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eeyonkee
Trad climber
Golden, CO
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Oct 25, 2006 - 11:38am PT
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Raymond. I guess I didn't quite get what you meant with One thing that is clear from this thread is that no expert on evolution participate in the discussion. It makes it on some what the same level as mountain mans global warming threads. The opinion of someone with no knoweledge on the subject is not very interesting. Many people here know much more than MM but the idea is the same.. It's my opinion that this thread has some very interesting things to say.
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Aya
Uncategorizable climber
New York
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Oct 25, 2006 - 11:54am PT
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I don't think you're understanding, Blight.
The ability to code the protein was NOT there. It did not "always do it", except in the trivial sense that once a mutation caused it to be read differently, it did. A mutation occurred that allowed the protein to be encoded.
I found this website. In addition to explaining far better than I ever could about how a frameshift mutation indeed creates new information (rather than just somehow "unlocking" pre-existing information), it has much more in depth information about the nylon digesting bacteria than I provided, including multiple links to if not full papers, then at least their abstracts (you could get the full papers at most libraries as they will have access to jstor, etc.). Hopefully they will explain it in a way such that you understand how a frameshift mutation indeed creates new genetic material.
Where did I say that if you didn't agree with me, you were wrong? What I'm saying is that you're demonstrating that you don't understand certain processes that are fundamental to the theory, and that based on those misunderstandings, you're dismissing the theory.
Again, please answer my questions, if only to demonstrate how much you do understand.
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graniteclimber
Trad climber
Nowhere
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Oct 25, 2006 - 11:56am PT
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"Now the problem facing us is to demonstrate that such changes are plausible in the time frames suggested by the data. Doing this is the really and truly interesting science. And it is the one key test of the theory. It is one thing to speculate that species A evolved from species B based on the same number of chromosomes but different DNA sequences. It is another thing entirely to propose a mechanism that allows for the change in the required amount of time allowing for the stochastic processes involved. In other words, there needs to be an explanation for the development of a new genetic sequence (mutations, and other mechanisms) that is biologically and chemically supportable and physically probable enough to occur in the time required."
TradisGood, You were seeking rigor yesterday. Can you articulate the hypothesis you are testing and what kind of proof you are seeking.
The mechanism is pretty well understood. Of course, since this is science, there is always room for improvement and future discoveries. Obviously, you're not going to be able to prove timing in in a laboratory experiment, nor by direct observation (unless you invent a time machine).
Your best hope is to look at the "molecular clock" hypothesis. This is based on the assumption (not completely provable) that mutations happen at a constant rate. But it does appear to correlate with the fossil record.
So again, what type of proof are you looking for?
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raymond phule
climber
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Oct 25, 2006 - 11:58am PT
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I agree that some stuff is interesting and I am curious about same stuff myself.
But I have a feeling that people like Blight and TIG wants to prove the truthness of evolution. The people on the forum have not enough knowledge to decide this...
I dont think that blight's claim that it doesn't exist proof is more important than MM's claim that global warming is a hoax.
Why are the forum so incredibly slow today?
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eeyonkee
Trad climber
Golden, CO
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Oct 25, 2006 - 12:04pm PT
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I would contend that if the world's best expert on evolution participated on this thread, he/she still could not prove its truthfulness - not to a layman anyway.
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TradIsGood
Fun-loving climber
the Gunks end of the country
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Oct 25, 2006 - 12:08pm PT
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Aya, I read the book about 3 years ago. I should not presume to be able to summarize it for you, since it is certainly not my field.
OK, I will try, placing far too much trust in my aging memory. I believe the gist of it is:
 Darwin did not identify a mechanism for the origination of a new species, but rather described that the environment can impose "preferences" for a phenotype which will be exhibited over time.
That existing explanations for the creation of new genetic sequences that would explain the evolution of the species were inadequate because there probabilities were not high enough to occur in the time frames that they needed to. That is, random mutations from radiation, breaks, resequencing, etc. and possibly some other mechanisms (?) were insufficient.
To fill in the gap, she and her colleagues were seeking new mechanisms which included changes resulting from symbiotic relationships, e.g. fungus in guts of termites that were able to "digest" cellulose on behalf of the host.
I am thinking that the role of viruses and their ability to act on proteins played a part (if it was not here, I do not know where I got that idea, because I sure do not read widely in this field :-) )
And to the Dawkins fan... I still think that he is being cute, not that there is not something to be learned from the approach. The organism is an expression of the genes, but only the most primitive life forms have only natural behavior (definition of primitive). The more advanced have a nurtural and community component that is not dependent solely on genes. This was alluded to as well by the poster discussing life that had the intelligence to alter its own environment. Having it, and actually expressing it seem a stretch for a pure nature position on selection -
see also the breeding argument - the gene has "control" entirely dependent on its "fitness" in the context of the desires of the "breeders".
80(?) My prediction is looking pretty good, so far.
Can we agree that it is hard to agree on what the theory is, so that it is nearly impossible to test it? :-)
Can we agree that there is still work being done in the field because it is not so firmly established as Newtons's law, quantum mechanics, and general relativity? :-)
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Aya
Uncategorizable climber
New York
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Oct 25, 2006 - 12:16pm PT
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Uhm, nobody can prove the "truthfulness" of evolution (although, I'm pretty sure that "evolution" isn't a liar).
Either way, it's a theory. You can't prove it. You can only support it. Such is science.
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graniteclimber
Trad climber
Nowhere
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Oct 25, 2006 - 12:25pm PT
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Blight implores us, "Please don't waste any more time on me."
This is perhaps the most intelligent thing that Blight has said in this thread and a suggestion well worth taking.
As you can see, I entered this thread defending Blight--not his position, but requesting that we just answer his questions and refrain from impugning him personally.
However, after seeing his behavior on past threads on evolution and religion, I have lost respect for him and believe that he is just a troll whose main intention is to try to disrupt intelligent conversation, not try to engage in it. If you'll go back to the beginning of this thread, you'll seee that he began this dialogue with insults.
Blight is not here with an open mind. He has made it clear that the only evidence that he will accept is the spontaneous development of a completely new organ. And by new organ, he wants something entirely different. As he has stated, even the development of a third eye would not satisfy him. As has been pointed out to more then once, the "proof" that he is asking for would tend to disprove evolution (macro-evolution anyway), and be more in line with intelligent design.
So if you want to persuage Blight, good luck in that.
You think you can use prevail using logic? Blight has specifically disclaimed logic. He calls it "the narrow set of cirumstances that the arbitrary set of rules we made up and called 'logic'"
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graniteclimber
Trad climber
Nowhere
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Oct 25, 2006 - 12:32pm PT
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Raymond, writes, "It makes it on some what the same level as mountain mans global warming threads. The opinion of someone with no knoweledge on the subject is not very interesting."
Raymond, so why are you here?
Shouldn't you be studying? Or working on something?
If your answer is, yeah, but this is more fun, well, you've answered your own question!
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Blight
Social climber
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Oct 25, 2006 - 12:44pm PT
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Aya, let me clarify: I'm looking for evidence of a new trait. by that I mean one that the organism didn't have before.
In the nylon eating bug case, the ability to produce enzymes was not new. It already did it. The ability to experience mutations was not new. It already did that too. The ability to use food sources for energy was not new. That already existed too.
The nature of the food source itself is trivial to the point of irrlevant since the organism has an existing mechanism for adapting to new food sources.
As for your questions, I'm sorry but I must have missed them, could you repost them please?
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graniteclimber
Trad climber
Nowhere
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Oct 25, 2006 - 12:45pm PT
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"80(?) My prediction is looking pretty good, so far."
"Can we agree that it is hard to agree on what the theory is, so that it is nearly impossible to test it? :-) "
The articulation of a rigorous theory is your game. I don't think there is much interest or effort in trying to do that by anyone else here. You were making some progress yesterday with a statement of the meachanism, but now that you've jumped tracks and looking at macro-evolution, all bets are off. Macro-evolution is not just one unified theory, it is a whole bundle of theories.
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TradIsGood
Fun-loving climber
the Gunks end of the country
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Oct 25, 2006 - 01:07pm PT
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I am happy to leave out macroevolution. I just think debating something that is not rigorously defined leaves everybody on uncommon ground, destined for ever to repeat the same stuff, or even failing that, simply have no way to agree that the theory is consistent with known observations or not.
We can't resolve the science by a vote, but we could resolve the issue of what the statement of the science is by a vote. When agreement on the statement is unanimous, then rigor is available to address the science. If not unanimous then those who agree on the statement can offer claims, tests, or refutations.
Right now, it seems we are at the stage where some think Newton's Law is
F = ma, and others are thinking
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Aya
Uncategorizable climber
New York
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Oct 25, 2006 - 01:59pm PT
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Aya, let me clarify: I'm looking for evidence of a new trait. by that I mean one that the organism didn't have before.
In the nylon eating bug case, the ability to produce enzymes was not new. It already did it. The ability to experience mutations was not new. It already did that too. The ability to use food sources for energy was not new. That already existed too.
There's no need to clarify; you were clear to begin with. Apparently I haven't been clear, so I'll try again:
The bacteria did not digest nylon previous to living in an environment where it was advantageous to do so. To be certain, as recently as about 100 years ago, the bacteria did not live in an environment where nylon existed, period. The bacteria did not produce those enzymes before. They did not digest nylon before. Other closely related bacteria who do not live in nylon-rich environments do not and can not digest nylon. They could not do something before, and now, do to a mutation, they can: isn't this the definition of new?
It seems to me that you're saying that this was not new because the mutation that allowed it to happen was a frameshift mutation: yes or no?
If a mutation occured that allowed the production of an enzyme that the bacteria previously did not produce is not acceptable as new to you, out of curiosity, what types of mutations WILL you accept as new?
The ability to experience mutations was obviously not new; the mere fact that the bacteria have DNA means that they are able to experience mutations: this is of course one of the central mechanisms of evolution. I don't understand why the ability to experience mutations (i.e. have DNA?) must now be new, as well? Please explain.
The ability to use food sources as energy is also obviously not new. Again, I don't see the relevance: the bacteria could not utilize nylon as food previously. A mutation allowed them to utilize it. Of course they can utilize food as energy? I am, after all, making the point that the bacteria developed the ability to digest nylon, not that they developed the ability to digest, period. How does this somehow negate the essential fact that the bacteria had a mutation that allowed them to do something (digest nylon) that they previously could not?
It almost seems that ultimately what you're saying is that since organisms have DNA already, any changes to that DNA are not new? Please clarify.
The nature of the food source itself is trivial to the point of irrlevant since the organism has an existing mechanism for adapting to new food sources.
So you concede that the organism has a mechanism for adapting to novel food sources. Can you please explain to me this mechanism?
As for your questions, I'm sorry but I must have missed them, could you repost them please?
They were the questions in the following post that I'll copy below.
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Blight, if you've actually read the studies and looked at the data in the Bennett et al studies, you'll see that it is very evident that the ability to survive at novel temperatures increased over generations (rather than being progressively lost).
E. coli are able to survive at wide temperatures, yes. However, with each successive generation, they were able to survive better than the previous ones. How do you explain this, if you dismiss the idea that mutations arose in the bacteria's genome that allowed it to live better at these new temperature regimes? Please keep in mind that the bacteria were originally all identical.
Also, if you want to say that the old populations progressively lost the ability to live at higher temperatures (you'll need to explain how this would work a little better, since the original populations were frozen, so did not change, while the other populations were growing in the new environments).
Finally, and most to the point, they most certainly did sequence the genomes of these bacteria, and found multiple mutation events - so I'm not sure which studies you read? Here is a link to one of their studies which is available online. Several of these gene duplication events were coincident with statistically significant increases in fitness. Again, how would you explain this result?
I suppose that you might dismiss these results because the mutation events they found were replications and deletions, rather than the spontaneous appearance of completely new DNA sequences - which is the "proof" (please recall that there is no such thing as absolute proof in science) you requested. Yes or no?
Re: Barry Hall. The point in that case is that the E. coli he started with could not hydrolyze lactose. "It already exists" is true - but not of the cells he was studying.
The lactose matabolism pathway that these cells evolved was completely novel - i.e. it did not exist in the original cells, nor does it exist in other E. coli that are able to metabolize lactose (via a different pathway).
There are plenty of other examples, of course, such as the mutations in certain Flavobacterium and Pseudomonas strains which allow the production of enzymes which degrade nylon. Nylon is a manmade substance, the bacteria are not normally able to digest it. The mutation (it's been sequenced) that arose allowed them to utilize nylon as a food source. This was a new gene sequence that coded for a new protein that allowed the digestion of a new food source. Here is a link to one of the papers showing the results of sequencing the mutation.
There are lots of other examples of bacteria with mutations that allow the digestion of new, manmade compounds. Quick google searches will yield these.
Please explain how these studies don't show the development of new processes via mutations?
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eeyonkee
Trad climber
Golden, CO
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Oct 25, 2006 - 03:59pm PT
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Seems to me, some folks have spent a lot of time bending over backwards to try to answer Blight's questions. A few of us have asked Blight to articulate a viable alternative to evolution. To make it easier I would frame it this way. The theory of evolution basically postulates that existing species are the result of descent with modification from earlier forms. This simple but powerful idea has great explanatory power. There is almost nothing about the nature and distribution of species on earth that cannot be explained, at least in a general way, by the theory. It was a viable and generally accepted theory for 100 years before the discovery of DNA. The discovery of DNA provided the mechanistic underpinnings that were missing (but more or less anticipated) in the original theory. With these new underpinnings, the theory had even more explanatory power.
My question to Blight. Do you believe that a supernatural being created all of the species as they are and that they are essentially immutable? If you do believe this, than how do you explain the fossil record which clearly indicates that billions to trillions of species have gone extinct. If you do not believe the first question, then what do you believe?
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graniteclimber
Trad climber
Nowhere
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Oct 25, 2006 - 04:40pm PT
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"I just think debating something that is not rigorously defined leaves everybody on uncommon ground, destined for ever to repeat the same stuff, or even failing that, simply have no way to agree that the theory is consistent with known observations or not."
Well yes, what did you expect? This is Usenet, um, I mean Supertopo after all.
Is it realistic to expect that a rigorous definition can be jointly reached in a discussion like this? I think it would be unlikely even if every person participating in this thread specialized in studying evolution. Maybe I'm just a cynic, but usually one or two people put things out there and others snipe and heckle and eventually (maybe) grudgingly agree, because they can't think of anything else to criticize or just out of laziness.
Let's go with the definition of "absolute fitness" at http://en.wikipedia.org/wiki/Fitness_%28biology%29 , using absolute numbers.
Anything else missing?
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raymond phule
climber
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Oct 26, 2006 - 04:13am PT
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"Shouldn't you be studying? Or working on something?"
So true, I should be writing an article...
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Blight
Social climber
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Oct 26, 2006 - 05:05am PT
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They could not do something before, and now, do to a mutation, they can: isn't this the definition of new?
I understand what you're saying, I'm simply disagreeing with you.
Here's an analogy: our immune system contains cells which have the ability to adapt to combat foreign bodies they've never encountered before. Is this evolution? Of course not, these cells have a preexisting mechanism which allows them to make superficial changes in response to their environment.
So to return to the nylon-eating bugs: I don't accept the ability to eat nylon instead of carbohydrates as evidence of evolution for the same reason; it's just the superficial result of a preexisting mechanism, not a new mechanism itself.
what types of mutations WILL you accept as new?
Ones which are new. Not seen before. A new limb, a new organ, a new trait. Something novel, sustainable, net positive and possible without interference. Evolutionary theory says such things arise. So why is there no evidence of this happening?
Now to your questions:
How do you explain this, if you dismiss the idea that mutations arose in the bacteria's genome that allowed it to live better at these new temperature regimes?
I don't dismiss the idea that mutations arose in the bacteria's genome. I dismiss the idea that this is a new trait.
Several of these gene duplication events were coincident with statistically significant increases in fitness. Again, how would you explain this result?
A good example of natural selection. Of course the genes in surviving organisms were passed on looking for.
I suppose that you might dismiss these results because the mutation events they found were replications and deletions, rather than the spontaneous appearance of completely new DNA sequences - which is the "proof" (please recall that there is no such thing as absolute proof in science) you requested. Yes or no?
No. I have little interest in DNA sequences because you know as well as I do that they're not fixed, even within an organism. I'm looking for sustainable evidence of the results of new DNA: a new organ, limb or trait as described above.
Please explain how these studies don't show the development of new processes via mutations?
Eating is not a new process, as I've said before.
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Blight
Social climber
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Oct 26, 2006 - 05:07am PT
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My question to Blight. Do you believe that a supernatural being created all of the species as they are and that they are essentially immutable? If you do believe this, than how do you explain the fossil record which clearly indicates that billions to trillions of species have gone extinct. If you do not believe the first question, then what do you believe?
No.
We're not discussing my beliefs, we're discussing the scientific evidence for evolution. If you want to discuss that, by all means take part.
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raymond phule
climber
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Oct 26, 2006 - 05:15am PT
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Blight, you are not giving any references to your view as usual.
Could you give a reference to a crediable source that have a similar opinion as you or have you thought about this all by yourself?
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