Your inner parakeet

2000px-Budgerigar_diagram-labeled.svgI love reading books written by Richard Dawkins. Quite ironically, he provides some of the very best material I could ever hope to find for use in discussions with my atheist friends about God and His creation, as well as existential science and evolution theory.

It turns out that virtually everything I might ever need for my argument in favor of a supernatural God can be found in his book The Greatest Show on Earth: the Evidence for Evolution, simply by following the advice of Dawkins and accepting many of his claims about the theory of evolution on face value.

For example, in his book Richard Dawkins claimed that humans share a now-extinct ancestor with the budgerigar (another name for the common parakeet) that lived approximately 310 million years ago, writing that “Every species is a cousin of every other. Any two species are descended from an ancestral species, which split in two.” (pg. 254)

That would mean every modern living organism must be directly related to every other living organism on earth by descent — with modifications, of course. Not only is your cousin a chimpanzee, but your slightly more distant cousin is allegedly the cucumber.

The most obvious question coming to mind about this idea would seem to be “how?”

Now my atheist friends have frequently suggested that I publish the evidence that disproves my cousinship to fruits and vegetables such as cucumbers and turnips so that I might earn fame, fortune, and even to win a Nobel Prize. However, the Nobel Prize does not honor a category for evolutionary biology, making the goal itself nonsensical, even if one assumes that the purpose of pursuing a career in science is to earn fame, fortune, and win the Nobel Prize.

Not even Charles Darwin would have won the Nobel Prize if the award had existed when he wrote On the Origin of Species. Ernst Mayr never won the Nobel Prize, and also noted that there is no prize for evolutionary biology, presumably to silence his own critics. Besides, by the time I received my PhD in something, I’d only be a few years away from retirement age.

Furthermore, Richard Dawkins hasn’t won the Nobel Prize for Physiology and Medicine, either. So winning one can’t be that big of a deal.

Ideas matter.southernprose_cover_CAFG Book sales matter. Being able to defend one’s ideas with logic, reason, and the support of available scientific ideas matter. An honest pursuit of existential truth matters. Prizes and book awards, not so much.

In case awards matter to other people and increase book sales, though, I will point out to the reader that the book shown on the right won a gold medal in an international book awards contest, as did collection of animal rescue short stories and the detective novel shown below.

Thus ends my brief foray into shameless self-promotion, which I freely admit only doing to irritate those critics of mine who often accuse me of relentless self promotion and trying to sell them a book that I’ve offered to give away.

This mentality reminds me of the classic line from Joseph Bologna in the movie Blame It on Rio: “Who packs, not to leave?”

DivineEvolutionCover_eBook_finalWho writes a book and manages to get published, but doesn’t want people to buy it?

Not that I’m complaining, but I think my accountant might still tell me today that Mick Jagger, Keith Richard, and Bob Dylan have all made more money off copyright permissions from Divine Evolution, my first book, that I have earned from sales to date. Writing is a labor of love that will eventually pay financial dividends to my estate, if not before.

Buy a book and read — it doesn’t have to be one of mine. Broaden your horizons. Try to learn something new. End of commercial.

Now back on point…

It has been frequently said that extraordinary claims require extraordinary evidence. The assertion that humans might be related even to parakeets and even plants by sex, isolation of genetics, and time certainly would qualify as an extraordinary claim.

Dawkins writes (about the alleged reptilian human/parakeet common ancestor),

“In the unlikely event that a fossil of this ancestral species was ever found, it would need a name. Let’s call it Protamnio darwinii. We don’t know any details about it, and the details don’t matter [emphasis added] at all for the argument, but we won’t go far wrong if we imagine a sprawling lizard-like creature, scurrying about catching insects. Now, here’s the point. When Protamnio darwinii split into two sub-populations, they would have looked just the same as each other, and could have happily interbred with each other; but one lot were destined to give rise to the mammals, and the other lot were destined to give rise to the birds (and dinosaurs and snakes and crocodiles).” (pg. 254-5)

Now in order to reach this allegedly indisputable conclusion that humans and parakeets have ancestors in common, we only need to look at the evidence, according to Mr. Dawkins.

This is excellent advice, in my opinion. Never forget that extraordinary claims always require extraordinary evidence. So what exactly is this evidence, and what does it tell us?

Forgive me for stating the obvious, but birds have beaks, wings, and feathers. Their bones are hollow, yet incredibly strong. Birds lay eggs. Most birds can fly. They have a specially-adapted digestive system. In other words, birds are very, very different than human beings that appear to be engineered specifically for the capability of flight.

Neither birds nor humans are closely related to insect-eating lizards, though. Sure, birds, lizards, and humans have central nervous systems and cardio-vascular systems as well as skeletons, hearts, brains, eyes, and other organs that may be found in virtually every living animal, but this hardly qualifies as evidence for being the product of common descent.southernprose_cover_AANO

Furthermore, Richard Dawkins admits that there is an “overwhelming illusion” of design we may observe in nature, but then dismisses even the possibility of design versus descent because of his personal bias towards atheism. To justify his assumption, he refers to alleged evidence of “bad” design like the routing of the vas deferens through the human body or the laryngeal nerve in giraffes. My dogs are theoretically not only my best friends, they are allegedly my cousins as well.

Does anyone else (besides me, of course) have a problem with the absence of logic being shown here? We are being asked — no, told to believe that humans are related to giraffes and parakeets through common ancestry, conditioned to believe that evolution theory is the only conceivable explanation for the existence of a human being.

We are told to basically ignore all the differences like feathers and wings and emphasize any perceived similarities. If we attempt to ask intelligent questions about the science, we are branded as evolution deniers, as if we know some great existential truth that we stubbornly refuse to admit.

Skepticism about science will not be tolerated. Only skepticism about religion is allowed.

Nevertheless, common ancestry means that the primary factors that cause such incredible diversity are sexual reproduction, isolation of the gene pool (usually due to geography), and time. Both Dawkins and Coyne clearly agree on the importance of those three factors, especially isolation, in the formation of new species. Quite frankly, we are being conditioned to believe that only descent can possibly explain how a lizard, a parakeet, and a human being are allegedly “related” to each other.

Dawkins insists that we should go and look at the evidence — perhaps he should take his own advice and speak with paleontologist Michael Benton. An excellent candidate for Protamnio darwinii might well be a dicynodont named Lystrosaurus, the primary terrestrial animal that survived the Permian extinction of about 250 million years ago, according to Professor Benton. What’s sixty million years in the Big Scheme of things, compared to the life span of a human being?

More time than we have to observe the alleged processes in action, that’s for sure. That is roughly the same amount of geologic time that has elapsed since the Cretaceous extinction killed off the dinosaurs. Most modern animal species we can observe today allegedly “evolved” within the last 65 million years, with a few notable exceptions such as crocodiles and coelacanths.

It would be absurd to deny the possibility that descent alone might explain the existence of both the ant and the anteater, the cotton plant and the boll weevil, because we know that species (or kinds) are perpetuated by sexual reproduction, which is of course, descent. But why should we assume descent must be the only possible contributing factor, when there is overwhelming evidence drawn from inference that suggests manipulation and design might also be involved?

My point is merely this: it is absolutely silly to assume that descent explains the relationship of humans to bananas, while details of the process by which it occurred remain completely unknown. My goal is not to persuade the reader he or she should not believe Darwin’s theory solves all problems — I’m asking for someone to explain how it works to me, so that I might believe, too.

Currently we don’t even seem to know how recent evolution occurred, for example how humans evolved from ape ancestors. The “smoking gun” evidence that advocates of evolution theory love to cite is the commonly believed fusion of human chromosome 2, which biologist Ken Miller has said appears to be so clear that it appears “something” joined two primate chromosomes together as clearly as if a piece of Scotch tape had been used to connect them.

However, when pressed to explain how a fused joining of those chromosomes could occur slowly over many generations, Professor Miller explained that the joining of those two chromosomes had no discernible impact on ape-to-human evolution. But how can an event with no known relationship to human evolution be claimed to provide evidence that it occurred? If the evidence that humans evolved from apes doesn’t explain how it happened, why should we believe that it even happened?

And if human chromosome 2 created by fusion didn’t cause ape-to-human evolution to occur, what did?

It’s very important to note that Richard Dawkins admits that we don’t have the slighted clue about what causes or allows macro evolution to occur, writing: “What actually happened at this epic parting of the ways (divergence from reptiles into species that evolve into both humans and parakeets), nobody knows.” (pg 255) How…inconvenient. Or convenient, depending on your point of view.

Doesn’t that seem like something vitally important to know before it becomes universally accepted to be an indisputable truth? How can we assume something could have only happened one way, if we don’t even have the slightest clue how that way actually works in the real world?

Remember, if evolution as Dawkins describes it really is true, you’re not only a cousin of a chimpanzee, you’re also literally the cousin of a cucumber. All dramatic (and beneficial) mutations only made possible by sex. Plus isolation of two gene pools from the same ancestral creature. And lots and lots of time, of course. Dawkins also wrote in his book that “Biologists use the word ‘speciation’ for the splitting of a species into two daughter species.”

The problem with what biologists call “speciation” is the definition of the word species, originally redefined by Ernst Mayr to mean animals that don’t reproduce for whatever reason, regardless of their kind. Doesn’t this sort of diminish the whole concept of selection? In ring species, is it true that the animals can’t reproduce, or could it be possible they don’t mate by choice? Is a bluebird absolutely unable to mate with a cardinal, or possibly just not attracted to them?

I don’t ask questions because I know all the answers…I’d only like to know them.

According to Dawkins, the cichlids of Lake Victoria have allegedly evolved into hundreds of new species of cichlids. But the cichlids haven’t actually become a truly new kind of organism. Only more diversity in cichlids can be observed, even 400,000 years after the lake formed.

The real question of speciation is this: how long does it take for tilapia to evolve into trout?  Remember that in open ocean waters, a decent fisherman might catch bass, trout, flounder, salmon, mackerel, or they might encounter countless other forms of marine life — or perhaps they might even hook an alleged fossil fish, the coelacanth. Will the cichlids of Lake Victoria ever evolve into something other than a cichlid?

During Richard Lenski’s experiments with e-coli bacteria didn’t evolve into a completely different organism with a new body plan. It didn’t even evolve into a different form of bacteria such as salmonella or listeria. The e-coli merely adapted to changes in its environment. The experiments do demonstrate the remarkable resilience and ability to adapt to a changing environment for a well defined kind of animal, but haven’t shown how truly new organisms emerge.

My atheist friends want to know how I can dismiss evidence of evolution seen in ERVs, meaning the endogenous retroviruses that may become part of the DNA inherited by offspring.

Under what circumstances might an infection from a virus have beneficial results to the host organism? Trying to think of candidates for viruses that may become permanently embedded in the host’s DNA, I’m only coming up with examples such as herpes simplex/Chickenpox thus far — viruses without beneficial effect on the host organism.

New information might get added to the genome, all right, but it’s more than likely detrimental in nature, if it’s viral.

The latest and greatest discovery in evolutionary biology is the identification of the miR-941 gene that allegedly “helps to explain how humans evolved from apes. It appears to have played a crucial role in the development of the human brain and may shed light on our use of tools and language.”

The problem is that the article making this stunning announcement also had this to say:

Scientists say, however, that this gene emerged, in a startlingly brief interval of evolutionary time, fully functional out of non-coding genetic material. This material has been termed “junk DNA.” [emphasis added] Previous to this study, it has been remarkably difficult to see this process in action.

In light of these new clams, perhaps calling Sir Fred Hoyle’s famous tornado-through-a-junkyard analogy a “fallacy” is the truly egregious logical error in this exercise. I just don’t believe that the traits which make humans special formed quickly and naturally came from AREs and junk DNA.

southernprose_cover_SHSIn his book The Greatest Show on Earth, Dawkins repeatedly encouraged his readers to imagine being private detectives investigating a crime scene. As it just so happens, that is precisely what I do for a living — I write detective novels, published using the pen name Rocky Leonard.

So I’ve had to train my mind to imagine crimes and then to solve them.

It seems intuitively more obvious to me that God, not good luck, has monkeyed around with our DNA.

God doesn’t make junk. Complexity exists for a reason.

Perhaps the most telling comment of all from Dawkins was this: “Once again, I must stress, the details [emphasis original] of my little story are pure fiction [emphasis added].” (pg. 256)

He follows that up with: “Most biologists will tell you that geographical isolation is the normal prelude to speciation, although some, especially entomologists, may chime in with the reservation that sympatric speciation can also be important. Sympatric speciation, too, requires some kind of initial, incidental separation to get the ball rolling, but it is something other than geographic isolation.” (pg. 257)

Given the stated importance of genetic isolation of two breeding populations within species boundary, does this mean that humans, in the age of worldwide travel, can no longer evolve on earth?

That thought seems to beg yet another question: must humans colonize outer space in order to be able to evolve into new species? How else might two different human gene pools get isolated long enough to diverge, in this day and age?

I know this article turned out to be long, but I wanted to cover as much territory as possible and get all of the residual questions off my chest, but to be perfectly honest, I don’t see future books about evolution or religion.

I’ve pretty much said all that needed to be said, and what I wanted to say. Until the announcement of next great evolutionary breakthrough, that is.

Perhaps when they claim to have discovered how gene mir-942 helped turn monkeys into men.

Willful ignorance

southernprose_cover_CAFG A couple of years ago, I faced the rather formidable challenge of engaging in public debate against Ed Buckner, former president of American Atheists.

Ed was very experienced in that sort of thing; it was my first and remains as of today, the only formal debate I’ve ever had in my life.

Therefore, my work was certainly cut out for me.

Fortunately for me, video existed on You Tube showing Ed present his best arguments while debating a Muslim scholar in the U.K. named Hamza Andreas Tzortzis.

So I took copious notes, seizing upon the opportunity to anticipate Ed’s best shots.

In fairness, Ed also should have been able to anticipate my best shots coming, if he’d bothered to read some of my work as the Atlanta Creationism Examiner.

In my opening remarks, I enumerated the seven points that Ed made that were the foundation his best arguments for atheism and then eviscerated them, point-by-point.

I sort of expected that once the logical flaws in Ed’s argument were systematically exposed and shredded before he’d ever opened his mouth, we would then be able to spend the remainder of our time arguing about points about the science that has now officially become the crux of my Counterargument for God.

Because I knew Ed to be quite an intelligent man, I will now confess that I was expecting the alleged “freethinker” would be a little bit more open-minded.

I foolishly assumed that Ed would be able to defend his own beliefs, rather than simply attacking what he supposed to be mine with every opportunity.Sadly, Ed disappointed me.

Also in my opening statement, I had suggested we conduct the debate without making reference to the Bible, saying we could “leave that anthology in the narthex.”

But Ed would have none of that. It turned out that his argument solely depended on attacking the Bible, which is most certainly not “God.”

I countered that the Bible should be thought of as nothing more than a useful tool, such as a hammer, and pointed out that a hammer would never be worshiped.

In reflection, I now realize why Ed was so compelled to focus his attack on Christian beliefs based on literal interpretations of the Bible and the Old Testament in particular. Ed realized if he wasn’t the offensive, his argument was quite vulnerable.

When the debate did temporarily stray into my science arguments, Ed got into some trouble by making factually incorrect statements. For example, he incorrectly exclaimed that Darwin never wrote the words, “Monkeys make men.”

It didn’t matter to him when I said that I’d just seen the Darwin exhibit at the Fernbank museum, which included a page from his notebook highlighting that exact phrase, and I was quoting it verbatim.

Ed seemed to naturally assume that I was somehow being deceptive or distorting the truth by telling it.

He wasn’t the least bit receptive to any possibility that my argument might have been formed using superior logic and constructed with more accurate information than that in his possession.

He must have assumed he would win the debate merely because I freely admit that I am a Christian.

Ed finally conceded his mistake on that one minor point, but that admission came privately, long after the debate was over.

But implying that I had somehow been deceitful wasn’t the worst part of our debate. I was more disappointed when Ed showed me a brief glimpse of his hypocritical side, admitting to his own willful ignorance. After all, he was the one who suggested that our epistemic duty was to seek knowledge and test the truth. Ironically, that had been the only one of his seven points arguing his atheist philosophy that I conceded was true.

However, when I offered Ed several examples of scientific research that he should investigate because he had made statements that conflicted with scientific evidence, he changed his tune and claimed that his real duty was only limited to topics of his personal interest.

In other words, Ed had no real interest in seeking truth. He was only there to win an argument, and I’m not even sure he accomplished that.

But if nothing else, he gave me plenty of fodder for the second half of my Counterargument.

Yet the debate against Ed was nevertheless quite instructive, and therefore well worth the time and effort I invested. I learned that one of the most prominent atheists in America was willing to admit he would not consider new ideas with an open mind, in spite of what he had claimed was his epistemic duty.

But what isn’t worth my time is having an argument on the internet with some character who calls himself “Doc Cos”, who lurks on a Facebook page called God on the Slide.

While Dr. Buckner was pleasant and quite cordial, and without question an authentic doctor, this “Doc Cos” person hides behind a pseudonym and only seems capable of personal attack.

His most frequently used descriptors of me are “idiot” or “liar”, which he invariably spews using poor grammar and misspelled words. The delicious irony of that faux pas is apparently lost on him.

The only reason this nebulous “Doc Cos” merits any mention outside of Facebook is because he accused me of willful ignorance.

This is the same man who refused to accept a free copy of my now award-winning book Counterargument for God so that his criticisms would no longer be littered with ignorant remarks.

However, if ignorance is bliss, Doc Cos is determined that he will live in ecstasy.

And then again recently, I was reading Tom Krattenmaker’s editorial piece for USA Today that asserted “Evolution is not a matter of belief” but an indisputable fact.

Krattenmaker wrote,

But here’s the problem: As settled science, evolution is not a matter of opinion, or something one chooses to believe in or not, like a religious proposition. And by often framing the matter this way, we involved in the news media, Internet debates and everyday conversation do a disservice to science, religion and our prospects for having a scientifically literate country.

Here’s a real problem with Mr. Krattenmaker’s assertion — there’s no such thing as settled science.

If science were ever “settled”, people would still be taught that the earth was flat.

Only a couple hundred years ago,the prevailing wisdom about combustion was phlogiston theory.

Within the last century, many of our smartest scientists and philosophers were convinced the universe was eternal beginning because they recognized the problems posed by the universe having an origin.

Then Edwin Hubble provided evidence of red shift, validating the Big Bang theory in the minds of an overwhelming majority of astronomers and physicists.

The consensus of opinion is now that [the universe] all started with a big bang, as the jingle for the television show of the same name suggests. Yet even today, not every physicist agrees with the Big Bang theory. There are competing theories, like the Big Crunch, and brane cosmology.

Now, I have been known to express my utter contempt for phrases such as “scientific consensus” or “peer review”, but with good reason.

Those are nothing more than buzzwords, simple phrases that censor competing opinions out from public consumption.

If you don’t believe me, read the true story of what happened to Boris Belousov.

Consensus is the death of original thought. A consensus of opinion in the scientific community may well exist about any given theory at some point in time, but there is no such thing as a theory that is immune to challenge. The challenge itself may very well fail, but the ability to challenge will always remain.

But what really irritated me the most with Mr. Krattenmaker was his assumption that my beliefs about evolution theory are borne of willful ignorance, as he insinuated in this passage:

As a progressive, I’m tempted to blame willful ignorance by those on the “other side” when I see the sharp rise in Republicans rejecting evolution, and the always-high percentage of white evangelical Protestants (64% in the Pew poll) who believe that humans were created by God in their present form; i.e. no evolution.

I would be more than happy to debate Mr. Krattenmaker about the science of evolution theory.

Because of the willful ignorance of people such as “Doc Cos”, I haven’t been able to even give away a free copy of Counterargument for God  to an atheist willing to read it, even thought it has won an award.

Alleged “freethinkers” like Mr. Krattenmaker mistakenly believe that the evidence for speciation is as conclusive as the evidence for natural selection.

But the real problem with speciation is not to think that humans and apes could be related by descent via sexual reproduction, simply given enough time. The real problem occurs after one realizes that the exact same biological processes allegedly explain the relationship of both humans and apes to the bananas we both like to eat.

People who believe in the possibility of Divine Evolution  could consider our cousin-ship to both turtles and turnips via sexual reproduction a questionable proposition at best.

And they may very well take umbrage at the suggestion that they suffer from mental defect merely for having a few doubts about how much Darwin’s theory can do about answering our existential questions.

On the other hand, antitheists such as “Doc Cos” revel in their own willful ignorance, smugly confident that their limited knowledge is somehow superior to an argument they don’t even know.

“Doc Cos” won’t even spend a couple of hours reading a book that was offered to him for free.

Sure, it’s easier to criticize what you don’t understand.

But if that isn’t a prime example of willful ignorance, what is?

A conversation about evolution with Dr. Benoit Leblanc

Counter_cover_smAfter I wrote an open letter to Dr. Jerry Coyne, Dr. Benoit Leblanc was kind enough to comment at length in response.

He wrote,

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.

Thank you, Dr. Leblanc for taking the time to write your thought-provoking response.

It seems that in your opinion, I failed to show proper deference to Dr. Coyne. I’m truly sorry if I gave you that impression. Perhaps the strong sentiments of derision and ridicule Dr. Coyne has expressed against religious beliefs likewise tainted my confidence in his ability to produce unbiased science.

The truth is that I do respect the work of scientists. I also respect medical doctors.

However, an advanced degree does not make one infallible.  Doctors and scientists are human beings just like me, and similarly capable of mistakes.

True stories: Twice in my life, I’ve received horribly inaccurate medical diagnoses. Once I had one doctor mistakenly claim that a relatively simple eye infection was caused by flesh-eating bacteria.

Another doctor once told me that he thought I might have leukemia.

Thank God, both were wrong. Nobody’s perfect, believe me. I quickly learned to trust, but also verify.

Forgive me if I’m wrong, but it seems that you agree my understanding of the science behind evolution theory was accurate on the major points of contention.

I’m supposed to simply trust the pontifications of Dr. Coyne, because you say he’s right. You also said that biology is not concerned with the hypothesis called abiogenesis.

In respectful disagreement, I wrote a separate blog piece explaining specifically why abiogenesis is important in the Big Picture.

Your protest to the contrary has been duly noted. But using your same cake analogy to illustrate my objections, the problem with accepting speciation on face value is that it is like saying a cake can exist without worrying about where you’ll find the eggs, milk, sugar, flour, cake pan, and the oven.

I prefer not to make bold assumptions that the necessary ingredients will magically appear on cue without the benefit of solid evidence to support such conjecture.

Dr. Leblanc, you’ve made it clear that the consensus of biologists has accepted speciation as fact. However, that seems to be nothing more than an appeal to authority.

With all due respect, so what? Consensus is not science.

Ironically, you seem to reject the consensus of paleontologists when it comes to the evidence used to support punctuated equilibrium theory. So, am I left to assume that consensus is only acceptable until it disagrees with your perspective?

You wrote that I was correct in my basic understanding of evolution theory, but insinuated that I’m completely wrong in the conclusions I have drawn. Presumably I am to defer to indoctrination by the “experts.”

I’ve already replied in another post introducing the Big Picture to your remarks about my fourth point, that life cannot evolve until it exists. There’s no need to belabor the issue since you’ve conceded that very important point.

Surprisingly, you seemed to take offense at the idea that I would ask a trained and presumably expert biologist specific questions about biology, his alleged field of expertise.

Should I be asking questions about space travel instead?

You wrote “evolution of species by means of natural selection is a ridiculously good theory” but frankly, offered no new evidence that Dr. Coyne failed to mention in Why Evolution is True.

Unfortunately, my understanding of speciation theory did not improve. Because you conceded that the parts of speciation theory I recounted from my understanding were accurate, I feel confident that if someone were to supply the missing information, I would be able to comprehend it.

When I specifically asked for the missing ingredient in speciation that allows a single, rat-like ancestor to morph into every known species of mammal within the last 200 million years, you gave me yeast and MYH16. No offense, Dr. Leblanc, but that doesn’t begin to answer my question.

With all due respect, I’m not demanding that you explain the speciation that allowed a turnip and a turtle to share common ancestry. I’d be perfectly happy if you could explain why lions and zebras split from a common ancestor. Both animals are mammals if I’m not mistaken, so both animals must have differentiated from the same rat. less than 200 million years ago, if evolution is true.

One to hunt, and the other to potentially become dinner. And, we still have mice, rats, elephants, dolphins, whales, dogs, cats, leopards, giraffes all related to that same mammalian LUCA.

In short, Dr. Leblanc, why does the food chain exist? That seems to be the real mystery behind speciation. Which came first, the cotton rat or the cotton plant?

Nevertheless, let’s concentrate on the first three issues that specifically involve evolution.

You began your letter to me by asserting that I approach the existential questions with a creationist/ID mindset. No problem.

It would be somewhat dishonest for me to suggest otherwise. After all, for two years I wrote online as the Atlanta Creationism Examiner. As long as we acknowledge that “your” argument, or the one of Coyne and Dawkins, is motivated by an atheist/pure materialism philosophy, I think that’s fair.

But please, don’t claim what Coyne or Dawkins preach is pure and untainted science. These men are both hardcore atheists, first and foremost. At the end of his Harvard lecture, Dr. Coyne openly admitted his beliefs have been shaped by his Marxist/socialist/atheist philosophy.

In his convoluted, pure materialist view of the world, Jerry Coyne would have you believe there is no such thing as moral responsibility. Because morality can only come from God, Dr. Coyne simply rejects the possibility and any evidence that might contradict his world view without giving the evidence any consideration.

There is where we differ.

You appear to have gotten the impression that I “counterattacked” Dr. Coyne because of my own animus about his views on religion. Let me reassure you; I asked my questions because I sincerely want to know if there was a real answer.

I could believe in theistic evolution, if only it were true. It would be much easier than inventing a new theory to fit all of the scientific evidence.

I’m diligently looking for that biological example like Kate the fertile mule for clear evidence of theistic speciation that gives some insight into how the phenomena is possible. I’m specifically seeking evidence that might refute my philosophy I’ve been calling iterative creation.

Biologists say transitional species; I say prototypes. And I’d be more than happy to justify that claim.

Now, since you mentioned the work of Sean Carroll, I’d be remiss if I didn’t point out that my experience has been to read about his work in theoretical physics. I am somewhat familiar with his “Arrow of Time” hypothesis about the multiverse and even find parts of it useful.

However, in a panel discussion on atheism, Dr. Carroll somewhat brazenly made the assertion that he knew what happened when we die.

Keep in mind, in this same conversation, Dr. Carroll said that we have to distinguish between proof and warranted belief. He also said that he was as certain that God did not exist as he was the sun would rise in the east the following day. He said a number of things on which we agreed, and then made statements I was absolutely sure he was wrong to make.

So, I wrote Dr. Carroll an email, asking him to explain what he thinks will happen when he dies since he claimed to know. When I asked if he was familiar with scientific evidence of corroborated veridical NDE perceptions, to my disappointment but no great surprise, Dr. Carroll boldly stated that he had no need to investigate claims that violated the laws of physics.

However, we are asked to blindly accept speciation theory as a fact, when in reality it violates the known “laws” of modern biology.We are expected to blindly assume that this universe arose from literally nothing, that dirt and chemicals became a living organism, because someone else said so. There is no “one size fits all” solution to life.

Unfortunately, polyploidy only seem to occur in limited species: namely plants, fish, and some amphibians. You seem willing enough to discuss the negative evidence used to attack belief in God but refuse to consider the positive evidence I can offer to support my counterargument.

When I ask you to consider the implications of what you blindly believe due to a consensus of your peers, you declared that physics and chemistry is not your concern, yet you rely on them to produce the biology you study.

With all due respect, in order to make any audacious claims about the nonexistence of God, you have to concern yourself with the Big Picture. You have to allow yourself to at least consider the possibility that God does exist.

My argument has never been that speciation is flat-out impossible. Virtually any idea you can have is theoretically possible. My counterargument is concerned with not the impossible, but which is more probable? I’ve got great evidence, but no one seems to care.

Admittedly your “croco-duck” would satisfy the issues that prevent my blind acceptance of speciation theory, but there’s no need to produce anything so dramatic. I’d settle for proper identification and explanation of the biological processes that allow dogs to split from wolves, or even how houseflies and horseflies share common ancestry.

Nothing fancy.

But sadly, you give me multiple species of yeast.

The splitting event of speciation itself remains a nothing but a glossed over detail. This creates the distinct impression in my mind that you believe something has happened without the faintest idea of how it might have worked. My point is simple; perhaps it is too simple.

If the mule, liger, zedonk, or wholphin weren’t biological dead-ends, speciation theory might actually be believable. From what you’re telling me, the ability to observe the type of speciation I need to see to accept that it happens without divine intervention simply isn’t possible in the time frames we have available.

Implying that “evolution deniers” are too stupid to understand how evolution works and the argument from majority opinion might cow some opposition into silence, but I am stubborn enough to resist any argument based purely on superior intellect–especially until it’s been proved.

Bluster and bravado aren’t enough to convince me. I need provable facts.

Author Sam Harris recently wrote a book insisting that free will is nothing but an illusion, echoing many of the absurd, unsubstantiated claims made by academia regarding neuroscience. In light of the clear, incontrovertible evidence of brain-free consciousness, his argument becomes utter nonsense.

Therefore, Harris insists that corroborated veridical NDE perceptions are actually hallucinations. When exactly did hallucinations become confused with accurate memories? The only way to justify such an egregious mistake is to refuse to investigate the claim.

Yet I am the one called a denier of truth. Quid est veritas?

You ask why I feel brazen enough to challenge Dr. Coyne in his specific field of expertise. I must admit, I refuse to genuflect before any other human being.

While I do respect the fact Dr. Coyne has earned a doctorate and written a best-selling book that claims to explain why evolution is true, I also recognize the fact he isn’t immune to making extraordinarily claims about religion in particular. If his bias can lead to clear mistakes in his understanding of religion, why not evolution?

Having read his book and watched several of his lectures, it seemed rather obvious that Dr. Coyne simply glossed over the most important details regarding speciation–for example, how did phyla come into existence? Why is there a food chain? How did complex systems like the central nervous system and respiratory system evolve from simpler organisms with different body plans, and why?

I’m not afraid to consider the possibility you could be correct about speciation theory, which is why I asked questions and read books purportedly describing the processes called evolution.

What I don’t understand is why you and others in the scientific community appear to be afraid of considering the possibility that intermediate species were created prototypes rather than beneficial but accidental mutations?

In your comment, you mentioned the possibility that humans descended from Neanderthals. Been there, done that.

If this shape-shifting you have suggested actually does occur, then man is not only related to the chimpanzee and the bonobo ape, but also to the banana we both like to eat. This common ancestry was solely performed through the biological process of sexual reproduction, simply when given enough time.

Assuming for a moment this degree of shape-shifting you take for granted is theoretically possible, the questions how? and why? immediately come to mind. This is usually when the “environmental niche” card gets played.

At this point in the conversation, I’m always reminded of a Monty Python skit about Harold the flying sheep. The interesting thing is, sheep do not so much fly as plummet.

In my simplistic, non-biologist way of thinking, speciation is only possible one of two ways. Either two members of the same species mate, or two members of different species mate. The offspring must be fertile and reproduce. There doesn’t seem to be a third option.

You and I seem to agree that the only way speciation can occur is if an isolated breeding population of an existing species either splits off or morphs into a different species.

In my book I made it clear that it doesn’t matter if you blindly want to believe Darwin’s theory. If you seek answers to existential questions, you soon realize that the question of how modern species came to exist only provides a piece of a puzzle, not the whole Big Picture.

If you can’t ever reach the point where life diversifies without invoking a God to create the universe or animate matter, speciation becomes a mere detail of how things may or may not have been implemented.

True, scientific tests tell us that the earth is several billion years old, and the universe much older. However, the fossil record also tells us that life hasn’t been around in abundance for billions of years, and multiple mass extinctions cut down on the amount of time new species emerge.

While time does solve some evolutionary problems, it creates the problem of the coelacanth. The exact same process that theoretically describes the rapid (in geologic terms) emergence of new species as well as stasis. The “rules” for rates of evolutionary change appear to be quite similar to the rules suggested by Butch Cassidy in a knife fight.

Evolution can’t predict that everything will happen. Well, if it does, then the theory becomes useless. Anything goes.

I can understand how Jack Horner can look at a chicken and think he sees a modern relative of Archeopteryx. I just don’t understand how he could claim to know for a fact that chickens evolved from dinosaurs.

If the processes of evolution are not directed, then basic statistical analysis dictates that a normal distribution of mutations would occur. Some would be beneficial, some deleterious, and some neutral.

That factor alone makes Darwin’s assumption of slow, gradual, almost relentless change most attractive.

However, the fossil record, with clear evidence of mass extinctions and numerous examples of stasis, makes punctuated  equilibrium theory appear far more attractive. Gould wanted to have it both ways, to be sure.

There seems to be a lot of “because of it can” sort of answers necessary to accept evolution as fact.

Forgive me for noticing, but it seems that you don’t really have any problems with my basic recitation of the alleged facts of evolution, but my interpretation of them.

I don’t have any problem acknowledging that the uniqueness of Australian species gives some credence to your argument that isolation is the key ingredient in the success of  speciation. However, I’ve got plenty of even better evidence to support my comprehensive argument that I call iterative creation.

I don’t deny the pure materialist argument can be made. My counterargument is that the pure materialist argument is fatally flawed. Corroborated veridical NDE perceptions, or brain-free consciousness, would utterly defeat the materialist argument, if true.

Our third point of contention was evidence of intelligent design versus evidence of design flaws. You claim that whale bones in fins mimic hand bones well enough to assume common ancestry.

That is a possibility, but why do you assume it to be the only alternative? There is ample evidence that many of your colleagues, in their own words, admit that the alternative, some form of creation, is simply “unthinkable.”

And that is the only reason for their disbelief.


An open letter to Dr. Jerry Coyne

Counter_cover_smDear Dr. Coyne,

I’ll do my best to get right to the point. Your reputation as one of the world’s foremost experts on speciation theory precedes you.

You are a well respected scientist and educator. I am but a student of those fields in science necessary for any attempt to answer my existential questions.

Although I’ve been called a teacher, my background is not in education. By profession, I’m an author, certainly not a scientist. My strong preference is for writing detective novels.

However, in the spirit of full disclosure, I should divulge that my most recent book, published this past Easter Sunday, has the title Counterargument for God.

I should probably also mention that your advocacy of naturalistic evolution is one of the arguments that I endeavored to counter and defeat in my book. I meant no disrespect.

It just happens that I have very good reasons for believing that you’re wrong to assume that supernatural intelligence played no role in your existence or mine.

Now, I’ve read Why Evolution is True, but I cheerfully admit that I don’t yet quite understand the biological processes allegedly at work. I still have a few questions about your specific field of expertise, if you’ll be good enough to answer them.

Your USA Today article written not too long ago asserting that you can be good without God gives me some hope that you will cooperate, even though I suspect David Berlinski may have doubts.

If I never ask my questions, you won’t have the opportunity to respond if you so choose.

True, you have expressed some disdain for creationists in the past. You may decide to ignore me, but that will only reinforce my suspicion that you can’t answer my questions.

And if it helps, as far as I’m concerned, we can leave the Bible and religion out of this discussion in order to focus purely on the science.

Let me reassure you, my mind remains quite malleable.

By your own broad definition offered at Harvard, apparently I fall into the forty percent category of Americans you have suggested are “dumb or perverse” for not believing speciation has occurred.

However, you didn’t call speciation theory by its proper name. You called it “evolution.” The terms are not synonymous.

Please look at my request for information this way — I’m giving you an opportunity to improve on that statistic that troubles you so much. Without further ado, let’s get started.

Evolution simply means change. Of course things change. The real question is, can organisms shape-shift, simply by means of DNA recombination achieved through sexual reproduction?

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

I’m fairly sure that I know how it’s supposed to work. Please allow me to illustrate my current understanding of the process, formed in part by reading your book.

A small population of one species becomes geographically segregated from other members of its species, isolating its gene pool. That population only breeds with other members of its population, never coming into contact with other members of the ancestor species, until a biological split occurs after many generations of genetic recombination. Mutations aggregate until new genes can be identified in the genome identified as belonging to the ancestral species that are unique to the descendent species.



Voila! We now have a new species of organism. It all sounds so easy.

It’s much too easy, in fact.

Please forgive my skepticism, but there seems to be a missing piece to the puzzle. The process I just described could be argued as nothing more than natural selection.

Certainly, these processes can explain variety within a species, but not the creation of a new and unique organism.

Given enough isolation, time, and genetic recombination, it’s quite easy to see how astonishing variety can occur with a given morphological form, but not how drastically different morphological forms emerge from common ancestry.

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.

Your theory of speciation asserts that with isolation of a gene pool and time for mutations to become permanent, apes produce something other than apes, like Australopithecus, for example.

Perhaps Australopithecus remained segregated, and over time split again to form Homo Habilis. It’s an interesting theory, but hardly a fact.

Homo Habilis

Homo Habilis

We are merely using the same evidence, comparative anatomy and genetics, to reach different conclusions.

The idea of naturalistic evolution becomes especially suspect when one realizes that from this same, basic biological function, organisms as diverse as trees, crabs, worms, eagles, gulls, flies, fungi, apes and humans allegedly share common ancestry. Sexual reproduction performed by two members of the same species, provided sufficient isolation and allowed enough time to mutate beyond all recognition, apparently allows organisms to shape-shift, if your theory is right.

When the parents are from different species, the offspring are invariably sterile. This means that speciation must occur when members of the same species procreate.

I don’t mean to disparage your work with Drosophila, but variation and adaptation within a genome isn’t the same thing as genetic mutation that becomes drastic morphological change, with all due respect. No offense, but I’m really just not all that interested in the sex life of fruit flies.

I’m already quite familiar with the mating process of two members of the same species. My wife and I have two children, and three grandchildren.

The stork didn’t deliver them; an obstetrician did.

Therefore, you may safely assume that I understand the mating and birth processes quite well. What I still don’t understand is how speciation could ever occur without violating those biological processes I have observed in situ.

Evi_cromagnon_largeTwo members of the same species produce fertile offspring and perpetuate the species. On those rare occasions when two members of closely related but different species mate, the result is a sterile hybrid.

Members of significantly disparate species, like humans and horses, usually don’t even try. That sort of true perversion often results in death.

Now if you can tell me how the biological process of sexual reproduction involving two flies of the same species could produce both fruit flies and butterflies, I’m all ears. If you can truly explain the relationship by descent of the butterfly to the butterfly bush, that’s even better.

If you will be so kind to explain the nature of the cousin-ship between the crab and the conifer in graphic detail, I promise to give you my undivided attention.

However, if you can’t identify the specific biological processes that allow these miracles, perhaps you should reconsider your claim that your theory of evolution is irrefutably true, because you obviously can’t prove it or adequately explain the process by which it occurs.

In Why Evolution is True you wrote,

Speciation is a splitting event, in which each ancestral branch splits into two twigs, which themselves split later, and so on, as the tree of life ramifies. That means the number of species builds up exponentially, although some branches are pruned to extinction. How fast would speciation need to be to explain the current diversification of life? It’s been estimated that there are 10 million species on earth today. Let’s raise that to 100 million to take into account undiscovered species. It turns out that if you started with a single species 3.5 billion years ago, you could get 100 million species living today even if each ancestral species split into two descendants only once every 200 million years. As we’ve seen, speciation happens a lot faster than that, so even if we account for the many species that evolved but went extinct, time is simply not a problem.

Time appears to take on magical qualities in your concise explanation. The problem is, you seem to have grossly misrepresented the amount of time available for these drastic processes to happen.

We both know that if speciation really took 200 million years to split one species into two, Lystrosaurus would never have evolved into dinosaurs, correct? There was only 150 million years between the Permian and Cretaceous extinctions, the age of the dinosaurs. And complex life wasn’t plentiful until the Cambrian Explosion, which occurred only 530 million years ago.

There have been multiple mass extinctions since. According to simple arithmetic, the rate of evolutionary change has to be much faster than what you have suggested. In actuality, there doesn’t seem to be any known rate of evolutionary change.

Which leads me to…

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?

Please excuse me for questioning your authority in this regard, but according to the paleontologists, the fossil record apparently doesn’t support the Darwinian idea that new species emerge through a series of slow, incremental changes.

That’s why Gould and Eldridge proposed punctuated equilibrium, isn’t it?

The repetitive pattern found in the fossil seems to be one of jerky, episodic events. New life seems to appear in an “explosion” of activity, followed by a long period of stasis and then mass extinction, correct? Forgive me if I’m wrong, but it seems that you have determined isolation of the gene pool is critical for true speciation to occur.

In fact, you also wrote in your book,

The idea that geographic isolation is the first step in the origin of species is called the theory of geographic speciation. The theory can be stated simply: the evolution of genetic isolation between populations requires that they first be geographically isolated. Why is geographic isolation so important? Why can’t two new species just arise in the same location as their ancestor? The theory of population genetics — and a lot of lab experiments — tell us that splitting a single population into two genetically isolated parts remains very difficult if they retain the ability to interbreed. Without isolation, selection that could drive populations apart has to work against the interbreeding that constantly brings individuals together and mixes up their genes.

So, if I understand you correctly, isolation or geography plays a crucial role in speciation.

As far as human evolution is concerned, using human evolution as the illustration, it seems the explanation you have suggested for how speciation occurs is that about four million years ago a small population of breeding primates split into apes and Australopithecus.

The new Australopithecus genome must have remained isolated for an extended period of time, because as you stated above, interaction while the two different species retained the ability to interbreed would cause the collapse the new genomes. Presumably, Australopithecus split into Homo Habilis and other intermediate species until homo sapiens emerged.

Perhaps your theory is theoretically possible, but it’s hardly an incontrovertible fact.

Dr. Coyne, how does this isolation occur in an ocean?

The cichlids in Lake Victoria didn’t differentiate into trout, flounder, bass, or mackerel — they “evolved” into roughly 600 varieties of cichlid. Yet the coelacanth allegedly hasn’t evolved for 340 million years, and it lives in the ocean.

The more we scrutinize speciation theory, the less it makes sense or seems possible.

My third question: 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?

My fourth, and final question: Until life exists, how can it evolve?

At Harvard, you suggested that evolution theory was “the supreme achievement of human intellect.”

Really? Are you sure? More impressive than flight, space travel, the invention of the wheel or the computer? But that wasn’t my question.

My question is, aren’t the Big Bang theory and abiogenesis hypothesis at least as important as speciation and natural selection?

When I first became interested in the science related to my existential questions, I realized that to understand the Big Picture, one must begin with the physics of the Big Bang. Without the origin of this special universe, there’s no reason to worry about the origin of life.

After exploring chemistry to learn what scientists know about abiogenesis, the origin of life, we can learn about paleontology and the history of life before studying biology to learn about modern life.

Until LUCA came into existence, Darwin’s theories were irrelevant.

Life can’t evolve until it exists. Period.

If you read my book, you’ll find that many of your colleagues are the ones suggesting that luck plays an extraordinary role in our existence, from the origin of the universe to which species survived a mass extinction.

That’s extraordinary, cumulative luck I find very difficult to believe. Order does not emerge from chaos by accident.

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?

Inquiring minds want to know…