Punctuated Equilibria theories

[TeleMad]

Biochemist: I got the refutation of the ribulose enzyme mutation from one of your links.

 

So when do you plan on posting this mysterious (and non-existent) refutation? All you've done is shown us MORE of your Creationist logic.

[TeleMad]

Biochemist: I do understand you have difficulty with biochemistry ...

 

You're funny.

 

Did you learn anything about phagocytosis yet?

 

Did you learn anything about autophagy yet?

 

Did you learn yet that proteins aren't transcribed?

 

Did you learn yet that ribosomes don't read DNA, but rather mRNA?

 

I usually get paid to tutor biology. Please send my your address so that I can send you a bill for services rendered. :-)

 

Biochemist: This is like taking the performance chip out of your BMW and throwing it away.

 

Only to a Creationist, like yourself.

 

The bacteria RETAINED a functional copy of the gene. So why are you THROWING AWAY the performance chip? Your analogy is not even close to being analogous, but then again, Creationists aren't known for their strong logic skills: as you are helping confirm.

[TeleMad]

TeleMad: No, it's not. It's recognized fact.

 

Biochemist: I, of course, can't help but note that you seem to think that reiterating unsubstantiated claims somehow improves their credibility.

 

More dishonesty on your part. My statement was made about a host cell's blindly synthesizing viral proteins from viral genetic material. Here you completely change the topic. Shame shame.

[TeleMad]

bumab: ... overall, however speciation is not the issue. PE deals with species producing new higher taxonomic levels.

 

Speciation is an issue. So are beneficial mutations. Have you not heard the bunk that Biochemist is spewing out?

 

He is using FLAWED Creationist logic as the basis for his arguments. The basics are an issue.

[TeleMad]

Biochemist: What is the next part to throw off of the BMW to improve it?

 

Keep using that valid analogy ... you're just making yourself look too ignorant to understand what actually happened.

 

1) The bacteria didn't lose anything: a functional copy of the original gene remained.

 

2) The bacteria gained something: a second copy of the gene that was then coopted to perform a different function.

[bumab]

Speciation is an issue. So are beneficial mutations. Have you not heard the bunk that Biochemist is spewing out?

 

Please don't quote me out of context for attacks on other members.

 

Speciation as different beak sizes, different dogs, whatever is not the issue. Nobody is saying new phyla can't arise without divine intervention either. Mechanisms to limit mutation (and thus limit speciation) which seem to disapear when needed are the issue.

 

Let's stop the character attacks. Your posts are extremely intellegent, why the virulence?

 

Obviously you think the traditional model (niche filling through gradulaist mechanisms) is valid. Great. PE operates on timescales that throw that in doubt, but don't neccessarily exclude it at all. That's the topic...

[C1ay]

You're funny.

 

Did you learn anything about phagocytosis yet?

 

Did you learn anything about autophagy yet?

 

Did you learn yet that proteins aren't transcribed?

 

Did you learn yet that ribosomes don't read DNA, but rather mRNA?

 

I usually get paid to tutor biology. Please send my your address so that I can send you a bill for services rendered. :-)

 

 

 

Only to a Creationist, like yourself.

 

The bacteria RETAINED a functional copy of the gene. So why are you THROWING AWAY the performance chip? Your analogy is not even close to being analogous, but then again, Creationists aren't known for their strong logic skills: as you are helping confirm.

 

Flaming != debate

 

See:

Also, we will not accept racist, sexist, hateful, or derogatory posts. Such posts may be deleted or edited without further notice. Violations of these ground rules might lead to banning without further notice.

[TeleMad]

bumab: Slowly changing genes will turn into novel genes given enough time. It's really the time-frame problem with PE: how do you get so many novel genes so fast? I'll bet there's a mechanism beyond randomness and natural selection.

 

Why? What evidence shows that mutations don't happen at a fast enough pace? Seem to me, to put it in simple terms, that we don't "see" most mutations under normal conditions because natural selection continually weeds them out. But consider fish that have moved permanently into the pitch black of caves: they rather quickly loose their functional eyes - it doesn't take anywhere near 10,000,000 years. Did the mutation rate on eyes shoot up? No, the selective pressures on eyes dropped! Why can't that general mechanism be at work? With reduced selective pressures, due to reduced competition, and a lot of new niches opened up for the species, more mutations are accepted than would otherwise be and the species' diversity increases much more rapidly than otherwise.

 

This is simplistic, but consider an analogy of evolution as being a march up a fitness hill, and consider the hill to be fixed (the fitness terrain does not remodel itself). Mutations, left unchecked, would drag the species down the hill to the bottom. In general, natural selection tends to stabilize the genetics of a population by weeding out the deleterious mutations so that the species can remain where it is. But then beneficial mutations occassionally occur and the species moves a notch up the hill (of course, natural selection has a hand in this too, by tending to retain such beneficial mutations). That helps visual how evolutionary progress occurs in general. But once a species is up on a hill, it can no longer navigate to other hills: that would require moving down the hill they are currently on. But if selective pressures are reduced, genetic diversity increases greatly in the species and it becomes "smeared out" along the hill's gradient; some members of the species are farther down the hill, and some may be down far enough that they can access another hill. When competition starts increasing again, one fraction of the species can be moving up the original hill and another fraction can be moving up a different hill.

[TeleMad]

C1ay: Flaming != debate

 

Neither is saying many things known to be wrong, like a "biochemist", who shall remain nameless, asserting that:

 

1) lysosomes use phagocytosis to take in materials

2) autophagy is a form of phagocytosis

3) ribosomes read DNA

4) proteins are transcribed

5) no beneficial mutations occur

6) a host cell doesn't 'blindly' synthesize viral proteins from viral genetic material

7) there is no evidence that a species ever arose by mutation.

8) the genetic information needed to code for arms, hands, and finger; neurons and brain; hearts, arteries, and veins; kidneys and ureters; cardiac, smooth, and skeletal muscles; wings, echolocation, and so on, was all somehow magically contained in the first prokaryote, and then somehow magically protected from mutations for 3 billion years while it sat there unused

 

Pretty ridiculous statements for a "biochemist" to make: most every one of those deals with simple BIO101 stuff - things any first year biology student should know to be wrong.

 

 

 

And stubbornly refusing to admit an error and instead trying to push blame off onto others - claiming they are ignorant, when in fact they are correct - is not debate either. And this is what the "biochemist", who shall remain nameless, did.

 

1) I provided tons of material from multiple biology texts that showed he was wrong about phagocytosis. Should have ended there. But nope. He continued to claim - ignoring the mounds of valid evidence that contradicted him - that he was right and I didn't know what I was talking about.

 

2) I explained that autophagy is not a form of phagocytosis, and that even the material he presented indicated this. But again, he continued to claim that he was right and I was ignorant.

 

5) I showed him a beneficial mutation - actually, several - and yet he continued to pretend they don't exist, and then plays ridiculous "BMW" games that aren't at all analogous to what happened in the experiments. He continued to claim that the beneficial mutations didn't exist, and that they were actually damage, and that because I believe they were beneficial I'm ignorant.

 

6) I made a straightforward statement that host cells 'blindly' synthesize viral proteins from viral genetic material, and he said I was wrong. I replied that it is well accepted fact that shouldn't be questioned. He responded by quoting me out of context, changing the topic to try make it look like I said something I didn't.

 

7) I showed multiple times that we have at least one excellent example of a new species arising by mutation: did he accept that? No. He continued to make his now-refuted claim.

 

8) I pointed out that his front-loaded prokaryote hypothesis is religion masquerading as science. No one here can show otherwise - he can't use science to support his position: science REFUTES it.

 

And then this anti-scientific, error prone "biochemist", who shall remain nameless, has the balls to claim I don't know biochemistry? It wasn't me who said that ribosomes read DNA, it wasn't me who said proteins are transcribed, it wasn't me who said that autophagy is a form of phagocytosis, it wasn't me who said that lysosomes take in materials via phagocytosis, it wasn't me who said that there are no beneficial mutations, it wasn't me who said that we have no evidence that any species ever arose by mutation, it wasn't me who proposed a hypothesis that biology strictly forbids. His derogatory statement about me was an unfounded attack and quite childish.

 

What this "biochemist", who shall remain nameless, did is not debate.

[C1ay]

Neither is saying many things known to be wrong, like a "biochemist", who shall remain nameless...

 

What this "biochemist", who shall remain nameless, did is not debate.

I don't care if all of his posts are dead wrong. Being wrong is not against the rules, continuously attacking the messenger is. For someone that usually comes off as a smart individual you seem to have trouble understanding the rules. Do you really find them that complicated?

[bumab]

Did the mutation rate on eyes shoot up? No, the selective pressures on eyes dropped! Why can't that general mechanism be at work? With reduced selective pressures, due to reduced competition, and a lot of new niches opened up for the species, more mutations are accepted than would otherwise be and the species' diversity increases much more rapidly than otherwise.

 

Again, this is simply a deterioration of a gene. It's a new mutation, sure. It's possibly beneficial, sure. It does not provide a barrier to breeding, however- the behavior of living in a cave does that. Regardless, it's not a new gene, it's simply a case where damaging mutations are accepted because eyes are no longer necessary.

 

Those CAN arise quickly in the traditional model. Integrated genes, which complementary protiens in complicated sequences arising in a novel fashion- say the evolution of lungs, perhaps- would be FAR harder to achieve on a short timescale. The cave fish example shows how quickly mutations can change a single gene. It doesn't create a new gene, however, just a modified version of the old one.

 

Gradually, it will become a new gene. The gradualist sequence from horse like animal to whale is pretty amazing. But that was on a longer timescale then we're talking about (also not involving a catacylsm, if that does indeed play a part), so it doesn't really apply.

 

We're not tearing down the tradional genetic model here, just adding on...

[Biochemist]

Did y'all se the new research article that Tormod just posted? It suggest dramatic pericentromeric gene shuffling in chromosome 2 (human) about 10-20 million years ago.

 

Pretty interesting.

[paultrr]

Did y'all se the new research article that Tormod just posted? It suggest dramatic pericentromeric gene shuffling in chromosome 2 (human) about 10-20 million years ago.

 

Pretty interesting.

 

Yes, it rather gives strong support to Punctuated Equilibria as far as theory goes. However, I also notice a lack of reasoning at the present to account for what the sudden bursts and gaps.

[bumab]

Yes, it rather gives strong support to Punctuated Equilibria as far as theory goes. However, I also notice a lack of reasoning at the present to account for what the sudden bursts and gaps.

 

In which case it's not much further along then we are. It's more just a nail in the coffin for traditional gradualism as the only way to speciate... always gets more complicated. :shrug:

[paultrr]

In which case it's not much further along then we are. It's more just a nail in the coffin for traditional gradualism as the only way to speciate... always gets more complicated. :rant:

 

Gradualism works for some aspects. But it is not the whole picture when it comes to evolution. I think there has been amounting a chain of evidence for a while now that something akin to PE is working when it comes to the evolution of life on this planet.

 

Again, however, I think the key is time and place which begs the question if perhaps the real source of these sudden bursts is not more a combination of events and conditions that generally we have never been able to duplicate in the lab. I keep coming back to a line from a certain movie about Life finding a way. Perhaps the key is that biological lifeforms can sence their environment and adapt to it. When we try lab experiments it is possible that life does not find a way because it may at some level sence that these conditions we try to impose are artificial in the first place. There is also the time span of such experiments. Let's face it even shorter periods of a few million years for change is something we cannot duplicate in our labs at present.

 

For all the posturing on both sides it is true that not only are most mutations at times fatal and that some mutational changes are not fatal. These two facts have always been a point of contention on both sides. Yet, what is missed is that both remain true. Another words they are a fact of life as we know it and somehow life finds a way to deal with both to its advantage.

 

No one to date has supplied a full answer to how PE works in the first place. Some major suggestions are out there. However, I think these suggestions are only part of the picture. I might suggest for anyone who has not seen the responces on the news relase to check something I mentioned out in my last responce there. Its been mentioned by other researches that climate was changing some 1.7 million years ago in the African region. I also brought up that a natural radioactive reactor existed in Africa around that same time period. That period was another one of those periods that fits under the PE model. With the climate changes came plant life changes in the local region. Again a lot of natural factors where involved that could all combine together to bring about that PE period in earth's history.

 

The point is that we having living organisms in a region undergoing real natural environmental changes and we have these rapid mutative changes taking place. Something keys those changes that we cannot seem to duplicate in our labs exactly. I might suggest that it would be a very odd God who at his whim decides things need to change. I'm am reminded of Einstein's words about God playing dice here. So I think what is need is more research on a natural explination for such rapid changes. The reason I mention this is at least the ID supporters here want their ideas examined by fellow scientists. One way to get them heard is to show the natural cause and effect path in the same general way us naturalists do so. One can have a belief set in one's mind that somehow a Creator was behind all this and still be able to show how all of this was done naturally. Science wants scientific answers, not magic invocation.

 

So my suggestion to the ID camp is avoid the magic, so to speak, and present the evidence. My suggestion to others is forget that a lot of these guys believe in some Creator and you do not. Try to see if there is something in their idea worth exploring a bit. We learn the most in science when we question the bounds of what we already know. Every major advancement in Science came when one person or more began to question what they already thought they knew(Newton, Einstein, etc).

[TeleMad]

TeleMad: First, what logic indicates that a reduction in selective pressure - which we know would be associated with a reduction in competition - could not allow for changes that would normally not be maintained in population, followed by one or more of these additional differences leading to change that would not have otherwise occurred? I know of none. That's logic: I could probably find some info in my texts about reduction in selective pressures (I believe there's some in relatino to the founder effect/founder-flush process) ...

 

Yep, and here it is...

 

”Second and most important, selection is relaxed during a population flush, because resources are in excess. If descendants of the founder can invade a new niche, they expand their numbers in a flush. Carson proposed that normally, some blocks of genes on chromosomes are tightly linked or “closed” to recombination because of some selective advantage conferred by this configuration. New genotypes produced by recombination within those closed areas have reduced fitness. In fact, the advantage conferred by balanced polymorphisms for inversion heterozygotes may derive from the protection of such closed gene complexes.

 

During the flush period, genotypes produced by recombination in closed regions of the genome may survive because selection is relaxed at such times. These new genotypic combinations may be incompatible with the normal closed system of the species, but they survive because there is reduced competition for resources. After a crash, the survivor’s reshuffled genome is acted upon by selection to produce a new combination of open and closed gene groups adapted to the environment. These periodic genomic reorganizations may affect the timing and/or order of gene expression, bringing about developmental changes that accelerate the pace of evolution.” (Concepts of Genetics: Fifth Edition, Klug & Cummings, Prentice Hall, 1997, p686)

[TeleMad]

TeleMad: Did the mutation rate on eyes shoot up? No, the selective pressures on eyes dropped! Why can't that general mechanism be at work? With reduced selective pressures, due to reduced competition, and a lot of new niches opened up for the species, more mutations are accepted than would otherwise be and the species' diversity increases much more rapidly than otherwise.

 

bumab: Again, this is simply a deterioration of a gene. It's a new mutation, sure. It's possibly beneficial, sure. It does not provide a barrier to breeding, however- the behavior of living in a cave does that. Regardless, it's not a new gene, it's simply a case where damaging mutations are accepted because eyes are no longer necessary.

 

YOU MISSED THE WHOLE POINT!

 

Some people here are looking for a new, mysterious way that the RAW MUTATION RATE INCREASES sharply, and I am saying that's not needed: another way to increase the rate of evolution by increasing the genetic variation of a species is to have SELECTIVE PRESSURES REDUCED. Either way, the number of mutations accepted into the genome increases, but the second way is quite logical and straightforward, and requires no mysterious new process.

 

PS: See my last post, where I posted a quote from my genetics text about the founder-flush theory.