Freethought & Rationalism Archive

Charles Darwin · 08-31-2003, 02:42 AM

Quote:

Originally posted by Doubting Didymus
You were asked several times to provide evidence of phylogenetic mismatches. You utterly failed, and instead displayed for us a series of abominable misquotes that are not even talking about the same thing, or anything like it. I say again: mismatches of significance to evolutionary theory are rare. Mismatches happen, and are the subject of many papers, but they are not problems unless there is no explaition for the mismatch. The fact that you insist on childishly dismissing all explainations offered as contrived handwaving does not make the explaination ineffective unless you actually support your case, which of course you cannot do. You are about rhetoric, and you do not care for real debate.

Utterly failed? Misquotes? Sorry, it was claimed thta phylogenies make for one of the compelling evidences of why evolution is a fact. I pointed out that there are plenty of mismatches, and was asked for examples. I gave a few. How were they "misquotes?"

You say they are not problems unless there is no explanation. Oh, there are plenty of ways to explain away any given mismatch. Whether a mismatch is not a problem, as you claim, is an interesting question. But it is not relevant to the point. The point is that the "fact" of evolution is supported by evidence which can be ambiguous and there are plenty of explanatory mechanisms. Why should we believe evolution is a fact when the evidence you cite is so flexible?

Quote:

Originally posted by Doubting Didymus
Not a bit of it. Please, all onlookers, pay your fullest attention to any evidential problems charles raises. It would do you all good, however, to note that much of it is empty rhetoric, and to ignore that when you find it.

Would you agree that that is a fairer sentiment?

Of course.

Charles Darwin · 08-31-2003, 02:47 AM

quote:
--------------------------------------------------------------------------------
Originally posted by Charles Darwin
What is it about this sentence that you don't understand:

"Animal relationships derived from these new molecular data sometimes are very different from those implied by older, classical evaluations of morphology. Reconciling these differences is a central challenge for evolutionary biologists at present." Science, 279:505

How did I utterly fail? Please be specific this time.

Quote:

Originally posted by Doubting Didymus
First of all, WHAT new molecular data is the article referring to? also, what is the problem with new molecular data updating old morphology - based trees? Did you expect phylogeneticists to have everything perfect first try?

Its not my dog, he didn't bite you, and besides you hit the dog first. You see you can't win for losing.

The evidence shows evolution is a fact, there are no significant mismatches, if you find any there will be explanations, and in any case what do you expect, perfection?

Charles Darwin · 08-31-2003, 02:52 AM

Quote:

Originally posted by Doubting Didymus
Ha! the 'new molecular data' referred to here is actually referring to molecular data period. An entirely new data collection method clarifies old mistakes, and this is supposed to prove that it is an unreliable method!

Charles, your quote is referring to the old mophological relationships that were found to be wrong when molecular phylogenetics first arrived on the scene back in the eighties. Some relationships that taxonomists had inferred turned out to be false when the molecular data showed up. That's not a mismatch at all, its just an update in our knowledge base. And before you say it: I am not just defining the mismatch away. If we went into a detailed morphological analysis on the updated trees, we would find that we were in fact wrong the first time based solely on the morphological data, and more close to the correct tree now. If that were not the case, it would indeed be reported as a mismatch (remember I am not denying that they exists, just that they are sufficiently rare and unimpressive in detail that they do not outweight the support that phylogenetics delivers)

So, as I suspected, the quote does not mean what you think it means. This is not a mismatch that contradicts common descent. Please try again.

Oh, can it be? You've outdone yourself! Now the mismatches aren't even real.

It is not my dog, he didn't bite you, and besides you the dog first, and besides besides, there is no dog.

"I am not just defining the mismatch away." That is exactly what you are doing.

Charles Darwin · 08-31-2003, 09:34 AM

Quote:

Originally posted by markfiend
I think our friend misunderstands the way cladistic trees are made.

If we take an example of some cars which we wish to classify; lets say we have three colours, red, green and blue, three engine sizes, 3 litre, 4 litre. 5 litre, and two seating patterns 2-seater and 4-seater. From these three traits we can classify 18 different "kind" of car: red 3-litre 2-seater, green 5-litre 2-seater, etc. etc.

How do we classify them in a heirarchy though? We could split them into 2-seater and 4-seater, then colour, then engine size or we could give engine size the highest priority, then number of seats, then colour, and so forth. We would be left with a number of possible trees, all of which would be valid to "classify" our cars. This is to be expected of a designed system, where traits can be applied to any or all of the designed machines.

The difference when it comes to biology, though, is that our traits are not distributed across all species like they are with cars. For example, all birds have feathers, so are grouped together at one level of the tree. Also all birds have backbones, so can be grouped with mammals, reptiles, amphibians and fish into "backboned animals" (vertebrates).

The thing is, that there are no non-vertebrates that have feathers, so we know that having a backbone has a higher priority in our classification than having feathers; feathered animals (birds) are a twig on the branch of backboned animals.

When we take a large enough number of traits like this, we can devise a tree where we know that a trait is a "twig-trait" or a "branch-trait".

Now this tree based entirely on morphology (shapes of living things and their structures) was all we had to go on until biochemical investigation of genes and proteins became feasible. The funny thing is, the trees derived from genetic analysis, from protein structures, and from morphology all agree to an astounding degree. (The "mismatches" that CD alleges are when people said, "Hmmm... I'm not sure whether this branch comes out here or there.")

Now the one correct tree is what is predicted from evolutionary theory, where all organisms descend from a single common ancestor. A creationary/ intelligent design theory (as my example of cars) predicts multiple equally valid trees. This is not found, so ID is refuted. QED.

You are not trying hard enough. There are some cars with a hatchback; others without. Some with a trunk, others without. Then include trucks, earth movers, mopeds, bicycles, airplanes, .... You get the point. I don't want to push the analogy beyond its point of usefullness, but you've erred in the opposite extreme.

Charles Darwin · 08-31-2003, 09:44 AM

Quote:

Originally posted by Doubting Didymus
Common descent predicts that an ancestor tree should exist. Nothing else (at least, nothing you're mentioned) predicts that result. Therefore the robustness of the ancestor tree confirms that there were, in fact, ancestors. Thus validating the theory that ancestral species existed, namely common descent.

If you want to refute this, you must either show that common descent does not in fact predict the tree to exist in the way it does, or that some other explaination exists that fits the data as well or better. That's how theories are normally treated in science, anyway.

Even evolutionists use manufactured objects as examples of hierarchies.

Charles Darwin · 08-31-2003, 09:53 AM

Quote:

Originally posted by God Fearing Atheist
Charles my friend, never have i seen someone so capable of talking out of both sides of their mouth. Either there is significant convergence, or there is not. So far, you seem to accept both simultaneously.

- A simply exassperated GFA

There is significant convergence, but there are also numerous and important mismatches (not just a few). None of which cannot be explained away by evolutionists. But they assume evolution is a fact and therefore assume that stretching for whichever explanation is always valid. Never is the theory itself questioned. There is no boundary line beyond which evolution is not allowed to go. Those who claim that this validates evolution are forced to trivialize these important mismatches, and are guilty of not actually setting a criterion for what constitutes confirmation and what does not.

lpetrich · 08-31-2003, 10:34 AM

Quote:

Originally posted by Charles Darwin
(origin-of-endosymbiosis scenario...)
You are coming through loud and clear. Your imaginary passage is painfully unlikely (not impossible though), yet your metaphysics forces you to accept it. This isn't science.

Except that cells living inside of other cells is not as unlikely as CD seems to believe. CD ought to do some studying of "intracellular parasites" some time.

Quote:

I wouldn't make the conclusion sound so trivial. It provides plenty of fuel to those evolutionists who are skeptical of endosymbiosis. Also, the conserved organelle in both prokaryotes and eukaryotes forces evolutionists line these species up (I do not know what the implications of this are).

That's a STUPID argument. CD, do you honestly think that biologists are unable to distinguish between endosymbiotic and non-endosymbiotic organelles?

Endosymbiotic ones can be recognized by their gene content; they have their own genomes, and their genes are most closely related to certain outside organisms. And some non-endosymbiotic organelles may be derived from endosymbiotic ones; some protists have hydrogen-releasing "hydrogenosomes", which are likely genome-less mitochondria.

lpetrich · 08-31-2003, 10:36 AM

Quote:

Originally posted by Charles Darwin
rRNA and tRNA sequences are not "non-coding." In any case, these sequences were not "involved in gene regulation and production of functional bits of RNA, like ribosomal and transfer RNA." That's the point.

They may be called "non-coding" if one means by that "not translated into a protein".

lpetrich · 08-31-2003, 10:43 AM

Quote:

Originally posted by Charles Darwin
Interesting. If the mismatches were not rare then it would be a problem for evolution? Unfortunately, the answer is not yes. Of course I don't know what you intend by the term "rare" but such mismatches are all over the place. One need only look. I was asked for examples, I gave some. There are plenty more.

It must be conceded that there are some circumstances that are likely to produce mismatches, like greatly varying rates of evolution and relatively rapid divergence However, there are ways for testing for such circumstances, such a rerunning a tree-finding algorithm with different randomly-chosen taxon-addition orders, and seeing which topologies consistently appear.

So I don't see why these difficulties support a poof-poof-poof theory of origins.

lpetrich · 08-31-2003, 10:46 AM

(on lateral transfer of photosynthesis genes...)

That is indeed an oddity, but if the genes are transferred in groups, then some of the coordination difficulty disappears.

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08-31-2003, 10:46 AM	#210
lpetrich Contributor Join Date: Jul 2000 Location: Lebanon, OR, USA Posts: 16,829	(on lateral transfer of photosynthesis genes...) That is indeed an oddity, but if the genes are transferred in groups, then some of the coordination difficulty disappears.

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