Group Think

From Researcher Condemns Conformity Among His Peers:




Conformity and group-think are attitudes of particular danger in science, an endeavor that is inherently revolutionary because progress often depends on overturning established wisdom. It’s obvious that least 100 genes must be needed to convert a human or animal cell back to its embryonic state. Or at least it was obvious to almost everyone until Shinya Yamanaka of Kyoto University showed it could be done with just 4.

The academic monocultures referred to by Dr. Bouchard are the kind of thing that sabotages scientific creativity.


4 responses to “Group Think

  1. Mike,

    More fun stuff from Eugene Koonin just published…

    Search for a ‘Tree of Life’ in the thicket of the phylogenetic forest

    I like the three authors openess and willingness to look at failures as well as the new horizon ahead and the range of opinions that are truly out there, but rarely mention in public media today. Its a big “we dunno” right now.

    A sample paragraph:

    The views of evolutionary biologists on the changing status of the tree of life (see [23] for a conceptual discussion) span the entire range from persistent denial of the major importance of HGT for evolutionary biology [26,27]; to ‘moderate’ overhaul of the tree of life concept [28-33]; to radical uprooting whereby the representation of the evolution of organisms (or genomes) as a tree of life is declared meaningless” [34-36].

    This is refreshing open discussion. Why can it not be discussed as such in Textbooks, Universities and even high school levels like this? Politics?

    “The moderate approach maintains that all the differences between individual gene trees notwithstanding, the tree of life concept still makes sense as a representation of a central trend (consensus) that, at least in principle, could be elucidated by comprehensive comparison of tree topologies.”

    Comparison of Tree topologies is not a bad idea, better than what we have.

    ” The radical view counters that the reality of massive HGT renders illusory the very distinction between the vertical and horizontal transmission of genetic information, so that the tree of life concept should be abandoned altogether in favor of a (broadly defined) network representation of evolution [17]. “

    From a computer science perspective, this makes more sense to me personally. Core Programs vs Called Subroutines or Nodes on a Network Trunk connected to Hubs, etc.

    “Perhaps the tree of life conundrum is epitomized in the recent debate on the tree that was generated from a concatenation of alignments of 31 highly conserved proteins and touted as an automatically constructed, highly resolved tree of life [37], only to be dismissed with the label of a ‘tree of one percent’ (of the genes in any given genome) [38].”

    I’ll never forget that quote; “the tree of one percent” nailed down the problem and also exposed the deception. Two birds/one stone.

  2. oops, forgot to end blockquote above…

    Here are a few more interesting highlights…

    “To avoid the uncertainty associated with the pruning procedure and to explore the properties of those few trees that could be considered to represent the ‘core of life’, we analyzed, along with the complete set of trees, a subset of nearly universal trees (NUTs).

    So, essentially, this to me seems a possibly biased study to begin with? I realize the need to narrow down candidates for study, but essentially this elliminates the fruit of the tree thats already fallen. Not intentionally, but they have little to work with that is not riddled with mutations and HGT, etc.

    “As the strictly universal gene core of cellular life is very small and continues to shrink (owing to the loss of generally ‘essential’ genes in some organisms with small genomes, and to errors of genome annotation) [45,46], we defined NUTs as trees for those COGs that were represented in more than 90% of the included prokaryotes; this definition yielded 102 NUTs.

    This gives us a hint of the current problem and why being open in the discussion is good. Science simply cannot deny the problem anymore is not just about concept, but of raw data input being modified over billions of years if you like.

    “Not surprisingly, the great majority of the NUTs are genes encoding proteins involved in translation and the core aspects of transcription (Additional data file 3)”

    I thought this might be interesting to you. Translation and transcription as “nearly universal trees” is interesting especially since the non-coded regions also are in these areas.

  3. and then… possibly the opening of the beginning of the end… a coup de gras to TOL….

    “However, the opposite side of the coin is that the consistency between the trees in the forest is high at shallow depths of the trees and abruptly drops, almost down to the level of random trees, at greater phylogenetic depths that correspond to the radiation of archaeal and bacterial phyla. This observation casts doubt on the existence of a central trend in the forest of life and suggests the possibility that the early phases of evolution might have been non-tree-like (a Biological Big Bang [36]). To address this problem directly, we simulated evolution under the CC model [39,40] and under the BBB model, and found that the CC scenario better approximates the observed dependence between tree inconsistency and phylogenetic depth. Thus, a consistent phylogenetic signal seems to be discernible throughout the evolution of archaea and bacteria but, under the CC model, the prospect of unequivocally resolving the relationships between the major archaeal and bacterial clades is bleak.

    Nor is reconciliation any clearer under the Biological Big Bang model. “Compressed Clado-Genesis?” Big Bang? Or just plain old Genesis? I realize they see this as millions of years still. I’m not going to argue about time. But I find it interesting there is an admission of genetic explosions or burst of information generation now in Biology openly discussed as possible alternatives. Glad to see it.

    “In summary, HGT is pervasive in the prokaryotic world, so that there are very few fully consistent NUTs.”

    Theres the rub. They were dealing with those few in this study. Outside the small 102 NUTs, there is no consistency in the forest at least for now in this study. And even the consistent ones may all be influenced by HGT.

    “Thus, the original tree of life concept is obsolete: it would not even be a ‘tree of one percent’ [38].

    Wow… thank you… finally. This is not only a huge admission, but a death “TOL” for Darwin’s original theory. So where does that lead them and/or the Design/UnDesigned debate?

    “Nevertheless, there seems to be a discernible signal of consistency between the trees in the forest of life, down to the deepest branching levels. Whether or not this central trend is denoted a tree of life could be a matter of convention and convenience, but the nature of this trend as well as the other trends that can be discerned in the forest merit further investigation.

    Certainly, lets open it all up again for many trends of related Design investigation. They’re willing to leave the metaphor TOL intact as a matter of “convenience” …. hmmmm. Even if it is “obsolete?”

    This is so refreshing. Everyone should now be allowed at the table without fear of losing jobs or glass ceilings due to holding minority opinions critical of Darwinian theory.

    Many Trees of Life in a Forest is similar to what Creationist have been saying for a long time. There should be a chance at common ground in some areas. That diversity exist within multiple Trees in the Forest of Life.

    The only thing left untouched after this paper and other recent findings is the inability to admit the big elephant in the room called Design.

    They did not kill off unguided evolution. Thats fine, it is not part of their research or the study.

    But, I think as you argued Michael elequently not long ago regarding Gradualism, the evidence now shifts to Design. And this is the final nail in the coffin.

    Wrapping up, current research and a shift in growing opinions show that essentially

    1) gradualism as defined by Darwin does not exist
    2) no single TOL, but multiple Trees
    3) regulatory systems as CORE across the spectrums
    4) non-coded regions become more important
    5) Selfish Genes tanked, obliterated
    6) a network of systems communicating programmatically
    7) Genetic differentiation across cells that are functionally dependent upon tissue type, organ type and transport.

    Because Biology for the longest time was not based in hard sciences, it has taken decades to allow cross-disciplinary research to attain new insights into life’s origins, blueprint and mechanims, plus networking complexity.

    And only recently with the advent of widespread use of computer technology and design has the concepts began to change over to recognition of Design attributes.

    It is fun to see this happening, to be alive at a time of revolutionary change in science ahead of us.

  4. One final comment or question finally related to your post about Conformity.

    Are we finally seeing the breaking down of the current Darwinian dogma? I hope so. Koonin’s, et al., study seem to indicate so.

    Now, if they’ll only admit that Design in biology can be a robust program for research.

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