Freethought & Rationalism Archive

lpetrich · 08-30-2003, 09:47 AM

Charles Darwin on family-tree discrepancies:
"The phylogenetic position of the platyhelminths within the metazoan tree is examined ..." C R Acad Sci III., 320:83

"The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear. ..." Nature, 387:489

However, this is an active area of research, as a result of the progress of gene-sequencing technology, and some new results have been emerging. Some old taxonomic ideas, like Protostomia and Deuterostomia, have continued to be supported, but there have been some rather startling new results, like the division of Protostomia into Ecdysozoa (molters) and Lophotrochozoa (those with lophophores [a certain sort of ring of tentacles for feeding] or trochophore larvae). Arthropods belong to Ecdysozoa and annelids to Lophotrochozoa, though they have often been thought to be closely related on account of their segmentation. However, those trochophore larvae are shared by marine annelids and mollusks, both in Lophotrochozoa.

And as to arthropods, one startling new result that has emerged is that Uniramia (insects and myriapods) is not a natural group. Insects are most closely related to the branchiopod crustaceans, a group which includes the well-known brine shrimp Artemia salina. Myriapods (centipedes and millipedes), however, are an early-branching group, comparable to crustaceans and chelicerates (spiders, scorpions, horseshoe crabs, etc.).

Charles Darwin · 08-31-2003, 01:23 AM

Quote:

Originally posted by lpetrich
Charles Darwin:
When you say life looks like it evolved you're begging the question. That is the question at hand.

How is it that living things fit into a family-tree-like hierarchy so well?

Is it some obscure whim? Or is it something else? Like descent with modification?

Whim? Created thinks such as automobiles and aircraft, as evolutionists have pointed out, form "family-tree-like" hierarchies, so why must we resort to the improbable notion of the most advanced machines arising on their own, to explain the observed hierarchy in biology?

Charles Darwin · 08-31-2003, 01:29 AM

Quote:

Originally posted by Doubting Didymus
Regarding phylogenetic mismatches: they are few and far between. They get a lot of airtime in phylogenetic publications because they are rare, unexpected, and worthy of receiving an explaination. It's not like these things are impossible under the evolutionary framework, just that it should be unlikely. For example, further study of the problem may reveal answers:

Correction: answers and explanations have already been provided. There is no "problem" with these mismatches (and no, they are not "few and far between" -- take a look at just the few references I supplied) from the evolution perspective. Evolution is a fact, and the anomalies and mismatches are the result of one or more of a dozen or so possible explanations evolutionists can draw on. But the ability to explain so much means the data are not compelling evidence for evolution. That has been my point.

Charles Darwin · 08-31-2003, 01:43 AM

Quote:

Originally posted by GunnerJ

CD replies:

So does the failure of endogenous retrovial insertions to confirm pre established trees disprove evolution?

No. This does not follow from what DD said at all.

Why? Because there are lots of reasons why, for example, an "HERV... shows up in gorillas and chimps but not humans." They have been listed. Thus, it's plausible that an HERV would not conform to the phylogenic tree for reasons other than the falsehood of evolution.

However, outside of evolution (by this we mean the fact of evolution, i.e., common descent) being accurate, there is no reason for HERVs to confirm the phylogenetic trees.

If you can't tell the difference between this and mere hand-waving and ad-hoc rationalization, then, well, there isn't much I can do to help you. [/QUOTE]

Actually, the only reasons given have been unacceptable from the evolution perspective (eg, the HERV inserted into the ape/chimp line after the human split-off; sorry that won't work). That's not to say that there is no explanatory mechanism. I'm sure they'll come up with something; or maybe they'll just sweep it under the rug.

You say "there is no reason for HERVs to confirm the phylogenetic trees." This is relatively new data, and we still do not understand it all that well. Evolution has an unfortunate history of pronouncing not-well-understood data as undeniable proof, only to later find out that the devil was in the details. Perhaps we should think a bit more carefully about the HERV data.

For if evolution is true, then there must have been a "punctuated equilibrium" type event or events to explain the jump in numbers. And the HERVs must have serendipitously played a role in evolution itself. And there'll have to be plenty of explanations for all the mismatches (see a quote a gave earlier, for example).

Finally, it is a scientific fact that some retro viruses have quite specific insertion site preferences. Is it not possible that HERVs which are found at homologous sites in different species share site preferences?

So why must we say that there is "no reason for HERVs to confirm the phylogenetic trees" aside from common descent? First of all, they don't always confirm those trees, and there are important exceptions; and secondly, there are reasonable alternative explanations which don't require making a mockery of science and natural laws.

Charles Darwin · 08-31-2003, 01:58 AM

Quote:

Originally posted by lpetrich
Charles Darwin:
(endosymbiosis -- most successful is naturally selected...)
I'm not doubting that we can contrive explanations, where we are free to imagine.

Let's imagine that we could go back about 1.5-2 billion years ago to where some early protist was eating last year's crop of cyanobacterium colony.

The endosymbiosis hypothesis states that one of those protists swallowed, but did not digest, some alpha-proteobacterium. That bacterium multiplied inside, living off of the protist's waste products, like acetic acid. One day, due to some membrane-synthesis defect, the bacterium's outer membranes became a bit leaky, allowing some synthesized ATP to escape and AMP, ADP, and inorganic phosphate to return for assembly. This ATP supplied extra energy, helping its host eat more cyanobacterium and grow more and reproduce more, assisting the reproduction of that bacterium.

And that's what I would expect to see -- that or something similar. As opposed to this:

One day, some protists popped into existence with a big *POOF!*. They looked like some existing protist inhabited by an alpha-proteobacterium, however.

"Charles Darwin", is this what you believe?

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.

Quote:

Originally posted by lpetrich

I was referring to membrane-bound organelles, independent of the plasma membrane, such as things like acidocalcisomes which are found in both some prokaryotes and eukaryotes.

That ONLY means that some organelles have not originated by endosymbiosis; I've yet to see anyone claim that they have that origin.

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).

Charles Darwin · 08-31-2003, 02:02 AM

Quote:

Originally posted by lpetrich
Charles Darwin:
Again, all you are doing here is parroting the standard evolution line. Segments that share greater similarity are assumed to have evolved more slowly, and are therefore assumed to have more functional constraint. ...

Why don't you look at discussions of protein structure and function some time? Real discussions, not creationist literature.

Not sure what you are referring to. I've been quoting from journals (eg, Science). Do you have a problem with Science?

Charles Darwin · 08-31-2003, 02:05 AM

Quote:

Originally posted by lpetrich

CD wrote: Then if evolution is true, why do segments in the human and mouse genome, which evolutionists say are functionless, show near identity?

These are noncoding sequences, which can be involved in gene regulation and production of functional bits of RNA, like ribosomal and transfer RNA.

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.

Charles Darwin · 08-31-2003, 02:07 AM

Quote:

Originally posted by Ape31
This has been a most amusing thread and I, like most here it seems, thought CD was a genuine (mustn't say creationist) anti-evolutionist.

However, he has shown a reasonable understanding of most of the arguments and has shown the ability to read and reference primary literature so the only conclusion I can draw is that we are dealing with a most excellent sock-puppet!

I must offer my most sincere congratulations on such a wonderful creation. :notworthy

Or did he evolve perhaps?

r.

If all else fails, pull out the ad hominums.

Charles Darwin · 08-31-2003, 02:11 AM

Quote:

Originally posted by Doubting Didymus
Phylogenetic mismatches are rare, and thus do not cause problems for evolutionary theory. You do not damage a major field of science with five questionable quotations, which I highly doubt you even understand.

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.

Charles Darwin · 08-31-2003, 02:33 AM

quote:
--------------------------------------------------------------------------------
Myself: Phylogenetics is a very precise science with well established guidelines. I don't see how you can call it handwaving.

Thee: "Until about 5 years ago, researchers considered the transfer of genetic material from one species to another an oddity. Since then, genome studies have shown that some genes have moved around quite a bit. [Note, no one has shown any such thing; this all hinges on the assumption evolution is true � CD] Even so, microbiologists assumed this would not be true for genes involved in translating DNA to RNA, for example, or sunlight to biomass; they couldn't see how genes of such mixed ancestry could possibly coordinate these complex processes. But that assumption 'doesn't seem to be true,' says W. Ford Doolittle, an evolutionary biologist at Dalhousie University in Halifax, Nova Scotia. The new work 'clearly shows that photosynthesis genes have moved from one organism to another,' adds Carl Bauer, a biochemist at Indiana University, Bloomington." Science, 298:1538."

Quote:

Originally posted by Doubting Didymus
I may have to take this as evidence that you havent got the foggiest idea what the hell you're talking about. You seem to have no clue about the biology involved here.

Please, dispel this perception for me. Tell me in your own words what the article is talking about. What kind of species does this happen in? What do you suppose is the mechanism of such gene transfers? Importantly, what on earth is the implication of finding genes of mixed ancestry in a species on the accuracy of phylogenetic research? Lastly, regarding your insert into the above quote: (genes have moved around quite a bit. [Note, no one has shown any such thing; this all hinges on the assumption evolution is true � CD]). In your opinion, can genes move between species as described in the above article, or is there no mechanism for such an occurance?

Sorry, I should have pasted in the abstract. The article is about photosynthetic prokaryotes of which there are 5 major groups. Looking at representative genomes from each group, the researchers were able to identify 188 reasonably-likely orthologs upon which to construct a phylogeny.

What they found was a rather striking lack of consensus. Of the 15 possible unrooted trees, they found good support for practically all of them (or should I say, no good support for any one of them). This remained true even when the data set was narrowed to subsets, such as hypothetical common function.

They also expanded their dataset with additional genome data, including non photosynthetic species. To summarize the results I'll quote the paper:

"These results bolster the idea that the evolution of photosynthetic genes has been disconnected from divergence and speciation in these organisms, confirming the extensive role that horizontal gene flow has played in prokaryote evolution."

and,

"The most unexpected result from this analysis is the distinct lack of unanimous support for a single topology. Plurality support is seen for the three trees (5, 10, and 15) that group together Synechocystis sp., C. aurantiacus, and H. mobilis separate from a distinct R. capsulatus and C. tepidum cluster. The data suggest that even strongly supported phylogenies and highly conserved genes from these organisms often show very different evolutionary histories."

Unexpected? Yes; but a problem for evolution? Of course, not. There is always HGT to call upon. Remember, this is evidence for the fact of evolution.

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08-30-2003, 09:47 AM	#191
lpetrich Contributor Join Date: Jul 2000 Location: Lebanon, OR, USA Posts: 16,829	Charles Darwin on family-tree discrepancies: "The phylogenetic position of the platyhelminths within the metazoan tree is examined ..." C R Acad Sci III., 320:83 "The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear. ..." Nature, 387:489 However, this is an active area of research, as a result of the progress of gene-sequencing technology, and some new results have been emerging. Some old taxonomic ideas, like Protostomia and Deuterostomia, have continued to be supported, but there have been some rather startling new results, like the division of Protostomia into Ecdysozoa (molters) and Lophotrochozoa (those with lophophores [a certain sort of ring of tentacles for feeding] or trochophore larvae). Arthropods belong to Ecdysozoa and annelids to Lophotrochozoa, though they have often been thought to be closely related on account of their segmentation. However, those trochophore larvae are shared by marine annelids and mollusks, both in Lophotrochozoa. And as to arthropods, one startling new result that has emerged is that Uniramia (insects and myriapods) is not a natural group. Insects are most closely related to the branchiopod crustaceans, a group which includes the well-known brine shrimp Artemia salina. Myriapods (centipedes and millipedes), however, are an early-branching group, comparable to crustaceans and chelicerates (spiders, scorpions, horseshoe crabs, etc.).

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