The Primordial Pond
(Part I)

Summary of the new theory:

The primordial pond (or ponds) existed eons ago. As the earth gradually cooled, many different environmental conditions would have existed. At some point, those conditions would have been conducive to certain chemical reactions, some of which could have involved the formation of DNA and related biochemicals. Over millions of years and in many different regions of the earth, the random associations of these chemicals produced ever more complex biochemicals and reactions. Genes were formed, as were the mechanisms for translating and replicating genes, eventually culminating in the random assembly of "seed cells" from which an organism developed, similar to the way an organism grows today from an initial single cell. The ponds would also have contained mechanisms (largely unknown today) that could have stabilized and protected the DNA.

The reason organisms have features in common is because the primordial pond that produced genome "X" had various copies of all the genes that went into the earlier genomes, i.e. "A," "B," etc. The chemistry of the pond was able to replicate DNA using the same biochemical mechanisms that are known today, but instead of the results being selected by the viability of living cells, the outcomes were random and ultimately selected later if a viable organism was formed. New organisms were produced by random combinations of these existing genetic sequences plus some unique sequences. Most random associations would fail at living instantly, some would fail later -- perhaps they could not reproduce, but a small few would live and adapt through microevolution (small changes and adaptation).

The "reuse" of previously manufactured genes and sets of genes led to the commonalities, and new, unique sequences led to the unique features of the organism. Note also, that there could be random multiple commonalities in organisms (that is, a new organism might share traits that were once used in the construction of numerous previous organisms). Macroevolution (descent from a common ancestor) cannot explain all the special cases and situations where one creature doesn't exactly fit into a nice spot on the evolutionary "tree." There are even arguments about where some creatures belong on a tree -- but this is easily explained by Senapathy.

Senapathy does not insist that ALL new species came about independently, only those that do not share body parts and genes with other species. That is, breeds of cats, dogs and wolves, different kinds of snails, and so on are related through adaptations.

From Dr. Senapathy:

See quotes in bold, below.



From Keith Robison: (Quoting Dr. Senapathy) "Yes, I do say that the genes for lots of proteins did exist in the random DNA sequences in the primordial pond. And I do postulate the formation of "seed cells" which develop into whole organisms. I challenge any one to read my theory completely and then to show how it is mistaken."

Your "seed cell/primordial pond" hypothesis is implausible for multiple reasons in this particular regard:

  1. Your theory claims to explain the sudden appearance of living forms over many millions of years. Your description of a primordial pond -- a rich soup of biomolecules, is commonly called in the biology business "bacterial medium". As soon as protists, fungi, and bacteria arrived (and we know they came early), your primoridal pond would be a feeding ground for numerous organisms. It would be contaminated with nucleases which would chew your posited long DNAs into short pieces. Abiotic origin of life scenarios are only plausible in a sterile environment.

  2. The development of many multicellular organisms is guided by chemical asymmetries laid down in the ovum by the mother. So not only would your seed cell have to form, it would need all these asymmetries (or somehow do without, but then switch over).

  3. You posit mammals emerging from this pond. Most mammals, of course, develop within the mother's body and are almost completely helpless before then, both molecularly (immune system) and physically. Your "seed-cell mammals" would have to somehow develop without being devoured or infected by the millions of species which emerged previously.

  4. Mammals contain a system of molecular imprinting, which is essential to mammalian development. If one and only one copy of certain genes is not tagged (probably by methylation), then the embryo fails to develop.
In summary, once the bacteria showed up, the party was over. Most multicellulars would never figure out which way is up, and us mammals would have made it through to the fetal stage, to be even more deletable morsels for the fish, and frogs, and bugs, ....


From Joachim Dagg: After constructing a very special primordial pond, from which the evolution of the diverse species is very easy, he will have to explain the evolution of this very special primordial pond.

JM: He does explain this. He spends a whole chapter on it, plus many other references throughout his book. And, the pond is not all that "special." We cannot create one today, but given the nasty condition of this planet back at that time, many ponds might have developed.


From Mike ( (via email) That is a very interesting theory but I don't like it for a few reasons. One is his belief that species originated from a single "random" prototype from the primordial pond. My problem with that theory is that it fails to explain all of the similarities among many organisms. For instance, is it just a coincidence that all mammals have basically the same structure and the same organs (with only relatively minor variations). The same thing goes for reptiles and fish even. The existence of such groups with a large degree of similarity suggests a common thread somewhere (but where?).

JM: You've guessed wrong, but that is understandable because his web page does not offer very much detail about the new theory. The book is over 600 pages long. He says there were many original organisms coming out of the pond -- perhaps billions, only a few million of which were at all viable. Once a genome was assembled and was "born," it became immutable, and all that we see today are either the original organisms or slight variations thereof. For example, all cats might be related. The test is: if two organisms have any unique body parts or unique genes, they are not related by evolution. Darwin saw only microevolution, and that does occur. He incorrectly assumed macroevolution. Actually, Darwin was not at all certain of macroevolution and admitted there were problems, and those problems continue today.

Some similarities will exist. The biochemistry of the cells must "work," so there are similarities there. At a higher level, all organisms must be able to reproduce, digest food, move around (to find food and mates), and so on. That should not be surprising -- all vehicles have wheels (1, 2, 3, 4, 18). Furthermore, once a viable genome was formed in the pond, it would be available to be replicated (in the pond) and parts of the genome could be reused. Mix and match, then add a few unique genes -- maybe the resulting genome would work, maybe not. The basic physical structures that are common to some animals are because of necessity or gene reuse.

Senapathy shows that there was a tremendous amount of DNA available for numerous primordial ponds, and in fact much more than necessary to find any gene, as long as the gene could be broken into pieces, exons, of length 600 nt or smaller, as most genes are. His whole theory is based on introns-early. The first organisms formed in the pond were eukaryotes. The key is that you CAN find genes in the pond if you allow "junk" DNA between the coding DNA. He supplies the math.

Example: Here is a "random" sequence of letters (yes, I cheated here, but he gives a true random example) Pretend the spaces (added for clarity) aren't there:

You can find the phrase (gene) "to be or not to be" in there, but only if you allow "junk" letters (introns) in between the words (exons). The math works out that the probability of finding a gene in a random sequence of DNA is related only to the longest exon (not the other exons) of the gene.

Once you have enough DNA to be reasonably assured of finding a particular gene "A" (Senapathy computes the necessary length of DNA based on the longest exon), then you can find ANY gene "B" (as long as the longest exon of "B" is no longer than that of gene "A"). This is not just guesswork -- there is math to back it up, and the amount of DNA needed is not a problem.

Some fish might be related at the micro level. However, other commonalties would be from the reuse (re-manufacture) of parts of the genetic material of previously viable genomes. The pond was not just a bunch of simple chemicals. It was rich in the chemicals of life. DNA, RNA, etc., so genetic chemistry could have occurred in the pond, although it would not be "living" -- it would just be random interactions of various life-type chemicals.

Mike: Since I haven't read his book, if this issue is addressed in it, Dr. Senapathy would probably say that natural selection dictated that those protypical organisms who possessed those basic structures would reproduce while those that did not have them would not. Actually, on second thought, it doesn't seem likely that he would suggest this because there are far to many holes in that.

JM: There would be many non-viable organisms produced by the pond. And some semi-viable that would die out fast. Those that survived would have had to be able to adapt to the changing environment, so some "natural selection" would occur, but only within a closed framework. That is, a bug might be able to change color (through selection of colors that gave it an advantage). Those changes are chemical, not genetic. You can breed sheep for longer wool, but only up to a point -- try to go too far and you get less wool or sterile sheep.

Mike: Also, the author says that it would be impossible for a mutation to occur in an organism that would introduce any new genes into the chromosome. I don't see why this could not happen. If I remember correctly, there are large areas of DNA which do not appear to code for anything. These extra portions of DNA could be considered extra storage space for any new genes which happened to be formed.

JM: That is a good question. Based on my understanding, the problem would be that you would have to change many, many sites, and in the process you might damage an existing gene. Most mutations are bad -- duplicate organs, missing organs, cancer, etc.

Mike: Overall, I think his theory has too many holes (from the surface examination of the introduction on that web page anyway).

JM: You really need to read his book. I cannot do it justice here. I promise you, the book contains many details, and he takes on all the issues you mentioned. Furthermore, it is full of non-disputed genetic information. There is a lot of "meat" in there.


From Dave Oldridge: Senapathy's theory does not require ... similarities to arrange themselves in a hierarchy. In fact, it tends to predict that they should NOT be so arranged when, in fact, they are.

JM: His theory does predict similarities and they would (or could) form a hierarchy, but not necessarily as strict a hierarchy as necessitated by macroevolution, if that did exist. According to Dr. Senapathy, random parts of previously-constructed, viable genomes can be reused in the construction of new organisms. Thus, there will be relationships between organisms. Some relationships result from the requirement for viability (e.g., the inclusion of life-supporting functions and organs), and some not (nifty body parts that may or may not help the organism to survive). You really should read his book. Some of you will jump on me ("Quit telling us to read his book!") but isn't that the only fair way to evaluate his theory?


From Keith Robison: Why did this pond survive for millions of years, but then disappear in the recent past? How did it remain in the presence of bacteria, fungi, and protists? Why can't we create one today? What biochemical assumptions does it make, and are they plausible in light of the known thermodynamic and chemical properties of biological macromolecules?

JM:I don't know if you could characterize it as "recently" disappeared, but it would have done so because (1) the DNA material in the pond was being consumed (or diluted through the construction of organisms), and (2) the conditions of the planet changed making the pond(s) less active.

Keith: Recently in geological time -- remember, Senapathy claims that this pond was active until the appearance of the mammalian orders in the fossil record. His proposed pond existed over a billion years (the time life has been on earth), and then went poof?

Think about the implications of your two suggestions. If #1 is true, then the original pool must have been enormous, in order to handle the enormous number of incomplete attempts ("hopeless monsters") which must have crawled out of it. If #2 is true, what changed? More importantly, what changed which didn't change between the emergence of bacteria and the emergence of mammals?

Why can't we create one today?

JM: We do not know the correct conditions, mixtures, etc. Perhaps someday we will be able to create one.

I have a few questions for you: Why it is so hard for evolutionists to accept that if life could occur by chance maybe once, then why not twice, or three times -- or millions of times? Even if you see convincing evidence of evolution, why could there not be millions of separate evolutionary trees? Wouldn't that make it easier for you -- that is, wouldn't it explain many of the admitted problems with linking various organisms together on that single tree? Senapathy says two things: (1) Darwin was only half right, and (2) there were many millions of original organisms. It seems to me that you could accept (2) without accepting (1).

Keith: Only a taxonomist could do justice to Senapathy's claims of "unconnectible" organisms, but I suspect you will find that them not so unconnectable. Unfortunately, the data necessary to apply the "Stoltzfus test" on these organisms is unlikely to be available at the current time.

JM: It is ironic that Dr. S. would likely have had a much easier time convincing Darwin himself of his theory (in light of current-day genetics knowledge) than today's Dawinists. Darwin seemed very perplexed about much of this. I think Darwin's basic theory (the selection of small adaptive changes within a closed framework) has been incorrectly extended to the Grand Scheme of Things (one common ancestor and the ability to evolve new body parts), and this extension has taken hold because there has been no better alternative, and there could not have been a better (more correct) alternative until recently because we didn't understand the construction of genes and so on until now.


From Joachim Dagg: Dr. Senapathy explains how his primordial pond is imaginable (at least to himself) and thinks that is enough to be scientific.

"I can imagine it in my sick brain, so it is probable!" is not the trick!

Principle of parsimony application example -- it goes like this:

  1. Count the assumptions necessary for Dr. S's primordial pond
  2. Count the assumptions necessary for our (the accepted) primordial pond
  3. Forget about that one which needs more assumptions
The accepted primordial pond needs no genes in it, no seed cells and all the other things Dr. Senapathy needs. After this primordial pond we apply on simple natural rule - the Darwinian evolution -- and everything else just happens by itself. Dr. Senapathy's verbal trials to make the evolution of complex features look improbable are cramped spasms. I think he missed the emergence of a totally new science popular under the name of chaos theory. This mathematical science found out, that a negative feedback cycle with mistakes occurring, is all necessary for a system to evolve. The cycle in biological systems is reproduction, the negative feedback is selection and the mistakes are mutations. As simple as that. Maybe some sophisticated mathematicians can even give you a radically mathematical treatment of this.


From Keith Robison: If his interpretation of it is to be taken at face value, then new species ought to be crawling out of ponds everywhere, all the time.

JM: No, certainly not now. The productivity of the primordial pond ceased long ago because of changing conditions (e.g., the environment, lack of enough DNA material). Senapathy makes this very clear in his book, although he does not attach a date to the demise of the pond.

Keith: Senapathy's pond is a pretty amazing place. Out of it emerged, complete, both obligate aerobes and obligate anaerobes. Parasites and their hosts. Sessile desert plants and sessile jungle plants.

Furthermore, if Senapathy's theory has any merit, it ought to be easy for him to demonstrate it in the lab by actually producing new species from an artificial "soup."

JM: He does not claim to know the proper conditions, but no doubt we will be able to do this some day. It did happen at least once, so there can be no doubt that it is possible. Along that same line, if it happened once, why not twice -- or a few billion times?

Keith: I've already supplied the answer -- because once decomposers show up, any primordial pond is doomed. Quite simply, abiogenesis conditions cannot coexist for long in the presence of life.


From Keith Robison: Conservation of gene order (synteny) has been observed between taxa which Senapathy claims are independent lines (such as rodents and humans or mammals and birds). Since the odds against the same gene order appearing randomly are immense, Senapathy claims that this is evidence for DNA from existing organisms being recycled back into his primordial pond. Ignoring for the moment the shear (sic :-) difficulties of chromosome-sized DNAs getting recycled, there is another problem -- many genes showing synteny differ by >10% !!

JM: How is this a problem, whether there is a greater or lesser similarity? The parts of viable genomes that are reused could be large or small, and the anatomical similarities could vary accordingly. Also, you assert that recycling large hunks of DNA would be difficult, but why? There are mechanisms that keep the DNA together and constant in cells, why could there not be similar mechanisms in the pond? You are assuming the pond is a hostile environment for DNA, but it could be just the opposite (at least during the period when the pond was productive). The pond, although not "living" would have the same bio-chemicals in it that make cellular life function.

Keith: I am not talking about anatomy, but sequence. What the sequences tell us is that all of your statistical calculations are flawed, because even a Senapathian model must allow for great changes in sequence over time.

Large DNA molecules are very sensitive to mechanical stress, and fragment easily. To manipulate large (>50Kb) DNAs in the lab, one generally takes great precautions. To manipulate very large DNAs (>1Mb), it is almost never done in solution because the DNA will snap into pieces. Primate chromosomes are 10's to 100's of megabases long. Many syntenic regions >>1Mb are observed between lines Dr. S would claim are independent (e.g. rodents and mammals), the expectation under a "chromosome recycling via pond" mechanism would be little if any synteny, and certainly not commonly on a multi-megabase scale.

JM: (reprise): You are assuming the pond is a hostile environment for DNA.

Keith: Because this is the most natural assumption. DNA is sensitive to:

  1. H+ ions
  2. Oxidation
  3. Free radicals
  4. Mechanical shearing
  5. Enzymatic attack
  6. UV & X-ray radiation
  7. Much, much more (most of the above attack the backbone; other chemicals attack the bases)
There is only one natural place which is likely to be able to build and maintain large DNA molecules -- the interior of a cell. Cells take great pains to build, repair, and store DNA so as to maintain it. All of this takes great amounts of biochemical energy and specific enzymes, which must be applied in a controlled fashion and protected >from other enzymes which will be present if other life is around.

Senapathy basically posits the existence of acellular life, and then claims that it coexisted for millions of years with cellular life. It also apparently lived in every ecosystem which currently exists, from the polar regions to rain forests to deserts.


From Dave Oldridge: If Senapathy's theory is correct what happened to all the DNA that twists the other way? If Senapathy is correct, shouldn't there be two major branches of living organisms around, not just one?

The fact is that there is a good deal of shared genetics between all living organisms, at least above the prokaryote level. It's surprising just how much genetic material humans share even with oak trees. Or at least it would be surprising if we didn't have a common ancestor. Now I realize Senapathy sort of accounts for all this by claiming that large chunks of genomes floated around in the primordial swamps, so to speak. As I said before, I'd be much happier if he could construct an example of this primordial swamp full of genomes and still happier if he could produce a couple of rabbits out of this hat. Then I'd say he had a really solid, working theory and the rest of the world should jump on the bandwagon (and give him a Nobel for his efforts). But so far what I'm seeing is a lot of speculation backed up by some non- rigorous mathematics. It may sell books, but it don't sell me.

Senapathy is arguing from the improbability of a particular end result (evolution doesn't predict or need eukaryotes) to the impossibility of the general pathways that led to that particular result. He does not take into account the myriad of other possible particular results that didn't happen.

JM: Again, Senapathy's theory of how life came about and various organisms formed does not require that macroevolution be disproved (the "negative"), but he starts out trying to do that in his book. We are now addressing Senapathy's theory (the "positive"), not the issue of Darwin, etc.

Dave: (reprise)It's surprising just how much genetic material humans share even with >oak trees. Or at least it would be surprising if we didn't have a >common ancestor.

JM: It is not surprising under Senapathy's theory, either.

Dave: Now I realize Senapathy sort of accounts for all this by claiming that large chunks of genomes floated around in the primordial swamps, so to speak.

JM: Not "sort of" -- not "so to speak." That is part of his theory, and he discusses it at great length.

Dave: As I said before, I'd be much happier if he could construct an example of this primordial swamp full of genomes...

JM: He does this in his book, but probably not to the detailed level that you would like, because....

Dave: ... and still happier if he could produce a couple of rabbits out of this at.

JM: Give me a break! You cannot expect that level of proof. If we must use your standard of measurement, then I should require you to produce observable macro-evolution. Be reasonable here -- there are certain things we cannot now see or do, but that should not automatically mean some theory or other is wrong. At least Dr. Senapathy uses numbers (many of which have been challenged here). But numbers and formulae can be discussed more objectively than broad statements like yours.

Dave: But so far what I'm seeing is a lot of speculation backed up by some non-rigorous mathematics. It may sell books, but it don't sell me.

JM: And that is how macroevolution appears to me. Show me the rigorous math that proves there was a common initial ancestor to all life that we see today. Again, you are assuming there is no math about this in Senapathy's book, but there is plenty. Please argue about those numbers.


Keith Robison: How do you explain all those big exons (there are many greater than 400 nts, as I have posted -- as big as 7Kb as I recall).

JM: Senapathy uses 600 nts as a typical longest value, but agrees there are some that are longer. What's wrong with that? If his average longest exon frequencies are wrong, what are the correct numbers?

Keith: As your calculation shows, Senapathy's pond contains >10^5-10^10 kilograms of high molecular weight, double-stranded >DNA. Biological systems are quite capable of generating this; >a serious challenge for any abiogenesis scheme is generating >the biomolecules (one was just published in Nature). Senapathy >says "no problem" -- and then assumes it will be polymerized, >double-stranded, and high-mw (or else his calculations croak >from "edge effects" -- you can't run a long gene into DNA which >doesn't exist). Furthermore, this DNA is being replicated, transcribed, >and translated.

JM: I don't understand. Please elaborate.


From Dave Oldridge: The cost of new body parts is enormous >compared with the cost of modifying what already exists. Really novel >structures are rare. Why is this so hard to understand?

JM: You are just making a statement with no basis. Even if there is a high cost, there ought to be new body parts showing up from time to time. What is the "cost," and why is it prohibitive? Please explain this to me without just making broad sweeping statements. Although you might not agree with Dr. Senapathy, he does base his arguments on science and his research, not on generalizations that just sound logical (e.g., "the cost ... is enormous").

Dave: Take a look, for example at Archaeopteryx. Every bone in the wings is also present in the forelimbs of Coelophysis. Is this just coincidence?

JM: According to Dr. Senapathy, it could be due to reuse. Dogs and cats both have four legs, and there are other similarities. Many are necessary simply for survival (e.g., legs for movement), and so are not present coincidentally, and should be no surprise.

Dave: The problem here is that Senapathy is not doing enough work. If he could demonstrate this in the lab and actually show us how to make it happen, I'd start to get a lot more comfortable with his ideas (and probably buy the darn book, even though I can't afford it).

JM: If you look at his book, you will see that he has, indeed, done a lot of work. However, he can no more demonstrate the formation of life in the lab than you can objectively demonstrate macro-evolution. He does, however, offer numerous detailed explanations for the pond, genes, life, and so on. So, go on, take the plunge. It won't impact your life that much -- just delay seeing a few movies. You just assume he does not offer much in his book.


From Shane McKee: (quoting JM) "What is the established fact that refutes Senapathy's seed cells?"

Shane: A complex multicellular organism, like a human or any other mammal for example, cannot be spontaneously generated in a pond. Even if the cells arose, they could not develop into an embryo, much less a fetus or fully-formed adult without the protection, nutrition, stimulation etc. of the uterus (staying with mammals).

JM: Initially, this was a big bother for me, too, but Dr. Senapathy discusses this in his book. The trouble is that we expect and assume that just the mechanisms we know about today must be present in the Senapathy model, but there are alternatives, and you need to keep an open mind. The short answer is: things were a lot different back then. Since few if any of you have read about this, I will quote from Senapathy's book (at page 308):

"The seed cell in analogous to the zygote. It has the ability to grow into an embryo and into an offspring in an appropriate environment such as that of the laid egg of an egg-laying animal, or the uterus of a mammal that supports embryo development. The seed cell, analogous to the developing zygote, could have developed into the offspring in a localized environment that could have existed in the primordial pond with its rich broth of biochemicals: proteins, lipids, carbohydrates, etc."

"It is quite possible that such environments provided nutrients for the seed cell analogous to the environments within the eggs of many mammals (such as the yolk). In fact, the majority of invertebrates and many vertebrates do not develop fully into the offspring within the egg, because the amount of the stored nutrients within the egg is insufficient. They develop first into larva, which then must find further nutrients from the environment -- and subsequently develops into offspring by metamorphosis."

"When we consider the case of the independent birth of mammals, it is reasonable to think that a conglomeration of a large number of cells and biochemicals in the primordial pond could have formed an environment akin to that of the placenta and uterus of mammals. There, a seed cell can differentiate into an embryo and a full-grown offspring. ... what we then need is the birth of the first few individuals of an organism to establish a population by mating."

JM: Dr. Senapathy then lists five observations that support the possibility of seed cell development in the pond (e.g., encapsulated eggs of oviparous animals, in vitro fertilization). (Pages 309-310)

To get multiple organisms, Senapathy suggests that perhaps "a successful seed cell can divide and multiply into many seed cells and produce many individuals of the same organism." Chicken or egg first? Egg first.

Aside: I can visualize a system whereby the first individual, or the first few, develop in a different way from subsequent individuals. Analogous to "vestigial organs," perhaps there are a set of genes still within us that are no longer used, but at one point, at the beginning of our development, were expressed and served to give our first ancestors the ability to grow and reproduce in a different manner from the way we do now. That is, why could there not be two or more "developmental programs" within our genomes, only one of which is expressed today, and the other lay dormant? Depending on the environment, the proper developmental program is used. [Reminder: this paragraph is mine, and so it does not necessarily reflect the views of Dr. Senapathy.]

Shane: The notion that, for example, a baby could haul its little way out of the pond (at 9 months), then make its life, and meet another similar baby, maybe 20 years later, and have more babies, is, frankly, ludicrous....

JM: See? You are assuming there must have always been a 9-month gestation period because that is all you see today. It may not have worked that way in the beginning -- you are just assuming it must have.

Shane: ...Think about it. Dr. Senapathy hasn't.

JM: Wrong! Any yet another incorrect assumption. He clearly has thought about this -- the problem is that you assume he has not, in part because you have not read his book.


From Dave Oldridge: Then why did Archie reuse so much of Coelophysis? And why isn't anything reusing it as much now? These are not just idle questions...they beg for answers before you can claim a full-fledged theory.

JM: According to Dr. Senapathy, the amount of reuse would depend on the time between seed cell births an the location of those births. See figures 8.4 and 8.8 on pages 314 and 323. Quoting: "Parts of the first successful genomes were included in newer genomes being assembled from the [universal gene pool], thereby making it easier to assemble newer genomes resulting in some organismal similarity." "The commonness of genes can be high enough for many organisms to be classified into groups of similar organisms resulting in a false and misleading scenario as though organisms are related by evolution." [page 320]

Dave: I just assume that if there was really all that much to it, the >whole community would be talking it up and doing research to verify or >disprove it. So far, though, I haven't seen much that we could actually >test. It seems more like a sort of "just-so" story.

JM: Things like this take time. Do you expect this to be like the cold fusion announcement? As for testing, some of this is being done now in the form of genetic sequencing. The data will be forthcoming.

Dave: Macroevolution at least doesn't incorporate much in the way of speculative stuff. The things deemed necessary for it to happen are KNOWN to happen all the time. Senapathy has proposed something we don't KNOW happened at all and has so far not tested the hypothesis in any fashion that I can see.

JM: You and I just don't agree on the definition of macroevolution, so let's not use that word. Those things that are known (through direct observation, for example) are not in dispute. For example, Senapathy has no problem with artificial selection or allowing that some species evolved from other species (for example, all frogs, or spiders), or that adaptations occur (e.g., moths changing color). None of that is a problem. However, you have no way to know that a frog and a rabbit are related through any direct evidence, and Senapathy asserts they are not.


From Dave Oldridge: I still say that, if there is anything to this theory, Senapathy ought to be able to come up with an artificial soup full of DNA and produce, at the very least, new (to the soup) species of prokaryotes every time the experiment is performed.

JM: It would not be prokaryote genes, we're introns-early here. The whole theory rests on the genes coming from the pond being eukaryotes.

Dave: He need not try to duplicate the whole procedure....I'd even be interested if he manufactured the soup already loaded with DNA molecules, as long as it was scrupulously sterile of living bacteria.

If his theory is so good, why isn't he performing these experiments? They're right in line with his credentialled expertise.

JM: He has done this via computer simulation with random DNA, and he reviews this work on pages 273-288. It did not involve a full-length run of DNA (10^30 nts), but enough simulated DNA was used to search for genes and other things.

On the other side of the coin, what kind of experimental or observational evidence would it require to completely discredit his theory? If he really wants that Nobel, he has to try for both. :-)


From Joe Morlan: OK. As I see it this theory proposes that every living and extinct creature crawled out of a primordial pond.

JM: No, that is an overstatement. As an approximation, Dr. Senapathy suggests that perhaps "several million" seeds cells have led to the billion or so species that ever lived (page 533).

Joe: The first human was nothing but a strand of DNA and it grew into a human baby. How did it do that?

JM: It was not just a strand of DNA.

Joe: How did this human baby take care of itself with no mother?

JM: I agree -- this is a bother for me, too. However, we can not assume that the first humans required nurturing the same way as human infants do today. But this is on my list of questions, and I hope Senapathy will address this in more detail.

Joe: Where is this pond? This theory predicts that no new species can ever arise without the pond.

JM: That is correct -- no new species will come from the pond because the pond (or ponds) are no longer productive.

Joe: All species past, present and future are in this pond. Yet speciation has been and continues to be observed without any pond. There is no evidence of any pond.

JM: Well, there had to be a pond in any case because life did start somewhere, at least once. Why not more than once? Senapathy does not say there can never be any new species, but (at page 533): "Except for similar variations of existing organisms [including some new species], no new creatures will ever arise again!"

Joe: Why are we discussing this?

JM: We are discussing this because Dr. Senapathy is a molecular biologist, and he deserves to be heard. We are discussing this because his theory sounds plausible, at least to me and a few other people (some of which are more familiar with biology than me). We are discussing this because people here are trying to show me why Senapathy is wrong, and I am trying to understand their arguments. We are discussing this because it is interesting, at least to a few people. We are discussing this because it deals with science. We are discussing this because it deals with evolution. We are discussing this to determine the validity of his theory. We are discussing this because this is the Internet and it is a good interactive medium for sharing ideas. Do you need any more reasons? Note: you do not need to participate.


From Don Cates: Please note that, as far as I can tell, Dr. S's theory would predict that the distribution of differences in the third base of these codons would be random across the different "independently born" organisms. However, this is not what is observed. Organisms that are considered to be close evolutionarily are more likely to have a higher proportion of same third bases.

JM: Let me quote from The Book a bit more (pages 438-440) which will explain Senapathy's position on this:

"Evolutionists believe that the same gene in widely different organisms has in fact evolved by descent with modification, simply based on the fact that there are nucleotide differences in the gene's coding sequence (amino acid differences in its protein) in various organisms -- which they assume are due to mutational changes during evolution. Molecular biologists compare the coding sequences of the same gene present in various organisms and show that the differences are most common at the third base position of the codons. This is precisely expected under our new theory: if the same gene were included independently in different organisms, it will undergo such mutations that either do not affect the basic function of the protein, or lead to a defective protein. That is, organisms that are independently born can have the same gene, and in each organism the gene undergoes random mutations producing normal variants of that gene independently of any other organisms, while all organisms remain immutable. Thus, the phenomenon of the presence of the same gene in various organisms and the presence of sequence variations in them -- which is claimed to be the strongest molecular evidence for the evolutionary theory -- can be explained by the theory of independent birth of organisms. This is also true for the similar portions of entirely distant genes."

"The same gene included in two entirely distinct genomes from the primordial pond can be changed in the two creatures, although these creatures originated independently. These changes can occur in those amino acid positions that can tolerate substitutions. Where amino acid substitutions are not tolerated, often changes in the third, most degenerate codon position are allowed. This is variation in an immutable genome within its confined genomic framework."

JM: So, to put it another way, Senapathy is saying that the evidence you say strongly supports evolution is, in fact, predicted by his theory, and that the evidence you are using has been assumed to be due to changes during evolution. I think this is called a tautology.(?). Anyway, please correct me if the evidence you mentioned is not what Senapathy was talking about.

Don: It's close but not quite. There are three parts.

  1. The similarity of functionally similar sequences.
      Maybe a problem for special creation.
      No problem (predicted) for Dr. S.
      No problem (predicted) for evolution.

  2. The existence and location of differences in otherwise similar sequences.
      A problem for special creation.
      No problem (predicted) for Dr. S.
      No problem (predicted) for evolution.

  3. The pattern of the DIFFERENCES across different organisms.
      A big problem for special creation.
      A problem (predicted) for Dr. S.
      No problem (predicted) for evolution.
Points 1 and 2 are addressed by the quote from Dr. S but 3 is not. I also feel he overstates evolution's incestuous relationship with and reliance on this data. It seems to me that it is near identical for evolution and Dr. S for points 1 and 2. Both predict it and can use it as evidence. But point 3 belongs to evolution and is a problem for Dr. S.

Again, the point is not that these similarities exist. They would also exist in "special creation" if the creator used the same basic blueprints for all its creations. What is important is the pattern of the differences across different organisms. This pattern is completely consistent with evolution but requires some sort of special pleading for both Dr. S and creationists.

JM: I think the special pleading is on your side. Although Senapathy did not use the word "pattern" (because he would say there is no pattern),...

Don: Then he is wrong.

JM: it not true that the pattern you mentioned has been the primary foundation for the evolutionary tree? If so, then you cannot argue that the evidence supports evolution when it was that evidence that was used to create the tree! Senapathy does you one further: he demonstrates why the similarities and differences exist.

Don: The point is that the tree existed before this info was available, generated from other data (fossils, etc.). Both Dr. S and evolution can give a "why" for this data (for the same reasons! Reuse of existing material). So this data is not the primary foundation for the tree, just very good confirmation. What you have not shown that Dr. S addresses is the following.

When I refer to differences below, I am speaking of differences in the base code that are purely arbitrary and have no effect whatsoever on the final output. Why are the number of differences greater between humans and kangaroos than between humans and dogs? Why are many of the differences between humans and kangaroos, and dogs and kangaroos, shared? (this is indicative of the pattern I was speaking of) For evolution, this is inevitable. How does Dr. S account for it?

Do you see why I think that this information poses a problem for Dr. S (and creationists)?

JM: I agree there is a problem here but, in my opinion, it is not with the independent birth theory. There have been numerous similar complaints about Senapathy's theory, and all but a few of them are addressed in his book.

Don: Does he address this?


From Shane McKee: It assumes a pond full of DNA, in which organisms develop, and out of which they crawl, fully formed.

JM: He does not assume a pond in the sense that he just starts from that point. He estimates how many nucleotides could have been available based, in part, on the amount of DNA present in all life today (about 10^41 nucleotides). He drops this to 10^30 nucleotides per pond. There is much discussion in his book about the characteristics of the soup -- this subject is not glossed over.

Also, he does not say the organisms simply "crawled, fully formed" out of the pond. The pond produced the seed cells from which the organisms developed (in the pond itself for fish, out of the pond for most others). After that, they reproduced on their own, one way or another (or both, if you get my drift).

Assumptions, assumptions (reprise). I note that you and a few other people conveniently assume things about Senapathy's theory that you can easily refute, yet you also complain that he assumes too much without having read his book. I am perfectly happy quoting, paraphrasing, and interpreting Senapathy's book here, but I get a little hot when some people say he's wrong without first at least asking what he has written on the subject.

Shane: There is no fossil evidence for such a pond. If it was productive for millions of years, we would expect to find some fossil evidence, together with the dead bodies of all the failures that sank to the bottom.

JM: Senapathy absolutely loves the fossil record because it completely supports his theory, utterly and totally, backwards and forwards. He even devotes a whole chapter to the subject (Chapter 11, pages 491-519). Here are some highlights:

As for the "dead bodies of all the failures" -- many are there as the fossils we find of extinct creatures. The vast majority of independently-born non-viable species that were able to at least survive for a while consisted of only one individual, so it is unlikely we'd ever find a fossil. However, if you do find one fossil of a particular type, maybe that is the only one. I don't know, do you?

Shane: Leaving that aside, a pond full of DNA is a very, very unstable product. As soon as the tiniest bug gets in, the DNA will be digested as the bug replicates. The DNA in a Senapathy pond might last a couple of weeks at best.

JM: Is "bug" a technical term for bacteria? :-). I'll assume that's what you mean and point out that this complaint has been raised to me before, most recently by Keith Robison. I left that item in limbo because it was a question I could not then answer based on Senapathy's book. However, I now believe that issue was not specifically addressed in the book because it was unnecessary. The basis of Senapathy's theory is that the first genes had introns and exons (necessary in order to obtain long reading frames -- but that's another topic of discussion). Hence, the first organisms were eukaryotes and there were no bugs, er, bacteria. Prokaryotes came later, and by that time, the ponds had been productive enough for life to continue. Even if you don't agree with the introns-early idea, tell me why the above scenario would not work if you assumed introns-early.

Shane: Using the Senapathy example, the first bug will eat all the DNA.

JM: Introns-early = bugs-late? :-)

Shane: It is not that I don't like Dr. S's hypothesis, it's just that it consists of too much stubble, and the shaving foam of Reality, coupled with Occam's razor, yield a very smooth shave. Evolutionary theory is more than adequate to explain what we see around us.

10/10 for trying. It's important to come up with wild and implausible ideas now and again. That's how progress can be made. You never know, it could be that the dying embers of the Senapathy hypothesis could provide a spark of inspiration for someone in the future.

JM: Wow, what a great lead-in. I've been hoping for this. Just last night on ABC's 20/20 (see? even the math works: "10/10" to "20/20"!), there was a story about the Australian physician who, circa 1986, had a "spark of inspiration" and figured out that practically all stomach ulcers were caused not by acid but by bugs, er, bacteria. His "wild and implausible idea" was denounced and laughed at by the rest of the medical establishment, the drug companies, and his wife. Everybody knew that acid caused ulcers, it was a fact. But most treatments were ineffective, and people were living with chronic problems. However, as we all know now, the doctor was correct, and the old acid theory is now a "dying ember." It took about five years for that relatively easy proof. So, just keep your mind open -- even those cold fusion experiments haven't been explained yet.

Shane Yeah. I saw that on QED, as did the rest of my intake of students in medschool a couple of years back. We laughed and laughed, because it was so misrepresented. The theory did not really encounter all that much resistance, and, what's more, this guy had the data to back up his claims.

Reuse of successful genomes in conventional evolution is done via the vehicle of organism bodies. In Senapathy's hypothesis, the extra element of a pond is added, with the concomitant (and in my opinion, insuperable) problem of regeneration of organisms from the pond. To exhibit a tree-like phylogenetic pattern, Dr. S's hypothesis must assume a fairly homogeneous pond for each group -- an elephant's gravepond, if you like, or a pelican's gravepond. Otherwise, we would have viable organisms with genes borrowed from different organisms, and each gene would show a different phylogenetic tree. For instance, a pelican could probably be viable with an elephant's cytochrome-C, and vice versa. Yet we don't see this across phyla. So each lineage would require a separate pond.

In my opinion, this is adding epicycle upon epicycle. It's fun, but is it science?

The discussion is continued in The Primordial Pond, part II.