Hoist on its own petard: ENV’s two “fake science” stories turn out to be genuine

Two articles exposing “fake science” claims have recently been published over at Evolution News and Views. One article attacks the fossil evidence for whale evolution, while the other seeks to discredit the claim that human and chimp DNA are 99% identical. Both articles suffer from serious scientific flaws.

“Fake science” Story No. 1: Whale evolution – too little time for it to happen?

Let’s start with whales. In an article titled, Fake Science: Whales as the “Sweetest Series of Transitional Fossils” an Evolutionist Could Ask For (January 3, 2017), David Klinghoffer writes (bolding mine – VJT):

Back in the day, paleontologist Stephen Jay Gould found in whales “the sweetest series of transitional fossils an evolutionist could ever hope to find.”…

…In truth, the “picture-perfect intermediacy,” which Gould commended as a weapon to be deployed against “creationists,” looks increasingly like a patchwork. The situation was made worse by the recent documenting of a 49-million-year-old Antarctic whale jawbone fossil that narrowed the window available for the evolution from a fully terrestrial ancestor to an unbearably rushed 1 million years.

If we go back to the ENV article linked to in the quote, we find that the age estimate of 49 million years for an Antarctic whale jawbone supposedly comes from a recently published scientific paper titled, Eocene Basilosaurid Whales from the La Meseta Formation, Marambio (Seymour) Island, Antarctica by Mónica Buono, Marta Fernández, Marcelo Reguero, Sergio Marenssi, Sergio Santillana and Thomas Mörs (Ameghiniana 53(3):296-315, June 2016). At the other end, the ENVarticle estimates that the supposed “fully terrestrial ancestors of whales” lived “at about 50 Ma [million years ago].” Take 49 million years away from 50 million years, and you get a maximum window of one million years for fully terrestrial mammals to evolve into fully aquatic whales – which is impossible.

Smashing the myth of the one-million-year window

The problem with this argument is that neither the 49-million-year figure nor the 50-million-year-figure is correct. Both figures have been thoroughly debunked in a brilliant little blog article by Bill Needle, titled, New Basilosaur Fossil vs The Discovery Institute! (November 21, 2016). Needle quotes from a 1998 article describing a newly discovered whale ancestor called Himalayacetus, titled, “A new Eocene archaeocete (Mammalia, Cetacea) from India and the time of origin of whales” by S. Banjpai and P.D. Gingerich (in PNAS, December 22, 1998, vol. 95, no. 26, pp. 15464-15468):

Himalayacetus is significant because it is the oldest archaeocete known and because it was found in marine strata associated with a marine fauna. Himalayacetus extends the fossil record of whales about 3.5 million years back in geological time, to the middle part of the early Eocene [53.5 million years ago (Ma)] [author’s parentheses]… When the temporal range of Archaeoceti is calibrated radiometrically, comparison of likelihoods constrains the time of origin of Archaeoceti and hence Cetacea to about 54–55 Ma (beginning of the Eocene), whereas their divergence from extant Artiodactyla may have been as early as 64–65 Ma (beginning of the Cenozoic). (Bolding mine – VJT.)

It should be noted that the Archaeoceti were not “fully terrestrial”: they were at least partially amphibious. Since the oldest known amphibious ancestor of whales appeared 54 million years ago (not 50 million years ago), the terrestrial ancestor of this creature must be even older than that.

What about the 49-million-year figure for the Antarctic whale? The problem is that the authors of the paper describing the fossil actually propose a different figure. They acknowledge uncertainties in the dating, but think an age of 40-46 million years is most likely. In their words (bolding mine – VJT):

Age control within the La Meseta Formation has been based primarily on biostratigraphy and suggests that its deposition spanned during much of the Eocene, but there is uncertainty about the precise age of particular units within this formation. In particular, the age of the lower part of the La Meseta Formation (TELMs 2-5), where MLP 11-II-21-3 was collected, is still disputed… TELM 4 includes a significant number of reworked shells, which could have biased the strontium-isotope data. The uncertainty is heightened by the small degree of variance in the global seawater curve for the early to the middle Eocene…

A younger age for TELM 4 and TELM 5 has been discussed as a feasible alternative to an early Eocene age in a number of publications…

In summary, considering that 87Sr/86Sr ratios provided for TELM 4 might be biased (because of potential reworking and oscillation of the marine Sr isotope curve during the Eocene), we interpret the age of the horizon that produced MLP 11-II-21-3 (i.e., TELM 4) as early middle Eocene (~46- 40 Ma; middle Lutetian to early Bartonian based on ICS International Chronostratigraphic Chart 2015; Cohen et al., 2013) and follow the most recent chronostratigraphic interpretation for the La Meseta Formation. This age is also more consistent with the published stratigraphic record of basilosaurids elsewhere.

In view of the uncertainties highlighted above, it would be foolish to attach any confidence to the original age estimate of 49 million years for the Antarctic whale jawbone, which was the figure reported back in 2011.

Let’s be conservative, and assume a figure of 46 million years for the whale. That gives us at least 8 million years (54 million minus 46 million) for terrestrial creatures to evolve into aquatic whales. The ENV article disputes the figure of 46 million years, arguing that an age of 49 million years is more consistent with the biostratigraphic data. But even if the original estimate of 49 million years were correct, we’d still have 5 million years for whales to evolve. That’s a geologically short time, but it’s a lot more than 1 million years.

As if that were not embarrassing enough, it turns out that the original Associated Press article by Michael Warren, which Casey Luskin blogged about in ENV back in 2011 actually refuted claims of a 1-million-year window for whale evolution. Allow me to quote a short excerpt from the Associated Press article (bolding mine):

Argentine paleontologist Marcelo Reguero, who led a joint Argentine-Swedish team, said the fossilized archaeocete jawbone found in February dates back 49 million years. In evolutionary terms, that’s not far off from the fossils of even older proto-whales from 53 million years ago that have been found in South Asia and other warmer latitudes.

That still leaves 4 million years for proto-whales to evolve into fully aquatic whales. And remember, these proto-whales would have been partly amphibious. Evolution from a terrestrial ancestor to a fully aquatic whale would have taken even longer. And for those who think that a few million years is not enough, I would advise them to read my Uncommon Descent article, Are 3,000 beneficial mutations enough to transform a land animal into a whale?” (February 2, 2016).

I conclude that the “1-million-year window” is a myth, and I hope that Evolution News and Views will have the grace to publicly acknowledge their error.

So much for whales. What about humans and chimps?

“Fake science” Story No. 2: Are humans and chimps 99% genetically identical?

In his ENV article, Fake Science: “About 99 Percent of Our DNA Is Identical to That of Chimpanzees” (January 3, 2017), David Klinghoffer dismisses the 99 per cent claim, which he evidently regards as socially pernicious, as he thinks it blurs the vast distinction between humans and chimpanzees:

Man, this is a piece of fake science that, in the popular media, has taken on a life of its own. With fine timing, our colleague Sarah Chaffee has lately offered a four-part interview with Discovery Institute biologist Ann Gauger on the 99 percent myth. The series for ID the Future is here, here, here, and here.

Are humans and chimps effectively identical in our respective DNA? The short answer is no, no way: not in our DNA, coding and non-coding, not in the way our genes are expressed, how chimps splice their DNA, the existence of human-specific genes, and more, not to mention how this all cashes out in terms of anatomy and behavior.

Errors in the chimpanzee genome?

I’ll confine my discussion to the first two parts of Sarah Chaffee’s four-part interview with Dr. Ann Gauger. In the first section, titled, How Chimps and Humans are Different, Pt. 1: The Genome, Dr. Gauger criticizes the sloppy of the Genome Consortium that did the sequencing for chimp DNA (bolding mine):

Now, sequencing is also complicated because there’s a certain amount of error rate that goes into reading nucleotides. Mistakes happen for various reasons. It’s not a perfect read each time you do it. So the way around that problem is to read through the sequence multiple times. And if five out of six times you get an A [adenine] in that position, then you’re pretty confident that it should be A. Well, they only did the chimp sequence with a 3.6-fold redundancy. That means they read through the same stretch of DNA three or four times. Now you can guess that getting one out of four wrong might be fairly convincing, but if you have two out of two, you’re not going to know which way you should go. It’s much more convincing if you do twelve reads, and you find two out of twelve have one read and the other ten are different. And you can say with pretty good confidence that the ten-read versions are correct. So what does this mean for the chimp genome? Only a 3.6-fold redundancy means that there is a chance that error has crept into the sequence.

What Dr. Gauger omits to mention is that the 2005 paper in Nature which reported the findings of the Chimpanzee Genome Consortium specifically addressed the question of accuracy, right after the paragraph highlighting the 3.6-fold redundancy that Dr. Gauger mentions above. Here’s what it says (bolding mine):

Nucleotide-level accuracy is high by several measures. About 98% of the chimpanzee genome sequence has quality scores of at least 40 (Q40), corresponding to an error rate of ≤10-4.

That’s an error rate of 1 in 10,000. I don’t think we need to worry too much about errors in the chimpanzee genome.

And to cap it all, Dr. Gauger’s figure of a 3.6-fold (or roughly four-fold) redundancy in the chimpanzee genome is out-of-date. In fact, a chimpanzee genome with six-fold redundancy is now available, making it much more accurate than Dr. Gauger suggested. The following quote is taken from the Pan troglodytes [chimpanzee] Web page of the McDonnell Genome Institute at Washington University (bolding mine):

The chimpanzee genome was sequenced to 4X coverage initially, in collaboration with the Broad Institute at MIT and Harvard. A male chimpanzee known as “Clint”, from the Yerkes National Primate Research Center was chosen as the reference chimpanzee genome. Our center subsequently produced additional (2X) whole genome coverage utilizing a combination of whole genome plasmid reads as well as fosmid and BAC end sequences. The total 6X genome sequence coverage has been assembled and is now being evaluated for quality prior to release to the public through established genome web browsers.

As far back as 2013, creationist Dr. Jeffrey Tomkins was aware that the “present chimpanzee genome assembly now includes a total 6-fold redundant coverage,” as he mentioned it in an article for Answers in Genesis. Dr. Gauger seems to have missed out on this item of news.

92% or 99% similarity?

In her interview with Sarah Chaffee, Dr. Gauger goes on to argue that the true level of genetic similarity between humans and chimps is no more than 92%:

The Genome Consortium that did the sequencing for the chimps, they calculated it as [a] 1.23% difference between us and chimps, or if you take into account the fact that not all humans have the same DNA sequence, 1.08%. Now obviously that’s a very, very low level of difference, but that’s just counting the differences that could be detected by their method of sequencing, and what that method of sequencing misses is small insertions and deletions. And according to some calculations, small insertions of a few bases – up to 100 bases – can occur at a frequency of 2 to 4% – so that already jumps us from 1 to 4 to 5% difference. Then there are other things that would not be counted well: large duplications in our genome, compared to chimps, represent 2.7% that wasn’t accounted for by that method of sequencing. So we’ve added 2 to 4% to 1% to 2.7%. Then there are other small differences. I would say that my best estimate is that we are at least 8% different in our DNA from chimps.

Professor Larry Moran wrote about insertions and deletions several years ago, in a 2012 post discussing the oft-cited claim that humans and chimps are 98% genetically identical:

Britton (2002) challenged that number by pointing out that humans and chimp genomes differed by a large number of insertions and deletions (indels) that could not have been detected in hybridization studies. He claimed that there was an additional 3.4% of the genome that differed due to indels. That means the the real difference between humans and chimps is closer to 5% and we are only 95% identical!

Much of the difference is due to insertion and deletion of members of gene families. One study shows that the human genome has 689 genes not present in the chimp genome…

At first glance this looks like 689 completely new genes have evolved in the human lineage since it diverged from our common ancestor with chimpanzees but looks can be deceiving. These genes are members of gene families and all that’s happened is that 689 orthologous genes have been lost by deletion in the chimp lineage or 689 new parologous genes have been “born” by gene duplication (or some combination).

In any case, as creationist scientist Dr. Todd Wood explains in a blog article titled, Chimp genome again (September 28, 2010), Britton was wrong in arguing that humans and chimps are only 95% genetically similar, due to insertions and deletions in the human genome. Wood illustrates his point with a hypothetical example (bolding mine):

Britten was wrong. His strategy of counting indels doesn’t actually make any sense at all. Consider a simple example. Say you have two sequences, one 50,000 nucleotides long and the other 55,000 nucleotides long. The only difference between them is a single insertion of 5,000 nucleotides. Otherwise, the sequences are identical. What then should the percent identity be? Should it be 90%, counting the 5000 nucleotide difference as 10% of the smaller sequence? Or should it be 91%, counting the 5000 nucleotide difference as 9% of the total sequence in comparison (55,000)? Neither one makes any sense, since the reality is that there is only one difference between the sequences. It’s a single insertion or deletion, representing one mutation. Why should we count that as 5000 differences when there’s only one mutation?

…[I]f you specify precisely what you mean, you can talk about the number of nucleotide mismatches between two genome sequences at some kind of optimal alignment (which, of course, is debatable as to how you get that optimal alignment). When you do that with the human and chimp genomes, the percent identity is well north of 95%. When you realize that there is no single human genome and start discounting polymorphisms from your counts, then the actual fixed nucleotide mismatches between humans and chimps are probably less than 1%, making a percent identity of >99%.

In his hypothetical example, Dr. Wood wrote as if there was only one mutation that accounted for all the insertions and deletions (indels) in the human genome. In reality, of course, “the actual number of mutational events is in the millions,” according to Professor Larry Moran’s blog article, What’s the Difference Between a Human and Chimpanzee? (January 23, 2012).

Dr. Todd Wood’s series of articles on human-chimp similarity can be accessed here, and is well worth reading:

RTB and the chimp genome Part 1
RTB and the chimp genome Part 2
RTB and the chimp genome Part 3
RTB and the chimp genome Part 4
RTB and the chimp genome Part 5
RTB and the chimp genome Part 6

And what about the “large duplications” discussed by Dr. Gauger, which are said to make up 2.7% of the human genome? These are simply places where two pieces of human genome align with only one piece of chimpanzee genome, or two pieces of chimpanzee genome align with one piece of human genome. So far from weakening the case for human-chimp similarity, they actually strengthen it, by showing that multiple pieces of the human genome may show a high degree of similarity to a piece of the chimpanzee genome, and vice versa.

Genes which are unique to human beings

In the second part of her interview with Sarah Chaffee, titled, How Chimps and Humans are Different, Pt. 2: Human-Specific Genes, Dr. Gauger talks about genes which are allegedly unique to human beings:

We have 20,000-or-some genes. We actually have a certain number that are unique to us, not present in chimps. Estimates vary as to how many there are, because it’s actually a moving target: scientists keep changing what they consider to be unique, and whether it’s a real gene or not. So some estimate 300, some estimate over 600 genes that are unique to humansAs many as 60 of these new genes didn’t come from existing genes, but apparently came from repurposing of other DNA, which we’ll talk about later….

I have already quoted Professor Moran’s explanation of how the large number of genes that are unique to humans may have arisen. But what about the 60 new genes that didn’t arise from existing genes?

I blogged about these 60 genes on Uncommon Descent, in a post titled, Double debunking: Glenn Williamson on human-chimp DNA similarity and genes unique to human beings (October 24, 2015). Briefly, what Williamson found was that these genes had non-coding counterparts in apes that were approximately 98.5% identical. Yes, that’s right: 98.5%.

Gene regulation

Later in her interview, Dr. Gauger talks about differences in gene regulation between humans and chimps:

In fact, there are substantial differences in expression of genes we share with chimps, just as King and Wilson, whom I mentioned earlier, predicted in 1975. And here’s an interesting fact: those differences in expression are particularly true in the brain. So what regulates that gene expression? There are these proteins called transcription factors, that bind to the DNA and either shut it off or turn it on. And roughly 1 to 3% of them are human-specific. So they’re going to be turning on different genes in humans than in chimps. So that contributes to our uniqueness. Not only do we splice our genes differently, we also have different gene regulation.

So by Dr. Gauger’s own admission, 97 to 99% of transcription factors are not human-specific, but are shared between humans and chimps.

Genetic similarities do not equate to similarities in anatomy and behavior

The ENV article by David Klinghoffer lists differences in “anatomy and behavior” as its final reason for rejecting claims of a 99% genetic similarity between humans and chimps. The logic of this passage escapes me. Unless you’re a reductionist, you would never be tempted to imagine that a 99% genetic similarity between humans and chimps would translate into a 99% anatomical similarity, let alone a 99% behavioral similarity. The vast intellectual and moral gulf between humans and chimpanzees should be abundantly obvious to anyone who has ever observed a chimp. The fact that we last shared a common ancestor with the chimp six or seven million years ago in no way negates the reality of this gulf. It’s what happened after our paths diverged that’s the most interesting chapter of the human story.

Conclusion

There is a saying that truth is not served by bad arguments. The two ENV articles on “fake science” which I have critiqued in this post turned out to be an expose that backfired badly, as key claims that were made in the articles were demonstrably wrong. Errors like these do not help the case for Intelligent Design. If you want to argue that whales were designed or that human beings are special, then that’s fine; but you should not build your case on a scientific house of cards.

221 thoughts on “Hoist on its own petard: ENV’s two “fake science” stories turn out to be genuine

  1. Patrick: Please list all the internal contradictions in evolutionary theory of which you are aware.

    It isn’t a scientific theory as it doesn’t have a way to scientifically test its claims.

  2. phoodoo: I don’t buy the continuous regress argument for a even minute.I don’t exist in the other world which needs examining and explaining, I only exist in this one.

    I am not fond of the possible world argument either.This universe is plenty.

    When I exist in some other world, then I can try to understand its cause and meaning.We can literally only strive to understand this one.

    I agree with that too.

    It is like trying to experience infinity, when you are finite.There really is no point.

    Looking at the night sky away from all lights is as close as I can get.

    However, my comment involves this universe. If intelligence is required for design, eventually you need an non designed intelligence.If meaningless chemicals result in that intelligence,ID is unnecessary. The only other option I can imagine would be that intelligence is non designed because it is uncaused.

  3. The vast intellectual and moral gulf between humans and chimpanzees should be abundantly obvious to anyone who has ever observed a chimp

    Vast compared to what? A starfish? A yeast cell? A spirochete? Considered against the full diversity of life on earth humans and chimps are almost indistinguishable.

  4. Mung: I absolutely agree with VJT that bad science doesn’t help the ID cause.

    But of course when bad science is all you have you have to run with it

  5. There is a saying that truth is not served by bad arguments.

    Truth has never been the aim of ID.

    Conflating their definitions and “conclusions” with the truth has been the goal. Bad arguments are all that serve their purposes.

    Glen Davidson

  6. Mung,

    It’s capable of containing within it’s purview other contradictory evolutionary theories.

    What like one person arguing for paraphyly and another for monophyly? That was your contribution when asked.

    One has to wonder how evolutionary theory resolves its internal contradictions

    Yes, there is nothing in evolutionary theory allowing such debates to be resolved. Nothing.

  7. vjtorley:
    Hi Sal,

    Thanks very much for the link to paleontologist Gunter Bechly’s talk:

    https://youtu.be/KcT61jEnJF8

    I’ll take a look at it tonight. Cheers.

    Sal and/or Vincent: I would very much like to see a post summarizing this very long talk and Bechly’s views. I’ve gone about a third of the way through it, and it’s a painful way to introduce the subject. He’s longwinded and he tends to digress and simultaneously begin mumbling toward the end of each point. And of course I disagree strongly with much that he says.

  8. Neil Rickert: It is pretty much meaningless to say “life is destined to achieve”, if you get to make up what was achieved only afterward.

    Thus I said your theory of evolution is impossible to articulate.

  9. Richardthughes,

    VJ hasn’t even explained WHY we shouldn’t expect to see a 1% difference in form in organisms, if there is a 1% difference in the genetic code which makes those forms, and this is the ONLY theory we are allowing to be taught in schools, so maybe we better first sort out what this ONLY theory is trying to say first.

    Its a falsifiable theory, right? Right???

    Guerilla skeptics in action.

  10. phoodoo:
    Richardthughes,

    VJ hasn’t even explained WHY we shouldn’t expect to see a 1% difference in form in organisms, if there is a 1% difference in the genetic code which makes those forms, and this is the ONLY theory we are allowing to be taught in schools, so maybe we better first sort out what this ONLY theory is trying to say first.

    Its a falsifiable theory, right? Right???

    Guerilla skeptics in action.

    Take a 100 equations with 50 arithmetic operators and 50 numerical constants. randomly change either an operator or a constant and compare the result to the original equations result. Do you get on average a 1% difference? You changed 1% of its genome…

  11. Regarding the charge that these papers by evolutionary biologists are “fake”, it is worth remembering that to ENV, most papers in evolutionary biology are “fake”. At UD, the ever-astonishing Denyse O’Leary hammers away at this by trumpeting cases of fraud in scientific research, as if that were the norm, and endlessly emphasizing that peer review doesn’t work.

  12. newton: Looking at the night sky away from all lights is as close as I can get.

    I can’t imagine a life where I have not spend at least one night looking at a clear night sky through, at least, a set of binoculars. Where you see one bright spot with the naked eye, you can perhaps see as many as 10 with a simple pair of binoculars. This experience of “depth” when looking at the stars, and the knowledge of the incomprehensible distances involved and the amount of time it takes for that light to travel here, will make hairs stand every time.

    It is nothing short of a transformative and deeply humbling experience. Even thinking about it can bring that experience on. A stange experience that can’t quite be described, a feeling of joy, without it being quite like what I’d call “pleasure”, a feeling of peace and relaxation, yet at the same time wild and able to make your heart pound, and a feeling of a deep connection, and understanding, of something overwhelming, yet so far away it can never be reached.
    I’m sure that if I was a religious man, I’d attribute this to an “experience of God” or “witness of the holy spirit” or something along those lines.

  13. phoodoo,

    Thus I said your theory of evolution is impossible to articulate.

    One shouldn’t regard personal failure as a reflection on everyone’s capacity. But this would explain why you had no contribution to make to the thread on that very topic. As I said third post in, phoodoo objects to something, but it is impossible for anyone to articulate what it is …

  14. REW: Considered against the full diversity of life on earth humans and chimps are almost indistinguishable.

    Wow- I could never get the two confused. And there isn’t any evidence that changes to a genome can account for the anatomical a physiological differences observed. And that means there isn’t any science behind the claim that chimps and humans share a common ancestor.

  15. Rumraket:

    It is nothing short of a transformative and deeply humbling experience. Even thinking about it can bring that experience on. A stange experience that can’t quite be described, a feeling of joy, without it being quite like what I’d call “pleasure”, a feeling of peace and relaxation, yet at the same time wild and able to make your heart pound, and a feeling of a deep connection, and understanding, of something overwhelming, yet so far away it can never be reached.

    “Awe”, perhaps?

    Nicely written, by the way.

    I’m sure that if I was a religious man, I’d attribute this to an “experience of God” or “witness of the holy spirit” or something along those lines.

    Thereby cheapening it.

  16. phoodoo,

    That explains why I had nothing to add on the topic of there being no theory of evolution? What I am supposed to add, another NOT theory?

    You are the one endlessly reasserting the notion “there is no theory of evolution”, as if it is a vital contribution to the evolution-Creation debate. There is a thread just for you to elaborate your meaning if you so choose. But instead you simply to repeat the assertion at the drop of a hat, in every thread but that one. OK phoodoo, got it. There is no theory of evolution. Now back to our normal programming.

    You seem to have nothing to add about where knowledge is stored in the genome, and about how you know that non-coding DNA has no function.

    I know that non-coding DNA has function. It would be ridiculous to assert otherwise. What is less secure are the notions that

    /1. Because some non-coding DNA has function, all of it does.
    /2. Every difference, be it in a functional or a nonfunctional region, is a functional difference.

    Suppose I wrote a brief program, in which it was functionally essential that a, b and c all had the same value.

    a:=b
    c:=b

    Or wrote it this way:

    a:=b
    c:=a

    Is that a functional difference?

    That is a completely uneducated and unfounded position. No wonder you don’t defend it.

    Despite the many words I use? You are a curious individual.

  17. Allan Miller,

    Oh course if you didn’t write the program, you have no idea what the programs purpose is, and you are not a computer programmer, you could have very little to say about what the program code does or doesn’t do.

  18. phoodoo,

    Oh course if you didn’t write the program, you have no idea what the programs purpose is, and you are not a computer programmer, you could have very little to say about what the program code does or doesn’t do.

    One can look at the functional consequences of a program without knowing how to write them.

    There must logically be some differences in some parts of the genome that make no functional difference, surely? It’s certainly true of iPods and other designed objects. Why not biology? This is the kind of cleft stick one ends up in in trying to simultaneously invoke a Design inference and deny Common Descent (on the continuing mistaken belief that the latter only works in non-functional regions).

    It’s Design, Jim, but not as we know it!

  19. Rumraket:

    It is nothing short of a transformative and deeply humbling experience. Even thinking about it can bring that experience on. A stange experience that can’t quite be described, a feeling of joy, without it being quite like what I’d call “pleasure”, a feeling of peace and relaxation, yet at the same time wild and able to make your heart pound, and a feeling of a deep connection, and understanding, of something overwhelming, yet so far away it can never be reached.
    I’m sure that if I was a religious man, I’d attribute this to an “experience of God” or “witness of the holy spirit” or something along those lines.

    Exactly. And it makes the whiskey taste better too

  20. phoodoo takes exception to my remark:

    Unless you’re a reductionist, you would never be tempted to imagine that a 99% genetic similarity between humans and chimps would translate into a 99% anatomical similarity, let alone a 99% behavioral similarity.

    He evidently believes that the default expectation is that 99% genetic similarity would translate into 99% anatomical and/or behavioral similarity. Let me give a simple example to show why this is not the case.

    We are all familiar with the notions of a genetic code and a genetic program. So let’s talk about programs. Let’s imagine there are two computer programs, A and B, and that 99% of their code is the same. Would anyone expect 99% of their output to be the same? Or would anyone expect the two programs to behave in the same way, 99% of the time? I think not. Why, then, would anyone have that expectation when it comes to the genetic programs that regulate and control our anatomical development as well as influencing our behavior?

  21. Rumraket: It is nothing short of a transformative and deeply humbling experience.

    I was middle aged before I saw a dark sky.

    I had never seen the milky way.

    I was reminded of Asimov’s Nightfall.

  22. Frankie: And there isn’t any evidence that changes to a genome can account for the anatomical a physiological differences observed. And that means there isn’t any science behind the claim that chimps and humans share a common ancestor.

    Right. So the differences between humans and chimps are not due to the differences in their genomes?

    Interrrresting. ….

  23. Sal and/or Vincent: I would very much like to see a post summarizing this very long talk and Bechly’s views. I’ve gone about a third of the way through it, and it’s a painful way to introduce the subject. He’s longwinded and he tends to digress and simultaneously begin mumbling toward the end of each point. And of course I disagree strongly with much that he says.

    Well, if you’re really interested in engaging and criticizing his points, you could take the time to watch 1.25 hours of what one of your ex-comrades has to say. You could then post a rebuttal at TSZ and show the superiority of your viewpoints.

    So far all you can do is criticize his style, not the substance of his claim. So what if he’s long winded or mumbling. Reminds me of some professors that I’m willing to listen to despite the way they communicate, because of the content of what they have to say.

  24. vjtorley: We are all familiar with the notions of a genetic code and a genetic program. So let’s talk about programs. Let’s imagine there are two computer programs, A and B, and that 99% of their code is the same. Would anyone expect 99% of their output to be the same? Or would anyone expect the two programs to behave in the same way, 99% of the time?

    Why VJ?

    How big is the code?

  25. Hi Vincent,

    Apparently no one else is going to point this out, so on behalf of Shakespeare fans everywhere, I’ll do so: the phrase is “hoist with his own petard”, not “hoist on his own petard.”

    It’s more than just a quibble. A petard was a small bomb for blowing doors open or breaching walls. You can be hoist “with” or “by” a petard, but “on” doesn’t really make sense.

    From Hamlet:

    For ’tis the sport to have the engineer
    Hoist with his own petard: and ‘t shall go hard
    But I will delve one yard below their mines,
    And blow them at the moon:

  26. Joe Felsenstein: Right.So the differences between humans and chimps are not due to the differences in their genomes?

    Interrrresting. ….

    So will it Joe? Will a 1% change in genome change an organism approximately 1%?

    I guess there must be more to an organism than its genome.

  27. for phoodoo’s benefit I’ll repost this from RichardHughes.

    Take a 100 equations with 50 arithmetic operators and 50 numerical constants. randomly change either an operator or a constant and compare the result to the original equations result. Do you get on average a 1% difference? You changed 1% of its genome…

    Care to give the test a try phoodoo? Post your results here and show ‘us’ all how wrong-thinking we are to doubt your notions!

  28. phoodoo: So will it Joe?Will a 1% change in genome change an organism approximately 1%?

    Attempting to treat this a serious question. There are single point mutations that can produce dramatic changes in phenotype – the mutation that results in achondroplasia for instance – and many mutations that do not affect the phenotype – mutations in non-functional DNA. And how would one go about estimating a percentage change in a phenotype? I’f I’m one percent taller than you? One percent more intelligent?

    I guess there must be more to an organism than its genome.

    Evidently!

  29. Alan Fox: And how would one go about estimating a percentage change in a phenotype? I’f I’m one percent taller than you? One percent more intelligent?

    I am not the one who said a 1% difference in the genome “obviously” wouldn’t result in a 1% difference in morphology, so why would you ask me that question, ask VJ.

  30. phoodoo: I am not the one who said a 1% difference in the genome “obviously” wouldn’t result in a 1% difference in morphology, so why would you ask me that question, ask VJ.

    Vincent understands then that the relationship between genotype and phenotype is not one-to-one.You seemed not to understand this.

  31. Hi Phoodoo,

    A simple Pascal program will illustrate my point. Here’s program 1.

    program PPAPorHerMajesty;

    var
    myname:string;

    begin
    myname:=’vincent’;
    if myname=’vincent’ then
    begin
    writeln(‘I have a pen, I have an apple.’);
    writeln(‘Uh! Apple Pen’);
    writeln(‘I have a pen, I have pineapple.’);
    writeln(‘Uh! Pineapple Pen’);
    writeln(‘Apple pen…’);
    writeln(‘Pineapple pen… uh!’);
    writeln(‘Pen Pineapple Apple Pen!’);
    writeln(‘Pen Pineapple Apple Pen!’);
    end
    else if myname=’phoodoo’ then
    begin
    writeln(‘Her Majesty”s a pretty nice girl’);
    writeln(‘But she doesn”t have a lot to say’);
    writeln(‘Her Majesty”s a pretty nice girl’);
    writeln(‘But she changes from day to day’);
    writeln(‘I want to tell her that I love her a lot’);
    writeln(‘But I gotta get a bellyful of wine’);
    writeln(‘Her Majesty”s a pretty nice girl’);
    writeln(‘Someday I”m going to make her mine, oh yeah’);
    writeln(‘Someday I”m going to make her mine’);
    end
    end.

    And here’s program 2, which is 99% similar to program 1. Only the initialization of myname is different in the code, yet the output is completely different.

    program PPAPorHerMajesty;

    var
    myname:string;

    begin
    myname:=’phoodoo’;
    if myname=’vincent’ then
    begin
    writeln(‘I have a pen, I have an apple.’);
    writeln(‘Uh! Apple Pen’);
    writeln(‘I have a pen, I have pineapple.’);
    writeln(‘Uh! Pineapple Pen’);
    writeln(‘Apple pen…’);
    writeln(‘Pineapple pen… uh!’);
    writeln(‘Pen Pineapple Apple Pen!’);
    writeln(‘Pen Pineapple Apple Pen!’);
    end
    else if myname=’phoodoo’ then
    begin
    writeln(‘Her Majesty”s a pretty nice girl’);
    writeln(‘But she doesn”t have a lot to say’);
    writeln(‘Her Majesty”s a pretty nice girl’);
    writeln(‘But she changes from day to day’);
    writeln(‘I want to tell her that I love her a lot’);
    writeln(‘But I gotta get a bellyful of wine’);
    writeln(‘Her Majesty”s a pretty nice girl’);
    writeln(‘Someday I”m going to make her mine, oh yeah’);
    writeln(‘Someday I”m going to make her mine’);
    end
    end.

    You can run both programs at http://rextester.com/l/pascal_online_compiler . It’s been a while since I last coded, but it’s still fun. Cheers.

    (Hope the indents work OK.)

    [Sigh. Looks like they didn’t. Anyway, you can still read it.]

  32. stcordova: Well, if you’re really interested in engaging and criticizing his points, you could take the time to watch 1.25 hours of what one of your ex-comrades has to say.You could then post a rebuttal at TSZ and show the superiority of your viewpoints.

    So far all you can do is criticize his style, not the substance of his claim.So what if he’s long winded or mumbling. Reminds me of some professors that I’m willing to listen to despite the way they communicate, because of the content of what they have to say.

    So you aren’t interested in discussing this unless I start? I can see why you’re generally unwilling to discuss creationism and pretty much ignore every thread I start on the subject. I would be happy to criticize the substance, but I’d rather not be talking to myself. Having you start the thread is my best bet that someone else will participate. Even you would be better than nothing.

    And I did watch the 1.25 hours. I don’t intend to watch the Q&A.

    I’ll start, just a little. He says that the nested hierarchy of life and fossil progression can be explained by an ordered sequence (a tree, more or less) in the mind of god, and justifies that by a reference to pattern cladism. But there are infinitely many ways to order information. Why pick the one uniquely predicted by common descent? Pattern cladism is supposedly the most efficient way to summarize information, but that’s only true if the information has nested hierarchical structure, and we’re still left to explain why it has that structure.

    Are you afraid to discuss this at length?

  33. Alan Fox: Vincent understands then that the relationship between genotype and phenotype is not one-to-one.You seemed not to understand this.

    No, Alan, I understand that. What I don’t understand is from a random mutations, natural selection viewpoint we should expect that to be so.

    If life is about a genome that gets mutations which cause change, it should be a 1 to 1 outcome.

    Of course we all know that its not.

  34. Hi keiths,

    Good point. I can see your logic, and most online dictionaries of idioms agree with you. Although it makes less sense, “hoist on his own petard” has also been used for a long time, according to Brewer’s Dictionary of Phrase and Fable (1898).

    http://www.bartleby.com/81/13079.html

    Hoist on his own petard. Caught in his own trap, involved in the danger he meant for others. The petard was a conical instrument of war employed at one time for blowing open gates with gunpowder. The engineers used to carry the petard to the place they intended to blow up, and fire it at the small end by a fusee. Shakespeare spells the word petar: “’Tis the sport to have the engineer hoist with his own petar.” (Hamlet, ii. 4.) 1
    “Turning the muzzles of the guns Magdala wards, and getting a piece of lighted rope [the party] blazed away as vigorously as possible… and tried to hoist Theodore on his own petard.”—Daity paper.

    End of quote. Wikipedia adds: “Shakespeare’s use of “petar” (flatulate) rather than “petard” may be an off-colour pun.”

  35. phoodoo: No, Alan, I understand that. What I don’t understand is from a random mutation, natural selection viewpoint we should expect that to be so.

    I disagree.

    If life is about a genome that gets mutations which cause change, it should be a 1 to 1 outcome.

    There’s no logic to that statement.

    Of course we all know that its not.

    How the information transferred in a zygote cashes out into the adult, functioning organism is a fascinating and ongoing question. Evo-devo has made a huge contribution but it’s work in progress.

  36. Hi everyone,

    People have been asking me about Gunter Bechly’s talk. I’m afraid that although it sounded promising at the beginning, it disappointed me at the end. The meat of Bechy’s argument (which starts around 1:09:00 and finishes at 1:28:00) has to do with coordinated mutations, and in particular, Bechy’s citation of Durrett and Schmidt’s 2008 paper at http://www.genetics.org/content/180/3/1501 .

    In brief, Bechy (who is a paleontologist, not a geneticist) relies on Behe’s reading of the paper and his own intuition that human and whale evolution would have required two or more coordinated mutations on multiple occasions, to arrive at a conclusion that there would not have been enough time available. He also quotes some figures from Sanford which support the same conclusion. Bechy relates that he was blown away by the fact that in a 2009 debate, Donald Prothero was unable to respond to Richard Sternberg on this issue – which is hardly surprising, as Prothero is a paleontologist (like Bechy).

    The problem is that Durrett and Schmidt don’t say what most ID advocates think they say. What they actually say is heavily qualified:

    “We now show that two coordinated changes that turn off one regulatory sequence and turn on another without either mutant becoming fixed are unlikely to occur in the human population… Our previous work has shown that, in humans, a new transcription factor binding site can be created by a single mutation in an average of 60,000 years, but, as our new results show, a coordinated pair of mutations that first inactivates a binding site and then creates a new one is very unlikely to occur on a reasonable timescale.

    “To be precise, the last argument shows that it takes a long time to wait for two prespecified mutations with the indicated probabilities.”

    To which my response is: OK. So what? Where’s the evidence that such mutations had to occur in the evolution of humans or whales?

  37. vjtorley,

    I didn’t find that to be the interesting part of the talk, nor, even if true, would it be evidence for progressive creation. It would just be evidence that known mechanisms could not account for some evolutionary change. It would do nothing at all to dispell the evidence for common descent.

    It’s common for creationists to conflate the separate issues of common descent and mechanisms of evolution. Don’t fall into that trap. You might let Michael Behe be your guide there. (And it’s hard for me to believe I typed that sentence.)

  38. Vincent,

    I think it’s simply because “petard” is an obscure word. Most folks don’t know (and don’t need to know) what it means. If you don’t, then “hoist on his own petard” sounds right. If you do, then “on” sounds wrong but “with” or “by” sound right.

  39. vjtorley:

    To which my response is: OK. So what? Where’s the evidence that such mutations had to occur in the evolution of humans or whales?

    The mutations don’t have to occur any more than a lock and a matching key have to occur. To the extent a system is coordinated, like the picture of the house of cards in the OP, there is difficulty in it emerging as a matter of principle.

    A house of cards doesn’t have to occur, but if it does, it requires emergence of at least two simultaneous, highly specific events, otherwise, if the cards at the base of the house of cards are not simultaneously there, the house of cards collapses.

    There is no requirement for a house of cards to exist, any more than there is a requirement for a specific mutation to exist. The issue is the difficulty of creating coordinate structures.

  40. Hi John Harshman,

    Thank you for your email. I agree with your point about common descent vs. mechanisms for evolution, but I regard the latter as a more critical issue. If you want to make a case for Intelligent Design then the former won’t interest you very much. That was why I focused on the Durrett and Schmidt paper: because ID advocates often (mistakenly) cite it as evidence for Intelligent Design.

    Hi Sal,

    I’ll defer to Professor Felsenstein here, but I’d like to note that:

    (i) Durrett and Schmidt don’t just speak of two coordinated mutations, but two very specific kinds of coordinated mutations – namely, “two coordinated changes that turn off one regulatory sequence and turn on another without either mutant becoming fixed,” and I know of no such mutations occurring in the course of human or whale evolution;

    (ii) more generally, I see no reason to believe that two coordinated mutations of any sort would have been required within any particular organ or system during the course of human or whale evolution;

    (iii) during the course of whale (and human) evolution, a lot of anatomical changes would have been occurring in parallel, in different organs and/or systems, where a small change in system A may have been followed by another small change in system B, followed by another change in A, another change in B, etc. To that extent, the changes would have had to have been in sync. But there wasn’t any set order: the change in B could have preceded the change in A, for instance, and it wouldn’t have made any difference. There would have been multiple (perhaps millions) of possible paths to the same destination. In other words, the evolution of one system was constrained by that of other systems in the body, but there wasn’t a specific sequence that the mutations had to follow. I don’t think this is a case where Durrett and Schmidt’s argument applies.

    Is there any scientist who’d like to comment?

  41. vjtorley:

    I know of no such mutations occurring in the course of human or whale evolution

    The issue is they would have to occur to create some of the coordinated systems we see to day.

    A case example: HOTAIR lncRNA.

    The regulatory sections are turned off in the eyelids, but turned off in the soles of the feet.

    That doesn’t have to happen, but it does. Hence the quality of skin in the eyelids is different than the soles of the feet. Not absolutely critical for survival, but it helps.

  42. Joe Felsenstein: So the differences between humans and chimps are not due to the differences in their genomes?

    The genetic differences would be due to differences in their genomes.

  43. keiths: Apparently no one else is going to point this out…

    Only thing worse than getting the science wrong is getting the poetry wrong!

  44. John Harshman: It’s common for creationists to conflate the separate issues of common descent and mechanisms of evolution.

    It’s not the creationists claiming there’s but one theory of evolution.

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