This is low, even for Dr. Michael Egnor, who has been an active apologist for the nonsensical anti-evolution propaganda over at the Discovery Institute. Egnor cannot seem to resist when he thinks he has caught someone in an error, and so he throws whatever faint whisper of logic or scholarship he has overboard (hardly noticeable, really) and sinks to new lows of intellectual buffoonery.

In this case he is responding to my discussion of the evolutionary tree of life – the fact that the fossil record and genetic evidence support the conclusion that all life is related through a pattern of branching descent. He refers to my summary of the current consensus of scientific opinion as an “astonishing gaffe.”

Punctuated Equilibrium

Egnor is using an old creationist trick – the deliberate misinterpretation of legitimate scientific debate about the details of evolution as if it calls into question the fact of evolution itself. He writes:

The fossil record does not show a “clear pattern of branching descent in the fossil record”, even “to the degree that it is complete.” The fossil record shows punctuated equilibrium, which is stasis in a species for millions of years, then disappearance of the species. New species arise, discontinuous with old species. Even isolated ‘transitional’ forms are rare, and gradual transitions are virtually non-existent.

Here we see that Egnor does not understand even the most basic evolutionary concepts.  New species that arise in the fossil record are not “discontinuous with old species,” unless he means by that the simple fact that they are recognizably distinct species, which makes the statement rather pointless – new species are new species. New species, rather, are derived from older species – they are morphological variations on existing patterns.

For example, vertebrates first arise in the fossil record in the late Cambrian, about 500 million years ago. Later in the fossil record vertebrate fish with jaws appear. Later still land vertebrates appear, with features of one branch of fish. These early terrestrial vertebrates have some features that all later land vertebrates will share. However, within this group of land vertebrates sub-groups appear over time, each with their own set of features that all of their members will have.

This kind of analysis looks at homology – features that are shared because they derive from a common ancestor. Homology is distinguished from analogy – features that look similar because of common function, but are different in the details. Homologous traits, on the other hand, share details that cannot be explained by shared function. Looking at life from this perspective we see a clear pattern of branching descent that follows a temporal sequence compatible with evolution from common descent.

Egnor’s statement that the fossil record does not show branching descent because it shows punctuated equilibrium misunderstands both concepts, the one has nothing to do with the other. Punctuated equilibrium is about what happens between the branching points (speciation events), not about the branching itself. PE states that species will be largely stable, in equilibrium with their environment, for most of their time on earth, but this stasis will be punctuated by relatively rapid (geologically speaking – 5-50 thousand years) speciation events. Darwinian gradualism, on the other hands, states that species are gradually changing throughout their existence. Both views, however, incorporate branching speciation. Both views have the same evolutionary interpretation of the nestled hierarchy of life.

What we do not see in the fossil record, however, is true discontinuity – the type that Egnor is talking about which would call evolution into question. We do not see the appearance of species with radically different body plans, or impossible (evolutionarily) chimeras with homologous traits from distinct branches. Nothing that would falsify common descent. If Egnor believes such a creature exists he should name it and claim his Nobel prize.

The Tree of Life

Not content to butcher punctuated equilibrium and misinterpret the fossil evidence, Egnor next sets out to completely misrepresent a New Scientist article about the tree of life. He writes:

Furthermore, molecular genetics has refuted Darwin’s “Tree of Life”— as Dr. Novella characterizes it, the “clear pattern of branching descent”— unequivocally. The generally pro-Darwinism magazine New Scientist, in its recent cover story, “Why Darwin Was Wrong About the Tree of Life”, pointed out that scientists are abandoning the vertical Tree of Life. Molecular biology is showing deep inconsistencies in Darwinists’ simplistic understanding of similarities and differences in biological structure:

He then gives quotes selected to mislead his readers as to what the article actually says. For example, he give the follow excerpt:

…Many biologists now argue that the tree concept is obsolete and needs to be discarded. We have no evidence at all that the tree of life is a reality…[t]hat bombshell has even persuaded some that our fundamental view of biology needs to change…The tree of life is being politely buried, we all know that…What’s less accepted is that our whole fundamental view of biology needs to change. Biology is vastly more complex than we thought…and facing up to this complexity will be as scary as the conceptual upheavals physicists had to take on board in the early 20th century…

Beware when Egnor uses “…”  – that usually means he is taking quotes out of context and excluding information that would help the reader understand what is actually being written. Read the full article yourself.

I must say at first that the New Scientist article went for maximal sensationalism and overstated the case. But even accounting for that, Egnor had to go out of his way to completely miss the bottom line.  From reading Egnor you might think there is recent evidence that calls evolution and common branching descent into question. Again – this is the old creationist trick of distorting progress toward a more complex and complete view of evolution with calling evolution itself into question.

The article is talking about the fact that in recent years scientists have discovered that horizontal gene transfer (HGT) is much more common than previously thought. What this means is that species, even after separating, can still transfer genetic material to other species, even distantly related.

Of course, Egnor does not point out that this is primarily talking about single-celled life. He left that bit out. This is crucial because he offered this as a counter to my contention that the fossil record indicates branching descent. There is no fossil record for branching descent among single-celled creatures.

This is also not new. We have known for a long time that bacteria swap genes. Yes, it is more extensive than previously thought, but so what. Like most things in science, nature turns out to be more complex than we at first imagine. Simple models need to be made more complex and subtle, but that does not invalidate the more basic knowledge, it just deepens it.

For example, we now know about epigenetics – factors other than the DNA that influence development. This does not mean, however, that DNA is not the primary molecule of inheritance. We now know about relativity – this does not mean that Newton’s mechanics are wrong, they are just incomplete.

What about multicellular life and HGT? Here is a quote from the article Egnor does not want you to see:

Nobody is arguing – yet – that the tree concept has outlived its usefulness in animals and plants. While vertical descent is no longer the only game in town, it is still the best way of explaining how multicellular organisms are related to one another – a tree of 51 per cent, maybe. In that respect, Darwin’s vision has triumphed: he knew nothing of micro-organisms and built his theory on the plants and animals he could see around him.

With multicellular life there is horizontal transfer – closely related species may mate and swap genes, for example. Also, viruses may pick up bits of DNA from one species and transplant them to another phylogenetically distant species.  This is old news. We are likely to discover more horizontal transfer than was previously known. Again – a big so what? Among multicellular life a vertical tree of branching descent is still the dominant pattern we see.

Further, the degree to which the tree of life is vertical vs a horizontal web of life is irrelevant to the question at hand – is evolution correct. That there are mechanisms of horizontal gene transfer in no way invalidates the fact of evolution. Nature almost always turns out to be more messy than our clean models of it.

Genetic Evidence

Egnor writes:

Molecular biology is showing deep inconsistencies in Darwinists’ simplistic understanding of similarities and differences in biological structure:

You would think that the molecular biology he is referring to is being done by scientists who are not “Darwinists”.  If you interpret “Darwinist” as Egnor does – anyone who accepts the modern synthesis of evolutionary theory, then this is dead wrong. The only thing that is simplistic is Egnor’s straw man of what evolutionists claim. It is evolutionary biologists who are discovering the rich complexity of life at all levels, and furthering our understand of the the complexities of evolution.

But to get back to the genetic evidence for branching descent, I have gone over this before. This is a home run for common descent. Here is a good talkorigins article on this topic, which states:

Humans and chimpanzees have the exact same cytochrome c protein sequence. The “null hypothesis” given above is false. In the absence of common descent, the chance of this occurrence is conservatively less than 10^-93 (1 out of 10⁹³). Thus, the high degree of similarity in these proteins is a spectacular corroboration of the theory of common descent. Furthermore, human and chimpanzee cytochrome c proteins differ by ~10 amino acids from all other mammals. The chance of this occurring in the absence of a hereditary mechanism is less than 10^-29. The yeast Candida krusei is one of the most distantly related eukaryotic organisms from humans. Candida has 51 amino acid differences from the human sequence. A conservative estimate of this probability is less than 10^-25.

Egnor has failed to address this evidence, or even show that he understands it. The dominant pattern within the genetics of various species is one of nestled hierarchies – branching descent. Yes – there are exceptions, which can be explained by horizontal transfer. That is a level of deeper complexity – it does not invalidate the overall evolutionary pattern, which is overwhelming.

Conclusion

Egnor concludes:

The evidence is so clear that Darwin’s “Tree of Life” is wrong that now even Darwinists are jumping ship.

So why would Dr. Novella publicly misrepresent the state of the science? Either Dr. Novella’s claim is the result of his ignorance of the relevant science, or it is an intentional misrepresentation.

Dr. Novella should explain his misrepresentation.

It is Egnor who has some explaining to do. He has misrepresented my position. He has misunderstood punctuated equilibrium. He has misrepresented the state of the fossil and genetic evidence. And he grossly misrepresented the New Scientist article.

Egnor should clarify what he actually believes, rather than just playing the creationist game of exploiting a poor understanding of the complexities of evolutionary theory to create the false impression that the fact of evolution itself is in doubt.

Egnor claims he is not a creationist, which is absurd on its face. But he should clarify his position. Does he accept common descent or not.  If not, how does he account for the dominant pattern of branching descent that we do see in the fossil record and the genetic evidence. If he thinks there are problems with evolutionary theory he should make a positive case for a viable alternative.

Of course he can’t. Egnor cannot win with legitimate scientific arguments, so instead he is trying to make this personal, as if my views are somehow aberrant. Rather, Egnor is at odds with the scientific community. He is perfectly at home with his creationist buddies, whose modus operandi is to distort, misrepresent, and selectively quote. Their purpose is not to enhance understanding but to sow confusion.