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Kirk Durston on the new “tree of life”

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Biophysicist Kirk Durston of Contemplations writes, re Tree of life morphs into … leaf?:

I studied that new tree of life for a while. It leaves me wondering how much is empirical observation and how much is conjecture. I would much rather see the imaginary parts removed and only the dots plotted. As one involved in bioinformatics, I know that one must be very careful to avoid ‘fitting’ the dots into a pre-conceived pattern. Would could just as easily (perhaps even more easily) fit the dots into clusters representing the various ‘kinds’ of life. My own perspective is that life should be mapped out in clusters of dots; leave out everything else for which there is no empirical evidence for. As my Ph.D. supervisor used to say, ‘If you haven’t got the data, don’t ‘suggest’ it in your paper.

But Kirk, not a Darwinian, was stuck with bare facts, not a grand narrative that everyone earns in school.

Meanwhile, from the New York Times,

Patrick Forterre, an evolutionary biologist at the Pasteur Institute in France, agreed that bacteria probably make up much of life’s diversity. But he had concerns about how Dr. Banfield and her colleague built their tree. He argued that genomes assembled from DNA fragments could actually be chimeras, made up of genes from different species. “It’s a real problem,” he said.

Oh, maybe not.

Picture a compost heap instead of a tree, and we’re good.

See also: Probability Mistakes Darwinists Make: Part I

and

Taxonomists savage their dead We knew speciation was a mess, just not that it was such a vicious mess.

2 Replies to “Kirk Durston on the new “tree of life”

  1. 1
    bornagain77 says:

    Of related note:

    unique ORFan genes are found in every new genome sequenced:

    ,,,”Typical bacterial species. The smallest part of the pie are the genes that all bacteria share. 8% roughly. This second and largest slice (of the pie, 64%) are the genes that are specialized to some particular environment. They call them character genes. By far the biggest number of genes are the ones that are unique. This big green ball here (on the right of the illustration). These are genes found only in one species or its near relatives. Those are the ORFans (i.e. Genes with no ancestry). They said, on the basis of our analysis the genetic diversity of bacteria is of infinite size.”
    Paul Nelson – quoted from 103:48 minute mark of the following video
    Whatever Happened To Darwin’s Tree Of Life? – Paul Nelson – video
    https://youtu.be/9UTrZX47e00?t=3820

    You can see the pie chart that Dr. Nelson used in his talk here on page 108 (figure 2) of this following article:

    Estimating the size of the bacterial pan-genome
    Excerpt Figure 2 pg. 108: At the genomic level, a typical bacterial genome is composed of _8% of core genes, 64% of character genes and 28% of accessory genes,,,
    http://www.paulyu.org/wp-conte.....genome.pdf

    Estimating the size of the bacterial pan-genome – Pascal Lapierre and J. Peter Gogarten – 2008
    Excerpt: We have found greater than 139 000 rare (ORFan) gene families scattered throughout the bacterial genomes included in this study. The finding that the fitted exponential function approaches a plateau indicates an open pan-genome (i.e. the bacterial protein universe is of ‘infinite’ size); a finding supported through extrapolation using a Kezdy-Swinbourne plot (Figure S3). This does not exclude the possibility that, with many more sampled genomes, the number of novel genes per additional genome might ultimately decline; however, our analyses and those presented in Ref. [11] do not provide any indication for such a decline and confirm earlier observations that many new protein families with few members remain to be discovered.
    http://www.paulyu.org/wp-conte.....genome.pdf

    The essential genome of a bacterium – 2011
    Figure (C): Venn diagram of overlap between Caulobacter and E. coli ORFs (outer circles) as well as their subsets of essential ORFs (inner circles). Less than 38% of essential Caulobacter ORFs are conserved and essential in E. coli. Only essential Caulobacter ORFs present in the STING database were considered, leading to a small disparity in the total number of essential Caulobacter ORFs.
    http://www.ncbi.nlm.nih.gov/pm.....201158.pdf

    of related note:

    Unexpected features of the dark proteome – Oct. 2015
    We surveyed the “dark” proteome–that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44–54% of the proteome in eukaryotes and viruses was dark, compared with only ~14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology.
    http://www.pnas.org/content/ea.....1508380112

  2. 2
    Dionisio says:

    bornagain77

    Interesting articles. Thank you for the references.

    BTW,

    These results suggest new research directions in structural and computational biology

    The more we know, more is ahead for us to learn.
    Complex complexity.
    Work in progress.

    🙂

    Also here:

    A key remaining frontier in our understanding of biological systems is the “dark proteome”—that is, the regions of proteins where molecular conformation is completely unknown. We systematically surveyed these regions, finding that nearly half of the proteome in eukaryotes is dark and that, surprisingly, most of the darkness cannot be accounted for. We also found that the dark proteome has unexpected features, including an association with secretory tissues, disulfide bonding, low evolutionary conservation, and very few known interactions with other proteins. This work will help future research shed light on the remaining dark proteome, thus revealing molecular processes of life that are currently unknown.

    surprisingly? why?
    unexpected? why?

    did they expect something else or nothing at all?

    🙂
    [emphasis mine]

    They also wrote:

    […] dark proteins may remain a sizeable and irreducible feature of the protein universe.

    The dark proteome is a key remaining frontier in the understanding of biological systems. This work will help focus future structural genomics and computational biology efforts to shed light on the remaining dark proteome, thus revealing currently unknown molecular processes of life.

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