gets a half of it, and the daughters of these cells get the half again, eventually this property will fade away. What we need instead is for these primitive cells to somehow be able to make completely new and accurate copies of themselves. They have to be able to store information about the structure of the molecule and transfer that information to its offspring.

How such a mechanism for storing and transmitting this kind of information came about is one of the unresolved questions about the origin of life. We know, however, that there is such a molecule in modern cells. This is a cell that accesses a blueprint for making more molecules. This molecule is called Deoxyribonucleic acid, or DNA.

DNA passes its information onto another kind of nucleic acid, RNA, and then the information goes from RNA into proteins. This is the way information works in modern cells. In this system, DNA acts as some kind of blueprint, RNA as the translator and proteins are the product of that blueprint. Proteins do much of the real work in modern cells.

Here we encounter a really serious problem, however. DNA could not have been the storage molecule that first arose in early life. Why not? The reason is that DNA can’t replicate itself. DNA requires a huge number of other proteins acting as enzymes to replicate. DNA in modern cells can be replicated but only if there are proteins to do the replication job. Proteins that could do that replication job might have arisen sometime in the early history of life on Earth, but they couldn’t have arisen before there was DNA to store their code. We need to postulate simultaneously the appearance of DNA that could store information about proteins and proteins that could replicate that DNA. Which came first, the chicken or the egg?

Neither could have come first because DNA and proteins can’t exist without each other in modern cells. Also, it is unbelievably improbable to think that just the right kind of proteins and just the right kind of DNA happened to arise spontaneously sometime in the early history of life.

What was need, instead, is for some kind of molecule that could do both of these things. A molecule that could replicate itself and it could do other useful things in the cell. Today we’re beginning to think that when life arose the molecule that did that was the nucleic acid RNA, or some early form of what we know today as RNA. Why we think that?

The RNA World

At the beginning of the 1960’s researchers have begun to suspect that RNA might have acted as the first blueprint or genetic material. In the laboratory, it is possible to put in some kind of RNA and then some building blocks, and under the right conditions the RNA replicates itself. RNA in the solution somehow acts as a template that helps the monomers come together in the right way and also polymerize.

A second breakthrough that led people to think that RNA might be the first information processing molecule came in 1983, when Thomas Cech actually discovered that, in modern cells, there are some kinds of RNA that do act as catalysts the way protein enzymes do. That is, they perform some important biochemical tasks in the cell. They are generally called ribozymes.

The important point is that these rybozymes are functioning as catalytic molecules just like protein enzymes. We’ve got two things now. We’ve got evidence that RNA can replicate itself and also evidence that RNA can have some sort of catalytic function. Taken together, these two sets of results suggest that in the very early stages of life, that magical point where a non-living protobiont somehow slipped over the edge into the state that we might want to call a living cell, happened in what we now call an RNA world. RNA actually dominated as the key biological molecule.

At some point after the RNA world, things changed. RNA had gotten the system rolling, but eventually DNA and proteins took over. DNA took over the job of being the information-bearing molecule. Proteins took over the job of doing all of the catalytic and other kinds of work in the cell. RNA became relegated to just an intermediate in the process.

Why this would happen is fairly obvious. Proteins are extraordinarily versatile molecules. They do an enormous number of tasks. Their versatility comes from the fact that they can assume all sorts of complicated shapes in a way that RNA can’t. Proteins clearly took over doing the real work in the cell because they were really good at it. DNA assumes a particular kind of chemical configuration that makes it really good at storing information in a way that RNA is not particularly good. Once we have DNA, it is much better than RNA at making more copies of itself and storing that information. So, it took over that job. RNA became just an intermediate.

I think that with this we have what is basically needed to the appearance of life. We’ve explained the origin of life, at least in part. Quite an accomplishment, eh? How do we get from these simple cells to platypuses and other things is another subject, and don’t worry, I’ll try to tackle it.

Return from Genetic Code to The Origin of Life

The Origin of Life, Part III: Primitive Cells

2009-11-08T03:55:00.000-08:00

The experiments of Miller, Fox, Ferris and others had shown that complex polymers could arise spontaneously on the early Earth. We know, however, that the organic molecules that make us up are not just a jumble of things floating around in a primordial soup, they are highly ordered. They come in highly ordered packages. There are many such packages in living systems, but the most fundamental one is what we call the cell. All living things are made of units called cells. Minimally, for something to be living, requires a barrier between the living part and the non-living part. That barrier is what would define the cell.

Is it possible that some cell-like structure could arise spontaneously on the early Earth? Here, too, laboratory experiments suggest that the answer is yes. A number of experiments have been done that demonstrate, under conditions that are not too rigorous, that you can get aggregations of molecules that would spontaneously form cell-like structures.

This kind of spontaneously made cells are called protobionts. You can actually make protobionts, it is not difficult to do. You can make them under a number of different kinds of conditions. For example, if you have the right kind of lipids, you can almost literally put them in water and they spontaneously form a package where there is a membrane of lipids that encloses some central space.

The most remarkable kind of protobiont, called coacervate, is one that has been made to self-assemble out of a solution that includes polypeptides, nucleic acids and polysaccharides. If you have the right conditions, you can make these to self-assemble into a cell-like object. What is really interesting about coacervates is that if you then throw into the mix some real biological molecules, a protein enzyme that you’ve taken from a real living cell, for example, the coacervates can take up those enzymes. They would bring them inside of themselves.

Those enzymes would start working inside the coacervates. What enzymes do is to process some kind of biological molecule into another. Once these enzymes have been taken up by these coacervates, it would also start doing the reactions and putting out the products. This is really getting remarkably close to something that we might want to call living.

I don’t say that we can make primitive cells. Nobody has actually made a cell that any biologist would look and say “oh, that’s a cell you just made”. People are trying to do that now, but it hasn’t been done yet. We can, however, make cell-like things and it doesn’t seem to be any big trick. These things spontaneously form, we know that for sure.

Return from Primitive Cells to The Origin of Life

The Origin of Life, Part II: Polymerization

2009-11-07T09:44:00.000-08:00

Okay, let’s go on with the origin of life. In my last post I talked about Miller’s experiment. The significance of this experiment was simply to show that non-biological processes could result in the formation of organic molecules, including amino-acids and nucleotides. These molecules that Miller got, however, were still relatively simple. They thus only represented a first small step.

Amino-acids and nucleotides by themselves don’t get us very far because we need to get these simple molecules linked together. They act as building blocks to make the more complicated stuff that we are really made up of. The technical term for this process is polymerization. In other words, complex organic molecules, like proteins, or DNA, are polymers. They are long chains of building blocks(monomers).

Miller was able to make the building blocks, but living things need those building blocks strung together in polymers.

Ordinarily, in living things today, there are a series of specialized proteins, called enzymes, that are responsible for building these polymers out of the monomeric building blocks. What happened in the early Earth in the absence of these specialized protein machinery that could possibly lead to polymerization?

Polymerization in Laboratory

The first evidence that this was possible came fairly early on in the late 1950’s, and it was worked by Sidney Walter Fox. Fox took Miller’s experiment one step further. He was able to take amino-acids that might have been created in an experiment like Miller’s and get them to start joining together but only under certain conditions. In just the right proportions, in just the right temperature, the right amount of time that you might heat them, he could get short polymers of amino-acids. We call a polymer of amino-acids a protein, but we also call it a polypeptide chain. That’s simply because the chemical bond that link these monomeric amino-acids to form that chain is called a peptide bond.

What Fox was able to do is to get fairly short polypeptides, showing that you can get spontaneous polymerization. The problem was that Fox could only do this under a very narrow range of conditions. In Miller’s work, you could just throw a bunch of stuff into those flasks, and you get some sort of organic molecule. Fox’s work, however, required much more controlled conditions, conditions that are unlikely to have been that of the early Earth.

Origin in Clay?

Fox and a number of other scientists, however, speculated that maybe you could get more spontaneous formation of polymers if you had some sort of non-biological catalyst. A catalyst is just a term that refers to something that makes a chemical reaction run faster. What Fox and others suggested was that maybe there was something that was non-biological that could catalyze these polymerization reactions. Specifically, what they suggested was that perhaps there were certain kinds of clays that acted as inorganic catalysts.

Why clay? It turns out that some kinds of clay, when they dry out, form very regular ladder-like structures. Furthermore, these clays would also have weak electrical charges on their surfaces. These weak electrical charges can adhere organic molecules. The idea here is that sometime in the early Earth, the shores of a primitive ocean had a bed of clay. As organic molecules that were being created in that primitive ocean got accumulated into the shore, they adhered to that clay. And the clay, because of its regular order and the spacing, would increase the probabilities that you get some sort of spontaneous polymerization.

Wow, that’s an interesting idea. Is there any evidence that this could work? We don’t know what the primitive Earth was like at that scale, but it turns out that recent work by James Ferris, who is at the Rensselaer Polytechnic Institute, has shown exactly that this process does work under abiotic conditions. In a laboratory, Ferris and his colleagues have been able to synthesize not only short polypeptides, but also short stretches of DNA from the component building blocks that were created from experiments like those done by Miller.

The proteins and DNA that Ferris and other have produced are not functional. These are strings of monomers that have been polymerized, but they don’t make any sense. It’s not like a string that would do anything like a real biological molecule might. Nevertheless, it is a start. We can postulate that biological polymers could arise spontaneously.

So, let’s imagine that we have complex polymers. Let’s imagine that we’ve got a primitive ocean brimming with a whole bunch of organic polymers, what has been called the primordial soup. Let’s imagine that even some of these polymers, by chance, have come together as strings that might even have some sort of useful biological function, like modern polymers. Where do we go from there?

The experiments of Miller, Fox, Ferris and others had shown that this is possible, but even with all of this we still don’t have anything approaching what we would want to call life. Why not? Because we know that the organic molecules that make us up are not just a jumble of things floating around in a primordial soup, they are highly ordered. They come in highly ordered packages. This is going to be the subject of my next post, cells. Stay tuned.

Return from Polymerization to The Origin of Life

The Origin of Life, Part I; Miller's Experiment

2009-11-07T08:12:00.000-08:00

As Richard Dawkins puts it, “the theory of evolution is about as much open to doubt as the theory that the Earth goes round the sun”. We can also be sure that all of the diverse forms of life we see around us today have arisen from some common, primitive, single original living entity. Our first problem is, then, how this living “thing” originated. In 1953, Stanley Miller conducted his famous (or infamous) experiment. At the time he was a graduate student at the University of Chicago. For decades, scientists had speculated whether the complex organic compounds characteristic of living things could have somehow been generated spontaneously on the early Earth. Spontaneous generation of organic compounds can’t happen today. This is because organic compounds are too fragile.

It is possible that, given enough time, a complex compound might just come together. If it did, however, it would immediately be taken apart. This is because today our planet is just filled with oxygen. Oxygen breaks down organic compounds. Oxygen pulls electrons out of organic compounds and turns them into inorganic compounds.

How can we even get the formation of any kind of organic compound, if as soon as anything begins to arise by chance, it is immediately taken apart? Well, this one is easy. If oxygen is bothering you, just get rid of it.

Before the Miller-Urey experiment, two scientists, Alexander Oparin and J.B.S. Haldane, independently suggested that the early Earth actually did not have much or any oxygen. Oxygen is all around us in the atmosphere, but they suggested that when the planet was formed, the first atmosphere that developed was entirely composed of just a few gases: hydrogen, methane, ammonia and water vapor. This would be as the atmospheres of the moons of other planets that have been described.

Oparin and Haldane independently suggested that the problem of spontaneous generation of organic compounds wasn’t really a big deal, because the early Earth did not have an oxidizing atmosphere. To test this hypothesis, what Miller did was set out to reproduce the conditions presumed to exist on the early Earth before life have arisen, and see if he could get the spontaneous production of organic compounds.

A Simple Experiment, Powerful Results

Miller’s experiment was set up this way: He had two flasks connected by a series of glass tubes. He had a lower flask in which he put water, and he heated this water gently with a little flame. He would cause the water to evaporate and create water vapor, which would circulate into a higher flask. In the upper flask, Miller also added a number of other gasses. He created an atmosphere similar to the one of the early Earth, consistent of hydrogen, methane, ammonia and wáter vapor.

The Experiment. Souce: Wikipedia.

Miller also exposed the gases in this upper chamber to a lot of energy by putting two electrodes that would create electrical sparks. He knew that he needed energy to create any kind of compound, certainly organic compounds.

This is actually a pretty simple experiment, and you can almost do this in your own house. All of these materials are easily available. You could replicate Miller’s experiment and results, which were spectacular. In only a couple of days, he found he could synthesize a whole range of different organic compounds, including some very complex ones, like amino-acids.

The scientific community immediately set out to replicate this. Many people replicated the experiment and it quickly became clear that depending on starting conditions, it was possible to spontaneously, without any preexisting organic molecule, produce all of the amino-acids that are normally found in living material. Most intriguingly of all, you could create nucleotides, which are the building blocks of nucleic acids, DNA and RNA.

The implication of Miller’s experiment and those that followed was that there appeared to be no trouble at all for complex organic compounds to arise spontaneously on the inorganic early Earth. This is a first stepping stone to the origin of life from non-living matter.

On the other hand, as exciting as this result was, the organic compounds that Miller created were still relatively simple compared to the stuff that we are made of. What else do we need to get something that we would call “living”? We have to take our synthesis of organic compounds even farther, beyond these organic building blocks, to get the varied extremely complex molecules that living systems are really made of. We will see how that was possible in the early Earth next time.

Return from Miller's Experiment to the Origin of Life

In the Beginning

2009-11-07T05:45:00.001-08:00

In the beginning... there was a singularity. Physicists tell us that the universe, as we know it, began between 10 and 20 billion years ago, at a moment in time they call the Big Bang. Our own star is comparatively young. Estimates are that it formed about 5 billion years ago. As our solar system was forming, cosmic dust gradually got swept up and began to form planets. Scientists estimate that our own planet reached its present size at about 4.6 billion years ago. That is generally taken as the age of the planet Earth.

In the beginning, planet Earth was a really miserable place. The way that the planet was formed, with ever larger and larger chunks of material slamming into it, created an enormous amount of heat. When the planet first formed it was melted. It was no place where one could ever conceive of life existing. Less than a billion years later, however, the fossil record clearly shows that life was there. This life was in the form of simple cells that resembled the bacteria we see around us today.

This is pretty fast work, especially when you consider that it took about a half a billion years just for the Earth to cool enough to actually have rocks and an atmosphere. In fact, some scientists now argue, based on fossil evidence, that life might have been present even earlier, as earlier as four billion years ago.

What we can take from this is that life appeared on the planet almost as soon as it was possible to do so. As soon as there were rocks to record the existence of life, we find evidence that life is there.

Where do these organisms come from?

In the beggining, life originated on the early Earth from non-living materials. All of the diverse forms of life we see around us today have arisen from some common, primitive, single original living entity. This is pretty deep stuff, a very cool idea.

There are alternatives to this account, of course. Many religious faiths hold that, in the beginning, life was bestowed on the planet by the work of a deity, but this is a pretty boring idea. Another alternative, one that has been suggested repeatedly over the years by a number of scientists, is the panspermia hypothesis. It suggests that the first life on Earth came from somewhere else in space.

Both of these alternatives, however, beg the question of how living matter could arise from non-living matter. That brings an important question into the table.

What’s the minimal difference between living and non-living materials? This is basically the same as asking “what is life?”. This question has been around for a long time. For me, however, with all the knowledge we have today at our disposal, to address this question is pretty simple.

So, what is life?

Life is defined by what is called organic chemistry. The most fundamental difference between living and non-living matter has to do with chemistry. Living things all have in common the fact that they are made of a particular class of chemical compounds. These are compounds that are built around the unique chemical properties of the element carbon. These kinds of compounds are called organic compounds. They are called that way because they are uniquely associated with living organic things.

There are only four kinds of organic compounds, broadly speaking. The first kind are amino-acids. These are the things that make up protein. The second kind of organic compound are the nucleic acids. These nucleic acids are DNA and RNA. The third class are the carbohydrates. These are what we commonly call sugars. The last general class of organic compounds are the lipids. Lipids are what we commonly call fats in many cases, but lipids can actually take a number of different forms.

These organic compounds have particular and quite sophisticated chemical properties that are unique to them. There is one property that is particularly remarkable, that is that the complex organic compounds that we find on the planet today, the stuff we are made of, is generally only produced through the action of living things. Another way to put this is that the creation of new organic matters depends on the existence of organic matter. You can’t make more organic compounds unless you got compounds to make them.

We can be quite confident given what we know about how the planet was formed the early Earth was entirely inorganic. Then, we have to ask: Where did the organic compounds that life depends on came from in the beginning? At this point, you might think that I’m going to throw Intelligent Design and Creationist arguments at you. I won’t, don’t worry. I’ll create some tension and leave that question unanswered, until next time, when we talk about the exciting, random and unintelligent origin of life.

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