Nick Matzke posted Entry 3080 on April 18, 2007 06:09 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/3070

A detailed eyewitness report on the Discovery Institute’s conference revival at Southern Methodist University last weekend has been published. This bit (p. 3) is particularly good:

At this point, we were fed up with the sheer lack of science being discussed. (Remember, ID theorists claim to support a science, not a religion.) So we held up our signs. They bore questions such as, “Why do we have wisdom teeth if they do not fit our jaws?” and “Why did it take 20 species of elephant to go extinct to get two species that survived?” and “Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?” to name a few.

Well, after holding up these signs for a while, the men on stage noticed and decided to answer one of them. They chose the last one, regarding ribosomes. Immediately, the only person on stage with any knowledge of biology, Michael Behe, took up the question.

His answer was that ID theory does not allow for explanations regarding interspecies commonalities such as those implied in the question.

In short, his answer was that he couldn’t explain it with ID theory.

But then he went on, describing how a Creator may have given humans similar ribosomes for no good reason. His logic was that when one sees a car with a radio, one can ask how that radio got there and there are many explanations.

One such explanation was provided by Behe, and it was so very realistic: He said the radio could’ve fallen from an apartment and landed in the car, suggesting that a Creator could have simply thrown ribosomes all over the place, and they just landed in humans by chance. Very likely, indeed.

Over the course of the event, two of my friends decided to stand up slightly and move a row ahead. When they did, they were manhandled by SMU’s finest officers and escorted out.

[…]

(HT: Red State Rabble via Afarensis)

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Comment #170728

Posted by Alan Kellogg on April 18, 2007 6:44 PM (e)

If God designed us the way we are, can I sue Him for my scoliosis?

Comment #170742

Posted by Inoculated Mind on April 18, 2007 7:49 PM (e)

Awesome opinion piece. I had dreamed of getting 100 people to show up wearing fake green beards to these kinds of events, but that would have been too esoteric.

I am simply amazed at the gall of these people trying to keep flyers from being distributed by hand. They ought to lodge a formal protest with the university against the sponsoring organization. The DI ought to get banned for behaving like that.

Interesting to hear Behe and the others finally becoming a bit more honest for a change. Too bad we don’t know the name of the ID Prop. who admitted that the DI’s mission was true.

Comment #170743

Posted by harold on April 18, 2007 8:00 PM (e)

By a coincidence (or “coincidence”), SMU is also going to be the site of the George W. Bush presidential library. Seriously.

I’m quoting from memory, but if I recall correctly, there are already protests that some kind of monstrous structure is going to disrupt the “graceful Georgian campus located in a well-to-do suburb”.

I’m not sure that the futurologists at SMU are doing a great job of forecasting. Maybe the Methodists at SMU should have asked the Baptists at Baylor for some advice about ID.

Comment #170746

Posted by Sir_Toejam on April 18, 2007 8:05 PM (e)

If God designed us the way we are, can I sue Him for my scoliosis?

most certainly.

the problem is in serving the summons.

Comment #170747

Posted by Sir_Toejam on April 18, 2007 8:06 PM (e)

By a coincidence (or “coincidence”), SMU is also going to be the site of the George W. Bush presidential library.

a library of comic books?

Comment #170752

Posted by Jedidiah Palosaari on April 18, 2007 8:21 PM (e)

I live in Seattle. Who wants to join me with some signs near the corner of 3rd & Pike?

Comment #170755

Posted by Paul Nelson on April 18, 2007 8:36 PM (e)

“Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?”

They do?

The mammalian mitochondrial ribosome (mitoribosome)1 has a smaller sedimentation coefficient (55 S), compared with the bacterial ribosome (70 S), and consists of large 39 S and small 28 S subunits (5). The former contains 16 S and the latter contains 12 S rRNAs as RNA components. The mammalian mitoribosome contains no counterpart for the 5 S rRNA found in bacteria. A recent physicochemical study has revealed that the rat mitoribosome has a large molecular mass (3.57 MDa) compared with that of the Escherichia coli ribosome (2.49 MDa) (6), which is explained by the fact that the protein to RNA ratio is completely reversed between these two ribosomes (7). The protein composition of the mitoribosome has been estimated to be about 75%, which indicates that large parts of bacterial rRNA domains have been replaced by protein components during mitochondrial evolution from a eubacteria-like endosymbiont in eukaryotic cell progenitors.

See T. Suzuki et al., “Proteomic Analysis of the Mammalian Mitochondrial Ribosome,” Jl Biological Chem 276 (2001):33181-33195.

Comment #170757

Posted by Doc Bill on April 18, 2007 8:48 PM (e)

Wow! Is this THE Paul Nelson of “ontogenetic depth” fame who PZ says is 3 years tardy with an answer to his question?

Perhaps, Paul, you could answer this question:

What would the “ontogenetic depth” be of a radio falling from an average sized apartment building onto

a) concrete
b) loose beach sand
c) a plate of cheese nachos

I await your reply.

p.s. If you are not THE Paul Nelson then forget the above and carry on. That is all.

Comment #170759

Posted by daenku32 on April 18, 2007 8:49 PM (e)

Maybe it’s my tiny brain, but my wisdom teeth haven’t caused me any trouble. (I know they are a bitch to keep clean, but the primary reason to pull them hasn’t surfaced). Not sure if I got an evolutionary advantage or what.

Comment #170760

Posted by Julie Stahlhut on April 18, 2007 8:49 PM (e)

Immediately, the only person on stage with any knowledge of biology, Michael Behe, took up the question. His answer was that ID theory does not allow for explanations regarding interspecies commonalities such as those implied in the question.

Oh, Zarquon. You’re frassin’ me, right? This man is a faculty member in a SCIENCE DEPARTMENT?

Hmmmm – Let’s see. You’re a faculty member in a Department of Intelligent Design. Your star graduate student is writing her dissertation proposal and suggests that it might be fruitful to explore the reasons for genetic and developmental homologies between species. (Okay, being in your ID department, she doesn’t realize there’s a literature on this subject, but at least she’s thinking.) What do you do?

A. Require her to remove the part of the proposal that suggests she’s curious about the subject and wants to investigate it.

B. Call the security people and have her kicked out of the building.

C. Write “Just move along, there’s nothing to see here” on her draft proposal and never bring up the subject again.

D. Pray for her.

E. All of the above.

Comment #170761

Posted by raven on April 18, 2007 8:50 PM (e)

Immediately, the only person on stage with any knowledge of biology, Michael Behe, took up the question.

His answer was that ID theory does not allow for explanations regarding interspecies commonalities such as those implied in the question.

In short, his answer was that he couldn’t explain it with ID theory.

Well at least Behe is honest about it. Got to give him a point here. Evolutionary thought can explain that and lots more. That is one of the reasons the theory was developed.

I’m liking my creo theory more and more. They have decided to suspend disbelief permanently and enter into a fantasy world. We all do this when watching a movie, TV, or reading a fiction book, temporarily.

It is probably harmless. They have a right to do so in a free country. They could just as easily have decided to be Jedi knights and wander around in robes carrying light sabers and looking for Sith Lords and their starship.

The big problem is trying to force this fantasy world on people who don’t want to enter into it by of all things, sneaking it into biology classes. This is wrong, immoral, illegal, foolish to our nation, and dumb. Just say no.

Comment #170763

Posted by Kevin on April 18, 2007 9:02 PM (e)

“By a coincidence (or “coincidence”), SMU is also going to be the site of the George W. Bush presidential library. Seriously.”

I think the word is

co-inky-dink.

Comment #170771

Posted by steve s on April 18, 2007 9:17 PM (e)

Comment #170746

Posted by Sir_Toejam on April 18, 2007 8:05 PM (e) | kill

If God designed us the way we are, can I sue Him for my scoliosis?

most certainly.

the problem is in serving the summons.

No problem. God is everywhere, so just throw the summons at anything. Yahweh, you got served..

Comment #170772

Posted by Pete Dunkelberg on April 18, 2007 9:18 PM (e)

RSR also implicitly raises the ancient mystery “If humans evolved from other primates, why are there still creationists”?

Comment #170777

Posted by B. Spitzer on April 18, 2007 9:31 PM (e)

“Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?”

They do?

The mammalian mitochondrial ribosome (mitoribosome)1 has a smaller sedimentation coefficient (55 S), compared with the bacterial ribosome (70 S), and consists of large 39 S and small 28 S subunits (5). The former contains 16 S and the latter contains 12 S rRNAs as RNA components. The mammalian mitoribosome contains no counterpart for the 5 S rRNA found in bacteria. A recent physicochemical study has revealed that the rat mitoribosome has a large molecular mass (3.57 MDa) compared with that of the Escherichia coli ribosome (2.49 MDa) (6), which is explained by the fact that the protein to RNA ratio is completely reversed between these two ribosomes (7). The protein composition of the mitoribosome has been estimated to be about 75%, which indicates that large parts of bacterial rRNA domains have been replaced by protein components during mitochondrial evolution from a eubacteria-like endosymbiont in eukaryotic cell progenitors.

See T. Suzuki et al., “Proteomic Analysis of the Mammalian Mitochondrial Ribosome,” Jl Biological Chem 276 (2001):33181-33195.

Yes, they do. If you sequence the RNA in a mitochondrial ribosome, the sequence is a much closer match to the RNA in the ribosomes of a proteobacterium than it is to the RNA in any other organism’s ribosomes. Also, antibiotics such as chloramphenicol will inhibit the mitochondrial ribosome and the ribosomes of bacteria, but they won’t affect the function of the ribosomes in the cytosol of your cells. (But try fitting all of that on a sign…)

Now, if the sign had said “My mitochondrial ribosomes are identical to bacterial ribosomes in every respect!”, that might be worth quibbling over.

–B. Spitzer

Comment #170779

Posted by DMA on April 18, 2007 9:34 PM (e)

Dr. Nelson,

Would you be so kind as to explain your reference’s figures four and five and the patterns found therein, without utilizing common descent? As a personal request, would you be so good as to explain them using Intelligent Design? I first heard of ID around about 1999, and I know it has been around for nearly 20 years now, but I’ve never heard it used to explain this kind of data. I’d also like an explanation for the following: “Among the 21 proteins in the small subunit, 13 proteins were identified as prokaryotic homologues and eight proteins were specific to the mammalian mitoribosome (Table I). The amino acid sequences of the human and mouse mitoribosomal proteins along with their counterparts from other animal mitochondria and prokaryotes were aligned as shown in Fig. 4. Significant homology between mitoribosomal proteins and their bacterial counterparts indicates that the distribution of proteins within the mitoribosome and the prokaryotic ribosome is similar, as observed in a previous study on 39 S large subunit proteins (22).” How about explaining ref 22? You had some reason for picking out this paper so I’m sure you’re quite knowledgeable about its contents so this should be no problem for you.

You did read it, right?

Comment #170782

Posted by Keanus on April 18, 2007 9:43 PM (e)

Sire toejam asked about Dubya’s library to be

a library of comic books?

Yes, but it will also include a remote, one oversize video screen, a library of John Wayne movies along with a sampling of porno films on CD but in plain brown wrappers, and a Barcalounger with cupholder for all the scholars to use.

Comment #170787

Posted by Sir_Toejam on April 18, 2007 10:02 PM (e)

don’t forget the beer bong and several available mirrors and handy one-sided razor blades.

can’t enjoy the library without refreshments, after all.

Comment #170788

Posted by Pete Dunkelberg on April 18, 2007 10:07 PM (e)

DMA wrote:

Dr. Nelson,

Would you be so kind as to explain your reference’s figures four and five and the patterns found therein, without utilizing common descent sense? As a personal request, would you be so good as to explain them using Intelligent Design?

DMA, if you were paying attention, you would know Professor Behe already did that. How could you forget the radio theory?

[Sorry, but I first read your question as “… without utilizing common sense”]. It just seemed to fit.

Comment #170789

Posted by Douglas Theobald on April 18, 2007 10:16 PM (e)

Paul Nelson wrote:

“Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?”

They do?

Yes Paul, they do.

Take any human mitochondrial protein you want, for instance S12:

>gi|16950591|ref|NP_203527.1| mitochondrial ribosomal protein S12 precursor [Homo sapiens]
MSWSGLLHGLNTSLTCGPALVPRLWATCSMATLNQMHRLGPPKRPPRKLGPTEGRPQLKGVVLCTFTRKP
KKPNSANRKCCRVRLSTGREAVCFIPGEGHTLQEHQIVLVEGGRTQDLPGVKLTVVRGKYDCGHVQKK

BLAST it: http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?PAGE…

(hint: use the swissprot database for easier viewing and faster search)

Note what organism the highest scoring non-mitochondrial protein is from.

Comment #170809

Posted by PvM on April 19, 2007 12:00 AM (e)

Just enough data to confuse the faithful while ignoring the rest. I see a hint of young earth creationism shining through. Sal, oh Sal where are you.

Comment #170820

Posted by sparc on April 19, 2007 1:07 AM (e)

BLAST it:

IDists never blast sequences, because they would have to concede common descent in doing so. They only blast their own logic.

Comment #170848

Posted by Frank J on April 19, 2007 5:27 AM (e)

[Behe’s] answer was that ID theory does not allow for explanations regarding interspecies commonalities such as those implied in the question.

Warning. Turn off your irony meters before reading further.

For at least 12 years Behe is on record admitting that “interspecies commonalities” are transmitted through “biological continuity,” his most recent rephrasing of the politically incorrect “common descent”. So, technically, ID has no need to explain them because it is not challenging mainstream science (evolution) with respect to that particular question.

This would have been a perfect opportunity for him to turn to those IDers who seem to deny common descent, ask them to specifically say how they think it happens instead, and once and for all shut up those of us who claim that ID is not science.

Comment #170849

Posted by the pro from dover on April 19, 2007 5:30 AM (e)

To Mr. Kellogg: You have scoliosis because of original sin. When you are raptured up to heaven at the end of times if you are a true believer your spine will be perfect. Any questions/-please consult your nearest premillenial dispensationalist..Your presence at this website; however, may bring your religious sincerity into question.

Comment #170855

Posted by Laser on April 19, 2007 7:05 AM (e)

Quoth the raven

I’m liking my creo theory more and more. They have decided to suspend disbelief permanently and enter into a fantasy world. We all do this when watching a movie, TV, or reading a fiction book, temporarily.

Indeed.

Nelson quoted

The protein composition of the mitoribosome has been estimated to be about 75%, which indicates that large parts of bacterial rRNA domains have been replaced by protein components during mitochondrial evolution from a eubacteria-like endosymbiont in eukaryotic cell progenitors.

Only someone who has permanently suspended disbelief would quote a paper that uses evolution as a mechanism as if it supported ID.

Comment #170858

Posted by Zachary Moore on April 19, 2007 7:43 AM (e)

Behe actually answered the question initially appropriately, saying that the current scientific understanding is that mitochnodria were mostly likely independent prokaryotic organisms that were symbiotically appropriated by eukaryotic ancestors.

Once granting this scientific explanation, Behe then claimed that science cannot explain how or why this symbiotic relationship was formed. His reference to radios falling into cars was his way of illustrating how unlikely it would have been for this relationship to form by random chance. The implication, of course, was that since science supposedly cannot explain it, and it was too unlikely to happen by chance, therefore the Designer must have taken the two organisms and placed them together, creating eukaryotic life.

Comment #170860

Posted by Ben (t.o.o.) on April 19, 2007 7:47 AM (e)

pro from dover:

Scoliosis from his original sin… but what do you have from yours?

Does the human intellect come from original sin as well? The ability to question the dogma fed to us from toddlerhood onward certainly sounds like a punishment Yahweh/Allah/Vishnu/Zeus/Odin/Zoroaster would have given us.

Comment #170863

Posted by David Stanton on April 19, 2007 8:14 AM (e)

“Behe then claimed that science cannot explain how or why this symbiotic relationship was formed. His reference to radios falling into cars was his way of illustrating how unlikely it would have been for this relationship to form by random chance.”

Really. So I guess the fact that there are some species of amoeba that have aerobic bacterial endodymbionts doesn’t count as “understanding”. Come on, this is not just something that happened a billion years ago. We can still observe this process going on and can duplicate it in the laboratory.

The “how” is engulfment by endocytosis. The “why” is mutualism. The endosymbiont benefits by getting a protected place to live and access to nutrients. The host gets an efficient mechanism of arerobic respiration and a source of ATP. That is why the relationship has been so stable and profitable.

Of course how or why are not nearly as important as the fact that it actually did occur. The genetic evidence is quite clear that it did, which Behe does not seem to dispute. Given that, how unlikely it would have been becomes irrelavent.

Comment #170867

Posted by FastEddie on April 19, 2007 8:59 AM (e)

“Maybe it’s my tiny brain, but my wisdom teeth haven’t caused me any trouble. (I know they are a bitch to keep clean, but the primary reason to pull them hasn’t surfaced). Not sure if I got an evolutionary advantage or what.”

If you can’t keep them clean, then they will definitely cause you problems eventually. I suggest pulling them one every 6 months or so. You get REALLY good drugs! I wish I had a few more to get pulled.

Comment #170868

Posted by barkdog on April 19, 2007 9:02 AM (e)

The Pro’s price for Original Sin must be a minor form of Cassandra’s curse if anyone is taking his last comment literally. Longtime readers know him for what he is.

Comment #170869

Posted by harold on April 19, 2007 9:28 AM (e)

David Stanton -

Although I strongly agree with you that the evolution of eukaryotic cells is a viable topic for science (and vehemently disagree with Behe’s hypocritical and politically motivated claim that it isn’t), unless I’m misunderstanding something, amoebae with symbiotic bacteria are a partial analogy at best.

This is because amoebae are already eukaryotes. They already have eukaryotic ribosomes, mitochondria, a nucleus, and so on. What we don’t see in the present, to the best of my knowledge, is any cellular life that has traits intermediate between eukaryotes and prokaryotes.

Paul Nelson -

Funny, I was going to point out the minor differences between eukaryotic and prokaryotic ribosomes for clarity.

Maybe if you actually read some real science carefully and objectively, you might enlighten yourself a little.

Comment #170870

Posted by JoeG on April 19, 2007 9:33 AM (e)

“Why do we have wisdom teeth if they do not fit our jaws?”

You could be a mutant- (think Jeff Foxworthy’s “You could be a redneck”)

If your jaw is too small to accomodate all of your teeth, you could be a mutant.

Also, pertaining to endosymbiosis:

” Many researchers think eukaryotes are the descendants of either bacteria or archaea, or some combination of the two. But genetic and protein evidence do not support this view, researchers report in Friday’s issue of the journal Science, published by AAAS, the nonprofit science society.”

“Instead, the data suggest that eukaryote cells with all their bells and whistles are probably as ancient as bacteria and archaea, and may have even appeared first, with bacteria and archaea appearing later as stripped-down versions of eukaryotes, according to David Penny, a molecular biologist at Massey University in New Zealand.”

See Can evolution make things less complicated?

Comment #170879

Posted by Glen Davidson on April 19, 2007 10:22 AM (e)

For at least 12 years Behe is on record admitting that “interspecies commonalities” are transmitted through “biological continuity,” his most recent rephrasing of the politically incorrect “common descent”. So, technically, ID has no need to explain them because it is not challenging mainstream science (evolution) with respect to that particular question.

Technically (for the few IDists who agree with Behe, that is), sure. With respect to any real explanation of phylogenies, from their continuity to their changes and splitting, he has a strangely dichotomous view in which “Darwinism” explains the evidence during recent evolution, “Design” is responsible for the past evolution, which is indistinguishable in regard to type of evidence from “Darwinism”, but which he deems to be IC (in real science we’d look at the evidence to determine if any hypothetical IC produced any obvious evolutionary differences, while in ID any desire to check their hypothesis is met by denial and intransigence).

Of course he wants to claim that his view is scientific and utilizes the evidence, it’s just that it doesn’t. You can’t rely upon the continuity provided by DNA to explain biological similarities while claiming that other similarities, and differences, just poofed into existence, all the while that you lack any reliable markers for the dichotomous “explanation”. IOW, ad hoc miracles used as “explanation” make ad hoc reliance upon regularities, when convenient, just as dicey as the miracles are. For miracles are what make inferences such as “common descent” unreliable and subject to unknown tampering with the evidence.

Glen D
http://tinyurl.com/35s39o

Comment #170885

Posted by Torbjörn Larsson on April 19, 2007 10:43 AM (e)

Inoculated Mind wrote:

Too bad we don’t know the name of the ID Prop. who admitted that the DI’s mission was true.

http://scienceblogs.com/pharyngula/2007/04/depar…:

Zachary Moore wrote:

“I wonder which of the four said it.”

It was Stephen Meyer, actually. I’ve got the exchange virtually transcribed in my notes, and I’ll be posting a lot of the question-and-answer session on my blog later.

Comment #170886

Posted by JoeG on April 19, 2007 10:45 AM (e)

Can genetic similarities also be explained by convergence? If “yes” that alone can explain the similarities observed in ribosomes.

Also is there any way to objectively test the premise that free-living bacteria can engulf another free-living bacteria and in the end wind up a eukaryote?

Comment #170889

Posted by Torbjörn Larsson on April 19, 2007 10:52 AM (e)

Glen Davison wrote:

Technically (for the few IDists who agree with Behe, that is), sure.

I wonder if that is correct? He has no evolutionary data or evolutionary mechanism that explains where and why his mythical barrier is. He may think he has a creo mechanism, but when he doesn’t use evolutionary theory as we know it but contradicts it.

I guess what I am saying is, in for a penny, in for a pound, as regards theories.

Comment #170893

Posted by Jim on April 19, 2007 11:11 AM (e)

“By a coincidence (or “coincidence”), SMU is also going to be the site of the George W. Bush presidential library. Seriously.”

To be fair, hosting a presidential library does not imply agreement with the administrations policies. This library could be a gold mine for historians for generations to come. The list of controversies in this administration is endless.

Since Bush is a Texan and a Methodist, it is quite reasonable for him to donate his papers to the largest Methodist university in Texas.

Regards,
Jim

Comment #170894

Posted by harold on April 19, 2007 11:13 AM (e)

JoeG -

Those are good questions.

It would be fascinating if some or all bacteria were descended from early eukaryote mitochondria, not the other way around.

I suppose that this would be vaguely analogous to the evolution of viruses, which are thought to have descended from cells. (Since viruses require intact cells for replication, it is much less controversial that cells most likely came first.)

Of course, if eukaryotes came before prokaryotes, that raises the big question of where eukaryotic cells came from. Note that this would not in any way weaken the theory of evolution, which applies to cellular and post-cellular life. Nor would it make “eukaryotic cells are complex so they must have been poofed into existence by magic” a valid scientific answer. (Although I’m a non-atheist who firmly believes that the origin of life is a natural, scientific question, it is theoretically possible, if strained, for someone to argue that a supernatural entity magically created the first life of earth, and evolution took over after that, without running afoul of definitive current science.)

The symbiosis argument is obviously still plausible. For one thing, if mitochondria were organelles first and independent bacteria second, how did they come to have their own DNA? (Of course, we can think of hypothetical answers to this, but it is a tough question).

As for whether survivors of consumption by predators can be ancestors to symbiotes with the predators, I can’t provide an example, but it sounds plausible, and I bet someone else will.

Comment #170895

Posted by Paul Nelson on April 19, 2007 11:13 AM (e)

Douglas and DMA,

If similarities are evidence of common ancestry, then dissimilarities are evidence of – what?

Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other? One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.

Doubtless there are many striking similarities between eukaryotic mitochondrial and bacterial ribosomes – the “match” of the SMU biology students’ poster. We also observe many differences, however. These bear on the central question of evolution (alluded to by JoeG), namely, the transformation of structure without loss of function.

For instance: it is possible to lose rRNAs (such as the 5S) from the ribosome molecular machine, and yet maintain function? How is this known?

Laser, I cited the Suzuki et al. paper not to support ID, but rather to get readers thinking about the questions above, and what it means (biologically) to say that two structures “match.” Incidentally, the passage you excerpted

The protein composition of the mitoribosome has been estimated to be about 75%, which indicates that large parts of bacterial rRNA domains have been replaced by protein components during mitochondrial evolution from a eubacteria-like endosymbiont in eukaryotic cell progenitors.

presupposes, but does not explain, how bacterial rRNA domains were swapped for proteins (under the hypothesis of the common ancestry of bacterial and eukaryotic mitochondrial ribosomes). Beware of assuming the point at issue.

I have to fly today to Dallas (!) to give a lecture, and so will be unable to add anything else to this discussion for a bit.

Comment #170900

Posted by Bill Gascoyne on April 19, 2007 11:36 AM (e)

To be fair, hosting a presidential library does not imply agreement with the administrations policies.

I’m not sure I’m ready to accept the notion that a president who so clearly values loyalty over competence would offer his library to an institution that didn’t lick his boots.

Comment #170901

Posted by Andrew on April 19, 2007 11:40 AM (e)

As I read Paul Nelson’s comments, I find it impossible to believe that he is not dissembling on purpose. His answers contain enough “jargon” to sound superficially plausible, but he avoids basic questions asked in a straightforward manner. To recap:

1. The protesters held up signs indicating the similarity between ribosomes in human mitochondria and bacteria;

2. Nelson confidently stated that they do not, in post #170755, ostensibly supported by a citation to a paper from Suzuki;

3. Numerous posters pointed out that (a) the evidence, including Suzuki’s paper, supports the original claim and not Nelson’s, and (b) that the Suzuki paper flatly contradicts ID;

4. Nelson responds, in post #170895, but does not address point (a) at ALL, and responds to point (b) only to give an answer on the level of Dembski’s “street theater” answer; “Oh, it’s okay, I just posted the reference to make you think.”

No, Paul, you didn’t. You confidently asserted that human mitochondrial ribosomes are not similar to bacteria, tried to slough it off with a science-y-sounding citation, and got called on it. You’re dead wrong, and your source does not support the argument you initially made.

Failing to acknowledge that, and worse, changing the subject – those are the hallmarks of a professional charlatan.

Comment #170908

Posted by CJO on April 19, 2007 12:00 PM (e)

worse, changing the subject

…and yet even worser, flying to Dallas!

‘sokay Nelson. You didn’t have anything to contribute to the discussion anyway.

Comment #170917

Posted by Paul Nelson on April 19, 2007 12:19 PM (e)

Andrew,

Does “uniformitarian” as a character string match “non-uniformitarian”? Well, yes, in one sense: the strings share 14 out of 17 letters, in identical positions (if one aligns them after the hyphen, and begins counting matches there). Better than 82 percent similarity.

Can one therefore substitute one word for the other in a text, without loss of meaning? No.

Evolution is not, au fond, a theory of similarity. It is a theory of transformation. Differences in two molecular complexes, or machines (the eukaryotic mitochondrial ribosome vs. bacterial ribosome) are as relevant as similarities, when assessing hypotheses about their origin and evolution. The Suzuki et al. paper gives evidence of differences between the two complexes, which must be weighed when evaluating theories about the origin of mitochondrial ribosomes.

To the airport.

Comment #170920

Posted by Sir_Toejam on April 19, 2007 12:22 PM (e)

Can one therefore substitute one word for the other in a text, without loss of meaning? No.

is that actually relevant to your claim?

No.

Comment #170921

Posted by Art on April 19, 2007 12:25 PM (e)

Nelson:

Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other? One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.

Hmm… if one were to show that the catalytic core of the eukaryotic ribosomal peptide synthase was fundamentally different from that of the bacterial ribosomal peptide synthase (such as not consisting of an RNA), one would pretty clearly conclude that they do not share a common ancestry.

Of course, this “experiment” has been done (although not exactly as Paul would suspect), and the results are why most people would not consider ribosomal and non-ribosomal peptide synthases to be derived from a common ancestor.

Let’s turn the question around for Paul and other ID proponents - how would you test the hypothesis that the bacterial and eukaryotic ribosomes share a common ancestry?

(Interesting side observation - the recent spate of posts by ID proponents here and elsewhere on this subject are remarkable in that they ignore the defining feature of the ribosome. Which is namely that it is an RNA enzyme, that the chemical reaction that is the raison d’etre of the ribosome is catalyzed by RNA. It’s no wonder that IDists choke on the evolutionary aspects of ribosomes, when they cannot bring themselves to acknowledge the fundamental nature of the enzyme.)

Comment #170922

Posted by Sir_Toejam on April 19, 2007 12:26 PM (e)

Evolution is not, au fond, a theory of similarity. It is a theory of transformation.

Nelson lecuturing on the form and function of evolutionary theory.

ROFLMAO!

that’s rich.

no, Paul, it actually IS a theory of similarity. hence common descent, remember?

ever looked at convergent and parallel evolution?

you should just stick to telling us over and over again how we get ID wrong, and reinvent your interpretation of it whenever you see fit.

Comment #170927

Posted by David Stanton on April 19, 2007 12:32 PM (e)

Harold,

The organism I mentioned lacks mitochondria. In that sense at least it is “intermediate” between prokaryotess and eukaryotes. That is why it is beneficial for it to have the symbiotic bacteria. I don’t know for sure that it has been demonstrated that that species lacks mitochoindrial as an ancestral condition. If so, that would be even stronger evidence for the endosymbiotic theory.

It is also my understanding that these types of experiments can be repeated in the lab with two prokaryotes. I will have to try to look up some references about this, unless someone else can help me out here.

As regards convergence, the genetic similarities cannot easily be explained by convergence. The probability is simply too low. In addition, the sequence data point to a particular group of purple bacteria as ancestral to mitochondria and there is good evidence form other types of data that this is probably the right answer. The animal mitochondrial genome is so degraded compared to any bacterial genomes that the hypothesis that bacteria could have been derived from mitochondria is also ruled out, unless this occurred very soon after the symbiosis event. Still, this could not have been the origin of all bacteria, since they appear significantly before eukaryotes in the fossil record. Likewise, we also know from sequence data that there was an independent origin of chloroplasts and chloroplast DNA, undoubtedly after the mitochondrial event.

The endosymbiotic theory is well supported by several different independent data sets. It is definately the most parsiminous explanation for all the data. Pretending that we don’t understand this at this point is, once gains, ignoring all the evidence.

Comment #170928

Posted by pondscum on April 19, 2007 12:38 PM (e)

The evidence for endosymbiosis is, IMO, quite compelling. For example, a prediction of the endosymbiotic model for the origin of mitochondria is that the inner and outer mitochondrial membranes should have different characteristics since the outer should be a remnant of the host cell and the inner should be similar to the plasma membrane of prokaryotic cells. Studies of have shown that the outer mt membrane is similar to ER (i.e., eukaryotic!) and the inner mt membrane is similar to the PM of prokaryotic cells. Furthermore, the case for an endosymbiotic origin of the chloroplast is even stronger (again, my opinion) than that for mitochondria. Chloroplasts have many of the same features that link mitochondria to the prokaryotes (circular DNA, 70S ribosomes). The evidence from numerous molecular phylogenetic markers makes a strong case for cyanobacteria as the primary endosymbiont. We even have an extant example of what an intermediate might look like. The Glaucocystophytes are algal protists that, at first glance, appear to possess chloroplasts. However, a closer examination reveals that the “chloroplasts” are actually cyanobacteria (some even with peptidoglycan cell wall material still present!) that are functioning like chloroplasts. As a consequence, these chloroplast-like structures have been termed cyanelles and are interpreted as another “experiment” in primary endosymbiosis. The evidence for secondary endosymbiosis (eukaryote + eukaryote) is also compelling. One of the best cases for secondary endosymbiosis is found in the Chlorarachniophyta. These green amoebae do indeed possess functional chloroplasts. Ultrastructural analysis of Chlorarachnion revealed a rather peculiar feature–in addition to a large central nucleus, a second, smaller nucleus is present. This smaller nucleus, now called a nucleomorph, is always associated with a chloroplast. In fact, the chloroplast (with its own double-membrane system) and the nucleomorph are surrounded by a separate membrane. The clear inference is that a heterotrophic amoeba engulfed a photoautotrophic green alga, resulting in the modern day Chlorarachniophyta. This interpretation is supported by molecular phylogenetic analysis of the various genomes present in the cells of Chlorarachnion. We also know that engulfment, without complete digestion is possible. A number of molluscs (e.g., some sea slugs) engage in kleptoplasty. As the name implies, these “animals” consume chloroplast-bearing organisms (usually algae). However, they harvest and retain the still functional chloroplasts, exploiting the capabilities of the stolen organelle. Eventually, the chloroplasts die, but the mollusc need only resume grazing in order to re-stock.

While we certainly don’t have all the answers, the study of eukaryote origins, within an evolutionary framework, has been a remarkably fruitful endeavor.

Comment #170930

Posted by Pete Dunkelberg on April 19, 2007 12:43 PM (e)

Andrew, please consider the possibility that you are being hasty vs Paul Nelson. For one thing, in post #170755 he said “They do?” which is not quite how you related it. More generally, Paul is a sincere Young Earther. He see things differently than you. Try re-doing your analysis from the point of view of Morton’s Demon. Should you apologize to Paul?

Comment #170931

Posted by David Stanton on April 19, 2007 12:46 PM (e)

“Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other? One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.”

The phylogenetic position relative to other groups based on DNA sequences is how these relationships were defined. This is how we know that mitochondria were derived from purple bacteria and chloroplasts from green bacteria such as cyanobacteria and not from a common ancestor from a single symbiosis event. If the sequences were more similar to any eukaryotic lineage, then we would not conclude a prokaryotic origin. Remember, this was not the easy answer. This theoiry had to be subjected to many different tests before it was accepted. It has already passed those tests.

Comment #170932

Posted by Torbjörn Larsson on April 19, 2007 12:58 PM (e)

Andrew wrote:

hallmarks of a professional charlatan.

Indeed. Since Nelson opted out of the discussion, I can only note the remaining hallmarks.

Paul Nelson wrote:

If similarities are evidence of common ancestry, then dissimilarities are evidence of – what?

I’m sure all scientists are fed up with IDiots insistence on false choices. Here two of them:

- Similarities can be evidence for several theories.

A simple example is when the square-law behavior for electric fields confirm both classical and quantum EM field theories.

- Dissimilarities doesn’t need to be evidence for any theory.

To be more precise, one must specify the theory and the test if dissimilarities should be used as evidence.

Paul Nelson wrote:

One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.

More false choices. Hypothesis testing tests against a null hypothesis, not a false choice.

The real question is what counts as a failed prediction. It depends on the specific test of course, as any scientist will tell you.

For an example we can use phylogenetic trees. By making a very constrained prediction of a small group of possible trees among the overwhelming amount of possibilities, the precision rises fast. To get to under 1 % imprecision in the standard phylogenetic tree, more than 18 of 30 branches needs to be correct as tested against the null hypotheses of randomness.

However, the tree is known to 38 decimal places, which is a much greater precision than that of even the most well-determined physical constants ( http://www.talkorigins.org/faqs/comdesc/section1… )!

Now, I’m sure the objection raised that the real question raised was about falsifiability, not unverified predictions against common defaults.

Well, trees gives that too. Anti-correlated, anti-hierarchical pattern would give statistically significant low so called CI values. But no one does. (See the same link.)
….…..
Really, DI has a lot of philosophers instead of scientists. But one would think one of these philosophers at least could understand the simple logic of false choices as applied to science. ;-)

Comment #170933

Posted by Sir_Toejam on April 19, 2007 1:06 PM (e)

Really, DI has a lot of philosophers instead of scientists

I’m sure any legitimate philosophy professor would be appalled to hear the DI described as containing philosophers rather than solopists.

Comment #170934

Posted by Torbjörn Larsson on April 19, 2007 1:15 PM (e)

scumpond: fascinating. [Yet another sentence I never thought I would utter. :-) ]

Pete: I find the applications of sundry demons in science fascinating. However, I would think YEC:ers see it differently. Oh, wait…

Comment #170936

Posted by Torbjörn Larsson on April 19, 2007 1:18 PM (e)

ST wrote:

philosophers rather than solopists [sic].

Oh. Well, I used Wikipedia (“PhD in philosophy”). Isn’t that a reliable source? ;-)

Comment #170948

Posted by Laser on April 19, 2007 1:43 PM (e)

Paul Nelson wrote:

Beware of assuming the point at issue.

Like you assuming God did everything?

Comment #170950

Posted by Pete Dunkelberg on April 19, 2007 1:48 PM (e)

David Stanton writes: “The organism I mentioned lacks mitochondria.” Could you please specify the organism? The eukaryotes previously thought to be primitively amitochondriate have been found to have small degenerate ones after all.

The paper brought up as a news item is last year’s. Penny’s website . Not everyone agrees with the standard endosymbiosis hypothesis yet. One of the big problems is simply that eukaryote diversity is severely understudied as yet.

Comment #170965

Posted by harold on April 19, 2007 2:38 PM (e)

David Stanton -

That’s quite interesting.

I had a vague feeling that there might be amoebae without mitochondria (should have remembered that from parasitology). However, I did a brief check and found lots of articles about amoebic mitochondria, so I disregarded the proddings of my unconscious mind.

This is a link to a very brief abstract of a relatively recent article that talks about endosymbiotic bacteria in amoebae, but not with regard to mitochondria per se.

http://www3.interscience.wiley.com/cgi-bin/abstr…

On the other hand, the link below leads to the abstract of a paper that suggests that modern amoeba lineages without mitochondria may be descended from ancestors that had them. In case this link just takes you to the pubmed homepage, the reference is below.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db…

Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1414-9

So the evidence for endosymbiosis is strong, but there is still some room for controversy. This is an area of ongoing scientific investigation, it would seem.

Comment #170969

Posted by David Stanton on April 19, 2007 3:07 PM (e)

Pete,

The organism I was referring to was Pelonyxa (not sure that is the correct spelling). Apparently there are many such amoeba that lack mitochondria. Thanks to Harold for the reference. If these organisms come from lineages that had mitochondria, then the question becomes - did they lose the mitocondria for some reason and then acquire endosymbionts, or did they acquire endosymbionts and then lose the mitochondria. Perhaps the reference cited will give some clue.

Comment #170971

Posted by harold on April 19, 2007 3:24 PM (e)

Paul Nelson sulked -

“Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other? One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.”

Short Answer - As you know, anything but similarity would fail to support common ancestry of the ribosomes.

Long Answer - As you know, when Darwin first articulated what was to become the theory of evolution, the very idea that bacteria existed was still the subject of debate, and the idea that they could cause disease was intensely controversial.

The theory at that time was morphology based. Still, scientists could easily distinguish superficially similar organisms that weren’t closely related and superficially different organisms that were, based on such core concepts as whether they were marsupials or placentals, or the like.

Soon, biochemistry expanded rapidly. The theory of evolution predicted similar, preserved biochemical pathways. Had different forms of life had radically different biochemical pathways, the theory might have been challenged. But great similarity was found among biochemical pathways throughout life.

Classical Mendelian genetics emerged. Again, it might have led to doubts about evolution, but instead, the evidence was confirmatory.

Molecular genetics and modern cell biology emerged. Again, it was clear what the the theory of evolution predicted. Again, it was clear that the theory of evolution could be cast into doubt if unexpected results emerged. Again, a powerful independent line of evidence not only supported, but expanded and strengthened, the theory of evolution.

In every case, of course, it was not just similarity across life that was detected, but the same pattern of relationships that were suppored. Rabbits are more related to weasels than they are to moss, no matter what metric you look at.

Others say you present a false choice. I disagree. It’s obvious what would count as evidence against common ancestry.

What degree of similarity across all of life do we need to infer common descent? That’s an intriguing question, which you may have meant to imply. The molecular genetic, biochemical, and cell structural commonalities across life are so overwhelming, and the degrees of relationship between lineages so obvious from so many independent lines of evidence, that the question is effectively moot except for details like trying to decide the relationship between different lineages of amoebae. Whatever the threshold is, we’re so far over any reasonable threshold that it doesn’t matter.

At this point, of course, the evidence of common ancestry is so powerful that in order to “overturn” it, a great deal of very strong, objective evidence (and not any amount of childish word-game playing) would be required. However, it is crystal clear that there is such a thing as evidence for common descent, that there is such a thing as evidence against common descent, and that what we see over and over again is evidence FOR common descent.

Comment #170975

Posted by harold on April 19, 2007 3:35 PM (e)

David Stanton -

That’s Pelomyxa; I googled it.

http://en.wikipedia.org/wiki/Pelomyxa

The current endosymbiosis explanation would be that they evolved from an ancestor that had endosymbionts, and then lost their mitochondria later, I presume. Whereas some other amoebic lineages did not lose their mitochondria.

Obviously, if there were some amoebic lineages with a primary lack of mitochondria - never had any ancestor that had them - that would support endosymbiosis even more. But the existence of these guys doesn’t argue against it.

I believe that the issue of which amoebae have mitochondria may be a bit more complex that our discussion has suggested, but I have to drag myself away from this topic.

Comment #170976

Posted by harold on April 19, 2007 3:38 PM (e)

David Stanton -

That’s Pelomyxa; I googled it.

http://en.wikipedia.org/wiki/Pelomyxa

The current endosymbiosis explanation would be that they evolved from an ancestor that had endosymbionts, and then lost their mitochondria later, I presume. Whereas some other amoebic lineages did not lose their mitochondria.

Obviously, if there were some amoebic lineages with a primary lack of mitochondria - never had any ancestor that had them - that would support endosymbiosis even more. But the existence of these guys doesn’t argue against it.

I believe that the issue of which amoebae have mitochondria may be a bit more complex that our discussion has suggested, but I have to drag myself away from this topic.

Comment #170982

Posted by Mr_Christopher on April 19, 2007 4:12 PM (e)

Paul Nelson, enough of this evilution talk, please tell us the story again where the Earth is only 6000 years old! The truth is out there and you’re just the man to tell the world! cue X-Files theme song>

Comment #170986

Posted by Kristine on April 19, 2007 4:29 PM (e)

@ Sir Toejam, re books for Bush Library: Bush’s Fart Joke Legacy.

“Turning to the Bush clan, we learn in Kitty Kelley’s book The Family: The Real Story of the Bush Dynasty that New Yorker writer Brendan Gill was once a guest of George H.W. and Barbara Bush at their summer house in Kennebunkport, Maine. Stumbling through the place late at night in search of something to read, the only volume he could find was The Fart Book.”

Wow, he and Bill Dembski share some, er, tastes.

Comment #170988

Posted by Sir_Toejam on April 19, 2007 4:39 PM (e)

Wow, he and Bill Dembski share some, er, tastes.

i rather suspect they share some acquaintances as well….

as an aside, I think I’m gonna go all Curt Gowdy on Paul from now on, and whenever he spouts off, will forever more start my responses with:

Whoa, Nelly!!

Comment #170995

Posted by ERV on April 19, 2007 5:06 PM (e)

Nelson–One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.

*giggle* Im having fun playing with a Sternberg paper (yes, THAT Sternberg) that says something similar with Repetitive Elements in our genomes.

Saying that some REs are functional and some REs arent functional is a tautology, rendering evilution an unfalsifiable just-so story! Game over, everybody go home! LOL!

Blech!

Comment #170998

Posted by Sir_Toejam on April 19, 2007 5:28 PM (e)

Saying that some REs are functional and some REs arent functional is a tautology, rendering evilution an unfalsifiable just-so story! Game over, everybody go home! LOL!

yeah, that relates to the false dichotomy argumentation method alluded to earlier in the thread.

it’s one of Slimy Slaveador’s specialties as well.

Comment #171008

Posted by Pete Dunkelberg on April 19, 2007 6:34 PM (e)

Saying that some REs are functional and some REs arent functional is a tautology…

Wow! Geniuses are springing up all over. But wait. Some means at least one. Oh well, false alarm on the genius.

Comment #171019

Posted by Torbjörn Larsson on April 19, 2007 7:29 PM (e)

Others say you present a false choice. I disagree. It’s obvious what would count as evidence against common ancestry.

I agree that it is obvious. Perhaps I took the point too far, not being a biologist, and trying to couch the point in terms a philosopher (or, as Sir_Toejam will have it, a solipsist) would react to. (And, I must confess, being able to use the word false a number of times. :-)

However, the material I referenced seems to have been written by another biologist.

In the general case I think the degree of obviousness depends on exactly what evidence and what test we are discussing.

In this case, I like the strength of your account much better than the weakness in mine. ;-)

Comment #171041

Posted by Don Smith on April 19, 2007 9:32 PM (e)

Paul Nelson wrote:

Does “uniformitarian” as a character string match “non-uniformitarian”? Well, yes, in one sense: the strings share 14 out of 17 letters, in identical positions (if one aligns them after the hyphen, and begins counting matches there). Better than 82 percent similarity.

Can one therefore substitute one word for the other in a text, without loss of meaning? No.

Wow! The perfect example of evolution by splicing to get new function! And the common descent is there for all to see!

With arguments like this, how do the IDers get anywhere at all?

P.S. Of course you can’t substitute “not A” for “A” a retain the same meaning. That doesn’t mean “A” and “not A” are not related. Hint: not is a relational operator.

Comment #171044

Posted by Sir_Toejam on April 19, 2007 9:45 PM (e)

With arguments like this, how do the IDers get anywhere at all?

good question.

Comment #171047

Posted by LEW on April 19, 2007 10:11 PM (e)

Paul Nelson wrote:

“Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?”

They do?

Funny stuff. I hear the argument “if things are similar, it’s because they have a common designer”, so we have mr. nelson telling us there must not be a common designer because the ribosomes don’t match.

Comment #171048

Posted by Sir_Toejam on April 19, 2007 10:22 PM (e)

now you know why “whoa nelly!” doesn’t spend much time here at PT

Comment #171066

Posted by BC on April 20, 2007 1:24 AM (e)

If similarities are evidence of common ancestry, then dissimilarities are evidence of – what?

If similarities were due to a common designer, then how do you explain shared errors? Looking at broken genes (like the one to synthesize Vitamin C, and a large number of olfactory genes), shows the same pattern of common descent as working genes. But, if there was no common descent, did God put broken genes inside similar organisms just to mess with us?

Comment #171080

Posted by SteveF on April 20, 2007 4:32 AM (e)

Why does Paul Nelson usually have to run off and get on a plane when questions get tricky?

Comment #171099

Posted by David Stanton on April 20, 2007 8:24 AM (e)

Once again Harold is correct. The evidence for common ancestry in all known life forms is so overwelming that it cannot really be doubted. Therefore, since all organisms did share a common ancestor at some point in the past, similarity is indeed evidence of common ancestry (usually) and dissimilarity is (usually) evidence of more distant relationships.

As to what would constitute evidence of independent origins, one could speculate. For example, if life was found on another planet, how could we tell that it was not a contaminant from earth but truly alien. Here are some speculative possibilities:

(1) Not cellular
(2) Not DNA based
(3) Drastically different genetic code
(4) “Multicellular” forms without organelles
(5) “Enzymes” not usually made of proteins

While none of these things might be absolutely conclusive by itself, a combination of them would certainly be difficult to reconcile with a common origin shared with life on earth.

And by the way, BC is also correct. If the organisms were based on the same structures and mechanisms found on earth and they shared the same genetic “mistakes” and “errors” shared by earth organisms, it would be extremely difficult, if not impossible, to argue for a comon origin.

Comment #171105

Posted by Paul Nelson on April 20, 2007 9:58 AM (e)

Replies and comments to various, from Dallas.

Steve F asked:

Why does Paul Nelson usually have to run off and get on a plane when questions get tricky?

Because I travel too much.

I asked:

Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other? One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.

Art replied:

Hmm… if one were to show that the catalytic core of the eukaryotic ribosomal peptide synthase was fundamentally different from that of the bacterial ribosomal peptide synthase (such as not consisting of an RNA), one would pretty clearly conclude that they do not share a common ancestry.

Ask yourself why – if their catalytic cores were different – one would infer separate ancestry.

Answer: the [biochemical] differences would be too great to allow preservation of function during the transformation of structure from a common ancestor. That is, the differences would violate what Francis Crick and Leslie Orgel called the Principle of Continuity: the only absolutely necessary condition for any evolutionary transformation is that essential function not be lost. No postulated evolutionary transformation can violate the Principle of Continuity.

Observed (real) differences between eukaryotic mitochondrial ribosomes and bacterial ribosomes do not count, for Art and others, as evidence sufficient to trigger the Principle of Continuity. That means they must know the Principle of Continuity has been satisfied: the changes required to transform the common ancestral ribosome into the different systems we see today are known to be biologically possible.

What’s the observational (or experimental) evidence that ribosomes could jettison a structural unit such as 5S rRNA, without loss of function?

David Stanton wrote:

The evidence for common ancestry in all known life forms is so overwelming that it cannot really be doubted.

Mike Syvanen and others have written here at PT about the increasingly lively debate now ongoing within evolutionary theory about the early history of life. The universal Tree, or universal common descent, has become a locus of controversy. Some investigators, such as Carl Woese and W. Ford Doolittle, strongly reject a single Tree:

The meaning, role in biology, and support in evidence of the universal “Tree of Life” (TOL) are currently in dispute (1–15). Some evolutionists believe (i) that a single rooted and dichotomously branching representation of the relationships between all life forms is appropriate (at all levels above species), because it best represents their history; (ii) that we can with available data and methods reconstruct this tree quite accurately; and (iii) that we have in fact done so, at least for the major groups of organisms. Other evolutionists question the second and third of these beliefs, holding that data are as yet insufficiently numerous and phylogenetic models as yet insufficiently accurate to allow reconstruction of life’s earliest divisions, although they do not doubt that some rooted and dichotomously branching tree can in principle represent the history of all life. Still other evolutionists, ourselves included, question even this most fundamental belief, that there is a single true tree. All sides express confidence in their positions, and the debate often seems to be at an impasse (see for instance refs. 9–12).

See W.F. Doolittle and E. Baptestse, “Pattern pluralism and the Tree of Life hypothesis,” PNAS 104 (February 13, 2007):2043-2049.

Don, a text in which the insertion mutation “non” occurred before “uniformitarian” would be a lethal mutation (so to speak), if the original text read “Charles Lyell was a uniformitarian.” By “loss of meaning,” I mean of course loss of true or intended meaning (normal function). “Charles Lyell was a non-uniformitarian” is meaningful, but false. In any case, the point of the analogy is to illustrate that similarity between objects within functional-conveying systems, whether English sentences or ribosomes, cannot be considered in isolation, or without respect to preservation of function. Saying that two systems share similarities does not entail that one can be transformed into the other.

Comment #171116

Posted by B. Spitzer on April 20, 2007 11:45 AM (e)

Ask yourself why – if their catalytic cores were different – one would infer separate ancestry.

Answer: the [biochemical] differences would be too great to allow preservation of function during the transformation of structure from a common ancestor. That is, the differences would violate what Francis Crick and Leslie Orgel called the Principle of Continuity: the only absolutely necessary condition for any evolutionary transformation is that essential function not be lost. No postulated evolutionary transformation can violate the Principle of Continuity.

Observed (real) differences between eukaryotic mitochondrial ribosomes and bacterial ribosomes do not count, for Art and others, as evidence sufficient to trigger the Principle of Continuity. That means they must know the Principle of Continuity has been satisfied: the changes required to transform the common ancestral ribosome into the different systems we see today are known to be biologically possible.

The “Answer” you give is incorrect. Phylogeneticists do not infer common ancestry or separate ancestry based on any information about continuity of function during the presumed evolutionary transition. You are conflating two questions. The phylogenetic question is “What is X most closely related to?” The anagenetic question is different; it is “How did X evolve to its current state?”

We infer common ancestry between the mitochondrion and bacteria not merely because they are similar. We infer common ancestry because the rRNA of the mitochondrion is much more similar to the rRNA in one particular type of bacterium than it is to any other type of rRNA. All mitochondrial rRNAs are very similar to those of proteobacteria.

We infer separate ancestry not when sequence X is different from sequence Y, but when it is independent of some set of sequences. If the mitochondrion doesn’t share common ancestry with a proteobacterium, it should be equally different from a proteobacterium as it is from, say, a bacterium in the Chlamydiales, or a bacterium in the high-GC Gram-positives, or a giant squid.

The fact that mitochondria are always more similar to proteobacteria than they are to other organisms– not just with respect to rRNA, but with respect to other characters as well– is very strong evidence for common descent. With that working hypothesis, we can begin to consider how the present-day mitochondrion might have evolved from a proteobacterial ancestor. But the inference that it did evolve from a proteobacterial ancestor doesn’t rely on a detailed understanding of how it occurred.

If you’re wondering, yes, as we try to understand how the transition occurred, it’s possible that we might discover that the transition is extremely improbable. That’s a second test that the hypothesis of common descent will eventually be faced with as we learn more about the details of ribosomal function. But, given the extraordinarily high similarity between the mitochondrion and proteobacteria, it’s only sensible to provisionally accept the inference that they are related by common descent unless and until that second test suggests otherwise.

While you’re here, Dr. Nelson, there is a question that I’ve been wondering about for some time. This isn’t intended as a “gotcha” question– it’s something that I really don’t know the answer to. Living organisms show a very strong pattern of hierarchically nested traits. I’ve heard the argument that “a common designer leads to common design”, but this doesn’t account for a hierarchically nested pattern. I’ve never heard any ID proponent try to explain that pattern in terms of design. In fact, I’ve never heard of any plausible explanation for that pattern other than common descent with modification. Do ID proponents have an explanation for this pattern? If so, what is it?

B. Spitzer

Comment #171121

Posted by Davbid Stanton on April 20, 2007 12:05 PM (e)

“Still other evolutionists, ourselves included, question even this most fundamental belief, that there is a single true tree.”

Paul,

Thanks for the reference. I guess these guys have the answer to your question about what would count as evidence against common ancestry.

Comment #171125

Posted by B. Spitzer on April 20, 2007 12:28 PM (e)

Mike Syvanen and others have written here at PT about the increasingly lively debate now ongoing within evolutionary theory about the early history of life. The universal Tree, or universal common descent, has become a locus of controversy. Some investigators, such as Carl Woese and W. Ford Doolittle, strongly reject a single Tree

Hypothesis 1: All living organisms today share common ancestry.

Hypothesis 2: All modern life arose from a single origin, as opposed to there being multiple origins, the descendants from which combined at some point early in life’s history.

Hypothesis 3: The Tree of life is dichotomous, as opposed to there being any lateral transfer or re-joining of separate lineages.

Hypothesis 1 is not the same as Hypotheses 2 and 3. Don’t pretend that it is.

I would not be surprised if Woese or Doolittle reject Hypotheses 2 and/or 3 for the events very early in the history of life. I don’t know of any serious scientist who rejects Hypothesis 1. If you feel that Woese or Doolittle specifically reject Hypothesis 1, present clear evidence for it.

Comment #171131

Posted by Sir_Toejam on April 20, 2007 1:34 PM (e)

Because I travel too much.

Whoa Nelly!

sometimes for YEARS at a time, right?

Comment #171132

Posted by Glen Davidson on April 20, 2007 1:34 PM (e)

While you’re here, Dr. Nelson, there is a question that I’ve been wondering about for some time. This isn’t intended as a “gotcha” question– it’s something that I really don’t know the answer to. Living organisms show a very strong pattern of hierarchically nested traits. I’ve heard the argument that “a common designer leads to common design”, but this doesn’t account for a hierarchically nested pattern. I’ve never heard any ID proponent try to explain that pattern in terms of design. In fact, I’ve never heard of any plausible explanation for that pattern other than common descent with modification. Do ID proponents have an explanation for this pattern? If so, what is it?

Here’s one answer that Nelson reportedly gave, while in Norway:

He [Nelson] further stated that evolutionary theory today has much greater explaining power than ID and that ID consequently should not be taught in schools.

http://scienceblogs.com/pharyngula/2006/09/paul_…

Who knows what he’s trying to do here? Does he really think that trying to make us explain every last detail, while he totally and egregiously ignores the overall patterns predicted by evolutionary theory and observed in the evidence, is really going to get him some place?

And are quote mines of Doolittle and Woese supposed to prove something? Yes, some say that there is “no single tree of life”, but Doolittle and Woese aren’t denying common ancestry or “trees of life”, they’re simply saying that the roots of the “tree of life” have acted promiscuously and fused in various ways.

Nelson’s like the other IDists, ignoring what he doesn’t like while making impossible demands of science. Much better than making a science of their ID which is currently lacking in “explaining power” (fully lacking, though he only admits that it’s partly lacking in that power). Just act as if you don’t know that the whole point of evolution is both change and derivation, and pretend that change is contrary to derivation.

We know, Paul, that similarities are evidence for common ancestry because we do know what counts as evidence against common ancestry. The Pinto is what counts as evidence against common ancestry. Both the Pinto and the Ferrari counts as evidence against common ancestry among cars, because no matter how well or poorly “designed” the cars are, they aren’t restricted to the use of ancestral parts and to the use of modified ancestral parts. And there is no excuse to cavil over the modification of “parts”, for we know much of how and why such parts are modified, so we know (for instance) that complete change of a functioning gene is not going to occur in vertebrates over the course of 100 generations.

It’s like any dependency, we compare overall similarities, perhaps noting nested hierarchies (Woese and Doolittle are merely denying this at some point in the distant past, not for any recent evolution, such as the Cambrian evolutionary period) or some other patterns, in order to determine derivation. We know in languages that some changes are likely due to evolutionary developments, and that others are due to horizontal transfers. There can be some ambiguity in such determinations (watch a court case on plagiarism for an analogy), however there are many clear-cut cases. We know that the Old French words in English didn’t evolve from Anglo-Saxon’s ancient roots, and we generally have no problem in determining the words which come from Old English.

IOW, we know that archaeopteryx fits the pattern of “naturalistic evolution” because it derives its wings from the forelimbs of reptiles, not from the wings of the unrelated (actually, less related) pterodactyl. We know that bats fit the predictions of evolution because their wings are adaptations of mammalian forelimbs, not adaptations of bird or pteranodon wings. That is what vertebrate evolution can do, it can adapt what exists in its lineage, and cannot “borrow” apparently good structures from other lineages.

In a way Paul is doing the opposite of what a good philosopher would do, which is to discuss how it is that we recognize patterns and make sound inferences from these patterns. Instead he’s asking us to disregard patterns due to his objections, and to be content with no explanation for homologies (or with an ad hoc “explanation” of design which produces effects dis-analogous from human design and adaptation of design). That is, they appear miraculously, just as he wishes to conclude, and we who do not believe in mere accident or miracle are thus wrong to insist that the evidence means something (like all IDists, he’s really nihilistic with respect to the “real world”, a “realist” only with respect to ideas). That this is contrary to his remarks reported from Norway, his admission that evolutionary theory has much greater “explaining power” (I only disagree with the statement to this degree—ID has no explanatory power, and evolutionary explanations can’t have “much greater” explanatory ability than something completely lacking in such ability), suggests that he either can’t keep his stories straight, or that he doesn’t care to do so.

Principle of Continuity: the only absolutely necessary condition for any evolutionary transformation is that essential function not be lost.

I don’t know what Crick claimed, however it is believed that in many cases essential function is lost when genes are duplicated. This frees up genetic material to effect some other function.

Be that as it may, function cannot generally be lost for very long, or even the framework of the protein that a gene might produce will degenerate into something that life can’t use.

So OK, function needs to be maintained for the most part. The reason that we assume that the principle of continuity was largely maintained is the huge and undeniably amount of evidence for evolution. This includes the fact that we see very few adaptations which appear to be “jumps”, as if one function were suddenly lost and a quite different one appeared (indeed, a specific instance where this seems (to them, at least) to have occurred is one of the arguments against the single tree of life by Doolittle and Woese). Most, if not all, “jumps” appear to be the result of horizontal transfers.

That is to say (and as Spitzer ably pointed out), we have tested to see if evolution and its known processes are responsible. Of course continuity of function can’t be shown to have been the case over the course of evolution in the details of every gene and organelle, but we can observe the general patterns and see that no glaring exceptions to those patterns is evident.

The sort of nickel-and-diming to death of evolutionary theory attempted by Paul and his ilk is kind of as if Paul were utilizing Biblical manuscripts which have been shown to belong to a certain textual family—and instead of his accepting the evidence of continuity in this textual family, he demands that each and every change be shown to have either happened, or at least to be plausible, even for the Hebrew words which are not known outside of the Bible.

Do any good scholars, or scientists, operate like that? No, because although questions may remain as to how change and continuity affected a family of texts, or a family of languages, one accepts the evidence in favor of continuity and change (from the patterns of derivation) and considers this to be an overall guide to understanding the texts, or languages. And yes questions may be asked of some difficulties, or putative difficulties, however denying the relatedness of German and English is so outrageous as not to be a starting point to any serious discussion.

Likewise with denying the relatedness of birds to reptiles, and of bats to other mammals. We know what would constitute evidence against evolution, one such group of evidences being the evidence for any sort of design analogous to that of humans (rational design, borrowing from “unrelated” structures, and novelty beyond anything seen in biology). For not only do we lack evidence for design, it is this lack of evidence that has been socially instrumental in the development of a model which can explain what design never could, the phylogenies and adaptations found throughout biology.

Glen D

Comment #171133

Posted by Sir_Toejam on April 20, 2007 1:37 PM (e)

Answer: the [biochemical] differences would be too great to allow preservation of function during the transformation of structure from a common ancestor. That is, the differences would violate what Francis Crick and Leslie Orgel called the Principle of Continuity: the only absolutely necessary condition for any evolutionary transformation is that essential function not be lost. No postulated evolutionary transformation can violate the Principle of Continuity.

Whoa Nelly!

because, as was pointed out earlier, the differences in this particular case that you are focusing on are not relevant to the issue of relatdness.

again, Paul, it’s quite dishonest, or horridly ignorant, of you to promulgate a theory of difference based on irrelevance.

so which are you being Paul, dishonest or just plain ignorant?

Comment #171134

Posted by Glen Davidson on April 20, 2007 1:46 PM (e)

Just to clear up an ambiguity in what I wrote here:

I don’t know what Crick claimed, however it is believed that in many cases essential function is lost when genes are duplicated. This frees up genetic material to effect some other function.

Essential function is typically lost (eventually) in only one set of the duplicated genes, of course. One gene continues the original function, the other is free to perform some other function, perhaps poorly at first but well later on.

Furthermore, it would be difficult to envision evolution working very well without such duplications occurring, and it so happens that evolutionary changes appear to have taken advantage of duplications many times (sometimes via whole-genome duplication). I suppose it remains for Dembski or Paul to build a coincidence detector to tell us how these known facts are actually meaningless, rather than supportive of evolution (then too, it seems to depends on whether it’s a time when Paul admits that evolution has explanatory power, or when he’s nickel-and-diming evolution in his intellectually gruesome manner).

Glen D
http://tinyurl.com/35s39o

Comment #171142

Posted by JohnK on April 20, 2007 2:18 PM (e)

Nelson cites:
W.F. Doolittle and E. Baptest(s)e, “Pattern pluralism and the Tree of Life hypothesis,” PNAS 104 (February 13, 2007):2043-2049.

The meaning, role in biology, and support in evidence of the universal “Tree of Life” (TOL) are currently in dispute (1–15). Some evolutionists believe (i) that a single rooted and dichotomously branching representation of the relationships between all life forms is appropriate (at all levels above species), because it best represents their history; (ii) that we can with available data and methods reconstruct this tree quite accurately; and (iii) that we have in fact done so, at least for the major groups of organisms. Other evolutionists question the second and third of these beliefs, holding that data are as yet insufficiently numerous and phylogenetic models as yet insufficiently accurate to allow reconstruction of life’s earliest divisions, although they do not doubt that some rooted and dichotomously branching tree can in principle represent the history of all life. Still other evolutionists, ourselves included, question even this most fundamental belief, that there is a single true tree. All sides express confidence in their positions, and the debate often seems to be at an impasse (see for instance refs. 9–12).

Anyone who cites this in front of the general public without mentioning the qualifiers in bold is being dishonest.
One guess as to what Nelson did in a recent Canadian interview which included Jerry Coyne, Dennis Lamoureux, etc.

Comment #171144

Posted by harold on April 20, 2007 2:29 PM (e)

Paul Nelson -

I notice you ignored my earlier post.

Let’s review the overall situation. The extreme similarity of bacterial and human ribosomes was presented as a drop in the ocean of evidence in favor of the common descent of modern life, a single drop in itself sufficient to demonstrate the vacuity of ID.

You aren’t arguing “for ID” in this thread. You’re merely arguing against this single tiny drop of evidence for evolution. Let’s not forget that a massive ocean of equally good evidence gave forth this drop, nor that, even if bacterial ribosomes did not share ancestry with eukaryotic ribososmes, that alone would hardly justify the adoption of ID, or the abandonment of the theory of evolution.

You wrote -

“Answer: the [biochemical] differences would be too great to allow preservation of function during the transformation of structure from a common ancestor. That is, the differences would violate what Francis Crick and Leslie Orgel called the Principle of Continuity: the only absolutely necessary condition for any evolutionary transformation is that essential function not be lost. No postulated evolutionary transformation can violate the Principle of Continuity.”

I’m not sure why Crick and Orgel said this. It’s often true, but not always. Gene duplications, followed by the evolution of a different function for one of the copies, have been advanced as an example. Many other examples abound (bats and birds use their “arms” to fly, seals use them to swim, humans don’t use them for locomotion at all except very early in life and under unusual circumstances, to demonstrate a facile one). However, my main argument is hardly with Crick, and there are cases where what he said does apply.

Moving on…

“Observed (real) differences between eukaryotic mitochondrial ribosomes and bacterial ribosomes do not count, for Art and others, as evidence sufficient to trigger the Principle of Continuity. That means they must know the Principle of Continuity has been satisfied: the changes required to transform the common ancestral ribosome into the different systems we see today are known to be biologically possible.”

Correct.

“What’s the observational (or experimental) evidence that ribosomes could jettison a structural unit such as 5S rRNA, without loss of function?”

Obviously, the fact that both bacterial and eukaryotic ribosomes do function can easily be observed.

I guess that settles that.

Comment #171150

Posted by Glen Davidson on April 20, 2007 2:47 PM (e)

And yes questions may be asked of some difficulties, or putative difficulties, however denying the relatedness of German and English is so outrageous as not to be a starting point to any serious discussion.

Just one more comment for the non-YEC (observable-process) evolution deniers: Denying that the relatedness of German and English is due to observable processes is also so outrageous as not to be a starting point for any serious discussion.

One might never be able to observe the processes effecting the evolution of languages and organisms (though it happens in both cases that we have observed apparently quite effective processes which explain what we see), yet at what point would anybody be justified in denying that observable processes could, in principle, be responsible?

Glen D
http://tinyurl.com/35s39o

Comment #171151

Posted by Sir_Toejam on April 20, 2007 2:49 PM (e)

yet at what point would anybody be justified in denying that observable processes could, in principle, be responsible?

at what point did justification play any role in the arguments of IDiots?

Comment #171154

Posted by BC on April 20, 2007 3:22 PM (e)

Paul Nelson wrote:

If similarities are evidence of common ancestry, then dissimilarities are evidence of – what?

First of all, there are times when “A” counts as evidence FOR theory X, but “not A” does not count as evidence AGAINST theory X. For example, if Joe is spotted in a particular minimart at 10:05 am, then it is evidence that Joe was in the neighborhood at that time. If Joe is NOT spotted in a particular minimart around that time, it does NOT count as evidence that he was not in the neighborhood at that time. Similarly, finding Noah’s Ark counts as evidence FOR a global flood, but NOT finding Noah’s Ark does not count as evidence against a global flood (it could’ve decayed, it might be elsewhere, etc). Hence, your statement, “If similarities are evidence of common ancestry, then dissimilarities are evidence of – what?” is formulated completely wrong because dissimilarities might count as evidence for nothing. In essence, you’ve built in an assumption into your question.

Second, the evidence for common descent can be contradicted by non-sensical genetic data. For example, it’s possible that studies of different genes could give deeply different phylogenetic trees (and by “deeply different”, I mean that non-sensical interpretations can’t be explained by one or two coincidental mutations). For example, Hovind takes aim at common ancestry with this quote:

Well, now, hold it. If you want to just pick one item and that’s supposed to prove relationship, did you know that human Cytochrom [sic] C is closest to a sunflower? So really the sunflowers are our closest relative folks. It depends what you want to compare. If you want to compare the eyes, we are closest to an octopus. Not a chimpanzee. Pick something. What do you want to compare? Human blood specific gravity is closest to a rabbit or a pig. Human milk is closest to a donkey. It depends on what you want to compare. Pick something. If there were not some similarities between us and other animals we could only eat each other. So God designed all animals from the code so we could eat other plants and animals and digest them. Not proof for evolution. It’s proof of a common Designer!

Unfortunately for creationists, while this situation could theoretically be true, it’s false - I’ve looked up the cytochrome-C data, and the octopus eye is not like the human eye. Would you agree that Hovind’s statement (if true) would constitute evidence against common descent? If so, can we look forward to you never again claiming that “One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.”

Comment #171155

Posted by Bilbo on April 20, 2007 3:29 PM (e)

Nick wrote: “Well, after holding up these signs for a while, the men on stage noticed and decided to answer one of them. They chose the last one, regarding ribosomes. Immediately, the only person on stage with any knowledge of biology, Michael Behe, took up the question.

His answer was that ID theory does not allow for explanations regarding interspecies commonalities such as those implied in the question.”

Nick, given that Behe accepts common descent, I find it difficult to believe that he gave this answer. As much as I respect your intellect and general honesty, I can’t help but suspect that you’ve left out part of Behe’s answer. Perhaps not on purpose. All of us are guilty of not remembering completely, from time to time.

Comment #171159

Posted by Paul Nelson on April 20, 2007 4:11 PM (e)

Brian Spitzer wrote:

Hypothesis 1: All living organisms today share common ancestry. […] If you feel that Woese or Doolittle specifically reject Hypothesis 1, present clear evidence for it.

Both Woese and Doolittle have consistently argued over the past decade that extant life on Earth descends from more than one cell (organism). On their view, there never was a universal common ancestor, meaning an organism to which all extant life traces its ancestry. For Woese, the original cellular ancestors of the three domains – Eukarya, Archaea, Bacteria – arose independently: their cellular architectures represent a polyphyletic geometry. Woese writes:

Extant life on Earth is descended not from one, but from three distinctly different cell types.

Carl R. Woese, “On the evolution of cells,” PNAS 99 (June 25, 2002):8742-8747.

For his part, Doolittle argues that the base of the tree of life represents a mangrove (multiple independent roots terminating in the prebiotic milieu), and, like a mangrove, no single root draws all the others together, as would be necessary under a strictly monophyletic geometry. Under the heading, “Is a single universal ancestral cell or species really necessary?” Doolittle argues

Thus, there is no more reason to imagine only a single first kind of cell as the progenitor of all contemporary life than there is to imagine only Adam and Eve as progenitors of the human species.

W.F. Doolittle, “The nature of the universal ancestor and the evolution of the proteome,” Current Opinion in Structural Biology 10 (2000):355-358.

Woese has taken to calling Darwin’s single Tree a “Doctrine” -– the capital letter is his -– and says “The Doctrine of Common Descent has deceived us.” I think ‘doctrine’ in this instance is not a term of praise. In his 2007 PNAS paper with Bapteste, cited above, Doolittle was worried enough that the heterodoxy of his current views would be exploited by ID Bad Guys (like me) to include comments at the end, saying that dropping Darwin’s single Tree picture didn’t mean that evolutionary theory writ large had failed. Of course he’s right: evolutionary theory from its inception has included mono- and polyphyletic geometries. Darwin, for instance, toyed with both.

JohnK – if you watch that Canadian program from the start, you’ll see Jerry Coyne claiming that all biologists accept the common descent of life from a single organism as a “fact.” My mention of the Doolittle paper was within that context, and precise. It is not true that all biologists accept Darwin’s single Tree (universal common descent) picture. Your charge of dishonesty is groundless.

Harold wrote, answering a question from me:

“What’s the observational (or experimental) evidence that ribosomes could jettison a structural unit such as 5S rRNA, without loss of function?”

Obviously, the fact that both bacterial and eukaryotic ribosomes do function can easily be observed.

You’ve assumed that different ribosomes share a common ancestor, and thus that any differences, such as numbers and types of structural rRNAs, evolved without disrupting function. That was however the point at issue. I asked if any experimental evidence existed, showing that ribosomal function would not be destroyed if a structural RNA were removed.

Gotta leave this discussion (work calls); sorry if questions were overlooked.

Comment #171162

Posted by Doc Bill on April 20, 2007 4:33 PM (e)

Paul Nelson, ducking the issue, wrote:

I asked if any experimental evidence existed, showing that ribosomal function would not be destroyed if a structural RNA were removed.

My question to Paul Nelson is this: Is there any experimental evidence showing that ribosomal function is the result of “intelligent design?”

Since I’m not interested in waiting until 2010 for an answer, I’ll provide an answer for Paul:

Paul Nelson’s proxy writes: No, Doc Bill, there isn’t experimental evidence for anything about ID. As you know, ID is a religious proposition that ribosomal function was designed by an unknown Intelligent Creator at an unknown time for an unknown purpose. I guess we’ll never know. By the way, have you ever looked at your hand? I mean, really, really, really looked at your hand. It’s like, wow!

Comment #171165

Posted by Stuart Weinstein on April 20, 2007 4:48 PM (e)

Paul Nelson writes:
“Douglas and DMA,

If similarities are evidence of common ancestry, then dissimilarities are evidence of – what?”

Subsequent evolution, including selection and drift.

Sheesh.

“Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other? One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.”

Can you arrange the patterns of similarity in a nested heirarchy? If not, then that is evidence against common ancestry.

Now, Paul, tell us again, how you falsify ID?

Comment #171187

Posted by B. Spitzer on April 20, 2007 6:26 PM (e)

My earlier post:

Hypothesis 1: All living organisms today share common ancestry.

Hypothesis 2: All modern life arose from a single origin, as opposed to there being multiple origins, the descendants from which combined at some point early in life’s history.

Hypothesis 3: The Tree of life is dichotomous, as opposed to there being any lateral transfer or re-joining of separate lineages.

Hypothesis 1 is not the same as Hypotheses 2 and 3. Don’t pretend that it is.

I would not be surprised if Woese or Doolittle reject Hypotheses 2 and/or 3 for the events very early in the history of life. I don’t know of any serious scientist who rejects Hypothesis 1. If you feel that Woese or Doolittle specifically reject Hypothesis 1, present clear evidence for it.

Dr. Nelson’s reply:

Both Woese and Doolittle have consistently argued over the past decade that extant life on Earth descends from more than one cell (organism). On their view, there never was a universal common ancestor, meaning an organism to which all extant life traces its ancestry. For Woese, the original cellular ancestors of the three domains – Eukarya, Archaea, Bacteria – arose independently: their cellular architectures represent a polyphyletic geometry. Woese writes:

Extant life on Earth is descended not from one, but from three distinctly different cell types.

Carl R. Woese, “On the evolution of cells,” PNAS 99 (June 25, 2002):8742-8747.

For his part, Doolittle argues that the base of the tree of life represents a mangrove (multiple independent roots terminating in the prebiotic milieu), and, like a mangrove, no single root draws all the others together, as would be necessary under a strictly monophyletic geometry. Under the heading, “Is a single universal ancestral cell or species really necessary?” Doolittle argues

Thus, there is no more reason to imagine only a single first kind of cell as the progenitor of all contemporary life than there is to imagine only Adam and Eve as progenitors of the human species.

W.F. Doolittle, “The nature of the universal ancestor and the evolution of the proteome,” Current Opinion in Structural Biology 10 (2000):355-358.

Based on what you’ve written here, it’s clear that Doolittle rejects Hypothesis 3 and Woese rejects Hypothesis 2.

Let me repeat myself: “Hypothesis 1 is not the same as Hypotheses 2 and 3. Don’t pretend that it is.”

And again, “If you feel that Woese or Doolittle specifically reject Hypothesis 1, present clear evidence for it.”

I’ll make my point even clearer, so that there’s no confusion: arguing that the history of life cannot be represented by a purely dichotomous tree with a single root is not the same as arguing that modern organisms do not share common ancestry. You seem to be claiming that there are modern organisms that never shared any sort of ancestor, cellular or pre-cellular. I do not believe that Woese or Doolittle would support you in this claim; I do not believe that the empirical evidence supports you in this claim.

Perhaps I am mistaken about the claim that you’re trying to make. If so, you have my apologies, but I would appreciate it if you would make your claim clear and precise.

B. Spitzer

Comment #171205

Posted by David Stanton on April 20, 2007 9:38 PM (e)

Paul,

How do Woese and Doolittle explain the fact that all three domains use exactly the same genetic code? How do they explain the nested hierarchy of ribosomal gene sequences? How do they explain all of the other shared commonalities if there were three independent origins?

Now drastically different genetic codes or complete lack of ribosomes in one domain, that would be evidence of independent origins.

Comment #171214

Posted by Pete Dunkelberg on April 20, 2007 10:48 PM (e)

Earlier I posted a link to the pdf, but with other links. Should have known that would get it held up.

W.F. Doolittle and E. Bapteste, “Pattern pluralism and the Tree of Life hypothesis”.

It’s about microbes, lateral gene transfer, and how far back the common ancestor was. There is or was enough lateral gene transfer so that a tree is not a complete model of prokaryote relations. This hardly implies the Designer did it. Lateral transfer means more evolution; evolution works even better than we used to know. Search for the paper at Sandwalk for more discussion.

Comment #171264

Posted by harold on April 21, 2007 9:19 AM (e)

Paul Nelson -

You wrote -

“What’s the OBSERVATIONAL (or experimental) evidence that ribosomes could jettison a structural unit such as 5S rRNA, without loss of function?”

Emphasis mine.

I wrote -

“Obviously, the fact that both bacterial and eukaryotic ribosomes do function can easily be observed. I guess that settles that.”

My tone may be light, but the fact is, this is a painfully obvious answer to your question as posed. Although 5s rRNA is not necessarily useless, ribosomes that lack it can be observed to function. Here’s a link to a basic discussion.
http://users.rcn.com/jkimball.ma.ultranet/Biolog…

I also wrote about the massive amount of other evidence for evolution; you chose to ignore that.

But you replied…

“You’ve assumed that different ribosomes share a common ancestor, and thus that any differences, such as numbers and types of structural rRNAs, evolved without disrupting function. That was however the point at issue. I asked if any experimental evidence existed, showing that ribosomal function would not be destroyed if a structural RNA were removed.”

Emphasis mine.

First of all, I never made an “assumption” about ribosomes in my life; it is the evidence that shows that ribosomes share a common ancestor.

Second of all, now you want an “experiment”. Of course, such an experiment is technically very possible. We can’t directly test that the earth goes around the sun by experiment (apologies if you perceive the heliocentric solar system as heresy); we can do indirect experiments only for that. We rely mainly on observation. But we could probably show, experimentally, what we already know observationally - that even in the abscence of a subunit, ribosomes will assemble and retain some function.

Probably such experiments have been done, not for the idiotic reason of responding to obsessive creationists, but to learn more about ribosomal physiology. In fact, there is a literature on the function of the 5s subunit.

But you don’t really want an experiment (you’d look for one yourself if you did), you just want to keep denying, largely by pretending that you said something other than what you originally said, that your point has been refuted.

You’ve been knocked out twice now. If you get up and begin swinging your fists again, you’ll be the only one in the ring, in an empty arena.

Comment #171396

Posted by harold on April 22, 2007 1:44 PM (e)

Well, I guess I was a bit more harsh than I intended during that last comment.

I certainly don’t feel guilt. Paul Nelson was being very slippery. First arguing against the similarities between the various types of ribosomes, while ignoring all the other evidence for evolution, and not providing the slightest insight into how ID explains ribosomes. Then changing his question when he got a very simple answer.

Still, I’m trying these days to be less curmodgeonly.

Comment #171403

Posted by David Stanton on April 22, 2007 2:37 PM (e)

Harold,

I don’t think you were being all that harsh. After all Nelson has definately been playing us.

Nelson claimed that you can’t use similarity as evidence for common ancestry if you don’t know what would count as evidence against common ancestry.

I replied that since all known organisms did share a common ancestor similarity is indeed evidence of common ancestry and I gave a list of criteria that could be used to infer that organisms did not share common ancestors.

Nelson replies that not everyone believes that all known organisms shared a common ancestor and cites references. Huh, I guess he knew all along what would constitute evidence against common ancestry.

I replied that this hypothesis does not account for the similarities between all known life forms. After all, none of the criteria I cited were fulfilled.

Nelson runs away without answering.

It’s always preferable to be civil. I do appreciate you guys putting up with me. But this guy just seems to want to play games.

Comment #171425

Posted by MPW on April 22, 2007 9:03 PM (e)

As fascinating and often amusing as this discussion has been, I’d like to drag things back to the OT for a moment. For those who haven’t followed up Nick’s link to the SMU Daily Campus in detail, there’s been ID content on the opinion page for every day in the past week. The reader comment sections have been very lively (if occasionally buggy on a technical level). IDists of the most ignorant and pugnacious sort are all over it. Friday saw an op-ed piece by a Spanish lecturer at the university. Choice excerpts:

“I, for one, am weary of this arrogant stranglehold on knowledge, and science so-called, as if there were a single scientist or philosopher anywhere in the world who was there when it all happened (evolution, creation, the Big Bang) and saw God not do it!”

“Scientific materialists have been force-feeding me their one-sided perspective on reality for way too long.”

“If there is a Creator, then what we see around us is at best the debris of the creation event, whatever form it may have taken. Would you put much confidence in a Theory of French Cuisine based only on an analysis of the egg and flour spillage on the countertop and floor?”

Really, I’m not making those up. Anyway, there’s plenty of pushback from sharper minds, but one or two people from around these parts would be welcome. Clearly there are a lot of eyes watching those pages, many of them probably people who don’t give much thought to this subject otherwise (unlike most people who come here, I would imagine). At the very least, it’s entertaining to read.

Comment #171498

Posted by John on April 23, 2007 11:25 AM (e)

Paul Nelson wrote:
“If similarities are evidence of common ancestry, then dissimilarities are evidence of – what?”

This is a creationist straw man. The evidence for common ancestry is not simply similarity. The evidence is the pattern and extent of similarities, which necessarily involves looking at differences too.

“Put another way, what molecular characters would show that eukaryotic mitochondrial ribosomes and bacterial ribosomes arose independently of each other?”

Their failure to fit into a nested hierarchy, of course.

“One cannot say that similarities count as evidence for common ancestry, unless one knows what would count as evidence against common ancestry.”

We don’t simply say the former, and we clearly know the latter.

You are a very dishonest man.

Comment #171918

Posted by Tyrannosaurus on April 25, 2007 11:21 AM (e)

Interesting announcement from UCI.

BACK TO DARWIN
Francisco Ayala, the UC Irvine biologist who won the National Medal of Science for groundbreaking work in evolutionary genetics and the origins of disease, will give a pair of free public lectures today and Thursday about Darwinism and intelligent design.

His first appearance comes at 7 p.m. today, when Ayala, a former Franciscan priest, gives a talk titled “Evolution and Religion: Concert, Not Conflict.” The lecture will be held in Schneiderman Hall, on Ring Road, next to McGaugh Hall.

On Thursday, Ayala will visit Chapman University in Orange to discuss “Darwin and Intelligent Design.” The talk gets started at 4 p.m. in Beckman Hall. He will accept questions from the audience after both lectures.

Comment #184742

Posted by brightmoon on June 26, 2007 6:33 PM (e)

childish word-game playing

yep that’s exactly how i would put paul nelsons short answer

however,i would like to see his long answer (and the subsequent refutations)

btw,does anyone know anything more about “hatena” and that sort of “precursor” secondary endosymbiosis that some japanese researchers found last year ?

there was a short article in Science about it