Evograd Blog Debunks YE Creationist Genetics Claims in Depth

The Internet debate between those who affirm and those who deny the evidence for evolution and an old earth usually takes place on the scale of fairly short articles which are accessible to the average reader. Some supposed evidences for a young earth, such as the changing magnetic field of the earth, or the amount of helium in the atmosphere, can be readily disposed of in just a few pages.

On the other hand, there are topics where the scientific issues are more complex and subtle. In such cases, it seems useful to present a comprehensive examination of all the main points in one write-up. For instance, one of the top 10 evidences for a young earth claimed by Answers in Genesis is the observation of soft tissue in some dinosaur fossil bones. To the layman, this seems to indicate that that these bones cannot be tens of millions of years old as mainstream science says. Rather than trying to address just a few of the scientific issues with soft tissue in a piecemeal manner, I decided to write a fairly long essay which discussed all of the key scientific findings up to that point. This enabled the efficiently addressing of all the substantive young earth claims associated with this topic, and provided a single reference to which readers could be directed.

Every few years some seemingly well-credentialed Young Earth (YE) creationist publishes a new book which is touted as the final demolition of evolution. The sweeping claims in such a book are then regarded as established facts by the consumers of YE creationist literature. It seems helpful in such cases to systematically work through such a book, and compare what the author claims to what the full data actually show. This sort of fair and thorough rebuttal will typically make no impression on dedicated YE creationists (since they rigorously filter everything through their particular interpretation of the Bible), but it can prove enlightening to someone who is on the fence, trying to sort out what the truth really is.

For instance, when John Sanford’s book, Genetic Entropy, was first published in 2005 it was hailed as the definitive proof that modern evolutionary theory is a complete failure. The central claim of that work is that all genomes are (and have been since The Fall) relentlessly deteriorating due to the buildup of unselectable harmful mutations. Jubilant YE creationists widely referred to that book to bolster their beliefs. The author was a respected retired botanist from Cornell. In my own case, a fellow evangelical Christian handed me a copy of that book in 2008, assuming that it would bring me over to the anti-evolution camp. At that point I had not made up my mind about the scientific case for or against evolution, and Genetic Entropy seemed convincing at first reading. Being a professional researcher, I wanted to read some in-depth critical review of the book, and then balance the pros and cons in my own mind.

However, I could not find a thorough critical review. In the end, I wrote my own chapter by chapter review of Genetic Entropy, as a means of clarifying issues for myself and to respond to my well-meaning YE creationist friend. The net result for me personally was to conclude that the evidences presented against evolution were complete failures, if all the facts (not some cherry-picked subset) are laid on the table. (It happens that writing that review of Genetic Entropy  was what launched me into blogging on faith and science – – since no other thorough scientific review of this controversial book seemed to be available, I decided to implement a WordPress blog to put it, and some other material I had drafted, out on the internet for the benefit of others.)

All of this goes to show why I am highlighting here the Evograd blog. The proprietor of this blog, a graduate student in evolutionary biology who prefers to remain anonymous, has produced a relatively few but very weighty studies which treat timely, highly technical subjects. I don’t think his work is as well known as it should be, considering how it directly and thoroughly confronts some key YE creationist claims.

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I first became aware of this blog when looking for commentary on Replacing Darwin, by Answers in Genesis’s Nathaniel Jeanson. This book appears to be the latest, greatest “demolition of evolution” touted by YE creationists. Jeanson has a PhD from Harvard, which is supposed to lend credibility to his work.

The only in-depth critique of this book I was able to find was by Evograd. He systematically exposes Jeanson’s erroneous assumptions and faulty logic. The first seven out of planned ten posts on the blog have been completed. (Evograd’s fans are waiting for the last three installments to appear, but more pressing matters have taken up his time). Replacing Darwin is a long, sprawling, and dense treatise, and so Evograd’s responses are likewise lengthy, diverse, and detailed. I’ll mention a few points here, but won’t try to summarize all the issues.

Part 6: Jeanson’s Fulcrum Fails” treats chapter 7 of Replacing Darwin. In that chapter Jeanson claimed that the actual, observed amount of mitochondrial mutational differences between various species is much, much lower than predicted by standard evolutionary timescales – – and therefore, the biosphere (and indeed the earth) must be much, much younger than posited by mainstream science. But…the Evograd blogger notes that Jeanson used a mutation rate for mitochondria that is about ten times too high, and also did not take into account the elementary math of how the apparent rate of substitutions will tend to slow down for more ancient lineages even if the actual rate is/was constant. These errors (and others) led Jeanson to grossly overestimate the mitochondrial mutations entailed by “standard” evolutionary theory. When those errors are corrected, the data are in fact consistent with evolution.

The seventh and latest installment, “Part 7: A Nuclear Catastrophe“ has links to all the previous posts in the series on Replacing Darwin. In this technically dense post which cites a wide range of relevant literature results, Evograd debunks a number of Jeanson’s claims concerning DNA in the cell nucleus.

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Tomkins on the Human Vitellogenin Pseudogene: Who Needs Signal When You Have Noise? – – Reptiles and birds produce eggs with substantial yolks. The yolk nourishes the embryo as it grows and matures in the egg, prior to hatching. The vitellogenin gene is involved in producing the yolk. That is its function in birds and reptiles, as can be clearly demonstrated. (In some species, this gene has been duplicated, so there is more than one copy of it in the genome, but the function is the same). In modern placental mammals like humans, there is no need for the function of the vitellogenin gene. Human embryos get their nourishment from the placenta, not from an egg yolk, so they have no need of the protein product of the vitellogenin gene. Thus, over the tens of millions of years since the emergence of modern placental mammals, most of this gene has mutated away. However, some mutated, nonfunctional fragments of the vitellogenin gene still appear in the human genome, in a location corresponding to the locus of the functional gene in chickens. Standard evolutionary science holds that mammals descended from egg-laying common ancestors with reptiles, and so finding these deactivated “pseudogene” fragments in this location is a confirmation of evolution. [1]

In response to this evidence for common ancestry, a YE creationist scientist, Jeffrey Tomkins, published an article in an Answers in Genesis journal, claiming that one of these gene fragments is in fact functional. Tomkins identifies it as a key part of a gene that affects neurological processes in the human brain. This claim has been cited as fact by YE creationists all across the internet, and used to deflect the evolutionary evidence of the vitellogenin gene. Enter Evograd: in this article linked above, he eviscerates Tomkins’ contention of functionality, showing that each of Tomkins’ seven lines of argument is utterly worthless. This is another virtuoso performance by the Evograd blogger, showing a keen grasp of subtle technical points and wide command of the relevant literature, combined with clear writing style and ability to focus on the most important issues.

More Evograd articles on the evolutionary significance of pseudogenes:

Dating Shared Processed Pseudogenes in Primates

Pseudogenes Testify to the Evolutionary History of Animals

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Articles dealing with human chromosome number 2.

This chromosome 2seems to represent a fusion of what in all other higher primates are two separate chromosomes (typically called 2A and 2B). In the human chromosome, the actual point of the fusion of the two original chromosomes can be discerned, pointing to common ancestry between humans and other primates.

Chromosome 2 Fusion and Bayes Theorem: Support for Common Ancestry After All

Chromosome 2 Fusion and Bayes Theorem: Addendum

[and also, in   Part 7: A Nuclear Catastrophe , Evograd demolishes Tomkins’ claim (retailed by Jeanson) that a functional gene spans the fusion site in Chromosome 2]

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Some other excellent reads on the Evograd blog:

Testing a Strong Prediction of Universal Common Ancestry

Human Genetics Confirms Mutations as the Drivers of Diversity and Evolution

 

Endnote

[1] A “pseudogene” is a recognizable DNA sequence derived from some functional gene, but which no longer expresses the original protein. For instance, humans have many nonfunctional genes (i.e. pseudogenes), which in other animals are functional genes involved for odor recognition. (Presumably as humans developed higher visual acuity, they became less dependent on sense of smell, and so natural selection was relaxed for retaining these olfactory genes). These pseudogenes, both the coding DNA and related regulatory regions, were originally fully functional (prior to accumulating disabling mutations), so it is not surprising to find that some bits of some pseudogenes have become used in the regulation of some other, still-functional genes in the genome. Opponents of evolution cite these discoveries of functionality as though they overturn the status of pseudogenes as pseudogenes, but that is misleading nonsense.

Per Wikipedia on the definition of pseudogenes:

Pseudogenes are segments of DNA that are related to real genes. Pseudogenes have lost at least some functionality, relative to the complete gene, in cellular gene expression or protein-coding ability. Pseudogenes often result from the accumulation of multiple mutations within a gene whose product is not required for the survival of the organism, but can also be caused by genomic copy number variation (CNV) where segments of 1+ kb are duplicated or deleted.[4] Although not fully functional, pseudogenes may be functional, similar to other kinds of noncoding DNA, which can perform regulatory functions. The “pseudo” in “pseudogene” implies a variation in sequence relative to the parent coding gene, but does not necessarily indicate pseudo-function. Despite being non-coding, many pseudogenes have important roles in normal physiology and abnormal pathology… Pseudogenes are usually characterized by a combination of homology to a known gene and loss of some functionality. That is, although every pseudogene has a DNA sequence that is similar to some functional gene, they are usually unable to produce functional final protein products.

[Housekeeping note: in deference to the primacy of his work, if a reader here is unhappy with some of the technical conclusions of the Evograd blogger cited above, please leave your comments on his blog, not mine]

About Scott Buchanan

Ph D chemical engineer, interested in intersection of science with my evangelical Christian faith. This intersection includes creation(ism) and miracles. I also write on random topics of interest, such as economics, theology, folding scooters, and composting toilets, at www.letterstocreationistists.wordpress.com . Background: B.A. in Near Eastern Studies, a year at seminary and a year working as a plumber and a lab technician. Then a B.S.E. and a Ph.D. in chemical engineering. Since then, conducted research in an industrial laboratory. Published a number of papers on heterogeneous catalysis, and an inventor on over 100 U.S. patents in diverse technical areas. Now retired and repurposed as a grandparent.
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10 Responses to Evograd Blog Debunks YE Creationist Genetics Claims in Depth

  1. Nitpicking: “Standard evolutionary science holds that mammals descended from reptiles”; not really, unless we expand the definition of “reptile” backwards to include the last common ancestor of reptiles (as generally understood) and mammals. But replace “retiles” with “egg-layihg ancestors”, and the argument survives intact

  2. jimvogan@juno.com says:

    Thanks for the introduction and link to Evograd. It was amazing how much work the author did to analyze the Tompkins paper. There should be some kind of scientific-public-service award for such efforts.

  3. evograd says:

    Thanks for the shoutout and very high praise! I noticed a significant boost to my blog’s traffic since you posted this. I’m really glad to see that my writing is appreciated, it makes all the effort I put into them worth it.
    I wish I could blog more often, but I’m determined not to let the quality slip so I will only write when I have the time and headspace to knuckle down to it. The long-form technical articles usually take months to write in my spare time, and it’s hard to find that spare time (a PhD programme is a lot of work, who’d a thunk it?). I may even take a little break from creationism in my next post and write about something a bit closer to my actual field of research. I know people want to see me finish the review of Jeanson’s book though, I haven’t forgotten about it!

  4. Jeff B says:

    “in Part 7: A Nuclear Catastrophe , Evograd demolishes Tomkins’ claim”.
    I’ve read through that article. I see no ‘demolishing’ going on.

    I can’t count how many times I’ve heard statements like “Behe has been ‘shredded'” or the likes, only to do the research and find that that is not the case.

    So here’s another one to add to the growing list of “pseudo-demoloshings”

    I’d say the future is bleak for the HC2 argument.

    • Jeff, I concluded my article with :
      ” Housekeeping note: in deference to the primacy of his work, if a reader here is unhappy with some of the technical conclusions of the Evograd blogger cited above, please leave your comments on his blog, not mine ”
      …. precisely to forestall such vague and useless comments such as you just left.

      If you have a genuine, specific technical objection to anything that Evograd wrote in his article, man up and go leave a comment on HIS site and see if he can handle it. I’ll be watching.

  5. Jeff B says:

    Scott,
    I actually have a sincere question. I’m putting together a creation talk for our church (and an article for a blog I’m going to create).

    I have one topic I’d like to make sure I research a bit before talking about it. I’d like to know the best examples of beneficial mutations, particularly ones that would be consider ‘upward evolution’, or good information adding mutations.

    Or, can you point me to a good person to ask?
    -Jeff

    • Jeff,
      I have not kept up with the latest here. A few thoughts:
      The fossil record indicates that evolution is, in general, a very slow process. Thus, it is not reasonable to expect to see new whole new genes appearing within the span of modern human observation. We do, however, sometimes observe cases where complex (i.e. multi-step) mutations to existing genes and regulatory elements gave rise to new functionalities.

      My 2017 article describes four such cases:
      https://letterstocreationists.wordpress.com/2017/11/04/evolution-before-our-eyes-complex-mutations-in-microbes-giving-new-functions/
      As noted in the article, these observed changes are relatively modest. They don’t meet the demand to see a crocodile turn into a duck before our eyes. But as noted already, that is simply not a realistic demand, given the slowness of evolution. That would be like disbelieving in plate tectonics because scientists cannot show you a solid continent suddenly ripping apart to form a new wide ocean all within the span of your lifetime. That is just not how these things work.

      The theory of evolution posits that many, many small changes in genomes, each one producing a viable organism along the way, end up producing large changes in phenomes. And when we look into the fossil record, allowing for its inherent incompleteness, that is exactly what we do find. We do not find animal life jumping from trilobites to rabbits. Rather, there appear first simple fishes with no jaws (basically swimming worms with simple spinal cord), then fish with jaws, then amphibian-like fish, then fish-like amphibians, then modern type amphibians, then reptiles, then mammals…. (see https://letterstocreationists.wordpress.com/2014/04/02/realistic-expectations-for-transitional-fossils/ ).

      In some cases, we can infer from the genomes of similar, seemingly related creatures some of the genetic sequences which allowed a new feature to appear over the past few million years. The article references, for instance, the Antarctic notothenoid fishes which have an unusual “antifreeze” glycoprotein (AFGP) which inhibits the formation of ice crystals in their bodies in the sub-freezing (-1.9 C) Antarctic waters. The AFGP is a polymer of a Thr-Ala-Ala glycopeptide monomer. It appears that in an ancestral copy of a trypsinogen protease gene the Thr-Ala-Ala region was expanded through multiple internal duplications. The exons coding for the protease sequences were lost, to yield the present form of the AFGP gene. If you reject macro evolution out of hand for religious reasons, you will not accept this sort of historical inference. But it does show that a sequence of small mutational steps, each plausible and of a type that is known to occur, could give as an end result a significantly altered genomic section with new, beneficial function.
      These are the sorts of evidences that convince practically everyone who does not have a prior religious commitment against evolution that indeed small mutational steps can accumulate over vast periods of time to result in large changes in body type. Behe claimed to have identified limits to evolution, but failed. Some of the examples in my 2017 article explicit disprove his thesis. And see https://letterstocreationists.wordpress.com/stan-4/ on some of his fundamental conceptual errors.

      Here is an article from 2009, where I note a few instances of observed beneficial mutations involving gene duplications, including one with yeast where some of the new genes were not identical to the original genes – – thus several novel genes were added to the genome, with beneficial effects to the organism. I also put some numbers around the pace of evolution.
      https://letterstocreationists.wordpress.com/stan-3-3/

      By straightforward measures of information, which most scientists would accept, a simple gene duplication is a mutation that adds information. The genome is like a recipe or other set of instructions for making something. It should not be treated like a novel or newspaper article. This is especially important in evaluating the impact of gene duplication, as discussed in my 2009 article above. And even more so, if other mutations are combined with gene duplication. So the creationists’ observation that “two copies of a newspaper article yield no new information” is probably true, but irrelevant. With a recipe, duplicating a step leads to a different product, and especially if you then alter one of the duplicated instructions. It seems self-evident that altering a recipe section from “Add one teaspoon sugar” to “Add one teaspoon sugar; add one teaspoon cinnamon” has increased the information content of the recipe, and makes for a materially different product.

      As described in the 2017 article, in Lenski’s long term E coli experiment, a gene was duplicated and in its new position came under the control of a different promoter than the original gene, which gave it a different functionality than originally. Then to give the bacterium its full capacity to metabolize citrate, there was a second mutation, to the dctA gene, enabling the reuptake of C4-dicarboxylates. So here we have the original gene still in place and functioning, and now an additional gene/promoter combination with a modified functionality (fully enabled by that second mutation). The result was that the organism acquired a new capability, to vigorously feed on citrate under oxidizing conditions. *Added* genetic material with modified function giving *new* capability= an obvious increase in genetic information.
      But opponents of evolution won’t accept that, so they devise their own special in-house measures for increasing information which carefully exclude nearly all actual observed mutations. Real, practicing scientists are not fooled by this sort of maneuver [see discussion in Endnotes to my 2017 article, e.g. on “moving the goalposts”]. However, this rhetorical maneuver allows anti-evolutionists, within the evangelical ghetto, to claim victory among their own people. And I don’t have the patience to argue this with folks who basically don’t want to accept evolution, even if they claim to be open-minded about it.
      Peace.

      P.S. If you cared to Google (I use DuckDuckGo, less snoopy), you can find more on this. Two random hits I found in first 30 seconds:
      ( A ) TalkOrigins used to be a cutting edge site for creation/evolution debate, but has not be updated much since about 2005. There is a link http://www.talkorigins.org/indexcc/CB/CB102.html which addressed the claim that “Mutations are random noise; they do not add information. Evolution cannot cause an increase in information.”
      Part of the response, which is similar to what I wrote, is:
      “It is hard to understand how anyone could make this claim, since anything mutations can do, mutations can undo. Some mutations add information to a genome; some subtract it. Creationists get by with this claim only by leaving the term “information” undefined, impossibly vague, or constantly shifting. By any reasonable definition, increases in information have been observed to evolve. We have observed the evolution of
      • increased genetic variety in a population (Lenski 1995; Lenski et al. 1991)
      • increased genetic material (Alves et al. 2001; Brown et al. 1998; Hughes and Friedman 2003; Lynch and Conery 2000; Ohta 2003)
      • novel genetic material (Knox et al. 1996; Park et al. 1996)
      • novel genetically-regulated abilities (Prijambada et al. 1995)

      If these do not qualify as information, then nothing about information is relevant to evolution in the first place.”
      ( B ) https://www.newscientist.com/article/dn13673-evolution-myths-mutations-can-only-destroy-information/
      “ The duplication of genes or even entire genomes is turning out to be ubiquitous. Without a duplication of the entire genome in the ancestor of modern-day brewer’s yeast, for instance, there would be no wine or beer. It is becoming clear that every one of us has extra copies of some genes, a phenomenon called copy number variation.

      The evolution of more complex body plans appears to have been at least partly a result of repeated duplications of the Hox genes that play a fundamental role in embryonic development. Biologists are slowly working out how successive mutations turned a pair of protoHox genes in the simple ancestors of jellyfish and anemones into the 39 Hox genes of more complex mammals.
      Can mutation really lead to the evolution of new species?
      Yes. Several species of abalone shellfish have evolved due to mutations in the protein “key” on the surface of sperm that binds to a “lock” on the surface of eggs. This might appear impossible, but it turns out that some eggs are prepared to be penetrated by deviant sperm. The same thing can happen in fruit flies, and likely in many other groups too. In yeasts, the mutations that led to some new species forming have not only been identified, they have even been reversed.

      The list of examples could go on and on, but consider this. Most mutations can be reversed by subsequent mutations – a DNA base can be turned from an A to a G and then back to an A again, for instance. In fact, reverse mutation or “reversion” is common. For any mutation that results in a loss of information, logically, the reverse mutation must result in its gain. So the claim that mutations destroy information but cannot create it not only defies the evidence, it also defies logic.”
      — – – — – – – – – – – – – – – – – – – – –
      There are more references, but I will just include two more. Note that both of these again note that by normal definitions of information, mutations can and do add information:

      ( C ) https://www.quora.com/Have-random-mutations-that-add-information-to-the-DNA-been-observed?share=1

      ( D ) https://thelogicofscience.com/2016/10/31/debunking-the-creationist-myth-that-mutations-dont-produce-new-and-useful-information/
      “ …. Thus, by simply rearranging the existing bases, we created new information which produced a different amino acid. In other words, we added genetic variation to the population, because the individuals who receive that mutation will produce Serine, while the result of the population is producing Leucine. Objecting to that by claiming that “no new information has been created” is really quite silly because the fact remains that individuals with that mutation are producing a different amino acid than everyone else. Something that codes for the production of an entirely different amino acid is, by any reasonable definition, “new information” (i.e., it is information that was not there before).
      A useful analogy to help you conceptualize this is to think about letters in the alphabet. The English language has 26 letters (bases), and we combine those letters to from words (amino acids). We then arrange those words into sentences (proteins), and we arrange those sentences into paragraphs (tissues). Ultimately, we can use those paragraphs to make books, essays, etc. (organisms). Now, according to creationists’ reasoning, it should be impossible to make any new information by simply rearranging those 26 letters, but that is clearly absurd. We can arrange them one way and produce the works of Shakespeare. We can arrange them another way and produce “The Origin of the Species.” We can rearrange them yet again and produce the script to a Stargate episode. Indeed, there are a virtually infinite set of possibilities, each of which contains different information, and the situation is no different for DNA. We can arrange the bases one way and get a dinosaur, and we can rearrange that code (via mutations) and get a chicken. We can rearrange it yet again and get a whale, human, tree, bacteria, mushroom, etc. This notion that making new arrangements of the four existing bases doesn’t produce new information is absurd because everyone agrees that different arrangements of those bases produce very different organisms.
      A big part of the problem here once again comes back to the definition of the word “new.” Creationists seem to think that evolution requires something that is completely and totally novel, such as a new base pair or, at the very least, an entirely new amino acid that has never existed anywhere before, but that is a straw man fallacy. Evolution does not require something that has never previously existed anywhere. Rather, it simply needs to have variation. Thus, any change to the genetic code is “new information” in an evolutionary sense, because it provides variation. A useful way to think about this is that evolution doesn’t need “new” information. Rather, it needs “different” information. In other words, all that it needs is a code that is different than the one that was there before. ”

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