Thursday, April 30, 2009

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

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 neutral mutations. 


On surface, the similar mutation rate idea seems to explain the equidistance result in terms of percent identity.  But one fatal weakness with this idea that was pointed out in my previous paper is that there is no independent evidence for this idea.  In contrast, there are ample evidence against this idea.  That observation alone has in part led me to invent the MGD hypothesis as the correct interpretation for the equidistance result.  The MGD interpretation came to me from logical reasoning based on basic biological principles.  Thus, I had deduced an important feature of the equidistance result from an axiom before I had a full grasp of the complete story of equidistance.  That feature is: most of the residue positions differing between one sister lineage and the outgroup are also different between another sister lineage and the outgroup.  In other words, suppose that sister species A and B are equidistant to the simpler outgroup C, where A and B has separated for much longer time than the time of separation between C and the common ancestor of A and B.  We would observe that most of the residue positions that differ between A and C are also different between B and C.  Below, I illustrate this fundamental feature of the equidistance result by using the example of cytochrome c which was used originally in 1963 to discover the equidistance result, with the baker’s yeast as the outgroup to the sister species of drosophila and human. 


Yeast blastp against drosophila:

Identities = 67/104 (64%), Positives = 78/104 (75%), Gaps = 0/104 (0%)











Yeast blastp against human:

Identities = 66/102 (64%), Positives = 79/102 (77%), Gaps = 0/102 (0%)











Drosophila blastp against human:

Identities = 80/102 (78%), Positives = 87/102 (85%), Gaps = 0/102 (0%)











Overlap variant positions among Sc, Dm, and Hs:







Overlap       xxx  xx  xx  x         x         x   xx   x        xx xxx







Overlap     x xxxx   x           x x    xxx x   x




The above alignment data show that yeast is approximately equidistant to drosophila (67/104 identity) and to human (66/102 identity).  If one carefully compares the alignments, one would find that among those 36 residue differences between yeast and human, 31 are also different between yeast and drosophila. 


This nearly complete overlap in mutated residue positions in two separate sister lineages is one of the two fundamental features of the genetic equidistance phenomenon (the other is of course the equidistance in terms of percent identity).  However, it, dubbed the overlap feature, has been completely ignored or overlooked in the past 46 years.  The molecular clock interpretation and the neutral theory were invented based on a complete ignorance of this feature.  They would not have been invented in the first place if people had paid attention to the overlap feature because they are clearly contradicted by this feature.  It is astonishing that this obvious contradiction has never been recognized for the past 46 years in a large field of study that has produced several dozen members of the National Academy of Sciences but is nonetheless completely misled by a false paradigm.


The molecular clock and the neutral theory cannot predict a majority of all mutant residue positions between yeast and human to be also mutant positions between yeast and drosophila.  The predicted number is at best 20 residue positions, far short of the observed 31.  This is easily calculated as follows:


As the above alignment shows, drosophila and human differ at 22 of 102 positions.  Among these, 17 drosophila or human positions are also different from yeast.  So, of the total 31 mutant/changed positions between yeast and human that are also altered between yeast and drosophila, 14 could be assigned to changes occurred during the time period when the common ancestor of human and drosophila has been separate from the yeast lineage but has yet to split out human and drosophila.  After the split of human and drosophila, the chance for a residue to be different between yeast and the human lineage or between yeast and drosophila or between drosophila and human is approximately 22/81 = 0.27.  (There are only 7 residues that are absolutely conserved among all life forms that contan cytochrome c.  So the positions that are changeable are 88 - 7 = 81).  The chance for the same residue position to be altered in both the yeast-human comparison and the yeast-drosophila comparison is 0.27 x 0.27 = 0.073.  Together with the 14 shared mutant positions accumulated in the common ancestor lineage of drosophila and human, this means that there should only be 14 + 6 =20 residue positions that are altered in both the yeast-human comparison and the yeast-drosophila comparison.


To get to 31, we must invoke that there are only 28 residues that are neutral (22/28 x 22/28 x 28 = 17).  This means that the observed distance between yeast and human or between yeast and drosophila or between human and drosophila represents nearly the maximum possible.  But a maximum cap concept on genetic distance is entirely missing in the practical application of the molecular clock and the neutral theory.  That concept is nonexistent in the past until the recent MGD hypothesis.


In short, while the molecular clock and the neutral theory may predict half of the equidistance result (equidistance in terms of percent identity), they cannot predict or are contradicted by the other half of the result where most of the mutant positions relative to the outgroup are shared between the two sister lineages.  Therefore, the molecular clock and the neutral theory are not at all valid explanation for the equidistance result.  This way of invalidating the existing theory did not occur to me until recently, which is why I did not include it in my previous paper that refutes the molecular clock interpretation of the equidistance result.  Ref. Huang, S.  “The genetic equidistance result of molecular evolution is independent of mutation rates.”


The MGD hypothesis is the only viable and complete explanation so far for the equidistance result.  It has proven to be the correct one as it easily passes the highest standard for a scientific theory, i.e. to explain all relevant facts and to have not a single factual and logical contradiction.  The example here with cytochrome c should provide the actual data for the simplistic illustration of the MGD explanation as shown in Table 1 of my MGD paper (Inverse relationship between genetic diversity and epigenetic complexity).   


BTW, an example of how the molecular clock interpretation was used in practice by the field to produce the famous 5 million year divergence time between human and chimpanzees, as first reported in 1969. Wilson AC, Sarich VM (1969) A molecular time scale for human evolution. Proc Natl Acad Sci U S A 63: 1088-1093.


Wilson and Sarich wrote in their 1969 paper:

“Table 1 shows that the four primate hemoglobins are about equally distinct in sequence from that of the horse. Therefore, the hemoglobins of monkeys on the one hand, and those of the apes and man on the other, have changed to about the same extent

since these species last shared a common ancestor.  These results are neither unique nor surprising. Others have already recognized that protein molecules often appear to have evolved in a regular fashion with respect to time. The bulk of the available sequence information is consistent with the hypothesis that for any given protein, such as hemoglobin, the probability of an amino acid substitution occurring in a given interval of time is the same in every lineage.”


The above shows that Wilson and Sarich interpreted the equidistance result (horse is equidistant to the primates in hemoglobins) by assuming the same mutation rate in every primate lineage.  From there, they went on to calculate a 5 million year split for humans and chimpanzees.  Now, given that I have proven that the molecular clock interpretation of the equidistance result is completely false, it follows that any result based on such interpretation is automatically false.  Indeed, my calculation based on the MGD hypothesis gave a human-pongid split time of 19.2 million years (manuscript in preparation).   



I thank my college classmate Dr. Wei Shen for discussion and correcting a mistake on the number of overlap residues in the first draft of this assay. 


Monday, April 27, 2009

Species are evolutionary accidents

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 products of natural selection, he is saying in one place that species is random accident while in another place that species is not random accident.

Statements by Jerry Coyne that natural selection is not random:
"This brings up what is surely the most widespread misunderstanding about Darwinism: the idea that, in evolution, “everything happens by chance” (also stated as “everything happens by accident”). This common claim is flatly wrong. No evolutionist—and certainly not Darwin—ever argued that natural selection is based on chance. Quite the opposite."

"Richard Dawkins provided the most concise definition of natural selection: it is “the non-random survival of random variants.”

Statements by Jerry Coyne that speciation is random:
"The study of speciation tells us that species are evolutionary accidents."

It is amazing that a scientific theory can be interpreted in two opposite ways by its followers. If a theory is like that, it is not genuine science but is rather philosophy or religion. On the random nature of evolution, Darwinists can be divided into three camps.

Camp 1, Evolution by accidents. Typical examples include Jacques Monod, Ernst Mayr,Stephen Jay Gould,Larry Moran.
Typical statements:
Larry Moran: "I think the term "evolution by accident" is an accurate description of how evolution occurs.......The "problem" is that writers like Richard Dawkins have made such a big deal about the non-randomness of natural selection that they risk throwing out the baby with the bathwater. A superficial reading of any Dawkins' book would lead you to the conclusion that evolution is an algorithmic process and that chance and accident have been banished. That's not exactly what he says but it sure is the dominant impression you take away from his work."

Ernst Mayr: "“If evolutionists have learned anything from a detailed analysis of evolution, it is the lesson that the origin of new taxa is largely a chance event. Ninety-nine out of 100 newly arising species probably became extinct without giving rise to descendant taxa. And the characteristic of any new taxon is to a large extent determined by such chance factors as the genetic composition of the founding population, the special internal structure of its genotype, and the physical as well as biotic environment that supplies the selection forces of the new species population.”

Camp 2, Evolution is not random. Typical examples include Richard Dawkins, Simon Conway Morris.
Typical statements:
Richard Dawkins: “the non-random survival of random variants.”

Camp 3, The logically impaired who claims evolution of new species is both random and nonrandom. Typical example, Jerry Coyne

If Darwinism is real science, it can only have one authentic position on the issue of randomness. That position belongs to camp 1.

Thursday, April 16, 2009

Molecular Clocks and the Puzzle of RNA Virus Origins

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 would reach a maximum in less than 100000 years and stays unchanged forever thereafter.

Some genes like proteases are conserved in viruses and all cellular life forms. In such genes, the genetic distance between two closely related and recently separated viuses, like HIV1 and HIV2, is equivalent to that between bacteria and eukaryia representing 2 billion years of separation. So, simple life forms can reach great genetic distance in very short time. Genetic distance between evolutionally distant viruses represents the maximum.


Are RNA viruses adapting or merely changing?
J Mol Evol. 2000 Jul;51(1):12-20.
Sala M, Wain-Hobson S.

Molecular Clocks and the Puzzle of RNA Virus Origins
Journal of Virology, April 2003, p. 3893-3897, Vol. 77, No. 7
Edward C. Holmes
Although the ultimate origins of RNA viruses are uncertain, it seems reasonable to assume that these infectious agents have a long evolutionary history, appearing with, or perhaps before, the first cellular life-forms (38). While the RNA viruses we see today may not date back quite this far, the evidence that some DNA viruses have evolved with their vertebrate hosts over many millions of years (24) makes an equally ancient history for RNA viruses a natural expectation. Yet a very different picture of RNA virus origins is painted if their gene sequences are compared; by using the best estimates for rates of evolutionary change (nucleotide substitution) and assuming an approximate molecular clock (21, 33), it can be inferred that the families of RNA viruses circulating today could only have appeared very recently, probably not more than about 50,000 years ago. Hence, if evolutionary rates are accurate and relatively constant, present-day RNA viruses may have originated more recently than our own species.

Saturday, April 11, 2009

Exceptional convergent evolution in a virus

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 completely consistent with a pongid clade with human as the outgroup. Common selection for evolution of high intelligence could lead to more identity between human and chimp than between human and orangutan.

Genetics. 1997 Dec;147(4):1497-507. Links
Exceptional convergent evolution in a virus.

Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, Gulati A, Ho C, Molineux IJ.
Department of Zoology, Institute of Cellular and Molecular Biology, University of Texas, Austin 78712, USA.
Replicate lineages of the bacteriophage phiX 174 adapted to growth at high temperature on either of two hosts exhibited high rates of identical, independent substitutions. Typically, a dozen or more substitutions accumulated in the 5.4-kilobase genome during propagation. Across the entire data set of nine lineages, 119 independent substitutions occurred at 68 nucleotide sites. Over half of these substitutions, accounting for one third of the sites, were identical with substitutions in other lineages. Some convergent substitutions were specific to the host used for phage propagation, but others occurred across both hosts. Continued adaptation of an evolved phage at high temperature, but on the other host, led to additional changes that included reversions of previous substitutions. Phylogenetic reconstruction using the complete genome sequence not only failed to recover the correct evolutionary history because of these convergent changes, but the true history was rejected as being a significantly inferior fit to the data. Replicate lineages subjected to similar environmental challenges showed similar rates of substitution and similar rates of fitness improvement across corresponding times of adaptation. Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed.

Also on the same topic
Genetics, Vol. 181, 225-234, January 2009, Copyright © 2009

Parallel Genetic Evolution Within and Between Bacteriophage Species of Varying Degrees of Divergence
Jonathan P. Bollback*,1 and John P. Huelsenbeck

* Department of Biology, Evolutionary Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark and Department of Integrative Biology, University of California, Berkeley, California 94720

1 Corresponding author: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, King's Bldgs., W. Mains Rd., Edinburgh, EH9 3JT, United Kingdom.
Parallel evolution is the acquisition of identical adaptive traits in independently evolving populations. Understanding whether the genetic changes underlying adaptation to a common selective environment are parallel within and between species is interesting because it sheds light on the degree of evolutionary constraints. If parallel evolution is perfect, then the implication is that forces such as functional constraints, epistasis, and pleiotropy play an important role in shaping the outcomes of adaptive evolution. In addition, population genetic theory predicts that the probability of parallel evolution will decline with an increase in the number of adaptive solutions—if a single adaptive solution exists, then parallel evolution will be observed among highly divergent species. For this reason, it is predicted that close relatives—which likely overlap more in the details of their adaptive solutions—will show more parallel evolution. By adapting three related bacteriophage species to a novel environment we find (1) a high rate of parallel genetic evolution at orthologous nucleotide and amino acid residues within species, (2) parallel beneficial mutations do not occur in a common order in which they fix or appear in an evolving population, (3) low rates of parallel evolution and convergent evolution between species, and (4) the probability of parallel and convergent evolution between species is strongly effected by divergence.

Thursday, April 9, 2009

Darwin’s logical errors

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 beauty and complexity of the co adaptations between all organic beings, one with another and with their physical conditions of life, which may have been effected in the long course of time through nature’s power of selection, that is by the survival of the fittest.”

“(Talking about human breeding, Darwin had this to say) Ultimately, after the lapse of centuries, these sub-breeds would become converted into two well-established and distinct breeds. As the differences became greater, the inferior animals with intermediate characters, being neither swift nor very strong, would not have been used for, breeding, and will thus have tended to disappear. Here, then, we see in man’s productions the action of what may be called the principle of divergence, causing differences, at first barely appreciable, steadily to increase, and the breeds to diverge in character, both from each other and from their common parent.
But how, it may be asked, can any analogous principle apply in nature? I believe it can and does apply most efficiently (though it was a long time before I saw how).”

The above is what Darwin wrote on natural selection in two separate places in his famous book. It astonishes me to see that he can equate human breeding with natural selection, without acknowledging any difference between the two. It does not follow at all logically that if human breeding can do amazing things, then natural selection over longer time can do even more amazing things. The unspoken assumption here is that time is the only variable. But it is not. Intention/intelligence/mind is the other key variable. If humans want to breed a drought resistant crop, they would not allow the crop experience cycles of drought and flood. But natural selection can do no such things. The natural cycles of drought and flood would never produce a drought resistant breed no matter how much time it is allowed to work its magical Darwinian power.

You cannot find a better proof for the kind of logical ability, or should we say illogical, that Darwin had. When he cannot do simple high school mathematics, what can you expect? What is truly amazing is this kind of logical lapses have been viewed as ‘science’ for 150 years.

Monday, April 6, 2009

Natural selection is random/chance, period.

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 away with such logical nonsense? The ID camps are equally poor in logic to allow this nonsense unchallenged (see Jonathan Wells debate with Massimo Pigliucci on youtube).

A thing is either chance or intentional. No third alternative. Laws are non-random and intentional products of law creators. If we don’t know either way the presence or absence of God, we simply cannot use natural laws as evidence of things that are nonrandom and nonintentional. A single random event is enough to make the outcome of a chain of events random. The selector in the natural selection processes is always random in a Darwinian God-less world. The natural selection process from the selector hot weather to death of heat sensitive variants is non-random. But the selector hot weather is random, which makes the end results of natural selection random. Calling the process non-random is not wrong but is meaningless. The end result is what matters, which can only be either random or intentional. The natural selection process is non-random but the end result could still be random if the selector is randomly caused.

Darwin followers mislead by changing the meaning of random for different terms in their theory without acknowledging it. The “random” as in variation does not mean the same thing as the “random” as in the phrase “non-random” that is used to label natural selection. The random in the former refers to the outcome of a complete chain of events from an initial mutation to the final expression of the variation phenotype. The random in the latter is only concerned with a part of a complete chain of events, i.e., the middle part linking the original event and the end result, which is the selection process linking the random selector and the end result of selection.

Mutation in DNA is followed by variation in phenotypes. Mutation is random but the biochemical process form mutation in DNA to the expression of the mutant phenotype is not random. It is correct here to call the mutant phenotype random, because there is a random event in the chain of events from beginning to end. If this definition of random used for mutation/variation is applied to selective death of mutants due to hot weather selection, we must call these death a random outcome of a chain of events that has one random event among them, the hot weather. In a chain of events, selector to selection-process and finally to end result, the end result is random so long the selector is random, regardless whether the process is random or not. If we do not care about the process in calling variation random, we must do the same in all other cases to be internally coherent with the concept random. This could only mean calling the result of natural selection random, if the selector is random. To call such result non-random is deceiving, fooling oneself, and incoherent. This is either logical lapse or deliberate cheating by Darwin followers. Neither is genuine science.

To be internally coherent with the word random, Darwinism can only mean this: random variations followed by random survival of fitter variants as a result of the natural selection process. (Emphasizing whether the process is random or not is meaningless here and only achieves the goal of confusing or misleading.) The two random words here in this sentence have the same meaning, and it is about the outcome of a complete chain of events. Contrast this truthful rendition of Darwinism with this popular but cheating version: random variations followed by non random survival of fitter variants as a result of the non random natural selection process. The first random means very different things from the other two random in this sentence. The lie here is that a non random process can only lead to a non random end result, when truth is that it can lead to both random and non-random results depending on the random nature of the selector.

Some quotes from Darwin followers:

Richard Dawkins:

Natural selection, the non-random survival of genes in gene pools (to put it in neo-Darwinian terms rather than Darwin's own).

Coyne is right to identify the most widespread misunderstanding about Darwinism as the idea that, in evolution, “everything happens by chance”. This common claim is flat wrong – obviously wrong, transparently wrong, even to the meanest intelligence (a phrase that has me actively restraining myself). If evolution worked by chance, it obviously couldn’t work at all.

Douglas Futuyma:
“Chance” does not mean lack of purpose or goal in science. If it did, we could say that absolutely everything in the natural world is by chance because we don’t see any purpose or goal in storms, in ocean currents, or anything else. Evolution certainly does involve randomness; it does involve unpredictable chance. For example, the origin of new genetic variation by mutation is a process that involves a great deal of chance. Genetic drift, the process I referred to earlier, is a matter of chance.

However, natural selection itself is the single process in evolution that is the antithesis of chance. It is predictable. It says that, within a specific environmental context, one genotype will be better than another genotype in survival or reproduction for certain reasons having to do with the way its particular features relate to the environment or relate to other organisms within the population. That provides predictability and consistency. So, if you have different populations with the same opportunity for evolution, you would get the same outcome.

Let us just pick Futuyma here and see how confused and incoherent he is.

If chance does not mean lack of purpose, it can only mean presence of purpose. So chance is purpose or presence of purpose in science. What kind of concept is that? Any real world examples of such stupid things? Then what is purpose and what is the opposite of purpose in science? There is unpredictable chance as in mutations. So chance here in science does mean lack of purpose since no one would say mutation has purpose, just qualified by unpredictable. Then is there such a thing as predictable chance?

Matter has no purpose, only mind has. In a world without mind, purpose is meaningless. Is there a thing that has purpose but no mind? Gravity laws have purpose and are nonrandom. But no one knows what/who created gravity laws. So, one cannot use gravity laws as an example of things that are both nonrandom and non-intentional.

If chance means lack of purpose, we cannot say absolutely everything in the natural world is by chance. Because if we say that, it would mean that we know there is no intention/God. And we don’t know that. There is nothing known in science that can exclude the coexistence of chance and intention in nature. Darwinism has not excluded God in the evolution process. The Darwinian story of evolution is incoherent for the simple fact that it has countless contradictions. It is contradicted by both the fossil record and the DNA record, the only types of evidence one could have for evolution.

So, in a Godless world demanded by Darwinian science, chance is given a meaning that has purpose. No human intuition could picture such a senseless thing. If Darwin followers must require us to accept senseless phrases like "chance means presence of purpose in science", it simple means that their theory is anti-intuitive. For all we know, genuine science like math and physics are based on intuitions. Anti-intuition is self-defeating. Nothing in science that is not ultimately intuitively sensible. Earth is flat is intuitive for ancient humans but is ultimately sensible too for modern humans.

The above proves that natural selection is as random as anything that is random. By Darwin followers' own criterion (if natural selection is random, it could not work), this in turn proves that Darwin's theory could not work. And it does not. Just take a look at the countless factual contradictions, as well as the numerous logical mistakes made by the Darwin followers.

MGD hypothesis peer review

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.

Re: JEZ-B-2009-02-0022

JEZ-B 2007 Impact Factor is 3.578.
Average time to first decision 41 days

Dear Prof. Huang:

I am sorry to inform you that your manuscript, Inverse relationship between genetic diversity and epigenetic complexity, has not been found acceptable for publication in JEZ Part B: Molecular and Developmental Evolution. I have enclosed the comments of the Associate Editor upon which this decision was based. I must emphasize that this decision is final.

You may also view the comments by loggin onto the JEZ Part B: Molecular and Developmental Evolution submission site: .

Thank you for allowing us to consider your manuscript.

There is a policy in place for the disposing of files from rejected manuscripts 180 days after the rejection decision, and that any appeal to the reject decision will not be considered after that time.


Prof. Gunter Wagner
JEZ Part B: Molecular and Developmental Evolution

Associate Editor Comments:
Dear Dr. Huang,

I have now had a chance to read your manuscript and I regret that I am not recommending publication in JEZ-B. While the ideas presented are very intriguing, several key elements lack rigorous definitions and, as written, are inconsistent with observations from across the tree of life. For example, the view of phylogenetic diversity is more consistent with the Scala Natura than current understanding of the tree of life and the nature of biological diversity on Earth. Similarly, the treatment of the term complexity is simplistic at times. For example, limb number is certainly one measure of complexity (e.g. snakes vs. other reptiles) but, if "complex organisms are here defined as those that have complex epigenetic programs" then organisms like ciliates, which rely on epigenetic mechanisms to scan the last generation's somatic genome in forming the next generation's somatic genome, may also be worth considering. As written, the manuscript reads as if humans are the pinnacle of both the tree of life and complexity. Further, the treatment of genetic distance is also simplistic at times, particularly given what we know about patterns and processes driving molecular evolution across genomes.

I do hope that this quick turn around enables you to find a more appropriate journal for your interested manuscript without any unnecessary delay.


Laura Katz

My response below:

Dear Dr Katz,

Thank you for reading my paper and offer your opinions. I explain here why these opinions may have merit from your point of view, which is the current Darwinian view, but have zero value from the point of view of genuine science, which is to explain facts with whatever theory that works the best.

You say: “several key elements lack rigorous definitions and, as written, are inconsistent with observations from across the tree of life. “

The key elements of the hypothesis are genetic diversity and epigenetic complexity. Both are clearly defined in my paper. The proof of this is that the hypothesis works in what counts, which is to explain all facts. The hypothesis explains all relevant observations known in evolution, as clearly presented in the paper. There is no inconsistency. Your specific examples of inconsistency are not about facts but about philosophical views.

You say: “the view of phylogenetic diversity is more consistent with the Scala Natura than current understanding of the tree of life and the nature of biological diversity on Earth.” Indeed my view is inconsistent with the “current understanding”, but that is precisely the merit of my view. Think about it, if it is consistent, it would have no chance of being true, since the “current understanding” is clearly false or incomplete or contradicted by countless facts, a claim made in my paper which you did not object in your review.

You next example about ciliates is based on misrepresenting my definition of epigenetic complexity. That definition is based on the number of epigenetic molecules and number of cell types. Ciliate is not a complex organism based on my definition, which is fully consistent with reality.

Your third example is about whether humans are the pinnacle of both the tree of life and complexity. Can you find a single observation that could invalidate this intuitively obvious notion? The scientific way of considering this issue is to come up with two opposite theories, one does not grant this notion and the other does, and see which one explains facts better. When this is done as in my paper, the MGD hypothesis handily beats all existing theories, a claim made in my paper which you also did not object in your review.

Your final example: “the treatment of genetic distance is also simplistic at times, particularly given what we know about patterns and processes driving molecular evolution across genomes.” What you know is much less than what you should know and is largely incorrect. Proof: What you know does not explain all the facts or has numerous contradictions. What I know may be simple but it does explain all the facts. And that is what a true theory should be, using simple concepts or axioms to explain a complex array of facts.

To summarize, I am very pleased with the fact that you cannot come up with a single observation that would falsify the MGD hypothesis, exactly as I predicted or as I claimed in the paper. (Don’t feel bad, you are hardly alone in this regard.) You did not object to my outrageous statement in the paper that the MGD explains all relevant facts and has yet to meet a factual contradiction. You also did not object to my outrageous claim that the MGD is a better theory than all existing ones based on the best and only criterion that counts, which is to explain all facts and is contradicted by none.

The above clearly shows that you have said nothing negative about the key claims of the paper. Thus, the paper would be publishable in any journal by any standard of science or reason. Given this, it is very easy to understand your negative view about the paper: yours is a religious view not science or reason. You and your cohort of Darwin followers have nothing personal to gain and everything to lose if you promote the MGD hypothesis. When there is a conflict between truth and personal interest, personal interest takes priority. That is just human nature and I would not fault you for that. I may act similarly if I were you. I am promoting the MGD because there is no conflict between truth and personal interest in my case. Of course, I may lose my job and grants but that kind of sacrifice is nothing compared to the reward of immortality and intellectual satisfaction by associating one’s name with truth.

Religion is a story that is incoherent in logic and facts but is still believed by its followers. This sentence would remain true if one substitutes the word ‘religion’ with ‘Darwinism or the existing evolution theory’. After more than two years of trying to publish in journals controlled or peer reviewed by the followers of the Darwinian religion who worship a dice-tossing God, it just reaffirms the obvious truth that reason and religion are incompatible and antagonistic.

Therefore, the only realistic way of publishing the MGD is a book. If Darwin changed history by publishing a book, it may well take another book to reset history.


Shi Huang