Gen_Entropy

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, one arbitrarily (as best they 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

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 Jesus Christ, by His Holy Spirit, bring you insight and wisdom in this challenging area.

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37 Responses to Gen_Entropy

  1. OgreMkV says:

    Hi, just a nit to pick. The bacteria in Lenski’s lab were not placed into a ‘challenging environment’. Citrate was added to all the growth medium as a stabilizer specifically because E. coli couldn’t metabolize it.

    When the mutant strain(s) appeared that could utilize it, they found a massive untapped niche and approached the classic exponential growth pattern.

    Other than that, this was well written and researched. Off to read the remainder.

  2. JoeCoder says:

    A minor point. I’m cautions about using the point from the Joseph & Hall Study to indicate that 5.75% of all mutations arriving are beneficial in nature. Most beneficial mutations work by eliminating energy-consuming functions that are not needed under the current fitness landscape. So they end up being deleterious in the long run when the fitness landscape changes and those functions are needed once again. As they state:

    “the protocol for measuring fitness may cause mutations that are deleterious in nature to be beneficial in the lab. In the complete medium of our growth assays, several metabolic pathways, such as those involved in amino acid synthesis, are not required. … Mutations that reduce or preclude production of proteins in these types of pathways might be beneficial to diploid mitotic growth rate, even though they represent deleterious mutations in nature.”

    And also:

    “the ancestral strain used in our experiment may have been poorly adapted to the experimental conditions. If this is true, a higher proportion of mutations are expected to be beneficial because the ancestral genotype was far from its fitness optimum”

    And finally:

    “dominance may have biased our estimates. If deleterious mutations are more likely than beneficials to be recessive, then they would appear underrepresented because we are measuring heterozygous fitness. This possibility is consistent with the empirical observation that most deleterious mutations are recessive”

    It would be interesting to know what percentage are truly beneficial and don’t act by removing unneeded functionality.

    The Joseph & Hall Study again for reference:
    http://www.genetics.org/content/168/4/1817.full

    • I agree, it is hard to quantitate beneficial mutations. For the reasons you note above, MA experiments may tend to overestimate them. For instance, Shaw et al. (2000 – -http://www.genetics.org/cgi/content/abstract/155/1/369 ) estimated about 50% of mutations in their a MA study of the plant Arabidopsis thaliana were beneficial. I did not cite this in STAN_4 because that just seemed way too high. You may be aware that Joseph and Hall, in order to verify their somewhat controversial results (5.75% beneficials), continued this study for another 1050 generations. With updated calculations, they found some 13% of mutations to be beneficial.
      Link to this abstract: http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=1919588

      That said, the starting point in the scientific quantification of the effects of mutations is to define some measurable measure of fitness, and watch how that moves as the experiment progresses. We can later argue about the meaning of these results, but first we should acknowledge the results themselves. Whether 5.75% or 13% or 0.1% is the best estimate of naturally-occurring beneficial mutations, it is clear that under well-defined conditions, the mutations/natural selection process is plenty powerful enough to provide and select mutations that are beneficial in the current environment. Genetic Entropy taught away from all that.

      My main objection to Dr. Sanford’s treatment of beneficial mutations is that he presented only studies that would be biased toward the low end of beneficial mutation incidence , with the conclusion that they are all essentially unselectable. That is just a falsehood.

      It is well known that in huge bacterial populations like the Lenski flasks, clonal interference makes the vast majority of beneficial mutations to be invisible. For instance, Perfeito et al. ran experiments (like Lenski) on E. coli, but in some cases kept the population sizes small population sizes to minimize the effect of clonal interference. In those cases, they found that 1 out of every 150 new mutations was beneficial. All this is known, but Dr Sanford presented only the Lenski results ( 1/ million beneficials) and two other near-zero beneficials studies, with the impression that represented reality. As a genetics professor, I expected that he would have known that clonal interference would lead to underestimation of beneficials in the Lenski experiments. And I expected that he would have acknowledged all the MA experiments as showing the power of natural selection in general, even if he wanted then to claim that natural selection cannot work on the smallest of deleterious mutations.

      Thanks for your comment.

  3. Martin Zukor says:

    Dear Mr Buchanan

    I do not share your Christian beliefs and am not a geneticist either (!) but I somehow feel indebted to you for your dedication, intelligence and what I can only term “good faith” in your work in this area. Truth (even or perhaps especially scientific truth) is not a straightforward affair but honest debate gets us closer.

    Bets wishes
    Martin Zukor

    • Martin, thanks for the kind words. You put it well – – some of these issues are not simple, but hopefully in the back and forth of debate all sides get aired and the truth can be discerned. Best wishes to you as well. -Scott

  4. Gerard Jellison says:

    Mr. Buchanan,
    I really enjoyed reading your “Genetic Entropy” critique. I’ve done some background research on Sanford’s work as well, and I was pleased to find many of my criticisms reflected in your writeup. We even found a lot of the same references! I recently posted my analysis as a one-star review on Amazon (it’s called “Disinformation Theory”). If you get a chance to read my work, I’d be happy to hear of any comments or criticisms you may have. And if you have an Amazon account and want to vote my reviews “helpful” (I posted for all three editions of Sanford’s book), that would be much appreciated as well. Critical reviews tend to get voted down by “no” votes by creationists, which means they don’t show up at the top of the page, and so get overlooked.
    Best wishes,
    Jerry Jellison

    • Jerry,
      I read through your review (kind of quickly, so I may not have gotten every nuance). It looked OK to me, so I did vote “helpful” as you requested. Good of you to put in the effort for this review. It’s hard to know if any mind are changed by these reviews — as you have seen already, a critical review of a YE creationist work usually garners attacking comments. But hopefully there are a few folks out there on the margin, who are motivated to find out the truth rather than just confirm their existing beliefs, who will benefit.

      Some suggestions to edit your review, which you can ignore if you want:
      (a) In fairness to Dr. Sanford, given that you take 1-2 paragraphs to discuss his academic career, he did more than just breed plants. You should mention that he was co-inventor of the “gene gun”, which was a pretty nifty, fundamental tool. Go look it up – -as a physicist, you’ll enjoy.
      (b) I don’t recall your mentioning perhaps the most obvious, non-technical disproof of Dr. Sanford’s contention that fitness is steadily spiraling down [since a ~ perfect creation around 4000 B.C., which is what Bible literalists believe, even if that was not explicitly stated in the book], which is that historical records which go back to Greeks c. 400 BC would indicate if human lifespans were much greater than in say 1500 A.D. (before modern medicine took off), or whether rabbits could leap tall buildings with a single bound back in 400 B.C., which was many thousands of generations ago for them. But no such pattern is found. Hence, fitness is not inevitably declining.
      (c) I don’t get any benefit from clicks on this site, but you might want to reference my STAN4 article here, since it goes into more depth than is normally possible with an Amazon review.
      Best regards,
      Scott

      • Gerard Jellison says:

        Scott,

        Thanks for reading my Amazon review and for your comments. As you say, the problem is to reach an audience that doesn’t already agree with everything we say. I’ve posted extensive critiques of three creationist books on Amazon, since I think that may be a good way to reach at least a few people “on the margin.” That’s probably about all one can hope for.

        I’ve been thinking, as you suggest, that my comments on Sanford’s background may come off as too harsh. One problem is that I’m bumping up against Amazon’s length limit for reviews, so I don’t have room for a lot of subtlety. There’s a lot more to say about that book (my original writeup was longer by a factor of three!). I actually did mention the gene gun, but it was so brief that I don’t blame you for not noticing it. I’ll think about softening my comments so they don’t sound so much like personal attacks.

        Regarding historical information on human longevity, I didn’t get into that because, according to Sanford’s Figure 14 (the Biblical lifespan chart), he doesn’t expect a big effect until you get to 1500 BC or so. But this whole thing is ridiculous…according to his chart, in New Testament times the genetically-limited lifespan was only about 30 years. In the time of the Greeks, it was maybe about 50 years.

        One could go back further, but I seem to remember that Biblical literalists claim support for a literal reading of the OT claims about longevity from other cultures. I think the ancient Egyptians (or somebody) have similar stories about their ancient rulers living hundreds of years. There must be a way to find credible evidence that people have never lived much longer than they do today, but I was reluctant to go down that rabbit hole. But I would be interested if you know of any god sources of information on lifespans in very ancient times.

        I can add a reference to your site in my “comments” section, since there’s no word limit there.

        Thanks again,
        Jerry

  5. Gerard Jellison says:

    Freudian slip…I meant “good” not “god sources of information”…!

    • Jerry,
      re lifespans, it may be of interest that at the time the Psalms were written (timing debated , but c. 400-1000 B.C.) , 70-80 years was considered maximum old age…from Ps 90:10, see
      http://biblehub.com/psalms/90-10.htm
      for discussion.

      http://brianclegg.blogspot.com/2012/02/35-year-lifespan-myth.html

      notes that, although average lifetime of ~ 30 years may have held for premoderns:
      … average figures can be very misleading. The historical figures are dragged down by a very high infant mortality rate. Before modern medicine, most children would not make it to adulthood. Similarly, many women died while giving birth, in their twenties or younger. If early deaths are excluded from the average, lifespans in the 50s, 60s and 70s were not uncommon

      You might find more on lifespans by googling it
      Best regards,
      Scott

  6. Gerard Jellison says:

    Scott,

    Thanks for the information. I saw that reference to Psalm 90 in your analysis. It’s interesting to know that 70-80 was recognized as the maximum even then. Also, David is traditionally considered the author of Psalms, and the Bible says David died at age 70.

    I don’t know whether Sanford uses King David as one of the data points on his Figure 14. A creationist article by someone named Lopez (who makes claims similar to Sanford’s) assumes David died about 1100 years before Jesus. Sanford’s plot has a lot of the same points as those cited by Lopez, but the dates are not perfectly consistent, so I don’t know if Sanford’s point at “21 centuries after Noah” is David or not. Anyway, using a date for David of about 1100 BC puts him right on Sanford’s curve; a later date makes the agreement less good (but not dramatically so, considering the slow decline of the second half of the curve).

    Thanks again.

    Jerry

  7. Roger says:

    Scott,

    I am not attacking you in any way but I do not I find your ability to think logically to be consistently inconsistent. Also I am not defending John Sanford so what I have to say isn’t about genetic entropy. In a debate or discussion of two opposing views you cannot argue as if your belief is the only credible belief. Yet this is exactly what you do repeatedly. It is circular reasoning in it’s most literal form. Just consider the following quote of yours.

    “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”

    Is this an established fact that John Sanford agrees with? If not then you need to establish that everything said in the above statement is true. This is how a discussion of opposing views of any value proceeds. You might as well say “I am right and you are wrong and that proves I am right”.

    If you believe the current popular understanding of the fossil record, life has evolved from single cellular life forms to what we have today over the last 600 million years. So 600 million years ago and older, only single cell organisms. Some of the first fish like the Coelacanth fish are virtually unchanged from 430 million years ago (as you point out). This is an utterly unimportant point from the Sanford side of the argument because he isn’t expecting it to evolve, only that fish (like Coelacanths) might have had longer life spans in the past. He doesn’t believe they have been around 600 million years anyway.

    It actually is destructive to yours.

    How did a highly evolved fish like a Coelacanth come into existence within the first 28% of this single cell until today time span and remained unchanged by the wildly different ecosystems it would need to adapt to and exist today in the same form. It has no major predatory abilities nor defensive abilities to give it an advantage. It is just a big juicy fish that did not evolve for 430 million years. I do not have a problem if evolution is a fact or if it isn’t but the Coelacanth didn’t care much for the following definition of evolution…

    evolution /evo·lu·tion/ (ev″ah-loo´shun) a developmental process in which an organ or organism becomes more and more complex by differentiation of its parts; a continuous and progressive change according to certain laws and by means of resident forces.

    Anyway there are many points you make that are just circular reasoning. You assume your view to be true which is fine but at times you are highly logical and yet at other times you are not. It is clear that you are blind to those times of being illogical so I am not going to try and go into some lengthy dissection of your writing. Pray for clarity on it.

    More importantly…

    The first impression of your response to the book was (you tried to cover over this later) that you were calling John Sanford a liar and that he was purposely misleading people. Which again I am not commenting on him, his book nor if he is a liar. If you think he is a liar then let it stand at that. If you don’t think he is then don’t say that he is. In this you are double minded. Consider your absolutely mean spirited, prophetic and condemning quote below as an example…

    “This is a sad end for a world-class researcher”.

    You cannot come back now and say he will happily continue to be a world class researcher… No you have condemned him to his sad end. Once a world class researcher but now a sad end.

    Something tells me that this is not the end of John Sanford.

    • Roger,
      I will offer a couple of responses to your remarks.
      (1) re: “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” – – – Essentially everyone who is able to examine the rock layers in a reasonable and objective manner comes to understand that they were laid down over many millions of years ago, not 6000 or 4500 years ago. As I discussed here https://letterstocreationists.wordpress.com/2013/03/16/unconformities-showed-geologists-by-1800-that-the-earth-was-very-old/ , geologists (many of them committed Christians) had realized from the rock formations that they had to be laid down over long ages, not in a single worldwide flood. Information from English canal surveyors showed the basic sequences of fossils that spanned these ages. I am fully aware that Young Earth Creationists like Ken Ham and John Sanford would dispute all this, but they simply do not tell the whole truth. I went into all this in great detail with the age of the Grand Canyon , https://letterstocreationists.wordpress.com/grand-canyon-creation/ , detailing the misrepresentations of the YE creationists, so I am not going to rehash them all here. The bogus evidences brought forth by YE organizations are debunked here http://www.talkorigins.org/origins/faqs-youngearth.html , and here http://oldearth.org/youngministry.htm .

      Sanford claims that the genomes of larger animals are relentlessly deteriorating because natural selection cannot weed out the continual small deleterious mutations in their genomes, so, yes, these observations are fatal to his case. As is the observation I made that thousands of generations of rabbits have come and gone in historical times, with no observed trends of genetic deterioration. There is just no evidence for general genetic deterioration in reasonably sized (e.g. >10,000 for mammals) populations where natural selection is allowed to operate (i.e. significant differential mortality, as there is in pre-industrial human societies).

      (2) As for Coelacanths evolving in say 200 million years from the wormish animals of the Precambrian, then not changing much since, that is exactly the sort of pattern predicted by basic population genetics. See here: https://letterstocreationists.wordpress.com/2014/04/02/realistic-expectations-for-transitional-fossils/
      ” Thus, it is far more likely that a new species would develop within a small, isolated population, especially if that population is under some environmental stress that would favor genetic changes. The odds of us finding fossils from that small, localized population is are nearly zero. If the new species becomes more fit than the old species, the new species will expand, and only then is likely to appear in the fossil record. But once a species is widespread and successful in its ecological niche, there will be diminished selection pressure for changes, so fossils of this now well-adapted species are likely to appear for perhaps million of years with showing little change.”

      You seem to believe that the pace of morphological evolution should be uniform, but there is no reason that that should be so

      (3) re “This is a sad end for a world-class researcher”. OK, let’s parse this out. Let’s start with “world-class researcher. ” Yes, John Sanford was that. I tried sincerely to honor his accomplishments.

      “Sad end”: here is this highly educated and capable guy, who should know better, writing explicitly as a Christian, who misrepresents the facts in order to bolster his case (I listed three of the clearest misrepresentations in this Genetic_Entropy article above). And by encouraging Christians to believe in a young earth and no macroevolution, he (along with the whole YE establishment) is setting today’s Christian teens up to reject their Christian upbringing when they find out that they have been lied to in this key area. For me, anyway, that is “sad.”

      Is this the “end”? Well, I suppose Dr. Sanford could repent and start telling the whole truth about genetics. I tried to give him that chance when I corresponded with him, back in 2010 before I released my letter on my blog, but he at that point mainly engaged in attacking my motives and defending his own rather than addressing the substantive points I raised. So, we’ll see.

      I appreciate the time you put into writing your thoughts here. For me, this is not a happy subject to have to deal with. I am just trying to do damage control as best I can. Peace….

      • Roger says:

        And I appreciate that you took the time to respond.

        You didn’t respond to anything important that I said. Simply two issues.

        3) The most important of which is your prophesy of the end of John Sanford’s career.That he didn’t have a chance to have a career at this point. You can be critical as you desire about his work but about his future is just against everything you say you believe. You could say this is a low point but you didn’t. I am not even familiar with who he is but I am making a prediction also. This is not his end as a respected researcher. If it turns out it is not his end I hope you will get out the prediction of others ruin business. Also you go back and forth on him being a liar.

        You said of Sanford in your above response to me, “who misrepresents the facts in order to bolster his case”

        1) Also that you employ circular reasoning such as saying something that John Sanford would argue to be not true to show him that he is wrong about what you believe to be true. This is just the poorest of reasoning and sounds more like you need this or that point to be true even though you cannot prove it. Proving the flood didn’t cause the layering of the fossil record doesn’t prove your interpretation of it. Again your logic is strange to me like bringing up the flood at all to explain this point. I don’t believe John Sanford’s understanding of the fossil record to be correct but neither do I believe yours. All of which is off topic.

        You said, “You seem to believe that the pace of morphological evolution should be uniform, but there is no reason that that should be so”

        No I just think it should logical.

        2)I don’t want to waste more time on Coelacanths but look up some of its fossil images and you will find some that look incredibly similar to the modern Coelacanth.

        http://madjellyfish.blogspot.com/2012/11/the-coelacanth-living-fossil-tetrapod.html

        I asked, “How did a highly evolved fish like a Coelacanth come into existence within the first 28% of this single cell until today time span and remained unchanged by the wildly different ecosystems it would need to adapt to and exist today in the same form?”

        Ask why this fish survived when so many species didn’t that were far more adaptable or had better defense mechanisms or were far more dominant predators. Then look at the periods they survived through. Radical changes of environment and again this fish is just a large, slow, great choice for dinner to many of the species in the periods it made it through. Review what lived in those periods.

        There are many other examples of nearly non evolving species that have no right to make it as well but just consider this one.

        This guy has been around without much change for most of the evolution from single cell until today. That doesn’t make any sense unless you just cannot think for yourself. Even if you don’t come up with an answer, it is okay. Sometimes we don’t have the answer.

        Think… actually pray… especially about point number 3) Please…

        OgreMkV… You write of what you know not…

        I’m out…

      • Roger,
        – re “your prophesy of the end of John Sanford’s career” – – I did not catch on earlier to why you objected to the “sad end” wording. Now I see that you took it as meaning that his career has altogether ended. Good point, that had not occurred to me. Better language would have been “sad come-down” or something like that. But I have taken that wording completely out of the main STAN4 article.

        – re “you go back and forth on him being a liar” – – First, the facts: In Genetic Entropy Dr. Sanford is
        ” 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. ” (If you want to correct me on any of these substantive issues, please feel free.)
        Sanford has therefore deceived his audience, so by definition he is a deceiver. Whether or not he is a “liar” depends on how conscious he was that he was deceiving others.

        It is reasonable to expect that, as a genetics professor, he would know that his representations here were false. However, having been a YE creationist myself, I am all too aware of the self-deception that goes with it, so I clearly exonerated him of conscious lying: “Sanford has first and foremost deceived himself… 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 assumed my readers would grasp the difference between fully-conscious lying, and the shadowy world of self-deception (that affects us all to some degree). Maybe that distinction was not clear to you.

        But again, to try to make it even more clear that I respected Dr. Sanford’s underlying intentions, I pulled that language out of the main essay. I only cited it here to show that even in the original version, I credited his misrepresentations to the usual YEC self-deception, not to deliberate lying.

        re Coelacanths: You still do not seem to understand that there is no necessity in evolution for a lineage to keep undergoing rapid morphological change (assuming it is reasonably adapted to its environment). None. If you grasped that, your objections would go away. You are welcome to your personal incredulity, but there is no logical difficulty in coelacanths evolving from Precambrian bilaterians to Cambrian primitive chordates to Ordovician jawless fishes to Silurian jawed fishes, then not changing a great deal since then.
        Even if you are a YEC, you have to acknowledge they have been around for at least 6000 years, so they cannot be poorly adapted. I understand that they live fairly deep in the ocean, which may be why they can continue to evade predators and keep on reproducing.

        “Radical changes of environment” – – well, things don’t really change all that fast in the deep ocean. Some lineages vanish and some don’t.

        That said, there will be slow genetic drift for any population which will manifest at some level in bodily changes, however slight and slow. This is exactly what we do see in the coelacanth lineage, as OgreMkV pointed out. The specimens we find today are not the same species, or even the same genus (as judged expert ichthyologists, using detailed morphological features) as the fossils, however similar these may appear to us amateurs.

        I may be wrong , but I will hazard a guess that your apparent resistance to evolution stems from a belief that it is incompatible with your Christian faith. I went through something of a crisis of faith myself as I began to realize that the “Darwinists” were telling the truth on genetics and fossils, and the Intelligent Designers and YECs were not. If you are interested, my reconciliation is told here: https://letterstocreationists.wordpress.com/2013/11/28/evolution-and-faith-my-story-part-2/

        A key insight was to realize that what I had been told that “If there was no historical Fall, there is no need for redemption” is total baloney. Oddly, the grand Reformed doctrine of the federal headship of Adam stems from a misreading of Rom 5 by Augustine (he did not know Greek well, and was working from a faulty Latin translation).

        Paul develops the universality of sin in Romans 1-3 with no mention of original sin. He moves from, “The wrath of God is being revealed from heaven against all the godlessness and wickedness of people, who suppress the truth by their wickedness… although they knew God, they neither glorified him as God nor gave thanks to him” (1:18-21) to “all have sinned and fall short of the glory of God” (3:23) quite apart from Adam. In all the gospel proclamations to both Jews and Gentiles recorded in the Book of Acts, there is not a single reference to Adam’s sin. The Fall is never mentioned in the sayings of Jesus. On the contrary, Jesus directed people away from religious speculations or blaming others, and towards a consciousness of their own shortcomings and their personal need for mercy. Something to think about, anyway.

        Best regards…

  8. OgreMkV says:

    As a point, saying that Coelacanths haven’t changed much in the past 413 odd million years is like saying that Earth hasn’t changed that much in 413 million years. Even a casual reading of the wikipage and references contained therein would reveal that Coelacanth is an entire order of fishes (kingdom, phylum, class, ORDER, family, genus, species) numbering with over 80 known species in 5 families and 22 genera.

    The coelacanths alive today (two species: Latimeria chalumnae and L. menadoensis) are as different as the coelacanths of the early devonian as birds are from their dinosaur ancestors.

    For example, here’s a fossil of Whiteia woodwardi http://www.dinofish.com/image16.htm

    And here’s an image of the modern Latimeria chalumnae http://www.arkive.org/coelacanth/latimeria-chalumnae/

    That’s just in a few seconds of looking. I’m sure a detailed search could turn up many more fascinating (and different) fossil coelacanths.

    While it’s true that the modern coelacanths seem to evolve more slowly than other vertebrates (especially terrestrial vertebrates (see : http://www.nature.com/nature/journal/v496/n7445/full/nature12027.html#f1)), it doesn’t mean that they aren’t evolving and changing. The estimate in that paper (comparing to the two extant species) indicates a species divergence time of 6 million years (possibly more given the general slowness of evolution).

    Again, according to that paper, “coelacanth proteins that were tested were significantly more slowly evolving (0.890 substitutions per site) than the lungfish (1.05 substitutions per site), chicken (1.09 substitutions per site) and mammalian (1.21 substitutions per site) orthologues (P < 10−6 in all cases)". Given that modern coelacanths have a 413+ million year genetic history, they are highly different from their early devonian ancestors.

    Just wanted to put that out there.

    • Ogre,
      Appreciate the meaty commentary on ceolacanths. So – – living coelacanths are different species, even different genus, from any of the many fossil samples.
      I looked at the Wikipedia article http://en.wikipedia.org/wiki/Coelacanth
      on this order of fish, which included this human interest angle on their discovery:

      “The fossil record of the coelacanth is unique because coelacanth fossils were found 100 years before the first live specimen was identified. In 1938, Courtenay-Latimer rediscovered the first live specimen, L. chalumnae, which was caught off of the coast of East London, South Africa. In 1997, a marine biologist was on a honeymoon and discovered the second live species, Latimeria menadoensis in an Indonesian market.”

      Best regards

  9. Michael says:

    Scott, I have enjoyed reading your blog. My story is the opposite of yours (i,e,an early life acceptance of Evolution theory transforming into a confirmation of Creationism). My expertise is in software design. I’m one of the team members that build the software that guides this nation’s space vehicles during atmospheric flight. My work building these complex codes has been humbled by my simplistic appreciation of the genetic code and the incredible complexity for even the simplest form of life. To believe in theories that life originated from nothing, to believe that the complexity of information that exists within the genetic structure of even the simplest life forms came out of “blind” chance, requires more faith than I could ever possess. There are no “reasonable” pathways for abiogenesis. Lee Spetner and Werner Gitt have fascinating books available that discuss life from an information theory perspective. I am a YEC. I believe in the inerrancy of scripture and the truth therein that even a child can fundamentally grasp. That is why I believe simply that when a “man” lifted his arms and stilled a mighty storm, or commanded that a blind man see, or that the lame walk; that there are powers far beyond my simple mind’s ability to grasp. My faith is simple…. like a child. But I will live eternally after this life, and you and I and all followers of Jesus Christ will have much time to debate these matters 🙂

  10. OgreMkV says:

    Why is it always engineers?

  11. Terry says:

    Michael writes, “To believe in theories that life originated from nothing, to believe that the complexity of information that exists within the genetic structure of even the simplest life forms came out of “blind” chance, requires more faith than I could ever possess. There are no “reasonable” pathways for abiogenesis.”

    But this is almighty God we’re talkng about. In his book, The Language of God, Francis Collins describes the anthropic principle and comments: “The existence of a universe as we know it rests on a knife edge of improbability.” And: “Altogether, there are fifteen physical constants whose values current theory is unable to predict. They are givens: they simply have the value that they have … The chance that all these constants would take on the values necessary to result in a stable universe capable of sustaining complex life forms is infinitesimal. And yet those are exactly the parameters that we observe. In sum, our universe is wildly improbable.”

    Well, this wildly improbable universe is actually here. So, if blind chance had its way, it’s not just organic life that would have an infinitesimal chance of existing but the universe itself of which it is part. If God can manage the whole universe, why can’t he manage abiogenesis? To say he can’t is to put him in a box marked ‘This is what I can understand’, so anything outside the box is impossible.

    In my draft book, ‘The God Debate – Dawkins in Denial’, I comments on Dawkins’ argument against God’s existence as follows: “In the God scenario, nothing in the physical universe would be improbable. On the contrary, given a deliberate all-embracing creative act, everything in the causal flow (except exercises of free will or supernatural interventions) would be inevitable. Even ‘accidental’ genetic mutations that drive organic evolution have causes; the fact that science currently has no way to predict them doesn’t alter that fact. So ‘statistical improbability’ can be viewed as a label masking our ignorance of the nature of the causal flow God preordained.”

    Properly viewed, evolution is a far smaller challenge to faith than a simplistic literalist approach to Genesis which fails to take account of either the massive physical evidence for evolution discovered in God’s second holy book, the book of nature, or the findings of modern biblical scholarship on how we should understand Genesis 1-11.

    • zenzeddmore says:

      “So ‘statistical improbability’ can be viewed as a label masking our ignorance”
      Or if you had had adequate training in statistical analysis you would understand how we come to the conclusion that X is random. In the case of mutations you can see there is no particular bias toward beneficial ones. Nobody on either side of this argument would disagree. If your “designer” is producing bad mutations at a prodigious rate and beneficial ones only rarely (as this is precisely what is observed), then why not hold him accountable for things like harlequin Icthyosis?

  12. Terry says:

    I should have written in the final para, “… evidence for evolution and an ancient earth …”

  13. zenzeddmore says:

    Sanford’s models are not realistic. Like Haldane before him he ignores that reproduction and selection are exclusively local phenomena. Sanford’s model rejects the obvious fact that selection is performed locally among near peers. (siblings in competition). Their near identical genomes are set against each other effectively eliminating the notion that slightly deleterious genes “add up”.
    Another thing that Sanford did not take into account, at least in humans, was the miscarriage rate. The vast majority of significant genetic problems get weeded out at the early embryo stage. The reported rate of early miscarriage is 30-70% and he completely ignored that.
    Haldane stated, “I am quite aware that my conclusions will probably need drastic revision”, & subsequent corrected calculations found that the cost disappears. He had made an invalid simplifying assumption which negated his assumption of constant population size, & had also incorrectly assumed that two mutations would take twice as long to reach fixation as one, while sexual recombination means that two can be selected simultaneously so that both reach fixation more quickly.
    Fossil evidence puts modern human as starting about 35,000 years ago. Would you say we degraded from Homo Habilis and he degraded from Australio pithicus? Because they were here first. Before that the last resemblance to man disappears. Go farther back and all trace of primates disappears. Ask Sanford to reconcile this with “genetic decay”.
    It’s quite a fallacy to posit that bad mutations only accumulate eventually leading to catastrophic genomic failure. Bad mutations only accumulate in branches from whence they originate. Other branches will not have that same mutation. Recombination can produce individuals who not only don’t have those bad genes, but who also have more copies of good genes.

    I would say Dear Mr Sanford, You have reality upside down. You seem to think that the best and strongest have the least chance of spreading their genes, that the strong will only produce weak, that population become less fit over time. This is all implied by your “genetic decay” mandate. How insane is that?

    Say you have a population of 1,000,000. Say 50% have bad mutations while the other 50% are neutral and only one in a million is beneficial. In any generation the 50% with bad mutations fail to breed leaving the ones with neutral genes (that 500,000) to breed. This particular generation, the one that had the good gene was accidentally killed by a freak lightning bolt. A generation passes with no beneficial mutation. Say a hundred generations pass with none of the organisms with the beneficial mutations surviving to breed. So what? All those neutrals are breeding happily away. And eventually there will be something with a beneficial mutation that survives and passes it down to half it’s offspring which deceases the chance of that mutation getting lost by a freak lightning bolt. It then gets pass down even more until before you know it ever member of some generation down the line has a copy of that gene.

  14. doug says:

    Stepping back to assess the big picture, copying errors produce chaos, not highly functional and complex systems. If the experimental data is showing that the genome is not deteriorating as would be expected in a solely natural system, this merely suggests that something supernatural is involved. Job 34:14,15 provides a clue as to what that something is.

    • Doug, your comment is sensible, but you are missing two important aspects. One is that copying errors can have a range of effects: they may be deleterious, beneficial, or neutral with regard to fitness. See the references in Stan3 and Stan4 that demonstrate that some mutations are indeed beneficial.
      Now, the deleterious mutations far outweigh the beneficials, as shown by mutation accumulation experiments where you deliberately prevent natural selection from functioning. Rather, in each generation you arbitrarily select one individual or one couple as the ones allowed to breed the next generation. In this case deleterious mutations accumulate, and fitness declines.

      But normally in the wild, deleterious mutations are purged by natural selection , as explained in the articles and in the comments above. This is readily understood within the framework of known physical laws. No need to invoke the supernatural.

      As a fellow evangelical Christian, I would like to respectfully suggest that you seek God in what is known, rather than trying to find gaps in our understanding that seem to require supernatural intervention. The god of the gaps approach has a long history of failure which dis honors the Lord. Jesus taught that “no sign” would be given to unbelievers except his resurrection, so we should not expect to find any genuine gap in the operations of the physical world that requires routine divine intervention.
      Best regards….

  15. doug says:

    Thank-you for your kind words in calling my comment sensible. I wish I could return the compliment, but your comment seems a bit naïve, at best. Please let me explain.

    We know a lot about how mechanistic systems work. Man’s creativity in the last 70 years or so has gone a long ways in designing increasingly complex computing machines.

    For example, we have incredibly complex computing systems. We know how to build them, we know how they work. Trillions of man hours of some of our most brilliant men and women have been invested in their design and implementation.

    Based on our current technology, we can design hardware to electronically manipulate information (stored as data) in response to other information stored as instructions (e.g. software /firmware of various kinds). We design other hardware to electronically or mechanistically receive data as input. Other electronic and mechanical systems can use generated data to display or even to control systems such as robotics, etc.

    This is all brilliant and interesting stuff. But there is nothing that mankind has designed that approaches the elegance and brilliance exhibited by the simplest form of life.

    Think about it, in life, the instruction codes (e.g. DNA) are passed down from generation to generation, but at each generation, all the hardware reproduces itself. And it scales itself too. Humans start as the union of a sperm and an egg, and from that two cell union, self creates a human body.

    Each cell considered alone is wonderful to behold. Every system in a cell is marvelously and elegantly designed. Many systems we are only beginning to understand and there are probably thousands we have not even discovered. Think of a simple system like transportation. How does the transport system of a cell know to copy RNA and transport it exactly to the location it is needed to build a protein. Who programmed the transporation system? Who controls it? How can you have a transportation system without a control system?

    Or think of the storage system. We are just beginning to learn about the complexity of how multiple layers of data are stored within the complexity of supercoiled DNA. How can you change a bit of data at one level, without affecting multiple levels of stored information? How do you design and utilize such a storage systems?

    And here you are, trying to convince me that this glorious design was created by the crudest of all tools—beneficial mutations. Seriously…

    Think about your explanation: Every once in a while a beneficial copy error occurs in one of the billions of bits of information stored in a DNA module. This beneficial error, somehow, gives the slightest reproductive advantage to a creature. Perhaps, after hundreds or thousands (or hundreds of thousands) of generations, this benefit spreads to an entire reproducing population and improves the gene pool. And this selection process is seriously complicated and delayed once we recognize that the selection needs to take into account other mutations that might spring up within the gene pool.

    And using this crudest of all tools, the wonder of life is created and improved upon? How many generations of beneficial copy errors does it take to generate just one of the marvelous hardware systems within a single cell. How many generations to you think you have to produce all this glorious innovation?

    Seriously! Have you ever run the numbers? You are going to use this process to generate the 3 billion pairs of DNA (a DNA structure that extends 39 inches) for a human? How do you put all the systems in place that even allow this process to begin? How does the hardware of the cell even know what to do with the instructions encoded in the DNA? How do you explain creation or improvement of systems that are undetectable or deleterious at the level of reproduction, until hundreds or thousands of simultaneous mutations have occurred?

    Perhaps if you could show me that a few generations of copy errors could turn a Windows PC into a Mac, I might begin to believe that this is an acceptable design strategy for life. But the only evidence you have mustered is the citation of a couple of papers that purport to show that, indeed, it is possible to have a single binary mutation that (by the way) tends to lessen, rather than increase, information in the genome.

    You have not even begun the process of demonstrating that this mechanistic approach to designing complex systems is feasible. Nor has anyone else.

    May God bless you in your journey back to Him.

    • Doug,
      First, I agree with you that there is no clear scientific understanding of how the first cells arose from plain chemicals, i.e. how “the wonder of life” was created. However, that is the subject of abiogenesis, not evolution. Normally evolution deals with changes from generation to generation of living things, usually starting from the first cells.

      Once those first cells with their marvelous capacity to metabolize, reproduce, and sustain changes in their genomes arose, their genomes can change, and change, and change some more. You seem to believe that significant changes in genomes can only make them worse (less fit). That would only be the case if we knew that the very first realization of a genome for a species was the best possible genome for it. But we do not know that, and in fact there are good reasons to believe that is not that case. Thus, you have no basis to maintain that ongoing mutations, coupled with natural selection to preserve the beneficial and weed out the deleterious ones, cannot continue to bring viable change and even improvements to the organism. You may express your incredulity over and over again, but that does not change the facts.

      This is the main reason that your computer programming analogy fails. With a normal computer program, which, say, was written to calculate a numerical result, there is only one right answer. If the program is properly composed and debugged, it will give that one right answer. From then on, any random change that has any effect on the program can only make it worse.

      But that is not the case with biological genomes. As far as we can tell, there is not a single “right” genome associated with a single “right” phenotype, such that any change will make it worse. This question is easily put to the test: take some population, any population that is big enough (say >10,000 vertebrates or >1,000,000 microbes, which had become adapted to one condition, and put them in some other condition, and let them breed and compete for survival. This has been done over and over and over again, and nearly always we observe mutations leading to improved fitness. I cited a number of examples of this . This proves that there is not one single “right” genome which is the best for all circumstances, and also proves that mutations to the genome (coupled with natural selection) can indeed improve the functioning of the organism.

      This also demonstrates another reason your computer code analogy fails. Throwing even one random change into a computer program typically makes it useless. But the genetic code is much more tolerant of changes, per the examples above. I just gave a few examples to illustrate what is out there. If you wanted to engage the literature, you could easily find more.

      You are living proof of the plasticity of the genome. You have about 100 mutational changes compared to the genomes of your parents. These are actual mutations, not just the usual gene shuffling of sexual reproduction. And you have about 1000 mutations compared to your ancestors ten generations back. And yet, here you are, reading your screen as a viable individual.

      These beneficial mutations come in all kinds. They some are single point mutations, which I agree would add no new information. But they also include insertion and deletions of nucleotides, and duplications of whole chunks of DNA, including genes. With some organisms, the entire genome can get duplicated, e.g. with polyploidy in plants. It appears you did not read through the Stan 3 reference I recommended. Here it is in full, for your clicking convenience. https://letterstocreationists.wordpress.com/stan-3-3/

      There I cited several “Examples of Recent Beneficial Gene Duplications”. Gene duplication is an obvious route to increasing the size of the genome. As the duplicated genes mutate and become differentiated from the original, this unquestionably increases the information content of the genome: instead of one Gene A, we now have Gene A and Gene A’. We know genes duplicate and we know genes can mutate to improve fitness. If you are in possession of information which demonstrates that duplicated genes CANNOT mutate and thereby become added, differentiated genes, you should inform the scientific community. Otherwise, you must agree that the gene duplication plus subsequent modification is a viable path to increase the information content of the genome.

      In fact, in some cases we don’t even need to wait for a subsequent mutation — sometimes the copied gene gets altered in the course of duplication. For instance, in the Brown, et al. study of yeast, they found that the evolved strain had multiple gene duplications, and that these new genes were altered compared to the parents: ” Here we have an increase in the number of functioning genes, which is beneficial to the organism. Moreover, the duplicated genes are chimeric: they combine the coding sequence of one parent gene with the promoter sequence of a different gene. Hence, the new genes are not completely identical to either of the parent genes. As discussed above, this gives some novelty and provides additional opportunity for modification of these genes.”

      In comparing the genomes of apparently related animals, one can find differences between them that can reasonably be understood in terms of past gene duplications and modifications. The “antifreeze” gene in certain fish is one of these cases:
      “The Antarctic notothenoid fishes 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 a trypsinogen protease gene was duplicated, and in one copy the The-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. Thus, a gene with an entirely different function was evolved.” [from Stan 3]

      This does not prove that this happened, and if you refuse on principle to believe that any such thing could possibly have occurred, that is fine. But you should know that when biologists peer into genomes they find thousands of such features that can readily be explained in terms of the types of mutations (including duplications) that we can observe occurring in organisms today. This is one of many reasons that nearly everyone with depth knowledge of biology and who is not wedded to a literal interpretation of Genesis find that evolution does a good job explaining the facts.

      I do understand how hard it is let go of the familiar and conservative-endorsed fiat creation of the species. But the church has had to do this on a number of issues. In Galileo’s day, Catholics and some Protestants were convinced that to let go of the literal passages describing how the earth was fixed on its foundations, and how the sun moved or stood still, would be a terrible compromise of unbelief. In the words of Cardinal Roberto Bellarmine (1615), “…to affirm that the sun is really fixed in the center of the heavens and the earth revolves swiftly around the sun is a dangerous thing, not only irritating the theologians and philosophers, but injuring our holy faith and making the sacred scripture false.” You will of course recognize that today’s anti-evolutionists make the same claims about the dreadful theological implications of evolution.

      Enough for now. Best regards…

      • doug says:

        Hi Scott,

        Thanks for taking time to respond. I feel like we are making good progress on defining areas of agreement and disagreement.

        We seem to have many points of agreement. I commend your candor and your concessions concerning abiogenesis. Perhaps rather than saying “there is no clear scientific understanding”, might it not be more accurate to say “there is no plausible materialistic explanation” for the beginning of life? Would not you agree that the best current explanation for the origination of life is supernatural? Don’t you think the existence of life is a clear indication of a creator? Unless you equate being a scientist with being an atheist, it is not a betrayal of science to acknowledge the obvious fingerprints of the supernatural. Galileo did so. Newton did so. Einstein did so. You can too.

        Since we seem to be in basic agreement about the origination of cellular life, I am glad to focus on origins of sophisticated interrelated systems in multi-cellular life.

        There is much here to agree on.

        I agree that natural selection exists, especially if you define natural selection as survival of the fittest, and you define “the fittest” as those who survive. It is a truism, a tautology. Natural selection is merely a way of saying there is “no intelligent selection”—i.e., what occurs (naturally) is what occurs.

        I also agree that mutations occur. I also grant (at least for the purpose of this discussion) that some mutations, at least in certain circumstances, might be beneficial.

        I also agree that life is highly adaptive. We can observe it. It is amazing.

        I suspect you might also agree with the following comments about adaptability. That is, we currently have some limited ability to design flexibility into a mechanistic system. But designing in flexibility requires tremendous sophistication. Our simple attempts pale in comparison to the amazing variety available in life. One of the most amazing features of life, and something that distinguishes life from mechanistic systems, is its ability to adapt. Don’t you agree this is a wonderful feature of life that distinguishes life from mechanistic systems?

        While we agree that life is adaptable, we perhaps differ on the amount of elasticity in that adapation.

        As I understand it, early forms of Darwinism were plausible because Darwin and others did not understand the mechanics of adaptability. For example, because of his ignorance of Mendel’s work in genetics, Darwin believed he could extrapolate the variation achieved by selectively breeding pigeons to provide an explanation for the origin of species. What he did not know was that the pigeon gene pool was what allowed for the variation achievable by selection. But there is a limit to the pigeon gene pool and thus limits to what types of features you can obtain by breeding pigeons. Can we agree on this?

        Neo-Darwinists tried to save Darwin’s notion of Origin of Species with the claim that random mutations can introduce beneficial changes to the genome. Once introduced, the most beneficial mutations are selected for, naturally. Neo-Darwinists use this mechanism and extrapolation to explain both the origin and diversity of species.

        It is this neo-Darwinist, modern evolutionary synthesis that likely separates us. I do not believe it. The two questions I would need answered to move me from my position are the following:

        First: Is the information introduced into the genome by mutations sufficient to explain the existence of the sophisticated interrelated systems that exist in multi-cellular life? For example, is random mutation a source of innovation sufficient to explain the existence of the information necessary to form our central nervous system, hearing, sight, circulatory system, reproductive system and on and on?

        Second–assuming (against all odds) that this information were to appear in the genome through random mutation–is natural selection an intelligent enough mechanism to recognize and retain this information and then use the information to “improve” the genome (whatever that means in a materialistic world view) while at the same time discarding information (arising from bad mutations or obsoleted by good mutations) detrimental to the genome?

        Regarding the second question, John Sanford, and others, make an excellent case that while “natural selection” is well suited to discard detrimental information harmful to the genome, it is not well suited to recognize, retain and utilize the information needed to design new sophisticated, interrelated systems.

        Regarding the first question, many have ably used mathematics to calculate the odds of using random events to produce useful information. For example, I recommend Lee Spetner’s book “Not by Chance”.

        I have found such works persuasive. When I look for helpful documentation from neo-darwinists, I don’t find any.

        The empirical data seems to be against them. For example, they have radiated thousands and thousands of generations of fruitflies. What they got were deformed fruit flies. It seems their attempts to stimulate the appearance of sophisticated interrelated systems through mutations have failed.

        In fact, it seems convention wisdom, even among Neo-Darwinists, is that the more mutations, the worse it is for us. Why else would we be concerned with radiation levels experienced by humans?

        There is also “just so” stories. You mention their existence. That is, Neo-Darwinists make observations about how things are or were and then present imaginative stories about how things could have come about based on mutation and natural selection. However, I don’t think it would be very hard for clever creationists to come up with equally (if not more) persuasive stories. So these tales do carry much weight with me.

        If you want to move me towards your position, you would have to do so by addressing the two questions listed above.

        Thanks again for your interest in the topic. I believe honest wrestling with these issues cannot help but point people towards God and the marvel of His creation.

      • Doug,
        Re: “Would not you agree that the best current explanation for the origination of life is supernatural? Don’t you think the existence of life is a clear indication of a creator? Unless you equate being a scientist with being an atheist, it is not a betrayal of science to acknowledge the obvious fingerprints of the supernatural. Galileo did so. Newton did so. Einstein did so.” – – Let’s look at how this “acknowledge the obvious fingerprints of the supernatural” approach worked out for Galileo, Newton, and Einstein.

        Galileo’s overarching position was that the Bible was given to teach ”how one goes to Heaven, not how the heavens go”, and “in discussions of physical problems we ought to begin not from the authority of scriptural passages, but from sense-experience and necessary demonstrations”. This view is in direct opposition to today’s Young Earth Creationism, which starts with its literal interpretation of the Bible and rejects any physical evidence which contradicts that interpretation. The main point at which Galileo let his theological views influence his science was in rejecting Kepler’s proposal of elliptical orbits for the planets around the sun. Galileo believed that only perfectly round orbits were worthy of the Creator. Wrong answer.

        Newton believed that God had personally set in motion the orbiting planets and comets of the solar system. Right or wrong, that belief did not affect his science. However, he could not account for the long term stability of the orbits of the planets in the face of gravitational interactions among themselves and the comets, so there he fell back on proposing that periodically God supernaturally reached in and readjusted the planets’ positions. This god-of-the-gaps approach is exactly what you are recommending for the origin of life: current science cannot explain X, so X must be a miraculous intervention. Science marched on, and eventually it was found no such supernatural intervention was required to maintain the planets in their orbits.
        Einstein described himself as an agnostic and as a pantheist, and explicitly denied a belief in a personal or supernaturally-intervening God. See https://en.wikipedia.org/wiki/Religious_views_of_Albert_Einstein . One way he let his religious views, such as they were, impact his science was to reject quantum mechanisms with its probabilistic formulations. According to Einstein, God could not possibly “play dice” with the universe. Wrong again: quantum mechanics has since been verified in all sorts of ways.

        All these examples demonstrate the wisdom of Francis Bacon’s advice to avoid mingling or confounding the learnings from Scripture and from science: “Let no man … think or maintain that a man can search too far, or be too well studied in the book of God’s word, or the book of God’s works, divinity or philosophy; but rather let men endeavor an endless progress or proficience in both; only let men beware that they apply both to charity, and not to swelling; to use, and not to ostentation; and again, that they do not unwisely mingle or confound these learnings together.” God-of-the-gaps does not honor our Lord.

        Re: “One of the most amazing features of life, and something that distinguishes life from mechanistic systems, is its ability to adapt. Don’t you agree this is a wonderful feature of life that distinguishes life from mechanistic systems?” This is a wrongly posed question. The adaptability of life is wonderful, but the ongoing metabolism of life is in fact mechanistic, i.e. occurs according to the regular laws of physics. Those laws embrace both deterministic processes and probabilistic processes (where any single event is random as far as we can tell, but there are established statistical patterns across large numbers of such events). Hundreds of thousands of scientists all over the world have been closely studying biological systems for decades, and no “non-mechanistic” event (i.e. something that violates the normal rules of physics) has ever been observed. Also, there is some adaptability in nonliving mechanistic systems – e.g. if you try to topple a spinning gyroscope, it will transform that push into a sideways motion and remain somewhat upright for an extended period.

        Re:” … But there is a limit to the pigeon gene pool and thus limits to what types of features you can obtain by breeding pigeons. Can we agree on this?” Yes, but only for short term breeding projects (e.g. hundreds of years for vertebrates). There you are pretty much limited by reshuffling existing genes (alleles). Longer term (millions of years) there is no such limitation, as that gives sufficient time for beneficial mutations to accumulate.
        Re: “Is the information introduced into the genome by mutations sufficient to explain the existence of the sophisticated interrelated systems that exist in multi-cellular life?” – Yes; in the course of 1+billion years, and combined with natural selection.

        Re: “is natural selection an intelligent enough mechanism to recognize and retain this information and then use the information to “improve” the genome (whatever that means in a materialistic world view) while at the same time discarding information (arising from bad mutations or obsoleted by good mutations) detrimental to the genome?” Yes (though substitute “effective enough” for “intelligent enough”) — I have supplied examples already of this, e.g. beneficial gene duplications, including changes to genes in the course of duplication. Going from Gene A to Gene A + A’ is an increase in genomic information. Again, whole genomes are sometimes duplicated, and then participate in the usual ongoing mutation/selection, which develops new, modified genes. You can find many more examples by reading the bio literature.
        (YE creationists cannot accept this, so they start making up criteria of “specificity” to ward off the reality of gene duplication and modification. They fool no one but themselves).

        I’ll add that looking at the acquisition by bacteria of resistance to antibiotics, like Spetner did, is not likely to yield good examples of information increase. Those organisms are having to combat a chemical which targets some metabolic pathway, so the short term survival response is often to inactivate some aspect of that metabolism. Also, irradiating fruitflies is not a good model of natural evolution – natural mutations are a rich mixture of point changes, insertions, deletions, moving sections of code around, and duplication, mediated by the cell’s transcriptional machinery. Just ripping DNA apart with radiation is not like that at all. One other point to note is that the existence of regulatory regions associated with genes can allow relatively limited mutations to change the body features without requiring the production of whole new genes.

        Re:” John Sanford, and others, make an excellent case that while “natural selection” is well suited to discard detrimental information harmful to the genome, it is not well suited to recognize, retain and utilize the information needed to design new sophisticated, interrelated systems.” – I read John Sanford’s book thoroughly, and found that nearly all of his assertions were false, directly contradicted by the facts. See https://letterstocreationists.wordpress.com/stan-4/ If you want to show me where I was incorrect in my assessment, please feel free.

        Re: “many have ably used mathematics to calculate the odds of using random events to produce useful information. For example, I recommend Lee Spetner’s book “Not by Chance”. “ — I am not planning to read yet another whole anti-evolution book. I have read a number of such writings, and they generally make the same mistake of implicitly assuming that there is only one genome to serve as an end point of the evolutionary process, and then making calculations of how improbable it is to get from there to here. If it were true that there is only one viable ending genome, I’d agree with many of their objections. It is indeed almost infinitely improbable to get from one starting point to any single end genome.
        However, as I pointed out earlier, there are many, many versions of genomes that are viable. All seven billion humans alive today have different genomes, with about 100 mutations per generation accumulated from their ancestors. So if a generation is 40 years or less, since say 3000 B.C. we all have at least 10,000 mutations, placed somewhere amongst the 3 billion sites of our genomes. You can play with the math on this, but you will find that the probability of getting your own specific genome is way, way low, and yet here you are. The fitness landscape is broad and lush, and there are vast numbers of viable genetic combinations along the way. That refutes the main YE creationist mathematical objections. Again, if you have information showing on the basis of pure mathematics that evolution is impossible, do let the scientific community know.

        More on “using random events to produce useful information.” – – in engineering, for instance, a designer might sketch out a trial profile for an airplane wing, say a plain skinny oval, and then let a program run which makes small random alterations in the design. Each new variation is tested for “fitness” by an aerodynamic simulation, and any variation which gives improved lift and drag characteristics is retained as the new basis. This will normally converge to good airfoil. In recognition to the similarity to evolution (i.e. random variations and a selection process), this is called a “genetic algorithm.” The non-symmetric airfoil is more informationally complex than a plain, symmetric oval. This is not intended to be a perfect analog to natural evolution, but it does prove that random events (harnessed with selection) can indeed produce useful information. This refutes YE creationist arguments to the contrary. There was intelligent design of the program, but the programmer did not design the program to solve for this specific airfoil. Once the algorithm was established and running, the random variation & selection process just went along by itself, and converged where it converged. Likewise, the Creator has providentially provided the mechanisms of random changes and natural selection in cells, such that adaptations and informational increase can occur within the natural world without continual miraculous tweaking.

        Best regards….

      • doug says:

        For those of your readers that are interested in a more rigorous (yet very accessible) examination of the very strong (e.g., airtight) scientific case against generating significant biological change (e.g., generation of a new protein) based on random mutation and natural selection, I recommend the following video.

  16. doug says:

    Hi Scott,

    Thanks for taking time to respond. Forgive me for pointing out, but at times discussion with you seems a bit like an interview with a politician. That is, politicians have talking points that they like to insert in response to questions. They do not necessarily answer the questions asked, they just are looking to insert their talking points.

    For example, I have never once raised the issue of the age of the earth. Yet, you continue to bring this up.

    Likewise, the questions I have raised about Neo-Darwinists have all been based on the sufficiency of the mechanism to get the claimed results. You, however, keep raising points about misinterpreting the Bible to come up with claims that clearly conflict with the observable evidence. Of course I do not believe it is correct to do so. I don’t why you even bring this up. I am assuming you are not intentionally trying to smear me or the positions I take. But your tactics seem a bit odd.

    And you bring up “God of the gaps argument”. Where does that come from? I did not raise it. It seems to me that you are the one that is exhibiting a strong philosophical bias. Take abiogenesis. There is no plausible materialistic explanation for the origin of life. There is a very plausible theistic explanation for the origin of life. You even seem to admit the evidence is not there to back up a materialistic origin of life. But your language, e.g., “there is no clear scientific understanding” muddles the obvious point. You appear to have a philosophical bias towards materialistic explanations—and hold them even when the evidence is overwhelmingly against you. Perhaps if enough clever minds work on it, we can come up with a just so story about the origin of life that is not as outlandish as some of the current ones that have to do with aliens or crystals. But until we do, is it that hard, as a Christian, to admit the explanation that best fits the evidence that we currently have is that the origination of life is a miracle of God.

    My main two questions you did make some comments on so I will comment back.
    1. On your assessment of John Sanford, I note I read John Sanford’s book, your assessments, and John Sanford’s response http://creation.com/genetic-entropy. I am not sure what I can add to these discussions. I found John persuasive and you much less so. If John’s defense does not move you—I do not see how any comments I make would move the discussion forward.

    2. Although, you say you have not read Spetner’s book you argue against some points he raises. If you are going to argue against someone’s position, you ought to do so based on what they actually wrote. That requires reading their material. BTW, Lee Spetner has a new book out. I ordered it. I think he is worth reading. It does not bother me that you do not follow my recommendations.

    I agree that many others that have written good books and articles discussing the likelihood of production of useful information by random generation.

    You say you have read some of these works—if so, I think you totally miss the point. For example, you raise the argument:

    “However, as I pointed out earlier, there are many, many versions of genomes that are viable. All seven billion humans alive today have different genomes, with about 100 mutations per generation accumulated from their ancestors. So if a generation is 40 years or less, since say 3000 B.C. we all have at least 10,000 mutations, placed somewhere amongst the 3 billion sites of our genomes. You can play with the math on this, but you will find that the probability of getting your own specific genome is way, way low, and yet here you are. The fitness landscape is broad and lush, and there are vast numbers of viable genetic combinations along the way. That refutes the main YE creationist mathematical objections. Again, if you have information showing on the basis of pure mathematics that evolution is impossible, do let the scientific community know.”

    The point you seem to miss is that when random generation is used, no matter how many useful combinations there are, the useful combinations are always overrun by the noise.

    Let me give you a very simple illustration. In the single sentence in the paragraph above, there are 183 characters, including spaces and punctuations. Given 183 characters, how many meaningful sentences can we come up with? A thousand? A hundred thousand? If you want more, choose a number. A million (10^6)? A billion(10^9)? A trillion(10^12)? A quadrillion(10^15)? Let’s be wildly generous and say there is a quadrillion meaningful messages you can generate using 183 characters. Don’t worry, I won’t make you write them all out.

    OK, now let’s find out how many different combinations there are. Let’s just stick with the punctuation I use (period, comma and space) and ignore capital letters. So for each space there are 29 (26 letters plus three punctuation) possibilities. The total number of possible combinations for 183 characters are 29^183.

    Do you have any concept how big 29^183 is? I don’t. Estimates for the number of atoms in the universe is only 10^81.

    So your likelihood of random generation of a meaningful combination by random chance in a 183 character sentence, using the assumptions above, is about (10^15)/(29^183). Do you know how vanishingly small a number that is?

    And that is when there are only 183 places. A DNA strand is 3 billion pairs!!!!! Let’s assume 4 possibilities (A,C,G,T) for each pair. Suppose we generously assume that your fitness landscape is 10^81 viable combinations (one for every atom in the universe), could a random process generate even one of these among the total combinations (e.g. 4^1000000000000000) in a quadrillion years, with selections made at the frequency of light? Seriously? You think so?

    And your model of evolution does not have to come up with a useful combination once. It has to continually find them. Among all the possibilities (4^1000000000000000), time after time it has to find useful combinations that move the genome forward. By randomness?

    And in the rare event a useful combination arises, natural selection (survival of the fittest) has to detect and retain it, discarding throughout a breeding population all the other useful (but not quite as useful) combinations it replaces. And what happens if it misses the useful combination? How long does it have to wait for the next one?

    This seems like a fairy tale to me. What do you have left to rely on but just so stories? I would suggest it requires a strong philosophical commitment to ignore the implication of these straightforward math calculations.

    God Bless.

    • Hi Doug,
      I will respond to your remarks in roughly inverse order. First, I agree that it would be impossible for a higher organism to sample every single possible genetic combination in a reasonable time. But why would that be necessary? It is not required. Enough viable new combinations get sampled for evolution to move forward. Please see references above.

      You can repeat and restate “…when random generation is used, no matter how many useful combinations there are, the useful combinations are always overrun by the noise “ as many times as you wish, but that statement is simply incorrect. Over and over again, real-time experiments show that beneficial mutations both occur and are selected for in populations with enough time for say, several thousand generations, and enough members for selection to operate. I have links in my articles to published studies on this. It is so straightforward that my daughter did this for a sixth-grade science fair – starting from one strain of bacteria, she evolved a new, salt-tolerant strain by exposing the generations to successively more saline media.

      If you want some quick visuals on this, check out Figure 6 in this paper by Lenski http://lenski.mmg.msu.edu/lenski/pdf/1994,%20PNAS,%20Lenski%20&%20Travisano.pdf
      . He put identical populations of E. coli bacteria in twelve flasks with a new, challenging environment, and just let them evolve for thousands of generations. Figure 6 shows that the fitness of all twelve populations have undergone beneficial (for this environment) mutations, and that these have been selected for. Figure 5 zooms in on the finer details of the progress of one of the twelve populations. You can see how the fitness bumps along at the same level for a while, until a new beneficial mutation takes hold.

      These clear experimental results trump any abstract arguments about how these results are impossible. That is one of my criticisms of John Sanford. It is fine for him to propose a model, but when the model results do not match reality, the honest and correct response of a scientist is to admit that the model is incorrect and modify it, not to deny reality, which is what he does.

      Re “God of the gaps” – the reason I bring this up is because that is precisely what you are doing with the origin of life, although you don’t seem to be aware of it. I tried to explain this to you last round, but perhaps I was unclear. Here is how it is stated in Wikipedia:

      ………The term God-of-the-gaps fallacy can refer to a position that assumes an act of God as the explanation for an unknown phenomenon, which is a variant of an argument from ignorance fallacy. Such an argument is sometimes reduced to the following form:
      There is a gap in understanding of some aspect of the natural world.
      Therefore the cause must be supernatural.
      One example of such an argument, which uses God as an explanation of one of the current gaps in biological science, is as follows: “Because current science can’t figure out exactly how life started, it must be God who caused life to start.”…………..

      Dietrich Bonhoffer explained why this is a bad idea theologically. He wrote of, “how wrong it is to use God as a stop-gap for the incompleteness of our knowledge. If in fact the frontiers of knowledge are being pushed further and further back (and that is bound to be the case), then God is being pushed back with them, and is therefore continually in retreat.”
      It is also bad thinking in general. The reason we scientists have jobs is that there is always something that we cannot explain yet. Sometimes these mysteries remain for many years. No science would get done if we all just threw up our hands and said, “I guess that phenomenon is just a miracle.” The scientific revolution began in Christian Europe, based largely on the conviction that God had chosen to make the physical world orderly and intelligible for humans.
      I grant that it is possible that now, at last, in the origin of life we have finally come to an occurrence in the natural world that falls outside the normal laws of physics and must be described as supernatural. However, that claim has fallen flat on its face so often over the last few centuries that I hope you can understand my reluctance to automatically endorse it here.

      Re: “materialistic bias” – – I am fine with specific miracles that meet New Testament norms (e.g. occurring in response to faithful prayer in the name of Jesus) and appear to be attested as such. For instance, on this site I have called attention to evidence for healing from MS (https://letterstocreationists.wordpress.com/2012/12/11/engineers-wife-healed-of-multiple-sclerosis/ ), healing of a nearly-deaf boy in Brazil (https://letterstocreationists.wordpress.com/2012/08/14/healing-of-nearly-deaf-boy-on-youtube/ ), growing out of short legs (https://letterstocreationists.wordpress.com/2011/03/10/healings-on-youtube-legs-growing-out/ ), and healing of deafness and blindness in Mozambique ( https://letterstocreationists.wordpress.com/2010/10/11/study-healing-miracles-in-mozambique/
      ). But mere lack of understanding of a physical phenomenon is different.

      Re: Young earth creationism – – I did not mean to imply that that is your position. I’m sorry if it seemed that way. I was noting that the usual source from which I hear these anti-evolution arguments is YE creationist ministries. I realize that some old-earth Christians also go along with these arguments.

      Re: “You, however, keep raising points about misinterpreting the Bible to come up with claims that clearly conflict with the observable evidence.” – – I realize there are exceptions, but every person I interact with who is against evolution is driven to that by their interpretation of the Bible.

      You were the one who brought up religion, with “May God bless you in your journey back to Him.” I do appreciate your good wishes, but this statement indicates that you consider someone who confesses Christ as his Lord and Savior and who accepts evolution as being away from God. This suggests that you are someone whose interpretation of the Bible militates against evolution. If so, that would explain why you are making “claims which clearly conflict with the observable evidence” ( e.g. the claim that “when random generation is used, no matter how many useful combinations there are, the useful combinations are always overrun by the noise” ). This is not at all meant as a criticism of you personally. That is the norm in many evangelical circles.

      It was only a few years ago that I was making exactly those sorts of claims. When I felt that a faithful reading of the Bible required rejection of evolution, naturally I gravitated towards reading anti-evolution books like Phillip Johnson’s Darwin on Trial, Huse’s The Collapse of Evolution, Sarfati’s Refuting Evolution, the intelligent design textbook Of Pandas and People, and similar works by Hugh Ross that helped me justify what I thought must be true. These books are still on my shelves.

      It was only after I thoroughly read books on both sides of the issue, and then read hundreds and hundreds of primary research articles to see who was telling the full story, that I was forced to the conclusion that all the available evidence supports evolution, and precludes a special creation of humans. As a PhD, research scientist I had the training and inclination to engage all these diverse studies. I realize not everyone has those advantages. Might I suggest that, instead of reading yet another book from Spetner that tells you what you want to hear, that you read Coming to Peace with Science, by Christian biology professor Darrel Falk. This is a peaceable, easy to understand , medium-length treatment of the issues.

      Although this has been a busy month, I have put considerable time into answering your scientific questions. I have provided specific examples, and links to further reading, to demonstrate the efficacy of beneficial mutations, natural selection, and gene duplication. However, long experience leads me to believe that someone who is wedded to a literal interpretation of Genesis is psychologically incapable of objectively engaging with all the facts. No need to answer me on this, but I encourage you to consider the extent to which your Bible interpretation model drives your view of evolution. That is most likely the real fundamental issue here.
      (You might respond that atheists are driven by similar, opposite concerns, and I agree. But the vast majority of confessing Christians who have opportunity to study geology and biology in detail come to the same conclusion as I have, which is that the facts fit macroevolution and not the various creationist schemes .)

      Bible interpretation is a whole other huge subject. A summary of what I have come to is here: https://letterstocreationists.wordpress.com/2013/11/28/evolution-and-faith-my-story-part-2/
      . That is my approach to being faithful to God’s revelation in His word and in His works. There may well be better interpretative grids than mine.

      If I can, I’d like to be of help to you as an individual. However, my larger concern is a climate of opinion in the church that teaches young people that evolution is incompatible with a biblical faith. I have heard of too many cases where young men who have been taught “If evolution is true, the Bible is false”, go to university, realize evolution is true, and, based on what they have been taught, conclude that the Bible is false. Jesus taught that it is a dreadful thing to cause a little one who believes in him to stumble. If I can influence one Christian parent or teacher or pastor to dial down the antievolution rhetoric, I will feel the work I put into this blog will have been worthwhile.

      Paul’s treatment of a different controversial issue may be relevant here: “Therefore do not let what you know is good be spoken of as evil. For the kingdom of God is not a matter of eating and drinking, but of righteousness, peace and joy in the Holy Spirit, because anyone who serves Christ in this way is pleasing to God and receives human approval. Let us therefore make every effort to do what leads to peace and to mutual edification.” Rom 14:16-19

      Blessings….

  17. doug says:

    Hi Scott,

    I do thank you for taking time. I also note you have been relatively gracious in our discussions. And perhaps because of this, I am hopeful you will understand my points, which are very simple—but which you seem to completely miss. I assume you are not intentionally misunderstanding. So let me try again. I will take your points in order.

    Here is your first point:

    The Mechanism that allows adaptation:
    You argue:
    “If you want some quick visuals on this, check out Figure 6 in this paper by Lenski http://lenski.mmg.msu.edu/lenski/pdf/1994,%20PNAS,%20Lenski%20&%20Travisano.pdf . He put identical populations of E. coli bacteria in twelve flasks with a new, challenging environment, and just let them evolve for thousands of generations. Figure 6 shows that the fitness of all twelve populations have undergone beneficial (for this environment) mutations, and that these have been selected for. Figure 5 zooms in on the finer details of the progress of one of the twelve populations. You can see how the fitness bumps along at the same level for a while, until a new beneficial mutation takes hold.
    These clear experimental results trump any abstract arguments about how these results are impossible. That is one of my criticisms of John Sanford. It is fine for him to propose a model, but when the model results do not match reality, the honest and correct response of a scientist is to admit that the model is incorrect and modify it, not to deny reality, which is what he does.”

    Granted that that E coli bacteria adapted to a challenging environment. That is not what is in dispute. The question that is in dispute is whether random mutation is a sufficient mechanism to explain the adaption. Just observing that an adaption occurs and then concluding (without further proof) that something must be the result of random mutation, is not a proof—it is at best a hypothesis. And when you use very simple math to calculate probabilities, you realize how improbable a mechanism randomness is for generating useful information. The probabilities against random mutations introducing useful information into the human genome are astronomical. These are not hard numbers to calculate.
    So honest scientists (who are not merely propagandists) should recognize that if the probabilities are vanishingly small that random mutations produce useful change, there must be other mechanisms or explanations that produce the adaptations we see.
    I don’t know definitively where the information for positive adaptations come from, but there are some places worth looking. For example, the adaption could be the result of an epigenetic trait. See, Wanner, B. L, (1985) Phase Mutants: Evidence of a physiologically regulated ‘change-in-state’ gene system in Escherichia coli, in Simon, M. and I. Herskowitz (eds.), Genome Rearrangement. Proceedings of the UCLA Symposium April 7-13 1984, where it is suggested that genomic rearrangements could be part of a control system in bacterial that produce heritable changes in response to environmental inputs.
    Your insistence on the creative potential of random mutations, against even the simplest, most obvious computations that show how unlikely this is, hinders searching for the real cause of such adaptations.

    Philosophical Bias:
    Here is what you claim about “God of the Gaps”
    “It is also bad thinking in general. The reason we scientists have jobs is that there is always something that we cannot explain yet. Sometimes these mysteries remain for many years. No science would get done if we all just threw up our hands and said, “I guess that phenomenon is just a miracle.” The scientific revolution began in Christian Europe, based largely on the conviction that God had chosen to make the physical world orderly and intelligible for humans.
    I grant that it is possible that now, at last, in the origin of life we have finally come to an occurrence in the natural world that falls outside the normal laws of physics and must be described as supernatural. However, that claim has fallen flat on its face so often over the last few centuries that I hope you can understand my reluctance to automatically endorse it here. “

    You totally miss the point of philosophical bias. I am not arguing God of the gaps. I am merely arguing that we need to follow the physical evidence wherever it leads, even if it leads us to where we do not want to go. Basically—let’s be honest about what the evidence says. I have a very open mind to the latest discoveries. If the best evidence points to a mechanistic explanation, I can accept that. If the best evidence points to a miracle—I can accept that. You claimed to have read Phillip Johnson’s Darwin on Trial, and this was his central point.
    The Darwinists, among which I presume I can number you, seem to have a closed mind. Darwinists have a priori ruled out the possibility God as the originator and sustainer of life. Darwinists won’t even admit the evidence for it. Even when the evidence is overwhelmingly against them (as it is in abiogenesis) most Darwinists will not admit it. On this point, you seem to be an exception. But you have read the literature—Most Darwinists, without any ability to even propose a mechanism, claim it is a fact that life rose from non-life (at least that is what is communicated to the public). That is not a fact, it is a philosophical bias, a wish, totally unproven, and totally contrary to what we know about life.
    It is dishonest to use the “prestige” of science to fool the public like this. Especially when there is so much at stake. We should be honest about what we know and what we don’t know.

    Biblical Interpretation:
    I apparently touched a nerve here on your past church experience. I cannot speak for whatever negative experience you have in the past.
    As far as discovery what happened in the distant past, I think Solomon summed it up nicely when He said:
    “and I saw every work of God, I concluded that man cannot discover the work which has been done under the sun. Even though man should seek laboriously, he will not discover; and though the wise man should say, ‘I know,’ he cannot discover.”
    There is a certain mystery to the past. We are not going to solve it in this life. The evidence is just not sufficient. We look to the physical universe, but forensic evidence can only take us so far. We look at the Biblical record, and it also provides only a paucity of information about these issues.
    Because of the relative paucity of information, it is easy to interpret the forensic evidence and the Biblical record to support a bias. I think there is plenty of blame to go around.
    What I dislike is propaganda. Some things we can know.
    For example, if you ever take time to run the numbers to calculate the likelihood of random mutations to provide any useful information you would recognize that this is not a rational explanation for designing something as complex as a human being. I suggest you take read outside the biological literature and you will have not trouble confirming how irrational the claim is.

    The numbers are not that hard. You do not need a doctorate to perform multiplication. Common sense should instruct you. Seriously, the human brain—one of the most complex and wonderful things in the universe–happened based on a long string of chance copy errors. To claim this—without any proof but noticing a couple point mutations in bacteria—is a fraud. You know better.

    I admit I sometimes get offended for the honor of my Creator. The claim that “science” knows categorically that the complexity of life, in all its forms, is a result of random mutations, is deception. We cannot know this is the case. If you indeed claim to know life is not His work (or at least you are unwilling to admit the possibility this is His work), this betrays your position and your heart.

    But I hope you are not that closed minded. And if not, your words should reflect that. We need honest thinking scientists to point out errors. I think you are on the wrong side of the argument on Darwinism. I am hopeful you will run the numbers and reconsider. Spetner’s work “Not by Chance” would be a good place to start.

    God Bless.

  18. doug says:

    I did want to add a postscript to my last comment. When I respond, I often sit down to the typewriter, write and post (without much review, as I am engaged in a number or things). But I am afraid, sometimes when I post so quickly, I forget my manners. As a result, I may overstate or incorrectly state your position. I read over this morning what I wrote, and I realize I could have been more gracious to you. For that lack, I apologize. Throughout this discussion you have been gracious, you have engaged the points I raised intelligently, and have communicated honestly your position. This has facilitated open discussion on this topic, which I greatly appreciate.

  19. Hi Doug,
    Re: “Granted that that E coli bacteria adapted to a challenging environment. That is not what is in dispute. The question that is in dispute is whether random mutation is a sufficient mechanism to explain the adaption. Just observing that an adaption occurs and then concluding (without further proof) that something must be the result of random mutation, is not a proof—it is at best a hypothesis. And when you use very simple math to calculate probabilities, you realize how improbable a mechanism randomness is for generating useful information. “

    The results of the “simple math” here depend entirely on the validity of the assumptions from which these calculations begin. In science, whenever possible we test the validity of the model assumption by looking at what the model predicts, and comparing it with the real world. If the model predictions do not match physical reality ,then we know the model results are invalid – either there was a mistake in the calculations, or (more likely) the assumptions were incorrect, So let’s be good scientists and test the hypothesis: Can random mutations be demonstrated to be beneficial ? If they can be so demonstrated in a reasonable trial, that would show that the assumptions that Spetner made were unrealistic, and his model is invalid.

    Elena et al. [“Distribution of Fitness Effects Caused By Random Insertion Mutations in E. Coli.” Genetica 102/103:349-358. (1998)] took a sample of the bacteria from one of Lenski’s E. coli populations which had been adapted to a glucose-only feed medium, and inserted bits of DNA at random locations in the genome. For the purposes of their experiment, they chose conditions that would do only that one kind of mutation (i.e. a single insertion, and nothing else). They made 227 of these mutants. They verified that these insertions were randomly spread throughout the genome, not concentrated in a few hot spots.

    Remold and Lenski [ “Contribution of individual random mutations to genotype-by-environment interactions in Escherichia coli” PNAS September 25, 2001 vol. 98 no. 20 11388-11393 ] then randomly chose 26 of these 227 mutants, and tested them for fitness in a new challenging growth medium, where maltose rather than glucose was the food. If Spetner is correct, then we should see no improvements in fitness here. If the fitness landscape is so terribly sparse, it would take a gazillion random mutations to land on a new, beneficial genetic arrangement. So what did Remold and Lenski find? While most of the mutations were deleterious (as expected), 3 out of the 26 randomly chosen random mutants “significantly improved fitness in maltose.” So 12% no 0%, of these random mutations were beneficial. This contradicts Spetner’s model prediction, and therefore his model is wrong. Again, you can repeat endlessly how impossible it is for random mutations to give adaptation, but the facts say otherwise.

    A notable set of beneficial mutations occurred in one of the twelve populations in Lenski’s long term E coli experiment. The growth medium in all these flasks contained some citrate, in addition to glucose. These bacteria normally are unable to metabolize citrate under aerobic conditions, although a metabolic pathway exists to feed on citrate under anaerobic conditions. In that one population, a strain arose which became capable of feeding on citrate in the aerobic conditions of the experiment. The mutations which gave this ability have been analyzed. I’ll let the investigator himself, Zachery Blount, describe this:

    “ …. My dear little Cit+ cells gained their ability to partake of the previously forbidden citrate by a genetic duplication involving a gene, called citT, which encodes a transporter protein that is used during anaerobic growth on citrate.
    This duplication did something very special. You see, one of the major aspects of gene regulation is that genes have associated regulatory DNA sequences, including what are called promoters that control when genes are expressed. The citT gene is normally controlled by a promoter that tells the cell to turn it on only when there is no oxygen present. As shown in the Figure below, the gene duplication put one copy of citT next to, and under the control of, a promoter that normally controls another gene called rnk. The rnk gene is normally turned on when oxygen is present. The new association between citT and the rnkpromoter – what we call the rnk-citT regulatory module – turns citT on when oxygen is present, and allows Cit+ cells to use citrate under the conditions of the LTEE. (To really feast on the citrate involved additional evolutionary changes, both before and after this rewiring, but I’ll leave that point aside for this post.) “

    So a gene was duplicated, and acquired a change in functionality. We started with Gene A, and now we have Gene A and Gene A’, where A’ is functionally different from A. By any reasonable definition, this constitutes a gain in genetic information, and happened to confer a big benefit on the organism. If you still want to claim that this particular gene duplication was NOT due to normal physical processes, then you need to provide some positive evidence instead of just repeating that some calculations based on some assumptions show it is impossible. I realize that if all this material contradicts your Bible interpretation you will not really be able to take it in.

    Re: “If the best evidence points to a mechanistic explanation, I can accept that. If the best evidence points to a miracle—I can accept that.” – – You appear to be so wedded to god of the gaps thinking that you cannot recognize that that is what you are doing. Here you changed the wording, but that does not change the essence. What does it mean for the “best evidence to point to a mechanistic explanation” ? If we had some preliminary evidence for a mechanistic explanation of something, it would no longer be a gaping gap in our understanding. To have a gaping gap normally means that we do not have even the beginnings of a mechanistic understanding, and so we cannot claim that “the best evidence points to a mechanist explanation”. You are saying that in that case we should invoke a miracle.

    Examples: ( a) Natives in South American jungle I read about (don’t remember name), who had no mechanistic understanding of disease as physical cause and effect. They therefore (following your reasoning) ascribed disease to supernatural entities. (They took this so seriously that if one of their tribe got struck down by disease, they assumed it was due to a curse from their rival tribes, so they would go kill one of their rivals for revenge; when Christian missionaries came, they shared the scientific vision of an orderly and intelligible universe, and put a stop to these revenge killings) . (b ) In 1900, geologists and biologists knew the earth had to be hundreds of millions of years old to account for today’s landforms and organisms, since they know erosion and mountainbuilding, and evolution, to be very slow processes. However, an earth that was hundreds of millions of years old would have lost all of the heat of its core to outer space, so there should be no molten rock beneath the crust and no volcanic activity. There was absolutely no known mechanism that could have kept the inner earth hot for so long. By your logic “the best evidence pointed to a miracle”. (It turns out the radioactivity of elements in the earth is what keeps it hot down there).

    So again, all you are saying is that if there is a gaping gap in our understanding, such that we cannot propose any credible mechanistic explanation at the present time (as is the case with abiogenesis), we should invoke the miraculous. This is precisely god of the gaps mentality.

    Re: “The claim that “science” knows categorically that the complexity of life, in all its forms, is a result of random mutations, is deception. We cannot know this is the case. If you indeed claim to know life is not His work (or at least you are unwilling to admit the possibility this is His work), this betrays your position and your heart.” – – Now we may getting down to the nub of our disagreements. You seem to feel that there is an antithesis between random events and the work of God. Thus, if life is His work, it cannot have come about via random mutations. That is incorrect. I respectfully suggest that your view of God is too limited.

    I encourage you to ponder Proverbs 16:33. In the King James this reads “The lot is cast into the lap; but the whole disposing thereof is of the LORD.” The Basic English Translation paraphrases this as “A thing may be put to the decision of chance, but it comes about through the Lord.” My faith in God is big enough that I believe that He can work providentially through events that are random, and also through events that seem to have come about deterministically from prior conditions. By “random” I mean events which from the human point of view are indeterminate. They may appear purposeless to us, but that does not mean they are outside God’s control or purpose.

    As noted, your genome contains thousands of random mutations accumulated over prior generations. Did these occur outside of God’s will and control? Or were they a part of producing the unique individual that you are, a man suited to the good works prepared for you before the world began (Eph 2:10). Random mutations are as much His work as anything else that happens.

    We understand fairly well the mechanisms of nucleation and condensation, and of air movements. There is nothing to indicate that rainfall is supernatural. Nevertheless, it is God who governs the distribution of rain, and it happened that He chooses to distribute rain on the just and the unjust (Mat 5:45).
    Perhaps you have been spooked by atheists who claim that the progress of evolution via random mutations (and natural selection, etc.) displaces God. Their claims are absurd. Let us reply to the bad reasoning of the atheists with good reasoning, not with bad science.

    Best wishes….

  20. doug says:

    Hi Scott,

    It does not seem you have correctly understood Spetner’s position or adequately explained my position.

    Let me first address whether you have demonstrated that “the assumptions Spetner made are unrealistic and that his model is invalid.”

    I have to start by asking what assumptions are you discussing and what model are you referring to?

    How would even know what Spetner’s assumptions are or his model is if you do not read his work?

    I am just now working through his new book, and I would have to say that as far as I can understand, none of the experimental data from Remold and Lenski you cite dispute what he says. Instead it seems to confirm it.

    Spetner (The Evolution Revolution, p. 51) cites a very interesting study by Hillenmeyer that appeared in Science in 2008. An experiment was performed on yeast in which each of its 6000 genes was deleted, one by one. Of these 6000 genes, 34% were found to be necessary for the proper function of the cells under normal conditions because their deleting was either lethal or led to growth defects. The remaining 66% of the deletions showed no effect under normal conditions. Almost all of these (63% of the total), however, showed growth defects under various environmental changes. The remaining 3% showed no effects in this experiment.

    Spetner’s point was this: experimental data such as this show that there are DNA sequences that have no effect on the functioning of the organism under ordinary circumstances, but which play a role under extraordinary conditions.

    The more general point is that there is a lot of inactive functionality within the DNA of single cell organisms that can be turned on or off as a result of stress to the cell or whatever.

    Certainly it would come as no surprise to Spetner that a study shows that when one starts making random changes to a cell, it might result in turning on or off some latent functionality in a cell that improves or hinders a cell’s fitness in maltose or other environments.

    I would suggest that his assumptions would expect such a result. The results certainly do nothing to show that his model is invalid.

    You summarize my position like this: “So again, all you are saying is that if there is a gaping gap in our understanding, such that we cannot propose any credible mechanistic explanation at the present time (as is the case with abiogenesis), we should invoke the miraculous. This is precisely god of the gaps mentality.”

    That is not my message at all. My message is not that God must be invoked when there are gaps in our understanding. Rather, my message is that we should not promote absurd and obviously wrong explanations to fill these gaps to discourage people from recognizing the necessity of God. Let’s be honest and forthright and shut down the propaganda.

    Look, if you don’t want to believe God created life, that is fine. But don’t lie and tell people “science” has proved life springs up naturally from non-life.

    Be open. Say philosophically we would like to believe that life springs from non-life, but there is no evidence that this is possible. Nevertheless, we would like to believe it, so we do. We will look for evidence. And if we ever find any we will fairly report it to you.

    Since this is a philosophical position, why involve science at all, since it is not on your side?

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