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.


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

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

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?

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

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

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

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

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

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

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

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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

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

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

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

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

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.

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