The Primordial Pond
(Part II)

Discussion (continued from Part I):

From Don Cates: It seems that in order to fit morphological data to Senapathian independent births, you've had to make them less and less "independent". The more you rely on "reuse", the less "independent". It's starting to approach the point where you can replace "pond" with "egg sack" or "uterus" and call it evolution.

"Poorly designed features"; structures like the human knee (chosen from bitter personal experience); are expected in evolution because choices are limited to modifications of preexisting structures and "good enough" will do, "optimal" isn't necessary. I can't believe that a well stocked "pond" couldn't provide a better knee than the hacked modification of a quadruped's knee that I have. I know this is an argument from incredulity, but one that I personally feel is well-founded.

From Keith Robison: Nucleotides don't easily come about -- they arise almost entirely via biological processes. This is a stumbling block for any origin-of-life theory. Senapathy's explanation is no explanation.

There's a more subtle extension of this -- how was all that random sequence formed and replicated? How were the mRNAs spliced, and the proteins translated? None of the processes are known to take place without the prior existence of proteins and specialized (i.e. information-bearing) nucleotide sequences. Repeat: These are all sticking points for all origin-of-life scenarios. Senapathy's scenario is particularly dependent on them.

Senapathy's book is nothing but a stew of assumptions, with a seasoning of untruths disguised with a thin glaze of facts.

There are plenty of intron-bearing eukaryotes which would have a good time ruining a pond. Second, if you assume a world without decomposers all the available carbon and nitrogen will be used up. Again, as I have pointed out before, decomposers are inevitable and necessary, and will destroy the pond. There is absolutely no hope for Senapathy's pond to survive a century of life, let alone millions of years+.

Also, as I have pointed out, even non-decomposer eukaryotes could quickly ruin an abiogenic mixture. All organisms shed nucleases and proteases, and even a dead critter falling in the pond would be disaster for it.

From Ralph M Bernstein: 1*) So, if I understand correctly, homologous genes in phylogenitically related creatures...

JM: Bzzt! You are presupposing evolution, but go on...

Ralph: ...that serve the exact same purpose exactly the same purpose should be identical? Right? This I need to know. Because if so, then this (Senapathy's stuff -- main supposition) is ALL wrong. If not, then you're saying "once out of the pool, and into an organism, genes shared equally, the genes can mutate and change" -- hence NON-immutable.

JM: Put us down in the "if not" category. Genes can change once out of the pool. Don't take that word "immutable" to the extreme. Obviously, there are changes in organisms. Artificial selection, adaptations, etc. But the fundamental characteristics of an organism do not change. Minor changes do, in fact, happen. That is what Dr. Senapathy means by "immutable."

Ralph: Come on Jeff, answer the question! They serve the same function in higher and lower vertebrates! Immutable means immutable. Say "sortakinda immutable" if that's what Senapathy means. Maybe he should release a "Senapathy's abridged and modified dictionary". What does this mean Jeff: "But the fundamental characteristics of an organism do not change." What are these? Are you confusing phenotype and genotypes? Do you mean genetic content, do you mean their morphological features? Generalizations en masse don't better your argument. So answer that question for me.

2*) I really like the pool idea-as I like to swim (being from Tucson). Does anyone know what happens if you leave DNA in water? Plain water? It eventually hydrolyses itself. DNA is a weak acid. so....if there was a pond with loose huge huge huge chunks of DNA (or, supposedly both DNA and RNA) they would soon, just by themselves, become lots of small chunks of DNA (barring the horrible damage that mechanical shearing does to the carefully prepared genomic DNA).

OK, so maybe salt conditions, etc. were right at the time, it was actually a large pool of Tris-EDTA (tm-sigma). The DNA/RNA just self catalytically threw itself together into monster chains (long-PCR?). Even so, Senapathy must have enzymes in this mix, otherwise no DNA replication. there must be some nucleases, because to initiate replication you must have nicks, and that's done with an enzyme. So if a nucleic acid protective method/system was around along time ago to protect DNA from itself and enzymes, why don't all organisms (that swam and crawled out of TE) use the same method to protect themselves today?

JM: I'd like to point out that life did happen, at least once. And some of the same problems you say Senapathy has with his pond would also apply to "Darwin's" pond. I keep asking: if life came about once, why not a million times? Anyway, to your question: here is what Senapathy says about the DNA in the pond:

(At page 214): "Today we can multiply DNA extremely efficiently.... the DNA molecule is highly stable even by itself in a test tube, indicating that such a stability is the inherent nature of the DNA molecule. Also, protective mechanisms similar to those existing in the chromosomes of living cells could have existed in the primordial pond. One would logically expect that DNA must have been abundant and very stable before complex cells were developed. ... there is still more support for the stability of DNA molecules in the primordial pond. ...DNA from mummified bodies has been stable for thousands of years... DNA is routinely boiled in the laboratory. ... there exist many microorganisms that live at high temperatures. ... Humans have only discovered a few of the methods for DNA synthesis and replication in the laboratory that Nature can carry out. Many more chemicals and conditions than can be created in the test tube could have existed in the primordial broth. It is extremely important that we should not underestimate the potential of the primordial broth, which must have contained millions of highly reactive organic chemicals of different types, sizes, and structures, brewing with all kinds of molecular catalysts."

From Ralph M Bernstein: (quoting Senapathy) ""Today we can multiply DNA extremely efficiently.... the DNA molecule is highly stable even by itself in a test tube, indicating that such a stability is the inherent nature of the DNA molecule."

Ralph: Not true. Only small pieces, and even these are subject to self-hydrolysis, and Senapathy proposes monster-size pieces.

"Also, protective mechanisms similar to those existing in the chromosomes of living cells could have existed in the primordial pond. One would logically expect that DNA must have been abundant and very stable before complex cells were developed."

This may be open to debate.

"... there is still more support for the stability of DNA molecules in the primordial pond. ...DNA from mummified bodies has been stable for thousands of years... DNA is routinely boiled in the laboratory. ... there exist many microorganisms that live at high temperatures. ... Humans have only discovered a few of the methods for DNA synthesis and replication in the laboratory that Nature can carry out."

Of the nearly hundred or so polymerases discovered and characterized, they are basically the SAME family a b and x polymerases, all having degrees of aa identity. Crystallized versions? Look the same. Only wacky ones are pol beta and tdt (x fam) that are still essentially sequence similar. How can these things be so similar? (Maybe see Ito J and Braiwaith, PNAS) Anyway, the point is...the method of synthesis is the same, Jeff, all processing in the same direction-constrained by the biochemical nature of the molecule itself!

"Many more chemicals and conditions than can be created in the test tube could have existed in the primordial broth."

Come on! This is just a plain monster assumption!

"It is extremely important that we should not underestimate the potential of the primordial broth, which must have contained millions of highly reactive organic chemicals of different types, sizes, and structures, brewing with all kinds of molecular catalysts."

This is the acceptable statement in this mix.

From Keith Robison: (quoting JM) "I'd like to point out that life did happen, at least once. And some of the same problems you say Senapathy has with his pond would also apply to "Darwin's" pond. I keep asking: if life came about once, why not a million times?

Keith: Repeat:

1. Life is highly improbable
2. Abiogenic mixtures are destroyed by life.

This is a joke -- right? DNA is highly vulnerable to numerous non-biological conditions:

1. acids (including itself)
2. UV light
3. mechanical shearing

One of Senapathy's top 10 hits -- it is an inarguable fact that any biological system is replaceable with a non-biological one which the pond is guaranteed to have. Yeah, right.

"One would logically expect that DNA must have been abundant : and very stable before complex cells were developed. ... there is still more support for the stability of DNA molecules in the primordial pond. ... DNA from : mummified bodies has been stable for thousands of years..."

Hmm, a mummy. Let's see. Dry (low hydrolysis). Dark (no UV). Solid (little shearing). And guess what, ancient DNA ain't exactly in good shape. It is well known in that field that what is obtained is generally a replica prepared by splicing together all the little fragments of DNA in the sample. Repeat: DNA is chemically unstable.

" ... there exist many microorganisms that live at high temperatures. ... Humans have only discovered a few of the methods for DNA synthesis and replication in the laboratory that Nature can carry out. ... Many more chemicals and conditions than can be created in the test tube could have existed in the primordial broth. It is extremely important that we should not underestimate the potential of the primordial broth, which must have contained millions of highly reactive organic chemicals of different types, sizes, and structures, brewing with all kinds of molecular catalysts."

In other words, assume the primordial broth had everything necessary, despite an utter lack of evidence. And you complain about our assumptions.

From Warren Gallin: So you are proposing that the DNA from successful organisms is recycled back into the pond?

JM: Well, Dr. Senapathy is, yes.

Warren: That is the only way that the re-use idea could fly. Does that meant that the ponds are accessible to dead organisms? If so, then it is also accessible to organisms that feed on dead organisms, i.e. they will rot. So this re-use argument doesn't work.

JM: This is a previous complaint, to which I suggested a solution ("there were no bugs") or there were other protecting mechanisms.

Warren: The point is that "re-use in the Darwinian sense is due to breeding and selection of whole organisms. What you are proposing is that pools of rotting meat spontaneously gave rise to new, variant organisms.

quoting JM: What I'm looking for is a definitive test that will determine which mechanism is correct. But it is not as simple as some s.b.e. people think because, if you come up with a test, you must consider how it might be passed by both theories. Most of the "evidence" people say refutes Senapathy is, in fact, just evidence that supports evolution -- and support of either theory does not automatically rule out the other. Also, just to avoid confusion, by "evolution," I'm just talking about long-term evolution (natural selection and descent with modification), not short-term (adaptation or artificial selection).

Warren: I think you haven't been reading the replies to your posts. They consistently propose tests that Senapathy's theory fails and Darwinian natural selection passes....

JM: I agree there have been some good criticisms, and a few have yet to be addressed. They are not forgotten. I point out, however, that most of the so-called problems with Senapathy's theory are due to (1) presupposition of descent with modification and/or (2) incorrect assumptions of the details of the new theory. Not all, but many.

Warren: ... Read over the critiques of the "seed" cell hypothesis, which requires not only the spontaneous generation of the DNA sequence of an organism, but also the spontaneous generation of all of the non-DNA components of a cell that are necessary for the information in the DNA to be translated into functional molecules (ribosomes, transcriptional enzymes, assembled lipid membranes). This isn't a minor objection that you can just cast aside by saying that things were different then than they are now.

JM: It has not been set aside. The caption to figure 8.3 summarizes other text in the book on this subject (at page 311):

"The genetic code and the genetic machineries such as transcription, splicing, and translation systems had been already established in the primordial pond before any living cells were formed. This pool also contained the DNA-recombination enzymes, such as DNA ligases found in today's living cells, that could recombine different pieces of DNA to help form many genomes. Thus, the primordial pond was a common pool of code, genetic machineries, and genes, from which different organisms could be derived. Consequently, they all used the same code and genetic machineries, but different sets of genes and, more importantly, different DG pathways leading to distinct independently born organisms."

From Don Cates: 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.

JM: OK, I've been sitting here reading your questions over and over. I still say you are presupposing descent with modification when you ask your questions. (You have in mind a certain relationship between humans, dogs, and kangaroos based on the "pattern" you have found.) Please consider your questions without thinking about evolution. To wit:

Don: Why are the number of differences greater between humans and >kangaroos than between humans and dogs?

JM: Tell me why, under Senapathy, it should not be greater.

Don: 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)

JM: Tell me why, under Senapathy, they should not be shared?

Don: For evolution, this is inevitable. How does Dr. S account for it?

JM: It is a result of the random reuse of DNA material.

You see a "pattern." I could give you a set of random stick figures or drawings that share some common characteristic (such as the number of pen strokes -- to make it "viable") and you could probably arrange them into some kind of a pattern. You are asking "why" the supposed pattern exists.

Don: Does he address this?

JM: He does, in many places. It is one of the major predictions of his theory: organisms will have some unique genes, they will have some shared genes (and junk DNA), and they will have some shares sets of genes. If you say there is a tree and try to "fit" Senapathy to that tree, you are presupposing something that is not part of Senapathy's theory.

Don: (reprise) I am speaking of differences in the base code that are purely arbitrary and have no effect whatsoever on the final output.

JM: Are you referring specifically to the non-coding, junk DNA? Here is something on that subject (page 443):

"The amount of DNA material included as genomes in the different seed cells can vary widely because each genome includes a different number of genes, and, more importantly, a different amount of nongenic, random sequence. Organisms independently born in the primordial pond need not have similar amounts of DNA in their genomes. The intergenic 'junk' DNA included in the different genomes could vary even far more significantly because of the manner in which each genome is separately assembled from the primordial genetic sequences."

JM: And, continuing, why the junk might still be there:

"The junk DNA originated in the primordial pond but could not be eliminated from the genomes of multicellular organisms for several biological reasons. One such reason is that the seed cell and the cells of the organism were built with the size of the genome that was organized originally, and has become biochemically, physiologically and mechanistically tied to that size of the genome. For instance, the size of the nucleus, and the size, organization, and number of chromosomes may be some of the possible reasons. Once this had happened, then the junk DNA became an integral part of the genome and the cell, and started to have size-related functions. Therefore, it has persisted in the genome to this day."

From: Shane McKee: A little pet peeve of mine is the Burgess Shale story. Don't get me wrong - I like S. J. Gould's stuff (some of it). But I don't think it's quite as spectacular a menagerie as it's made out to be. For example, hallucigenia turned out to be an upside-down worm-of-sorts, and not the weird beastie it was first thought. Anyway... as for the intermediates for limbs etc., I think there is plenty of evidence, fossil and embryological, for them. The old 'embryology recapitulates phylogeny' argument is pretty weak at best, but similar embryological processes underlay the formation of a bat's wing and a human arm. No new body parts - only the relative growth parameters have changed. Evolution can do that. As regards feathers, it's a pretty sound bet that at least some dinosaurs had them long before they were used for flight.

Re: bugs in the ponds: How long can you leave a pint of milk out of the fridge? Or a bowl of curry? Either it goes off, or something eats it (in fact, both amount to the same thing). The ponds are inherently unstable in the presence of the simplest cell.

But even a eukaryote can bust DNA. Ask any paramecium. You don't even need a prokaryote. Aside from that, there is plenty of evidence for prokaryotes billions of years before the ponds were allegedly spawning mammal seed cells.

I don't think introns-early or introns-late make much difference. If it can be eaten, something will eat it, whether it's eukaryote or prokaryote. The timing of intron inclusion is at best a side-issue until the practicalities are resolved.

From Warren Gallin: He is not only assuming that a huge amount of DNA is spontaneously generated in a small volume, (and as a number of others have pointed out, this is chemically impossible), he is also assuming that all of the proteins and lipids necessary for cellular function are also spontaneously forming at high concentrations, and in addition, that no proteins that would adversely affect the functions of the required proteins are being produced at the same time (another event that is chemically impossible).

I say that he assuming that because the information in the DNA can not be translated into functional proteins without the presence of large numbers of identical copies all of these proteins to mediate the transcription and translation, so even if he doesn't explicitly state it, he is implicitly assuming this and it is essential to the theory.

I know what you are going to say: "Give me numbers, tell me why these are impossible", Right? Well, Keith has already gone over and over the problems with Senapathy's assumptions and modeling, and I suggest that you read some basic biochemistry textbooks and learn about what is known about the energetics of protein synthesis and folding. There is a huge amount of information that is easily accessible and I don't think that this group is a good forum for teaching basic biochemistry.

From Ingrid Jakobsen: I've been to a few talks on molecular archeology recently. These talks all mentioned that DNA doesn't survive in fragments much longer than 300 nucleotides outside a cell. (One speaker said: "if you can PCR fragments longer than 300 bp, you know you have contamination"). I find the idea of 10^20 bp strands of DNA "just floating around" ludicrous. For me, the theory doesn't even get off the ground.

From Don Cates: (quoting JM) OK, I've been sitting here reading your questions over and over. I still say you are presupposing descent with modification when you ask your questions. (You have in mind a certain relationship between humans, dogs, and kangaroos based on the "pattern" you have found.) Please consider your questions without thinking about evolution."

Don: I am presupposing nothing. The pattern is there. It is not arbitrary. Looking at the code for identical proteins in different organisms, we see that there are differences. Remember, these are different codes for the same identical proteins. This is possible because there are 64 codons for 20 amino acids and there is a great deal of redundancy for some of the acids.

JM: Yes, and Dr. Senapathy discusses this at great length. The codon degeneracy and other redundancies that form major aspects of evolution proofs are also predicted by the new theory. You are assuming that any proof of evolution must refute Senapathy (and that is because you are presupposing Darwinian evolution). But evidence for evolution is NOT evidence against Senapathy.

Don: But you're leaving out the crucial part. I do not deny that (from your description) that Dr. Senapathy also predicts the existence of codon degeneracy etc. But since you went to some pains to state that any pattern I saw in these differences were imposed by me on randomly appearing similarities, I will assume that this pattern does pose some problem for his theory. The main point of my quoted post was the real existence of this pattern of differences, not the existence of the differences.

JM: I'm not exactly sure what you are getting at, but I don't deny that there are patterns that you can see. However, the problem is the source of those patterns. They could have come from the random assembly in the pond. The "random" assembly does not necessarily mean a random result (no eggbeater) because the source material (reused genomes) form the basis of the following organisms, and there are obvious constraints imposed by viability.

The closest similar example I can think of is the controversy over cancers supposedly induced by electric fields. People see a cluster of cancers (a "pattern") and then look for a common cause and see the electric power lines. The problem is, there will be clusters in any random arrangement. In evolution, people see a pattern of characteristics and genes, and attribute that to natural selection. I know this example isn't exactly the same thing, but it is close in the sense that the observations may not prove the hypothesis, even though they fit the hypothesis.

Don: Choose an organism at random and arrange the rest according to the number and location of differences with this organism and with each other and you get a pattern. It turns out that this pattern matches pretty closely the pattern independently generated by organizing by physical and chemical structure.

JM: (Reprise) Proof for evolution is not an automatic refutation of Senapathy. Also, I will refer you to my previous post and the Senapathy quotations therein from page 434.

Don: If humans and dogs share a more recent ancestor than they do with the kangaroo, then they also share that ancestor's differences from the kangaroo. So humans and dogs have their differences and each of them have those differences plus their common ancestor's differences when compared to the kangaroo. ... As you state below, Dr. S posits the random reuse of DNA. Why do the human and dog have many of the same differences from the kangaroo if these differences are random?

JM: You are making the same assumption as has Shane. There is no eggbeater in the primordial pond. That is, there is no requirement that "random" reuse is completely mixed up reuse. The fact that humans and dogs have shared differences with the kangaroo is also predicted by Senapathy because the random reuse is not coming out of an eggbeater.

Don: If it's not thoroughly mixed, it's not random. As I stated once before, with the amount of reuse going on to explain the evidence, I see very little difference between Dr. Senapathy's theory and evolution. Replace the term "pond" with "egg" and they are virtually identical.

Please correct me if I am wrong but I am under the impression that the "ponds" existed for a short time relative to the amount of time that has passed since they disappeared. If this is true, then since these random neutral substitutions should be taking place both in the "pond" and in the organisms outside the pond, the number of differences should be greater (much) between the dog and human than between either of them and the kangaroo (more time has passed). But it is the other way around.

JM: How do you know "more time has passed"? Mostly because of the "tree" based on those differences, right? Bong! Then you are presupposing evolution again, and unfairly using that data as "proof." That is, you have this data and you form a tree based on the data, then you turn around and ask me to explain why the tree fits the data.

Now, you will probably say that you have other data that also supports the same (or similar) tree. But for me to be impressed by a "similar pattern" (i.e., for this to refute the new theory), you must show me that the two sets of data are not correlated (under Senapathy's theory). That may be difficult to do in a such a "wild" theory (in the sense of having organized, directed chaos in the pond). And for the data to support evolution, you must also so me that these two sets of data match the same tree.

Here's Dr. Senapathy at page 218: "Eons ago, in turbulent ponds scattered across a still hot and partially molten earth, organic chemicals were being synthesized far more fiercely and ferociously than in today's laboratory flask. All of these organic chemicals were boiling, broiling, hydrating, dehydrating, complexing, condensing, precipitating, breaking, and recombining in a dizzyingly random dance of chemistry gone mad! Use all of the words for processes that chemists today use to synthesize organic chemicals in the laboratory -- condensation , diazotization, amination, hydration, halogenation, pyrrolysis, and so on. All of these and more occurred spontaneously, and prolifically, in the millions of ponds that were sometimes mixing and sometimes isolated. Reactions ensued not for just a few hours or days, or even years, but for several millions of years."

JM: Somebody is sure to jump on me: "that sure sounds like an eggbeater to me!" No, no, please.

From Warren Gallin: Come on Jeff, think about what you have written here. If all of the patterns match, then the correlation is compelling. There is nothing in the Senapathy theory that predicts that all of the phylogenetic groupings derived from the fossil record should match the phylogenetic groupings from a wide variety of different genes with little or no physiological connection. This "gene reuse idea that you keep touting goes directly against the essence of the Senapathy argument, that all the organisms arise without natural selection other than the final viability test of the complete organism coming out of the pool.

Numerous people have pointed out that the spontaneous assembly of a whole multicellular organism (actually two because you need a male and female at the same time) is inconsistent with the most basic, well defined biochemistry and physiology. Your sole response to this too date has been of the order of "Things were different then" That carries no weight. Are you really meaning to imply that the laws of physics were different from the origin of the universe up until a few million or even hundred thousand years ago, and then changed to what they are today? That's what it sounds like.

Jeff, no-one who has spent more than a year in any biological chemistry lab would [agree that DNA is stable]. Long chain DNA is not stable under these conditions. Cell membranes are not stable under these conditions. Most proteins are not stable under these conditions. Single cells are not stable under these conditions. Are we talking about different laws of physics again here? Without a doubt this is the most transparently flawed piece of Senapathy justification yet, and the competition is stiff.

By the way, if the Earth's surface is molten, there won't be pools of water percolating somewhere (or has the boiling point of water changed recently too?).

In addition, since according to the Senapathy theory the ponds have been spewing out new life forms at different times (thus the correlation between the theory and the fossil record) that must mean that these special conditions existed at least up until the formation of the last new "kind" found in the fossil record (by the way, you or Dr. S. have never defined what constitutes the boundary between kinds, other than the odd waving of a hand of the order of "some, but not too much") So, since the hominids are found a maximum of a couple million years ago, and no evidence for modern man until much more recently, the argument seems to be that there were localized areas of spitting bubbling water spewing out full blown life forms from about 3 billion years ago until 2 million years ago, and then things changed.

What we have here is a theory of special creation, no more, no less. Calling it something different doesn't make it something different.

Can we kill this thread, or take it to talk.origins where it belongs?

From Don Cates: Imagine if the EM-cancer pattern were more like this.

• We have a very large sample of people whose genetic and environmental backgrounds are very homogeneous except for the level of EM that they have experienced in their life.
• 95% of those experiencing a level of exposure (LX) greater than 100 (some index of exposure) have cancer.
• 80% of those who have 80 < LX < 100 have cancer.
• 65% of those who have 60 < LX < 80 have cancer. ... (down to)
• 5% of those who have 0 < LX < 20 have cancer.

JM: I don't agree. In the EM case, you are comparing two variables (LX and the number of cancers) to determine their correlation. You plot the two and look for a pattern. Based on what you see, you can determine the correlation of the two variables, and hence decide if they are dependent or independent variables. ...

Don: Well, you introduced the "EM radiation - cancer" analogy to try and show a deficiency in the pattern recognition part of my argument. I introduce a scenario which I think more accurately represents the analogy and you state that the analogy is not a good one. I never thought it a good analogy, but I think my formulation of it is more accurate than yours.

JM: ...In the evolution case, however, you are comparing a genetic pattern with the position a creature has on the "tree." However, those genetic differences were used to create the tree (or a derivative of those differences expressed as traits, no?), and hence they are correlated by default.

Don: NO, NO, NO. How many times must I say it? The codon differences I am talking about have NOTHING, diddly, zip, nada, squat, to do with any expressed difference. The pattern of these differences creates a tree. The expressed differences form another tree. These two trees match up very well.

From Wesley R. Elsberry: Jeff, you do have something of a point here. However, it doesn't work to the advantage of Senapathy's outlook. The theory of common descent is consistent with any of a large number of possible "trees" that could be determined from the data. It is also inconsistent with a far larger number of possible "trees" that could be determined from the data. So far as every example has demonstrated, the evidence is consistent with the prediction of a hierarchical pattern of differences made by the theory of common descent. Common descent predicts the pattern rather than the actual "tree". This hierarchical pattern is a necessary (though not sufficient for absolute establishment) condition of living systems derived through common descent.

The point is that this condition is not necessary to Senapathy's theory. Any tree at all is consistent with Senapathy's theory once you allow for complete flexibility in invoking "reuse". The fact of the matter is that for the current diversity of living things, the number of "trees" consistent with common descent is highly constrained, while the number of "trees" consistent with Senapathy's theory is relatively unconstrained and thus extremely large. It is easy to see that if Senapathy's theory is true, the probability of a "tree" emerging from the data that is consistent with common descent is very small. In this case, arguing "Reuse!" is analogous to writing in "Then a miracle happened!" on a test to cover a lapse of memory. Sure, it's consistent; it just doesn't happen to also be responsive.

If you are going to fault examination of the pattern of relationships based upon circularity, it is only right that you also forego critiques based upon that point ("reuse" as a presupposition of Senapathy's theory).

From Don Cates: (quoting JM) How do you know "more time has passed"? Mostly because of the "tree" based on those differences, right?

Don: No. Because from what you say above, the time from the kangaroo's emergence from the pond to the dog and human's emergence is much less than the time from then until now.

  Let:
    Tk = time of kangaroo's emergence.
    Td = time of dog's emergence.
    Th = time of human's emergence.
    Tn = now.

Then the amount of shared neutral differences between dog and human and kangaroo should be proportional to Td-Tk for the pond + Td-Tk for the kangaroo. [=2*(Td-Tk)]. The dog-human differences proportional to Th-Td for the pond + Tn-Th for the human + Tn-Td for the dog. [=2*(Tn-Td)]. The total dog or human to kangaroo differences proportional to 2*(Tn-Tk). So the number of unshared dog and human vs. kangaroo differences should be proportional to 2*(Tn-Td). From your information, (Tn-Td) >> (Td-Tk). So there should be many more unshared differences than shared ones. This turns out not to be the case.

JM: What, exactly, did I say that led you to those numbers? I do not know if Tk < Td < Th, but I will agree that all three are much less than Tn. Please explain again.

Don: You stated that the length of time that the "ponds" existed and were productive was much less than the length of time since then. The number of neutral codon differences should be proportional to the length of time that the different organisms have been separated. Once the kangaroo has left the pond, it and the pond will begin to differ. When the dog leaves, it will inherit the pond-kangaroo differences and start to accumulate differences of its own from both the pond and the kangaroo. There would be no way to distinguish between these differences. But when the human leaves, it too will inherit the pond-kangaroo differences and share these with the dog. The dog-kangaroo differences shared by the human will be proportional to the length of time from the kangaroo emergence to the dog emergence. The unshared differences will be proportional to the length of time from the dog's emergence to now. Since Dr. Senapathy's theory posits a relatively short time frame for genetic separation of these species, the shared/unshared ratio should be very small; and it isn't, as far as I know.

JM: Yikes! I just fell off my chair! :-) Up to now, you've been presupposing evolution in rather small ways, but this time you've reached critical mass! :-) Don't you see it yourself?

Where in the world did you ever get the idea that you can measure pond birth dates by looking at proportions of shared differences? You've got the pond spitting out creatures and undergoing chemical changes like its a machine programmed with your tree. Practically every sentence was a major transference of evolution. The new theory is NOT evolution. To wit:

1. "Codon differences should be proportional to the length of time that the different organisms have been separated" -- No!

2. "When the dog leaves it will inherit the pond-kangaroo differences..." -- No!

3. "...and start to accumulate differences of its own from both the pond and the kangaroo" -- No!

4. "When the human leaves, it too will inherit the pond-kangaroo differences and share these with the dog." -- No!

5. "The dog-kangaroo differences shared by the human will be proportional to the length of time from the kangaroo emergence to the dog emergence" -- No!

6. "The unshared differences will be proportional to the length of time >from the dog's emergence to now" -- No!

7. "Since Dr. Senapathy's theory posits a relatively short time frame for genetic separation of these species, the shared/unshared ratio should be very small" -- No, no, no!

Have you considered reading the book yourself? You are obviously interested enough in the new theory to actively participate in these discussions, and we all have been expending considerable time and energy on writing our posts -- I know what it takes. So, I would think you'd be willing to invest the time needed to really learn about the theory, if for no other reason than you would be able to more effectively argue against it.

Before you start in on me, I will admit that I'm still learning about evolution -- that's why I came to this forum in the first place -- and between you and the others I have picked up a lot. But, I'm not relying solely on this forum to teach me what I need to know so I can understand and evaluate evolution, and neither should you regarding Senapathy's theory.

From Keith Robison: Climb back on that chair! You are apparently assuming complete stasis in the pond, which is basically ridiculous. Changes will accumulate in the DNA due to replication errors and chemical mutagenesis. Errors will also accumulate over time during the propagation of a species. Such evolution (change over time but ignoring selection) is INEVITABLE. It is perfectly legitimate for Don to try to apply it to Senapathy's scenario of reuse (which is, of course, contradictory to Senapathy's claims regarding independent birth of genes).

From Don Cates: My point is that when the reuse level gets really high it is indistinguishable from "descent with modification" + "selection".

JM: Correct, but the mechanism is the issue: in pond, or out. At page 528: "We should note that we are not against the concept of molecular evolution in the primordial pond. We do not say that evolution did not occur at the level of the prebiotic organization. Instead, we say that all the molecular evolution happened prebiotically and not within organisms. We are opposed to the claim of Darwin and the evolutionists that all creatures originated from one or a few original creatures by organismal descent with modification. We are against the concept of organismal evolution of unique creatures, by whatever mechanism this is claimed to have happened."

From Warren Gallin: So the original quote, which you provide from the Senapathy book, describes the pools existing on the molten surface of the newly formed planet. Can you elaborate on how this is possible?

JM: The surface of the earth cooled very slowly over a long time. During that period, the ponds would have been able to form, and the changing conditions (temperature, atmosphere, chemicals, etc.) would provide a wide variety of conditions, some of which would be conducive to the formation of biochemicals, and ultimately life. There would have been tremendous opportunities through the large area (maybe the whole earth) and the long time for things to happen. Nobody, not me, not Senapathy, not Darwin, not you, can answer exactly how or when these things happened, but we can come up with plausible ideas. To expect Senapathy to detail everything is unfair -- you do not expect Darwin to do that (he didn't). However, Senapathy provides much detail, based on his own research over many years, for the most important parts of the theory -- the formation of genes from random DNA.

From Keith Robison: (quoting JM) In the evolution case, however, you are comparing a genetic pattern with the position a creature has on the "tree." However, those genetic differences were used to create the tree (or a derivative of those differences expressed as traits, no?), and hence they are correlated by default.

AAAAAAAAAAAARRRRRRRRRRRRRRRRRGGGGGGGGGGGGGGGHHHHHHHHHHHH!!!!!!!!!!

Jeff, will you PLEASE stop making this argument -- it is completely out of touch with reality, and several of us have pointed this out repeatedly. Yes, if there was 1 tree, then it would be valid. But we have many trees, from many unlinked genes. And, with minor exceptions, they are all the same, and when a fossil tree is available they correlate with that as well.

It is the fact that you see the same pattern over and over which is such strong evidence for common descent -- and one source of highly useful predictive power (i.e., you can roughly predict what an unknown gene will look like based on the same gene from other organisms and a tree of those species -- and plan your experiment accordingly).

From Warren Gallin: There was plenty of time for the prebiotic synthesis of biomolecules; there has been work on this for years. The problem, I repeat, is that no known, hypothesized or possible conditions could allow the spontaneous generation of a) kilogram quantities of extremely long chain DNA in high concentrations and b) intracellular concentrations of all of the proteins required to make a seed cell, repeatedly for several billion years. That is what the Senapathy theory requires, and that is why I say you are espousing a non-physical explanation for the origin of biological diversity, i.e. special creation.

From Dave Oldridge: (quoting JM) In the evolution case, however, you are comparing a genetic pattern with the position a creature has on the "tree." However, those genetic differences were used to create the tree (or a derivative of those differences expressed as traits, no?), and hence they are correlated by default.

Dave: No....this is wrong. The "tree" is created by a number of methods. Genetics is only one element (although a large one). Let's examine the consequences of Senapathy's hypothesis:

1. Genes are re-used, so they ought to show up all over the place.
2. The genes are not re-used with any PARTICULAR order or pattern, merely as they are found in situ in the pond.

Check out Morris Goodman's work on cytochrome-C back in '82.

"We should note that we are not against the concept of molecular evolution in the primordial pond. We do not say that evolution did not occur at the level of the prebiotic organization. Instead, we say that all the molecular evolution happened prebiotically and not within organisms.

And that is simply counter to present-day observations of living organisms and to the fossil record. I keep wondering who "we" are and why "we" are "against" evolution in the conventional sense.

If the primordial pond was primordial, then it was long gone when humans and (other) apes appeared on the scene. Or do these primordial ponds keep appearing from time to time?

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