Thursday, July 15, 2010

New fossil finds on ape-monkey common ancestor supports my molecular dating while contradicts all others'

New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys. Iyad S. Zalmout, William J. Sanders, Laura M. MacLatchy, Gregg F. Gunnell, Yahya A. Al-Mufarreh, Mohammad A. Ali, Abdul-Azziz H. Nasser, Abdu M. Al-Masari, Salih A. Al-Sobhi, Ayman O. Nadhra, Adel H. Matari, Jeffrey A. Wilson & Philip D. Gingerich. Nature 466, 360–364 (15 July 2010)

This new paper on a common ancestor of ape-monkey from 29-28 million years ago in Nature this week fully supports my molecular dating as found in this preprint here (, while contradicts all other previous dating results on the ape-monkey divergence time. The dating in my paper is 29.7 million years (MY). Dating results by others using completely different, in my view flawed, methodology are self-conflicting and either too late (23 MY) or too early (30-35 MY). Any methodology that can turn solid factual data like DNA into conflicting interpretation of reality has of course self-proven itself false.

My paper has been through a number of submissions and I have not seen a valid criticism on the key points of the paper. The paper is now in the hands of a journal editor and below is part of my cover letter explaining my paper, which should help people understand the difference between my method/result and others’ and why others’ are incorrect from both a theoretical point of view and a practical point of view that they are contradictory to the new fossil finds.

Molecular phylogeny methods are based on the neutral theory. But the neutral theory should never have been invented in the first place for macroevolution if people had not overlooked the overlap feature of the genetic equidistance result that originally inspired the molecular clock and in turn the neutral theory. More on this exceptional new finding, see my newly published paper, Huang S (2010) The overlap feature of the genetic equidistance result, a fundamental biological phenomenon overlooked for nearly half of a century. Biological Theory 5: 40-52.

Since the neutral theory has no concept of a maximum distance, all these methods include a large amount of sequence alignment information that are non-informative and hence contribute to the high noise level that can sometimes overwhelm the signal. Also, these methods require false or uncertain assumptions that treat macroevolution the same as microevolution. It is thus fully expected that these methods cannot possibly produce a true molecular phylogeny of macroevolution. In fact, they have all self-proven themselves incorrect by repeatedly turning solid factual data into conflicting interpretations of reality, one of which must be false. The data in molecular phylogeny is just sequence facts and cannot possibly be wrong so long one is not making sequencing errors. Thus the only way to produce a false result or conflicting results in molecular phylogeny is through an incorrect method, including any method that does not have any correct means and principles of identifying only the informative data. One good example of endless conflicting results produced by the existing methods is the position of tarsiers, which some studies group with prosimians whereas others with simians, despite the fact that all these studies used the same kind of method but just different set of genes. A correct method should have ways of selecting the informative data and either produce only correct results or no results if informative data are not available.

The manuscript here used a new method ‘the slow clock’ to resolve key questions of primate phylogeny. Since the method has no uncertain assumptions and uses only informative genes, the slow evolving ones not yet reaching maximum genetic distance, it is immune to turning factual data into false or conflicting interpretation of reality. Indeed, the new primate molecular phylogeny here produced by the new method matches closely with the original interpretation of the fossil records by paleontologists.

You don’t really need to be reminded of this of course but I still suggest that you must use the highest standard of science to compare my story versus the existing theory/methodology. One must judge a story only by how contradiction-free it is. It is really the minimum scientific standard and the only practical way to distinguish a scientific truth from a religious belief. Thus, you only need to give me one single contradiction to my theory/methodology for me to withdraw my manuscript. That by the way should also be the only scientific way to reject the manuscript. I am eager to have the reviewers to help me either improve the manuscript or thrash it.

The following novel results in my manuscript are the contradictions to the existing theory/methodology but are not to mine. You and the reviewers must express your views on these results or offer an explanation if it happens to be different from mine. 1) Chimpanzee is closer to orangutan or gorilla than human is in DNA. 2) Slow and fast evolving genes produce different phylogeny. 3) The clock/neutral theory is a mistaken interpretation of the equidistance result of Margoliash. 4) Given 3), the existing interpretation of ape-human relationship is based on false theory and cannot possibly be true. One simply cannot imagine that the field has been all along on the right track when a major mistake had been committed right from the start. Neither can one imagine that the field can continue business as usual now that the mistake has finally been caught after nearly half of a century. Essentially no conclusion or interpretation on macroevolution from the molecular evolution field in the past half of a century can be regarded as correct or conclusive. 5) The fact that octopus is closer to human than cockle is, or that bird is closer to human than snake is in DNA contradicts the existing theory/methodology. The fact that chimpanzee is closer to human than orangutan or gorilla is therefore cannot be used to infer closer genealogy to human, just like one cannot infer closer genealogy between bird and human than between snake and human.

Finally, the newest version of my paper has a lay abstract as follows:

Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers

Author Summary:

Molecular phylogeny methods are based on the neutral theory of evolution, which was originally inspired in a large part by the genetic equidistance result of Margoliash in 1963. But the neutral theory should never have been invented in the first place for macroevolution if people had not overlooked the overlap feature of the genetic equidistance result. Therefore, the field of molecular phylogeny has been on the wrong track all along, and a complete reevaluation of all molecular phylogeny results is in order. The maximum genetic diversity hypothesis is a more coherent and complete account of evolution, and was here used to resolve key questions of primate phylogeny. The analysis shows that humans are genetically more distant to orangutans than African apes are and separated from the pongid clade 17.3 million years ago. Also, tarsiers are genetically closer to lorises than simian primates are, suggesting a tarsier-loris clade to the exclusion of simian primates. The validity and internal coherence of the primate phylogeny here were independently verified. The results as a whole show a remarkable and unprecedented concordance between molecules and fossils.

Monday, July 5, 2010

Paper on the overlap feature is now published

The Overlap Feature of the Genetic Equidistance Result—A Fundamental Biological Phenomenon Overlooked for Nearly Half of a Century no access
Shi Huang
Biological Theory Winter 2010, Vol. 5, No. 1: 40–52.