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Friday, June 24, 2005

Urmetazoa rising

Nature has an interesting short review this week about the search for the urmetazoan, the last common ancestor of all animals. The search isn't for a fossil, of course, since the urmetazoan would have been minute, soft, and rather nondescript, but is instead a plunge into the genomes of extant simple forms, like choanoflagellates and sponges, to extract the common elements of their molecular circuitry. There's a brief summary of what we've learned so far, but what I found most enticing is the promise of what is to come.

Like choanoflagellates, the urmetazoan's single-celled ancestors may have used signals relayed by proteins called tyrosine kinases to sense changes in the outside world. Cell adhesion might have helped unicellular organisms to form simple colonies — colonies that may have been an intermediate step between single cells and true multicellularity. The urmetazoan may then have recruited these genes for new purposes. "Evolution is an extremely dynamic system and paradoxically a very lazy one," says palaeobiologist Simon Conway Morris at the University of Cambridge, UK, who studies the origins of metazoans. "It will co-opt whatever it can."

But this raises a puzzling question. If the toolkit was already there, why didn't animals evolve sooner? The answer seems to be that the catalyst for multicellular animal life may not have been genetic but environmental — in the form of rising global oxygen levels.

Whatever the trigger, researchers hope that the completion of the choanoflagellate genome sequence, expected later this year, will yield fresh insights into the biology of this momentous transition. Genome sequences are also expected for the sea anemone Nematostella vectensis and the simplest known living animal, Trichoplax adhaerens. Trichoplax is just two cells thick, has only four cell types and looks like a giant multicellular amoeba. Its genome promises to be the smallest of any animal yet measured and should define the minimum set of genes needed for animal life. Sea anemones, which have a more advanced body plan, could yield information on the genetic mechanisms underlying body-plan formation.

Isn't that exciting? Predictions from evolutionary biology are leading us directly to detailed analyses of the function and origin of fine details of the molecules in diverse organisms—and that is the power of good science.


Pilcher H (2005) Back to our roots. Nature 435:1022-1023.


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Comments:
#29651: — 06/24  at  09:41 AM
I wonder what the IDers would make of this? I challenge the educated ones, mostly lawyers, to explain how ID "theory" would account for such discoveries.



#29654: Krauze — 06/24  at  10:00 AM
Hi TC,

"I wonder what the IDers would make of this?"

Totally unrelated, I've just blogged about this very article at Telic Thoughts:

Front-Loading and the Urmetazoan



#29655: — 06/24  at  10:09 AM
Maybe. This view, however, is in conflict with the molecular data, which consistently places Placozoans among the more derived metazoans (Abouheif, Zardoya, & Meyer 1998; Collins 1998, 2002; Kim, Kim, & Cunningham 1999; Peterson & Eernisse 2001). If this is the case, Placozoa must have undergone an extreme degree of reducing selection, losing such non-trivial features as "specialized muscle cells, nerve cells, and a fixed anteroposterior axis" (Jenner 2004, 374).



's avatar #29656: John M. Price — 06/24  at  10:11 AM
<raving creationist>

Predictions from evolutionary biology? I think NOT!

Every God fearing human knows that that ain't so! Evolution is a tale of the past based on strong faith and biblical hatred.

REPENTENCE is needed to remove this blaspheming thought!

Think of your soul, man of hubris! Think of your soul!

</raving creationist>



#29658: — 06/24  at  10:24 AM
If the IDer(s) "front-loaded" for an eventual biota like today's, why the hell was the atmosphere not bio-oxygenated over a billion years earlier? Surely this would be child's play for the unimaginabley talented Front-Loader(s)? Why kill off over a billion years worth of laboriously evolved anoxic lineages?



's avatar #29660: PZ Myers — 06/24  at  10:42 AM
"Front-loading" is complete and utter bullshit. It doesn't make sense, it contradicts how we know molecular biology works, and there is no evidence for it anywhere, nor is there any known mechanism for preserving large quantities of unused genetic information intact within a genome for billions of years. Fans of it usually have to resort to a bizarre deterministic view of inheritance that is absurdly fixed--they are a kind of faux-scientific Calvinist.

So there you go, tc99mman. What will the IDers make of it? They will invent a mountain of pseudoscientific BS.

PZ Myers
Division of Science and Math
University of Minnesota, Morris



#29663: — 06/24  at  10:59 AM
"The answer seems to be that the catalyst for multicellular animal life may not have been genetic but environmental — in the form of rising global oxygen levels."

Presumably outer cells robs inner cells of oxygen, at least without a circulatory system. So it may take a long time for multicellulars to develop, longer than most stars live.

Which would be a pity - there is a lot of real estate out there that will not see much evolution. Does that makes IDers happy (not much evolution) or sad (not many worshipers), one wonders?



#29669: — 06/24  at  11:13 AM
Something relevant which was raised for discussion on the BBC science MBs (though the thread will have been deleted many months ago):
http://www.ceab.csic.es/~maldonado/INV-BIOL-04.pdf



#29672: Krauze — 06/24  at  12:24 PM
Myers, with his comment about "preserving large quantities of unused genetic information intact within a genome for billions of years", shows that he really doesn't know what front-loading is about. As the Nature article shows, precursors to structures used by multicellular creatures can have a different function in unicellular organisms, where they can be co-opted for their current role.



#29680: — 06/24  at  01:19 PM
Behe's little original 1996 "front-loading" suggestion in DBB did imply stocked-up genetic material. Myers, a biologist in the reality-based community, can't be blamed for "really not knowing frontloading", i.e. not keeping up with the latest ad hoc version of Mike/Julie Gene/Thomas.
Address the bio-oxygenation question, Krauze. People are talking about bio-oxygenating the Martian atmosphere over a matter of centuries. Surely the mighty frontloading IDer(s) could have done the earth's in 10 million years?



's avatar #29681: PZ Myers — 06/24  at  01:29 PM
No, I've actually read their nonsense about "front-loading". It doesn't work. The genes in choanoflagellates and humans are similar, but different. The idea that the magical designer loaded up some urmetazoan with Wnt genes and flagella with the idea that it would produce Homo sapiens, or something like it, is nonsense. Mainly what it produced is other simple forms.

PZ Myers
Division of Science and Math
University of Minnesota, Morris



#29692: Krauze — 06/24  at  02:19 PM
Hi Fed Up,

"Behe's little original 1996 "front-loading" suggestion in DBB did imply stocked-up genetic material. Myers, a biologist in the reality-based community, can't be blamed for "really not knowing frontloading", i.e. not keeping up with the latest ad hoc version of Mike/Julie Gene/Thomas."

So Myers was perfectly comfortable speaking authoratively on a topic he hadn't kept up with since 1996?

"Address the bio-oxygenation question, Krauze."

Sorry, but I'm not your servant, of whom you can demand to "adress" what suits your fancy. My interest in this thread sprung from the comment by "tc99mman", who asked, "I wonder what the IDers would make of this?" So, I linked to what this particular IDer makes of this particular subject.



#29694: — 06/24  at  02:22 PM
But you haven't read enough of their latest nonsense about 'front-loading'.
Krauze mentions it's now hip to co-option - Wnt could have come from a mutated coopted duplication, the flagella from a coopted secretory system, the evolution of evolvability biases certain types of mutation, and back front-loading goes into something indistinguishable from the weird Simon Conway-Morris version of evolution except the IDer(s) can also hide temporarily in any gaps in knowledge. Asking questions about the super-genius but drunken IDer(s) is the only way to embarrass them into silence.



#29696: Krauze — 06/24  at  02:26 PM
Hi PZ,

"No, I've actually read their nonsense about "front-loading"."

Then how did you get the idea that it involved "preserving large quantities of unused genetic information intact within a genome for billions of years"?

"It doesn't work."

You're entitled to your subjective opinion.

"The genes in choanoflagellates and humans are similar, but different."

Yes. And?

"The idea that the magical designer loaded up some urmetazoan with Wnt genes and flagella with the idea that it would produce Homo sapiens, or something like it, is nonsense."

My post said nothing about "Homo sapiens, or something like it". How did that particular interpretation of my post get into your reply?

"Mainly what it produced is other simple forms."

Yes, not all lineages evolved multicellularity. However, the non-teleological approach gave us no reason to expect that structures adapted to the needs of unicellular organisms should be of such use to multicellular animals.



#29703: — 06/24  at  03:41 PM
The "non-teleological approach gave us no reason to expect" co-option and exaptation as a process of evolution?
Unbelievable. Thanks for posting that comment here. Much more convenient than wasting time at your blog.

And no one in the world can 'speak authoritatively' on the vague, ever-changing, amorphous concept of frontloading. Not even Mike Thomas, who has come a long way since he was writing admirably of fixity-of-kinds creationists Bohlin and Lester.

As anyone who can scroll can see, Krauze, you're just lying when you imply I said Myers "hadn't kept up with frontloading since 1996". I implied he doesn't waste time reading the very latest of ID's infertile ejaculations.
And how would anyone get the idea ID frontloading involved large quantities of genetic information preserved for billions of years? Which prominent IDer said this, Krauze?
"Suppose that nearly four billion years the designer made the first cell, already containing all of the irreducibly complex biochemical systems discussed here and many others. (One can postulate that the designs for systems that were to be used later, such as blood clotting, were present but not "turned on". In present day organisms plenty of genes are turned off for a while, sometimes for generations, to be turned on at a later time.)"



#29706: Krauze — 06/24  at  04:18 PM
Hi Fed Up,

"The "non-teleological approach gave us no reason to expect" co-option and exaptation as a process of evolution?
Unbelievable. Thanks for posting that comment here. Much more convenient than wasting time at your blog."


It's a historical fact that scientists, working under a non-teleological paradigm, did not expect the high degree of genetic conservatism in the genetics underlying the bodyplans. Here's Mike Levine:
"When I was a student, there was a sense that all animals did things differently. If a gene was conserved between different animals, or between plants and animals, it was considered to be boring. How could it be interesting, because all animals and plants are different from each other? So, certainly, creating distinct forms of life couldn't depend on a common set of molecules. And so to see that genes that are doing such profound things in the fruit fly -- making head from tail, stomach from back, thorax from abdomen -- are conserved, related in other animals ... this was just not predicted by anybody. At least nobody that I ever read."

Or how about Brian Hall?
"Important as these developments were, they were carried out against the then current wisdom that organisms differ because they possess unique genes not found in other organisms - lobster genes for lobsters, human genes for humans, and so forth.

The discovery of homeobox genes turned this approach upside down and inside out. The body plans of lobsters and humans, flies and fish, barnacles and mice, are initiated using the same families of genes that are conserved across the animal kingdom."

"As anyone who can scroll can see, Krauze, you're just lying when you imply I said Myers "hadn't kept up with frontloading since 1996". I implied he doesn't waste time reading the very latest of ID's infertile ejaculations."

Which is different from what I said how?

"And how would anyone get the idea ID frontloading involved large quantities of genetic information preserved for billions of years? Which prominent IDer said this, Krauze?"

That's a quote from Behe's 1996 book. But remember that "nonsense" by other IDists that PZ claimed to have read since.



's avatar #29707: PZ Myers — 06/24  at  04:35 PM
You ID guys are all a bunch of frauds, aren't you?

Exaptation and cooption were expected and predicted evolutionary processes. What you've brought up here is not evidence against that.

We did not expect the degree of conservation seen in the molecules underlying body plans. That was a surprise. We actually expected, given a half billion years, all of the sequences would have been so chewed up by time that all of the homology would be invisible. Of course, that was an expectation formed before anyone had a chance to really look at genetic sequences and get a solid feel for rates of change; when we actually had the tools to look at these things, that's when we learned how well patterns had been preserved.

Note, however, that Intelligent Design creationism said nothing either way about what we'd find. And also note that the discovery reinforced evolution: we found a molecular record that was stronger and clearer than anticipated, allowing us to see relationships better.

Also note that these revolutionary discoveries did not drive Hall and Levine away from evolution, or anyone else for that matter. Those discoveries of molecular homologies have driven a revolution in molecular genetics and developmental biology that drew those disciplines more closely into the evolutionary fold.

Only an incompetent ass would quote Hall and Levine, or consider the amazing new work in molecular genetics, as part of a case for Intelligent Design creationism. You're just parroting stuff you don't understand blindly.

PZ Myers
Division of Science and Math
University of Minnesota, Morris



#29716: Krauze — 06/24  at  06:04 PM
Hi PZ,

At first, I almost thought you were disagreeing with my point:

"Exaptation and cooption were expected and predicted evolutionary processes. What you've brought up here is not evidence against that."

But when the smoke cleared, it turned out you weren't:

"We did not expect the degree of conservation seen in the molecules underlying body plans. That was a surprise. We actually expected, given a half billion years, all of the sequences would have been so chewed up by time that all of the homology would be invisible."

Indeed. But where did this expectation come from? After all, "[e]xaptation and cooption were expected and predicted evolutionary processes."

"Of course, that was an expectation formed before anyone had a chance to really look at genetic sequences and get a solid feel for rates of change; when we actually had the tools to look at these things, that's when we learned how well patterns had been preserved."

Yes, the increased accuracy of data forced scientists to abandon the expectations derived from a non-teleological understanding of evolution.

"Note, however, that Intelligent Design creationism said nothing either way about what we'd find. And also note that the discovery reinforced evolution: we found a molecular record that was stronger and clearer than anticipated, allowing us to see relationships better."

I never said that the results didn't reinforce evolution; as I've said on my profile, I'm an evolutionist.

"Also note that these revolutionary discoveries did not drive Hall and Levine away from evolution, or anyone else for that matter."

Nor did I claim that they did.

"Only an incompetent ass would quote Hall and Levine, or consider the amazing new work in molecular genetics, as part of a case for Intelligent Design creationism."

I'm not arguing for creationism.

And I didn't claim that the quotes from Hall and Levine supported ID. I quoted them to support my point that the genetic conservatism wasn't expected. You already said you agree with this, so why so miffed?

I gotta' admit, PZ, you're not doing good. You get front-loading wrong, think that my post was arguing for the front-loading of "Homo sapiens, or something like it", and now you have me a confused with an advocate of creationism. Try paying more attention to the posts you're responding to, and less attention to your stereotypes of how IDists should behave.



#29723: — 06/24  at  07:07 PM
So, Krauze seems to be saying that exaptation and cooption
are misnamed. These processes are actually part of the "grand design." My question is, Is this "designer" a natural or "super" natural entity? If natural, then one is prompted to ask about the origin of this "designer." If "super" natural, then, we are discussing religion, not science. (Unless Krauze will claim that science has both a materialistic (natural) and "super" natural methodology. This puts it in the category of religion.)
I suspect that the IDers think that they have found "fingerprints" of the "designer" in organisms and biological processes. Evolution seeks to explain using methodological naturalism. ID, invoking a higher (super) entity, is practicing a mixture of natural and "super" natural methodology, not science. Thus, the resorting to arguments from ignorance and appealing to a "designer" of the gaps. Wrongheaded tenacity is no virtue. Krauze is not dealing in science. If teleology is science, please explain the connection? I do not see it.



#29741: — 06/24  at  10:48 PM
I am not sure about Trichoplax being a living fossil. The time scale is forbidding, it seems improbable that any organism could protect its niche against evolved competitors for so long with no change. Trichoplax may be a reduced version of something more complex.

If I may throw in my 2 c., in another thread we seem to have agreed that the number of basic viable types is limited and that evolution follows the same path time after time. Space-travelling extraterrestrials may have an humanoid form. This is not "front-loading" but I would not dismiss the idea that once you get evolution in march on a planet like this, you end up with an organism similar to us. Or to be more bold, once you have a big-bang thing started, you arrive by natural processes alone to a planet like this where self-reproducing organisms will appear, that in time will evolve into something like us. The thought of God manipulating molecules is unnecessary and infantile.



#29746: — 06/25  at  02:43 AM
Huh...I was always under the impression that the common ancestor of sponges, cnidarians, Ediacarans and the rest of us was unicellular--that we all developed multicellularity independently. Is that an outdated view, or did I just have it wrong in the first place?



#29760: — 06/25  at  07:24 AM
Krauze is merely another in a short list of Mike Gene/Julie Thomas worshippers. Previous members included Nelson Alonso, DNAunion(Rick Pierson), Jack (of ARN), and Peter Nyikos. What do they have in common? They cite Mike Gene's writings as if they were gospel truth that ID generates positive research results (they have not). They cite Mike Gene's in toto to respond to critiques (when they do not). They cite scientific research to support Mike Gene's prophecies (and as are typical behavior for believers of prophecies, facts are often forced to fit their fantasies). Finally, like zealots, they defend their idol to the end.

Anyway, the biooxygenation question is quite important to "front loading ID evolutionists," since Julie Thomas addressed it in her nitrogenase article. He specifically predicted that these Designers would use molecular machines to terraform the Earth. It stands to ask why they missed Mars en route to our solar system. It also stands to ask why they used machines that were so sensitive to oxygenation. Significant evidence indicates the Designer of "front loading ID evolutionists" had very little foresight or teleological input into the evolution of life. I guess I can call myself a "Random Design evolutionist." =)

For more smackdown of Julie Thomas's thesis, go here: http://www.iidb.org/vbb/showthread.php?t=72089

BTW, no one should find any credibility that Krauze is an "evolutionist." Adopting this label was merely part of a rhetorical game. See evidence, here: http://telicthoughts.com/?p=75 Case in point, "Intelligent Design evolutionists" abhor the politics behind ID. They recognize that teleology has been around for quite a long time. Yet, they continue to adopt the ID label, and participate in the anti-evolution dialogue with zeal. Why maintain such close ties with such shady groups and engage in their tactics? After all, could "Intelligent Design evolutionists" not call themselves, e.g., Aristotlean Telelogical evolutionists? Maybe, "Intelligent Design evolutionists" have better things to do (like coming up with research for a positive ID theory) than attack Richard Dawkins and the Smithsonian Institute?

No, I think PZ got it right. These people are liars and frauds.



#29808: Krauze — 06/25  at  05:22 PM
Hi TC,

"So, Krauze seems to be saying that exaptation and cooption are misnamed."

I don't remember saying that. In fact, I was the first to use the term cooption in this thread.

As for the rest of your questions, they have all been adressed at our blog. Also, since none of them actually have anything to do with the subject of this thread, which you yourself asked for an IDer's take on, I hope you'll understand why I'll refrain from answering them.



#29809: Krauze — 06/25  at  05:31 PM
Hi Jaimito,

I agree with you about Trichoplax; we should be wary of treating this as a model of the pre-multicellular state.

By the way, it should be noted that the essay that you quote is located at Mike Gene's homepage. I wonder if Wad will also accuse you of being a Mike Gene worshipper. wink

"The thought of God manipulating molecules is unnecessary and infantile."

You're entitled to your theological views, but I don't share them.



#29812: Krauze — 06/25  at  06:09 PM
Okay, let's look at "Wad of ID"'s response. He characterizes me as being a "Mike Gene/Julie Thomas worshipper" who "cite Mike Gene's writings as if they were gospel truth" and defend my "idol to the end." What evidence does "Wad" present for this characterization? That's right, none at all.

In fact, as one with the most intimate knowledge about my own motivations, I know that Wad's characterization is wrong. So where did Wad get it from?

Wad thinks that "the biooxygenation question is quite important", yet I beg to differ. Had it been the case that I had claimed that front-loading had answered all its question and demanded that everyone else adopt it as their position, he would have had a point. But I didn't.

My interest in this thread was prompted by "tc99mman", asking "what the IDers would make of this", so I linked to a post containing my ID interpretation of the article. Neither in the post nor in my comments here have I claimed that these results prove design, nor have I demanded that Wad or anyone else adopt my position.

In fact, it appears that no one are actually interested in discussing the topic of this thread. PZ wants to talk about creationism and how "incompetent" I am; "tc99mman" wants to talk about whether the designer is natural or supernatural; and "Wad of ID" wants to talk about biooxygenation and my motivations.

Finally, Wad thinks my calling myself an ID evolutionist is merely part of a rhetorical game, and suggests that I should call myself an "Aristotlean Telelogical evolutionists". Of course, if I were to follow this "advice", Wad would probably just accuse me of being an Aristotle worshipper and of hiding my Trojan horse in another Trojan horse.



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