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Andrea Diem-Lane is a tenured Professor of Philosophy at Mt. San Antonio College, where she has been teaching since 1991. She received her Ph.D. and M.A. in Religious Studies from the University of California, Santa Barbara. Dr. Diem earned her B.A. in Psychology from the University of California, San Diego, where she conducted original research in neuroscience on visual perception on behalf of V.S. Ramachandran, the world famous neurologist and cognitive scientist. Professor Diem has published several scholarly books and articles, including The Gnostic Mystery, When Scholars Study the Sacred and When Gods Decay. She is married to Dr. David Lane, with whom she has two children, Shaun-Michael and Kelly-Joseph. Also available as e-book. Republished with permission.

Explaining Evolution

Darwin's DNA: A Brief Introduction
to Evolutionary Philosophy, Part I

Andrea Diem-Lane

One of the difficulties in explaining the theory of evolution is where to start. I have noticed over the years in teaching this subject at the undergraduate level that most students don't really know much about Charles Darwin and they certainly know less about the mechanism of natural selection. Usually, I have a fairly vocal contingent of fundamentalist Christians who tend to believe in the literal interpretation of Genesis and therefore believe that God created the world in six days. Some accept an old earth hypothesis (five billion years old); whereas others believe that the world is only several thousand years old.

Given this mixture in my class, my husband, David, who is also a Professor of Philosophy, suggested a way that not only reaches students of varying persuasions but ends up actually convincing them, even if only partially, of the viability of evolutionary theory.

Whenever you have to present a controversial idea, he has noticed it is best to begin with what we all know and what we all agree upon. Thus, he advised that I ask for a student volunteer and use him or her as my example.

Let's imagine that the young man's name is Shaun. He is 18 years old. The first question we pose is a simple one. Why does Shaun physically look the way he does? Excepting his clothes and hygiene and other personal choices, my students invariably say “because of his parents.”

And that is certainly true and nobody tends to dispute the fact that his parents were the key to his physical looks. But what is it that his parents bring to the equation? The simple answer, of course, is that Shaun's father (let's call him Christopher) contributes sperm whereas his mother (let's call her Catherine) an egg. Both substances are quite small. A human sperm for instance (including both its head and its tail) is roughly 55 microns, so tiny that it is 25,000 times smaller than a golf ball. At this point, we start to see one of the first hallmarks of science and one that is often misunderstood: reductionism. The contribution that Shaun's parents made to their offspring doesn't come at the phenotype level (that is merely the replicating appliance), but rather at the genotype particulate. We have scaled down from a 6”1 body and a 5”4 body to precisely what those larger frames house—a sperm and an egg. Now we have literally “reduced” Shaun's parents to the arena where the information they share is more easily accessible and localized.

One metaphorical way of putting this is to imagine that Christopher and Catherine are individual books, filled with all sorts of historical information. Their desire is to recombine their books and produce a new edition. Since human sexual intercourse is literally the intertwining of two fairly large body forms so that a transmission of information can catalytically induce a viable recombination to occur, we can readily see that what makes a child is essentially the intersecting of binary forms of data.

The larger question that arises in this metaphor (with its real world applications) is how to decipher Catherine's and Christopher's contributions to the book they named Shaun. In what language are their books written? Are they the same language or different? What is the alphabet or rudimentary notation wherein their respective knowledge is inscribed?

Today, unlike in Darwin's day, we can actually answer these queries with remarkable accuracy. Although an egg and a sperm are compositely varied, the essential code they contain is written in a biological language known most famously by its initials: D.N.A. or more properly deoxyribonucleic acid. This language comes in four letters, easily remembered with the acronym C.T.A.G. Here “c” stands for cytosine, “t” for thymine, “a” for adenine, and “g” for guanine.

Thus, Catherine and Christopher shared books which had a common four lettered language. These letters further comprised whole pages numbering in the tens of thousands known as genes which formed twenty-three chapters known as chromosomes. Our entire book is known as a genome.

Shaun is, therefore, the result of two genomes (books) recombined which results in a unified outcome of 25,000 plus genes (pages), 23 chromosomes (chapters), all written in DNA (a four letter alphabet).

Sexual selection, however, is merely the start of why Shaun looks the way he does. Since obviously his mother could have chosen another author to help write her memoirs and in so doing produce a completely different son with a unique set of genes. Shaun isn't merely a duplicate reconfiguring of his parent's deoxyribonucleic acid. Occasionally, when DNA is copied throughout one's body it makes a copying error, what is known as a mutation. This can simply be a one letter change. Instead of ATGGTTTGATGTC, one might get ATGGTTGATTGTC. While at the level of just script it looks somewhat inconsequential, but in terms of applied genetics such minor variations can loom large.

Why mutations occur is a deep subject, but not an insurmountable one, especially if you have an understanding of Heisenberg's uncertainty principle and how quantum mechanics is based on indeterminacy. The introduction of “chance” (or occasional mutations) into the genome is important because it causally explains how a child can indeed be unexpectedly and unpredictably different than his parents. In other words, sexual selection is just one component in what makes up Shaun's physical characteristics. DNA mutations are another. There are two fundamental ways to mutate a gene. The first way is through environmental damage. As the Learn Genetics website, sponsored by Genetic Science Learning Center at the University of Utah, explains:

Ultraviolet light, nuclear radiation, and certain chemicals can damage DNA by altering nucleotide bases so that they look like other nucleotide bases.

When the DNA strands are separated and copied, the altered base will pair with an incorrect base and cause a mutation. In the example below a "modified" G now pairs with T, instead of forming a normal pair with C.

Environmental agents such as nuclear radiation can damage DNA by breaking the bonds between oxygen (O) and phosphate groups (P).

Cells with broken DNA will attempt to fix the broken ends by joining these free ends to other pieces of DNA within the cell. This creates a type of mutation called "translocation." If a translocation breakpoint occurs within or near a gene, that gene's function may be affected.

The second way is by DNA replication. As the same website elaborates:

Prior to cell division, each cell must duplicate its entire DNA sequence. This process is called DNA replication.

DNA replication begins when a protein called DNA helicase separates the DNA molecule into two strands.

Next, a protein called DNA polymerase copies each strand of DNA to create two double-stranded DNA molecules

Mutations result when the DNA polymerase makes a mistake, which happens about once every 100,000,000 bases.

Actually, the number of mistakes that remain incorporated into the DNA is even lower than this because cells contain special DNA repair proteins that fix many of the mistakes in the DNA that are caused by mutagens. The repair proteins see which nucleotides are paired incorrectly, and then change the wrong base to the right one.

At this junction, most of the class is still with me, since they can readily concede that sexual selection and chance play a huge role in producing children. What is not so apparent is how a four lettered language could produce the wide array of complexity that we see in the human species. In other words, how can such diversity arise from only four varying molecule clusters?

To explain it better, I start again with what we know and then posit a query. The English language has 26 letters and from that can we get a wide diversity of published materials? The answer is an easy yes. Just go to the local library and you can see what diversity such a language can bring—ranging from Cosmopolitan magazine to US weekly to the New York Review of Books to Surfer's Journal. All telling different stories, yet all written in the same English alphabet utilizing A's to Z's. But what would happen if we only had 2 letters, not 26; could we still have the same wide diversity? Usually, at this moment, my students shake their heads with a face of disapproval, wrongly imagining that more letters would mean greater diversity.

Such is not the case, however. If we only had two letters or two numbers (0 and 1), we could, in point of fact, reproduce our entire alphabet and our entire English set of words, sentences, paragraphs, and books. Indeed, we could recapitulate any system of information that has appeared on earth. The very basis of computer programming is predicated upon a string of 0's and 1's. The internet itself can be seen as a huge ocean of cascading binary bits, triggering off an electron dance near the speed of light where information reaches innumerable portals.

The mythic universal library, so hauntingly brought to life in Jorge Borges' famous short story, “The Library of Babel,” which was written before the advent of the World Wide Web, indicates an almost infinite range of information. W.V. Quine, the late professor of philosophy at Harvard University, ironically pointed out that letters were actually unnecessary, since even a dot and a dash could suffice and all the texts of the world could be replicated by such a simple binary. As Quine summarizes, “The ultimate absurdity is now staring us in the face: a universal library of two volumes, one containing a single dot and the other a dash. Persistent repetition and alternation of the two is sufficient, we well know, for spelling out any and every truth. The miracle of the finite but universal library is a mere inflation of the miracle of binary notation: everything worth saying, and everything else as well, can be said with two characters. It is a letdown befitting the Wizard of Oz, but it has been a boon to computers.”

Even here, one could argue that Quine didn't go far enough, since all one would need is a dot and its absence. The dash itself being unnecessary since a thing and its absence is sufficient to be its own binary system.

Thus, it comes as a surprise to my students to realize how easy it is to get such wide diversity from a simple language or code. But even though sexual selection and genetic mutations can explain much, they are not sufficient to explain a much larger process called natural selection, for which Charles Darwin is rightly famous.

Natural selection, as defined by Darwin in his famous On the Origin of Species, is:

Owing to this struggle for life, any variation, however slight and from whatever cause proceeding, if it be in any degree profitable to an individual of any species, in its infinitely complex relations to other organic beings and to external nature, will tend to the preservation of that individual, and will generally be inherited by its offspring. The offspring, also, will thus have a better chance of surviving, for, of the many individuals of any species which are periodically born, but a small number can survive. I have called this principle, by which each slight variation, if useful, is preserved, by the term of Natural Selection, in order to mark its relation to man's power of selection. We have seen that man by selection can certainly produce great results, and can adapt organic beings to his own uses, through the accumulation of slight but useful variations, given to him by the hand of Nature. But Natural Selection, as we shall hereafter see, is a power incessantly ready for action, and is as immeasurably superior to man's feeble efforts, as the works of Nature are to those of Art.

Natural selection, though precisely defined by Darwin, has led to some unnecessary confusion since it mistakenly implies a conscious act on the part of nature to pick and choose. Rather, it may be more properly understood as natural elimination and anything that can survive that global and unending process is, because of such survival, sufficient (not necessarily “best”) to continue on. Viewed in this purview, evolution by natural selection isn't so much about “fittest” or “strongest” or “best,” but rather as contingently successful. With the operative word here being contingent since what is viable in one environmental niche may not be so in another.

What cannot be denied are the vast odds against life to survive under such harried conditions. That anything does survive tells us much about both the environment from where it arose and the competition it had to go head to head against in order to live long enough to pass on its code. Natural selection or natural elimination or survival of the sufficient (however, we describe this winnowing process) is fundamentally a description of how organic life struggles for a temporary respite from ultimate annihilation. We can witness this struggle right now in the world we live in. We hear of an earthquake in China, where thousands are summarily killed, and yet several individuals, defying astronomical odds, survive. We hear of powerful and relatively new viruses, such as HIV, which can kill millions after years of incubation. And, yet, there are a few who seem to ward off its terminal sentence and live relatively long and healthy lives, even without the introduction of new drugs.

How is this possible? Variation. Natural selection only works if there are variations among organic life, where a panoply of potential body types live and die. Those that do survive this gauntlet (and the gauntlet, lest we forget, is unending), do so only temporarily and only under certain conditions. It is under this severe testing that we can start to see how certain adaptations are better suited than others. Further, if those adaptations can produce viable offspring that carry on such favorable traits then they will have a built-in advantage over competitors that do not. This isn't a static sort of testing, however, since environments change over time and new adaptations due to wide variability arise and compete anew.

As Darwin so beautifully summarized nearly 150 years ago:

It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

Now going back to Shaun, we have realized three key factors which have determined why he looks the way he does: sexual selection, genetic mutation, and natural selection. Play this out in your own life. Right now you are being tested by nature, even if completely unknowingly. Either you are going to have offspring that carry on your unique DNA configuration or you are not. If the former, you are in competition with other likeminded brethren in pursuing a potential mate. If the latter, you have basically given a Trumanesque-like gesture to millions of years of competitive successes that led up to your very being. You have said, “The buck stops here.” And, barring some future resurrection of your DNA in unseen ways, the book that was you will go into the non-circulating library of forgotten achievers.

But sexual success, while necessary, doesn't insure lineal success, since as we have pointed out a random genetic mutation could mean that your child won't live long enough to procreate. And, even if your child does live long enough there are many other factors to consider, including new environmental conditions (such as global warming), new strains of virulent bacteria and viruses, and any host of unpredictable variables that may arise in the unforeseen future—all of which can wipe out even the most successful of genetic programs.

All of this competition has led to a natural “editing” of what we see today. If something survives, you know a priori it has been edited or pruned by the very competition which led to its survival. Knowing the conditions from where we originally arose is a central key to understanding why we survive as we do in the present.

Shaun, therefore, is in the most literal sense a genome with a long history, one which was shaped by factors which we cannot access fully today, but which nevertheless give hints of its long sojourn on terra firma.

Every strand of DNA contains a unique history of its journey and what must have transpired to shape it into its present incarnation. Thus, Shaun's history doesn't start with parents, or with his grandparents, or with great grandparents, but rather goes thousands, nay millions, of years back in time.

It is right here in the lecture when I ask Shaun about his ancestry. Where were you born? Where are your parents from? Where did your ancestors come from?

Nobody is indigenous to America. We all came from somewhere else. In Shaun's case, we found out that he could trace his family lineage back to Ireland and Germany. But that also is not the final resting place for his DNA. We now know that all human beings living today trace their genetic history some 90,000 plus years back to the heartland of Africa. Shaun is in this sense (as we all are) African-American, even if his latter day sojourn may have resting places in European countries. As the entry on human migration in the MSN Encarta puts it:

Early humans first migrated out of Africa into Asia probably between 2 million and 1.7 million years ago. They entered Europe somewhat later, generally within the past 1 million years. Species of modern humans populated many parts of the world much later. For instance, people first came to Australia probably within the past 60,000 years, and to the Americas within the past 35,000 years. The beginnings of agriculture and the rise of the first civilizations occurred within the past 10,000 years.

Shaun is literally a f…ing success. Nobody in his genetic past screwed up (pun intended). At each stage where it counted most, Shaun's elemental sequences survived and not once was there a premature extinction or death. If so, he wouldn't be here today. If so, none of us would be alive today. The very fact that you are reading this book can be taken prima facie that you are one of the great success stories in human history, indeed in all of organic history. You have won nature's lottery. . . at least so far.

Imagine how many strands of DNA never made it. Imagine how many countless sperms and eggs never reached fruition. Imagine how many life forms lived and then died before they could transmit their genetic code? Imagine the odds against you and it becomes readily apparent that the very fact you have beat such odds is a clear indication that your unique genome has some fundamental traits that have led to such success. Those traits are called adaptations. Whether you like it or not, you must be sufficiently adapted to your present circumstance or you wouldn't have been able to arrive here.

You are one of the winners.

Given this amazing history and your amazing plasticity to survive nature's twists and turns, the real question that arises is not why but how? What is it about you that has led to you? In other words, you are a distinguished survivor. And how is it that you survived this competition and others did not? Or, more generally, what traits do Homo sapiens possess that has allowed them to last this long?

But before we probe further into that question, another one still begs to be answered. How far back does our genetic code go? Almost all fundamentalist Christians, who believe in a literal interpretation of the Bible, more or less accept evolution by natural selection within a range.

What most of them object to in class is the idea that the human species evolved from some earlier primate species. As one bright Christian argued, “Yes, I can accept micro-evolution, varying adaptations and changes within a species, but what I cannot accept (and which would go against my beliefs) is the idea that one species mutated or evolved into another. I see no evidence of such a thing in the fossil record. Where are all the transitional forms? Human beings are unique.”

To tackle this issue head-on in class and to answer the good questions put forth by my student, I first point out what is not so obvious at first. All of evolution, at least in terms of DNA sequencing, is at the micro level.

Instead of thinking of phenotypes (the bodies which house our genetic codes), focus on genotypes which are incredibly small. So small, in fact, that we cannot see even one complicated strand of DNA with our naked eye.

At the molecular level, deoxyribonucleic acid isn't concerned with our macro issues of whether something is a defined species or not. At these tiny scales, it is merely a question of biochemistry. And since humans and chimpanzees and dolphins and bananas all share the same language code (remember, it comes down to a four letter molecular alphabet), at the microscopic level there isn't a thick brick wall dividing DNA into invariant species categorizations which has a sign to all intruding and stray polynucleotides: Stay Away. No, rather it is more akin to alphabet cereal (though this cereal only has the letters C, T, A, and G) or alphabet soup where the letters are free to roam wherever they please within the medium of milk or broth. It isn't a question at this realm of a whether a species can mutate into another, but rather if adenine (“A”) can bond with thymine (“T”) in a complementary base pairing (it can), or if cytosine (“C”) can bond in a similar way with guanine (“G”)—it can also. In other words, the macro issue of species never emerges at this quartered off biochemical level. Rather, it is a word used after the fact to describe built-up differences of DNA sequencing. The DNA itself is the same and thus the notion of speciation isn't about C or T or A or G, but rather about how these already given molecular clusters form into larger scaffolding projects. Thus if you accept micro-evolution within a species, you have already de facto accepted evolution itself, since all DNA manipulation (which is how evolutionary change occurs over time in organic beings) is at the micro level. As the Brown University Course on Evolution explains it:

For evolutionists the revolution in DNA technology has been a major advance. The reason is that the very nature of DNA allows it to be used as a "document" of evolutionary history: comparisons of the DNA sequences of various genes between different organisms can tell us a lot about the relationships of organisms that cannot be correctly inferred from morphology. One definite problem is that the DNA itself is a scattered and fragmentary "document" of history and we have to beware of the effects of changes in the genome that can bias our picture of organismal evolution.

Two general approaches to molecular evolution are to 1) use DNA to study the evolution of organisms (such as population structure, geographic variation and systematics) and to 2) to use different organisms to study the evolution of DNA. To the hard-core molecular evolutionist of the latter type, organisms are just another source of DNA. Our general goal in all this is to infer process from pattern and this applies to the processes of organismal evolution deduced from patterns of DNA variation, and processes of molecular evolution inferred from the patterns of variation in the DNA itself. An important issue is that there are processes of DNA change within the genome that can alter the picture we infer about both organismal and DNA evolution: the genome is fluid and some of the very processes that make genomes "fluid" are of great interest to evolutionary biologists. Thus molecular evolution might be called the "natural history of DNA.

As for why we don't see as many transitional forms as one might expect, this too is a misleadingly framed question, since it implies that such should be easy to find. Quite the opposite is true. The fact that we have found as many as we have is astounding itself, given that the theory of evolution has only been accepted for less than two centuries. And even while accepted in the scientific community, how many researchers are there worldwide trying to unearth these very rare and precious documents of our ancestral past? My husband, David, who is a fond lover of Coca Cola, makes a fitting analogy here. He remembers back in the late 1950s and 1960s when cans of coke did not have the opening tabs we have today. Rather, one had to use a can opener (usually with one opening larger than the other). When can opening tabs were introduced they were clumsy and slightly dangerous. But Coke can tops have undergone an extensive evolution. As one writer on the subject explains it:

In the early 1960's the Pittsburgh Brewing Company introduced “Iron City Beer” in 'self-opening cans.' The concept was pretty novel—just pull up on a tab and you had an open can of beer in your hand! No accessories like a 'church key' or bottle opener necessary—imagine that! These early pull tabs were known as “zip tops” and were disposable. But because of the rough edges of the aluminum, the cans often left people with cuts on their fingers, lips and even noses.

By 1965 the design was changed to the ring style, which I'm sure every metal detectorists has seen his or her share of. The ring style was even easier then the zip top; just put your finger into the ring, yank forward and have your beverage with less potential for physical injury—even better!

Needless to say, the swift evolution of the zip top to the ring tab revolutionized canned beverages. By the mid-60's over 75% of all cans produced in the U.S. had a pull-tab opening.

Ten years after the “ring” version of the pull tab was introduced, an answer to this environmental and safety nightmare finally came. The “stay tab” style was introduced in 1975 by the Falls City Brewing Company, and they were here to stay—literally. These ring-style-stay-tabs are what we can see on every can of coke and beer in the grocery store today. Unfortunately, they don't stay quite as well as the designers would have liked. But at least this style doesn't force people to throw the tab aside… they actually have to do a little work to get it off.

However, today there are many students in college who are unaware of the evolution behind opening tabs on coke cans and other soft drinks. Indeed, there haven't been just three stages in this evolution but many small incremental changes, most of which have gone unnoticed. If you look just at a Coke can of the 1950s and a Coke can of today, you might ask where did all the transitional forms go? How easy would it be to find each and every modification over the last fifty or so years?

Unless you are an avid collector it wouldn't be easy at all, since most of the cans have been discarded and thus their respective histories have been smashed or buried. I bring up this analogy because there are millions of such canned fossils waiting to be found but it would take inordinate amounts of time and patience to unearth them, if one hadn't already kept a record of it as the cans were improved over time--and this is about an object for which we have tremendous amounts of information. Imagine how difficult it must be to find transitional forms of our ancestors that lived millions of years ago? So many conditions have to be right for us to be lucky enough to find even one example, much less several.

Kathleen Hunt elaborates on this her website on transitional forms in the fossil record:

The first and most major reason for gaps is "stratigraphic discontinuities", meaning that fossil-bearing strata are not at all continuous. There are often large time breaks from one stratum to the next, and there are even some times for which no fossil strata have been found. For instance, the Aalenian (mid-Jurassic) has shown no known tetrapod fossils anywhere in the world, and other stratigraphic stages in the Carboniferous, Jurassic, and Cretaceous have produced only a few mangled tetrapods. Most other strata have produced at least one fossil from between 50% and 100% of the vertebrate families that we know had already arisen by then (Benton, 1989)—so the vertebrate record at the family level is only about 75% complete, and much less complete at the genus or species level. (One study estimated that we may have fossils from as little as 3% of the species that existed in the Eocene!) This, obviously, is the major reason for a break in a general lineage. To further complicate the picture, certain types of animals tend not to get fossilized—terrestrial animals, small animals, fragile animals, and forest-dwellers are worst. And finally, fossils from very early times just don't survive the passage of eons very well, what with all the folding, crushing, and melting that goes on. Due to these facts of life and death, there will always be some major breaks in the fossil record. Species-to-species transitions are even harder to document. To demonstrate anything about how a species arose, whether it arose gradually or suddenly, you need exceptionally complete strata, with many dead animals buried under constant, rapid sedimentation. This is rare for terrestrial animals. Even the famous Clark's Fork (Wyoming) site, known for its fine Eocene mammal transitions, only has about one fossil per lineage about every 27,000 years. Luckily, this is enough to record most episodes of evolutionary change (provided that they occurred at Clark's Fork Basin and not somewhere else), though it misses the most rapid evolutionary bursts. In general, in order to document transitions between species, you specimens separated by only tens of thousands of years (e.g. every 20,000-80,000 years). If you have only one specimen for hundreds of thousands of years (e.g. every 500,000 years), you can usually determine the order of species, but not the transitions between species. If you have a specimen every million years, you can get the order of genera, but not which species were involved. And so on. These are rough estimates (from Gingerich, 1976, 1980) but should give an idea of the completeness required. Note that fossils separated by more than about a hundred thousand years cannot show anything about how a species arose….

But even with these severe limitations, archaeologists have already unearthed a number of very impressive transitional fossil remains. This is quite remarkable, as we have pointed out, given the inordinate difficulty inherent in trying to discover biological remnants that are still intact.

Here is just a partial list of transitional forms among amphibians:

Temnospondyls, e.g Pholidogaster (Mississippian, about 330 Ma)—A group of large labrinthodont amphibians, transitional between the early amphibians (the ichthyostegids, described above) and later amphibians such as rhachitomes and anthracosaurs. Probably also gave rise to modern amphibians (the Lissamphibia) via this chain of six temnospondyl genera , showing progressive modification of the palate, dentition, ear, and pectoral girdle, with steady reduction in body size (Milner, in Benton 1988). Notice, though, that the times are out of order, though they are all from the Pennsylvanian and early Permian. Either some of the "Permian" genera arose earlier, in the Pennsylvanian (quite likely), and/or some of these genera are "cousins", not direct ancestors (also quite likely). Dendrerpeton acadianum (early Penn.)—4-toed hand, ribs straight, etc. Archegosaurus decheni (early Permian)—Intertemporals lost, etc. Eryops megacephalus (late Penn.)—Occipital condyle splitting in 2, etc. Trematops spp. (late Permian)—Eardrum like modern amphibians, etc. Amphibamus lyelli (mid-Penn.)—Double occipital condyles, ribs very small, etc. Doleserpeton annectens or perhaps Schoenfelderpeton (both early Permian)—First pedicellate teeth! (a classic trait of modern amphibians), etc.

We have a mistaken notion about evolution because we tend to think only at the level of large body types, forgetting that the real changes occur at the biochemical level and even the smallest change there can have a dramatic impact on its eventual housing. While morphological evidences of evolution should by definition be scarce and difficult to precisely piece together (given that ideal conditions must be met on a series of fronts), the most remarkable evidence for evolution is found exactly where it should be uncovered: at the level of DNA.

Sean Carroll has written a popular account of this wonderful breakthrough in evolutionary biology entitled The Making of the Fittest. The Howard Hughes Medical Institute provides a nice summary of Carroll's work:

For decades, scientists studying evolution have relied on fossil records and animal morphology to painstakingly piece together the puzzle of how animals evolved. Today, growing numbers of scientists are using DNA evidence collected from modern animals to look back hundreds of millions of years to a time when animals first began to evolve. One of those leading the charge is molecular biologist Sean Carroll.

Carroll's research focuses on the way new animal forms have evolved, and his studies of a wide variety of animal species have dramatically changed the face of evolutionary biology. Using genetics and the tools of molecular biology, he is looking back to the dawn of animal life some 600 to 700 million years ago. It is so long ago that there are virtually no fossils or other physical clues to indicate what Earth's earliest animals were like.

"Evolution encompasses all of biology—it is our big picture," Carroll said. "When I was a student, we had a grand picture of animal evolution from the fossil record, but no knowledge whatsoever of how new animal forms arose. That is the mystery that I want to tackle."

Carroll's studies have uncovered evidence that an ancient common ancestor—a worm-like animal from which most of the world's animals evolved—had a set of "master" genes to grow appendages, such as legs, arms, claws, fins, and antennas. Moreover, Carroll noted, these genes were operational at least 600 million years ago and are similar in all animals, from humans to vertebrates, insects, and fish. What is different, however, is the way these genes are expressed, leading some animals to develop wings, and others to grow claws or feet.

"We found the same mechanism in all the divisions of the animal kingdom," Carroll noted. "The architecture varies tremendously, but the genetic instructions are the same and have been preserved for a very long period of time."

Carroll is also probing the common fruit fly, Drosophila melanogaster, to elucidate how genes control the development and evolution of animal morphology, or form. This innovative approach to studying evolution has led scientists to a more detailed understanding of how animal patterns and diversity evolve.

By analyzing the genetic origin of the decorative spots on a fruit fly wing, Carroll has discovered a molecular mechanism that helps to explain how new patterns emerge. The key appears to lie in specific segments of DNA, rather than genes themselves, that dictate when during development and where on an insect's body proteins are produced to create spots or other patterns.

The same molecular mechanism is likely at work in other animals, including humans, and helps to explain the pattern of stripes on a zebra or the technicolor tail of the peacock. Carroll and his colleagues chose to study the evolution of the wing spot on fruit flies because it is a simple trait with a well-understood evolutionary history. While ancient fruit fly species lack spots, some species have evolved spots under the pressure of sexual selection. The wing spots offer a survival advantage to males, who depend on the decorations to "impress" females to choose them in the mating process.

The discovery is important because it provides critical evidence of the way that animals evolve new features to improve their chances of reproductive success and survival. "We now have convincing proof that evolution occurs when accidental mutations create features such as spots or stripes that impart an advantage for attracting mates, hiding from or confusing predators, or gaining access to food," Carroll explained. "These accidents are then preserved as small changes in the DNA."

At this point in the lecture, most of my students are nodding their head about the logic of evolution, even though they may not agree with all the pointed details.

Evolution by natural selection is, as Daniel Dennett rightly pointed out in his book Darwin's Dangerous Idea, based on the notion of methodological naturalism, whereby one attempts to explain all phenomena by its constituent parts. Paul and Patricia Churchland have called this approach intertheoretic reductionism. Take any physical object and you have two fundamental options in trying to explain it. Either it is material or it is not. If the former you try to ground your explanations in physics, chemistry, biology, psychology, and sociology—with an eye and ear to the ground from which these emergent structures arise. If the latter, you are engaged in a metaphysical enterprise, where things are explained not by other material substances but transcendent, even spiritual, realities. Dennett has invoked a nice metaphor to explain these different approaches: science is a crane like approach, and follows an algorithmic (step by step procedure) mindset, even if one is allowed all sorts of wild imaginings provided they are ultimately tested and verified by empirical experiments. Religion, on the other hand, is a sky hook and tends toward non-algorithmic explanations.

This is why evolution is such a powerful idea. It explains so much so simply. Dennett has called it the single greatest idea in the history of human thought, since it serves as the backbone for almost every one of the sciences—from astronomy to neuroscience. As Theodosius Dobzhansky, one of the architects of the neo-synthesis of evolutionary theory in the mid-20th century points out, “Nothing in biology makes sense except in the light of evolution.”

It is right at this juncture that I raise a larger philosophical issue in my lecture. If evolution by natural selection (and other selective or eliminative forces) can indeed explain why Shaun looks the way he does, can it also help explain why Shaun thinks the way he does?