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Archived Comments for: Estimating the phylogeny and divergence times of primates using a supermatrix approach

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  1. Real reason for endless production of conflicting results

    Shi Huang, Central South University

    19 November 2009

    On the position of tarsiers, the paper wrote:”The majority of molecular evidence supports the latter grouping [4,10-13], although a large number of molecular studies still provide support for the Prosimii concept [14-18].”

    When a method or technique can lead to two opposite results repeatedly and seemingly endlessly while only one of the two can be true, it is time to ask whether something is fundamentally missing with our method. Let us start from the very beginning and examine the assumptions for our method. The key assumption for all sequence similarity based methods is that sequence dissimilarity always correlates with time of divergence. Well, is this true? We don’t have to be a specialist to know that this is sometimes true and sometimes not. Thus, for our method to be able to produce accurate and uncertainty-free result, it must take into account the reality that sequence dissimilarity sometimes does not correlate with time of divergence. But unfortunately, no existing methods have done that. Thus, none of them can produce results of 100% certainty. Many of the sequence comparisons are not informative and should and must be excluded from our method. When they are not as is the case with all existing methods, they contribute to the high noise level that can sometimes overwhelm the signal. It is by accident that these methods sometimes give correct results and sometimes wrong results and no one knows why the difference or when to view such a result correct and final. Therefore, we have the peculiar non-scientific situation specific to the field of phylogeny that is not seen in any other branch of science: no one is taking anyone else’s result as the final say. Never mind that we only have one true phylogeny of life on Earth. Once you know it, it is done and no more work needed. The existing methods are perfect for keeping some of us employed forever but will never give us truth. Truth is not judged by a quantitative difference in the number of studies that support it versus those against it. The correct method should produce zero number of studies that is against truth.

    By the own admission of the leading experts, the existing methods are flawed in the sense that they can easily produce incorrect results that are totally out of the hands of the scientists:
    “Unlike the case in physics, the predictive power of a model in biology is quite low. It seems to us that if the prediction (e.g., a phylogenetic tree reconstructed) of a model is correct in 80% of the cases, it is a good model at least at the present time.” From Masatoshi Nei and Sudhir Kumar, 2000, Molecular Evolution and Phylogenetics, (p85):

    Well, this typical attitude of molecular evolution biologist is not science, at least by the standard of any other branch of science. When a result is only 80% certain, it can be completely wrong. We either know or we don’t know. Knowing 80% means we don’t know. We are much better off without it because it often leads the non-specialist into the wrong idea that we know with 100% certainty. Does not everyone think that we are 100% certain that chimp is closest to humans when in fact we are only 80% certain and can therefore be completely wrong?

    Of course, biology does not have to be different from physics. The present situation merely means that we have not known enough yet. When we know better, we should be able to have a model that is correct in 100% of the cases. I have now offered the slow clock method as the best candidate for a method that takes into account all reality and is capable of 100% certainty (1). While your result, like many others, does support my result on tarsiers using the slow clock method (1), I do not view your result as confirming mine, because your method is flawed. By using the same kind of method, another group could easily produce a result opposite of yours by just picking a new set of genes (this of course has been done many times already). I of course do not view such result as valid contradiction to mine just like I do not view yours as valid support.

    Huang, S. (2009) Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers. Available from Nature Precedings,

    Competing interests