A History Of Life, Part IV

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

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

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

“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

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

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

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

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

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

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

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

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

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

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.


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

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

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

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

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.

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