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Punctuated Equilibria theories


bumab
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...I use a broader definition of ID, which refers to any theory in which "intelligence" is pre-existing with no explainable mechanism for its existence.
This is interesting. By your definition, all of empirical experience is included in ID, since we have not established initial casuality for anything. I am not sure your definition is useful but feel free to use it. Just keep in mind that I am going to label you an ID proponent in any post where do do not establish initial causality. That would be all of your posts, I think. This will make the ID folks happy, because it means that folks like Lindagarette and Freethinker are ID proponents.
...and there are a number of theories from the dissatisfying anthropic to the more intreguing but still naturalistic multiverse theories that explain them rather easily.
Explains what easily? First cause? These theories say nothing about initial causality. They just kick the problem back further in history. That is all I did too.
..What you are describing here is a computer program that is far more complex than anything yet written by man
Intrigueing. I don't believe you meant to say this. The trivial parts of DNA behavior that we understand currently are already orders of magnitude more complex than any program written by man. Surely you don't think otherwise. DNA code is:

1) extraordinarily tight, in that a very small body of code handles a massive amount of processing

2) extraordinarily flexible, in that the number of services delivered and conditions covered is unbelieveably large

3) extraordinarily reslilient, even to the point of being self healing

4) extraordinarily well integrated, in that a common storage and processing architecture is used for all main programs and subroutines,

5) extraordinarily simple, in that all processes are founded on permutations of 4 machine-level instructions, with the "higher" level language being only 20 instructions.

6) Even the subroutines are tight, averaging 200-600 "lines" of code (i.e., residues in a typical protein)

 

Do keep in mind that the description above would apply to any single life form. The very same processing architecture applies to all life forms, which raises the sophistication of the architecture up several orders of magnitude further. Comparing the sophistication of DNA to anything done by man is laughable. Are you going to compare DNA coding to SAP? Powerpoint? The PacBell billing system? Those are pinpoints in complexity compared to the DNA architecture in the simplest bacterium.

 

My main point is that DNA in any one species is so complex already that assembling the coding for all species into a single life form does not really increase the complexity very much. What are there? A billion species? This would probably not raise complexity by 10^9, given the processing overlap.

...that just *appeared*...
Everything just "appeared". So what?
... is there *any* naturalistic process at all that could even be imagined that would cause that big bang to happen...
There is not a "naturalistic" process for the genesis (no pun intended) of either big bang.
...I guess it would be a good explanation of PE, but It also seems, um, awfully overcomplicated:
Maybe, but 1) every time we learn more about the fundamentals of DNA it gets orders-of-magnitude more complex, 2) there really is no other explanation for PE. It is ludicrous (probabilisitically) to assume that rapid "mutatations" happen under cataclysmic stress, unless there is some intrinsic propensity for life forms to act that way. I just bit the bullet and described the intrinsic propensity. The notion that the majority of biological coding existed at the first life form is a byproduct of trying to explain the empirical data.
...it kinda fails Occam's Razor....
That would be true if we had a simpler explanation that was consistent with observed facts. I don't think we do. I think this is the simplest explanation.
...The really hard to explain explosions are all proving to be post-major-cataclysm (gotta love those asteroids!), but that just provides lots of environmental pressure and lots of niches to fill.
Again, the triumph of hope over experience. This does not provide a mechanism for the adaptation post cataclysm. This is a data point, not a mechanism. By all "rules" of natural selection, cataclysms should eradicate species, not generate new phyla. By any measure, a cataclysm should decrease the number of individuals available for mutation. A cataclysm provides more niche space, but less genetic capacity to respond to the niche space. That is the essence of the problem that is not reasonably addressed by the mutation model.
...I don't see is why your extremist "gotta all be preprogrammed" is *necessary* to explain PE....
All of this is to provide a mechanism to explain PE adaptive speed. The notion of genetic loading at a Biological Big Bang is an unnecessary extrapolation, but a logical one.
An explanation based on mutations accumulating, being tested, selected re-expressed, etc, provides the same end result without demanding that no additional information was added along the way.
Except that this mechanism is at odds with the well structured tendency for cells to repair their own mutations, reject foreign proteins, and adapt rapidly. This model fails logically. You could argue it is simpler, but is is at odds with experimental evidence. Newton was pretty close (and simpler), but not corrrect: data overturned Newtonian mechanics. The data is overturning mutative adaptation.
... even Darwin pointed out that its not that one species turns into another, but that the new species splits *off* and both can exist, possibly separately or even together.
Sorry, but Darwin's opinion is hardly relevant. He was before the discovery of DNA, and your point is not related anyway. Nothing in my model requires species to go extinct or precludes branching. I just suggested a mechanism for rapid speciation. We don't use Newton's views to critique Feynman. Feynman had a lot more data than Newton had.
And as Bumab points out, single gene changes can result in major changes.
Again, this supports my case. If a single gene change produces a massive morphological change, it shows exactly how complex a single gene change is.
...Just because there are mechanisms that reverse out mutations...does *not* mean that *all* mutations are reversed out. ...
Buff- I don't know why you are stuck on this. I never said all mutations are revered out- you keep repeating that. I said that mutations have almost nothing to do with speciation. The accumulation of serial positive mutations concurrent with the (obligatory) destruction of serial nonfunctional mutations is so unlikely as to be untenable. No one has ever done the math on this to make it remotely feasible. There are a number of simplistic computer models (like the one that TeleMad referenced about eye development) that are easily refuted since they ignore major obstacles and complexities. Even though Gould did not say it, I think that Gradualism, as a mechanism for speciation, is not supported any any data set: Paleontological or biochemical.
...trying to prove that certain meta-genes in lower forms map exactly onto expanded genes in higher form ...
This is probably not true. The lower genes are probably swap-permutations of higher genes. This would be similar to attempting to show that if you twist a Rubik's cube 50 times, you can show the connection to the 50-generation-earlier parent configuration. Except we are turning thousands/millions of Rubik's cubes concurrently (to make the analogy the correct order of magnitude), and the cubes are about a micron across. This is a tall order....
...simply find gene sequences in all their various forms for say, eyes, and if there are simple variations that cannot be shown to exist in other places, you may have proof of an included mutation. All you'd need is one to invalidate your theory.
This is not rational, Buff. There might be a gene (or a gene shred) that carries through multiple species generation. This is consistent with the BBB hypothesis. It certainly does not refute it. But most base sequences probably did NOT preexist, but the Rubik's cube swapping that generates new genes is PART OF THE CODE, not an accident. The problematic issue for Gradualism is the speed of production of new, fully functional genes. And there are millions (literally) of these. If a higher function gene shred was maintained in earlier life forms where there was no selective reason for the previous life form to maintain the shred, it would support BBB, not Gradualism. And if a new functional gene shows up quickly via a rubik's-cube-like swapping mechanism, it supports BBB, not Gradualism.

 

There is almost no data to support Gradualism. And there is a mass of data to obviate it.

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This is interesting. By your definition, all of empirical experience is included in ID, since we have not established initial casuality for anything.
No, you just conveniently turned what I said on its head, silly! You dyslexic? I said "intelligence" which you just ignored... As you skipped over, I say there are naturalistic explanations for the universe's parameters. The rest of us think intelligence and DNA evolved. You're saying here that they did not!

...and there are a number of theories from the dissatisfying anthropic to the more intreguing but still naturalistic multiverse theories that explain them rather easily.

Explains what easily? First cause? These theories say nothing about initial causality. They just kick the problem back further in history. That is all I did too.

Again, "huh?" Explains the handful of initial parameters G, c, e, h, etc. hit go button. You're insisting that "explainable mechanism" is the same as causality, and while thats a neat rhetorical device, its disingenuous. I'm not asking at all for causality, I'm asking for a mechanism that could create it, and that's a *very* different thing. You are trying to hide a very big elephant behind the curtain, and its showing!
Intrigueing. I don't believe you meant to say this. The trivial parts of DNA behavior that we understand currently are already orders of magnitude more complex than any program written by man.
Dyslexia: read it over again: I *am* saying that DNA is more complex than any computer program...
Do keep in mind that the description above would apply to any single life form. The very same processing architecture applies to all life forms, which raises the sophistication of the architecture up several orders of magnitude further....My main point is that DNA in any one species is so complex already that assembling the coding for all species into a single life form does not really increase the complexity very much.
So what? Yeah, DNA is pretty incredible. Alot of those basic mechanisms evolved over 3 BILLION years and we've got no record of them cuz like bananas, they have no bones. But I still say you're 1) incredibly trivializing the differences we do see in both the dna and the morphology of still existing species with no justification other than repeating "theres no proof of gradualism". That statement is nice, some of us agree with it partially, but it sure doesn't look like dna is a completely static thing that has not changed in 4 billion years. That's a real stretch...
...I guess it would be a good explanation of PE, but It also seems, um, awfully overcomplicated
Maybe, but 1) every time we learn more about the fundamentals of DNA it gets orders-of-magnitude more complex, 2) there really is no other explanation for PE. It is ludicrous (probabilisitically) to assume that rapid "mutatations" happen under cataclysmic stress, unless there is some intrinsic propensity for life forms to act that way.
You've really not been reading my posts then. I am NOT saying that "a whole bunch of mutations happen instantly under stress". I'm saying that pre-existing mutations *express* themselves under stress, which is almost *exactly* the same mechanism you're describing, except in my case, I'm saying that the these parts of the DNA came from accumulated mutations where you're insisting that all of them were in the first prokaryote.

 

Let me repeat this, because you're obviously ignoring it and I hate being misquoted:

 

I am NOT saying that "a whole bunch of mutations happen instantly under stress". I'm saying that pre-existing mutations *express* themselves under stress, which is almost *exactly* the same mechanism you're describing, except in my case, I'm saying that the these parts of the DNA came from accumulated mutations where you're insisting that all of them were in the first prokaryote.

 

Secondly, yes, DNA is pretty amazing. You know what though? The programming properties you listed end up being the *simple* parts! We've got lots of research on self replication and repair, but most of it is done in hardware, and the software folks are too lazy to incorporate it (I know, I've had to fire a lot of them!)! I'm in awe of DNA's complexity, but the properties you've described are a useful base to start everything else that's happened since. There's still no excuse in my book to put anything other than self-replication, input-driven modification, and self-repair in the first prokaryotes and hit the go button. Why does that prokaryote need to have instructions for a human brain, let alone what we may become? Moreover, according to your model, we just need to turn a few bits of the sequences on and we'll turn into a dinosaur or back into a prokaryote, right?

Newton was pretty close (and simpler), but not corrrect: data overturned Newtonian mechanics. The data is overturning mutative adaptation.
No, Newton was *modified*. Newton did not propose a cause, he did propose a mechanism that mass has an intrinsic quality of attraction which obeys the equations he provided describing the mechanism. Einstein modified it by describing another layer in which the conveyance of the mechanism was descibed as warping of spacetime. I know you want to portray Gradualism and PE as mutually exclusive, but as others have posted, thats really not necessary at all, unless you really do believe that "mutation has absolutely no effect and is always cancelled out" and I don't see anything in the literature that agrees with that point of view.
Again, this supports my case. If a single gene change produces a massive morphological change, it shows exactly how complex a single gene change is.
Well, it also argues against your position as well, because if a mutation does occur in a single gene, then it can produce a large morphological change. Again, you have done nothing to show that *all* such changes are eliminated and return to the "original prokaryote programming."
Buff- I don't know why you are stuck on this. I never said all mutations are revered out- you keep repeating that. I said that mutations have almost nothing to do with speciation. The accumulation of serial positive mutations concurrent with the (obligatory) destruction of serial nonfunctional mutations is so unlikely as to be untenable.
This makes no sense at all. I grant you said earlier that you agree mutations occur. You also have said they have no effect on speciation. You also say that they can be reversed, which we both agree on. But if they are *are not* reversed out, how can you argue with a straight face that over time they continue to have *no effect* on permanent morphological changes?

 

I guess even if I grant you that one, the whole concept that no matter how many mutations there are, the system always reverts to the "original prokaryote programming" indicates that the mechanism predicted every possible environmental pressure as well as the programming necessary to decide how to do it, since you have also indicated you don't believe selection has anything to do with it either. Like I say, a pretty amazing program you're describing.

There are a number of simplistic computer models (like the one that TeleMad referenced about eye development) that are easily refuted since they ignore major obstacles and complexities.
That's an opinion, and it is based on the view that there can be no effect from accumulated mutations, so the rest of us are free to disagree on this point.
Even though Gould did not say it, I think that Gradualism, as a mechanism for speciation, is not supported any any data set: Paleontological or biochemical.
I think its very significant that he did *not* say that. In fact everything that I read by him indicates that the notion of Gradualism that he disagreed with was indeed directly related to rates of change and mechanisms for accumulation and expression of mutations. If you've got some quote from him somewhere that indicates he believed in your concept that mutation has no effect at all, I'd love to see it.
... the Rubik's cube swapping that generates new genes is PART OF THE CODE, not an accident. The problematic issue for Gradualism is the speed of production of new, fully functional genes.
Again, if you keep refering to Gradualism as "the instantaneous mutation of genes resulting in immediate morphological changes showing constant gradual change in morphology over time," which is quite frankly the same as the rest of us, you can't turn around and say that anything that involves a mutation process is Gradualism, therefore it must be false. This is completely illogical. None of us here are defending the traditional, strict definition of Gradualism, we're describing mechanisms that include mutation model that like I say, has an expression mechanism that's not too different from yours. The only thing that's really puzzling is your abhorence of mutation in any form. Its fine to say that the pure Gradualist view is not proven, we agree with that, but to say that because of that, any mechanism associated with Gradualism needs to be discarded makes no sense whatsoever.

 

Cheers,

Buffy

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No, you just conveniently turned what I said on its head, silly! You dyslexic? I said "intelligence" which you just ignored...
It seems this discussion is now completely wrapped around the axel on at least 4 separate topics. I will need to recompose a straight thesis again when I get an hour.
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Oy!

 

A plethora of confusion.

 

The positions (correct me if I'm wrong):

 

Bio: Mutation cannot explain morphological changes because DNA itself is programed to resist mutations. Thus, mutations cannot provide any viable changes in the species, since they are inherently selected against by the DNA itself. Therefore, the information for those changes must already be present, like an insider, or a spy, and only gets expressed when some stress comes along.

 

Buff: Mutations accumulate gradually, according to the traditional model, and are only expressed when an environmental stress allows those mutations to be expressed in beneficial ways. Traditional PE.

 

Me: A mutation causing gene, or some structure that causes rapid mutation, could be activated after an environmental stress, thus providing for the rapid speciation we see after an extinction event. This would be selected for because any organism with it would pass it along quite successfully, even though the offspring would be very divergent. It's a selfish gene argument.

 

I think only Buffy is standing on established ground, but I share Bio's adversion towards acceptance, based on the difficulty of randomly aquiring successful, useful, and viable protiens that wouldn't be attacked like all other new protiens AHEAD OF TIME. The mutations required to create the vast morphological changes would have to, according to gradualism and traditional PE, be already present (built up) in the introns and other non-coding regions of the DNA. This would require them to already be functional, which is a stretch.

 

Neither gradulaism nor PE has a satisfactory explanation for the fossil record, as I see it. The jumps around the mass extinction events are simply too rapid for gradualism to explain, and PE has no real mechanism.

 

Bio solves this conundrum by saying it's all pre-programmed, everything was set up already in the beginning. It really is pushing the problem back further in time, but it's also turning that problem into a 200 pound gorilla.

 

I solve the problem by saying there could be a yet undiscovered mechanism (most likely genetic) that creates mutations INTENTIONALLY after an environmental stress of a magnitude to open up many niches. This would solve the problem by creating rapid change in genetic structure, but, not mutagen gene has been discovered. Heck, I doubt people are looking. Perhaps something to do with cancer...

 

Buffy says there is no real problem.

 

Sufficient summary?

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Man Bumab, you're good! I'd say that I agree with how you've summarized my position. I guess I have more "faith" in what can happen over time. I really think the junk dna has an important role in building up new steps, and while there's proven mechanisms for undoing bad mutations, I've done enough neural network coding (aka "viral coding" for you kiddies), to know that time does have a huge impact: the "mutation police" have rules, but unless they pass *some* of the mutations through, the system (in my experience, the neural net) has to tolerate some changes. So what you see is the cop going "nope, nope, nope, nope, nope, okay, nope, nope, nope, nope, nope, nope, nope, nope, nope, nope, nope, nope, okay..." etc. so you get enough time, and you've got some useful stuff sitting there in the middle of an already useful gene that is currently "off". Then you go through a stress, it gets turned on, if it helps the organism survive the stress, the newly activated gene survives. Note also the lather-rinse-repeat notion going on here: that gene could get turned on, prove to be deleterious as is, but its still sitting there in the original species turned off, it gets mutated again, turned on again and this time it works, so the if-at-first-you-don't-succeed rule of learning works quite effectively, because the branching ensures that both the orignal configuration (off) AND the new configuration (turned on) survive to "test" the proposed mutated gene.

 

Okay, I'm no biologist, I'm an amateur, but I have made things like this work with silicon and code, and to me its amazing how *well* they work even with hardly any time spent "learning"...seeing it happen can be very convincing, so forgive me for thinking this model is "obvious."

 

Cheers,

Buffy

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This is a great summary, Bumab, particularly because you got Buff to agree with your digestion of her position. Let me add a couple of comments:

Bio: Mutation cannot explain morphological changes because DNA itself is programed to resist mutations. Thus, mutations cannot provide any viable changes in the species, since they are inherently selected against by the DNA itself. Therefore, the information for those changes must already be present, like an insider, or a spy, and only gets expressed when some stress comes along.
I actually have no problem with mutation driving morphological change occasionally. I just suspect that it never launched a new phylum. Further, the main problem (actually, the only problem) I was trying to address is the mechanism for PE. My suggestion is that the only credible mechanism for a rapid transition (e.g., a couple of hundred thousand years) to a new phylum is for the parent species to have a codified transition to the daughter species. The corollary to this notion (which need not be accepted) is that if all daugher species are codified by their parent species, then all species came from one parent. This is not neccessary to accept to understand the proposed PE mechanism. It is just a logical corollary.
Buff: Mutations accumulate gradually, according to the traditional model, and are only expressed when an environmental stress allows those mutations to be expressed in beneficial ways. Traditional PE.
And my contention is that this does nothing to address PE. There is (almost) nothing in the Gradualism model that suggests an acceleration of acceptance of mutation after cataclysms. The increase in newly noncompetitive niches should be more than offset by the aggregate loss of genetic source material to mutate. I do not think this is a viable PE mechanism.
Me: A mutation causing gene, or some structure that causes rapid mutation, could be activated after an environmental stress, thus providing for the rapid speciation we see after an extinction event. This would be selected for because any organism with it would pass it along quite successfully, even though the offspring would be very divergent. It's a selfish gene argument.
Bumab- I think your position and mine are not differentiable. If a gene causes a "mutation", it is not a mutation. It is a predefined genetic expression. I am suggesting (as you are, I think) that there is more to the genetic code than the primary codon sequence. I am suggesting that the likely alterations to the code (which I described above as "rubik's cube swapping" ) are part of the code as well. Otherwise, the incidence of material, viable mutation in higher life forms would be nearly zero. Since they do exist and not just occur, but recur with some regularity, they are not accidents. They are part of the "code". The "code", in this context is not just the extant codon sequence. It includes the likely new sequences that will occur after the likely code swaps.
I think only Buffy is standing on established ground,
Yes, it looks like she can't take the heat of heresy.
... but I share Bio's adversion towards acceptance, based on the difficulty of randomly aquiring successful, useful, and viable protiens that wouldn't be attacked like all other new protiens AHEAD OF TIME. ...Neither gradulaism nor PE has a satisfactory explanation for the fossil record, as I see it.
Agreed. Although I don't think that Gould attempted to identify a mechanism when he identified the PE issue. He just named the problem.
Bio solves this conundrum by saying it's all pre-programmed, everything was set up already in the beginning. It really is pushing the problem back further in time, but it's also turning that problem into a 200 pound gorilla.
True. But that problem is not (currently) out of synch with observed data. Gradualism is out of synch with observed data.
I solve the problem by saying there could be a yet undiscovered mechanism (most likely genetic) that creates mutations INTENTIONALLY after an environmental stress of a magnitude to open up many niches. This would solve the problem by creating rapid change in genetic structure...
Bumab- If you just delete the notion of "mutation" from your text you have exactly my solution. You ALSO have the problem that the INTENTIONAL changes exist in all parent species, and hence roll back to the source of all parent species. You have the 200 pound gorilla too.

 

One more note: Buff- You mentioned that the mutations "had" to roll back to get back onto the coded "'track". That would not really be necessary. Any successful, beneficial mutation would then exist as a species until it "mutated" again, existed in stasis, or died out. It would not affect the "coded" evolutionary track which would exist in parallel.

 

I just suspect it never happened this way.

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I'll be dipped. If this is what I think it is, it seems in line with what I've always thought: Creationism and gradual evolutionism are both wrong. Creationism ignores ancient evidence and gradual evolutionism plays dice with very long odds and doesn't account for many new species in a short period of time. Evolution happens in spurts.

 

Correct me if I'm wrong (like you won't?), but are you saying that some event comes along and reshuffles the genetic deck to the next stable configuration? The implication being that the next series of stable configurations are a 'higher' form of life? Any idea what the form of stress happens to be? Is it a blast of radiation or just starvation?

 

Also, this would not contradict what James Putnam has been saying.

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G'day folks,

 

I just lost my entire post bar the last few words, yet again! You'd think even an old geezer would become proficient in the end! Oh well, Too bad.

 

Buffy I'm afraid you'll have to put up with me on your side. I can't help emphasising the critical importance of your appreciation of the length of time and number of generations involved when considering evolution. When talking of species we're dealing genetically with god knows how many powers of magnitude of readings of the four letter code. Your neat little - cop going nope, nope,... - example passes Ockham's for me. By the way anyone know any solid, recent update on PE especially in reference to that so called fossil record.

 

Bio and bumab, I'm a bit bemused with your difficulty re viable mutations. Are you saying new species equals new proteins? I've been led to believe this isn't at all essential, just variations in the usage of protains etc. will ensure vast change. Bio, would you care to estimate the order of magnitude of the readings of our genetic code that makes up our lives, elsewhere I've already owned up to my arithmetical failings. It is this reading of our codes that helps us to self-repair as you have noted but this ability enables adaptation as well as species statis surely?

 

Perhaps it pertinent at this point to restress the role of natural selection or, if you prefer, the environment in ordering speciation. I view current species as current viable possibilities, we are all potentialities responding, interacting with the world other than us. Stable environment, stable species, varying conditions diferentiation within species etc. The range of variation within species can be considerable, surely ideally placed to try out any new niche that may open? The proponents of gradualism I respect never claim some form of smooth, steady pace of incremental change.

 

Bio, re. your theory and my simple question in my last post. I'm bemused that you're not happy with the second prokaryote as our ancestor. After all doesn't 3 odd billion years of how many generations of single celled existence create the opportunity for the incredible genetic complexity that took multu-cellular life with such gusto? cheers gub.

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...are you saying that some event comes along and reshuffles the genetic deck to the next stable configuration? The implication being that the next series of stable configurations are a 'higher' form of life? Any idea what the form of stress happens to be? Is it a blast of radiation or just starvation?...
Rather than just offering conjecture, I would like to stick with what we know. We know, for example, that any sequestered family will tend to incur a higher likelihood of anomalies. This is at least partially due to matching recessive alleles in the children (this is why siblings and cousins can't marry). But there could be other mechanisms as well. Hence, we may not know all of the mechanisms for the sudden morphological change after a family is sequestered, but we see it in most species, including humans.

 

Ergo, we have a known effect of dramatic, viable morphological change in sequestered families. Cataclysm would cause a large number of sequestered familes in many species concurrently. That is my suggestion, based on the observations that we have, for the main mechanism of speciation. And this has almost nothing to do with serial mutation.

 

Notably, this mecahnism does not require a cataclysm. A cataclysm just tends to raise the likelihood. This model matches the fossil record.

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Hey, I empathize with your loss of posts, Gub. I have lost several myself.

....Are you saying new species equals new proteins? I've been led to believe this isn't at all essential, just variations in the usage of protains etc. will ensure vast change. Bio, would you care to estimate the order of magnitude of the readings of our genetic code that makes up our lives, elsewhere I've already owned up to my arithmetical failings. It is this reading of our codes that helps us to self-repair as you have noted but this ability enables adaptation as well as species statis surely?
Let me start by saying that we understand a relatively small portion of intracellular biochemistry. Like most sciences, the new things that we learn in biological sciences always raise more questions than they answer. This is dissimilar to physics, where leading physicists will actually openly discuss having a "theory of everything" and some will contend that string theory (even though still open to evaluation) is that theory.

 

There is no such position in biochemistry. Every additional material discovery surfaces other issues that bump up intracellular complexity by another order of magnitude. With that preamble, let me bore you with 12 steps of biochem 101 for a second, and then pull out some of the anomalies.

 

 

 

 

  1. DNA is a sequence of four nucleotides (guanine, cytosine, adenine, thymine)
  2. Three nucleotides in a sequence form a codon. Each of the 64 possible codons "codes" for one of 20 amino acids.
  3. There are an infinite number of amino acids possible in chemistry. Only 20 are used in living systems- pretty much the same 20 irrespective of the life system. Amino acid anomalies are extremely rare.
  4. DNA only codes for proteins and RNA. Proteins are the little machines to do things. RNA pretty much only helps to "transcribe" the DNA to make the proteins. Everything that is done in the cell is either done by a protein, or done by something built by a protein.
  5. DNA is hence a little machine that builds machines (ribosomes) that build machines (proteins) that build machines (everything else). Since DNA builds itself, you could add at least one more generation on this sequence.
  6. A typical protein is about 300-400 amino acids. They range from probably about 50 to over 10,000, but 300 is a good average. The set of codons that code for a protein is a gene. Ergo, a typical gene has 300x3 DNA bases in it, or about a thousand.
  7. Most proteins are highly specific. In most proteins (that have been tested) most individual amino acid residues cannot be changed at all or the protein stops functioning. Most proteins have exactly one substrate, exactly one output, and several speed modulators that control the rate at which the protein functions. Proteins that are acting in this fashion are called enzymes. This is differentiated from proteins that are part of our mechanical structure.
  8. Proteins are manufactured in a single-thread long string, but this 300 amino acid residue string "folds up" into a ball. It has to be in exactly one ball shape. Most proteins (all?) could fold up into different ball shapes which would be dysfunctional. They usually don't because other proteins ("chaperone proteins" ) manage the fold-up of the new protein to keep it the correct shape. Some diseases are thought to be errors in fold-up (e.g.,Alzheimers, cystic fibrosis) more about that issue at:http://www.faseb.org/opar/protfold/protein.html
  9. Human DNA is about 3.6 billion nucleotide bases, but there are thought to be only 30,000-40,000 functional genes. Even if there were 100,000 functional genes, that would account for 100 million bases. The other 3.5 billion are just standing by. That is, the ratio of stand-by DNA to functional DNA is probably higher than 40:1. More on that here:http://www.biology.eku.edu/FARRAR/gen-prot.htm
  10. Most proteins do not act alone. They act in a defined sequence of actions. Glycolysis, the Krebs cycle, the urea cycle, beta oxidation of fats: All of these are multi enzyme processes where the output of one enzyme is the input to the next. I will use the Krebs cycle as an 8-enzyme example (just because it it so famous). Picture here:http://www.bmb.leeds.ac.uk/illingworth/metabol/krebs.htm
  11. Most proteins systems need to be physically associated with each other to function. Hence, there are specific transport systems that transport proteins to their work site within the cell. These transport systems need to recognize the protein and "know" its appropriate location.
  12. Enzymes occasionally break, or need to fluctuate in quantity. When they do, the DNA is triggered to produce more of the enzyme. A typical human chromosome is about 78 million bases, and is folded at least ten times (into at least a thousand parallel threads of DNA). The DNA is triggered to "unfurl" just a small portion of base pairs, "unzip", and let the ribosomes zip along it the make a new protein. The new protein is then chaperoned into a ball, transported into location, and usually inserted into a specific location in the target machinery.

Now the math:

 

Granted, the math I will present is related mostly to the human genome. Frankly, at the level of detail we are talking about, it would apply pretty well to bacteria as well. Bacteria don't have genomes quite so big, and have substantially less non-coding DNA (maybe 10% versus human 98%) but the numbers are still impressive.

 

 

  1. To get a functional protein by mutation: you would need at least 200 specific amino acids in specific sequence out of 300 in the protein (it is actually more like 260 on average, but I am making it simpler). This would be randomly 1 in 20^200, or about 1 in 10^260. Heck. To be conservative, let's make it a couple of trillion trillion trillion trillion times more likely, and make it 1 in 10^200.
  2. Proteins do not work alone, so figuring 5 enzymes in a sequence (being conservative, typical is 6 to 8), this give us 1in 10^1000.
  3. Keep in mind that there are thousands of separate interdependent enzyme systems and structural construction systems. I am not including the calculations for other logically required systems. Any additional required system would be a multiplier (yes, that would be 1 in 10^1,000,000). Sheesh.
  4. I have no idea how to calculate the odds of a chaperone protein, since we would have to know the odds of a specific protein folding incorrectly without one. Let's give this one a pass.
  5. I have no idea how to calculate the odds of recognition in the protein transport systems. We would have to know the requirment for transport, versus the degree of activity if the enzyme system was floating freely. Heck. Let's give this a pass too.
  6. I have no idea how to calcualte the feedback loop for production of additional protein from DNA, but this one probably dwarfs all of the previous numbers. Remember that we have to expose the specific thread of DNA to let the ribosomes zip along it. The DNA unfurls on signal, and this means that one single loop of perhaps 1000-2000 codons out of maybe 70-80 million bases in a chromosome is exposed. I didn't mention that related enzymes are often associated in adjacent genes (called an "operon") and are transcribed as a set, rather than as a single enzyme. I already accidentally gave us a pass for the probability of 5 or 6 adjacent genes of 1000 codons being arranged together on a string of 80 million bases (about 25 million codons). But the real problem is that ANY mutation to the chromosome would tend to mess up this complex unfurling arrangement. So we have to allow for not just the 1 in 10^1000 problem of a mutation to create the enzyme system, but we have to make sure any of the series of mutations to establish the enzyme system does not mess up the feedback unfurling of several thousand OTHER genes on the same chromosome. No guess for the odds here.
  7. We have not yet discussed the "lysosome problem". Cells are remarkably efficient scavengers, in that they destroy useless junk routinely. This means that the lysosomes (or other scavenger pathways in lower lifeforms) recognize foreign from non-foreign chemicals. This means that a new random protein would likely get scavenged. If it didn't, the cell would be swamped in non-functional proteins. I can't find any information on the efficiency of the cell scavenger process, but certainly a minority of proteins in the cell is non-functional. Otherwise, an organism would spend most of its energy (and food consumption) on production of non-functional material. Clearly not the case. Even if we assume that every 1 in 10^6 mutations was functional (a ludicrously positive assumption) we have to assume that lysosomes destroy the vast majority of these. The lysosome has to recognize these as non-foreign to let them remain. For each enzyme in the sequence. This would be mandatory, or the house of cards falls apart.
  8. I brought up bacteria above, and that they have perhaps 10% non-functional DNA. Using them as examples of prokaryotes, it sure is odd that these archaic, simplistic systems are so efficient. Is it odd that the progenitors are so genomically efficient and yet the sophisticated, higher systems are not? If we have systems to reverse mutations in DNA (we do) and to eradicate foreign proteins (we do), why don't we have systems to eradicate nonfuncitonal DNA? My suggestion is that we probably do. I suggest this "non-coding" DNA is not nonfunctional. It is required.

Too long an answer to your question. But anyone who wants to advocate improved morphology by mutation has to get the 1 in 10^1000 number (not to mention the 1 in 10^1,000,000 number) down to something like 1 in 10^6 to 1 in 10^8 to make it have any chance of playing a role in speciation. As a biochemist, I have no idea how do do that intelligently.

Perhaps it pertinent at this point to restress the role of natural selection or, if you prefer, the environment in ordering speciation. I view current species as current viable possibilities, we are all potentialities responding, interacting with the world other than us. Stable environment, stable species, varying conditions diferentiation within species etc.
Agreed. All we are talking about is "How?"
Bio, re. your theory and my simple question in my last post. I'm bemused that you're not happy with the second prokaryote as our ancestor. ...
I actually have no problem with the second prokaryote. I just picked the older one to give us more time. I have no fact basis to pick one over the other.
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Thanks BIO, Bumab, Buffy et al (hmmm, lots of Bs there) - Nice thread guys. And I can understand Buffy's idea of mutations lying dormant until a stress situation appears. Really excellent work. Damn.

 

The effect of all of this is that my model is collapsing (I've been wrong - well, sort of right for the wrong reasons, but still wrong!). What a hatefull thing to have to admit. I have to assess the damage.

 

@#$&!

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Just read your 101 post BIO and I want to thank you for the synopsis. Quite interesting.

 

Is there any chance that we aren't dealing with a random set of events in the actions where the pieces combine to make new configurations? Specifically, is there any evidence to suggest that something like another property, so far undetected, is stacking the deck? Something akin to feedback by an organisms surroundings which presents the nature of those surroundings as a sort of 'guide'?

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...Bio, re. your theory and my simple question in my last post. I'm bemused that you're not happy with the second prokaryote as our ancestor. After all doesn't 3 odd billion years of how many generations of single celled existence create the opportunity for the incredible genetic complexity that took multu-cellular life with such gusto?
One more point on the math in this. 4 billion years is only 10^14 generations assuming an average generation is 20 minutes (using an E coli as our average generation time) which I suspect is being gracious. I am not sure how to estimate how many serial mutations are necessary to get from our abiogenic prokaryote to humans, but it is at least one for each of our 40,000 genes. I suggest 100,000 mutations is pretty conservative (I think a million to 100 million is more likely). At 100,000 mutations, we would have to have a positive, retained mutation every billionth generation. Most arguments to explain retention suggest that the systems are incrementally valuable, This would significantly increase the number of positive mutations required to establish a "selectable" mutative path. If it took 100 interim viable steps for each human gene, that would be about 10 million positive mutations, or 1 positive, retained mutations in 10 million generations (still assuming a generation is 20 minutes).

 

And that assumes even, gradual mutation, which it at odds with the fossil record. I think the arithmetic here is untenable.

 

We do get demonstrable morphology changes in E coli (under stress) in about a thousand generations. This is the link that Buff posted from Scientific American that showed a sudden 30% increase in cell size. But this is reproducible, so my contention is that this is not a mutation. It is codified in the E. Coli genome.

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Is there any chance that we aren't dealing with a random set of events in the actions where the pieces combine to make new configurations?
The core of my hypothesis is that none of this is random. All speciation events (well,the vast majority) are specified in the code of the parent species. That way, you can get significant morphological change in as little as one generation.
... is there any evidence to suggest that something like another property, so far undetected, is stacking the deck?...
We have already bought up several in this thread. Empirically, the fact that speciation tends to bunch around cataclysms argues against gradualism. Further, we have many examples of known, recurring morphological anomalies that occur in a single generation. I have argued that if they recur, they are not mutations. They are likely outcomes, based on the code of the parent. Examples like trisomy 13 (Downs syndrome) , or the cases where insects or amphibians get extra legs in a single generation are examples of likely, recurring anomalies that are codified in the parental species DNA.
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...doesn't 3 odd billion years of how many generations of single celled existence create the opportunity for the incredible genetic complexity that took multu-cellular life with such gusto?.
OK, last one on this.

 

The first mammals are thought to be the small shrews that arrived at the beginning of the Triassic period. This is about 250 million years ago. Most of these species will probably have generations that are more like a year, hence 250 million generations. They also have far smaller "litters" than lower life forms. If we assume (generously) 10 viable mutations in series for each functional human gene to get from the Triassic shrew, that would be 250,000,000 generations /(40,000 genesx10 serial mutations) = one successfully updated gene every 625 generations. This means that we now have to get retention of genes every 10^3 generation in the species that are most likely to reject foreign substances. It would also imply a new hominid (genetically) about every 10,000 years, assuming 15 year generations. That would be a bunch of differnet hominids.

 

Hmmmm.

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Sorry BIO, I don't mean to appear dense (and perhaps can't help that), but I was not referring to the parent genes. Is it possible that outside environmental factors are directly manipulating reorganization through some property we cannot, as yet, detect? Or, are you saying that something in the makeup of the parent genes is receptive to large change?

 

Perhaps both? That would seem to imply a direct influence between environment and genetic makeup. That would also seem to imply a sort of awareness of environment at the genetic level.

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Sorry BIO, I don't mean to appear dense (and perhaps can't help that), but I was not referring to the parent genes. Is it possible that outside environmental factors are directly manipulating reorganization through some property we cannot, as yet, detect? Or, are you saying that something in the makeup of the parent genes is receptive to large change?
I have been thinking the former, but I am open to anything. The core of my argument is that the biochemical infrastructure of a cell is so incredibly complicated, that putting all of the information in all of life into one cell does not really change the aggregate complexity all that much. Ergo, the first viable cell could have coded for all species.

 

If you would like to posit an external influence that could do what you are suggesting, I am all ears. OK, eyes.

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