Evolution is out of time

I discussed this a bit on last night’s Darkstream, but because my grasp of the technicalities of how genetics work is close to nonexistent, I didn’t even try to delve into the details. It’s much better to simply read the linked articles; I leave it to those more versed in the subject to determine how valid the reports of the massive gap between the oft-reported 98 percent estimated similarity between the chimp and human genomes and what genetic scientists are actually seeing now as their ability to analyze the various genomes improves.

The first exhibit is an interview with a creationist geneticist, which will no doubt be improperly dismissed by scientistry fetishists with an appeal to the genetic fallacy.

Dr. Tomkins: My motivation started when I arrived here and was given the task of researching the human-chimpanzee similarity issue because people ask about this in churches. They hear the claim that humans and chimps are 98 to 99{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} similar. People want to know if that’s true. Before working here, I’d not investigated that issue. I ran a genome center for over five years and investigated various plants and animals but never the human-chimpanzee comparison. I went into it with an open mind and began reading all the literature on the subject—this started about eight years ago. I looked at the top six scientific publications that proposed a 98 to 99{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} DNA similarity between modern humans and modern chimpanzees.

Brian: A 98 to 99{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} genetic similarity between modern humans and modern chimps—why is that important?

Dr. Tomkins: It’s very important to theoretical evolutionists. The 98 to 99{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} claim is a theory—it’s speculative. They need a similarity that close to have humans and chimps evolve in the alleged three- to six-million-year timespan from a supposed human-chimpanzee common ancestor. Their statistical models need that 98 to 99{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} similarity.

Brian: What did you find in the literature?

Dr. Tomkins: The first thing I noticed when I began reading these articles was that researchers were throwing out a lot of data. They were cherry-picking the areas of DNA between humans and chimps that were highly similar and throwing out areas, including areas that would not line up properly. Areas that don’t line up are dissimilar. When I researched the data, I was coming up with DNA similarities between 81 to 86{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} when I included the dissimilar data. I published a paper on this.1 This is way outside the realm of theoretical evolution.

Brian: What should the evolutionary community say about this?

Dr. Tomkins: They have reacted to a lot of my research since that first paper. There’s a lot of DNA sequence data that is publicly available in databases. I began working with the data myself, and over a number of years I refined my techniques. I used an algorithm developed by evolutionists that turned out to be a bad algorithm—so there’s been a lot of trial and error. But I finally got to the point where I published a paper in 2016.2 It was the most comprehensive study I’ve done yet, and I looked at all 101 data sets that went into originally building the chimpanzee genome.

I sampled 25,000 sequences at random from each of the data sets and then began analyzing and comparing them to human. Over half of the data sets were extremely similar to human, and the other half were extremely dissimilar to human. It appeared the initial chimpanzee genome was contaminated with human DNA, which is a huge problem in genomics.

There’s a number of studies by secular researchers showing that many public DNA databases, from bacteria to fish, have significant levels of human contamination. Human DNA literally gets into the samples. Contamination is a major issue. Human DNA comes from researchers’ fingers, coughing, sneezing, etc., and it gets into the samples. Now researchers are taking greater steps to alleviate that problem. This was especially prevalent back in the earliest phases of genome projects, when the chimpanzee was sequenced.

Brian: Wouldn’t some of the human DNA that made it into the raw data affect the results of any comparison analyses?

Dr. Tomkins: It has a huge effect because the chimpanzee genome is stitched together using the human genome as a scaffold. It’s like a puzzle—researchers used the human DNA “picture on the box” to assemble the chimp genome. The chimp DNA sequences used were all about 750 bases long. Not only was the chimp genome built using the human genome as a guide, it also has human DNA contamination in it, so it showed a lot of similarity from the contamination.

Brian: Even with those factors in place that skewed the data to a more human genome, is it closer to the 98{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} or the 86{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} maximum you observed?

Dr. Tomkins: It’s difficult to determine because it is a flawed product. I based my research on human-chimp similarity on the half of the data sets that appear to have much less human DNA. Based on my work, I’m seeing not more than an 85{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} DNA similarity of chimpanzee to human, and that’s a maximum. It’s probably less than that.

The second exhibit is even more interesting, because an evolutionary biologist who is the Professor of Evolutionary Genomics at the University of London has been seeing much the same thing in his review of the various chimp-human genomic studies:

When assessing the total similarity of the human genome to the chimp genome, we also need to bear in mind that roughly 5{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} of the human genome has not been fully assembled yet, so the best we can do for that 5{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} is predict how similar it will be to the chimpanzee genome. We do not yet know for sure. The chimpanzee genome assembly is less well assembled, so in future we may assemble parts of the chimpanzee genome that are similar to the human genome – this is another source of uncertainty to keep in mind.

To come up with the most accurate current assessment that I could of the similarity of the human and chimpanzee genome, I downloaded from the UCSC genomics website the latest alignments (made using the LASTZ software) between the human and chimpanzee genome assemblies, hg38 and pantro6. See discussion post #35 for details. This gave the following for the human genome:

4.06{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} had no alignment to the chimp assembly
5.18{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} was in CNVs relative to chimp
1.12{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} differed due to SNPs in the one-to-one best aligned regions
0.28{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} differed due to indels within the one-to-one best aligned regions

The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b}

In order to assess how improvements in genome assemblies can change these figures, I did the same analyses on the alignment of the older PanTro4 assembly against Hg38 (see discussion post #40). The Pantro4 assembly was based on a much smaller amount of sequencing than the Pantro6 assembly (see discussion post #39). In this Pantro4 alignment:

6.29{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} had no alignment to the chimp assembly
5.01{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} was in CNVs relative to chimp
1.11{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} differed due to SNPs in the one-to-one best aligned regions
0.28{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} differed due to indels within the one-to-one best aligned regions

The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 82.34{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b}.

Thus the large improvement in the chimpanzee genome assembly between PanTro4 and PanTro6 has led to an increase in CNVs detected, and a decrease in the non-aligning regions. It has only increased the one-to-one exact matches from 82.34{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} to 84.38{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} even though the chimpanzee genome assembly is at least 8{e5873ef35c49232e29b64cdfe957a2c94da2fd9855660473ec610b770b20216b} more complete (I think) in PanTro6.

I have already shown that it is highly improbable that the speed of mutational fixation is sufficient to account for the estimated 98 percent similar relationship which needs to account for 30 million fixed mutations since the Last Chimp-Human Common Ancestor, so this massive increase in the observed difference between the two genomes, which is presently calculated to end up somewhere between 84.38 to 93.43 percent, is enough to not only drive the final nail in the Neo-Darwinian coffin, but wrap it in iron bands, encase it in concrete, and drop it into the Marianas Trench.

Because what we’re seeing here is inept statistical wizardry that involves everything from contaminated evidence to cherry-picked data and the ridiculous assumption that literally ALL of the remaining unknown areas will, in the future, be found to perfectly align with orthodox Neo-Darwinian theory. And the priests of TENS are still desperately clinging to that improbable assumption even though it was only proved to be correct for 25.5 percent of the area that was filled in over the course of the seven years that passed between the publications of PanTro4 and PanTro6.

Of course, no one here will be even remotely surprised to observe that Prof. Buggs’s original 2008 prediction was too low because, in the 2005 paper upon which he relied, the biologists got the math wrong.