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Punctuated Equilibria theories


bumab
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Punctuated equilibria was proposed as a distinct theory by Niles Eldredge and Stephen Jay Gould in 1972. It is a theory of evolution which states that changes such as speciation can occur relatively quickly, with long periods of little change equilibria in between. This theory is one of the proposed explanations of the evolutionary patterns of species as observed in the fossil record, particularly the relatively sudden appearance of new species in a geologically short time period. The other alternative is phyletic gradualism.

 

The problem I see is it explains the small jumps that are observed in fossil lineages within or between closely related fossil species, not the transitions between major categories of organisms. As such it is more an alternative view on the subject of variance within a specific species with little solid answer on where the different species evolved from themselves.

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....The problem I see is it explains the small jumps that are observed in fossil lineages within or between closely related fossil species, not the transitions between major categories of organisms. As such it is more an alternative view on the subject of variance within a specific species with little solid answer on where the different species evolved from themselves.
My take on PE is that is describes the problem but does not offer a solution. PE just characterized the fossil record as mostly inconsistent with Gradualism. I don't believe Gould and Eldredge ever proposed a technical solution to the problem.
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My take on PE is that is describes the problem but does not offer a solution. PE just characterized the fossil record as mostly inconsistent with Gradualism. I don't believe Gould and Eldredge ever proposed a technical solution to the problem.

 

No, they didn't. However, I can see aspects of their idea that makes a bit of sence also. I would also add that the idea of the original life having the basic code for everything is if memory serves me not new. PE is an alternative to gradualism that is considered within mainline evolutionary thought. There are also a few who subscribe to it out there.

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g'day Bio,

 

Where do you find the time? Thanks for your 101 thread, a good primer for many of us besides me I suspect. I shall read up when I get a chance. (sigh!). Would you mind defining the bio 101 or an even more exact definition of Mutation for me in the meantime? My Collins version does not explain the use you put it to, it's way too vague? What exactly is the process of the genetic change you are arguing for? Are you saying that the gene is precoded to respond to a new stimulus to rework its program to form a preconceived result? (Pardon my simplicity I'm just trying to get at the central thrust of your position).

 

If I've finally half caught on to your concerns I'm beginning to understand Buffy's response (actually my head's spinning a bit and it ain't the apple brandy last night! I didn't have any). Putting your bang aside for a moment (whew), the essence of your disagreement with mainstream gradualism would be it fails to address the issues involved with it's simplistic non descriptive assertions and its modelling appears to be at variance with the fossil record. Sigh, quite probable, judging on our past behaviour, more on that in another thread. cheers gub.

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...Would you mind defining the bio 101 or an even more exact definition of Mutation for me in the meantime?
Thanks for the note, Gub. Let me start with a reference to the Wikipedia definition of mutation: http://en.wikipedia.org/wiki/Mutation

 

This definition includes a reference to mutations that are "intentional". I think that is not commonly accepted as is definition of mutation, but I could be wrong. Mutations are generally regarded as random damage to existing genetic material that results in a change in the genome. Most mutations are bad, and result in termination of the cell.

 

In contrast, some dramatic genetic outcomes are not truly mutations, but merely the association of recessive alleles in normal sexual reproduction. Allele from wikipedia:http://en.wikipedia.org/wiki/Allele

 

Many of the anomalies that humans see when families mate are these sorts of anomalies.

 

I am hypothesizing a new category of genetic code. We have a reasonable understanding of genes, and their transcription into functonal proteins. My suggestion is that genetic material has a propensity for specific reconfigurations that create new functional genes. That is, DNA has information in it that is other than the primary codon sequence. It also has a "shadow" sequence that is a set of codons that are highly likely (compared to random mutation) to become functional genes after sequestration of a small number of individuals. Imagine a recessive allele that encourages direct DNA modification. That is, a recessive gene causes new swaps in DNA sequence that spawn other genes.

 

This is all conjecture. But it is time that we recognize that we have not proposed a solution to the experiemtal evidence that presents itself in the fossil record. The most likely scenario is that small populations do something different. We know that small populations are more likely to express recessive alleles. I am suggesting that some recessive alleles that tend to express after cataclysms alter their source genetic code. This alteration cannot be random, because it occurs too quickly. The tendency to alter, and the specific next step in the alteration is part of the genome of the parent.

 

Make sense?

...I'm beginning to understand Buffy's response (actually my head's spinning a bit and it ain't the apple brandy last night! I didn't have any).
Now would be a good time to start with the brandy. Remember I only brought this up because Buff goaded me into it. This is really all her fault.
...the essence of your disagreement with mainstream gradualism would be it fails to address the issues involved with it's simplistic non descriptive assertions and its modelling appears to be at variance with the fossil record. ..
You got it. I think Gradualism is fundamentally bunk.
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Thanks for the note, Gub. Let me start with a reference to the Wikipedia definition of mutation: http://en.wikipedia.org/wiki/Mutation

 

This definition includes a reference to mutations that are "intentional". I think that is not commonly accepted as is definition of mutation, but I could be wrong. Mutations are generally regarded as random damage to existing genetic material that results in a change in the genome. Most mutations are bad, and result in termination of the cell.

 

In contrast, some outcomes that dramatic are not truly mutations, but merely the association of recessive alleles in normal sexual reproduction. Allele from wikipedia:http://en.wikipedia.org/wiki/Allele

 

Many of the anomalies that humans see when families mate are these sorts of anomalies.

 

I am hypothesizing a new category of genetic code. We have a reasonable understanding of genes, and their transcription into functonal proteins. My suggestion is that genetic material has a propensity for specific reconfigurations that create new functional genes. That is, DNA has information in it that is other than the primary codon sequence. It also has a "shadow" sequence that is a set of codons that are highly likely (compared to random mutation) to become functional genes after sequestration of a small number of individuals. Imagine a recessive allele that encourages direct DNA modification. That is, a recessive gene causes new swaps in DNA sequence that spawn other genes.

 

This is all conjecture. But it is time that we recognize that we have not proposed a solution to the experiemtal evidence that presents itself in the fossil record. The most likely scenario is that small populations do something different. We know that small populations are more likely to express recessive alleles. I am suggesting that some recessive alleles that tend to express after cataclysms alter their source genetic code. This alteration cannot be random, because it occurs too quickly. The tendency to alter, and the specific next step in the alteration is part of the genome of the parent.

 

Make sense?Now would be a good time to start. Remember I only brought this up because Buff goaded me into it. This is really all her fault.You got it. I think Gradualism is fundamentally bunk.

 

The intentional deals with cellular control during the processes such as meiosis or hypermutation. Think of genetic engineering there. Normal mutations involve copying errors in the genetic material during cell division and by exposure to radiation, chemicals, or viruses. It might also be mentioned that not all mutations results in death of the cell. There are germline mutations, which can be passed on to progeny and somatic mutations, which often lead to the malfunction or death of a cell and can cause cancer. People often forget that there are two known types.

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Thank you for the opportunity BIO. I really like your idea that all life configurations are already somehow coded into genetics right from the start.

 

One other possibility is that the genome is somehow susceptible to a frequency of radiation or to a form of 'radiation' that we haven't become aware of yet. Terahertz lasers are a case in point.

 

I will accept the possibility that sometimes I tend to overdue patterns a little bit and try to connect too many dots, but might there not be a connection between James Putnam's suggestion that 'the information is in the photon' - and the genome? I keep coming back to the fact that life is 'aware' of something and that something is a stable configuration of photons.

 

Perhaps all structures in nature have some kind of radiational signature.

 

If that is true, then it might be true that the fundamental particle is a heck of a lot more complicated than we might think.

 

That’s it. I got nothing more.

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...I will accept the possibility that sometimes I tend to overdue patterns a little bit and try to connect too many dots, but might there not be a connection between James Putnam's suggestion that 'the information is in the photon' - and the genome? I keep coming back to the fact that life is 'aware' of something and that something is a stable configuration of photons....
I should mention that I have nothing against James Putnam's assertion of information loading all the way back to the Big Bang. It is just a long way form being supported by evidence.

 

The solution I am suggesting here is not intended to be that grandiose. I am just trying to take a list of things that we know are true, and draw the simplest line through them to get a hypothesis. This one is actually testable.

 

Buffy has contended that my solution is overly complex. I understand her point, but I disagree. I think that Gradualism has failed on its merits, and is no longer consistent with observed fact. We have consistently underestimated the complexity of biological systems, and overestimated the quantity of things that could happen by random chance.

 

I have offered nothing in my hypothesis to address the apparent complexity of the initial life form (whatever that was). Abiogenesis was always a probolem, and I have essentially made the problem worse with my hypothesis. But solving abiogenesis was not my intent. I was only trying to propose a credible solution to the Punctuated Equilibrium problem. I will bet anybody a beer that the same mechanism that underlies PE is the one that underlies the vast majority of other (non PE associated) speciation as well. And I think Gradualism ain't it.

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Goodness, I go away for a few days and end up pages behind! Well, I still don't have time to get through all I've missed, but I thought I'd clear up my proposal.

 

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.

 

My position is different from what you are proposing in a fundamental way. While you are proposing that all the possible changes are already encoded, and thus in place ahead of time, I made no such assertation. All my mechanism involved was a gene or genes that increased the rate and level of mutations given the right environmental stimuli (a catacylsm, for example). I still invoke random mutations as a key to explaining PE, but there needs to be a way to explain how those random mutations could come to a head to quickly and effectivly in certain time periods. I don't think my proposal is as radical as your, Bio, it's more an extension of current theory, rather then a new theory in and of itself.

 

Well, I'll be back tomorrow to read this thouroughly. Nice work so far, from what I've glanced at!

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I should mention that I have nothing against James Putnam's assertion of information loading all the way back to the Big Bang. It is just a long way from being supported by evidence.
BIO, I agree, if that matters.

I think the problem I am having is my own fault. You are talking about the way life forms become new life forms. I have been focused on the connection between the changes in awareness between the old form and the new and didn't realize it. (I guess that proves that a person can be unconscious and conscious simultaneously). I have a very heavy bias toward the awareness aspect of life being heavily involved in not only 'the reason for' but also the 'progression' of life.

My thinking is that if we want to understand the (change in) form, we need to understand the (change in) function. It seems that PE would agree with 'dire need' driving a change in awareness. Is it then possible that genetic changes can be triggered by the capacity of awareness? This would be an internal feedback mechanism driving genetic changes.

Do you know of any evidence to suggest that parents involved in certain types of work have offspring with similar 'non-standard' strengths/weaknesses?

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...While you are proposing that all the possible changes are already encoded, and thus in place ahead of time, I made no such assertation. All my mechanism involved was a gene or genes that increased the rate and level of mutations given the right environmental stimuli (a catacylsm, for example). I still invoke random mutations as a key to explaining PE.......
Ah, I understand- sort of a "slightly less random" solutions. Any ideas for a mechanism?
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I saw something on slashdot the other day about parents in traditional female roles, like teachers and nurses, tending to have more female kids.

 

The traditional view is nothing the parent does during life affects the offspring, since the genetic code really doesn't change between conception and reproduction. Evolution thus can't happen on an individual level, bu rather through generations.

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Ah, I understand- sort of a "slightly less random" solutions. Any ideas for a mechanism?

 

Not even slightly less random, just MORE. A mechanism would be a gene (or gene group) that could do a number of things: Simply increase the amount of mutations, or the severity of those mutations. Or a gene that even turns off the spell checking protiens (another way to allow for more mutations). Or something else.

 

In any case, a gene like that would most likely be selected for after a cataclysm because more niches are available for mutant offspring. Since more things will survive and fill out a niche (to the exclusion of others), most any mutation that still forms a viable entity would survive. After cataclysms, predators often suffer the most, so most offspring would survive in the long run (I'm proposing).

 

So it's a little less dramatic then your idea, Bio. Perhaps there's another mechanism to produce a majority of beneficial mutations, but I wouldn't even begin to guess where that ability would come from. DNA doesn't have that ability- it can't just say "Hey, that might work, let's try that" or anything. If there is a mechanism, however, so much the better. I was staying within reasonably traditional mechanisms, just proposing there's a mutation inducing gene which is active at certain times.

 

If it exists, it would be present in almost all organisms, since that gene would bottleneck into most populations following the disaster.

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Not even slightly less random, just MORE. A mechanism would be a gene (or gene group) that could do a number of things: Simply increase the amount of mutations, or the severity of those mutations. Or a gene that even turns off the spell checking protiens (another way to allow for more mutations). Or something else....
I understand. This is a really interesting idea. I am going to muse on this for a while.
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FYI-

 

I found a pretty interesting article here:

 

http://www.skeptic.com/01.3.prothero-punc-eq.html

 

that reviews the thinking on PE at it 20th anniversary in 1992. I think it is a pretty good review of the core issues, and includes some dicussion of the way that Gould and Eldredge later viewed their initial presentaion of PE.

 

The overriding conclusion of the piece is that allopatric speciation (the tendency of sequestered populations to speciate) has been corroborated well in the intervening 2 decades (1972-1992) and the gradualists have nearly ceded the field except in the asexual reproduction schemes of lower phyla.

 

I remain convinced that it is difficult to continue to maintain that gradualism by mutation is reasonable. Gradualism by other means (e.g., temporally frequent allolpatric speciation) is feasible, but gradualism by mutation looks poorly supported.

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I remain convinced that it is difficult to continue to maintain that gradualism by mutation is reasonable. Gradualism by other means (e.g., temporally frequent allolpatric speciation) is feasible, but gradualism by mutation looks poorly supported.

 

True, but the objections you raised earlier are still valid. This like lysozomic activity actively controlling foreign protiens, or the whole issue of getting protiens to work in concert in a short period of time, still beg an explanation. Also, most higher animals are built to withstand mutation in other ways- spellchecking, apostisis, etc. Why is it that at certain times, mutation rates suddenly increase on the individual level? Allopatric speciation explains how those mutations stick around (i.e. are not dilluted out of the gene pool), but not how those mutations come to be.

 

Perhaps individual mutation rates are that high normally, but I have my doubts about that.

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