An open letter to Dr. Jerry Coyne

You admit you don’t fully understand the science of biology and then attempt to school a respected expert in the field why his conclusions on biology are wrong? Is that the point of this piece? I don’t see any other one.

Dear Mr Leonard,

I hope you won’t take umbrage at my attempt to answer your questions, even though I am not in the same league as Dr. Coyne. I am however a biologist, and having taught for the past ten years the molecular mechanisms that make evolution possible, I may be able to shed some light on a few points.

Let me start by saying that your curiosity does you credit, and even though I understand that you come at this with a creationist/IDer mindset, I laud you for at least askng questions.

I also hope that I won’t come across as pedantic, but I must admit something: very often, people with limited training in biology will be puzzled by things that are so basic to those trained in the art that these may adopt a condescending tone when answering questions. I hope that won’t be the case here. There is an anecdote I’d like to tell: many years ago, my wife and I had dinner with our landlord, a kindly mathematician from Heidelberg university. Making conversation, I asked what he was working on I knew that it had to do with some kind of high-level arithmetics, but being a biologist and not a true math-head I was quite the novice in that field. He took a second to think about it, then smiled charitably and said, apologetically, almost, “… you would not understand”. Which, of course, was true. It’s not that, seeing me as untrained, he thought I was stupid or ignorant but knew that I lacked the information and the experience required to understand what he was working on. Of course, biology is, by and large, easier to relate to than mathematics… but personally, I find it strange (though not totally unexpected, since the matter of where we came from is interesting to everyone) that people who would never argue with their mechanic about what’s wrong with their car would find it perfectly sensible to tell a trained biologist that he doesn’t know what he’s talking about.

But let’s go back to your questions.

The first one you have is “can organisms shape-shift, simply by means of DNA recombination achieved through sexual reproduction?”

The answer is yes, of course, and this is true even without sexual reproduction. Shape-shifting is in fact a very simple trick to perform, and a speciation event is far more ground-shaking than simply modifying the shape of a creature. For example, among those we have studied over the past thirty years are the many genes involved in establishing body plans and organ and limb development. These genes are the ones that dictate at what time during development and in which part of the body this or that protein will be synthesized, and in which quantity. One of the most fascinating aspect of developmental biology is that most organisms share a very large part of these genes (and the closer two species are, the more alike these genes are too). What may change is that due to a small mutation in this regulatory sequence or to a small deletion in that one, the level of expression of one or more of these genes may vary between a human being and, say, a chimpanzee.

For example, there is a particular gene called MYH16 which codes for a type of myosin, a protein found in muscles. This gene is shared by all primates and has a crucial role in the development of a powerful temporal muscle, allowing most primates to have very strong jaws. In humans, the gene is there too, and its promoter is perfectly functional… meaning that our body tries to make the protein. But sometimes in our fairly recent past, an ancestor of modern humans suffered a mutation in that gene; two DNA bases were lost, which resulted in a truncated protein being synthesized. This truncated protein is non-functional, and the result is that our temporal muscle is small and weak. The good thing (in hindsight) is that what we lost in cheweing power we may have gained in another way. First, the mutation was not that harmful, since it occured (and was allowed to spread) roughly at the time our ancestors discovered the use of fire, and our diet changed in such a way that strong jaw muscles were no longer such an important factor in our survival. Second, the lack of a strong jaw made it less important to preserve a thick, small and strong skull for it to act as an anchor point; this allowed further genetic changes (and these have been and are still investigated, to much enthusiasm) that made the human skull bigger, allowing further development of the brain. That brain itself, by the way, is not the result of hundreds or thousands of near-impossible happy accidents; it mostly cames from simple mutations that allowed neuronal precursors to divide a few more times in the human cortex than they do in less brainy mammals. And so from the simple loss of two base pairs, a chain of events was made possible that made it possible for us to get our modern brain (which is, in itself, such a benefit to our reproductive success that it was of course preserved).

Other examples of simple mutations that lead to massive changes in body plans abound, and I’d be remiss if I failed to recommend the works of Dr. Sean Carroll, a specialist of the link between development and evolution (a discipline referred to as evo-devo in biology circles). His books “From DNA to diversity” is quite informative. Apart from the odd mutations in developmental genes of the Hox family that will lead to flies having legs on the head or an extra pair of wings (certainly a massive shape-shifting event, and one occuring in one generation), we have things like a slight delay in expression of such genes in the development of vertebrate embryos, leading to chickens having fewer neck vertebrae than geese, or like snakes (which should have legs, really) failing to develop them because limb buds fail to develop on account of certain molecular signals that are lacking. (Some throwbacks in the python family manage to grow small limbs, though, because not all mutations have an all-or-nothing effect on the phenotype and that some may be partly rescued by the effect of other genes; furthermore, it shows that snake ancestors had legs and that the genetic machinery to grow them is still partly present).

Shape-shifting is also illustrated by the amazing different forms than the plant Brassica olearacea can adopt; by carefully isolating certain individuals and allowing them to breed only among themselves, you’ll get things as different as cauliflower, cabbage, Brussels sprouts or broccoli. And that’s without even having to go through a speciation event! Now you made mention of varied forms developing within a species, so the above probably didn’t come as a surprise; I suppose a more drastic change, especially one occuring in a short time, would be seen as more convincing. I can understand why it would be great to be able to breed fish in a classroom and have them turn into ostriches in one generation, and say “see kids? That’s how new species appear”. But that’s not how species appear, that’s not how Darwin thought species appear, and that’s not how any biologist believe species appear. Although it is possible to bring about a radical change in an organism with just one mutation, it won’t turn the affected individual into a member of a new species. It would simply be a mutant. For speciation to occur, sufficient modifications must accumulate to make the “new model” incapable of breeding with the old one, and I would expect that events occur in the reverse order: first there is reproductive isolation, and only later will changes accumulate. But these changes do accumulate. The flipper of the whale, for example, has the same bones as do the legs of a land mammal; and going back through the fossil record, we find a succession of increasingly less whale-like ancestors who have more and more leg-like appendages. All due to the expression of the same lot of genes, but at slightly different times. (And yes, we can play with this process in the laboratory, although in a ham-fisted and clumsy way. Not because it’s fun to grow six-legged amphibians, but because if we can learn to control limb growth and formation we have a hope of regrowing amputated human limbs the same way we can now regrow amputated frog limbs; certainly a worthy goal).

But back to your questions.

“My first question: How does the theory of speciation actually work in real life?”

The flippant answer would be “quite well, thank you”, but i get your meaning. And your basic understanding of the process is sound: groups reproductively isolated from similar groups will eventually grow apart, genetically speaking, due to genetic drift, the accumulation of different mutations, and very likely different selection pressures. We could also add hybridization and polyploidy to the mix, since they are fairly frequent in plants. (Triticale, for example, is a cross between wheat and rye. It resembles both of its parent species but is now its own plant).

A famous paper in the journal Science (“Hybrid speciation in experimental populations of yeast”) showed that crossing two yeast species, although not a very successful process because most of the offspring end up infertile, could give rise to a a few individuals of a new breed that would be fertile with itself but not either of the parent species (the very high number of yeast cells in a culture makes the experiment more feasible than if we used, say, elephants). Now I agree that it’s not as spectacular as would be the crossing of a crocodile with a duck producing a fertile dragon, but it allows us to observe real speciation in action. The lack of photogenic results does not make such experiments less spectacular.

The common ancestry of certain structures, already obvious to the physiologist, was enriched by the analysis of gene expression in (for example) certain limbs. We can see how a differently-shaped arm or hand can become a wing in bats, a different type of wing in birds, a flipper in dolphins or a leg and hoof in horses. More spectacular, we also have a fairly good idea of how a certain structure helping arthropods to exchange gas with their environment (“breathing”, to make it short) likely became a little sturdier, a little thinner, and ended up as the insect wing.

You say “quite frankly, the idea that sexual reproduction involving two members of the same species could produce a different species seems to violate our known “laws” of biology. Humans produce baby humans, apes produce baby apes, and so forth.”

Yes, that is a common observation. But then, the idea is not a speciation event occurs when two parents from species A suddenly beget a new member of species B. A species doesn’t “appear”, biologically speaking (although we use the term in the fossil record, for if a species takes a mere million year to develop, it might just have “appeared” as far as geological time is concerned). Species develop and end up different from a parent species the same way a sentence changes little by little in the game of telephone and ends up sounding very different. We’re talking incremental, often unnoticeable change. No two dinosaurs ever saw a chicken burst forth from their egg (and a good thing too, as they probably would have just eaten it) but progressive generations of dinosaurs who looked imperceptively less and less dinosaur-like and more and more bird-like gave birth to little critters that looked very much like them; only when comparing the great-great-great-(…)-great-grandparents to their great-great-great-(…)-great-grandkids could we say that a definite change took place. And since evolution usually occurs over spans of millions of years, there is a lot of time for these events to take place. (Although they don’t *have* to. Some shapes, probably quite well adapted to an environment that is pretty stable, do not change much over time -although unseen details like internal biochemistry or a taste for vanilla- may change a lot. Crocodiles, turtles, sharks, coealacanths, look a lot like their distant ancestors did; whales do not. Trilobites were also around for a very long while, and while they are emphatically not as homogeneous as some might think, they had a pretty stable basic Bauplan).

Now I realize that I’m mostly talking about how current biology explains how the world’s living things came to look like they do, but this might just be a just-so story unless we can make predictions. So let’s do just that. Let’s consider the human genome. It is riddled with the remains of retroviruses, small genetic parasites that enter our cells and manage to have their own tiny genome integrated into our chromosomes. And once they’re in, they stay there. So if, say, my grandfather was once infected by a retrovirus that saw its genome inserted in position #123 of chromosome 1, and that grandad passed that particular chromosome 1 to my mother, and that she in turn gave it to me, I will cary a copy of the retrovirus at that exact spot. It will become a “marker” of my grandad’s chromosome 1, bequeathed to the generations that follow him. Now if I am in turn infected by such a retrovirus, and that it integrates at position #456 of chromosome 1, the chromosome 1 I give to my kids (if they inherit that particular one and not my other chromosome 1) will carry two markers: one at position #123, and one at position #456. A few generations down the line, people looking at their chromosomes will be able to draw these conclusions: those with the marker at position #123 but not at position #456 will very likely be descendents of my grandfather, but won’t be my own descendents; those with the markers at #123 and #456 will likely be not only descended from my grandad, but from me as well.

Since these integration events are spurious, they are a good “neutral” way to link some families to others. And the interesting thing here is that if we look at many, many human lineages, we find that the more distantly related peope are, the fewer markers they have in the same positions (and we’re talking about hundreds of thousands of positions, here, and many millions if we account for transposons, which are not viruses but do pretty much the same thing). You can see where I’m headed, I’m sure: if we extend our sampling to closely-related but non-human species, like the bonobo or the chimpanzee, the family tree-like distribution continues: apes do have tons of ancient retroviruses inserted right where humans have them too. And if we go higher, we continue to see a steadily declining co-localization, strongly suggesting that as species diverged from each other, they left with common patterns of retroviral distributions that they later added to on their own. It is far more parcimonious to conclude that the co-localisation that closely parallels the accepted tree of life hints at infections that occured long ago and were maintained in daughter species than to come up with a way viruses would go around and independently infect species, integrating their genome in exactly the same spots every time.

On to your second question to Dr. Coyne.

“My second question: how do you reconcile the long periods of stasis indicated by the fossil record with the Darwinian idea of slow and gradual change?”

Okay, first, let me something that would be heretical if there was really such a thing as a “Darwin religion”. Charles Darwin did not know everything. Charles Darwin is not the be-all and end-all of evolutionary theory. “On the origin of species…” was a door-opener, the same way Columbus opened a whole new era of exploration for European -even if he mistakenly thought he had reached India. Charles Darwin came up with an amazingly simple, amazingly logical, and incredibly powerful way to explain the very real fact that species appear and vanish, and that lifeforms change over time. But he had no access to genetics (it didn’t exist in his days), had no idea what a chromosome was, was not even aware that there was such a thing as DNA, and did not know that mutants could spontaneously appear. His idea of a long, very gradual change made a lot of sense -but it’s not the end of the story. And in fact, even with that taken into account, natural selection would predict that if the environment doesn’t change, there is little reason for a species to do so.

We now know that this is of course an over-simplification. But the Hardy-Weinberg equilibrium concept, which is to population genetics a rough equivalent of what the Ideal Gas Law is to gases, does say that in a very large population where everybody breeds equally and each allele is tramsitted independently, and where mutations do not occur, and which is not affected by sudden environmental pressures, all the alleles of the population should stabilize their frequency within one generation. In layman’s terms, it means “evolution stops”. So long periods of statis are not particularly surprising: they are predicted by biology’s own laws.

That being said, and with all due respect to Stephen J. Gould and Niles Eldredge, I am not personally a fan of the punctuated equilibrium theory. That stasis can exists for very long periods, yes, that is expected and observed. That it is the rule and that gradual change is the exception, I have a problem with; the evidence is not all that convincing, particularly since we have several examples of continuous changes in the fossil record. Another great biologist, Ernst Mayr, was quite hostile to the concept; but whether one camp or the other is right, or whether both are only partially right, none of them argues against the reality of evolution.

You say “if I understand you correctly, isolation or geography plays a crucial role in speciation.”

That is quite accurate, but we’re talking about reproductive isolation, here, which may be facilitated by, but does not require, physical isolation. We know that humans with a look so different that they were at one time considered a different species (the Neanderthals) probably did not breed frequently with “modern” Homo sapiens; very recent papers even suggest that such attempts were rarely sucessful. However, we have discovered in the last few years that a low percentage of genes in a typical European genome comes from Neanderthals. That’s an exciting discovery, showing that a group that was probably on its way to become its own species was partly “reabsorbed” into the main branch of the family, while the shoot died out. The same happened to a group we know only by its genes, the Denisovans.

As for how isolation occurs in the ocean, another of your interrogations, it occurs the same way it does on land… but probably in an even more pronounced way, because distances are so much greater. Not all marine species migrate all over, and those that do usually do so at specific times of the year and along specific routes. The same holds true for birds who, like fish, could potentially have the capacity to spread evenly all over the globe but do not.

The isolation aspect also makes it very easy to understand why there were no placental mammals in Australia. The continent was isolated before they appeared, carrying only prototherian and metatherian animals with it.

Your third question to Dr. Coyne is as follows: “In your lecture at Harvard, you offered examples of the vas deferens tube location in humans and allegedly vestigial organs as examples of poor “design” by nature. You were using comparative anatomy to form your professional opinion. Yet when someone such as myself suggest that sophisticated innate abilities such as echo-location navigation, observed in both bats and dolphins, offers us an excellent example of brilliantly intelligent design, again using comparative anatomy, the suggestion is met with scorn and ridicule. Why is comparative anatomy useful for you to interpret as evidence of unintelligent design, while more obvious examples of intelligent design are declared a beguiling illusion? Could it be due to your personal bias toward atheism?”

I can’t speak for Dr. Coyne, but in my opinion he’s mostly saying that the idea of a designer idea is less compatible with obvious flaws than is that of natural selection. Biologists love the living world. Biologists are awed by the living world. Biologists take a never-ending pleasure in seeing how well-adapted most species are to their environment. But that some biological systems work so well (even if one skips over the fact that some don’t) is in no way a proof of design. And I really, really don’t know how comparative anatomy is supposed to help the designer argument; if anything, it would seem to do the opposite. Take the dolphin, for example, and its echolocation capacities. These capacities are shared by many cetaceans, as would be expected from common descent and similar ways of life. In some species they are very efficient, in others less so; in all cases, they do seem to provide an advantage. These echolocation skills are not shared with sharks, though. Furthermore, they seem to make dolphins susceptible to certain perturbations that send them beaching themselves; certainly an omnipotent designer would have made a better sonar, or one that doesn’t go on the fritz? Let’s consider two possible sources for the appearance of design: either the refinement of a form or function that increase a creature’s chance to pass its genes to further generations, which is what biologists think is jhappening, or outright design. The first view is very tolerant of less than perfect systems, even if with time we expect that they should have the chance to get better an better at what they do; the second view logically demands immediate perfection (at least if the designer is all-powerful and all-knowing). Meanwhile, we have human eyes that do a bang-up jobs at allowing us to see, but that have photoreceptors pointing the wrong way, that are prone to presbytia, glaucoma, detached retina and cataracts… A successful enough “design”, but not one that couldn’t be made better. And of course, there is the matter of knowing all the possible intermediates between a single-cell photoreceptor and a fully working camera-like eye. The “small improvements” idea is just simpler, because even if it requires more knowledge to be reached, it doesn’t present a logical dilemma.

Your fourth question is the least contentious one, because it deals with matters that lie outside of evolutionary biology. “Until life exists, how can it evolve?”

The answer is, of course, “it can’t”. Evolutionary theory is not concerned with abiogenesis, although its principles do apply to the evolution of increasingly-efficient unliving replicators (such as self-replicating nucleic acids) that may, in time, acquire characteristics that we associate with living creatures. Such is the power of the natural selection concept: in a population of replicators that can accumulate mutations, the replicators that gain a replicative advantage will, by definition, replicate better.

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I’m not convinced that the theory of evolution is the supreme achievement of human intellect, personally, although I understand the enthusiasm shown here. I’m pretty sure that general relativity is even more impressive, although I don’t truly understand it for lack of sufficient mathematical skills. I do believe the theory of evolution trumps flight, space travel, the wheel and the computer, though, because these remarkable technological achievements do not really change the way we think about ourselves or our place in the universe. (Calculus, the periodic table, the heliocentric theory or the big bang theory would be in the same league as natural selection, though, as far as I’m concerned. They redefine reality).

Life can’t evolve until it exists. That is true. But that’s like saying a cake can’t exist until it is baked. We do know that life evolves, and going backward in time we see how today’s organisms descended from previous life forms, all the way to an era with no plants, no animals, no eukaryote, even, and at some point very likely no bacteria. What came before? Although these Ur-ancestors left no fossils, we can make educated guesses. The discovery of self-replicating molecules is not a proof, but offers a possible explanation. The sad thing is that we may never be totally sure, despite a lot of plausible hypotheses; there might be things that are so far removed from us in terms of time and space that the best we can hope for is a credible conjecture buttressed by many facts. But definite certitude? That may not be always attainable. And I’m fine with that. It leaves the door open to new knowledge that may come up eventually. Drawing a line somewhere on the map of our knowledge and writing, instead of “terra incognita”, something like “from here on, it’s magic”, does not strike me as scientific, nor very sensible.

“So, in light of what we know, how can you say that speciation is a fact, when in reality it doesn’t seem to be a particularly good theory?”

Well, because in light of what we do know (and not what you appear to think we know), speciation is a fact, and the evolution of species by means of natural selection is a ridiculously good theory. I’m sorry to say it so bluntly, but that’s the way it is. It is such a good theory, in fact, that all of modern biology stands on it.

I hope this will have proven useful, and thank you for maintaining an inquisitive attitude.

Mr. (Dr.?) Leblanc,

That was an excellent and amazingly well put together response that deserves praise. I myself only hold an undergraduate degree in evolutionary biology and am nearly finished with my medical degree and start my clinical training next year, but evo bio is still a love and a hobby of mine (hence why I read WEIT and came to be directed here).

I hope that Mr. Leonard pays heed to it and reads it carefully for it truly does address quite completely his stated concerns.

I’ll merely add that it has been my experience that amongst those like. Mr. Leonard (as opposed to the fire-and-brimstone young earth creationist type) it seems that there is a lack of appreciation of just how incredibly long a period of time life has been evolving for. A minimum of 4.3 BILLION years is mind-boggingly long. Yes, a finch growing a larger beak over the course of a few hundred years may seem trivial, but give those very same processes MILLIONS and BILLIONS of years and the effects can – and are – truly astronomical and amazing. The Cambrian explosion is not a “mystery” to evolutionary biologists in the sense that deniers would wish it were. It is a mystery because we find a spurt of speciation indicating to us that a novel fitness peak was reached which allowed for the spurt and must have spread far and wide. What exactly that fitness peak was is a “mystery” which solving would give us further insight into life; was it a new protein fold? a new protein motif? a new way of handling superoxides produced in oxidative phosphorylation? an environmental change? all of these? Deniers like to frame it as a “sudden” event, an “explosion” such that natural processes could not account for it – it was much to “quick” ergo goddidit. But something on the order of 70-80 MILLION years is sudden only from a geological sense – not from any other reasonable sense. With a new fitness peak in play that is indeed ample time for significant speciation to occur and hardly “sudden” in the sense used by deniers of evolution.

The intuitive sense of how big is “big” and how big something can get (or how old something is) tends to be VERY misleading. Dr. Sam Harris made an excellent point where he asked a simple question: If you take a piece of A4 paper and fold it in half, and then fold the halves successively 25 times, how thick would the subsequent piece of paper be? (In other words, 25 successive doublings of the thickness). For my example, I’ll assume very thin paper of only 0.1mm in thickness.

Have the answer you think is right? How much would you like to bet you are in the right ballpark? Or even the right order of magnitude?

If you guessed “More than 100,000 LIGHTYEARS thick” then your intuition may be better than I gave you credit for. Yes, in doing the math you find that 0.1mm folded in half 25 times (0.1mm*10^25) is, in fact, 105,702.341 lightyears thick.

But I digress.

To expound on something you wrote on Mr. Leblanc about development which I believe is also missed by many naysayers of evolutionary theory. PZ Myers said it well that genes are not a BLUEPRINT for an animal but a RECIPE. What does this mean? I can give you a blueprint for an angelfood cake and you can reproduce it. I can give you another for a pound cake and you could reproduce that. Or a souffle. But if you asked the ingredients – the “genes” of the cake, if you will – you find they are nearly the same – flour, sugar, butter, water, eggs, etc. Yet vastly different “forms” arise because you use the ingredients in different proportions, mix them differently, and bake them differently. Throwing in minor changes (berries or chocolate) can also yield significantly different outcomes.

And THAT is what speciation is and discovering that is yet more evidence to support evolution rather than design.

Lastly, I’ll expound that reproductive isolation not only needn’t arise from geographical isolation or from changes in the environment, but can arise because of an already existing environmental niche that simply hasn’t been exploited yet. Land being a prime and primary example. It is almost certain life arose in the seas – the land was always there. It didn’t suddenly appear and nor did the seas suddenly disappear in order to drive selection pressure for land animals. It was merely that life became sufficiently capable to be able to expand to land and resources and competition sufficiently scarce in the sea that a new niche was taken advantage of. And once that began – slowly at first, with cautious and temporary forays onto land – a whole new environment of niches arose to be exploited.

Thank you for the kind words Mr. Leblanc. Truly, your students are lucky to have you as a teacher.

And of course, please feel free to use the cake analogy – though as I said I derived it from the writings of PZ Myers myself (though I doubt he would mind it being used to educate folks about evolution).

I have been involved in “debates” about evolution for a few years now and have learned the “tricks” as well as the implicit mistakes made be deniers and detractors. I also am quite active in doing the same vis-a-vis so-called “alternative medicine” since in both cases the arguments can seem quite superficially sound and appealing (and, of course, my chosen field is clinical and research medicine). Throwing more science jargon around is simply not as convincing, but drilling down to meat of it and exposing the tricks and explaining in simple terms the implicit assumptions that are false does have a salubrious effect. The Cambrian explosion being one of them in the same way that “it’s just a theory” is another, albeit the former much more subtle and less oft addressed.

Thank you for the well wishes and the same to you.

I am curious to see if Mr. Leonard responds and if so in what manner. It has been my experience that in such cases, despite a priori claims of open mindedness and willingness to accept evolution should sufficient cause be given, the claimant never seems to be satisfied that the evidence provided is sufficient but instead merely ignores such well put together explanation as yours while continuing to claim the other party (in this case Dr. Coyne) still hasn’t answered the questions. Hopefully Mr. Leonard demonstrates more intellectual honesty than that.

And yes, I am specifically calling you out Mr. Leonard, not in a pejorative or mean spirited way, but because of my reasonably extensive experience in such matters. My comment may make you feel uncomfortable but try and recognize it is not because I am being mean spirited but because it is likely forcing you to come close to addressing the cognitive dissonance you hold about evolutionary theory. I look forward to your response.