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Dawkins’s claim: “every gene delivers approximately the same tree of life” contested at Nature Portfolio Ecology & Evolution

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It’s just not like that, says a Queen Mary U prof. He points to this vid:

and writes,

The lay-person reading this, or watching the video above, is given the clear impression that every gene or pseudogene in every living organism gives essentially the same phylogenetic tree, when analysed with its homologs from other species. This is simply not true.

If this were true, then phylogeny building in the genomic era would be a walk in the park. But, as many of my readers will know from personal experience, it is not.

If this were true, terms like horizontal gene transfer, incomplete lineage sorting, introgression, and molecular convergence would be rare curiosities in the genomic literature. But they are common (click on the links in the previous sentence to see searched for these terms on Google Scholar).

If this were true, commonly-used phylogenetic software like ASTRAL, ASTRID and BUCKy, designed to deal with gene tree incongruence, would be seldom used. But they are used often.

I hardly need to labour my point to the present audience. Dawkins’ statements are simply wrong. Gloriously and utterly wrong.

Richard Buggs, “Obsolete Dawkinsian evidence for evolution” at Nature: Ecology & Evolution

You know, Dawkins may be losing his shine. New Scientist was making similar types of noise last October. It’s now okay to say when there’s something wrong with this stuff.

See, for example: The Selfish Gene is no longer cool. At New Scientist: “Some researchers think the solution lies in an idea called cultural group selection. Forget shared genes, they argue: selection can favour cooperative groups if the people within them share enough culture.” Darwin has left the building and returned to his estate.

This is New Scientist we’re talking about. And that’s Dawkins’s Selfish Gene.

So maybe science really is self-correcting. We’ve had lots of reasons to wonder if that’s just a myth. You know, nonsense drop-kicked from one journal article to the next doesn’t inspire confidence.

If they can set the record straight about the Tree of Life stuff, maybe a lot of other things would start getting straightened out.

3 Replies to “Dawkins’s claim: “every gene delivers approximately the same tree of life” contested at Nature Portfolio Ecology & Evolution”

  1. 1
    bornagain77 says:
    March 28, 2021 at 2:48 am

    A New Model for Evolution: A Rhizome – May 2010
    Excerpt: “Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,,
    Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations.”
    – Didier Raoult – has been referred to as the ‘Most Productive and Influential Microbiologist in France’
    http://darwins-god.blogspot.co.....izome.html

  2. 2
    bornagain77 says:
    March 28, 2021 at 4:43 am

    Richard Buggs also did this very interesting bit of research where he found that the genetic similarity between humans and chimpanzees is not nearly as great as Darwinists had claimed,

    Geneticist: On (Supposed 99%) Human-Chimp Genome Similarity, There Are “Predictions” Not “Established Fact” – July 31, 2018
    Excerpt: 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.,,,
    The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%
    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 percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 82.34%.
    – Richard Buggs
    https://evolutionnews.org/2018/07/geneticist-on-human-chimp-genome-similarity-there-are-predictions-not-established-fact/

    Richard Buggs’s research, ‘surprisingly’, almost perfectly matches other research that was conducted by Jeffrey Tomkins

    New Chimp Genome Confirms Creationist Research
    BY JEFFREY P. TOMKINS, PH.D. * | FRIDAY, SEPTEMBER 28, 2018
    Excerpt: The first time they constructed a chimp genome and compared it to humans, they claimed 98.5% DNA similarity based on cherry-picked regions that were highly similar to human. However, an extensive DNA comparison study I published in 2016 revealed two major flaws in their construction of the chimp genome.1
    First, many chimp DNA data sets were likely contaminated with human DNA, especially those produced in the first half of the chimpanzee genome project from 2002 to 2005. Second, the chimpanzee genome was deliberately constructed to be more human-like than it really is.2 Scientists assembled the small snippets of chimp DNA onto the human genome, using it as a scaffold or reference. It’s much like putting together a jigsaw puzzle by looking at the picture on the box as a guide. Since many chimpanzee data sets likely suffered from human DNA contamination, the level of humanness was amplified. I studied the 2005–2010 data sets that showed less human DNA data contamination and found they were only 85% similar to human at best.1
    Just this year, scientists published a new version of the chimpanzee genome.3 This new version incorporated an advanced type of DNA sequencing technology that produces much longer snippets of DNA sequence than earlier technologies. It also involved better protocols that greatly reduce human DNA contamination. And most importantly, the authors report that the DNA sequences have been assembled without using the human genome as a scaffold.
    They also acknowledged the flawed nature of previous versions of the chimp genome:
    The higher-quality human genome assemblies have often been used to guide the final stages of nonhuman genome projects, including the order and orientation of sequence contigs and, perhaps more importantly, the annotation of genes. This bias has effectively “humanized” other ape genome assemblies.3
    This confirms what many creationists have been pointing out for years.
    Curiously, the authors of the new chimp genome paper said very little about the overall DNA similarity between humans and chimpanzees. However, the University of London’s specialist in evolutionary genomics, Dr. Richard Buggs, evaluated the results of an analysis that compared this new chimp version to the human genome and discovered some shocking anti-evolutionary findings.
    Dr. Buggs reported on his website that “the percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%” and “4.06% had no alignment to the chimp assembly.”?4 Assuming the chimpanzee and human genomes are about the same size, this translates to an overall similarity of only about 80%! This outcome is way outside the nearly identical level of 98 to 99% similarity required for human evolution to seem plausible.
    http://www.icr.org/article/new.....t-research

  3. 3
    martin_r says:
    March 28, 2021 at 12:43 pm

    University of Oregon (2020):

    “Researchers find flaws in how scientists build trees of life”

    “In a new paper placed online April 15 ahead of print in the April 23 issue of the journal Nature, they argue that long-used approaches for reconstructing evolutionary paths are deeply flawed.”

    ““Our finding casts serious doubts over literally thousands of studies that use phylogenetic trees of extant data to reconstruct the diversification history of taxa, especially for those taxa where fossils are rare, or that found correlations between environmental factors such as changing global temperatures and species extinction rates,” Louca said”

    “”I have been working with these traditional types of models for a decade now,” Pennell said. “I am one of the lead developers of a popular software package for estimating diversification rates from phylogenetic trees. And, as such, I thought I had a really good sense of how these models worked. I was wrong.””

    https://around.uoregon.edu/content/researchers-find-flaws-how-scientists-build-trees-life

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