Genomics Tree of life

Science mag admits, DNA studies shake tree of animal life

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File:Sea walnut, Boston Aquarium.jpg
leidyi (sea walnut)/Steven G. Johnson

From Nautilus,

Late last year, the animal evolutionary tree quaked at its root. A team led by Joseph Ryan, an evolutionary biologist who splits his time between the National Genome Research Institute in Bethesda, Md. and the Sars International Center for Marine Molecular Biology in Bergen, Norway, analyzed the genome from a comb jelly, Mnemiopsis leidyi, a complex marine predator with muscles, nerves, a rudimentary brain, and bioluminescence, and found that the animals may have originated before simple sponges, which lack all of those features. 

See also: Comb jelly DNA sequence offers “unintuitive facts” about evolution…

Animal that stages light display is 600 million years old?

Sea creature, nearly 600 mya, wobbles current classifications of life

We are all denounced in the article as “temporal chauvinists” for expecting precisely what we were told in school to expect of allegedly Darwinian evolution—increasing complexity:

If comb jellies evolved before sponges, the sponges might have lost the complexity that the ancestor uniting them and comb jellies possessed. Or, that ancestor—the ancestor of all living animals—had the genes to build brains and muscles, but did not form those parts, and neither did sponges. If this is true, then comb jellies deployed the genome they inherited to build a brain, nervous system, and muscles, independent of other animals. There’s some support for this possibility: A unique set of genes seems to underlie comb jellies’ muscles.

Both hypotheses run counter to scenarios in which organisms evolve to be increasingly complex.

Casey Dunn, an evolutionary biologist at Brown University in Providence, R.I. who took part in the still-contentious comb jelly project, now doubts all notions of increasing complexity. Instead, he says the environment selects whatever form handles the challenges at hand, be it simple, complex, or plain ugly.

Gosh, he sounds a bit like that guy in a Thomas Hardy poem who lost his faith, due to reading critical works:

Since thus they hint, nor turn a hair,

All churchgoing will I forswear,

And sit on Sundays in my chair,

And read that moderate man Voltaire.

No one is allowed to ask just where the very early life forms got the complexity. It may be relevant that physicist Sean Carroll, a convert to the multiverse, is quoted on the folly of expecting the arrow to move in only one direction, so we may hear some very unusual hypotheses from such sources in the years to come.

Comb jelly lights:

8 Replies to “Science mag admits, DNA studies shake tree of animal life

  1. 1
    bornagain77 says:

    The quote at the end of the article will make you take a double take:

    Evolution, You’re Drunk (Go Home) – January 30. 2014
    Excerpt: When asked whether de-evolution, a reversal from the complex to the simple, happens frequently, Dunn replies, sure. “But,” he adds, “I wouldn’t call that de-evolution, I’d call it evolution.”
    http://nautil.us/issue/9/time/.....oure-drunk

    The one paper they cited in the article that was relevant to the primary Darwinian claim of increasing complexity (evolution as it is meant in the proper sense) was reminiscent of Behe’s ‘First rule’ paper:

    Also from the article: “Jernvall’s team induced mutations in genes involved in tooth formation in mice, and found that most of the mutations caused teeth to become simpler than they usually are. To form a more complex tooth (with more bumps), the team had to induce multiple molecular changes at once. The results suggest that reductions in complexity should evolve more easily than increases in complexity.”

    On the difficulty of increasing dental complexity – 2012
    http://www.nature.com/nature/j.....10876.html

    See if you can spot the similarity to Behe’s paper,,

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    Michael Behe finds Loss of Function Mutations Challenge the Darwinian Model – Casey Luskin August 24, 2013
    Excerpt: “Because of the many ways in which a gene can be altered to lose function, the LOF mutation would have a rate several orders of magnitude greater than that of the GOF mutation for the duplicated gene.”
    http://www.evolutionnews.org/2.....75591.html

    In fact their ‘multiple mutations needed for increased tooth complexity’ paper also fits in quite well with Gauger and Axe’s work:

    More from Ann Gauger on why humans didn’t happen the way Darwin said – July 2012
    Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population.
    You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect.
    Facing Facts
    But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes.
    http://www.uncommondescent.com.....rwin-said/

    In fact, it fits in with the overall principle of Genetic Entropy (i.e. de-Evolution):

    Genetic Entropy – Dr. John Sanford – Evolution vs. Reality – video (Notes in description)
    http://vimeo.com/35088933

    Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load:
    Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space.
    http://bioinformatics.cau.edu......aproof.pdf

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – May 2013
    Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11].
    1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696.
    2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19.
    3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358.
    4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144.
    5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47.
    6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117.
    8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526.
    9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685.
    10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079.
    11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    http://www.worldscientific.com.....08728_0006

  2. 2
    bornagain77 says:

    Even the fossil record, when looked at in detail instead of with Darwinian rose-colored glasses, contrary to popular belief, reflects what we would expect from the lab results we see:

    The Cambrian’s Many Forms
    Excerpt: “It appears that organisms displayed “rampant” within-species variation “in the ‘warm afterglow’ of the Cambrian explosion,” Hughes said, but not later. “No one has shown this convincingly before, and that’s why this is so important.””From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,”….(Yet Surprisingly)….”There’s hardly any variation in the post-Cambrian,” he said. “Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn’t vary in the post-Cambrian trilobites.” University of Chicago paleontologist Mark Webster; article on the “surprising and unexplained” loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago.
    http://www.terradaily.com/repo.....s_999.html

    In fact, the loss of morphological traits over time, for all organisms found in the fossil record, was/is so consistent that it was made into a ‘scientific law’:

    Dollo’s law and the death and resurrection of genes:
    Excerpt: “As the history of animal life was traced in the fossil record during the 19th century, it was observed that once an anatomical feature was lost in the course of evolution it never staged a return. This observation became canonized as Dollo’s law, after its propounder, and is taken as a general statement that evolution is irreversible.”
    http://www.pnas.org/content/91.....l.pdf+html

    A general rule of thumb for the ‘Deterioration/Genetic Entropy’ of Dollo’s Law as it applies to the fossil record is found here:

    Dollo’s law and the death and resurrection of genes
    ABSTRACT: Dollo’s law, the concept that evolution is not substantively reversible, implies that the degradation of genetic information is sufficiently fast that genes or developmental pathways released from selective pressure will rapidly become nonfunctional. Using empirical data to assess the rate of loss of coding information in genes for proteins with varying degrees of tolerance to mutational change, we show that, in fact, there is a significant probability over evolutionary time scales of 0.5-6 million years for successful reactivation of silenced genes or “lost” developmental programs. Conversely, the reactivation of long (>10 million years)-unexpressed genes and dormant developmental pathways is not possible unless function is maintained by other selective constraints;
    http://www.pnas.org/content/91.....l.pdf+html

    Dollo’s Law was further verified to the molecular level here:

    Dollo’s law, the symmetry of time, and the edge of evolution – Michael Behe
    Excerpt: We predict that future investigations, like ours, will support a molecular version of Dollo’s law:,,, Dr. Behe comments on the finding of the study, “The old, organismal, time-asymmetric Dollo’s law supposedly blocked off just the past to Darwinian processes, for arbitrary reasons. A Dollo’s law in the molecular sense of Bridgham et al (2009), however, is time-symmetric. A time-symmetric law will substantially block both the past and the future.
    http://www.evolutionnews.org/2.....f_tim.html

    Evolutionary Adaptations Can Be Reversed, but Rarely – May 2011
    Excerpt: They found that a very small percentage of evolutionary adaptations in a drug-resistance gene can be reversed, but only if the adaptations involve fewer than four discrete genetic mutations. (If reverting to a previous function, which is advantageous, is so constrained, what does this say about gaining a completely novel function, which may be advantageous, which requires many more mutations?)
    http://www.sciencedaily.com/re.....162538.htm

    “Also that mammalian life was richer in kinds, of larger sizes, and had a more abundant expression in the Pliocene than in later times.”
    Von Engeln & Caster Geology, p.19

    Don Patton – Entropy, Information, and The ‘Deteriorating’ Fossil Record – video (Notes on giant fossils in description)
    http://www.vimeo.com/17050184

    A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago – Wolf-Ekkehard Lönnig – December 2011
    Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species.
    Per ENV

    Even humans, contrary to popular belief, are devolving, not evolving:

    If Modern Humans Are So Smart, Why Are Our Brains Shrinking? – January 20, 2011
    Excerpt: John Hawks is in the middle of explaining his research on human evolution when he drops a bombshell. Running down a list of changes that have occurred in our skeleton and skull since the Stone Age, the University of Wisconsin anthropologist nonchalantly adds, “And it’s also clear the brain has been shrinking.”
    “Shrinking?” I ask. “I thought it was getting larger.” The whole ascent-of-man thing.,,,
    He rattles off some dismaying numbers: Over the past 20,000 years, the average volume of the human male brain has decreased from 1,500 cubic centimeters to 1,350 cc, losing a chunk the size of a tennis ball. The female brain has shrunk by about the same proportion. “I’d call that major downsizing in an evolutionary eyeblink,” he says. “This happened in China, Europe, Africa—everywhere we look.”
    http://discovermagazine.com/20.....-shrinking

    Genetic Entropy in Human Genome is found to be ‘recent’:
    Human Genetic Variation Recent, Varies Among Populations – (Nov. 28, 2012)
    Excerpt: Nearly three-quarters of mutations in genes that code for proteins — the workhorses of the cell — occurred within the past 5,000 to 10,000 years,,,
    “One of the most interesting points is that Europeans have more new deleterious (potentially disease-causing) mutations than Africans,”,,,
    “Having so many of these new variants can be partially explained by the population explosion in the European population. However, variation that occur in genes that are involved in Mendelian traits and in those that affect genes essential to the proper functioning of the cell tend to be much older.” (A Mendelian trait is controlled by a single gene. Mutations in that gene can have devastating effects.) The amount variation or mutation identified in protein-coding genes (the exome) in this study is very different from what would have been seen 5,000 years ago,,,
    The report shows that “recent” events have a potent effect on the human genome. Eighty-six percent of the genetic variation or mutations that are expected to be harmful arose in European-Americans in the last five thousand years, said the researchers.
    The researchers used established bioinformatics techniques to calculate the age of more than a million changes in single base pairs (the A-T, C-G of the genetic code) that are part of the exome or protein-coding portion of the genomes (human genetic blueprint) of 6,515 people of both European-American and African-American decent.,,,
    http://www.sciencedaily.com/re.....132259.htm

    Verse and Music:

    Psalm 104:29-30
    When you hide your face, they are terrified; when you take away their breath, they die and return to the dust.
    When you send your Spirit, they are created, and you renew the face of the ground.

    Phillips, Craig & Dean – You Are God Alone (Lyrics)
    http://www.youtube.com/watch?v=iDN3EFjrQac

  3. 3
    Robert Byers says:

    DNA as evidence for actual relationships is just a line of reasoning.
    Creationists must remember that a creator working with a common blueprint would have common DNA for common things.
    There is no evidence that DNA likeness equals common ancestry. its just speculation.
    Darwin mentioned this point about a common idea from a creator behind like body plans. He dismissed it in a single sentence but brought it up.

  4. 4
    Robert Byers says:

    DNA as evidence for actual relationships is just a line of reasoning.
    Creationists must remember that a creator working with a common blueprint would have common DNA for common things.
    There is no evidence that DNA likeness equals common ancestry. its just speculation.
    Darwin mentioned this point about a common idea from a creator behind like body plans. He dismissed it in a single sentence but brought it up.

  5. 5
    Robert Byers says:

    DNA as evidence for actual relationships is just a line of reasoning.
    Creationists must remember that a creator working with a common blueprint would have common DNA for common things.
    There is no evidence that DNA likeness equals common ancestry. its just speculation.
    Darwin mentioned this point about a common idea from a creator behind like body plans. He dismissed it in a single sentence but brought it up.

  6. 6
    bornagain77 says:

    Various Creatures with Photocytes by Matthew Coghill on Prezi
    http://prezi.com/cerg_tftffo8/photocytes/
    A photocyte is a cell that specializes in catalyzing enzymes to produce light (bioluminescence).,,,Researchers once postulated that ATP was source of reaction energy for photocytes, but since ATP only produces a fraction the energy of the luciferase reaction, any resulting light wave-energy would be too small for detection by a human eye
    http://en.wikipedia.org/wiki/Photocyte

  7. 7
    tjguy says:

    BA writes:

    Evolution, You’re Drunk (Go Home) – January 30. 2014
    Excerpt: When asked whether de-evolution, a reversal from the complex to the simple, happens frequently, Dunn replies, sure. “But,” he adds, “I wouldn’t call that de-evolution, I’d call it evolution.”
    http://nautil.us/issue/9/time/…..oure-drunk

    No one, not even creationists, argue with that kind of evolution, or to put it more accurately, with de-evolution.

    In fact, we believe in it more than they do, but that DOESN’T make us evolutionists.

  8. 8
    ppolish says:

    Would a Precambrian comb jelly have increased or decreased Darwin’s doubt?

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