Major topic areas:
From Dr. Periannan Senapathy
Date: 21 Mar 1995
Since I posted my original announcement of this new theory three weeks ago, many good questions have appeared in various forums pertaining to evolution, molecular biology and paleontology. I am happy to respond to them here collectively. Keith Robison, Andrew McRae, Tom Holroyd and Greg Buchannan have asked particularly insightful questions, and I thank them -- and everyone -- for their interest and thoughtful contributions to the discussion.
Before answering specific questions, I would like to restate the two primary objectives of my book. In the first part, I believe I have shown that no known mechanism of genetic mutation can evolve new genes for unique protein functions or new developmental genetic programs (DGPs) for unique body parts in any multicellular organism. Please note that the simplest single cell, assumed to be the ancestor of all life on earth, is supposed to have given rise to all these organisms purely by random mutational mechanisms. I have devoted an entire chapter of the book (96 pages, 103-199) to a detailed analysis of all these mutational mechanisms -- from transposition, crossing-over and exon-shuffling to the different types of gene-duplication, chromosomal aberrations, DNA recombination, point mutation, pleiotropy and others -- and an assessment of their ability to evolve new genes and new genetic networks. The analyses show that these mechanisms can easily produce a huge repertoire of normal variants of each gene, and can produce defective genes, but can never produce a qualitatively new gene or a new DGP. The many normal variants of a particular gene prove only that the protein coded by that gene is tolerant to many amino acid sequence variations, without changing its fundamental structure or its biochemical function. Defective genes can lead to congenital and genetic disorders and cancer. But none of these mechanisms can produce a new gene or a new anatomical structure, and therefore genetic mutations cannot produce new, unique organisms.
From these analyses I conclude that genetic mutations are an innate and unavoidable biochemical property of the DNA molecule and genes, and exist in the genomes of distinct organisms without changing the constancy of the set of genes or the fixity of the DG pathway of the genome of every distinct organism. That is, even if numerous distinct organisms had originated by independent assembly of their genomes from a common pool of genes in a primordial pond, the very same set of genetic mutations and rearrangements would exist in these independently originated organisms -- simply changing the physical nature of the genome, but not its constant set of genes or its DGP. The large amount of junk DNA sequences between genes and the intronic junk sequences within genes would be changed, and even the physical positions of genes within chromosomes, but not the genes themselves (except to their normal variants), nor the genetic networks in which these genes are organized. This notion that such genetic changes are evidence of ongoing molecular evolution has simply been uncritically accepted, but in fact these changes are only physical, not functional. Please note that no systematic scientific analysis of this pervasive assumption -- scrutinizing all the known mechanisms of genetic mutation and rearrangement -- has even been attempted until now.
In the second part of the book, I explain in great detail how the genomes of all distinct organisms could have occurred independently in the primordial pond. The common belief is that it is highly improbable for even one gene to arise at random, purely by chance, in the primordial pond's random genetic sequences (ref: Monod J, 1970, Chance and Necessity, 1972 edition, Vintage Books, New York; Dawkins R, 1986, Blind Watchmaker, WW Norton, New York, p 46; Kupper B, Information and the Origin of Life, 1990, The MIT Press, Cambridge, Mass, pp 59-62). In fact they say that even a short gene would have been utterly improbable even in a mass of DNA equal to the mass of the whole universe. But since life on earth is a reality, they simply assume that the first primitive ancestral living cell occurred by some improbable freak accident. Moreover, this presumed improbability of genes and life directly from inanimate matter is cited as evidence that all life diverged from just that one primitive ancestral cell. No evolutionist that I know of -- and I have searched hard -- has ever proposed a mechanism for the origin of the genes and genome of the first cell. Even modern evolutionists do not explain the origin of the first cell, and begin their explanation assuming that the first ancestral cell "somehow" originated on earth.
But to the contrary, my research shows that the chance occurrence of multitudes of genes was actually inevitable in a small primordial pond. The main difference between the previous computations and my own is that my analyses incorporate the structural features of eukaryotic genes -- namely their split exon-intron architecture -- which is perhaps the most crucial factor in these analyses. My approach also incorporated other important insights into gene and protein structures, such as codon degeneracy and amino acid degeneracy. My research, using actual DNA and protein sequences of the genes of living organisms from the DNA and protein sequence databanks (the GenBank and the Protein Information Resource), and many types of computer simulations, demonstrates that fully formed genes could exist abundantly in a reasonable amount of random genetic sequences that could be available in a primordial pond. In fact, an entire chapter of the book (72 pages, 221-293) is devoted to a systematic derivation of this premise.
Accommodating the split-gene architecture -- now generally acknowledged to be a fundamental feature of genes -- in these calculations and analyses really changes everything. Please note that this has never been done so far, since its discovery in 1978. With this new evidence, it becomes apparent that numerous split-genes were indeed statistically inevitable within only a small amount of DNA -- and certainly within the DNA expected to be available in a primordial pond. And if we can establish the origin of numerous fully formed genes in a primordial pond, it then becomes entirely plausible that many fully formed genomes formed spontaneously, by a sort of random "mix and match" process.
Chapters 6, 7 and 8 of the book provide ample evidence to conclude that primordial Earth's rich biochemical environment contained all of the enzymes necessary to facilitate the combination and recombination of genes and multi-gene segments into complete genomes. Of course, only a tiny fraction of the genomes thus formed were at all viable, and those that were meaningless would never have found expression as organisms. But again, statistical models demonstrate that so many billions of prototype genomes were likely to have been formed in this way, that many millions of them would have been viable and meaningful.
I know that my conclusions are at odds with what scientists in many disciplines have believed for a very long time, and I must say that I fully expected this controversy, as well as much of the sarcasm and name-calling. But my conclusions are drawn from a series of related premises that I have developed or verified by my own research and by the published and accepted work of others. My own findings include:
I will now respond to specific comments and questions from forum participants.
I can tell that some of my critics have at least browsed the book, but many of their comments indicate that they have not read it completely, and/or very carefully, since they ask questions that are specifically answered in the book.
Keith Robison writes:
>In order to clear the decks, Senapathy first tries to show that Darwinian evolution is simply impossible. Pages 35-37 (and again 157-9) attempt to prove that the transformation of one gene into another by random point mutation would require a time greater than the age of the earth. This is founded on an improper use of serial probabilities: i.e. Senapathy is arguing that the probability of finding two mutations in the same gene is the product of the mutation rates (probabilities). What this analysis ignores is that mutations occur within populations, and recombination can combine two such mutations onto a single molecule. In short, Senapathy's analysis assumes a serial process, when in reality it is parallel.
Keith thinks that point mutations occurring in a particular gene in different individuals would converge into a single individual by recombination of these various sequence changes through sexual mating. This is the usual argument given in general by molecular evolutionists. But when we scrutinize the probability for this process to happen by means of random mutations, random recombinations and crossing-over during meiosis, we see that it is simply improbable for a new gene to evolve by this manner. Molecular biologists have calculated that the mutation rate is between one per million and one per billion per nucleotide per generation. This indicates a rate estimate of one mutation in an average gene every 200,000 years (ref: Alberts, B. et al, 1983, Molecular Biology of the Cell, Garland Publishing, Inc., New York & London, page 214). Multiple sequence mutations that occur at different sequence positions in a particular gene in various individuals of a population should all converge into one single molecule -- i.e. in one single individual. Similar changes have to occur in multiple genes and all these multiple changed genes should converge into one individual, and this calculation should also incorporate the very low meiotic DNA recombination rate.
The probability for combining all this into one individual to have any meaning in the process of evolution is astronomically low. To my knowledge no one else has done a systematic calculation anywhere in the literature incorporating all the above to show how long it would actually take for all the mutational mechanisms to converge all the mutations into one single molecule (even taking all the parallel changes). Even if many different mutations would converge into a single molecule, it would still be a variant of the original gene, but not a new gene, when we take into account the biological selection mechanisms. Even molecular evolutionists know full well that partially new genes en route to evolving fully functional new genes (called incipient genes) have no selection value in evolution and are not preserved (Richard Dawkins, ref above; and Bernd-Olaf Kuppers, ref above, page 87), so only fully formed genes could be selected. This, as even Bernd-Olaf Kuppers puts it, is an unsolved and unsolvable problem for molecular evolutionists.
Keith's next comment concerns gene-duplication:
>Senapathy also provides explanations for how a number of genome-modifying mechanisms cannot be significant contributors to evolution. His discussion of gene duplication claims that this cannot be a significant contributor to evolution, because if it were we should see enormous numbers of pseudogenes in the genome (p.141). This ignores the possibility of unselected sequences being overwritten by other sequences. Hence, under evolutionary assumptions only recent pseudogenes are expected to be detectable.
By what molecular mechanisms does Keith mean that sequences are being overwritten? By unequal crossing-over, point mutation, gene-conversion, transposition? By whatever means, if evolution of new genes has to be achieved by tinkering with randomly duplicated genes by random mutations within the duplicated genes, on statistical basis we should see many, many more duplicated genes undergoing such evolution than we see today in the genomes of living organisms. Again, if sequences are being overwritten, the inability of incipient genes (a partially new gene in the process of formation of a fully new gene) being selected would show that it is extremely improbable to evolve new genes if unselected genes are being overwritten. Under such circumstances, it is simply improbable to evolve a new gene by tinkering with a duplicated gene within the short time-frame in which the distinct organisms are said to have evolved. In any event, please note that Keith agrees that his explanation is offered "under evolutionary assumptions."
The reality is that the set of genes of any organism is essentially constant. A genome is changed by the many types of mutations including point mutation and gene-duplication, but only to change the intergenic junk sequences and introns to a great extent. Even the protein coding exons can mutate up to about 90% without changing the structure or the function of the proteins they encode (due to the high tolerance of every protein to amino acid sequence variation) -- all without evolving new genes or new organisms. This physical genetic-flux -- occurring independently in distinct, independently originated organisms -- is mistakenly cited as the molecular mechanism of evolution, but the evidence simply does not support that conclusion. These genetic changes are the cause for the normal "individual variations" in the population of an organism. As I mentioned before, any other genetic change would only lead to a defective organism, not to a new organism.
Again from Keith Robison:
>The book is frequently internally inconsistent. After spending pages upon pages proving that it is impossible for developmental pathways to evolve, he spends pages 344-346 explaining how they must evolve. The problem is this: under Senapathy's theory, not only must whole genes arise from random sequence, but they must have all the correct regulatory signals. Similarly, after spending many pages explaining how developmental-genetic pathways are inviolate and cannot be modified significantly, he spends pgs 347-348 describing how different genes could be assembled in different forms to produce different developmental-genetic pathways.
While I say that random mutations cannot evolve new genes by organismal descent with modification (i.e. within the genomes of living organisms), how do I say that new unique genes could simply occur fully-formed in a primordial pond, so that they could self-assemble into various genomes? Again, I have devoted a whole chapter to this specific question and giving a detailed answer: The occurrence of abundant genes in the primordial pond was inevitable. And another chapter describes how these fully-formed genes simply occurring in random primordial genetic sequences could self-assemble to form many genomes nearly simultaneously. Note that this discussion is not molecular evolution within the organisms, as Keith has misunderstood. The two phenomena are entirely distinct and their probabilities are monumentally different.
In fact, I describe detailed computational analyses to show that fully formed split-genes (which are typical of all the eukaryotes, including all multicellular animals and plants) could simply occur in a small finite amount of random DNA in a primordial pond. During my work towards understanding the processes by which genes could occur fully-formed and by which genomes could be self-assembled, I worked out the details as to why it is extremely probable for eukaryotic genes to occur in random primordial DNA sequences, and why it is simply improbable for prokaryotic genes to occur in these sequences. Note also that all the structural features of genes predicted by this theory (by computer simulation analyses of genes) are precisely and completely found in almost all of today's living organisms. This theory on the origin of split-genes, published in two separate articles in the PNAS, has also been commended in New Scientist. (You can now read these New Scientist articles in my web pages: http://www.genome.com/ibo/newsci1.htm and http://www.genome.com/ibo/newsci2.htm)
In fact, the reputed protein structural biochemist and crystallographer Dr. Colin Blake of Oxford University has said that this theory comprehensively explains the origin of the split genes of eukaryotes from random primordial DNA sequences and the origin of the splicing process (ref: Holland, S.K. and Blake, C.C.F., 1990, Proteins, Exons, and Molecular Evolution, In Intervening Sequencing in Evolution and Development, Stone, E.M. and Schwartz, R.J., eds., Oxford University Press, New York, page 32): http://www.genome.com/ibo/cblake.htm.
Obviously this finding solves a problem that has been unsolvable for traditional evolution theory and its modern variants, which all base their analysis of life on earth on the presumed precedence of prokaryotic genes and prokaryotic genomes. Please note that it is this incorrect assumption that makes evolutionary biologists unable to explain the origin of even the simplest living cell.
In fact, I show in the book that given a small finite quantity of random genetic material, then we could find almost all the genes for proteins with almost any biochemical function in it. Then it is not difficult to demonstrate the possibility that these genes could self-assemble into numerous genomes. Again, please note that I am not saying that the self-assembly produced only viable genomes capable of giving rise to viable organisms. To the contrary, I give probabilistic considerations that show even if one in a million such randomly self-assembled genomes could give rise to any meaningful multicellular masses, still the genes present in that finite DNA in a primordial pond would be able to give rise to billions of complete genomes leading to the independent origin of multitudes of organisms. In fact, such a scenario fully explains why the same genes as well as utterly unrelatable genes are present in the numerous unrelatable organisms. And in fact, this is the only way that we can explain the mix-and-match mosaic scenario that we observe from the living organisms today. The point I am trying to make is that the scenario of life on earth, including the presence of similar DNA sequences in widely distinct organisms has been misinterpreted because evolution has long been mistakenly regarded as an established fact.
Keith Robison again:
>Senapathy brings up the tired old rhetoric about the impossibility of evolving an eye, arguing it is more likely for an eye to spring in toto from the primordial soup. Recent computer simulations have shown how a very slight the required selective gradient is for the evolution of a focusing eye from a simple photosensitive spot.
Yes! I certainly say that it is far more likely to assemble the genes for constructing an eye directly from the primordial pond's vast gene pool than to evolve an eye starting from a primitive organism that lacks even a photoreceptor. This fundamental theme of organizing the genes for even morphologically complex organs directly from the primordial pond is precisely what the new theory is all about. The book provides many valid scientific principles and corroborations to demonstrate this thesis. Certainly no computer simulation is acceptable unless it characterizes mutational process at the level of DNA, genes and proteins. To my knowledge no one has ever demonstrated the evolution of a complex eye by any kind of simulation involving the fundamental blueprint of DNA and genes, and in my view no one ever will.
Tom Holroyd (email@example.com) writes:
>Work in artificial evolution using computers (GP and GA) has shown that crossover is a more important mechanism for variation than simple point mutations. If pre-Cambrian organisms simply replicated themselves, then the emergence of sexual reproduction could have ushered in a large increase in variation -- what we now call the Cambrian Explosion.
>Senapathy's theory suggests an even more dramatic mechanism than the shuffling of genes via sex. As I understand it, sets of genes became capable of spontaneous self-assembly into genomes, some of which produced viable organisms. Instead of crossover between similar genomes, there was wholesale re-creation of the genome from a large set of genes each generation. I like the idea of self-assembly.
Thanks for understanding the possibility of self-assembly of genes into genomes that could produce viable organisms.
Again from Tom Holroyd:
>I think Senapathy underestimates the amount of variation that is possible with ordinary Darwinian evolution. Computer simulations using only mutation would, indeed, not produce the required amount, but as stated earlier, crossover is a more potent force.
In fact, cross-over can only reshuffle or re-sort the many variants of a constant set of genes in a genome, leading only to individual variations. As described above, even all the known mechanisms of genetic mutation and rearrangement collectively cannot explain the origin of distinct organisms. I do agree, however, that these mutational mechanisms are capable of changing every independently born organism into a set of similar organisms, which are now classified into genus and/or family.
Greg Buchanan (firstname.lastname@example.org) writes:
>I agree that there is evidence for micro-evolution based on studies and observations by Darwin. However, I don't see how micro-evolution is proof for macro-evolution. To say that a finch develops a different shaped beak due to environmental change is one thing. To say that that same finch originated from a less complex form is quite another.
I equate micro-evolution to the changes that occur within every distinct, independently born organism by means of all the mechanisms of genetic mutation and rearrangement. These, as we discussed above, can only lead to the normal individual variations and to the similar species of every distinct organism, that are now classified into the genera and families. Beyond that, what is termed ("macro evolution") in evolution theory is simply based on belief. Based on 1) the inability of genetic mutation to explain macro-evolution, 2) the ability of my new theory to explain the origin of many genomes independently from the primordial pond, and 3) the appearance of all distinct organisms (all phyla, and most classes and orders) right in the Cambrian explosion, we can see that the concept of macroevolution is false, and it did not, does not, and will not occur.
The problem of the origin of higher taxa is well known to evolutionary biologists (ref: Eli C Minkoff and Douglas J Futuyma, authors of two popular text books on evolutionary biology, both entitled Evolutionary Biology). The explanations offered for this problem so far -- from Richard Goldschmidt's Hopeful monster hypothesis to Stephen Gould's and Niles Eldredge's Punctuated Equilibrium -- are only truly speculative interpretations of the scenario. The scenario is therefore subject to newer interpretations by alternative theories -- if any can offer a valid genetic explanation.
Andrew MacRae (email@example.com) says:
>The Cambrian was brief on a geological scale, but a) it does have a succession of faunas over a significant period of time (i.e. they are not simultaneous).
The succession of fauna within the Cambrian explosion opposes evolution theory, which demands that from a single primitive organism all the distinct organisms in the explosion should have evolved within the short geological period. From all known accounts of molecular biology, this is simply improbable and unexplainable. As Stephen J. Gould notes (1989, Wonderful Life, W.W. Norton, New York), complexity existed right at the beginning of the Cambrian explosion, and this is enigmatic for evolution theory:
>This "Cambrian explosion" marks the advent (at least into direct evidence) of virtually all major groups of modern animals -- and all within the minuscule span, geologically speaking, of a few million years [pg 24]. ... This chronology poses the two classic puzzles of the Cambrian explosion -- enigmas that obsessed Darwin and remain central riddles of life's history: (1) Why did multicellular life appear so late? (2) And why do these anatomically complex creatures have no direct, simpler precursors in the fossil record of Precambrian times? ... Darwin has been vindicated by a rich Precambrian record, all discovered in the past thirty years. Yet the peculiar character of this evidence has not matched Darwin's prediction of a continuous rise in complexity toward Cambrian life, and the problem of the Cambrian explosion has remained as stubborn as ever -- if not more so, since our confusion now rests on knowledge, rather than ignorance, about the nature of Precambrian life. [pgs 56-57] In fact, the Ediacara softbodied fauna is barely Precambrian in age and, according to evolutionists, may represent a failed independent experiment in multicellular life. (Although according to my theory this fauna is a separate pond life.) In any event, Gould asks: >So if the true ancestors of Cambrian creatures lacked hard parts, why have we not found them in the abundant deposits that contain the soft-bodied Ediacara fauna? [pg 59] It is obvious that many complex organisms existed right at the beginning of the Cambrian explosion for which evolution theory has no explanation.
The span of new organisms within the Cambrian is well explained by my theory. In fact I have stated that the genomes of many organisms were assembled nearly simultaneously and not in a day or a year. This process would lead to the origin of many organisms over a short span of geologic time, which would reflect what is observed in the Cambrian explosion.
Again from Andrew MacRae:
>It is important to realize that there may be more to the Cambrian Explosion than what is obvious at face value. It is currently being intensively studied, so it is a bit premature to start drawing definitive conclusions about what exactly happened -- in my opinion anyway -- beyond the fact it appears to be a period of exceptionally rapid evolution/diversification.
I agree. As Andrew says, applying what is obvious at face value to fit the evolution theory is also incorrect. At the same time, the observations of Cambrian explosion can fit well with my theory, if he would read my theory in detail. I may be premature to start drawing definitive conclusions about what exactly happened, but at least my theory opens up an entirely new possibility based on molecular biology.
Andrew says that the Cambrian Explosion appears to be a period of exceptionally rapid evolution/diversification. Please note that this concept of rapid evolution is a statement which does not actually fit with any molecular biological evidence. In fact, there can be no rapid evolution, which probably most evolutionary biologists know. To evolve all the complex organisms classified into all the distinct phyla within a period of five million years (for that matter, even in a hundred million years) is highly improbable. We can prove this easily when we do computations as to how the new genes and DGPs of the various distinct creatures could evolve in all these organisms starting from a single cell.
Also, as Stephen Gould says, it appears that the eukaryotic single cell itself had originated right before the Cambrian explosion, which demands that the first and all the rest of the multicellular organisms that appeared in the explosion be evolved within the five million years (ref: Gould, S.J. , 1977, Ever Since Darwin, W.W. Norton, New York, page 115):
>UCLA paleobotanist J. W. Schopf believes that he has evidence for eukaryotic algae in Australian rocks about a billion years old. Others contend that Schopf's organelles are really the postmortem degradation products of prokaryotic cells. If these critics are right, then we have no evidence for eukaryotes until the very latest Precambrian, just before the great Cambrian explosion of 600 million years ago.
It should also be noted that the Cambrian explosion was thought to span 20-30 million years until 1993, when the application of a new uranium-lead dating method demonstrated that it is actually confined to the much shorter duration of five million years (ref: Bowring, S.A. et al., Calibrating rates of early Cambrian evolution, Science, 261:1293-98). This shrinking of the Cambrian explosion period poses an even greater problem to evolutionary biology.
Another important thing we should remember here is that the numerous distinct organisms that originated in the Cambrian explosion have never really changed, and have remained indeed essentially the very same organisms in the many dozens of millions of years since then. Would we expect this if evolution through random genomic mutations is an ongoing process?
Quoting an earlier post of mine, Andrew says:
"But, again, [punctuated equilibrium] does not offer a genetic or molecular mechanism, and, in fact, it does not work when scrutinized at the gene level." >This is news to me. One of the reasons for proposing smaller, isolated populations as a mechanism for speciation was the ability of mutations to have a greater potential effect in a smaller population.
I have analyzed this carefully in the book to show how this does not work when scrutinized at the gene level. My comments above pertain to this.
Another comment from Andrew MacRae, again quoting me:
"The question of life's origins is truly a multidisciplinary one: encompassing many fields including molecular biology, statistics & mathematics, paleontology, and zoology. I also studied zoology, including invertebrate zoology, and found that there are indeed numerous distinct organisms that are totally unrelated." >This is simply incorrect. For example, zoologists classify echinoderms, chaetognaths, hemichordates, and chordates as separate phyla, but have always recognized the close similarities in development, symmetry, cellular, and many other features between these groups (they are all deuterostomes). They are quite clearly a related group versus other phyla.
If we could agree that many phyla are unrelated, it is certainly a good starting point. Then we can see that my theory is able to explain at least the independent origins of the many phyla. If we could agree on this, then I could easily explain how even apparently related organisms within a phylum could originate from their genomes -- which could have assembled some common genes from the common gene pool of the primordial pond. In fact, my book explains how this is the only way the scenario of organisms could be explained, and not by evolution.
Andrew MacRae again (and again quoting me):
"Please note that zoologists themselves conclude that these creatures are unrelated, except that they have to say that these unrelatable creatures must have somehow evolved from one another, merely to fit the evidence to the prevailing evolutionary paradigm." >No. They have many similarities, and these are usually pointed out in invertebrate zoology texts.
May I then point you to the zoology text books that describe the phylogenetics of each phylum and the organisms within them -- for example, Zoology by Mitchell, Mutchmore and Dolphin (ref: Mitchell, L.G. et al., 1988, Zoology, The Benjamin/Cummings Publishing Company, Menlo Park)? When we peruse this book, especially the phylogenetics section of each phylum, it clearly shows how the different phyla are absolutely unrelated based on the anatomy of organisms. I have quoted many of these zoology texts in my own book, which elaborately describes how this sort of unrelatedness applies to even organisms classified within classes and orders. As regards to the cellular and biochemical similarity, my theory describes how this is precisely expected if the different genomes were assembled from a common pool of genes in a single primordial pond, sharing genes and biochemical mechanisms through this process.
>You have quite a bit more research to do before you can say your model accurately reflects the evidence, let alone refute evolutionary theory.
Certainly I agree. At least I am able to present a scientific theory that can be a viable alternative to evolution theory, and I am pleased that I could open up a new scientific discussion to understand the origins of life and diverse organisms. I would only request people to look at my new theory objectively (and completely), and analyze the existing data to prove or disprove its scientific validity.
Thanks again to everyone. I will prepare a similar "consolidated" reply to the next batch of substantive comments and questions, and will post again.... Anyone preferring to discuss these matters privately may e-mail me at: firstname.lastname@example.org.
[top] -- [home]