Freethought & Rationalism Archive

tgamble · 04-03-2002, 05:58 AM

posting by creationist

Quote:

An analysis of the tree of life at its most basic level (kingdoms) indicates that organisms do not share common descent (Pennisi, E. 1999, Is It Time to Uproot the Tree of Life? Science 284: 1305-1307)

A few dozen microbial genomes have been fully sequenced and the results indicate that there is no clear pattern of descent. Certain species of Archea ("ancient bacteria that are best known for living in extreme environments) are more closely related to species of eubacteria ("common" bacteria) than they are to members of their own kingdom. In fact, many microbial species share genes found in eukaryotes (non-microbial organisms characterized by the presence of a nucleus in the cell).

Many evolutionists are now suggesting that gene transfers were so common in the past (a convenient non-provable hypothesis) that a tree of life for microbial species can never be discerned from existing species. Such proposals remove evolutionary theory from being tested, and remove it from scientific criticism."

quote from above:

Quote:

"An analysis of the tree of life at its most basic level (kingdoms) indicates that organisms do not share common descent"

me:

If that claim is true, evolution has just been proven wrong. What's the real deal here?

The article appears to be online but I'm having problems getting at it.
<a href="http://www.sdsc.edu/mpr/compbio_jc/cbjc_s1999.html" target="_blank">http://www.sdsc.edu/mpr/compbio_jc/cbjc_s1999.html</a>

[ April 03, 2002: Message edited by: tgamble ]

[ April 03, 2002: Message edited by: tgamble ]</p>

MrDarwin · 04-03-2002, 07:14 AM

Quote:

A few dozen microbial genomes have been fully sequenced and the results indicate that there is no clear pattern of descent.

Quote:

An analysis of the tree of life at its most basic level (kingdoms) indicates that organisms do not share common descent (Pennisi, E. 1999, Is It Time to Uproot the Tree of Life? Science 284: 1305-1307)

I've rearranged the quotes to emphasize that the conclusion does not follow from the observation. Inability to discern a pattern of common descent does not falsify common descent; we still believe that bacteria came from pre-existing bacteria, which at some point shared a common ancestor. However, it does pose a serious problem for defining the term "species" at the microbial (or at least prokaryotic) level.

Evolutionary theory has not been falsified, but it has proven more complicated than anybody ever thought. But regardless, this does not affect the theory of evolution with respect to eukaryotic organisms one bit. This is somewhat similar to the origin of life question: most biologists believe life had an entirely naturalistic origin, but even if it didn't (e.g., life was planted on this planet by extraterrestrials or by a supernatural force), evolution would still have happened.

Peez · 04-03-2002, 07:23 AM

tgamble quotes:

Quote:

An analysis of the tree of life at its most basic level (kingdoms) indicates that organisms do not share common descent (Pennisi, E. 1999, Is It Time to Uproot the Tree of Life? Science 284: 1305-1307)

A few dozen microbial genomes have been fully sequenced and the results indicate that there is no clear pattern of descent. Certain species of Archea [sic] ("ancient bacteria that are best known for living in extreme environments) are more closely related to species of eubacteria [sic] ("common" bacteria) than they are to members of their own kingdom. In fact, many microbial species share genes found in eukaryotes (non-microbial organisms characterized by the presence of a nucleus in the cell).

I could not access the article, but this quote is confused. If a species is "more closely related to species of eubacteria than they are to members of (Archaea)" then they are members of Eubacteria by definition. Archaea are not "ancient" any more than Eubacteria, though (as the name suggests) they may be more similar in phenotype to those early life forms. "Eubacteria" means "true bacteria," not "common bacteria" (though most common bacteria are members of the Eubacteria). Eukaryotes are not all non-microbial (Amoeba, Paramecium, Euglena, many algae, Giardia, to name just a few microbial eukaryotes). Of course many microbial species share genes found in non-microbial species, and many prokaryotes share genes with eukaryotes, and many Eubacteria share genes with Archaea and Eukarya, this is evidence for evolution. Note that Archaea are considered to be more closely-related to Eukarya than to Eubacteria, even though Archaea and Eubacteria are both prokaryotic.

Quote:

Many evolutionists are now suggesting that gene transfers were so common in the past (a convenient non-provable hypothesis) that a tree of life for microbial species can never be discerned from existing species. Such proposals remove evolutionary theory from being tested, and remove it from scientific criticism."

Nope. The transfer of genes from one species to another was recognized before this: it raises some interesting issues but is not really a problem for evolution. For example, the mitochondria found in almost all eukaryotes evolved from Eubacteria. As for it being "common," the ease with which organisms can be assigned to kingdoms based on their genetic make-up falsifies this assertion.

Quote:

"An analysis of the tree of life at its most basic level (kingdoms) indicates that organisms do not share common descent"

Wishful thinking, but not true.

Quote:

If that claim is true, evolution has just been proven wrong. What's the real deal here?

I would not go that far. If gene transfer across species was common, it would make tracing lineages with genetics more complex, but it would not invalidate evolution at all. The evidence for common descent would remain (and might even be strengthened, not that it needed to be), and the theory of evolution would simply be refined (Dawkins' selfish gene model would fit in nicely).

Quote:

The article appears to be online but I'm having problems getting at it.
[URL=http://www.sdsc.edu/mpr/compbio_jc/cbjc_s1999.html[/URL]

It appears to be at a restricted site.

Peez

[ April 03, 2002: Message edited by: Peez ]

[ April 03, 2002: Message edited by: Peez ]</p>

Oolon Colluphid · 04-03-2002, 07:51 AM

tgamble, where did you get this from? Not the Computational Biology Journal Club I�d guess?! Reason I ask is, you�ve not made it clear which bits if any are supposedly from the Science article cited. (And you will have trouble getting it, you need to subscribe

.) so, from what you posted:

Quote:

An analysis of the tree of life at its most basic level (kingdoms) indicates that organisms do not share common descent (Pennisi, E. 1999, Is It Time to Uproot the Tree of Life? Science 284: 1305-1307)

Nope. The article indicates, not that there�s not been common descent, but just that discerning its really really early patterns ain�t easy. As the summary of the article says:

Quote:

When full DNA sequences opened the way to comparing many different genes in different organisms, the comparisons proved confounding. Rather than clarifying the tree that seeks to show how life evolved, they often produced new trees that differ from the traditional tree and conflict with each other as well. Now some microbiologists, pointing to evidence that microbes have swapped genes wantonly over evolutionary history, say that many of these genes are an unreliable guide to evolutionary history and the old tree is still basically sound. But others think it's time to uproot the old tree and are proposing candidates for new trees based on specific features of the genome and cell structure. And still others worry that gene swapping has turned the tree of life into a tangled briar whose lineages will be next to impossible to discern.

To continue...

Quote:

Many evolutionists

Having read the article, I�d quibble about �many�...

Quote:

are now suggesting that gene transfers were so common in the past (a convenient non-provable hypothesis)

Hahaha! Creationists know all about those... trouble is, gene transfer is a well-documented fact in modern bacteria... and it�s reasonable to assume that things, genome-wise, were a lot sloppier in the early stages of evolution.

Quote:

that a tree of life for microbial species can never be discerned from existing species.

It�s �may never�, not the emphatic �can never�, but fair enough. But it�s hardly the disaster for evolution that the creationist spin-doctors make it sound. The original article continues:

Quote:

This new tree of life pleases some researchers, particularly those who already have reason to suspect that the current tree might be misleading. For example, Maryland's Robb says he's often suspected that the placement of the hyperthermophiles, microbes that live at extremely high temperatures, toward the bottom of the tree might be an artifact resulting from assumptions about how fast these microbes evolve and on their initial discovery in extreme environments reminiscent of what early life might have experienced.

That placement was based in part on the finding that the DNA in the ribosomal genes of the organisms has lots of guanine and cytosine bases, an indication that their genomes had been around long enough for certain bases to become overrepresented. But it turns out that these bases tend to dominate in the genomes of organisms living in extreme environments, as they help stabilize DNA (Science, 8 January, pp. 155, 220). Thus, these DNAs do not necessarily tell the true story of evolutionary relatedness. [...] [M]any researchers think it's too early to reach any firm conclusions about early evolution from the new genomes. "We just don't have that high a resolution for ancient [events]," says EMBL's Bork. To try to resolve the issue, both he and Philippe advocate not only looking at more genomes but also working to understand better how genomes change through time.

Fraser agrees that more needs to be learned about the molecular mechanisms that underlie evolution. At this point, she says, the only thing that can be said with any certainty "is that the story is by far more complicated than is suggested by the ribosomal DNA tree."

In other words, it just ain�t clear. Which rather different from saying...

Quote:

Such proposals remove evolutionary theory from being tested, and remove it from scientific criticism."

Erm, it would hardly remove all evolutionary theory, just some bits to do with very early life. And anyway, nothing whatever is being removed from testing and criticism. The whole article is about scientists criticising each other�s hypotheses, and about finding ways of resolving it, as the quote above shows.

Quote:

"An analysis of the tree of life at its most basic level (kingdoms) indicates that organisms do not share common descent"

I don�t know where those quote marks came from, but that sentence sure as hell isn�t in the Science article. Of course.

The nearest to it is the article�s subheading:
�More genomes have only further blurred the branching pattern of the tree of life. Some blame shanghaied genes; others say the tree is wrong.�
What�s the betting that is what mutated into the cretinist �quote�?

The Science article in a nutshell: �It�s more complicated than we thought.�

Quote:

(from tgamble I guess):

If that claim is true, evolution has just been proven wrong.

Oh come on tg, you�ve been here long enough to realise that at most, even if that quote were correct, all it would mean is that plants, animals, fungi, bacteria etc, were not related to each other. That�s still a hell of a lot of evolution. Are you sure you�re not a closet creationist?? But anyway, that particular quote is NOT IN THE ARTICLE.

Interestingly, the Pennisi article has been cited a number of times. Here�s the abstract of one, Lin and Gerstein, �Whole-genome Trees Based on the Occurrence of Folds and Orthologs: Implications for Comparing Genomes on Different Levels�, in Genome Research, Vol 10 Issue 6, 808-818, June 2000:

Quote:

We built whole-genome trees based on the presence or absence of particular molecular features, either orthologs or folds, in the genomes of a number of recently sequenced microorganisms. To put these genomic trees into perspective, we compared them to the traditional ribosomal phylogeny and also to trees based on the sequence similarity of individual orthologous proteins. We found that our genomic trees based on the overall occurrence of orthologs did not agree well with the traditional tree. This discrepancy, however, vanished when one restricted the tree to proteins involved in transcription and translation, not including problematic proteins involved in metabolism. Protein folds unite superficially unrelated sequence families and represent a most fundamental molecular unit described by genomes. We found that our genomic occurrence tree based on folds agreed fairly well with the traditional ribosomal phylogeny. Surprisingly, despite this overall agreement, certain classes of folds, particularly all-beta ones, had a somewhat different phylogenetic distribution. We also compared our occurrence trees to whole-genome clusters based on the composition of amino acids and di-nucleotides. Finally, we analyzed some technical aspects of genomic trees -- e.g., comparing parsimony versus distance-based approaches and examining the effects of increasing numbers of organisms. Additional information (e.g. clickable trees) is available from <a href="http://bioinfo.mbb.yale.edu/genome/trees." target="_blank">http://bioinfo.mbb.yale.edu/genome/trees.</a>
(My emphasis)

And from Huynen, Gupta, Doolittle et al, �Lateral Gene Transfer [LGT], Genome Surveys, and the Phylogeny of Prokaryotes�, in Science 286: 1443a-1443:

Quote:

LGT of genes that are not yet present in a genome, and the parallel loss of orthologous genes in distant phylogenetic branches, reduce the phylogenetic pattern in the gene content. We argue that the rate of these processes is not so high as to preclude a phylogenetic view of genome evolution. Genome phylogeny based on gene content disregards the evolutionary history of genes. It is analogous to distance-based phylogenies of sequences that disregard the origin of amino acids. In the absence of a model of sequence or genome evolution, such approaches have been shown to be very useful. In discussions about genome phylogeny and gene phylogenies, it is difficult to see the forest (genome phylogeny) for the trees (gene phylogenies). Higher order approaches that are complementary to gene phylogenies and that stress the complete genome aspect and the relations between the genes should be taken into consideration.
(Again, my emphasis)

Quote:

What's the real deal here?

Creationist lies and misinformation. Why, what did you think would be the deal?

Oolon

Oolon Colluphid · 04-03-2002, 08:01 AM

Peez, there's a PM waiting for you.

This message will self destruct shortly...

Oolon

tgamble · 04-03-2002, 08:41 AM

"Are you sure you�re not a closet creationist??"

Of course not.

"But anyway, that particular quote is NOT IN THE ARTICLE."

good. thanks for the info.

And all I meant was that since evolution is generally common descent, common descent being wrong would mean evolution being wrong.

What I posted is what some cretinist posted on another board. I suspected it was BS. I just wanted some more info. I am not now, nor have ever been a creationist.

[ April 03, 2002: Message edited by: tgamble ]</p>

tgamble · 04-03-2002, 08:47 AM

"I don�t know where those quote marks came from, but that sentence sure as hell isn�t in the Science article. Of course."

um, they came from me. I was quoting part of what I posted and commenting on it.

MrDarwin · 04-03-2002, 09:09 AM

I also had some trouble discerning which were your comments, which were the creationist's comments, and which sentences were directly quoted from the article. (Part of the problem is that there is a closing quotes at the end of the third paragraph, with no corresponding opening quotes.)

Oolon Colluphid · 04-04-2002, 12:02 AM

No problem, tg! I really didn't think so, but the way you posted it made me wonder! Keep 'em coming, looking that article up made me read it, and it was fascinating! (To anyone who wonders why we bother refuting cretinists, the answer's right here: you learn a lot of real science in the process!) But, uh, next time... could you make it a bit clearer who's saying what please?

Oolon

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04-03-2002, 08:01 AM	#5
Oolon Colluphid Contributor Join Date: Sep 2000 Location: Alibi: ego ipse hinc extermino Posts: 12,591	Peez, there's a PM waiting for you. This message will self destruct shortly... Oolon

04-03-2002, 08:41 AM	#6
tgamble Veteran Member Join Date: Sep 2000 Location: St. John's, Nfld. Canada Posts: 1,652	"Are you sure you�re not a closet creationist??" Of course not. "But anyway, that particular quote is NOT IN THE ARTICLE." good. thanks for the info. And all I meant was that since evolution is generally common descent, common descent being wrong would mean evolution being wrong. What I posted is what some cretinist posted on another board. I suspected it was BS. I just wanted some more info. I am not now, nor have ever been a creationist. [ April 03, 2002: Message edited by: tgamble ]</p>

04-03-2002, 08:47 AM	#7
tgamble Veteran Member Join Date: Sep 2000 Location: St. John's, Nfld. Canada Posts: 1,652	"I don�t know where those quote marks came from, but that sentence sure as hell isn�t in the Science article. Of course." um, they came from me. I was quoting part of what I posted and commenting on it.

04-03-2002, 09:09 AM	#8
MrDarwin Veteran Member Join Date: May 2001 Location: Washington, DC Posts: 4,140	I also had some trouble discerning which were your comments, which were the creationist's comments, and which sentences were directly quoted from the article. (Part of the problem is that there is a closing quotes at the end of the third paragraph, with no corresponding opening quotes.)

04-04-2002, 12:02 AM	#9
Oolon Colluphid Contributor Join Date: Sep 2000 Location: Alibi: ego ipse hinc extermino Posts: 12,591	No problem, tg! I really didn't think so, but the way you posted it made me wonder! Keep 'em coming, looking that article up made me read it, and it was fascinating! (To anyone who wonders why we bother refuting cretinists, the answer's right here: you learn a lot of real science in the process!) But, uh, next time... could you make it a bit clearer who's saying what please? Oolon

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