Defenseload

Molecular Biology Primer

I’m going to embark on a six-part series of podcasts to present, as simply as possible, the molecular evidence for evolution. I’m extremely grateful for Dr. Douglas Theobald’s work in compiling not only these evidences, but two dozen additional evidences which can be found at www.talkorigins.org. Usually when people think of the evidence for evolution, they think of fossils. And certainly, fossil evidence is very substantial, making the case almost by itself, but we should be interested to know that evidence can be found in places other than under the ground- it can also be found inside all of us. That is- in the molecules that make up our bodies. Now, since the nature of this evidence is pretty technical, I want to preface it with a brief primer, so that I can flesh out the relationships between the relevant molecules that I’ll be discussing. So, hang with me as best as you can, because the evidences that will be piling up in the next few weeks are really astounding, in my opinion.

Molecular biology is a fascinating component of the biological sciences. It was born in the early part of the twentieth century out of a desire to find some way to unite the related fields of biological chemistry, microbiology (the study of microorganisms such as bacteria), genetics, and virology. The goal of molecular biology is to study biological systems by analyzing their macromolecular components. I’ll assume that most of you know that a molecule is nothing more than the smallest amount of any substance that still retains its properties, but what are macromolecules? They’re called “macro” molecules because unlike a molecule of, say, water, which is made up of only three atoms, macromolecules are composed of anywhere from dozens to thousands to millions of atoms, depending on the molecule. There are essentially four classes in biology- proteins, carbohydrates (sugars), nucleic acids (DNA), and lipids (fat). They are also somewhat unique in their ability to form polymers, or long chains of repeating segments. The longer the chain is, the larger the molecule.

Proteins perform most of the basic biological tasks in organisms- they form the internal structural support of cells, link cells together, cut up and assemble other proteins or nucleic acids, provide communication pathway between the inside and outside of a cell, immobilize and target invading microbes for destruction, and convert energy currencies to run the whole show. Carbohydrates and lipids are used primarily for energy storage, although they do a number of other things as well- I don’t want to slight those people who are interested in lipid biology- I come from a lipid background myself, and I know how essential they are, but I’d like to jump ahead to the final macromolecule, nucleic acids, and its connection with protein expression.

Nucleic acids form the central aspect of the replication of life. DNA is a nucleic acid, and is the beginning of the process that ends in production of a particular protein. DNA is a polymer, which means that it’s a long chain of subunits. These subunits, or nucleotides, come in four types, called adenine, cytosine, guanine, and thymine. These are usually abbreviated to the first letters of their name, A,C,G, or T. A DNA molecule is made up of only these four nucleotides, and they can be placed in any order. DNA molecules are millions of nucleotides long, which basically makes them very long string-like molecules. Unless they’re being copied, DNA molecules are usually wound up tightly around themselves- sort of like a telephone cord that’s been stretched too far and too many times. These wound up DNA molecules are called chromosomes- and humans have 23 pairs of them, or 46 total. The sequence of nucleotides that makes up a chromosome is copied every time a cell divides- in the process called mitosis. Mitosis occurs whenever new cells are being made- and this is happening in your body all the time. Skin cells, hair follicles, liver cells, muscle cells, bone marrow cells- all these cells are undergoing mitosis as you listen to this.

Mutations are mistakes in DNA replication. The molecular machinery that copies DNA during mitosis is not perfect, and it is susceptible to a number of factors, including radiation, certain chemicals, or viruses. Radiation, especially ultraviolet radiation, tends to affect adjacent thymine bases, so it’s not completely random, but it’s very close. But there is also a base rate of mutation that occurs randomly but at a measurable average rate, that results in one base being switched with another during copying. In humans, this rate is at about 1 mistake per 100 million base pairs every generation. This is about 175 total mutations per individual. If one of these mutations occurs in one of the cells that is transferred to the next generation- we call these “germ cells” and they would be either sperm in the male or eggs in the female- then the mutation is incorporated into the genome of the next generation.

This is an important concept- since we observe time and time again that inheritance is the mechanism for transfer of mutation from one generation to the next, we can infer genetic relationships between organisms based on shared mutations. For example, let’s say that your grandfather was the first person to have a unique and dominant mutation, call it “Mutation X”, which was passed on to all of his children, including your father, and then on to you. You happen to meet someone who claims to be a long-lost cousin, but how do you know? If you were to compare your DNA sequence to this supposed cousin and find that they had Mutation X as well, that would be genetic proof that you share the same grandfather. Thus, shared DNA sequence implies shared ancestry.

OK, so that’s how DNA works, but how do you get protein from DNA? Well, as I’ve mentioned before, the DNA sequence of most organisms is divided up into transcribed and non-transcribed parts. The transcribed parts are called “genes.” Gene transcription is the process by which an RNA copy is made of a DNA sequence. RNA is similar in structure to DNA, but it isn’t used as the genetic storage molecule. Instead, it’s used as an intermediate to ferry copies of the DNA sequence out of the nucleus of the cell and into the main part of the cell, where protein is made. RNA is kind of like a librarian who goes into the basement of the library, makes a photocopy of a book, and then brings the photocopy to a person who requested it. It’s basically an exact copy of the original gene, but constructed out of RNA nucleotides, instead of DNA nucleotides. These copies are called transcripts, because we talk about RNA being transcribed from DNA. The RNA travels from where the DNA is stored in the nucleus out into the main part of the cell, where protein is made.

Proteins are also polymers, or long chains of subunit molecules. Instead of being made out of nucleotides, however, proteins are made out of amino acids. Now, whereas there are only four different nucleotides that are incorporated into DNA, there are twenty different amino acids that are incorporated into proteins. That means that it would be impossible to have a 1:1 relationship between a nucleotide and an amino acid sequence- there just are too many amino acids. So what’s the solution? The solution is that there is a kind of code in the nucleotide sequence that requires it to be subdivided into three nucleotide groups. This way, a sequence such as AGTCTCGAATCC would be read, AGT, CTC, GAA, TCC. These groups of three nucleotides are called codons, because they are the individual units of the genetic code. Since there are 64 possible codons, that makes plenty of possible amino acid counterparts- too many, in fact. Since there are 64 possible codons but only 20 possible amino acids, that means that there are multiple codons that correspond to the same amino acid. The RNA sequence is used directly to make the amino acid sequence, in a process called translation.

Amino acids are themselves somewhat similar is structure to a nucleotide- there is a base structure that is composed of an amino group and a carboxylic acid group- hence the name, amino acid. But each amino acid also has room for another group, called a side chain- and it’s the various structures of the side chain that make one amino acid different from the other. Some amino acids are electrically charged, and some have no charge. Some amino acids associate well with water, others are repelled by water. Some amino acids are very large, and others are very small. All of these factors come into play during the final product, the protein molecule. Ultimately, a protein is just a long chain of amino acids, just like DNA is a long chain of nucleic acids. But instead of staying a long, floppy string of amino acids, proteins fold up into specific conformations, depending on the specific amino acids that are used to make them. Chemical bonds between different amino acids cause parts of the chain to stick together, specific orders of amino acids can cause the chain to fold back and forth or spiral around itself, much like DNA does. Because of all this folding, each protein has a different appearance, or what we call a structure. And it’s this structure that makes a protein able to do the specific things that it can do- all the things that I mentioned at the beginning of this episode.

All right, that’s a lot of information to soak up. Let me just go over the basics again. DNA is made up of a chain of four different nucleotides. The nucleotide sequence is transcribed into RNA, which is then translated into an amino acid sequence. The translation is carried out by virtue of the genetic code, in which 64 different 3-nucleotide codons are translated into 20 different amino acids. The specific order of amino acids confers physical and chemical properties to the final protein, influencing the way it is folded up into its final structure. And the structure of the protein is directly related to its function.

Available link for download

Molecular Evidence 2 DNA Functional Redundancy

All right, this is the second podcast in a series of six that I’ve planned on the molecular evidence for evolution. I’ll be using Dr. Douglas Theobald’s resource on Talk.Origins.org pretty heavily, so you can follow along with me there if you like.

The second piece of evidence is DNA functional redundancy.

The basic concept behind this piece of evidence is very similar to that which I discussed last week, which should be pretty obvious since they both have very similar names. They’re so similar that I’ll go ahead and review the basic argument behind last week’s evidence, since it has relevance here. All organisms share a number of proteins which are universally necessary for basic life processes; these proteins are called “ubiquitous proteins.” Because of the functional redundancy implicit in the structure/function relationship of amino acid sequences, there are a vast number of potential sequences for any given ubiquitous protein. Since the only mechanism for sequence similarity between organisms is common ancestry, similar amino acid sequences imply a phylogenetic relationship. As a specific example, I pointed out the ubiquitous protein cytochrome C, which has the exact same amino acid sequence in humans and chimpanzees, which strongly indicates common ancestry between the two species. The sequence similarity of cytochrome C between humans and just about every other species is higher than would be predicted if evolution is not a valid hypothesis. Thus, protein functional redundancy is strong evidence supporting evolutionary theory.

DNA functional redundancy is basically the same phenomenon, but instead of comparing amino acid sequences of protein, the underlying DNA sequences are compared. Now, you’ll remember from the Molecular Biology Primer two weeks ago that the amino acid sequence of a protein is determined by the nucleic acid (that is, DNA) sequence found in the corresponding gene. The nucleotide sequence of a gene is transcribed into an RNA message, which is then translated into an amino acid sequence, forming a functional protein. All right, and I’m sure you also remember that the genetic code which translates nucleotides to amino acids also reads the nucleotide sequence in groups of three, called codons. Since there is a 1:1 relationship between codons and amino acids, that means that there’s a 3:1 relationship between nucleotides and amino acids. If you haven’t already guessed it by now, the short answer to the question of DNA functional redundancy is that you take the strength of the evidence for protein functional redundancy and raise it to the power of 3.

I’ll try to explain a few of the details of this before getting into specific examples again. You’ll remember from the Molecular Biology Primer that I said that there are 64 different codons. You get this by raising the number of different nucleotides, 4, to the power of 3, which is the number of individual nucleotides in a codon. You’ll also remember that I said that there were only 20 different amino acids that are used to make proteins. Obviously, this means that you have 44 more codons than you actually need, if you were trying to be as efficient as possible. Theoretically, codons could be assigned completely at random, and the genetic code could be different for different organisms. If it were true, it would be an excellent refutation of evolutionary theory, but this is not what we observe. Interestingly, we find that for any three-nucleotide codon, the identity of the third nucleotide is less important for determining the corresponding amino acid than the first two. This phenomenon is referred to as codon degeneracy. Degeneracy means that for just about any codon, the third nucleotide can be changed to something different without affecting the corresponding amino acid that will result from translation. For example, the amino acid alanine has a four-fold degenerate codon, since any codon starting with guanine and cytosine will result in the translation of alanine. That is, you can find GCT, GCC, GCA, or GCG in the sequence of a gene, and all four will be eventually translated as an alanine. Other amino acids are less degenerate-tyrosine, for example, is only translated by codons beginning with thymine and adenine and ending with thymine or cytosine. The other two degenerate codons, the ones ending in adenine or guanine, are reserved as signals telling the transcription machinery to stop- they’re basically called “stop codons.”

So what does all this coding redundancy imply? Well, when all is said and done, it basically means that there are an astronomical number of ways that one could encode just about any given gene, without changing a single amino acid of the final protein sequence. Thus, there is no reason to assume, a priori, that any two organisms would have the same nucleotide sequence for any particular gene, even if they had the exact same amino acid sequence. Let me stress that again. Two different species with the exact same amino acid sequence for a protein have no biological reason, outside of common ancestry, to have high similarity between their corresponding nucleotide sequences. There isn’t even a name (I think) for the number of different possible nucleotide sequences. You just have to use exponents and powers of 10.

Well, let’s go back to the same example I used last week- cytochrome C. This, again, is a ubiquitous gene- it’s found in all living organisms. For this gene, the number of possible nucleotide sequences for any given amino acid sequence is higher than 10^49. That’s quite a lot. And remember, the human and chimpanzee cytochrome C sequences are exactly the same. So, there’s 10^49 different nucleotide sequences that could exist for the human and chimpanzee genes. Now, what happens when we compare the human and chimp sequences? We find they’re only different by 4 nucleotides. That’s only 1.2% different between them. The chance of this happening without common ancestry is infinitesimally small. And this evidence supports the existing fossil evidence. Most fossil evidence estimates that humans and chimpanzees separated from a common lineage somewhere around 10 million years ago, maybe sooner. We can measure the background mutation rate in humans (and other mammals), and we’ve shown it to be about 1-5 every 100 million nucleotides per generation. Since the average primate generation is 20 years, the predicted difference between a chimpanzee gene and a human gene is less than 3%. For cytochrome C, this prediction is undoubtedly fulfilled. And this is true for most other genes too- every gene that I’ve looked at, no less. In fact, I’d like to challenge anyone who’d like to disprove this evidence to find a gene that shows more than 3% difference- I’ll even do the work for you, even thought it’s easy to do by yourself.

Fortunately, the good people at the American National Center for Biotechnology Information (which can be found at the difficult to remember address of “ncbi.nlm.nih.gov”- I’d recommend just typing in “NCBI” to your Google search) have done everyone the service of publishing the entire human genome and the entire chimpanzee genome online. You can, if you like, download the entire human genome right to your computer. Burn it on a CD. Upload it to your iPod. Whatever. But the great thing is that you can use tools that they provide on their site to directly compare the sequences for yourself. You don’t need to take my word for it. But there’s not enough time now for me to tell you exactly how to use the website, so you can either spend some time fooling around with it on your own, or you can see what I’ve done with it. There’s a new resource website that I’ve started that has some gene comparisons including cytochrome C that you can look at for yourself. Just go to: http://www.drzach.net/evolution101/. I know, I know- another website to remember. I’ve tried to keep links reasonably redundant between the Freethought Media site, the blog, and this resource site- you can decide which one you want to bookmark. I’ll be updating the resource page with more information eventually, including a tutorial on how to use NCBI’s tools to analyze sequence similarity on your own. I’ve also tried to compare genes between as many organisms as are available, including orangutan, gorilla, cow, pig, dog, zebrafish, mouse, rat, etc. Comparing all these different organisms allows me to construct a genetic cladogram, and the predictions based on genetic similarity reinforce the phylogenetic relationships predicted by anatomy.

So, to review, DNA functional redundancy shows that the extra layer of redundancy implicit in the coding of DNA reinforces the evidence from protein functional redundancy, and makes it even less likely that organisms share similar DNA sequences for any reason other than common ancestry. This one-two punch of protein and DNA evidence has hopefully been convincing- next week we’re going to leave the strong evidence within the coding part of the genome and look at some equally strong, if not stronger evidence within the noncoding part of the genome.

Available link for download

Molecular Evidence 3 Transposons

All right, this is the third podcast in a series of six that I’ve planned on the molecular evidence for evolution. I’ll be using Dr. Douglas Theobald’s resource on Talk.Origins.org pretty heavily, so you can follow along with me there if you like.

The third piece of evidence is from transposons.

Now, you’ll remember that back in episode 106, we looked at junk DNA, and what it meant. Well, for the past two weeks we’ve been looking at the coding part of the genome, essentially the genes themselves and the products of their transcription, that is, proteins. For the next three weeks we’re going to leave those evidences behind in the coding part of the genome, and we’re going to look at the noncoding part, which some people call “junk.” That’s right- one man’s junk is another man’s treasure, and so-called junk DNA is a treasure of evidence, very powerful evidence in support of evolutionary theory.

Well, what is a transposon? A transposon is a mobile section of DNA. What I mean by saying that it’s “mobile” is that it can literally change its position within the genome. I’m afraid that there really aren’t any good analogies for this, so I’ll just have to resort to some bad ones. You remember that before I said that the genome is kinda like a magazine, where the genes are articles which are separated by pages and pages of advertisements. Well, you know those annoying advertisements that, instead of being printed in the pagestock, are printed on little cards and just kinda stuck in the magazine, near the spine? Or maybe one side of the card is glued to the page with that flimsy, rubbery glue that you have to peel and pull off at the same time? That’s basically what a transposon is. In the same way that those little cards are mobile advertisements, a transposon is mobile DNA.

Let’s say that you’ve got one of those annoying sticky cards in your magazine, and you pull it out. But then you accidentally drop both the card and the magazine, and they both land together. The card is going to be restuck in the magazine, but probably not in the same place. It might be stuck to the front cover. It might be stuck on another advertisement page that had nothing to do with where it came from. Or, it might be stuck on the story that you were reading, obstructing a couple paragraphs and preventing you from finishing the article. Well, that’s also what happens with transposons. A transposon can be cut out of the genome and then reinserted someplace else. The genome is a pretty big sequence, so there’s lots of places a transposon can reinsert. Sometimes a transposon will reinsert at another noncoding region. Actually, this is usually what happens, since there’s so much more noncoding DNA than there is coding DNA. But sometimes a transposon can reinsert in a coding region, and disrupt a gene. Now, in the same way that the stuck card in your magazine prevents you from reading the story, the inserted transposon prevents the gene from being transcribed, effectively turning it off. You might also think of a transposon like a pop-up ad on a website that pops up out of nowhere and obscures the content that you’re trying to see on the page.

Now, one of the obvious questions at this point is: why in the world do transposons exist? They seem pretty annoying, from a strictly genetic perspective, and they also seem dangerous, since by inserting into a gene a transposon could cause a debilitating mutation or disease. And indeed, this is the case- transposons are mutagenic, and are associated with a number of diseases, including hemophilia, severe immunodeficiency, and cancer. So why do transposons exist in genomes at all? Well, you can think of a transposon as existing as a separate selective entity to its host genome- almost like a DNA parasite. Now, admittedly, this is a hard concept to grasp, since we’re talking about a chunk of DNA and not something typically associated the word “parasite,” like a mosquito or a tick. But remember that even though it’s easier for us to think of concepts in black and white terms, science isn’t quite so discrete. Transposons come in two basic types: class I transposons, which are also called “retrotransposons,” and class II, which are simply DNA transposons. Retrotransposons function by allowing their sequence to be transcribed into RNA. It’s at this point that a retrotransposon does something odd- it reverse-transcribes the RNA sequence back into DNA, and this DNA copy of the original retrotransposon sequence is then integrated back into the original genome, but at a different location. Both of these functions are carried out by enzymes whose genes are encoded for within the retrotransposon sequence itself- pretty clever. In fact, this is the same way that retroviruses like HIV work- except that a retrotransposon never leaves the cell in a virus particle. You can almost think of a retrotransposon as a virus that made itself comfortable within an organism and decided never to leave. DNA transposons use a different enzyme called transposase, which actually cuts out the genomic transposon sequence and puts it back into the genome in a different location. This skips the whole process of reverse transcription of RNA that retrotransposons use, but you get the same basic effect.

Retrotransposons themselves come in two basic types- long and short. The longer ones are called “long interspersed elements,” or “LINEs.” The shorter ones are called “short interspersed elements,” or “SINEs.” LINEs contain the two enzymes necessary for the reverse transcription and integration that I already mentioned- called, predictably, “reverse transcriptase” and “integrase.” SINEs, on the other hand, don’t carry these genes, and so are dependent on LINEs for their propagation. You can think of the enzymes used by the retrotransposons as a “copy and paste” function, just like in a word processor. The transposase used by the DNA transposons is more like the “cut and paste” function, however. And I’m sure you know that if you cut and paste words in a document, you may screw up the meaning of the text, but you’re not going to significantly add or subtract to the length of the text. If you copy and paste, though, you’ll find that not only have you screwed up the meaning of the text, but you’ve also added overall length to it, and depending on how many times you paste, you may have added a lot of length to it. And that’s what we see with retrotransposons- both LINEs and SINEs are found all throughout the human genome, for example, and are responsible for nearly 30% of the total size of the genome. 30%! That’s a lot of space wasted on DNA parasites.

But it’s not all for naught. Because so much of the genome is made up of these predictable sequences, and because these sequences occur randomly in different places in the genome, transposons offer an excellent way to identify individuals genetically. I’m sure you’ve heard of technology like “DNA fingerprinting,” or something similar, that is used to establish paternity using a genetic test. These tests take advantage of the fact that two different individuals in a population having the transposon sequences in the exact same location is extremely rare, so much so that you can conclude genetic relation based on similar patterns of genomic transposons. Well, I’m sure you’re all astute enough to realize that if transposons can be used to establish a hereditary relationship between a father and his offspring, it can also be used to establish a hereditary relationship between two organisms from different species! Remember, the only observed mechanism for two organisms to have similar genomic sequence is through heredity, and so if two different species can be shown to have similar genomic sequences, then we can conclude that they share a common ancestry. So we hypothesize that if evolutionary theory is correct, and different species share common ancestry, then closely related species will share common transposon insertions. So let’s look at the evidence.

We’ll look at one of the common SINE retrotransposons, called the Alu element. This is a sequence only about 300 nucleotides long, and it found in all mammal species, and particularly in humans, where it composes close to 10% of the entire genome. In alpha-globin gene cluster, 7 separate Alu elements are known to exist, and all seven are found in the exact same location in the corresponding chimpanzee gene. According to our hypothesis, corresponding transposon sequences imply shared ancestry, and thus this evidence supports evolutionary theory.

So, to review, transposons are mobile DNA sequences that create distinct insertion patterns that allow us to distinguish hereditary links between individuals of the same species, as well as to establish common ancestry between organisms of different species. Once again, the evidence of common transposon insertions in humans and chimpanzees strongly supports the evolutionary hypothesis. Next week, we’ll look at pseudogenes, and how these broken genes also support evolutionary theory. Take care!

Available link for download

Molecular Evidence 1 Protein Functional Redundancy

All right, this is the first podcast in a series of six that I’ve planned on the molecular evidence for evolution. I’ll be using Dr. Douglas Theobald’s resource on Talk.Origins.org pretty heavily, so you can follow along with me there if you like.

The first piece of evidence is protein functional redundancy.

Proteins are, as a group, completely essential for life’s function, but there are some proteins that are more essential than others. These proteins perform very basic but essential tasks that all organisms require for life. We can call these proteins, “Ubiquitous Proteins.” These ubiquitous proteins are completely independent of an organism’s specific function or ecological niche- all organisms from bacteria to humans have these proteins, and they do the same thing no matter where they’re found.

Now, if you remember the previous podcast, the Molecular Biology Primer, you remember me talking about the relationship between protein structure and function. I didn’t get into much detail last time, but I’ll expand on it a bit more here, because it’s a pretty crucial concept for this piece of evidence. The function of a protein is determined by its structure. Imagine that we have an enzyme, which is a chemically active protein, that has the function of cutting other proteins in half. To create a conceptual model in your mind, imagine that the protein is basically like a pair of scissors. The function of a pair of scissors, to cut things, is determined by its structure, which is essentially two blades and a fulcrum, or pivot point. A pair of scissors has a pretty basic structure AND function, and so it’s not too hard to make different variations on the basic structure without changing the function too much. For example, you can make the scissors out of steel, iron, brass, or even plastic. You can make the handles longer, or shorter. You can make the blade longer or shorter. You can even have left-handed, versus right-handed scissors. So it’s pretty safe to say, if you want to cut something, you have a pretty wide variety of choices if you need a pair of scissors.

In the same way that you can vary the way you make a pair of scissors without giving up its basic function, you can vary the way you make a protein without giving up its basic function. Remember, a protein is made by constructing a long chain of amino acids, and each amino acid is distinguished from the others because of its unique side chain. That makes each amino acid slightly different from all the others both chemically and physically. Some amino acids are large, some are small, some are electrically charged, some are not, some attract water, and some repel water. Depending on specific interactions between different amino acids in the chain, the protein will twist around itself and fold up in a very specific structure. Now comes the tricky part- you can get two very similar structures from two very different chains of amino acids. To help you follow along with me, try out another conceptual model- imagine that a protein, instead of being constructed from amino acids, is constructed from Legos. (I hope I’m not violating any copyright here) Maybe I should say “small plastic construction blocks that are similar to Legos.” Whatever. Anyway, let’s say that you have a huge box of Legos, but the whole box only containes 20 different pieces. If I ask you to build me a pair of scissors out of Legos, how many ways do you think you could put the pieces together to get a decent Lego model of scissors? I haven’t actually tried this, but you could probably get pretty many, right? Probably a whole bunch. OK, well, in the same way that you can use many different combinations of Legos to give the same endproduct, you can use many different combinations of amino acids to give the same basic protein function. A more technical way of saying this is that for any given protein, there are many different amino acid sequences that are functionally redundant.

OK, this is all well and good, but what does it mean in terms of evidence for evolution? Well, you remember that I started by talking about Ubiquitous Proteins. These are proteins that are so essential to the basic functions of life that they can be found in every living organism. That is to say, their function is absolutely necessary, and what did we just learn about function? It can be produced from many different combinations of amino acids. So ubiquitous proteins are also functionally redundant in terms of amino acid sequence.

Now, before we look at the evidence, it behooves us to come up with hypotheses. This is part of the scientific method, and very essential. Without a hypothesis, we can’t draw meaningful conclusions- we’re just making observations. Now, we need to have two hypotheses- an evolutionary hypothesis and a null hypothesis. If the data support the evolutionary hypothesis, then we can conclude that evolution is the best explanation for the data. However, if the data support the null hypothesis, then we can conclude that evolution is not the best explanation for the data.

The null hypothesis posits that the evidence will show that amino acid sequences of ubiquitous genes will not be highly similar between any two given organisms. We know that the null hypothesis is possible because of the nature of protein function to be caused by many, many different variant amino acid sequences- that for any given protein, there are many amino acid sequences that are functionally redundant. Thus, since there are so many possible amino acid sequences for any given ubiquitous protein, there is no reason why each organism could not have a completely different amino acid sequence for any given ubiquitous protein. But, let’s say that the null hypothesis isn’t true- what other phenomenon could the evidence show? Well, if the evolutionary hypothesis is true, then different organisms are related to each other by heredity. Since, as I’ve mentioned before, the only mechanism which has been shown to result in similar sequences between organisms is heredity, the evolutionary hypothesis posits that the evidence will show that amino acid sequences of ubiquitous genes will be highly similar between different organisms.

So, let me just go over those two hypotheses one more time before we look at the evidence. If evolution is not true, then we would expect to see that the amino acid sequence of a ubiquitous protein would be completely different in different organisms. If evolution is true, however, then we would expect to see that the amino acid sequence of an ubiquitous protein would be more similar between organisms that are closely related. And the more similar the sequence, the closer the hereditary relationship. OK, let’s look at the data.

Cytochrome C is a ubiquitous gene that is found in all organisms, including animals, plants, and bacteria. It’s an essential gene for cellular metabolism, and helps to provide energy for all life processes. Cytochrome C fulfills the prediction of ubiquitous proteins- that is, it is extremely functionally redundant. Many different amino acid sequences have been shown to fold up into the basic structure required for Cytochrome C function, and in fact among bacterial strains, completely different amino acid sequences are redundantly functional. Experiments in yeast show that if you remove the yeast’s own Cytochrome C protein, you can replace it with Cytochrome C from humans, rats, pigeons, or even fruit flies, and it works fine. A study was published that shows there are, in fact, over 10^93 different possible amino acid sequences for Cytochrome C. That’s more possible sequences then there are atoms in the Universe. So, Cytochrome C is very functionally redundant, and it would be possible for every single different organism to have a completely different amino acid sequence, if evolution is not true.

So what do the sequence comparisons show? Let’s compare humans and chimpanzees. If evolution is true, then chimpanzees are our closest relative, but if evolution is not true, we’re no more related to chimps then we are to crickets. But if you compare the amino acid sequence of humans and chimpanzees, you see that they are exactly the same. Exactly the same. And when you compare human Cytochrome C to that of other mammals, you find that there is only about 10 amino acids difference between them. The chance of this happening without shared heredity is about 1 in 10^29. If you compare human Cytochrome C with the organism the least related to us, outside of bacteria, you find that there’s only about 51 amino acids difference between us. The chance of this happening without shared heredity is about 1 in 10^25.

To review, protein functional redundancy is the phenomenon by which many different amino acid sequences can give the same function in any particular protein. This phenomenon means that closely similar amino acid sequences between organisms implies shared heredity. Examination of the amino acid sequence of a ubiquitous protein shows that different organisms have a greater sequence similarity than would be expected by chance, and thus supports the evolutionary hypothesis.

Available link for download

Molecular Evidence 4 Redundant Pseudogenes

All right, this is the fourth podcast in a series of six that I’ve planned on the molecular evidence for evolution. I’ll be using Dr. Douglas Theobald’s resource on Talk.Origins.org pretty heavily, so you can follow along with me there if you like.

The fourth piece of evidence is from redundant pseudogenes.

A pseudogene is very similar to a regular gene at the DNA level, but with one crucial difference- it never gets transcribed. You can think of a pseudogene as a vestigial molecular structure- sort of like how the appendix is a vestigial organ in humans. Vestigial means that a structure is in degenerate, or atrophied, or somehow imperfect state. For example, the human appendix is basically a degenerate cecum, which is an essential digestive organ in mammals which eat lots of plant matter. You can get along fine without your appendix, but we still have them as an evolutionary carryover from a more herbivorous ancestor.

In the same way, pseudogenes are evolutionary carryovers from our ancestors, and we have them for a few different reasons. The first kind of pseudogenes are called “processed” pseudogenes. You’ll remember from last week’s episode that there are important enzymes used by retrotransposons, which allow them to copy and paste themselves throughout the genome. These enzymes, reverse transcriptase, and integrase, function by taking an RNA transcript, which is a copy of the original gene, and copying it back into a DNA form, which is then integrated back into the genome. This process is beneficial to retrotransposons, since it’s the only way that they can proliferate. But the same enzymes that work on retrotransposon RNA transcripts can work on other RNA transcripts as well. Since all genes are transcribed from the genome into RNA transcripts, there is the potential for reverse transcriptase and integrase to take a random RNA transcript, turn it back into DNA, and stick it back in the genome somewhere. Now, you might think, great, extra copies of a gene! That’s got to be a good thing, right? Well, not really. You’ll remember from the Junk DNA episode that I talked about regulatory sequences that exist in the noncoding DNA surrounding a gene. These regulatory sequences are actually quite important, and without them, you don’t get proper expression of a gene. Since integrase is fairly random in the way that it inserts DNA into the genome, what you end up with is a copy of the original gene stuck in a place that is of absolutely no value- it can’t be expressed there, since there aren’t the proper regulatory sequences.

The second way that pseudogenes can form is through gene duplication. This process occurs through improper recombination of chromosomes during the reproductive process called “meiosis,” which is necessary for sexual reproduction. Most organisms are considered “diploid,” which means that they have two copies of each chromosome. For sexual reproduction, the number of chromosomes in a germ cell has to be reduced to one copy for each chromosome, and meiosis accomplishes this through a mechanism that I won’t detail just yet. One of the stages in meiosis involves recombination between both copies of a chromosome before they’re separated, during which each can swap DNA sequences with the other. Picture two identical twin girls, one wearing a blue headband and one wearing a red headband. If they were to exchange headbands, they’d look basically the same, except for that one small change. That’s similar to what happens with chromosomes, in which sister chromatids exchange DNA. But sometimes mistakes can happen, and the exchange isn’t completely equal. Imagine the twin girls again, exchanging headbands, but only one girl is able to make the exchange. What you’d end up with is one girl with no headbands, and the other girl with two. For chromatids, this means that sometimes one can end up with two copies of a gene, which can get passed on to future generations. In addition to chromosomal recombination errors, sometimes whole chromosomes can be doubled, again due to a problem with the meiosis mechanism. This kind of thing rarely happens in animals, and is usually very detrimental. Down Syndrome is also known as Trisomy 21, which means that an extra copy of Chromosome 21 is present and causes developmental problems. Chromosome duplication, also known as polyloidy, is more common in plants. Recently, evidence has been found that long segments of the human genome exist as replications, although the mechanism for this process is unknown. Whatever the case, be it recombination or segmental duplication, these duplicate genes represent a pretty significant portion of the genome- over 15,000 duplicate genes according to a recent review out of the University of Michigan, which is close to 2/5 of all genes.

The final way that a pseudogene can arise is through evolutionary forces. Just like the ancestral cecum shrank down into an appendix because the evolutionary necessity of having a way to digest a large volume of plant matter was no longer present in human evolution, the lack of selective pressure for a particular gene can make it more likely that mutations and other changes can occur without sacrificing evolutionary vigor. To borrow from the cliché, “if you don’t use it, you lose it.” For an essential gene, a mutation that causes it not to work is likely fatal, or at least decreases the ability of that organism to procreate. Either way, mutations in essential genes have a hard time staying in a population. But if a gene isn’t necessary- let’s say, a gene that synthesizes an essential molecule in a population where that same molecule is available in abundance in the common food sources. In that case, mutations that disable that gene aren’t any more likely to occur on an individual basis, but they are more likely to increase in frequency within the population because there’s no selective pressure to maintain a fully-functioning gene. You’ve probably already guessed this, but this is the reason why duplicated genes often become pseudogenes- if you have two copies of an essential gene, there’s no selective pressure to keep both of them free from mutations- you only need the one. This is why many pseudogenes are found in close proximity to fully functional copies of the normal gene- there’s no pressure to keep both copies functional.

So why is this relevant? Well, for one thing, the formation of pseudogenes is controlled by random processes, whether by retropositioning or duplication. So there’s no good reason why two completely different organisms would have the same pseudogenes in the same genomic locations… other than common heredity. But wait, there’s more! Because of the fact that pseudogenes are largely nonfunctional, they pick up mutations at about the same rate as other noncoding DNA. And as you already know, the acquisition of individual mutations is itself a random process, so there would be even less reason for different organisms to have identical pseudogenes in the same locations with the same mutations… other than common heredity. So let’s look at the evidence.

There are, in fact, many shared pseudogenes between humans and primates, including the enolase pseudogene, hemoglobin pseudogene, sulfatase pseudogene, and the steroid 21-hydroxylase pseudogene. In this last pseudogene, an 8-nucleotide deletion has been found in both the human and the chimpanzee versions of the pseudogene, which in both is responsible for deactivating the gene function. Outside of common ancestry, there is no reason why humans and chimpanzees would share the same pseudogenes, and especially no reason why they would share the same inactivating mutations. This evidence strongly supports evolutionary theory.

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Molecular Evidence 6 Objections to Molecular Evidence

All right, this is the final podcast in a series of six that I’ve planned on the molecular evidence for evolution. I’ve been using Dr. Douglas Theobald’s resource on Talk.Origins.org pretty heavily, so you can use that to follow along with the previous five episodes if you like.

To get to this point, I’ve introduced you to the basics of molecular biology, I’ve explained why function follows from structure, why structure follows from sequence, and why sequences are functionally redundant, both with amino acids and with nucleic acids. I’ve shown you sequence homology between different species, verifying the evolutionary hypothesis. I’ve also taken you through noncoding DNA sequences, analyzing three different kinds of molecular artifacts which also verify the evolutionary hypothesis. Every last bit of genetic information that’s contained in your genome indicates that you share a common ancestor with chimpanzees and other primates, by any conceivable measurement.

Genetic information has an advantage over other kinds of evidence, such as fossils. Fossils are the result of genes that existed in the past, but the genetic information we analyze in living organisms is very much a part of the here and now. It’s a living, breathing (literally) piece of evidence. We can measure it, find out how it works. If you compare the fossils of two different kinds of dinosaurs, for example, which both have the same kinds of foot structure, we can hypothesize that they were related phylogenetically, but that’s all we can do. If we were to take two different kinds of organisms today, we can do the same thing, but we can go one step further- we can compare their DNA. Every physical structure that exists as a part of their body is the result of their particular genes- their genotype. The physical manifestation of that genotype is called a phenotype. So, a gene which codes for a protein which regulates beak shape in a bird is part of its genotype, and the shape of the beak is the phenotype. For living organisms, we can correlate genotype with phenotype, and since heredity is the only known mechanism for shared genotype, it’s so much more powerful than just comparing the way animals look.

Despite the power of genetic evidence, there are still detractors, people who don’t accept the conclusion that the molecular evidence supports the evolutionary hypothesis. This is just one of those things that happens in Science- not everybody is going to accept your conclusions. That’s okay, and it happens with just about everything. There are people who don’t accept the HIV hypothesis of AIDS- they don’t believe that the Human Immunodeficiency virus is what causes AIDS. There are also people that don’t accept the cholesterol hypothesis of cardiovascular disease- they think that you can eat as much cholesterol as you want and you won’t get a heart attack. Some of these criticisms come from scientists- the scientific community in general isn’t monolithic and dogmatic, at least it’s not supposed to be. There are always conflicting hypotheses in Science, and it often takes a long time before there’s sufficient experimental evidence to show that one hypothesis is right and the other is wrong. Whatever the case, when the evidence piles up, scientists generally all get behind the hypothesis that the evidence supports, and the conclusion is, for all practical purposes, a closed issue.

This is the case for evolution. The evidence supporting evolutionary theory has been piling up for a couple centuries now, and it’s basically a closed issue in the scientific community. It’s like the HIV hypothesis of AIDS or the cholesterol hypothesis of cardiovascular disease- there’s just no debate among scientists; the evidence is overwhelming.

The reason why I’m making this point is because I want to make it clear that the objections raised against evolutionary theory don’t come from scientists. They come from people with an ideological and theological presupposition that demands a rejection of evolution- of course, I’m talking about creationists. If you have noticed, there’s a critique of Dr. Theobald’s reference at Talk.Origins that is written not by another scientist, but by a lawyer, named Ashby Camp. Why would a lawyer be interested in critiquing scientific evidence for evolution? Well, it just so happens that Mr. Camp is not just a lawyer, he’s a Church of Christ minister and avowed creationist who wrote his critique for the website TrueOrigin.org, which is subtitled, “exposing the myth of evolution.” Clearly, Mr. Camp has a theological interest in portraying evolution as false- he views evolutionary theory as incompatible with his own theology, and therefore must choose one or the other. Obviously, he’s chosen to assert his theology- but this is not always the case. Dr. Kenneth Miller is an evolutionary biologist who finds the science of evolutionary theory compatible with theology, and he writes about this in his book, “Finding Darwin’s God,” which I can recommend highly as a popular introduction to evolutionary theory, especially for those who are under the same assumptions as Mr. Camp.

Since arguments against scientific theories from theology can’t offer competing scientific evidence, they almost always employ a type of argument commonly referred to as an “argument from ignorance.” These are very attractive, but are also logically fallacious. They’re easy to spot, too- all you have to do is listen or watch for someone to start talking about something that Science “doesn’t know,” or talk about something which “may be possible,” even though there’s no evidence to support the conclusion now. The implication is that since something is not known to be the case, it is not the case, or vice versa. Since these arguments against Science often come from a theological perspective, they’re also known as “God of the Gaps” arguments, because the idea is that there is some gap in scientific knowledge that is explained only by assuming that a deity is responsible for that phenomenon. Coming from a theological perspective makes these kinds of arguments no less fallacious, however, and if you run across any kind of criticism of this sort, be sure to pay attention for the arguments from ignorance, or the “God of the Gaps.”

This kind of argument is precisely what we see from Ashby Camp. When confronted with the evidence from protein functional redundancy, he says, “how could one be sure that God would not conserve amino acid sequences (or the underlying codons) when creating cytochrome c in separate species? After creating cytochrome c in the first organism, it certainly is conceivable that he would make changes to that blueprint only when necessary for his purpose. In other words, the default in this instance may be similarity rather than dissimilarity. There is no basis for demanding that God introduce novelty for novelty’s sake.” In other words, since we don’t know that God did not create cytochrome c functionally redundant in different species, he must have done so. Did you catch the argument from ignorance? When confronting the evidence from DNA functional redundancy, he says basically the same thing, “how could one be sure that God would not conserve codon sequences when creating cytochrome c gene in separate species? After creating the cytochrome c gene in the first organism, it certainly is conceivable that he would make changes to that blueprint only when necessary for his purpose. In other words, the default in this instance may be similarity rather than dissimilarity. Again, there is no basis for demanding that God introduce novelty for novelty’s sake.” Same argument from ignorance, and it’s just as fallacious the second time around.

The same mistake is repeated for the rest of the evidences. Regarding transposon, he says, “God may have had a functional reason for initially placing them at the same chromosomal location in separately created species. He also may have had a functional reason for designing certain transposons with an insertion bias for certain loci.” Regarding redundant pseudogenes, he says, “maybe lateral gene transfers occurred in the past through a mechanism that targeted a specific location in recipient cell DNA and that did not leave viral sequences near the inserted pseudogenes. Perhaps this mechanism is no longer operating, as a result progressive degeneration, and the viral action we see today is a distorted remnant of that originally designed process.” Regarding endogenous retroviruses, he says, “God may have had a functional reason for initially placing them at the same chromosomal location in separately created species. He also may have had a functional reason for designing a system to favor the insertion of certain ERV sequences at certain loci.” Did you catch all those “maybes” and “perhaps?” That’s right, obvious giveaways that he’s arguing from ignorance.

And it’s also the special case of the argument from ignorance, the God of the Gaps. For every piece of evidence, Mr. Camp makes the statement, “God may have a purpose for doing so that is beyond our present understanding.” In other words, Mr. Camp is making the claim that there is some kind of gap in our scientific knowledge about molecular biology in which some yet unknown purpose may have been intended by God.

This should be pretty easy for you now. When it comes to criticisms of the evidence for evolution, keep your ears open for arguments from ignorance, and that special case, the God of the Gaps. If you do that, it should be pretty easy for you to shut down critics who use logical fallacies as their only weapons. Well, this is it for the Molecular Evidence for Evolution. I hope this has been interesting and instructive, and more than that, I hope I’ve motivated some of you to check out the evidence for yourselves. Next week, I’ll be back to answering questions. Take care.

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