Punctuated Equilibria theories

[Biochemist]

Originally Posted by TeleMad

.. what right do you have to ask someone else to demonstrate a new body plan, when your replacement "theory" has the genetic information..poofing into existence all at once in the first prokaryote?

This issue has been dealt with previously in this thread. I was trying to formulate a credible hyposthesis to address the issues described in the fossil record, and usually characterised as "punctuated equilibrium". I was not trying to address abiogenesis.

1. There is absolutely no evidence for rapid mutation-based speciation, or for that matter, ANY speciation based on mutation
2. There is apparently a sudden arrival of new body plans in the fossil record
3. The fossil record is characterized by long periods of stasis.
4. We have demonstrated many biochemical mechanisms to extend and modify existing genes, and all of them have a high degree of specificity. There is no evidence that they are mutative. They could as likely be part of the genetic program.

My conclusion (based on extant fact) is that the notion of rapid speciation based on complex mutation strains credulity. Further, there is also absolutely no empirical evidence supporting it.

If you elect to reject a hypothesis based on the empirical evidence because you dissapprove of the implications, that is not science. It is faith. You have articulated this faith-based position previously, and you are welcome to hold it. I have no issue with faith based positions.

FYI, I don't think anyone has offered a reasonable explanation for abiogenesis anyway.

[TeleMad]

Originally Posted by Biochemist

Don't change the subject.

I didn't change the subject. I replied to what I was asked about. I discussed same kind of thing you yourself discusseed in this thread.

[TeleMad]

Originally Posted by Biochemist

There is absolutely no evidence for rapid mutation-based speciation, or for that matter, ANY speciation based on mutation

False. I already provided an example: a new species arising in nature and the transition being duplicated in the lab, in just 4 generations.

Biochemist:There is apparently a sudden arrival of new body plans in the fossil record

I may have missed it, but didn't see you give an exact definition of term "body plan". Got one?

Biochemist: The fossil record is characterized by long periods of stasis.

And we know that not all evolutionary changes get preserved in the fossil record. For example, industrial melanism and changes in beak morphology in Darwin's finches.

Biochemist: We have demonstrated many biochemical mechanisms to extend and modify existing genes, and all of them have a high degree of specificity. There is no evidence that they are mutative. They could as likely be part of the genetic program.

Sorry, but that statement sounds kind of like double-talk to me. Are you denying that mutations can modify existing genes?

Biochemist: My conclusion (based on extant fact) is that the notion of rapid speciation based on complex mutation strains credulity. Further, there is also absolutely no empirical evidence supporting it.

By COMPLEX mutation? Why COMPLEX? We have examples of rapid speciation based on mutation: there's the one example I gave, and any others that probably exist but I am not personally aware of.

Biochemist: If you elect to reject a hypothesis based on the empirical evidence because you dissapprove of the implications, that is not science. It is faith.

False. You're trying to substitute a miracle for science. I reject that.

Biochemist: You have articulated this faith-based position previously, and you are welcome to hold it. I have no issue with faith based positions.

And now you try some good old equivocation. I've seen you play your childish tricks on others in this thread.

It is your anti-science, religious position that is based on faith: a completely different kind of "faith" than one has in science.

[paultrr]

I might not get to see the answer for another month or two since I will be traveling some, but, you're replacement theory as someone else has termed it seems to still be evolution of sorts with the difference being all the primary genetric coding was already there in the first cells. So my question would be, and forgive me if this has already been given, just how and where did those first primitive cells with all that genetic code come from?

I ask this question because I believe this is where most scientists would begin to take major exception on. I am assuming in the back of my mind that when it comes to explaining the origin of those first cells you revert to claiming a devine act. Forgetting for a moment that a majority of us scientists tend to see no evidence of a devine being of any sort it still seems to me that in the end run the only thing this alternative theory manages to do is shift the big question of where did it all come from back beyond the historical record period. The rest of the way up it isn't that much different from evolutionary theory at all. That rather returns the problem with the theory back to what most of us see it as anyway. That being an evolutionary version of special devine creation. It also if one discounts the "God" equation suffers from the same problem creationists tend to claim we have of explaining how non-living became living.

[paultrr]

Standard evolution has life evolving from simplier forms to higher forms. The type of model you propose has life evolving from something complex enough to contain all the genetic code for everything into simplier forms where there is a specific genetic code in each organism. Now, even assuming for the moment that somehow the bridge between non-living and living was accomplished by some Creator or God the general gist of say the Bible is that man is the highest form of life on this planet while the general gist of you're approach would be that man is a specialized off-spring of something far more complex genetically. At least standard theistic evolution kept the pattern of higher forms from simplier forms as does normal evolutionary teaching in general.

As far as the preserved historical record goes when it comes to genetic evidence the two latter are more in line than you're own proposal. Genetic analyses published in New Scientist have revealed that nearly 75% of human genes have some counterpart in nematodes-millimeter-long soil-dwelling worms. Roy Britten, a biologist at the California Institute of Technology, said in a study that is published that a new way of comparing the genes shows that the human and chimp genetic similarity is about 95 percent. Generally, by genetic evidence, while both lines have a common ancestor we are far closer genetic wise to chimps than to nematodes and the complexity of the genetic material between both species is vastly different. Nematodes in general predate our line and the lack of complexity tends to argue against you're own theory.

So even if one wants to propose some theory in which one finds a progression simular to evolutionary theory based upon an initial special creation event one is still forced to accept the general idea of life evolving from the simplier to the more complex. At that point the only difference is one theory assumes life had to evolve from the non-living to the living and one theory assumes some special agent was involved in that process. The problem from a scientific perspective again boils down to showing evidence in the first place that such an agent exists from out of the natural evidence itself. Here most creationists and other religious perspectives simply lack the evidence that demands a verdict. Without that evidence one is simply presenting evolutionary theory admixtured with a faith based assumption of an outside agency. Up to the faith assumption one has science. Beyond that point one has a belief system being presented as science. At the least it's simply an alternative theory of evolution which is fine to a point. However, it raises the question of why bother to argue with the evolutionists in the first place since one would have 99% in common teaching with the remainder 1% stemming from faith which more properly belongs a subject of home and Church teaching.

Telemad is correct that you are substituting faith based ideas into the mix. Some of those faith based ideas simply do not pan out via genetic research itself when you look at the genetic differences as far back as we can study them. It's that lack of solid evidence more than the "creator" invocation that get's the argument going in the first place. Most general older theistic evolutionists had far less arguements out of the scientific community in general than the intelligent design camp has today. The reason is they stuck with the scientific evidence and simply offered a special agent or creator as a solution on how non-living matter became living. The only part one encountered an argument on was showing proof for that special agent in the first place. However, in fairness, given the lack of solid evidence in the record for that crossover period from non-living to living they could also argue that we had little evidence ourselves.

My suggestion is that the ID camp stick to tried and true science if they want recognized. They are welcome to hold the belief that the bridge between point was somehow accomplished by devine intervention or agency. I might suggest that perhaps they ought to experimentally try simular paths to those evolutionists have attempted to explain that bridge point in perhaps a way to amass evidence that some outside agency had to be involved. A lack of a positive result in many carryed out experiments is evidence in itself. To my knowledge evolutionists only attempted experiments to bridge such a gap between living and non-living over a very short period of time. A wider range experiment trying different conditions would be in order to more properly address that area.

[Biochemist]

Originally Posted by paultrr

I might not get to see the answer for another month or two since I will be traveling some, but, you're replacement theory as someone else has termed it seems to still be evolution of sorts with the difference being all the primary genetric coding was already there in the first cells. So my question would be, and forgive me if this has already been given, just how and where did those first primitive cells with all that genetic code come from?...

Paultrr-

1) Any discussion of speciation is evolution, irrespective of mechanism.
2) I was not trying to address any issues related to abiogenesis. I was trying to view empirical evidence and posit a mechanism to address the rapid speciation as represented in the fossil record. My hypothesis was that most speciation is likely to be driven by programmed code changes in the parent species, not some sort of random mutation. Although mutations certainly exist, the evidence for mutation driving speciation in animals is essnetially absent.
3) If parent species genes code for for daughter species genes, the implication is there that all "parent" code rolls back to a "super parent" in the first prokaryote. Maybe. But my only point was that mutation based speciation is inconsistent with the fossil record. I think it is time that we consider other mechanisms that are consistent with our current knowledge of intracellular biochemistry and are more closely aligned with the fossil record.
4) Nothing about this argument was driven by theism. It is only based on empirical observations. There are probably dozens of specifics that could be tested. It is true that some of the anti-theists on this site see a risk of God at every turn, and react adversely to the risk of support for theism. That is just bias, not science. I am just to looking logically at the extant data and suggesting a slight change in perspective. I am sure that Zohaar will suggest this is even better aligned with his interventionist view.

[Biochemist]

Originally Posted by TeleMad

You complaining because you feel science can’t explain a walk up a relatively smooth incline to reach the top of a mountain, whereas your replacement involves a single leap from base to summit!! Only Superman, or gee, maybe God, could make that leap your replacement requires.

I said nothing of the sort. You are obfuscating.

What I suggested was that existing theory is inconsistent with empirical evidence. The evidence for mutation-based speciation is absent, and the fossil record is characterized by extended periods of stasis puncuated by sudden arrival of new body plans in animals. There is nothing new in this.

I just suggested that we recognize that in the 30+ years since Gould and Eldredge published their seminal articles on puncuated equilibirium, we have learned a lot more about biochemistry. There is now a substantial body of knowledge that suggests that many mechanisms that alter genes might not be mutative, even though we ofter assume that they are (in the absense of evidence).

If you want to draw a consousion about abiogenesis from this, have at it. Goodness, you could even start your own thread on it. God. Extraterrestrials. Meteorite dust. Primordial lightening. I was making no assertions about abiogenesis. I was using extant data to posit a mechanism for PE.

[paultrr]

Originally Posted by Biochemist

Paultrr-

1) Any discussion of speciation is evolution, irrespective of mechanism.
2) I was not trying to address any issues related to abiogenesis. I was trying to view empirical evidence and posit a mechanism to address the rapid speciation as represented in the fossil record. My hypothesis was that most speciation is likely to be driven by programmed code changes in the parent species, not some sort of random mutation. Although mutations certainly exist, the evidence for mutation driving speciation in animals is essnetially absent.
3) If parent species genes code for for daughter species genes, the implication is there that all "parent" code rolls back to a "super parent" in the first prokaryote. Maybe. But my only point was that mutation based speciation is inconsistent with the fossil record. I think it is time that we consider other mechanisms that are consistent with our current knowledge of intracellular biochemistry and are more closely aligned with the fossil record.
4) Nothing about this argument was driven by theism. It is only based on empirical observations. There are probably dozens of specifics that could be tested. It is true that some of the anti-theists on this site see a risk of God at every turn, and react adversely to the risk of support for theism. That is just bias, not science. I am just to looking logically at the extant data and suggesting a slight change in perspective. I am sure that Zohaar will suggest this is even better aligned with his interventionist view.

My general problem is one has to propose a mechanism by which evolution or change and development of different species takes place. Given that most of the ID camp makes the faith based assumption that God or a creator is behind it all(why I assumed the other), and yet, proposes that the path followed is evolutionary based then exactly what mechanisms do you think we should invoke as a possible solution? I might add that there are some modern examples of mutation producing what we could define as a species difference where interbreading is no longer possible. I mentioned simular in another post here though I've forgotten the exact link. Generally these cases would be simular to say chimps and humans where they all share a common ancestory and still are in the same general line. So I would suggest that while perhaps mutations do not provide an answer for everything and there may well be other aspects involved that one must come up with at the very least historical evidence and modern case examples of exactly the replacement mechanism or mechanisms one's theory would put forth.

If anything I take more exception with the idea often put forward that perhaps the early life had the coding for everything already there given that nothing in the record of genetic evidence lends support to that.

[bumab]

While I don't buy the precoded genetic hypothesis either, it's fair to notice the ID and relgious aspects of the conversation were not brought in by Bio.

As you said, Paul, there are places where mutation doesn't seem to work. Precoding is a valid alternative. It has it's problems, which we were discussing rather well before this tanget (not brought on by you, of course). I would like to see this thread get back on topic, personally.

New protiens (produced by mutation or not) must survive the intercellular machinery that guards against foreign protiens and invaders. How, and how could that machinery have evolved (or not) concurrently with the life it facilitated? Could a break down in that machinery have produced the fossil record of morphological growth spurts we observe?

[Biochemist]

Originally Posted by paultrr

My general problem is one has to propose a mechanism by which evolution or change and development of different species takes place. ..If anything I take more exception with the idea often put forward that perhaps the early life had the coding for everything already there given that nothing in the record of genetic evidence lends support to that.

Underlining Bumab's point, none of the original interlocutors on this thread brought up God until someone did after post 150 or so.

The issue on the table is purely evidenciary. It has nothing to do with theism, or ID.

1) The fossil record does not support a gradual, mutative pattern. Phyla (and, in fact, Orders) spring up suddenly
2) No one can demonstrate that mutations are beneficial
3) No evidence for mutation-driven speciation exists at all
4) We have many documented mechanisms for genetic change that are all highly specific (in terms of sites of alteration of the genome)

Ergo, my hypothesis is that the genetic code of the daughter species is carried (mainly) in the genetic code of the parent species. We do not know what the trigger is (during cataclysmic events) that excites the parent genome to spawn a daughter species. But we do know mechanisms that increase the quantity of genetic material, and several mechanisms that alter it in tightly defined ways (discussed above).