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Stupid Christian Article on Evolution

bokonon said:
Organisms which have no complex nerve function are not likely to have genes for complex nerve function. If these genes are expressed in the organisms which have no complex nerve function, they are obviously coding for something other than complex nerve function.
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But, in fact, the original article didn't mention 'complex nerve function'...
 
bokonon said:
I'd account for it by something akin to what randman seems to have been saying: a lot of the genetic diversity we see today originated in more primitive organisms which reproduced more quickly, exchanged genetic material more promiscuously, and were subjected to more diverse selection pressures than many of the more complex organisms which carry those genes today.

It suggests to me that some common ancestor of the water flea and the human possessed many of these common genes. The evolutionary branch leading to fruit flies found many of these genes unnecessary, and left them on the cutting room floor. The branches leading to humans and water fleas continued to find them useful, and tended to conserve them.
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Thanks. Is that kind of thing likely to confuse calculations of relatedness?
 
sphenisc said:
Thanks. Is that kind of thing likely to confuse calculations of relatedness?
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It's likely to change them. Lots of phylogenetic trees are being redrawn as more genomes are being sequenced, and there is some disagreement about just how some organisms should be classified in relation to others -- if organism 1 has genes A and B, organism 2 has genes A and C, and organism 3 has genes B and C, did they all originate from a common ancestor which possessed genes A, B, and C, with 1 losing C, 2 losing B, and 3 losing A? Or did all three begin with A and B, with 2 and 3 gaining C, and 2 subsequently losing B? With thousands of genes per organism, and questions about what is a new gene and what is an allele of the same gene, you can see that things can get very complicated very quickly.

The burgeoning field of bioinformatics is providing new tools which can be used for comparative genomics and functional genomics. I think it's a fascinating field, with lots of interesting questions which won't be answered a week from Tuesday.
 
bokonon said:
It's likely to change them. Lots of phylogenetic trees are being redrawn as more genomes are being sequenced, and there is some disagreement about just how some organisms should be classified in relation to others -- if organism 1 has genes A and B, organism 2 has genes A and C, and organism 3 has genes B and C, did they all originate from a common ancestor which possessed genes A, B, and C, with 1 losing C, 2 losing B, and 3 losing A? Or did all three begin with A and B, with 2 and 3 gaining C, and 2 subsequently losing B? With thousands of genes per organism, and questions about what is a new gene and what is an allele of the same gene, you can see that things can get very complicated very quickly.

The burgeoning field of bioinformatics is providing new tools which can be used for comparative genomics and functional genomics. I think it's a fascinating field, with lots of interesting questions which won't be answered a week from Tuesday.
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Don't forget the joys of horizontal gene transfer, which makes interpreting the results even harder.
 
Phylogenetic trees suffer from a basic methodological flaw: They assume that each species has two daughter species. (This is based on the math behind such trees; if you want to play around with it look up PAUP in Google. It's a free mulitvariant statistical modeling program used by many paleontologists.) This is not, however, actually true. Any single species can have numerous subpopulations, some or all of which can become new species. This makes the math messy. One way to get around it is to do bootstrapping/jack knifing style tests for robustness, and any branch that occurs in less than a certain % of the results is collapsed; however, it's still an open question how we should deal with the biological messyness inherent in speciation.

PAUP's website offers a great discussion on the subject of phylogeny/cladistics, including the math behind it and the biological reasoning for the math. There are a few assumptions these methods make that are questionable, but we've got to assume SOMETHING. For example, PAUP generally considers evolution to be difficult--meaning novel traits arise infrequently. In practical terms, it means that it'll try to minimize the number of times a new trait arises. From a biological perspective it's an open question as to whether or not that's true; for example, I know of some bacteria which increase their mutation rates under some conditions, and such an increase in mutation rates will likely lead to two strains independantly developing the same mutations. Or, for another example, I'm willing to bet that under the long-term bacteria evolution study which gave us Nylonase, if we ran another test along side it we would eventually get the same gene to arise. It goes back to my comments about physical and engineering constraints. All of that said, however, we need some way to do the math. Until we can work out mutation rates, or exact timing of when novel traits arose (see my next paragraph), it's not a bad assumption to assume that mutations arise as infrequently as possible. It at least gives us a framework, a hypothesis to test.

If you want my opinion (with the obvious caveats that A this is merely one person's opinion, B I'm biased as all get-out, and C this would make my job much, much more important [similar to B but worth mentioning on its own]), I think that we should treat cladograms and phylogenetic trees as hypotheses, to be tested via the fossil record. Biology is very good at showing us the last few hundred years. Most speciation events we're interested in occurred long before that, and the science that studies that sort of thing is paleontology. This obviously can only be done in certain instances (not going to find many fossil fruit flies, for example, while I feel perfectly justified laughing at anyone who attempts to create a phylogeny for clams without including the fossil record), but where it can be done the fossil record provides an excellent way to test our trees. Even better, it's a completely different science, meaning that the biases, while they may partially overlap, will to some extent cancel each other out.
 
Is there any reason why this coral could not have once been a more complex organism but its niche lifestyle meant it had no need for some of its complexity and so abandoned them but retained the genes?
 
Ladewig said:
I am willing to listen to other explanations. Do the explanations you are referring to begin with the claim that the world is less than 10,000 years old and that we should expect to see a genetic bottleneck 4500 years ago? Do the explanations include humans and dinosaurs living contemporaneously? Because if they do, then I am prepared to dismiss them immediately as being in conflict with mountains of evidence showing an ancient Earth.
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randman said:
Depends on which camp you ask.
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Evasion noted. So which Creationist camp is the best one and why? They can't all be right. How shall one judge the validity of their conflicting claims?
 
Bad vibe said:
Is there any reason why this coral could not have once been a more complex organism but its niche lifestyle meant it had no need for some of its complexity and so abandoned them but retained the genes?
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It seems quite possible, as its larval stage is nektonic, and the adult stage settles down to a sessile existence (like barnacles).
 
Wow, so much info - a lot going over my head but I didn't mean to derail with the whole dinosaur thing. The dinos being thousands of years dead and not millions of years dead could be a thread all of it's own - possibly discussing the details of dating techniques - but I was really just trying to contrast then and now.

Basically, there weren't dogs and people - now there is. Do you have an alternative theory to where they came from? Note again that not having an alternative theory is not a weakness (that would a logical fallacy I encounter a lot in the religion threads) but again - I'm curious. If it's something along the lines of "supernatural big-daddy in the sky magiced us into existance", then tell me I'm off topic and stick to the evolution. Most young earthers would say that there's always been people and dogs because the earth doesn't go back past thousands of years - but that's not the vibe I'm getting from you.
 
randman said:
Ok, let's talk over a 500 million year period. Evolution predicts the slow accumulation of genes during that time, right? Exceptions noted but the first organisms didn't start out with all the genes that exist today according to darwinism. They evolved via an adaptionist process where mutations occurred and selective advantage promoted species and so with new traits and species, new genes evolved.

That's evolution, right?
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What is your theory?
 
Mister Agenda said:
Boy, that would have been such a letdown if it wasn't obvious a mile off. My experience has been that the Socratic method, in the hands of anyone but Socrates, is a particularly prolonged and tortuous form of asshattery.
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I hadn't previously known that "Socratic method" meant "an endless, tedious repetition of the same questions, leading inexorably to a rather dreary 'gotcha'".
 
And when the answer repeatedly comes back no, ignoring that and declaring that it's yes. That part was particularly endearing.
 
The core of Randman argument is so desperatly vague simplistic, though, that it is pretty much useless.
What is genetic complexity? It is simply the number of genes? Some species are tetraploids, meaning they have four copies of chromosomes rather than two and hence, twice as many genes.
Are they suddenly twice as complex than their closest relative? Even if polyploidy is generally reserved for "lower" animals and life form and lethal to more complex ones?

There is also the fascinating and rather wonderful example of the Ambystoma salamander.
There is a small sub-species of these little guy that is all female. They often reproduce by gynogenesis: all the genetic material of the eggs comes from the female. This is, however, a recent evolutionary development and the egg still depends of contact with a spermatozoon for activation. The genetic material of the spermatozoon is discarded, though while all the one from the female is conserved and the egg is all female...
Well... most of the times. Sometime, maybe to preserve some genetic brassing or not too drift too far away from the parent population, the genetic material of the male is integrated. Sometime in a classic manner, half of the genetic material of the female being discarded. And sometime it is a mix of the two with the spermatozoon bringing is haploid set and the egg otherwise keeping the integrality of the mother's genetic material, leading to a triploid organism.

It's quite cool, but that means that the genome's number of genes do jump up by a full half on a regular basis, do go back to level on the next generation. What does it mean in term of complexity and evolution?
Unless, of course, number of genes in a specific organism means little per se...
 
Simon39759 said:
Pierre-Paul Grassé.

First of all, you do realize that he was not a creationist, right?
He was a neo-Lamarckian.

Basically, his point was that mutations did not equal evolution. That population could remain evolutionary stagnant for a long time despite mutations.

That part is quite correct, that is because a mutation is not always beneficial for the whole population.
Furthermore, the benefits of a mutation is environment, ie selection, dependent. So a beneficial mutations in the lab is not necessarily a beneficial one in the population in the wild.
Mutations are the fuel of evolution, but natural selection is the engine driving it forward.

A big point of Grassé was that of living fossils, organisms that were seemingly untouched by evolution despite living in a different environment.
We now know that he was wrong.
First of all, a relatively stable environment is required for 'living fossils', if the environment change too much, either the species evolve or go extinct.
More importantly, his work was conducted before the achievements of molecular biology. So, if the fossils he looked at remain mostly unchanged, he concluded that they did not evolve. But now we can look in more detail and we can see that populations do evolve all the time. These evolutionary changes might not always leave fossilized traces, but now that we can look more closely at their genome, we can see that evolution do, indeed, occur.
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Indeed the creationists abuse of Grasse is so common it's got an entry on the Talk Origins FAQ.
Not surprisingly, Grasse is quoted FIVE TIMES in The Revised Quote Book, because he wrote of the "myth of evolution, considered as a simple, understood, and explained phenomenon."

However, the editors of The Revised Quote Book neglect to tell their readers that in the same book by Grasse from which they have quoted, Grasse also stated in the most unequivocal terms: "Zoologists and botanists are nearly unanimous in considering evolution as a fact and not a hypothesis. I agree with this position and base it primarily on documents provided by paleontology, i.e., the history of the living world ... [Also,] Embryogenesis provides valuable data [concerning evolutionary relationships] ... Chemistry, through its analytical data, directs biologists and provides guidance in their search for affinities between groups of animals or plants, and ... plays an important part in the approach to genuine evolution." (Pierre P. Grasse, Evolution of Living Organisms, Academic Press, New York, 1977, pp. 3,4,5,7)

Of course, Grasse also tipped his hat to the French "father of evolution," Lamarck, stating: "Lamarckism, which is no less logical than Darwinism ... is a tempting theory ... and we would not be surprised to learn from molecular biology that some of its [Lamarckism's] intuitions are partly true...it should be considered today a way of thinking, of understanding nature, rather than a strict doctrine entirely oriented toward the explaining of evolution." (Pierre P. Grasse, p. 8)
The authors of The Revised Quote Book lifted Grasse's phrase, "the myth of evolution," out of context, trying to deceive others into believing that Grasse was doubtful of evolution even though he stated he "agreed" with the "nearly unanimous" scientific consensus that "evolution" was an historical scientific "fact." Grasse simply disagreed with explanations of exactly "how" evolution occurred. He felt the "how" part was not a "simple, understood, and explained phenomenon."
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Creationists have to resort to such deceit as they have no real arguments of their own.....
 
Bad vibe said:
Is there any reason why this coral could not have once been a more complex organism but its niche lifestyle meant it had no need for some of its complexity and so abandoned them but retained the genes?
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You need to read the original paper and some other work to understand why they don't think that's the case. Also, it's not just the coral. It's a general pattern being repeated elsewhere. That's why I included the 2nd quote from someone else not really talking about the coral. I think the comment is quite amazing though it's been difficult to even involve the interest of people here.

He stated that the creatures that gave rise to plants and animals have more types of genes than are available today. When you think of that, it is quite an amazing comment which completely upends the NeoDarwinian narrative.

Instead of novel genes emerging with the adaption of through mutations of beneficial traits, which is the basic NeoDarwinian narrative, this guy is saying the genes were all there before there were even plants and animals.

That's quite an astonishing statement.
 
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