The Golden Gnomon 黄金识子 Huang-jin Shi-zi

Why naming an axiom may seem pompous but is not

2011-08-09T11:31:00.000-07:00

My friend Joe, a biology professor at a US public university, gave me some great feedbacks after I emailed him my essay “The second axiom of construction and the second axiom of biology” as posted here on July 9, 2011. Below, I post his email feedbacks and my responses, which deal with axioms and the random nature of natural selection. My essay: “The Second Axiom of

Making the existing model obsolete

2011-07-13T10:17:00.000-07:00

Numerous scientists in the past 150 years have repeatedly challenged the Darwinian macroevolution theory (few has problems with the microevo part though for which Darwin and 4 others deserve our great respect). And many in the future will continue to challenge it until it falls, with ever more devastating facts and reasons. Actually, if one wants to

Second Axiom of Construction and Second Axiom of Biology

2011-07-09T13:37:00.000-07:00

The Second Axiom of Construction and the Second Axiom of Biology posit that any system can allow a certain degree of random noises or errors in its building blocks, and such limited degree of random errors may confer zero, negative, or positive values to the functioning/survival of the system under certain random environmental

It is through intuition we discover

2011-04-27T01:29:00.000-07:00

Intuition or axiom is the foundation of mathematics and physics, but has been until the first axiom of biology lacking in the science of biology. Darwin philosopher Daniel Dennett is fond of saying how wonderful is Darwin's "strange inversion of reasoning", and he is very proud of the anti-intuitive nonsense that randomness/errors/noises can create complex systems of great

Nature news today: Human remains spark spat

2010-12-31T22:32:00.000-08:00

Below is my comment at the Nature website on the Nature news report today "Human remains spark spat" about the latest 400000 year old modern human fossils from Israel. http://www.nature.com/news/2010/101231/full/news.2010.700.htmlThe authors' conclusion is obviously the same as being reported by the press: "We offer the most reasonable conclusion based on the statistical evidence: that they

Others have also noticed the difference between fast and slow evolving genes in phylogeny inference

2010-12-30T17:43:00.000-08:00

The anthropology blogger Dienekes at http://dienekes.blogspot.com had a recent post on Dec 30, 2010 noticing the major difference between slow and fast evolving genes in calculating the time of origin for humans. It is reassuring to see that others have come to the same conclusion as I have regarding the difference between slow and fast genes. The mere existence of the difference between slow

Latest fossil evidence in support of our molecular dating of modern human origin

2010-12-28T16:48:00.000-08:00

As described by my blog post on May 25, 2010, our molecular results based on the MGD hypothesis suggest that modern humans have been a single species since ~2 million years ago (manuscript in preparation). The multiregional hypothesis is correct and the out of Africa hypothesis is mistaken. This week's report of 400000 year old remains of modern humans fully support our work. Middle

Very good points by Nigel Goldenfeld and Carl Woese

2010-11-26T00:33:00.000-08:00

I just finished reading a very good recent paper by Nigel Goldenfeld and Carl Woese, Life is physics: evolution as a collective phenomenon far from equilibrium. http://arxiv.org/abs/1011.4125Carl Woese of course is famous for defining the Archaea bacteria in 1977. Below I comment on some of their writings which I found remarkable.Goldenfeld and Woese: "In short, a unified view prevents the

Kimura said that the strongest evidence for the neutral theory is the molecular clock

2010-11-24T21:15:00.000-08:00

A recent comment from a reviewer of my primate phylogeny manuscript again said the same thing as Scott Page has said over at Nature Precedings where my manuscript is posted that “the concept of the moleculr clock has little bearing on molecular phylogenetic studies that do not enforce a molecular clock criterion in their analyses.” Thus, there is a strong consensus in the field that even if the

Laws of Biology

2010-11-20T06:35:00.000-08:00

As is well known, there are no laws in biology as in physics, which is the reason I called an idea of mine the First Axiom of Biology. Recently, however, I noted that there are in the recent literature four laws of biology. One paper is titled The three laws of biology by Trevors and Saier. http://saier-14451.ucsd.edu/~saier/bimm122/reading122/TheThreeLaws.pdf One book is titled Biology’s First

Models of micro- and macro-evolution and the overlap feature

2010-10-14T22:11:00.000-07:00

I hope the following figure serves as an easy to grasp illustration of the evolution process according to the MGD hypothesis.A. Microevolution......................................0123456789........................0123xxxxxx..........................................B ________________________ B...............A'__________________.......0123xxxxxx..........................................A ________

Some paper concludes that complex organism has more functional bases

2010-08-14T19:06:00.000-07:00

The conclusion of a recent paper last week, in particular this last sentence from the paper’s abstract, says: "This suggests that, rather than genome size or protein-coding gene complement, it is the number of functional bases that might best mirror our naïve preconceptions of organismal complexity." (1)The paper is still in part based on the neutral theory that is not true in my opinion for

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

2010-07-15T11:00:00.000-07:00

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

Paper on the overlap feature is now published

2010-07-05T13:45:00.000-07:00

The Overlap Feature of the Genetic Equidistance Result—A Fundamental Biological Phenomenon Overlooked for Nearly Half of a Century Shi HuangBiological Theory Winter 2010, Vol. 5, No. 1: 40–52.http://www.mitpressjournals.org/doi/abs/10.1162/BIOT_a_00021

A sister relationship between European and an East Asian-African clade

2010-05-25T04:28:00.000-07:00

I gave a talk on May 14, 2010 at the Institute of Paleontology and Paleoanthropology, Chinese Academy of Sciences, titled "Molecular evidence for the multiregional hypothesis of modern human origin and a sister relationship between European and an East Asian-African clade". Professor Xinzhi Wu, one of the major proponents of the multiregional hypothesis, was my host. see this website for the

Genetic equidistance as shown by a list of most conserved proteins

2010-03-16T06:12:00.000-07:00

I am reading a popular textbook on bioinformatics, “Bioinformatics and Functional Genomics” 2009 by Jonathan Pevsner, in preparation for a course I am going to teach. On the topic of evolution and phylogeny, the book shows a table of a list of 20 most conserved proteins found in yeasts, worms, and humans. The table was taken from an old paper by the Bork group (1). The original table, which I

Africans and East Asians are strikingly similar

2010-02-19T13:15:00.000-08:00

The maximum genetic diversity (MGD) hypothesis considers the molecular clock and the neutral theory incorrect for macroevolution. Thus the genetic relationship or SNP diversity data among human races has yet to be correctly interpreted. We are presently working on a correct one based on the MGD hypothesis. This week Nature published genome sequences of a few South Africans. "Complete

The universe evolves from simple to complex, concludes a physicist

2010-02-08T20:06:00.000-08:00

I recently read the book "The Wrinkles in Time" by the Noble Laureate physicist George Smoot. I found his view of evolution of the universe from simple to complex to be in complete harmony with the facts of biological evolution. It seems to me there is a universal law of evolution that underlies all changes with time, regardless of life or non-life. There has to be one

New manuscript on the overlap feature of the genetic equidistance result

2009-12-11T22:30:00.000-08:00

I am submitting this week a manuscript by me entitled “The overlap feature of the genetic equidistance result, a fundamental biological phenomenon overlooked for nearly half a century”. The work establishes an overlooked feature of a fundamental result that directly triggered the molecular clock and neutral theory, the dominating theory in the field of molecular evolution. If this old result

What CNE means for the neutral theory?

2009-12-11T22:29:00.000-08:00

A new paper of interest this week:McEwen GK, Goode DK, Parker HJ, Woolfe A, Callaway H, et al. (2009) Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates. PLoS Genet 5(12): e1000762. doi:10.1371/journal.pgen.1000762Some general features of CNEs are well summarized by this paper on CNE (conserved non-coding elements). It says: “These elements (CNE) appear

Building Complexity and the main pattern in evolution

2009-12-06T04:33:00.000-08:00

Building complex and robust machine may have more ways than just one. To have backups or overlapping systems is one way of doing it, the most stupid and awkward way. Instead of a single engine in a small plane, a more complex large plane may have 4 engines with 2 of them as backups. But is that the nature’s way for using DNA to build complex life? Do we have an extra heart or brain or any

Darwin's theory is coherent and hypothesis generating? Can a theory be proven true?

2009-12-06T04:28:00.000-08:00

Stanley Sessions responded to my comments at Nature Precedings:http://precedings.nature.com/documents/2887/version/1#comments"I think I understand at least some of what you are getting at…wonderful! I think of the schizoid pickle physics is in right now compared to biology, the latter thanks to the remarkable coherency of evolutionary theory. However, you get into some dangerous territory when

On the standard for truth and the role of communication in disseminating scientific ideas

2009-11-24T00:31:00.000-08:00

Someone wrote an article on the talent of Darwin in amassing support for and in communicating the idea of Darwinism. Sessions, Stanley and Macgregor, Herbert. (2009) The Necessity of Darwin. Available from Nature Precedings, http://hdl.handle.net/10101/npre.2009.2887.1I responded by saying that ideas are more important than amassing facts and communication. And I got a counter response that

Real reason for the endless production of conflicting results on tarsiers

2009-11-13T22:22:00.000-08:00

A couple of weeks ago, a new paper by Chatterjee et al. appeared on primate phylogeny that groups tarsiers with prosimians. “Estimating the phylogeny and divergence times of primates using a supermatrix approach” Helen J Chatterjee, Simon YW Ho, Ian Barnes, and Colin GrovesBMC Evolutionary Biology 2009, 9:259 doi:10.1186/1471-2148-9-259I sent the following comment titled “Real reason for the

The MGD hypothesis in brief

2009-10-28T03:57:00.000-07:00

A colleague recently asked to briefly summarize the MGD in laymen terms and its distinction from the modern evolution theory. I gave it a try in the following.1) The reality of maximum genetic distance/diversity (MGD): For any gene with a biological function, certain mutations that destruct the function will not be tolerated by the organism while those neutral or beneficial ones will. So

An old paper and the MGD

2009-10-28T03:29:00.000-07:00

In recent email discussions with one of the pioneers of molecular evolution, I became aware of a 1986 paper that suggested the idea of a limit on protein sequence divergence, similar to the MGD. But these authors only recognized a limit for bacteria but failed to see similar limit also exists for nearly all organisms regardless of time of divergence, so long evolution is long enough or more than

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

2009-09-22T13:32:00.000-07:00

I posted a new manuscript at Nature Precedings: http://precedings.nature.com/documents/3794/version/1 titled: Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers AbstractInterpretations of molecular data by the modern evolution theory are often sharply inconsistent with

My comment on CAPS finally appeared on Cell website

2009-09-14T07:56:00.000-07:00

It took more than two weeks and a push note from me for Cell to finally publish my comment on CAPS related to the recent Cell paper: "Protein Sectors: Evolutionary Units of Three-Dimensional Structure". See my comment on the Cell website here: http://www.cell.com/comments/S0092-8674%2809%2900963-5 My push note to Cell below: Dear Editor, It has taken a lot longer than

Complexity Associated Protein Sectors (CAPS), new evidence for the MGD hypothesis

2009-09-01T13:21:00.000-07:00

A Cell paper two weeks ago reports an important and beautiful result on protein sequence conservation and evolution (1) (free open access http://www.cell.com/fulltext/S0092-8674(09)00963-5) The result contradicts the modern evolution theory but is a precise prediction of the more complete evolution theory, the maximum genetic diversity hypothesis (MGD) (2, 3). The

Darwinists self destruct when self defend

2009-08-28T10:47:00.000-07:00

Let us do a few necessary/inevitable logical deductions from the typical claims of a Darwinist like Ken Weiss and others and see where they may lead us. Ken Weiss: “Any rule an evolutionary biologist can come up with, nature can break.” The rules/hypotheses of Darwinists include a few like the following: 1. The very rule itself that ‘any rule an evolutionary biologist

Either chance or intention (no other alternatives), in Darwin's own words

2009-08-21T20:09:00.000-07:00

In Darwin's words: "I cannot look at the universe as the result of blind chance, yet I can see no evidence of beneficent design, or indeed of design of any kind." "This [conviction in the existence of God] follows from the extreme difficulty or rather impossibility of conceiving this immense and wonderful universe, including man with his capacity of

All existing evolution theories have/allow contradictions and hence are non-testable

2009-08-19T12:36:00.000-07:00

Darwin followers never said that their theory has no exceptions. Here are a few typical claims: “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.” Masatoshi Nei

Natural selection is random but artificial selection is not

2009-08-19T11:00:00.000-07:00

Contrast between natural selection (NS) and artificial selection (AS). Artificial selection has human mind as the selector. It was used by Darwin as an analogy to natural selection. Darwin used the term once in his work On the Origin of Species:Slow though the process of selection may be, if feeble man can do much by artificial selection, I can see no limit to the amount

The origin of the flawed notion that natural selection is not random/chance

2009-08-12T09:23:00.000-07:00

I am very interested to find out who first said that natural selection is not random/chance but is the very opposite. I re-read Darwin's original book and did not find it there. The earliest source for this flawed notion that I could manage to find is the 1982 book by one of the founders of Neo-Darwinism, Ernst Mayr, "The Growth of Biological Thought: Diversity, Evolution, and Inheritance".

Latest gene knock out works confirm the MGD hypothesis

2009-07-27T10:56:00.000-07:00

A recent news focus article in Science discusses knock out works that are inexplicable by the existing paradigm of evolution. But, as I explain below, they are easy predictions of the MGD hypothesis. Genomic clues to DNA treasure sometimes lead nowhere By Don Monroe, July 10, 2009, Science 325: 142-143 The first paragraph summarizes the basic findings that the

Pervasive Natural Selection in the Drosophila Genome?

2009-06-11T13:04:00.000-07:00

There is new review paper openly attacking the neutral theory: Sella G, Petrov DA, Przeworski M, Andolfatto P (2009) Pervasive Natural Selection in the Drosophila Genome? PLoS Genet 5(6): e1000495. doi:10.1371/journal.pgen.1000495 The authors essentially concludes that the neutral theory is largely false in the Drosophila system. The implication is obvious, if it is false

Molecular evidence for the hadrosaur B. canadensis as an outgroup to a clade containing the dinosaur T. rex and birds

2009-05-15T12:06:00.000-07:00

Molecular analysis of collagen sequences from an 80 million year old hadrosaur B. canadensis and a 68 million year old dinosaur T. rex suggest that the two dinosaurs belong to a clade to the exclusion of birds I have written a review (http://www.amazon.com/review/R160K7033BB22Y) of Jerry Coyne’s book ‘Why evolution is true’ and criticized the author for not distinguishing between the facts of evolution and the Darwinian theory of natural selection. The facts are true but the theory is far from true as it has countless contradictions, which means that it is actually false, at

On the collagen sequence of the Campanian hadrosaurs (duck-billed dinosaur) B. Canadensis

2009-05-11T08:24:00.000-07:00

Collagen sequences from an 80 million year old dinosaur were published recently. Schweitzer et al., 2009, Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. Canadensis, Science, 5927, pp. 626 - 631 Below I analyzed the 8 peptide sequences reported. My analysis showed that B. Canadensis is an outgroup to a T.rex-bird clade, consistent with

A more accurate rendering of Table 1 in the MGD paper

2009-05-07T08:35:00.000-07:00

The following modification of Table 1 of the MGD paper take into account those positions that are shared between species due to common adaptation to a common environmental selection, depicted by ‘#’. Variant positions are denoted by 'x'. This more realistic rendering explains both equidistance and overlap features. It explains why not all variants between Hs and Dm are also variants between

The last straw for Molecular clock

2009-05-06T17:04:00.000-07:00

I sent the following email yesterday to a small groups of colleagues.Dear colleagues with an interest in human evolution (students, postdocs, and professors): I thought you may find the following two short comments informative and interesting (both are posted on the Internet). 1. Molecular clock at best explains half the story on ‘genetic equidistance’ and at worst

The overlap feature of hemoglobin

2009-05-06T16:45:00.000-07:00

Hemoglobin was used in 1962 by Zuckerkandl and Pauling to derive data that led to the molecular clock idea. Here I examined the overlap feature using human Hemoglobin alpha 1 (AAK61216, hba1) to compare with horse and chicken, in a way similar to what Zuckerkandl and Pauling had done. Hs, Human [Homo sapiens]Ec, Horse [Equus caballus] Gg, Chicken [

The molecular clock should never have been invented in the first place for macroevolution

2009-05-06T08:38:00.000-07:00

Two kinds of sequence alignment can be made using the same set of sequence data. The first aligns a recently evolved organism such as a mammal against those simpler or less complex species that evolved earlier such as amphibians and fishes. The second aligns a simpler outgroup organism such as fishes against those more complex sister species that appeared later such as

Evidence for an ancient adaptive episode of convergent molecular evolution

2009-05-05T08:25:00.000-07:00

Castoe et al., “Evidence for an ancient adaptive episode of convergent molecular evolution” PNAS, April 29, 2009, published on line, doi: 10.1073/pnas.0900233106 Abstract: …..These results indicate that nonneutral convergent molecular evolution in mitochondria can occur at a scale and intensity far beyond what has been

Genomics, Evolution, and Pseudoscience: T. rex protein degrades further

2009-05-05T08:20:00.000-07:00

Genomics, Evolution, and Pseudoscience: T. rex protein degrades further

Molecular clock, pseudoscience, and Steven Salzberg

2009-05-04T13:10:00.000-07:00

I have left several comments before on Professor Steven Salzberg’s blog: http://genome.fieldofscience.com/2008/08/t-rex-protein-degrades-further.html He is a professional in the business of molecular clock and molecular evolution. But he has a hobby of carelessly calling the research of some scientists ‘pseudoscience’. (granted that he may have

More on the MGD interpretation of certain facts

2009-05-01T19:31:00.000-07:00

I am showing below yeast and neurospora cytochrome c alignment to explain an observation that is not covered in detail in my MGD paper but is covered in principle. The observation is that not all variant residues between two complex species are also variant between two simple species, when Table 1 of the paper seems to indicate that all variant residues between two

Molecular clock at best explains half the story on ‘genetic equidistance’ and at worst explains none

2009-04-30T11:55:00.000-07:00

The genetic equidistance result (sister species are equidistant to a simpler outgroup) has been interpreted by a tautology, the molecular clock hypothesis, which says that vastly different lineages have very similar mutation rates. The neutral theory was invented to explain the molecular clock by postulating that the vast majority of residue differences between species are

Species are evolutionary accidents

2009-04-27T10:00:00.000-07:00

Logical incoherence is what often characterizes Darwinian science and the statements by Darwinian scholars. The latest example is the writing of Jerry Coyne in his book "why evolution is true". In one part of the book (p118), he makes the case that evolution by natural selection is not random. In another part (p176), he says that "species are evolutionary accidents." Since species are

Molecular Clocks and the Puzzle of RNA Virus Origins

2009-04-16T09:31:00.000-07:00

There is a paradox for RNA virus origin. Because the high mutation rate of these viruses, the large genetic distance between two unrelated viruses can be arrived at in very short time frames, like less than 100,000 years. This is a challenge to the molecular clock but is evidence for the MGD hypothesis. Two viruses may share a common ancestor many million years ago but their genetic distance

Exceptional convergent evolution in a virus

2009-04-11T16:04:00.000-07:00

This paper showed nicely that common selection can lead to extensive identity in DNA sequences. Thus, sequence comparison cannot always be used for inferring time of separation. This is exactly the point made by my MGD hypothesis. When we see a human and chimp identity of ~98%, we must first ask how much of that is due to common selection. The MGD says that there is a lot. The data are

Darwin’s logical errors

2009-04-09T12:35:00.001-07:00

I reread a part of Darwin’s book on the topic of natural selection to see if he ever said that natural selection is not random. I did not find it. But I was astonished to find that his logical lapses could ever got printed for all to see.Darwin wrote:“Slow though the process of selection may be, if feeble man can do much by artificial selection, I can see no limit to the amount of change, to the

Natural selection is random/chance, period.

2009-04-06T14:21:00.000-07:00

Darwin followers admit that random/chance cannot work, but calls natural selection nonrandom or the very opposite of chance. But they would never say natural selection is intentional or purposeful. So, is there such a thing that is nonrandom and non-intentional in nature? None what so ever in human experience. No one in history has a word for such a meaningless concept. How can anyone get

MGD hypothesis peer review

2009-04-06T13:12:00.001-07:00

I am sharing the latest peer review of my paper. It should help people understand the simple fact that while peer review does promote progress within a paradigm, it also prevents revolutionary progress or paradigm shift. 01-Apr-2009Re: JEZ-B-2009-02-0022JEZ-B 2007 Impact Factor is 3.578.Average time to first decision 41 daysDear Prof. Huang:I am sorry to inform you that your manuscript, Inverse

Human mutation rate associated with DNA replication timing, by Stamatoyannopoulos

2009-03-28T14:49:00.000-07:00

Human mutation rate associated with DNA replication timing, Nature Genetics, 41: 393-395, 2009Abstract:Eukaryotic DNA replication is highly stratified, with different genomic regions shown to replicate at characteristic times during S phase. Here we observe that mutation rate, as reflected in recent evolutionary divergence and human nucleotide diversity, is markedly increased in later-replicating

Meat intake and mortality, by Sinha et al

2009-03-24T10:23:00.000-07:00

A large study on meat and mortality was published today (Arch Intern Med, 2009, 169: 562-571.) The paper concludes that "Red and processed meat intakes were associated with modest increases in total mortality, cancer mortality, and cardiovascular disease mortality." But my careful review of the paper suggests that it is total meat intake rather than color that is important, consistent with my

The mode and tempo of genome size evolution in eukaryotes

2009-03-15T14:01:00.000-07:00

This old paper from 2007 was just brought to my attention by a netter discussing the MGD and the latest Science paper on high mutation rate of small genomes. This 2007 paper shows that large genomes show higher rate of large DNA segment duplications, insertions, rearrangments, etc, so called high rate of genome evolution in large genomes. These events are in fact both genetic and epigenetic,

Extremely High Mutation Rate of a Hammerhead Viroid by Gago et al

2009-03-06T08:27:00.000-08:00

This Science paper confirms the MGD hypothesis. The author stated: "Such error-prone replication can only be tolerated by extremely simple genomes such as those of viroids." The simpler the organism, the more mutations it can tolerate. Science 6 March 2009: Vol. 323. no. 5919, p. 1308 DOI: 10.1126/science.1169202 Prev | Table of Contents | NextBREVIAExtremely High Mutation Rate of a Hammerhead

The DNA-encoded nucleosome organization of a eukaryotic genome by Kaplan et al

2009-01-17T16:41:00.000-08:00

This paper supports the MGD hypothesis.Nature advance online publication 17 December 2008 | doi:10.1038/nature07667; Received 2 October 2008; Accepted 26 November 2008; Published online 17 December 2008The DNA-encoded nucleosome organization of a eukaryotic genomeNoam Kaplan1,9, Irene K. Moore3,9, Yvonne Fondufe-Mittendorf3, Andrea J. Gossett4, Desiree Tillo5, Yair Field1, Emily M. LeProust6,

Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites by Sasaki et al

2009-01-17T16:31:00.000-08:00

The paper by Sasaki et al in Science supports the MGD hypothesis. Indel rate is inversely related to point mutation rate. Indel is more of an epigenetic event. Originally published in Science Express on 11 December 2008Science 16 January 2009:Vol. 323. no. 5912, pp. 401 - 404DOI: 10.1126/science.1163183Prev | Table of Contents | NextREPORTSChromatin-Associated Periodicity in Genetic Variation

Dr. Francisco Ayala's response and my rebuttal

2008-12-28T13:39:00.000-08:00

I posted the following on Amazon.com, http://www.amazon.com/review/R8WB8ZQSOUVGCIn case anyone is interested in what the NAS experts may respond to my email to them, I here make public the response from NAS member Dr. Francisco Ayala who headed the NAS panel that wrote the booklet. I also post here my rebuttal. I have yet to hear from Dr. Ayala again after my rebuttal of 11/18/2008, suggesting

Misleading teachings in “Science, Evolution, and Creationism, A view from the National Academy of Sciences, 2008”

2008-11-11T11:36:00.000-08:00

Today I sent an email to Jay Labov, cc. Francisco Ayala, of the National Academy of Sciences, asking them to correct a misleading statement on molecular evolution.Dear Jay:I find it sad that a group of scientists of the NAS caliber simply cannot make a true statement in the field of molecular evolution. I have written to you in 2005 about a misleading (part truth part lie) statement in the 1999

Complete Neandertal mitochondrial genome by Green et al. Cell

2008-08-29T17:00:00.000-07:00

The paper shows that for amino acid or non-neutral sequences neandertals are more distant to an outgroup than modern humans are. This confirms what my earlier paper has found for neandertals, dinosaurs, and mastodons.

Response to a comment on my fossil paper and to the recent Cell paper on Neanderthals

2008-08-22T15:14:00.000-07:00

leigh van valen commented at Nature precedings on my fossil paper"There is ample evidence for a variable clock. Unless the divergence from constancy here is greater than what is found elsewhere, the paper unfortunately adds nothing useful."My response below:Thank for you this opportunity to address a common mistaken reaction to my paper. I will also here respond to the recent Cell paper on

Interesting papers from the Editor in Chief of Medical Hypothesis

2008-07-10T14:44:00.000-07:00

I enjoyed very much the following two papers by Bruce G. Charlton, Editor in Chief of Medical Hypothesis. False, trivial, obvious: Why new and revolutionary theories are typically disrespected Bruce G. Charlton, Medical Hypotheses 2008; 71: 1-3Summary:An old joke about the response to revolutionary new scientific theories states that there are three phases on the road to acceptance: 1. The

Fossil paper published

2008-07-08T13:29:00.000-07:00

The paper titled "Ancient Fossil Specimens of Extinct Species Are Genetically More Distant to an Outgroup than Extant Sister Species Are" is now published, Riv. Biol. 2008, 101: 93-108I am very happy to get these words published in a peer reviewed journal: "Therefore, while the molecular clock hypothesis is consistent with some data from extant organisms, it has yet to find support from ancient

The Maximum Genetic Diversity Hypothesis posted on Nature Precedings

2008-04-02T15:17:00.000-07:00

The latest version of the paper on the maximum genetic diversity hypothesis is now posted on Nature Precedings. It can be cited as: Huang, S. Inverse relationship between genetic diversity and epigenetic complexity, Submitted. Available from Nature Precedings at http://hdl:10101/npre.2008.1751.1I also posted a related paper introducing the 45 year old outstanding puzzle of evolution, 'the

Fossil sequence paper posted on Nature Precedings

2008-03-12T15:36:00.000-07:00

Today, Nature Precedings posted my paper on Neanderthals/dinosaurs/mastodons that falsify the molecular clock hypothesis. The paper can now be cited in publications as follows: Huang, S. Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are. Available from Nature Precedings at http://precedings.nature.com/documents/1676/

The Maximum Genetic Diversity Hypothesis

2007-05-30T15:49:00.000-07:00

I submitted two papers in April 2007 on a new evolution hypothesis, the Maximum Genetic Diversity Hypothesis (MGDH). The molecular clock hypothesis is really a tautology in many cases. The MGDH offers by far the only logically sound explanation for the remarkable molecular evolution phenomenon that sister species are roughly equally distant to an outgroup. The first paper titled "On genetic

Ancient fossil specimens of extinct species are more distant to an outgroup than extant sister species are

2007-04-17T11:09:00.000-07:00

Shi Huang，Ph.D.Program on Cancer Genetics and EpigeneticsThe Burnham Institute for Medical Research10901 North Torrey Pines RoadsLa Jolla, CA 92037AbstractThe molecular clock hypothesis was proposed 45 years ago to explain the remarkable molecular evolution phenomenon that sister species are roughly equally distant to an outgroup. The hypothesis predicts that ancient specimens cannot possibly be