Lenoxus,
"Yet if one accepts that it could, there’s not much more to say — nylonase was bound to happen sooner or later, no matter how many “casualties” occurred in the process."
Lenoxus, You'd have to accept that it could happen for sure. In the first reference Mario linked, Dembski's saying there was a sufficient number of correctly placed stops to preserve FCSI and redundancy in the segment that got shifted that it seems it was possible, but that this is so rare that it doesn't point to it being THE mechanism to evolve a whale. And also that this could be a sign of intelligent front loading or something, because it's so freakishly convenient to have such a setup. That's my interpretation, I don't want to speak for him. So the thing to do would be to look at other frameshifts in nature.
Regarding tradeoff's not stopping evolution, the point is you need to get off the ground before you can fly with natural selection.lamarck
August 17, 2009
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Was that a joke?Davem
August 17, 2009
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Lenoxus
I guess that would be why modern-day whales breathe underwater. It’s hard to imagine what else they’d do — just sort of go to the surface for breaths?
They don't breathe underwater, they need to come to the surface.Davem
August 17, 2009
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If the hippo was extinct and they found fossils of it along with evidence of it's aquatic lifestyle, it would be heralded as an ancestor of the whale.Davem
August 17, 2009
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Nylonase bug discussed here:
https://uncommondescent.com/archives/348
and here:
http://www.overwhelmingevidence.com/oe/forum/design_inferenceMario A. Lopez
August 17, 2009
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Huh, it seems like with the nylonase things the arguments go along the lines that there's no way one mutation could provide such a complex, positive, and information-rich benefit. Yet if one accepts that it could, there's not much more to say — nylonase was bound to happen sooner or later, no matter how many "casualties" occurred in the process.
As for the question of negative results from the mutation, I imagine there probably were tradeoffs for the organism in terms of digesting other substances. (Pretty much all changes to an organism involve tradoffs, but that alone isn't enough to stop evolution.)Lenoxus
August 16, 2009
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Frost,
Good comment, but then the question becomes:
What is the possibility of a frameshift mutation producing something more than chaos? It doesn't matter if this enzyme is common to this bug. What matters is how long and complex the "digestive" pathway was and if this enzyme was in close proximity or some such thing, to enable a one mutation easy shift over to perform this new function.
It's not about the phenotype or what chemicals are in the body, but instead what's happening in the genome.
Keep in mind another bug used a different enzyme to eat nylon in a lab experiment. Reference wiki.
A single point nucleotide mutation on an existing functional gene would seem a much more amenable and realistic solution to this change in eating habits, than making the gene into scrambled eggs and viola, the exact thing needed is produced.
Disagree or any thoughts?
Also anyone could jump in with a good challenge to what I'm saying if you knew how long the frameshift was, and so maybe not much existing FCSI damage if it's very short.
Turns out there's 400 frameshifts providing FCSI in humans. All the more evidence for my side I'd think.lamarck
August 16, 2009
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Frost,
Good comment, but then the question becomes:
What is the possibility of a frameshift mutation producing something more than chaos? It doesn't matter if this enzyme is common to this bug. What matters is how long and complex the "digestive" pathway was and if this enzyme was in close proximity or some such thing, to enable a one mutation easy shift over to perform this new function.
It's not about the phenotype or what chemicals are in the body, but instead what's happening in the genome.
Keep in mind another bug used a different enzyme to eat nylon in a lab experiment. Reference wiki.
A single point nucleotide mutation on an existing functional gene would seem a much more amenable and realistic solution to this change in eating habits, than making the gene into scrambled eggs and viola, the exact thing needed is produced.
Disagree or any thoughts?
Also anyone could jump in with a good challenge to what I'm saying if you knew how long the frameshift was, and so maybe not much existing FCSI damage if it's very short.
Turns out there's 400 frameshifts providing FCSIlamarck
August 16, 2009
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In regards too nylonase- it is the result of an existent enzyme that occurs in certain bacteria- and can result or appear from a mutation - and so is therefore used as an example of mutations creating a positive or beneficial novel adaptation. Well the problem is that the enzyme that results in the ability to dissolve nylon is common in certain kinds of bacteria. SO it is more like saying someone developed the mutation for red hair when there are already people out there with red hair. Yes it can happen but it is more common than the kind of revolutionary novelty to explain the emergence of novel body structures and forms. Also there has not been much research into what is any negative effects that mutation may confer. The gene that protects against malaria also causes anemia - and the positive/negative trade off of mutation can become very grey sometimes in how it actually progresses a species. 99% of all species are dead and extinct- yet according to the theory of DE there was just enough luck to get us here. Nylonase hardly elucidates the question of emergence of specified complex novelty- and especially at the macro level.
The question is always about guided vs unguided- and I personally dont think nylonase falls down in favor of either side.Frost122585
August 15, 2009
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Lenoxus, yes nylonase is that to me. One thing I'm unsure about is if a frameshift always means the whole gene shifts one letter over, or just part.lamarck
August 15, 2009
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Mr. Nak,
For some reason I didn't see what you were getting at with #1 yesterday.
So yes I agree that there's a possibility that large bodies with more parts would have a harder time changing.
Maybe one way to start studying this would be to look at # of base pairs between humans and chimps and compare that to number of pairs between two smaller and less complex related species. If more base pairs are needed between humans and chimps then maybe it's true.lamarck
August 15, 2009
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Mr Lamarck,
I would put is as phyla reduction was natural competiton/actuarial reality, while the lack of new phyla is less modularity/niches already being filled.
I don't think you can always assume that every niche is filled. Some mutations open up niches. The most obvious example is living on land. In the ocean there are niches for motile and sessile life, living on the surface, the floor, or free swimming, burrowing, etc.
I agree that the modularity hypothesis is speculation at this point. We need to dissect the machinery of vo-devo to make it more than that, but at least that is a direction for a research program.
I personally find the coincidence of multiple body plans appearing att the same time as body plans become reliably fossilisable to neat. i agree with the author of "In the Blink of An Eye" that a lot of body plan experimentation went on while bodies were still to small and soft to fossilize well. There could have been even more body plans tried and lost before we ever get a clue. It is frustrating that hundreds of millions of years of history is a blank slate. Or shale. Whatever. :)Nakashima
August 15, 2009
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lamarck: So for you, nylonase is perhaps an example of ID, rather than an evolutionist refutation pulled from the dark corners of science? Excellent. I always get a tad annoyed when IDers refuse to see any ID happening in the world today, on the non-uniformitarian assumption that all of it is "done". I think I would feel that way even if I were an IDer…Lenoxus
August 15, 2009
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Lenoxus,
I'll explain what I know, but let me know if something isn't understood because I have a clear understanding of at least what I think I know.
1. Nylonase made a whole new gene. This concept isn't understood by many IDers. There's an arbitrary cutoff point between a small change in a gene and a whole new gene and nylonase clearly fit the bill because it was a frameshift. All it's base pairs switched partners. And miraculously this coded for something significant which this bug found advantageous, eating nylon. It was a bug in a pond next to a nylon factory.
This is a whole other level than a gene duplication and resulting insertion or deletion in a codon. This too is an information gain technically. But this couldn't account for the massive complexity of the genome built up over time. Because the change is likely near neutral and so doesn't matter. This is the vast majority of beneficial mutations. Also we're talking about large structures forming and a large amount of mutations coordinating is needed over a small amount of time.
Unless of course your talking about this one in a million chance of a successful frameshift mutation which also codes for something very beneficial. If this happened all the time there would be no questions about whale evolution. So that's what's meant by a whole new gene. Everything changes, AND it codes for something significant which will last. AND this all happened in 20 years. We know this because nylon was invented this century. As an aside, this to me is further confirmation that the genome is preprogrammed to flexibly adapt in some way. Or that the organism's intention matters in the equation. I just can't believe this happened because of luck, there has to be something else going on.
2. GE is genetic entopy
3. Agreed on the whales.lamarck
August 14, 2009
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lamarck:
Aside from a couple examples (nylonase is one) where morphological changes aren’t taking place, or large changes take place.
How do you know that nylonase do / don't have less information available as a result of the mutations? How is the information content measured, since I assume you don't mean the total amount of DNA?
So GE asks, how are whales evolving?
What is meant by "GE"?
And a large change DOES to some degree have to happen all at once, or go vestigial.
I guess that would be why modern-day whales breathe underwater. It's hard to imagine what else they'd do — just sort of go to the surface for breaths? Some similar ad-hoc mechanism? That would just be weird. They clearly wouldn't survive being stuck in the middle like that. :)Lenoxus
August 14, 2009
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Mr. Nak,
What accounts for phyla reduction would then be:
1. Things were more modular.
I understand it insofar as it's utter unfounded speculation.
2. Niche filling on the food chain.
This idea would always be an automatic stopper to phyla radiation, or species radiation for that matter. It wouldn't matter if there were five phyla or fifty, it's all one big food chain for any ecosystem.
So that could be an answer for phyla reduction, except that the same idea never allows for there to be any radiation. So it can't be true, unless the cambrian explosion was ID'd.
Keep in mind that the niche/food idea would have to be always applicable in every case, because whatever mechanism is at work in phyla reduction, is working very absolutely, as I covered when I talked about the graph. So that's why I can safely say that the niche/food argument isn't true. Or it is true, but then automatically the cambrian explosion was ID'd.
I liked your answer though it was interesting.lamarck
August 14, 2009
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Mr Lamarck,
The "radiation, then dimunition" pattern won't normally repeat, because the sophisticated descendants of the few remaining entities (phyla, car makers, etc) are still more sophisticated than any newcomer.
In terms of the phyletic explsion of the Cambrian, there is one explanation that at that time the modules of body plan development fit together in a looser way than today. This allowed many different body plans to be developed rapidly which allows the exploratioin of more niches. If this hypothesis is correct, we won;t see any reradiation at the level of phyla because all phyla now have much more rigid developmental programs than their ancestors did 500 million years ago. So if you opened up a niche by (for example) wiping out all the spiders from the world, a descendant of termites or flies would rush in and grab the free lunch before any new phyla could form to exploit the free lunch. No new phyla, but maybe a new order of termite.
Is that any clearer?Nakashima
August 14, 2009
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Mr. Nak,
But we're looking at the net effect, taking in vast amounts of time and vast ecosystems and life variation. This is enough time to discern a pattern.
Are you then postulating that no pattern would have emerged, and that we will in the future see again 53, then 2 then 500 then 40 phyla?
Wouldn't this fluctuation be seen in the fossil record and is it? I doubt I wouldn't have heard about that. I'm talking about NO new phyla since cambrian and ALL phyla within a few million years, minus one aleady existing phyla. There's no variation on that graph.
"That pattern of radiation and then dimunition in number is very common."
In number of what? Species?lamarck
August 14, 2009
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Mr Lamarck,
That pattern of radiation and then dimunition in number is very common. You can see the same thing in car manufacturers or computer makers. In the early days a lot of tinkering is good enough, because really nobody is very good. Then one or a few start to distinguish themselves and starve out the competition.
Another aspect of it is the random chance that lineages go extinct. Lets say there was a group of 10,000 'first humans'. Mitochondrial Eve isn't one of them, she lived much later. What happened to that wonderful radiation of humanity? By random chance, their descendants haven't survived. That's not genetic entropy, that's just actuarial statistics in action.Nakashima
August 14, 2009
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And a large change DOES to some degree have to happen all at once, or go vestigial.lamarck
August 14, 2009
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Lenoxus,
"I’m trying to grasp what, if anything, might be the specific relevance of genetic entropy to whale evolution."
Part of genetic entropy is looking at the complex info in the genome and asking how it got there when all we see is loss of information when good mutations happen.
If you look at the genome, and believe it codes for all the variation happening, then you'd think we'd see more complexity going into the genome concurrent with good mutations, but we don't. Aside from a couple examples (nylonase is one) where morphological changes aren't taking place, or large changes take place.
Those couple examples are only small changes to existing structures.
So GE asks, how are whales evolving?lamarck
August 14, 2009
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I should also add that I don't believe in Sanford's 1000 generation meltdown, or however many it is. But I don't know that he does either. It could be that he's simply presenting the math based on what's known. I don't know I haven't read his book myself.
But too much emphasis is put on this part of the book. Sure, it IS called "genetic entropy", but the other part of the title is "and the mystery of the genome". Sanford is a top shelf geneticist, I'm sure he's aware of trilobites.lamarck
August 14, 2009
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Mr. Nak,
"Sorry, I don’t see the support for genetic entropy in that study at all. Where is the quick mutational meltdown? How is a family of thousands of species, lasting for 270 million years, evidence of rapid genetic failure?"
There were over 50 phyla created in the cambrian explosion, and there's 30 something now. Also since then there's been no new phyla I believe. So these two points are part of Sanfords book. No new real variation allowed, and decrease in species.
I'd like to know what evolution says about why reduced phyla, because from what I know of this is circumstantial evidence for entropy.lamarck
August 14, 2009
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Is there some sense that, around halfway to their becoming “fully whale”, an evolving cetacean species should “run out” of information/variability/whatever, and thus would be “stuck” between two worlds until an intelligent force could contribute the needed genetic information?
First of all, assuming the present day whale is "fully whale" suggests that the species is no longer evolving, that today's mammal is what was intended, what was in the design.
Secondly, suggesting that a species would evolve in dissimilar environments with no adaptive variations, because it was intended to 'end up' as 'fully whale, or fully hippopotamus, presupposes these species will be identical in another million years.
How does the lack of a transitional fossil record indicate the evolution of this species was "stuck"?Overburden
August 14, 2009
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I'm trying to grasp what, if anything, might be the specific relevance of genetic entropy to whale evolution. Is there some sense that, around halfway to their becoming "fully whale", an evolving cetacean species should "run out" of information/variability/whatever, and thus would be "stuck" between two worlds until an intelligent force could contribute the needed genetic information?
Earlier, Frost said something interesting:
First of all virtually any organism can evolve into any other organism via mutations and the like given enough imagination time and a well designed fitness landscape- but it is the improbability of those positive necessary mutations occurring that ID challenges.
This seems to be a somewhat related idea. The thing about probability is that, despite our intuition on the subject, nothing prohibits a long sequence of individually unlikely events from occurring — especially if earlier rare events tend to "stick" as they do with genetic heredity, while common events are usually filtered out by natural selection. (Given that, such sequences altogether expected.) It's not like a Pakicetus would have to "re-invent" the aquatic lifestyle in passing genes to each of its babies. If every individual change is plausible despite being unlikely, what's the problem with having a bunch of those changes occur?
And how should we interpret the existence of the intermediary fossils, if in fact the fossils are genuine? (From much of the commenting here, I do get a subtext that they might not be genuine, that Dawkins is sort of pulling them out of his butt. For example, jerry earlier referred to "[pulling] a couple rabbits out of the hat. Oh, I mean whales". Later, there was a mention of Nebraska Man. The title of this post is one I assume to sarcastically suggest that these are not "really" transitionals.)
In that quote, Frost is also suggesting that the landscape might itself be "well designed" — a possibility often implied by people here at UD responding to computer simulations of evolution. Yet no ID theorist has specifically proposed that notion — why not?
In any case, I personally don't agree that "any organism can evolve into any other organism" — this is why evolutionists often bring up chimeras such as mermaids and flying horses, or, say, a species with the a long non-coding sequence shared by distant cousin species. (What if whales shared one with birds, but it was absent from all the intermediary species!) To this, IDers might respond by bringing up platypuses, and so the great conversation proceeds!Lenoxus
August 14, 2009
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Mr Nakashima,
Mr Wisker,
Was there a polar continent during that era?
No. That would happen later in the Ordovician, as Gondwanaland wandered over the pole, resulting in even more glaciation.Dave Wisker
August 14, 2009
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BA77 ——-conclusion of the study?—— the propensity to radiate was significantly higher in lineages whose precursors emerged from more ancient adaptive radiations than in other lineages”
http:/
Cherry-picking that doesn't support your argument. From the same conclusions, not conclusion:
The implication is that speciation itself (not just coexistence) is driven by ecological opportunity, inconsistent with predictions of speciation through drift and ecologically neutral sexual selection.
Somewhat fishy fact-finding, I'd say.Overburden
August 14, 2009
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Mr Wisker,
Was there a polar continent during that era?Nakashima
August 14, 2009
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Oops. The source of the quote is here:
Bottjer, DJ JK Schubert, & ML Droser (1995). Comparative evolutionary paleoecology: assessing the changing ecology of the past. In Biotic Recovery From Mass Extinction Events, MB Hart, ed.Dave Wisker
August 14, 2009
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Mr Nakashima,
I agree with you that trilobites are one of the last groups one would want to use as an example supporting the genetic entropy thesis (as well as ancient bacteria, as I have pointed out elsewhere).
Here is an interesting tidbit regarding the ecospace and genome hypotheses:
As an intriguing postscript, Valentine (1995) has recently concluded, through an analysis of the Hox/Hum homeobox genes, that the current understyanding of the molecular basis of development provides no support for the genome hypothesis, and that the ecospace hypothesis is more consistent as an explanation for the concentrated origin of phyla during the Cambrian explosion.
That is, the more consistent hypothesis is that the ecospace of the Late Cambrian was full, and competetive exclusion precluded more innovation at the phylum level.
But what about bornagain's suggestion that ecological opportunity would be greater in the Late Cambrian? A little research on his part would have shown that there is evidence of a glacial period at that time. Basic paleoecology tells us that glacial periods result in significant amounts of seawater locked up as glacial ice on land. This results in lowered sea levels, which in turn reduce the area of continental shelves, where much of the marine life lives, creating increased competition and extinction levels. With a packed ecospace suffering restriction, food webs established earlier will collapse, resulting in mass extinctionsDave Wisker