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Does Professor Larry Moran (or anyone else) understand macroevolution?

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Professor Larry Moran thinks macroevolution isn’t terribly hard to understand, if you take the time to do some reading on the subject. He also thinks that Professor James Tour, the world-famous organic chemist who has declared that he doesn’t understand macroevolution, is lazy and opinionated.

Professor Moran singled out Professor Tour for attack in a recent post titled, A chemist who doesn’t understand evolution. (Before I continue, I’d like to thank Professor Moran for linking to my article, A world-famous chemist tells the truth: there’s no scientist alive today who understands macroevolution, in his post.) Here’s a relevant excerpt from Moran’s post:

Normally you’d have to be an expert on evolution in order to claim that all other experts are wrong. I wonder why an organic chemist thinks that he is qualified to make such a claim? It seems a bit strange, don’t you think? …

I’m not an expert on macroevolution but I think I understand the issues and the debate over whether macroevolution can be fully explained by population genetics (and/or natural selection). [see Macroevolution].

I don’t think it’s all that difficult to understand if you make a bit of an effort. It has nothing to do with any doubts about whether evolution explains the history of life. It has to do with whether there are additional mechanisms and events that are required in order to account for macroevolutionary change. Events like asteroid impacts, continental drift, speciation, and perhaps species sorting. I don’t understand why an organic chemist couldn’t figure this out if he really wanted to…

Ignorance is curable. If that’s the only problem facing James Tour then he could do no better than read Stephen Jay Gould if he really wants to understand macroevolution. He will get a heavy dose of “pondering and thoughtfulness.” I don’t think he’s up to it. I don’t think he really wants to learn.

In today’s post, I, a non-scientist, am going to make the audacious claim that Professor Moran, an eminent biochemist, doesn’t really understand macroevolution, even though he has written an article about it and doesn’t think it’s particularly hard to understand, if you are willing to try. I sincerely hope my article will cause Professor Moran to reconsider his views, but it’s never an easy thing to convince someone of something that they’re inclined to resist. Wish me luck!

My case, in a nutshell

The essence of my case can be summarized as follows. First, since macroevolution can be roughly defined as evolutionary change at or beyond the species level, you can’t really understand what macroevolution is unless you have a proper understanding of what a species is. Recent evidence shows: (i) that the current scientific understanding of what constitutes a species is severely deficient; (ii) that species can be characterized by their unique genes and proteins, and (iii) that because each species has hundreds of these unique genes and proteins, the task of explaining how new species arise is much harder than biologists had previously imagined.

Second, you can’t claim to understand what makes something go – a car for instance – unless you also understand what makes it stop. Scientists such as Professor Moran claim to understand the mechanism of macroevolution, but for most of geological time, that mechanism has been in stop-mode, and they have no idea why, as they themselves freely admit. What that means is that there must be some vital X-factor that helps drive macroevolution, which their theories haven’t taken into account.

Third, you can’t really claim to understand a mechanism for getting from A to B unless you can demonstrate – at least with back-of-the-envelope calculations – that the mechanism is capable of getting from A to B in the time available. If you are unable to produce the required calculations, then your claim to understand how the process works is tantamount to nothing more than hand-waving. As it turns out, scientific arguments that there’s plenty of time for macroevolution are fundamentally flawed, which means that evolutionary biologists are back at square one.

What is macroevolution?

Philosopher of science John Wilkins, in his Talk Origins article on Macroevolution, approvingly cites the definition given by Professor Jeffrey S. Levinton, of Stony Brook University: “I define macroevolution to be ‘the sum of those processes that explain the character-state transitions that diagnose evolutionary differences of major taxonomic rank‘” (Levinton, J. S. 2001. Genetics, paleontology, and macroevolution. 2nd ed. Cambridge UK: Cambridge University Press, p. 2). On this definition, macroevolution “includes the study of speciation, but it is hardly restricted to it,” for as Wilkins notes: “The scope of macroevolution rises very far above that level.” But the level of the species is clearly where macroevolution starts.

Professor Larry Moran, in his 2006 essay on macroevolution, opts for a simpler definition of the term, given by the Oxford zoologist, Professor Mark Ridley:

Macroevolution means evolution on the grand scale, and it is mainly studied in the fossil record. It is contrasted with microevolution, the study of evolution over short time periods., such as that of a human lifetime or less. Microevolution therefore refers to changes in gene frequency within a population …. Macroevolutionary events are more likely to take millions, probably tens of millions of years. Macroevolution refers to things like the trends in horse evolution described by Simpson, and occurring over tens of millions of years, or the origin of major groups, or mass extinctions, or the Cambrian explosion described by Conway Morris. Speciation is the traditional dividing line between micro- and macroevolution.
(Ridley, Mark (ed.). 1997. EVOLUTION. Oxford UK: Oxford University Press, p. 227)

Since (according to both definitions) speciation marks the dividing line between micro- and macroevolution, it follows that in order to understand macroevolution, you need to know what a species is, in the first place.

What is a species?

Philosopher of science John Wilkins has done an excellent job of summarizing the current scientific understanding of what a species is, in his articles, A list of 26 Species “Concepts” (Evolving Thoughts blog, October 1, 2006) and How many species concepts are there? (The Guardian, 20 October 2010). The following brief quotes will serve to convey the tenor of his thought:

… I think there is only one concept – “species”, and all the rest are conceptions, or definitions, of that concept…

It’s an old question in biology: what is a species? Many answers have been given over the years – I counted 26 in play, and recently a new one, the “polyphasic” concept (basically a consilience of many lines of evidence) has been introduced in bacterial and other microbial contexts, and which may apply to macrobial species too.

But on another count (where I asterisked what I thought were independent concepts in that list) there are 7 species concepts: agamospecies (asexuals), biospecies (reproductively isolated sexual species), ecospecies (ecological niche occupiers), evolutionary species (evolving lineages), genetic species (common gene pool), morphospecies (species defined by their form, or phenotypes), and taxonomic species (whatever a taxonomist calls a species).

But notice that some of these seven are in fact not concepts of what species are, that is, what makes them species, but instead how we identify species: by morphology, or the practices of taxonomists…

With these two causes of being a species, we can now narrow down the number of concepts to two: ecospecies or biospecies. To be honest, I don’t like calling the reproductive concept “biological” – all species concepts in biology are biological, and so I call them “reproductive isolation concepts”. Let’s call them “reprospecies” for short…

But wait! There’s a philosophical matter to clear up. These causal explanations are just that: explanations. They are not the concept of species. There was a concept of species before we had any clear idea of what they might be. We identified species in the 15th century that are still regarded as species, and there wasn’t the slightest hint of an explanation in the air at the time. And it’s an old concept, too, although the first simply biological definition of “species” (a Latin word that means “form” or “appearance”) waited until 1686 when John Ray defined it…

There is some power, a generative capacity, to make progeny resemble parents, and it seems to rely upon seeds. I call this venerable view, the generative conception of species, and I hold that it was not only the default view before Darwin, but Darwin himself held it, as do all modern biologists (exception below). I argue this in my two 2009 books (summarised in my recent paper). It is what it is that the explanations explain. So technically there is only one species “concept”, of which all the others, the 2 or 7 or 27, are “conceptions“…

That species all exist does not imply that all species have some essential property (any more than because we can usually identify what an organism is implies there is something that all and only organisms share). This philosophical error is called “essentialism”

In modern philosophy, there is an ongoing debate over whether one can have vague and fuzzy sets or kinds, but for science we need only a little logic and metaphysics: If we can identify mountains, rivers, and organisms, we can identify species, and they will tend to have a “family resemblance” (Wittgenstein’s most apt phrase in this context). (Emphases in green mine – VJT.)

The important thing for our purposes is that evolutionary biologists unanimously reject the traditional, “essentialist” view that there is some essential property shared by all species, and only by species. Recent scientific discoveries, however, have provided an unexpected boost to essentialism: species, it seems, are objectively real, after all.

What a species is: the case for essentialism

For those readers who haven’t already heard of him, I’d like to introduce Dr. Branko Kozulic, a scientist who received a Ph.D. in biochemistry from the University of Zagreb, Croatia, in 1979. From 1983 to 1988, Dr. Kozulic worked at the Institute of Biotechnology, ETH-Zurich, in Switzerland. For about fifteen years, he worked for a private Swiss biotech company, of which he was a co-founder. He currently works for Gentius Ltd., a company based in Zadar, Croatia. In addition, he teaches at the Faculty of Food Technology and Biotechnology in Zagreb. His professional interests center mainly on methods used for the analysis, detection, characterization and purification of biological macromolecules. Dr. Kozulic has published about 30 scientific papers to date, and he is also the inventor or co-inventor of numerous patents, 18 of which were issued in the USA. Dr. Kozulic formerly served on the Editorial Board of Analytical Biochemistry, and he is currently a board member of Food Technology and Biotechnology. Dr. Kozulic also serves on the editorial board of the Intelligent Design journal Bio-Complexity.

Dr. Kozulic is the author of a 2011 VIXRA paper titled, Proteins and Genes, Singletons and Species. The 21-page paper is impressively well-documented: it lists no less than 165 references. In the abstract of his paper, Dr. Kozulic refers to the recent finding that lends unexpected support to the view that all species share an essential property:

Recent experimental data from proteomics and genomics are interpreted here in ways that challenge the predominant viewpoint in biology according to which the four evolutionary processes, including mutation, recombination, natural selection and genetic drift, are sufficient to explain the origination of species. The predominant viewpoint appears incompatible with the finding that the sequenced genome of each species contains hundreds, or even thousands, of unique genes – the genes that are not shared with any other species. These unique genes and proteins, singletons, define the very character of every species.

The notion that species can be identified by their unique proteins and genes can be applied to bacteria and eukaryotes alike:

A recent study, based on 573 sequenced bacterial genomes, has concluded that the entire pool of bacterial genes – the bacterial pan-genome – looks as though of infinite size, because every additional bacterial genome sequenced has added over 200 new singletons [111]. In agreement with this conclusion are the results of the Global Ocean Sampling project reported by Yooseph et al., who found a linear increase in the number of singletons with the number of new protein sequences, even when the number of the new sequences ran into millions [112]. The trend towards higher numbers of singletons per genome seems to coincide with a higher proportion of the eukaryotic genomes sequenced. In other words, eukaryotes generally contain a larger number of singletons than eubacteria and archaea. [Eukaryotes are organisms whose cells have a nucleus, unlike bacteria – VJT.] (p. 16)

Based on the data from 120 sequenced genomes, in 2004 Grant et al. reported on the presence of 112,000 singletons within 600,000 sequences [96]. This corresponds to 933 singletons per genome. In 2005, Orengo and Thornton reported on the presence of about 150,000 singletons in 150 sequenced genomes [72]. In 2006, within 203 sequenced genomes and 633,546 nonidentical sequences Marsden et al. identified 158,798 singletons [97]; thus the singletons made 24% of all sequences and there were on average 782 singletons in each genome. In 2008, Yeats et al. [73] found around 600,000 singletons in 527 species – 50 eukaryotes, 437 eubacteria and 39 archaea – corresponding to 1,139 singletons per species… [T]he results of the above calculations are sufficient for an unambiguous conclusion: each species possesses hundreds, or even thousands, of unique genes – the genes that are not shared with any other species.

The presence of a large number of unique genes in each species represents a new biological reality. Moreover, the singletons as a group appear to be the most distinctive constituent of all individuals of one species, because that group of singletons is lacking in all individuals of all other species. The conclusion that the singletons are the determinants of biological phenomenon of species then follows logically. In [his] System of Logic, John Stuart Mill outlined his Second Canon or Method of Difference [133]: “If an instance in which the phenomenon under investigation occurs, and an instance in which it does not occur, have every circumstance in common save one, that one occurring only in the former; the circumstance in which alone the two instances differ, is the effect, or the cause, or an indispensable part of the cause, of the phenomenon.” (p. 18)

If species do in fact share some essential property, as Dr. Kozulic contends, then any adequate macroevolutionary account of how new species evolve has to explain this property. However, Kozulic argues that the appearance of hundreds of functional proteins in a new species, whether simultaneously or sequentially, is tantamount to a mathematical miracle:

Experimental data reviewed here suggest that at most one functional protein can be found among 10^20 proteins of random sequences. Hence every discovery of a novel functional protein (singleton) represents a testimony for successful overcoming of the probability barrier of one against at least 10^20, the probability defined here as a “macromolecular miracle”. More than one million of such “macromolecular miracles” are present in the genomes of about two thousand species sequenced thus far. Assuming that this correlation will hold with the rest of about 10 million different species that live on Earth [157], the total number of “macromolecular miracles” in all genomes could reach 10 billion. These 10^10 unique proteins would still represent a tiny fraction of the 10^470 possible proteins of the median eukaryotic size.

If just 200 unique proteins are present in each species, the probability of their simultaneous appearance is one against at least 10^4,000. Probabilistic resources of our universe are much, much smaller; they allow for a maximum of 10^149 events [158] and thus could account for a one-time simultaneous appearance of at most 7 unique proteins. The alternative, a sequential appearance of singletons, would require that the descendants of one family live through hundreds of “macromolecular miracles” to become a new species – again a scenario of exceedingly low probability. Therefore, now one can say that each species is a result of a Biological Big Bang…

If Kozulic is right here, then evolutionists have been overlooking the real problem of speciation all these years. The problem of how populations achieve reproductive isolation is dwarfed by the much greater problem of how hundreds of new, chemically unique functional proteins and genes appear with the emergence of each new species.

Of course, there are some obvious scientific questions that need to be resolved here. For instance, do these new functional proteins and genes appear simultaneously in a lineage, or sequentially (e.g. one at a time)? (If the latter alternative were proven true, it would lend support to a naturalistic explanation for their origins; whereas the former alternative would point to an infusion of information from an intelligent outside source.)

Another scientific question that needs to be answered is to what degree Dr. Kozulic’s proposed definition of “species” coincides with the definition(s) currently used by biologists. For instance, what about the thousands of species of cichlid fish, which are acknowledged even by creationists to be related to one another, and to constitute a “natural kind”, even though this “kind” is currently classified by taxonomists as a family of organisms, rather than a genus or a species? It would be interesting if it turned out that all cichlid species shared the same proteins and genes, despite their reproductive isolation from one another. Or what about ring species, such as the herring gull? Do they share the same genes and proteins, too?

Naturalistic hypotheses regarding the origin of chemically unique proteins and genes in a species

Now, I am aware that explanations have been proposed for the existence of chemically unique functional proteins and genes in a species, which have no known parents. Science journalist Helen Pilchard puts forward one hypothesis, in her blog article, A happy ending for orphan genes:

The majority of orphan genes, it now seems, lack obvious parents because they’ve sprung up from junk DNA. The idea, once considered totally implausible, is gathering credence as scientific papers pinpoint the non-coding sequences and processes that have forged these foundlings.

Our cells may be constantly experimenting with new genes all the time – ‘testing’ random stretches of non-coding DNA to see if they can produce anything useful. The cell’s cytoplasm is bustling with well-coordinated activity, so most of the proteins manufactured from these sequences won’t fit in. The wannabe gene won’t be selected for, and reverts to plain old, non-coding DNA. But once in a while, junk DNA throws up something useful. The sequence may then start to pick up useful mutations, and over millions of years of natural selection it becomes shaped it into a fully functional gene.

This sounds like an interesting proposal. What would make it a lot more convincing, however, is some number-crunching. How many “experiments” can the non-coding DNA in our cells perform, over a period of, say, one million years? How many fully functional genes would we expect Nature to generate during that period, in the human line? Can we even demonstrate the feasibility of one new gene arising during that time?

Dr. Ann Gauger, of the BioLogic Institute, also discusses several naturalistic hypotheses in her very balanced article, Orphan Genes: A Guide for the Perplexed (Evolution News and Views, July 30, 2013):

2. Will similar sequences be found in other genomes, as we obtain more data? This could be the case if orphans are simply the result of our having sampled too little of worldwide genomic diversity. Orphan genes could be examples of once common genes now lost in most other species, or they could be far voyagers, come from other life forms and integrated into new contexts (this is especially possible among bacteria). This is unlikely to be the case for all orphan genes, however, because we keep discovering more as we sequence more genomes.

3. Will orphan proteins show structural similarity, if not sequence similarity, to known proteins? This would suggest that orphan genes started out with sequence similarity, but have lost it because of rapid adaptive evolution or, alternatively, long-term neutral evolution. The current answer would seem to suggest that at least some orphan genes have no known structural similarity. It is too soon to say whether that will always be the case.

4. Given the fact that such surprising species- or clade-specific proteins exist, it raises interesting questions about where orphans come from. Some might have come from gene duplication followed by rapid adaptive evolution… If that is the case we should see traces left behind in the orphan protein’s three-dimensional structure. Some propose recruitment from non-coding DNA by a combination of mechanisms, including insertion of transposable elements. This is possible, but it would require that the insertion or other mechanism(s) be lucky events in order to produce a stable, functional protein, that is, one that is of use to the organism. Exactly how lucky is one of the issues we are debating.

Finally, Dr. Gauger considers the “elephant in the room” which evolutionary biologists don’t want really to discuss: Perhaps we see so many species- and clade-specific orphan genes because they are uniquely designed for species- and clade-specific functions. Dr. Gauger concludes: “What now needs to be determined is whether or not naturalistic processes known to be operating are actually capable of generating so many new proteins.”

The zebrafish (Danio rerio, pictured above, courtesy of Wikipedia) is an animal whose “orphan genes” have been extensively studied (see for instance Yang, L. et al., 2013. Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish. BMC Genomics. 14 (65): 1471-2164.) The orphan genes of zebrafish, ants and other animals are discussed by creationist geneticist Jeff Tomkins (who obtained his Ph.D. from Clemson University) in a fascinating series of articles on his Designed DNA blog. Tomkins writes:

The myth to explain the presence of orphan genes involves a completely fictional process called de novo gene synthesis. This is the supposed random mutational creation of fully functioning genes from noncoding DNA sequence – real quick.

The circular form of illogical reasoning for the evolutionary paradigm of orphan genes and it’s counterpart ‘de novo gene synthesis’, goes like this. Orphan genes have no ancestral sequences that they evolved from. Therefore, they must have evolved suddenly and rapidly from non-coding DNA via de novo gene synthesis. And, are your ready? De novo gene synthesis must be true because orphan genes exist – orphan genes exist because of de novo gene synthesis. As you can see, one aspect of this supports the other in a circular fashion of total illogic – called a circular tautology.

I claim no expertise on the subject, but my overwhelming impression (as a layman and non-specialist) is that Professor Moran has failed to effectively discredit the work of scientists like Dr. Douglas Axe (see also here and here) and Dr. Ann Gauger (see here and here) on the evolution of new proteins and genes.

Clearly more research needs to be done on the origin of genes and proteins which are both chemically unique and peculiar to one species. I shall leave the question there for now. Suffice it to say that while this question remains unresolved, it would be premature for any scientist to say that they understand macroevolution.

Even leaving this problem aside, however, there is another reason why it is scientifically absurd for anyone to claim that they understand macroevolution.

Macroevolution: What makes it start and what makes it stop?

Imagine a young boy who observes his father turning the ignition key to start a car. “Great!” he thinks to himself. “Now I know what makes a car go.” What the boy doesn’t know, however, is that the car will not go if it runs out of gasoline; nor will it go if the battery runs flat. Which brings me to my point: in order to properly understand what makes a thing go, you also need to understand what can make it stop.

Sadly, biologists have yet to reach this level of understanding with macroevolution, as paleontologist Professor Donald Prothero (pictures above, courtesy of Wikipedia) candidly admits in an article titled, Stephen Jay Gould: Did He Bring Paleontology to the “High Table”? (Philosophy in Theory and Biology, Volume 1, December 2009). Writing as a paleontologist, Prothero expresses his frustration that “neontologists” – biologists who only study living things which are alive today – remain blissfully unaware of the fact that ecosystems can undergo drastic changes over the course of geological time, while the species comprising those ecosystems don’t undergo any evolutionary change at all. Prothero is bewildered as to why macroevolution grinds to a halt in these cases:

By the mid-1980s, a consensus had emerged within the paleontological community that nearly all metazoans [i.e. animals – VJT] (vertebrate and invertebrate, marine and terrestrial) show stasis and punctuated speciation through millions of years of geologic time and strata, with only minor possible examples of gradual anagenetic change in size (Geary 2009; Princehouse 2009; Hallam 2009; Jablonski 2000, 2008). That has been the accepted view of paleontologists for more than 20 years now.

Yet one would never know this by looking at the popular accounts of the debate written by non-paleontologists, who still think it is a controversial and unsettled question. Even more surprising is the lack of response, or complete misinterpretation of its implications, by evolutionary biologists. Since the famous battle at the 1980 macroevolution conference in Chicago, neontologists have persisted in misunderstanding the fundamental reasons why paleontologists regard punctuated equilibrium as important. Many have claimed that people like Simpson (1944) and others were thinking along the same lines, or that gradual change on the neontological time scale would look punctuated on a geologic time scale. They miss the point of the most important insight to emerge from the debate: the prevalence of stasis. Before 1972, paleontologists did try to overemphasize examples of gradual evolution, and they expected organisms to gradually change through geologic time, as they do on neontological time scales. But the overwhelming conclusion of the data collected since 1972 shows that gradual, slow, adaptive change to environments almost never occurs in the fossil record. The prevalence of stasis is still, in my mind, the biggest conundrum that paleontology has posed for evolutionary biology, especially when we can document whole faunas that show absolutely no change despite major changes in their environments (Prothero and Heaton 1996; Prothero 1999; Prothero et al. 2009). That fact alone rules out the “stabilizing selection” cop-out, such as the effort by Estes and Arnold (2007) to invoke stabilizing selection to explain stasis, with no mention of the fact that the fossil record shows much stasis in the face of climatic change. For years now paleontologists and neontologists alike have struggled to find (unsuccessfully, in my opinion) a good explanation for why virtually all organisms are static over millions of years despite huge differences in their adaptive regime. be good examples of short-term microevolutionary change, but they simply do not address what the fossil record has shown for over a century.

So what does Professor Prothero propose? He mentions species sorting, which Wikipedia handily defines as follows:

Species sorting is a theory which states that each species will eventually have its own ecological niche as two species cannot occupy the same niche for an unlimited amount of time without extinction. One will be more competitive than the other species. Therefore, if two species with the same niche were left in the same area, eventually one of the species would evolve and participate in resource partitioning.

All well and good; but one has to ask: why, during the times of environmental upheaval which Professor Prothero describes above, didn’t we see a diversification of niches? Why didn’t species branch off? It appears to me that the process of species sorting, which was favored by Stephen Jay Gould and which Professor Moran also refers to in his 2006 essay on macroevolution, fails to resolve the paleontological puzzles that we find when we examine the fossil record.

In short: if scientists currently lack an understanding of what makes macroevolution stop, then how can they possibly claim to understand what makes it go?

Is there enough time for macroevolution?

No scientist can credibly claim to have a proper understanding of macroevolution unless they can produce at least a back-of-the-envelope calculation showing that it is capable of generating new species, new organs and new body plans, within the time available. So we need to ask: is there enough time for macroevolution?

At this point, I imagine Professor Moran may want to cite a 2010 paper in Proceedings of the U.S. National Academy of Sciences (PNAS), titled “There’s plenty of time for evolution” by Herbert S. Wilf and Warren J. Ewens, a biologist and a mathematician at the University of Pennsylvania. (I say “may” because Wilf and Ewens are Darwinists and Professor Moran is not.) Although their paper does not refer to them by name, there’s little doubt that Wilf and Ewens intended their work to respond to the arguments put forward by intelligent-design proponents, since it declares in its first paragraph:

…One of the main objections that have been raised holds that there has not been enough time for all of the species complexity that we see to have evolved by random mutations. Our purpose here is to analyze this process, and our conclusion is that when one takes account of the role of natural selection in a reasonable way, there has been ample time for the evolution that we observe to have taken place.

Evolutionary biologist Professor Jerry Coyne praised the paper, saying that it provides “one step towards dispelling the idea that Darwinian evolution works too slowly to account for the diversity of life on Earth today.” Famous last words.

Shortly after the publication of Wilf and Ewens’ paper in 2010, Dr. Douglas Axe, director of the BioLogic Institute, Dr. Axe wrote a devastating critique of Wilf and Ewens’ paper in a 2011 post titled, Breaking News from the Academy: There’s Plenty of Time for Evolution! (January 13, 2011). Dr Axe is certainly a qualified scientist in the field: after obtaining a Caltech Ph.D., he held postdoctoral and research scientist positions at the University of Cambridge, the Cambridge Medical Research Council Centre, and the Babraham Institute in Cambridge. He has also written two articles for the Journal of Molecular Biology (see here and here for abstracts). He has also co-authored an article published in the Proceedings of the National Academy of Sciences, an article in Biochemistry and an article published in PLoS ONE. His work has been reviewed in Nature and featured in a number of books, magazines and newspaper articles, including Life’s Solution by Simon Conway Morris, The Edge of Evolution by Michael Behe, and Signature in the Cell by Stephen Meyer.

I’d now like to quote a brief excerpt from Dr. Axe’s critique of Wilf and Ewens’ paper:

…[H]ere we have a new research paper that reads very much like a mathematically embellished version of the simplistic “METHINKS IT IS LIKE A WEASEL” argument put forward twenty-five years ago by Richard Dawkins [2].

In case you missed it the first time around, here’s my two-sentence synopsis. Although it would take eons for unassisted random typing to generate the Shakespearean line METHINKS IT IS LIKE A WEASEL, the task becomes very manageable if something can select the best line from among the many lines of random gibberish, where ‘best’ means most resembling METHINKS IT IS LIKE A WEASEL (however slight that resemblance may be). Couple this with the ability to breed slight variations on what was just selected, and voilá!— a line from Shakespeare materializes right before our eyes.

It’s an old argument with an embarrassingly obvious flaw. Yes, meaningful text can evolve very rapidly if selection has foresight or (equivalently) if miraculously helpful fitness functions can be assumed. But alas, neither of these happy circumstances follows from the impersonal kind of selection that Darwinists are committed to.

Dawkins’ illustration makes this abundantly clear, in spite of his intent. He proposed (in my antique copy of his book, it’s on page 48) that this:


is somehow manifestly more fit than this:


but I can’t imagine why it would be, unless the selector (like Dawkins) knows exactly where he wants to go with it. If he does… well, that’s called intelligent design.

In the end, whether evolution has plenty of time or not depends on what you want to ascribe to it. It copes well with the most favorable adaptations conceivable (those offering substantial benefit after a single nucleotide substitution), but even slightly more complex tasks involving just two or three mutations can easily stump it [3,4]. The key question, then, is this: What, of all life’s marvels, can be accounted for in terms of the single-change adaptations that Darwinism explains? And the answer, if we take Dawkins’ illustration seriously, is: Nothing that approaches the complexity of a six-word sentence.

You don’t need a biology degree to see that this leaves Darwinism in a difficult position. In fact, oddly enough, it seems that biology degrees only make it harder to see.

Finally, a 2012 paper, Time and Information in Evolution, by Winston Ewert, Ann Gauger, William Dembski and Robert Marks II, contains a crushing refutation of Wilf and Ewens’ claim that there’s plenty of time for evolution to occur. The authors of the new paper offer a long list of reasons why Wilf and Ewens’ model of evolution isn’t biologically realistic:

Wilf and Ewens argue in a recent paper that there is plenty of time for evolution to occur. They base this claim on a mathematical model in which beneficial mutations accumulate simultaneously and independently, thus allowing changes that require a large number of mutations to evolve over comparatively short time periods. Because changes evolve independently and in parallel rather than sequentially, their model scales logarithmically rather than exponentially. This approach does not accurately reflect biological evolution, however, for two main reasons. First, within their model are implicit information sources, including the equivalent of a highly informed oracle that prophesies when a mutation is “correct,” thus accelerating the search by the evolutionary process. Natural selection, in contrast, does not have access to information about future benefits of a particular mutation, or where in the global fitness landscape a particular mutation is relative to a particular target. It can only assess mutations based on their current effect on fitness in the local fitness landscape. Thus the presence of this oracle makes their model radically different from a real biological search through fitness space. Wilf and Ewens also make unrealistic biological assumptions that, in effect, simplify the search. They assume no epistasis between beneficial mutations, no linkage between loci, and an unrealistic population size and base mutation rate, thus increasing the pool of beneficial mutations to be searched. They neglect the effects of genetic drift on the probability of fixation and the negative effects of simultaneously accumulating deleterious mutations. Finally, in their model they represent each genetic locus as a single letter. By doing so, they ignore the enormous sequence complexity of actual genetic loci (typically hundreds or thousands of nucleotides long), and vastly oversimplify the search for functional variants. In similar fashion, they assume that each evolutionary “advance” requires a change to just one locus, despite the clear evidence that most biological functions are the product of multiple gene products working together. Ignoring these biological realities infuses considerable active information into their model and eases the model’s evolutionary process.

After reading this devastating refutation of Wilf and Ewens’ 2012 paper, I think it would be fair to conclude that scientists don’t currently have an adequate mathematical model explaining how macroevolution can occur within the time available.

Professor Moran may want to argue that the neutral theory of evolution which he champions is immune to some of the criticisms leveled at Wilf and Ewens’ paper. Fine; but what he really needs to show is that a process of random genetic drift acting on neutral mutations could generate macroevolutionary change within the time required. Where are the calculations?

Details, details

In his post, , Professor Moran disparages Professor James Tour for insisting that biologists supply “chemical details” explaining how macroevolution is possible.

Does he really think that evolutionary biologists are obliged to supply “chemical details” proving that whales evolved from land animals or that humans and chimpanzees share a common ancestor? Are all chemists this stupid?

I wonder if he is equally skeptical about whether the Earth goes around the sun given that we can’t supply chemical details? I wonder what he thinks about plate tectonics?

Given the apparent difficulty of accounting for the appearance of hundreds of chemically unique genes and proteins which have no “parents” in each new species, I think Professor Tour is well within his rights to demand details at the chemical level. How do these new genes get generated? If that’s not a chemical question, then what is?

The comparison with plate tectonics also misses the mark. Granted that we don’t know exactly how continental plates move, what is indisputable is that they do move. What’s more, it only requires a simple pencil-and-paper calculation to show that they could have spread out from the giant supercontinent of Pangaea within a period of 200 million years. Unfortunately, no such calculations are forthcoming from the scientific advocates of macroevolution.


I have listed several grounds for thinking that no scientist today can claim to understand the process know as macroevolution. That being the case, it is grossly unfair of Professor Larry Moran to criticize Professor James Tour for having the honesty to admit that he does not understand it, either.

'That being the case, it is grossly unfair of Professor Larry Moran to criticize Professor James Tour for having the honesty to admit that he does not understand it, either.' Not 'grossly unfair', vjt. Not even, 'unfair'. It would have to rise above the level of imbecility, to warrant designation as 'unfair', in whatever degree. Axel
Joe, I have repeatedly pointed out "the Noah's Ark problem" to Sal. I would not be surprised to find that I was among the first, if not the very first, to raise it here at UD. It's always been one my major objections to Sal's YEC'ism. Sal's response has been to delete my posts. Yet now he wants to adopt it as his own. What a hypocrite. Mung
scordova@5 - Thanks for the great articles! One possible scenario that I've toyed with is that felines once had a high degree of genetic variability---from pussycats to panthers and a smooth continuum of gradations between. As felines adapt to different ecosystems or are challenged by extinction events, the gradations between them disappear, leaving only a few specialized and regional types. The analogy that I picture is like an old hair comb with 90% of the teeth randomly missing. The teeth that are gone are no more ancient than the ones that are left. The spine of the comb is the source for all felines. Just a thought. -Q Querius
Hi dr466, Thank you for your post. In response to your question about miracles: I think we should be careful of imputing to God miracles which are not mentioned in Scripture itself. If a particular interpretation of the Flood narrative in Scripture requires God to have wrought additional miracles, not intrinsically connected with the Flood itself, which are nowhere hinted at in Scripture (e.g. depositing millions of varve layers in the course of less than a year, depositing a layer of iridium in rock sediments worldwide, disposing of an enormous quantity of heat after the Flood, and accelerating the rate of movement of the continents by a factor of 100,000) then it is almost certainly wrong. On the other hand, we are bound by the words of Christ Himself, Who told us that there was a Flood and an Ark. That much, we must take as certain. Regarding the miracle of water turning into wine, St. John presents it as vera historia, and as a sign by which readers might know Who Jesus really was. The story of Jonah, taken by itself, might be interpreted as an allegory, but Jesus referred to it as an historical fact, so it must have been one. Unlike the currently favored YEC interpretation of the Flood narrative, it does not require God to have worked any extraneous miracles. The miracle of the sun standing still in the time of Joshua (and later, Hezekiah), need not have involved the earth ceasing to rotate (an event which we would expect to find archaeological signs of); as Christian apologist Glenn Miller has pointed out, it may have been a local miracle, whereby God refracted the sun's rays in that portion of the globe so that the sun appeared to shine for longer than usual. In any case, I think it is best to avoid being overly dogmatic about one's own interpretation of Scripture. "In essentials, unity; in non-essentials, liberty; in all things, charity." Cheers. vjtorley
VJT, 169,049 and counting, there's life in the old thread yet! KF kairosfocus
I'm curious - having "disproven" Noah's Ark, will we now move on to explaining why, scientifically, Jesus couldn't have changed water to wine? Or how Elijah couldn't really have made the sun stand still? Or how Jonah couldn't really survive 3 days in the belly of a big fish? While I applaud the efforts of people like Woodmorappe to show that it was physically possible to fit enough genetic stock to explain today's variety, Noah's Ark is clearly a miraculous event. After all - how do 8 people collect and keep alive 16,000 animals until the ark is ready? By the time they gathered the last few, the first ones would be long dead. Are we now free to pick and choose which parts of the Noah's Ark story required a God-miracle, and which didn't? Much like the inerrancy of Scripture, Noah's Ark is a matter of faith - either you believe God can do it, or you don't. No amount of science, on either side, is going to change your mind. As for Professor Moran's comments - all he does is interpret the meaning of the word "understand" as "know a bunch of just-so stories of how macroevolution occurred", and then slime Professor Tour for wanting actual details on the exact mechanism and process instead of being satisfied with the wish-upon-a-star storytelling. I'm unimpressed. drc466
Mung, YECs don't deny evolution as evolution is entailed in baraminology. What YECs deny is universal common descent and that natural selection can increase biological information. Off of the Ark organisms would not have had to evolve new body plans that required new body parts. Joe
YECs are closet macro-evolutionists because of the Noah’s Ark problem.
And pointing this out to Sal in any thread he authors here at UD results in his personal censorship. So while he can admit this truth here, and suppress it in his own threads, I have to wonder. One of my objections to the YEC position is that they deny evolution while they yet rely on it. a self contradiction. The light seems to have gone off, finally, in Sal's mind. But the apology to me is still wanting. Mung
VJTorley, As far as YECs being closet macroevolutionists, I found exactly the sort of article written by a Christian Darwinist in my denomination that states the problem better than I. How to squeeze 10,000 bird species onto Noah's Ark. Joking aside, YECs really are in a position of having to find an alternate mechanism of macro evolution. That's why they have modest interest in small-scale front loading. They are interested in the hybridization of Galopagos Finches, and it would be an interesting question if each finch variety evidence Orphans among members. Allen MacNeill is very well read on the topic and he might be able to offer insights. scordova
It’s interesting that you should mention the Ark problem, Sal. That problem had occurred to me
YECs are closet macro-evolutionists because of the Noah's Ark problem. :-) When Dr. Nelson showed all the orphan genes at ICC 2013 in varieties of ants, I could sense a feeling of unease because of the Noah's Ark problem. The guys I talked to quickly saw the problem. Orphan genes are a two-edged sword for YEC, but a single-edge sword for ID.
To me, the idea of equating “kind” with “family” sounds rather radical on Biblical grounds: after all, the Bible speaks of wolves and foxes in quite different ways, without a hint that they are of the same kind. Interestingly, lions and leopards are distinguished too (Isaiah 11:6-9). An old-earth creationist wouldn’t have to worry about the space problem on the Ark anyway, as there would have been no need to fit in all those dinosaurs!
Well said! I most certainly have my personal beliefs, but my motto is "follow the evidence where it leads". For the time being, for everyone, there is no model that is problem free. The evidence is saying to me, "we don't know enough, we have our beliefs, but we see through a glass darkly." scordova
VJT: Yes, tapering, but it looks like the plateau with growth is going to have a significantly higher rate than hitherto. I don't know if that will be some hundreds per week, but that alone will keep it climbing. We can also see an echo effect on the WACs, which are also now having an accelerated upward drift. Indeed, in the past several weeks, moved from 28+ - near 32 K, several hundreds a week. KF kairosfocus
F/N: Re Moran on Tour:
Does he really think that evolutionary biologists are obliged to supply “chemical details” proving that whales evolved from land animals [ a --> Not observed, and particularly by blind watchmaker processes at realistic rates in available time] or that humans and chimpanzees share a common ancestor [ b --> not observed, and not explained on vera causa plausible blind watchmaker mechanisms acting in reasonably available time on credible pop sizes]? Are all chemists this stupid [c --> ad hominem, targetting one of the ten most cited chemists in the world, who is an expert on the synthesis of complex organic molecules]? I wonder if he is equally skeptical about whether the Earth goes around the sun [1 --> directly observed] given that we can’t supply chemical details [2 --> relevant details are gravitational, not chemical, save insofar as atoms have masses linked to nuclear composition, leading to masses of planets, said masses being known, distances observed, acting laws confirmed to have relevant scale since torsion balance measurements in C18]? I wonder what he thinks about plate tectonics [3 --> Directly observed, with rates of plate motion measured and adequate to explain source in original continents across a few 100 My, though with ultimate root forces . . . probably convective and perhaps in part tied to RA decay and heat . . . not fully understood]?
I trust that Dr Moran can see the material differences between a, b, c and 1, 2, 3. In particular the tendency to compare the degree of certainty attaching to blind watchmaker theories of macro-evo and the observation of planetary orbits around the sun is sadly revealing. KF kairosfocus
Hi kairosfocus, Thank you for your posts. The 1980 news clip was accompanied by a footnote which contained a reference to Stephen Jay Gould's essay, "The return of hopeful monsters" at http://www.andrew.cmu.edu/user/jksadegh/A%20Good%20Atheist%20Secularist%20Skeptical%20Book%20Collection/Gould_The_Return_of_Hopeful_Monsters_sec.pdf so I looked it up. It contained a very revealing paragraph:
Indeed, if we do not invoke discontinuous change by small alteration in rates of development, I do not see how most major evolutionary transitions can be accomplished at all. Few systems are more resistant to basic change than the strongly differentiated, highly specified, complex adults of "higher" animal groups. How could we ever convert an adult rhinoceros or a mosquito into something fundamentally different. Yet transitions between major groups have occurred in the history of life.
Dr. Paul Nelson refuted this suggestion in a comment he made over at Why Evolution is True, at http://whyevolutionistrue.wordpress.com/2012/12/11/a-marshall-mcluhan-moment-with-creationist-paul-nelson/#comment-338131 :
Mutations that disrupt body plan formation are inevitably deleterious. (There’s only one class of exceptions; see below.) This is the main signal emerging from over 100 years of mutagenesis in Drosophila. Text from one of my Saddleback slides: 1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows. 2. Thus, to change — that is, to evolve — any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring. 3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo. Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes.
A few pro-Darwin commenters suggested that neutral mutations in the early stages might do the trick. I wish they'd provided a few more examples. The only good one they cited (tweaking the Hoxd13 gene in zebrafish to produce a leg-like structure instead of a fin - see http://www.sciencedaily.com/releases/2012/12/121210124521.htm ) was engineered by scientists, and we don't know whether it would have been beneficial, neutral or deleterious in the wild. By the way, I think the readership of my post on Dr. Tour is finally leveling off. It looks like it'll peak at 168,000. Had to happen sooner or later, I guess... vjtorley
167,766 kairosfocus
in order to properly understand what makes a thing go, you also need to understand what can make it stop.
That is in any sufficient causal factor cluster, there must be a complete set of necessary, on/off enabling factors. (Think, fire triangle or at a more sophisticated level, tetrahedrons.) A key logic of cause point. KF kairosfocus
Hi Sal, I had a look at your articles, which made for some interesting reading. I agree that the research questions you proposed would be excellent ones to follow up, and I'd like to see the results myself - especially for the big cats. In its article on Panthera, Wikipedia states:
Panthera probably evolved in Asia, but the roots of the genus remain unclear. Genetic studies indicate that pantherine cats diverged from the subfamily Felinae between six and ten million years ago. Fossil records point to the emergence of Panthera just 2.0 to 3.8 million years ago.
This article on Science News by Tina Hesman Saey (September 18, 2013) also came up on a Google search (https://www.sciencenews.org/article/tiger-lion-and-domestic-cat-genes-not-so-different ):
All present cat species last shared a common ancestor about 11 million years ago. Usually genomes get scrambled as species evolve, says Jong Bhak, a bioinformatician at the Genome Research Foundation in Suwon, South Korea, who was one of the study leaders. But when the team compared the genome of a 9-year-old Siberian tiger named TaeGeuk to that of domestic cats, the researchers found few big differences. That probably means that cats both big and domestic "are very well adapted, successful evolutionary machines," Bhak says. But many subtler changes set big cats apart from other animals. Big cats share 1,376 genetic changes not found in other animals and people, the researchers discovered. Among those genes are many related to digesting meat – not a surprise, Bhak says, given that cats are obligate carnivores. Genes involved in muscle strength, sense of smell, visual perception and nervous system development are evolving rapidly in Siberian tigers, the team found.
And from a former zookeeper writing under the handle "Leolupus," who has studied animals all his life, here's this comment, in response to a question on Yahoo (How genetically similar are Lions and Tigers?) at http://uk.answers.yahoo.com/question/index?qid=20081129051321AAQ0lh9 :
...Like most hybrids, ligers and tigons are nearly always sterile, because the parent species have different numbers of chromosomes (meaning that the hybrid cannot produce functional sex cells), but occasionally a female will be fertile. However, genetic testing suggests that lions and leopards diverged from each other more recently than any of the other Panthera species - meaning that lions are actually more closely related to leopards than they are to tigers (lions and leopards can also hybridise, producing a leopon). It may surprise you to learn that humans are more closely related to chimpanzees and bonobos than lions and tigers are to each other. Genetically speaking, we should be in the same genus as chimps and bonobos - placing ourselves in a separate genus to all other animals is more to do with human arrogance than genetics.
I wonder if he's right on that one, though: according to Timetree, lions and leopards diverged only 2.9 million years ago, whereas humans and chimps diverged 6.3 million years ago. Finally, here's a recent article from Nature by Yun Sung Cho et al. (Nature Communications 4, Article number: 2433, doi:10.1038/ncomms3433, published 17 September 2013), titled, "The tiger genome and comparative analysis with lion and snow leopard genomes" at http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html , which should be right up your alley:
The Amur tiger genome is the first reference genome sequenced from the Panthera lineage and the second from the Felidae species. For comparative genomic analyses of big cats, we additionally sequenced four other Panthera genomes and tried to predict possible big cats’ molecular adaptations consistent with the obligatory meat eating and muscle strength of the predatory Panthera lineage. The tiger and cat genomes showed unexpectedly similar repeat compositions and high genomic synteny, and these indicated strong genomic conservation in Felidae. These results could be supported by the recency of the 37 species-Felidae radiation (<11 MYA)(15) and well-known hybridizations in captivity among subspecies in Felidae lineage such as liger and tigon. By contrast, the ratio of repeat components for the great apes was considerably different among species, especially between human and orang-utan(28), which diverged about the same time as felines. The breaks in synteny that we observed are likely occasional rare sporadic exchanges that accumulated over this short period (<11 MYA) of evolutionary time. The paucity of exchanges across the mammalian radiations (by contrast to more reshuffled species such as Canidae, Gibbons, Ursidae and New World monkeys) is a hallmark of evolutionary constraints.
Judging from Figure 1b in the article, tigers have certain genes which cats lack, but I couldn't ascertain whether tigers had any genes that lions or leopards lacked, let alone whether they had any orphan genes. From the foregoing quote, it seems that there has been a lot more "intelligent engineering" in the line leading to humans than in the line leading to lions. It's interesting that you should mention the Ark problem, Sal. That problem had occurred to me. Personally I don't know how much of the Noah story I'd take as literal: the only Flood hypothesis I've come across which fits the Biblical time scale is the highly controversial Noah's comet hypothesis, which would place the Flood in 2807 B.C. However, that wouldn't have been a flood that covered the entire globe, but only coastal areas around the globe. In any case, I dug up the following quote from an article by Tas Walker at http://biblicalgeology.net/Answer/How-did-Noah-fit-all-the-animals-on-the-Ark.html :
Woodmorappe in his book 'Noah's Ark: A Feasibility Study' (available on Amazon) calculated that the number of animals would have been less than 16,000, assuming that a biblical kind is roughly equivalent to the group of animals we call a genus today. However, if the biblical kind is equivalent to the family grouping, then there would have only been 2,000 animals. Probably it was somewhere in between... And the size of the Ark? It was huge. It had a capacity of over 500 railroad cattle cars, enough to carry more than 120,000 sheep. So there was plenty of room on the Ark for the animals, for their food and water, and for Noah and his family.
To me, the idea of equating "kind" with "family" sounds rather radical on Biblical grounds: after all, the Bible speaks of wolves and foxes in quite different ways, without a hint that they are of the same kind. Interestingly, lions and leopards are distinguished too (Isaiah 11:6-9). An old-earth creationist wouldn't have to worry about the space problem on the Ark anyway, as there would have been no need to fit in all those dinosaurs! vjtorley
Dr. Torley, Regarding the macro-evolution of orphan genes, after Paul Nelson spoke about Orphan genes at ICC 2013, a few of us had an informal conversation about whether orphan genes can be found in members of a species that can interbreed and hybridize, whether orphan genes are a sufficient marker to actually distinguish a taxonomic class. We basically concluded it is a little too early to tell because we simply do not have enough data. The reason YECs would not want orphan genes to necessarily be a marker of a separate species is that Noah's Ark would be overwhelmed if there are too many species! In an ironic twist, if orphans turn out to be the convention of defining a species, the YECs would be in the unfortunate position of hoping for macroevolution! Here is a simple starting point and open research question: Are there orphans and unique proteins for the panthera genus: Tigers, Leopards, Lions, Cougars, Tigons, Ligers, Panthers, etc. As far as I know, it seems many if not all can still interbreed and hence, it is dubious that we can really say they are not the same "species" Same for: Brussell sprouts, kale, cabbage, broccoli A speculation is if each major races in a species (like lions and tigers in the Panthera genus) have orphans but can still interbreed, one can hypothesize the founding ancestor had all of the orphans and then subsequent generations lost or modified them. The problem is it is too early to tell. The general view is it is easier to lose an orphan than gain a novel one as Ann Gauger suggested. I wrote two short essays on related topics. Regarding the Panthera Genus and Brocolli: De-origination of species Regarding Orphan Genes (aka macro evolution of orphan genes and regulatory elements): New Mechanism of Evolution - POOF scordova
Larry Moran is one of those who preach "We know it happened and we just have to figure out how. But no one really cares how because we know it happened." Earth to Moran- Gould isn't any help as he didn't know anything about the mechanism of macroevolution. Only developmental biology can help you with macroevolution and it ain't cooperating. Joe
166,753, picking back up the pace . . . kairosfocus
F/N: I think the thread of discussion here on is also relevant to this thread and should be linked. KF kairosfocus
VJT, first, we are now at 166,727+, a breakout. Second, it is time for a still smoking gun, the 1980 NYT article (which BTW was praised by Gould as being fair, informed and accurate). I therefore invite inspection of the Sewell clip, as is marked up here. After this is on the table, we can then see that for a generation, the top level of the relevant fields have had to acknowledge the force of the cluster of issues put on the table by Gould, Eldredge et al. Issues that through the rise of ID are pointing in a far more radical direction than they envisioned. It is time to face sobering facts and drop the dismissive rhetorical tactics. KF kairosfocus

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