Response to John Sanford’s Defense of Genetic Entropy, March 2013

BACKGROUND

Back in 2008-2009, a friend gave me a copy of John Sanford’s book, Genetic Entropy. He told me that it thoroughly disproved evolution, and urged me to read it, and use my scientific training to advance the Young Earth (YE) creationist cause. So I did read it. At first, I was impressed. There were diagrams and references and well-written arguments claiming that genomes are inevitably deteriorating: beneficial mutations are too weak and natural selection is not effective enough to counter the steady influx of deleterious mutations. Also, Dr. Sanford’s personal story is compelling. Like me, he has found personal wholeness in giving his life over to the lordship of Jesus Christ. His practical accomplishments in plant breeding and co-inventing the “gene gun” command the highest scientific respect.

There is reason to believe (see e.g. here), however, that the earth and its biota have been around for many millions of years, which is hard to square with genetic deterioration. So I did some independent reading on the topics raised in Genetic Entropy. What I found was that this book on important occasions misrepresented matters in order to promote its thesis.

As one example of what troubled me in Genetic Entropy, here is what it initially says about the concept of “synergistic epistasis” (a phenomenon which is believed to more-efficiently weed out deleterious mutations):

It is a sophisticated-sounding expression, signifying nothing. It has all the appearance of a deliberate obfuscation. Literally translated, synergistic epistasis means “interactive interaction”.

Here Dr. Sanford characterizes synergistic epistasis as a completely meaningless concept, trying to belittle it. But that is a knowing falsehood, since he shows elsewhere in the book that he knows perfectly well that synergistic epistasis is a well-established, meaningful concept.

I wrote up my findings in a letter to my friend. This turned out to be a pretty long letter, as it also contained a critique of Michael Behe’s The Edge of Evolution, and over 100 references. I realized it came out being rather critical of Genetic Entropy, so I decided to run it past Dr. Sanford to give him a chance to refute any of its assertions.

CORRESPONDENCE WITH DR. SANFORD 2010-2012

I therefore sent him a copy in January, 2010, and we corresponded back and forth a couple of times between then and June, 2010. Dr. Sanford sent me preprints of a couple of papers on simulating population genetics.

Although I gave him ample opportunity, Dr. Sanford did not address the specific assertions in my letter about his book. Nearly all of his correspondence was occupied with defending his motivations and questioning mine. Finally, about nine months after I had initially sent him the manuscript for his review, I published it on my blog, as https://letterstocreationists.wordpress.com/stan-4/, or “STAN-4” for short.

In late 2012, Dr. Sanford kindly sent me prints of two more papers in late 2012, and defended his treatment of Kimura’s graph (see below). His papers are interesting and deserve discussion. Even if his models produce results that do not correspond to reality, that very fact can promote additional insights into population genetics.

Dr. SANFORD RESPONDS PUBLICALLY: MARCH, 2013

In early March, Dr. Sanford posted a critique of my STAN-4 letter here, http://creation.com/genetic-entropy . I was interested to see if he had, since 2010, been able to more fully engage with the evidence that I had presented. He came up with ten points that he felt summarized my letter, and addressed them in reverse order, from 10 down to 1.

Getting into long, detailed internet debates is typically fruitless, so I will not try to address everything he writes. But let’s have a look. I’ll mainly put Dr. Sanford’s words in italics to distinguish them.

10. What other geneticists say: … Let me begin by going to the very end of my book (Appendix 1), where I quote key papers written by the leading experts within the field of population genetics. Scott refers to this as my “final shotgun-blast of misrepresentation to the gullible reader”…. Is man presently degenerating genetically? It would seem so, according the papers by Muller, Neal, Kondrashov, Nachman/Crowell, Walker/Keightley, Crow, Lynch et al., Howell, Loewe and also myself (in press). Scott suggests this is foolishness and dismisses the Crow paper (1–2% fitness decline per generation)… The most definitive findings were published in 2010 in the Proceedings of the National Academy of Science by Lynch. That paper indicates human fitness is declining at 3–5% per generation… Can Scott find any qualified geneticist who asserts man is NOT now degenerating genetically? There is really no debate on current human genetic degeneration—Scott is 100% wrong here, and is simply not well informed.

Response:

Many experiments show that when one shuts down the normal operation of natural selection (which depends on differential mortality, or at least differential reproductive success), the fitness of the population declines. This is seen in fruit flies , yeast, etc., where instead of letting them have lots of offspring of which only some survive and reproduce, the researcher arbitrarily (as best she or he can) picks say one breeding pair or one yeast bud to continue each generation. This is called a mutation accumulation experiment, since there is little chance for deleterious mutations (apart from lethals) to be purged, or for compensating or beneficial mutations to be rewarded.

The global empirical observation is that with a largish population and differential reproductive success, fitness holds up just fine, but if you shut down normal selection, fitness and genomes deteriorate. The fact that genomes deteriorate in a mutation accumulation experiment does not support the notion that genomes deteriorate in a natural situation.

I did not and do not dispute that James Crow and other scholars have expressed the belief that human genomes are deteriorating, but that pertains to MODERN TIMES ONLY. They state clearly that the reason they believe the human genome is deteriorating is that the world, especially the more industrialized segment, is now running something like a mutation accumulation experiment, with few children per family, and with these children kept alive by medical interventions, and with new chemical mutagens around. They do not believe that human genomes were deteriorating before now. Thus, this in no way supports Dr. Sanford’s key claim that all genomes are deteriorating all the time. James Crow has gone on record to clarify that “My comments had to do with only the recent past (a few thousand years).”

As I noted in STAN-4, in his first reference to Crow (p. 45), Dr. Sanford acknowledges that Crow bases his concern on recent relaxed natural selection. However, that crucial factor is omitted in his subsequent references to Crow, which gives the impression that Crow agrees with Sanford that mutation accumulation is a general problem for the human race. Over a hundred pages later, in pp. 171-172, Dr. Sanford selects a whole page’s worth of quotes from Crow, focusing on the most alarming sentences. Dr. Sanford’s commentary is that Crow’s speculations amount to “an amazing confession about the reality of genomic degeneration.” This implies that Crow’s work in some way supports Sanford’s contention that the human genome is inevitably declining, with or without natural selection in operation. That is grossly misleading, but as of March, 2013, Dr. Sanford still does not admit that.

The same goes for most of the other references cited by Dr. Sanford where he cites all sorts of dire quotes about genomic deterioration. Either they, like Crow, are simply noting that if you turn off natural selection in humans you get mutation accumulation, or they are observing that whatever simplistic genetics model they are working with did not match reality (i.e. the models showed uncontrollable buildup of deleterious mutations). Dr. Sanford’s mistake is to believe the model instead of observed reality. The proper response for a physical scientist is to fix his model.

That is probably the most important technical issue here. Dr. Sanford’s key claim is that small deleterious mutations are ever-building, and cannot be compensated for, and that must result in ever-decreasing fitness. The problem is that on any time scale we use, this prediction is at odds with observations, for most large populations where normal natural selection is operating. There may be exceptions, but the general rule is that populations are able to cope perfectly well with minor deleterious mutations, whether or not we understand exactly how.

The models he is working with simply do not represent reality accurately. I do not know exactly where the model assumptions are lacking — that is what genetics researchers are paid to do. Evolutionary/molecular biology is enormously rich and multi-layered, and every decade brings forth major new insights.

Most recently, Dr. Sanford calls on a paper by Michael Lynch:

The most definitive findings were published in 2010 in the Proceedings of the National Academy of Science by Lynch. That paper indicates human fitness is declining at 3–5% per generation.

Does this support the notion that genomes generally deteriorate? Not at all. As with Crow and the others, Lynch’s concern is based on the unnaturally low differential mortality in modern society which largely shuts down natural selection compared to pre-industrial man. Lynch writes,



“the mean phenotypes of the residents of industrialized nations are likely to be rather different in just two or three centuries, with significant incapacitation at the morphological, physiological, and neurobiological levels. Ironically, the genetic future of mankind may reside predominantly in the gene pools of the least industrialized segments of society.”

To wrap up this section, here is what a fair treatment of these alarming quotes might look like. I offer this for a revised version of Genetic Entropy:

“ It is well established by mutation accumulation experiments that drastically reducing differential mortality or reproductive success usually leads to a decline in fitness. A number of prominent geneticists, such as Muller, Crow and Lynch have noted the decline in birth rates and infant mortality in industrial society. They suggest that because natural selection is not being allowed to operate as it once did, this situation is analogous to a mutation accumulation experiment and therefore they expect a decline in fitness in humans in modern societies. They have no firm evidence that this is in fact occurring, but it is a reasonable conjecture. They do not believe that humans in more traditional societies, with high birth rates and high child mortality, are experiencing declines in fitness.”

7. Human life span has recently been increasing:

It is obviously true that human longevity has increased in recent centuries, but that is not due to evolutionary advance. It is clearly due to improved diet, sanitation, and modern medicine. We have figured out how to keep people from dying in infancy and extended the life expectancy for those who catch many diseases associated with middle-age. Thus, the average has gone up. The maximum possible lifespan has not gone up. This is a simple concept.

Here is what I wrote in STAN-4:

“ Average human life spans at birth are estimated as 20-30 years for classical Greece and Rome and for medieval Britain, compared to 30-40 years in the early twentieth century and about 65 years now. This measure includes childhood death. Environmental factors such as increases in nutrition and medicine over the last two hundred years likely explain the increase in the past three centuries, but the relatively steady values before 1700-1800 A.D. indicate the human race has not been deteriorating.

Although average life spans have increased, maximum life spans have remained about 105−122 calendar years throughout recorded history. In Old Testament times, 70-80 years was considered a ripe old age (Psalm 90:100). This hasn’t changed a lot since then. All this contradicts Sanford’s assertion that the human genome is deteriorating. “

So here Dr. Sanford is repeating the inconsequential part of what I wrote, namely that environmental factors can explain the increase in average life spans in the past for centuries.

The important part as far as evaluating the genetic entropy thesis is that, as best we can tell, average life spans were about the same in classical Greece and Rome (say 400-100 B.C. for classical Greece) and for medieval Britain ( say 500-1400 A.D.), and that maximum life spans have not varied appreciably for the last 3000 years. All this contradicts Sanford’s assertion that the human genome is deteriorating.

6. Genetic entropy is not obvious in lab experiments or in nature: It is true that most lab experiments do not show clear degeneration.

It is good to see Dr. Sanford acknowledging that. Since it is an important generalization in this controversy, it is surprising that this was not clearly stated in Genetic Entropy. And beyond lab experiments over the last century or two, we have descriptions of plants and animals by Greek and other ancient naturalists that do not indicate that these organisms were much more fit 2000-3000 years ago. So widespread genetic entropy has not been evident over the past 2000+ years.

But Scott should realize that anything alive today must have been degenerating slowly enough to still be here, even in a young earth scenario. All three of the downward decay curves I show in my book indicate that degeneration slows dramatically as it becomes more advanced.

The claim here is that genomes are relentlessly deteriorating, but we cannot detect it.

I’m sure that genetics simulation programs can be adjusted to show that the fitness of all sorts of organisms, from bacteria to elephants, starting from some idealized mutation-free state, could fall dramatically from 4000 B.C to say around 500 B.C., then almost level out. I do not find that compelling support for genetic entropy.

The fossil record clearly shows that fish have been around in more or less the same form for some 400 million years, and reptiles for over 200 million years, showing that genomes are not uniformly deteriorating. The thesis that genomes are relentlessly deteriorating at some meaningful rate can only be sustained under the assumption of a young earth. That should be clearly stated.

5. Duplications have biological effects:

This is obviously true, but how is it relevant? Like the accidental duplications that happen in emails and student essays, duplications are almost universally deleterious. Very rarely, some are beneficial. A few rare beneficial duplications cannot offset the many accumulating deleterious duplications, let alone all the other accumulating mutations.

How is it relevant? The key significance of gene duplications is not that they are more or less effective at warding off deleterious mutations, but, as I pointed out, that they furnish a plausible pathway for increasing the size of the genome and allowing the formation of new genes. (Dr. Sanford does not agree, but as I noted, his arguments against the potential for gene duplication are flawed.)

4. Mutation accumulation experiments suggest extremely high rates of beneficial mutations:

Mutation accumulation experiments are a very poor way to understand deleterious mutation accumulation. Such experiments do not study actual mutations, they only study performance of strains (the supposed ‘mutations’ are only inferred). In the papers of this type I have examined, zero mutations are actually documented. All that is observed is differential performance of strains. Non-genetic causes, including epigenetic effects or gain/loss of viruses in some bacterial culture, etc., cannot be precluded. More to the point, since the overwhelming majority of mutations are very subtle and do not express a clear phenotype, almost all mutations will be invisible in these experiments, which only monitor gross differences in performance. Only high-impact mutations can be observed in such experiments, and these represent a biased sampling of the actual mutational spectrum. Furthermore, high-impact deleterious mutations will still always be selected away in such experiments, no matter how hard the experimenter tries to preclude natural selection. Therefore there will be a strong tendency to preferentially observe only high-impact beneficials. Since the crux of the genetic entropy argument involves the low-impact deleterious mutations (which will always be invisible in such experiments), these types of experiments have no relevance to this discussion.

Naturally, what is observed are the actual fitness effects. Even if we tracked every mutation that occurred in a mutation accumulation line, we would not be able to make much useful sense of it, since the function of every nucleotide is not known. Researchers have been able to make inferences about fitness distributions from mutation accumulation experiments. Granted, most of the fitness “buckets” they use are out in the range of significant effects. But they can make reasonable extrapolations back to the realm of low-impact mutations. Agreed, that high-impact deleterious mutations such as lethals will be selected away, but (a) that is real life, and (b) researchers know how to take that into account in their analysis. Dr. Sanford mainly has to appeal to the effects of deleterious mutations whose effects are undetectable, either in controlled laboratory settings (as he acknowledges), or in the wild (no evidence that the rodents 10,000 generations ago, say 1000 B.C., were much superior to today’s rodents).

3. Just how rare are beneficial mutations?

Scott speaks as if I do not acknowledge there are beneficial mutations. I acknowledge them very openly in the book, but I also insist that beneficials must be very rare compared to deleterious mutations (as do nearly all geneticists). The critical question is “how rare?”

That issue, “how rare?”, is indeed critical. That is why I was so dismayed at the treatment of this topic in Genetic Entropy. Yes, the bare existence of beneficial mutations are acknowledged, but in a manner which would convince the lay reader that beneficial mutations are essentially ineffectual:

“I have seen estimates of the ratio of deleterious-to-beneficial mutations which range from one thousand to one, up to one million to one. The best estimates seem to be one million to one (Gerrish and Lenski, 1998). The actual rate of beneficial mutations is so extremely low as to thwart any actual measurement (Bataillon, 2000; Elena et al.,1998)….essentially all beneficial mutations (to the extent that they actually happen) must be ‘un-selectable’. “

Without rehashing it all, the particular studies he chose were such that they would yield estimates of beneficial mutations on the low side. There were other studies in the literature available in 2007 which showed significantly higher rates of beneficial mutations. In one of these studies (Remold and Lenski), 12% of the mutations were found to be beneficial in one growth medium. This Remold and Lenski study was a follow-up to the Elena et al paper which Dr. Sanford did cite, but apparently he was unaware of it. There are additional studies that came out shortly after the publication of Genetic Entropy which also show high, e.g. over 5% percent, levels of beneficial mutations, as noted here. So regardless of what was known to Dr. Sanford in 2007, in the light of these studies I would expect him now to explicitly retract his prior characterization of beneficial mutations as being very rare.

Whatever the quantified amounts are, to represent essentially all beneficial mutations as “un-selectable” is misleading in the extreme. Dr. Sanford was well aware of the Lenski experiments, where for twelve out of twelve flasks of E. coli, the fitness rose significantly from its initial value after the bacteria were put in a challenging new growth medium. Note that Lenski started with a single clone, so we cannot claim that it was the promotion of some initially-present strain in the population was responsible for the enhanced growth as time went on. Rather, it was due to the accumulation of beneficial mutations, which were clearly “selectable.”

Dr. Sanford objects to the form of the mutations in the Lenski experiment, and some of his points do bear consideration. But let’s start with being honest with the observed phenomena in those experiments.

We see similar adaptations practically any time a population is challenged with a new environment. “Fitness” is logically always defined relative to the environment that the organism is currently occupying, and it is unreasonable to require that an organism can be optimally fit for more than its current environment. When a bacterium that is transferred from environment A (where it had become habituated) to new environment B, we expect it to lose some of its fitness for A as it adapts (via beneficial mutations) to environment B. So the fact that today’s Lenski bacteria would compete poorly if stuck back into a wild environment is nothing to complain about.

YE creationists often confuse fitness with genomic complexity. There is nothing in evolutionary theory that demands that a beneficial mutation will necessarily preserve or increase genomic functionality, or that bigger genome are necessarily better. Onions and some amphibians have much bigger genomes than humans. Often, an adaptation involves change of expression or regulation of a gene; sometimes it involves the silencing of a gene; sometimes it involves the duplication of a gene (three examples of beneficial gene duplication described here).

…This means that random changes in specifications will disrupt information with a very high degree of certainty. This has become especially clear ever since the publication of the ENCODE results, which show that very little of our genome is actually ‘junk DNA’. : Actually, the ENCODE results showed that only about 20% of our genome is genetically functional.

2. Kimura’s Figure:

Scott makes a huge deal about my reference to a figure in Kimura’s work. He misrepresents me by arguing I misrepresented Kimura (I did not claim Kimura agrees with me). But this is a rabbit trail; the argument is not about Kimura. The crucial issue is about defining the correct distribution of mutation effects. For deleterious mutations, Kimura and most other population geneticists agree the distribution is essentially exponential. Figure 3c in my book (based upon Kimura) shows an exponential-type distribution of deleterious mutations, with most deleterious mutations being ‘nearly-neutral’ and hence un-selectable (effectively neutral). But, as I point out, Kimura’s picture is not complete, because degeneration is all about the ratio of good to bad mutations. Kimura does not show the beneficial distribution, which is essential to the question of net gain versus net loss! When I show the beneficial distribution (while Kimura did not do this, I suspect he would have drawn it much as I did), anyone can see the problem: the vast majority of beneficial mutations will be un-selectable (Figure 3d).

Below is the figure in question, as it appears in Genetic Entropy and in Dr. Sanford’s recent article.

Mutation Distribution, from Genetic Entropy

The left hand curve is a fair representation of what Kimura might have drawn for the distribution of deleterious mutations. In Kimura’s work, he did not draw in anything for the beneficial mutations. Dr. Sanford added the tiny curve on the right to represent beneficial mutations. These are so minuscule as to be essentially all in the non-selection zone.

If Dr. Sanford had just presented this tiny curve as his opinion, that would be fine. But that is not what he did. He implied that this tiny curve represented what Kimura would have put in for beneficial mutations. First he wrote, “In Kimura’s figure, he does not show any mutations to the right of zero – i.e. there are zero beneficial mutations shown. He obviously considered beneficial mutations so rare as to be outside of consideration.” Then, looking at this tiny curve and noting that essentially all beneficial mutations would fall in the effectively neutral zone, Dr. Sanford wrote, “So selection could never favor any such beneficial mutations, and they would essentially all drift out of the population. No wonder that Kimura preferred not to represent the distribution of the favorable mutations!”

Dr. Sanford is clearly claiming that Kimura would agree with him here (“He obviously considered beneficial mutations so rare as to be outside of consideration”). This is what any lay reader would take away from this. And even now (see quote above), Dr. Sanford writes, “I suspect he [Kimura] would have drawn it much as I did “. So he is still claiming that Kimura would have represented the beneficial mutations as so miniscule as to be non-selectable.

The problem here is that this is not at all how Kimura would have drawn the curve of beneficial mutations. As I stated in STAN-4, Kimura wrote, “Under the present model, effectively neutral, but, in fact, very slightly deleterious mutants accumulate continuously in every species. … Whether such a small rate of deterioration in fitness constitutes a threat to the survival and welfare of the species (not to the individual) is a moot point, but this can easily be taken care of by adaptive gene substitutions that must occur from time to time, say once every few hundred generations.” Thus Kimura clearly believed that there would be beneficial mutations which are strong and numerous enough to be selected and to compensate for the accumulation of deleterious mutations. There is no question, therefore, that he would draw the curve of beneficial mutations out to the right, fat enough to show a solid probability of occurrence. (The reason Kimura did not draw in the beneficial mutation curve is that in his primitive mathematical model, the presence of any beneficial mutations would make it blow up, not because he believed beneficial mutations to be negligible.)

Kimura, and most other biologists, would likely draw the vast majority of beneficial mutations falling in the non-selection zone, but would also include a non-negligible “tail” distribution of selectable beneficial mutations. This is the exact opposite of Dr. Sanford’s version, and that is why this is important. Genetic Entropy tells the reader that there are essentially no adaptive mutations: “… essentially all beneficial mutations (to the extent that they actually happen), must be “un-selectable”. That is simply not true, and Dr. Sanford knew this, e.g. from the Lenski experiment.

* * * * * ** * * ** * * * ** * * ** * * ** * ** * * *

The issues come thick and fast in this final section. I will respond as best I can. Again, Dr. Sanford’s words are in italics.

1A. Sanford is a liar:

Scott repeatedly asserts that my book is all about deliberate deception, and I am fundamentally a liar. He bases this upon two things: a) there were a few references he thinks highly relevant, which I failed to cite and which he says proves I have withheld and suppressed evidence; b) He argues I must surely know that beneficial mutations happen, that natural selection happens, and also that long term lab experiments do not show rapid degeneration. Therefore, I must be dishonestly pretending to be ignorant of these things in order to deceive the ignorant. He has not considered these possibilities: a) given the mountain of relevant literature, I might legitimately miss a few papers; b) I do not share his view on which papers are significant.

There are various instances of deception or misrepresentation in Genetic Entropy. We have rehashed some of these in this present post: pretending that synergistic epistasis is meaningless; misrepresenting Kimura’s stance on beneficial mutations ; presenting the human genome deterioration concerns of other scholars without adequately clarifying that they apply only to industrial, not pre-industrial societies; presenting beneficial mutations as too miniscule for any meaningful adaptive impact. The last two items are substantive. The way the human genome is handled gives the reader the impression that most scientists agree that genomes are irreversibly deteriorating, and the dismissing of beneficial mutations would teach the reader that there can be essentially no adaptive mutations.

I wrestled with what to make of these knowing misrepresentations, since I had reason to believe that Dr. Sanford is a sincere scientist and Christian. I made it clear in STAN-4 that I attributed these misrepresentations, not to deliberate lying, but to the genuine inability of folks in the grip of YE creationism to see anything contrary to it: “The thoroughgoing deceit that characterizes Genetic Entropy is explained by the fact that Sanford has first and foremost deceived himself. This is a sad end for a world-class researcher. This is a classic example of “Morton’s demon,” the genuine inability of young earth creationists to see or hear the vast constellation of physical facts that contradicts their mental construct of the world.”

I believe what I wrote there to be true, but since it seems objectionable I have since deleted that whole section from STAN-4, and reworded to show more clearly that I do not believe that the misrepresentations in Genetic Entropy were a deliberate attempt to deceive.

Re: I might legitimately miss a few papers

I assumed that a veteran professional genetics professor would have background knowledge, and would do a thorough job looking at references, e.g. on beneficial mutations, in order to represent them accurately in a book. Just poking at this in my spare time, I easily found references that showed beneficial mutations were by no means too “low to thwart any actual measurement.” When I saw the three studies that Dr. Sanford picked to represent beneficial mutations, it was difficult to believe that this choice was not skewed to show what he wanted to show. However, if he is stating here that he did not do that, I accept that and apologize for any implication that he may have deliberately withheld literature he had in hand.

1 B. He cites a great many papers which only speak of the obvious: beneficials do happen, selection does happen, adaptation does happen. Any high school student knows these things. My argument only begins AFTER acknowledging these obvious things.

In Genetic Entropy he did not “acknowledge” these things, in any meaningful sense – – by characterizing beneficial mutations as too low to measure and as essentially un-selectable, he represented them as irrelevant to real genetic processes. It is unfortunate that he overreached here in trying to bash evolution, because that cuts his credibility for his core arguments about accumulation of un-selectable mutations.

1 C. Scott and I corresponded briefly before his posting, and I tried to explain to him why his criticisms were not correct. I did not find him to be a very good listener as I tried to explain how he was misrepresenting me. I then sent him a series of preprints (in press), which extensively and conclusively addressed all his objections. Upon reading his essay now, I can see he did not bother reading those preprints, which are very rigorously written scientific research papers.

As noted above, in this correspondence he did not address my specific concerns, apart from trying to defend his treatment of Kimura. He noted, fairly enough, that Kimura probably didn’t think through some implications of relying on a few big beneficial mutations to compensate for many deleterious mutations, but Dr. Sanford did not come to grips with the fact that he had effectively invoked Kimura’s authority for representing beneficials as all effectively un-selectable.

I did read his papers. Dr. Sanford has apparently forgotten that I (trying to be helpful) wrote back and offered some comments on how he might reshape the presentation of his results to make his papers more likely to be published. While they were interesting, I did not find these papers to be impressive evidence that all genomes are deteriorating. As I wrote to him in February, 2010:

“In nearly every case where we can observe or make reasonable inferences about the progress of a reasonable sized population (say > 2000 breeding individuals for eukaryotes, bigger for prokaryotes) where natural selection is allowed to run its course, the populations do just fine for as long as we can detect – certainly over many thousands of generations. Genomes do NOT deteriorate. …There is no good in waving around simulation results in which genomes deteriorate as though that proves genomes are deteriorating, when in fact they are not. If your model does not return results like reality, there is something wrong with your model, either the assumed fitness distributions or the incorporated assumptions of the model itself.”

This book cost me a great deal. I basically laid down my reputation and my career in order to say what I believe to be the truth.

That is admirable.

In our personal correspondence, Scott closed our conversation saying he intended to present me as being intentionally deceitful.

As noted above, in my essay I specifically exonerated him from being intentionally deceitful.

I believe he should apologize and withdraw these personal attacks.

I remain troubled by the misrepresentations in Genetic Entropy. However, as noted above, I have edited STAN-4 to state even more clearly that I am not suggesting that Dr. Sanford is deliberately deceiving:

“It has been troubling to discover various instances of misrepresentation in Genetic Entropy. However, I do not believe this to be any deliberate attempt to deceive. It has been widely observed that someone who is in the grip of young earth creationism can get somewhat disconnected with reality. By all accounts, John Sanford is a sincere and godly man, a respected figure in genetics research who has accepted the price of ridicule to promote what he believes.”

As noted, I do apologize for (and have altered) wording which suggested that Dr. Sanford was aware of some relevant literature that he did not present.

In terms of the scientific issues, I would ask Scott to append this response to his blog attack.

I have provided a link in STAN-4 to Dr. Sanford’s response.

WHY BOTHER ?

An honest treatment of the physical evidence in geology and physics shows the universe and earth to be billions of years old, with a well-defined history. The sedimentary rock layers were laid down over many millions of years, not in a single world-wide Flood. The fossil record is inherently incomplete (very few organisms get fossilized, and scientists have examined only a small fraction of the total sedimentary rocks), yet the fossils show that large animals have existed for hundreds of millions of years. Evidence for simpler life-forms is found in rocks over a billion years old. Comparative genomics gives clear indication of common ancestry, e.g. between humans and chimpanzees.

The motives of most Young Earth creationists are basically good. I know, because I used to be one. They are trying to be faithful to God’s word, in the face of a hostile secular establishment. Unfortunately, the physical evidence simply does not support a young earth, and so YE creationism is forced to take a very selective, ultimately dishonest approach to it. This is detailed here for the case of the Grand Canyon.

If someone refuses to accept an old earth or evolution, that is largely their business. But in many churches and Christian families, young people are told, “If evolution is true, then the Bible is false.” These young people are then set up to lose their faith when they discover the earth is old, and evolution is how we got here.

On the internet one can find anguished mothers telling of the day their seventeen-year-old son told them that he had found evolution to be true, and therefore there was no need for God. There is no reason that God could not have used evolution as a means to create today’s biota, so there is no scientific or logical basis for this therefore. This therefore derives straight from misguided Christian attempts to defend the literal Genesis narrative; atheists naturally make use of Christian assertions like “Only God could do XXX” or “Evolution is incompatible with a Creator” to bash the faith.

Ultimately, most of the blame for these tragedies lies with the men in YE creationist organizations who trade on their scientific credentials to deceive lay Christians into believing that the Young Earth/anti-evolution viewpoint matches physical reality. The way for Christians to teach their kids to deal with evolution is not to deny it, but point out that God often works through extended processes (think: sanctification and parables of seeds growing).

My daughters are now adults, with vibrant Christian faith. As they were growing up, we exposed them to the full range of writings by C. S. Lewis. He (at least provisionally) did not dispute biological evolution. What he did was refute the ungodly implications that unbelieving philosophers tried to draw from evolution.

Genetic Entropy contributes to the Young Earth deception, and this is why I have taken the time (there are other things I could be doing) to research and write my original letter to Stan, and later post this essay on my blog. I respect Dr. Sanford as a researcher and a brother in Christ. I take no pleasure in pointing out the misrepresentations in his book as he attempts to make his case against evolution.

I hope in my blog posts to help Christians understand that the physical evidence really does support evolution and an old earth, but also that the truths of the gospel do not depend on how God elected to create humans. If you consider that you started your existence as a tiny sack of chemicals, a microscopic single-cell egg with only half of full human DNA (think about it….) , that helps clarify that it is not so important whether some distant ancestor shared 99.9% or only 98% DNA base pairs with you.

It can be most dismaying for a Bible-believing Christian to confront the fact that the Genesis creation story is not an accurate description of the development of the earth and its inhabitants. I deeply sympathize, have gone through this crisis myself. I offer on this blog the resolution I have found, e.g. re Adam and Eve, and the “firmament” in Genesis 1. It mainly boils down to taking II Timothy 3:16 seriously about God’s purposes for the Scriptures.

For those that have read this far, congratulations on your perseverance. May the Lord bring you insight and wisdom in this challenging area.