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 humans… As 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.