PZ Myers posted Entry 1813 on December 22, 2005 10:49 AM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/1808

Panderichthys

Panderichthys is a widely recognized transitional form in tetrapod evolution (you know, one of those transitional fossils we're so often told don't exist). A description of a specimen with a well-preserved pelvic girdle has just been described in Nature, and it tells us some more about the history of tetrapod locomotion.

Panderichthys is an interesting animal—it definitely looks more like a fish than a salamander, but its fins are stout and bony, and other characteristics of its skeleton clearly ally it with the tetrapods. In the shift from an aquatic to a fully terrestrial life, the limbs and their supporting pectoral and pelvic girdles had to undergo major changes. In fish, the pectoral girdles are coupled to the skull, while the pelvic girdles are small and 'floating' in the musculature. To bear the animal's weight, the pectoral girdles lost their connection to the skull, and both became thicker, stronger, and more closely bound to the axial skeleton. The fins themselves had to change from a fan of slender fin-rays to more solid load-bearing digits. In Panderichthys, we see a mixture of these changes in process.

Continue reading "Panderichthys rhombolepis" (on Pharyngula)

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Comment #64075

Posted by Karen Spivey on December 22, 2005 11:39 AM (e)

Of Panderichthys and People!

Comment #64133

Posted by Vasha on December 22, 2005 1:25 PM (e)

I agree, Panderichthys seems to make almost as good a mascot as a panda. I mean, here we have a fish with legs! (Which I believe is something creationists have specifically ridiculed the nonexistence of). Even better, it has legs in the front, fins in the back - both at once makes transitionality strikingly visual. How can this be used?

Comment #64192

Posted by The Ghost of Paley on December 22, 2005 3:28 PM (e)

PZ Myers wrote:

Panderichthys is a widely recognized transitional form in tetrapod evolution (you know, one of those transitional fossils we’re so often told don’t exist). A description of a specimen with a well-preserved pelvic girdle has just been described in Nature, and it tells us some more about the history of tetrapod locomotion.

Interesting fossil, as is the immaculately preserved Acanthostega. Just one problem: Morphological studies of lungfish, including analyses of their skull characteristics, preclude their direct ancestry to tetrapods. Thus, biologists proposed the coelacanth - like Eusthenopteron as the direct ancestor instead. With Jenny Clack’s discoveries, it all seemed to fit together: Coelacanth->Eusthenopteron->Acanthostega->Ichthyostega, a relatively smooth transition. And Panderichthys added further support to this story. The last piece: a genetic test of some sort. Good news! Modern Coelacanths and lungfish were available to check this yarn. And that’s when all hell broke loose. It seems the genes don’t support the fishy tale. Some studies did group the Coelacanths with the tetrapods. Others preferred placing them with bichir. Still others were all mixed up. Poor, poor, fishies. Where will you go now that Darwin has tossed you back into the sea?

Comment #64193

Posted by PZ Myers on December 22, 2005 3:33 PM (e)

I think you’re a little confused. Follow the link and take a look at the cladogram.

Comment #64199

Posted by Steviepinhead on December 22, 2005 4:07 PM (e)

Not to mention, O Insubstantial One, that–instead of wasting your time over here–you’re “supposed” to be linking to your asserted answers to Lenny’s questions over on Tara’s “So, is it over?” thread.

What seems to be the problem?

Comment #64200

Posted by The Ghost of Paley on December 22, 2005 4:10 PM (e)

PZ Myers wrote:

I think you’re a little confused. Follow the link and take a look at the cladogram.

I saw the cladogram, but this does not represent the majority point of view, morphology-wise. I think a careful reading of Zimmer’s book will highlight the difficulty in the Lungfish/Amphibian transition; in fact, I think he makes the same point about lungfish skulls that my source does. In any case, check out the evo predictions prior to the molecular studies - it’s a classic case of an ad hoc adjustment to avoid falsification.

Comment #64204

Posted by Russell on December 22, 2005 4:24 PM (e)

In any case, check out the evo predictions prior to the molecular studies .

Indeed, that sounds like a worthwhile exercise. So, are you directing us to Zimmer’s book to find those predictions?

- it’s a classic case of an ad hoc adjustment to avoid falsification

or possibly, the making of a prediction to test a hypothesis, learning from the results of that prediction that the hypothesis was faulty, and then coming up with a new one, better fitted to all the available data. How embarrassing! Clearly what’s needed is a more solid basis for our hypotheses, like the Bible, for instance.

Comment #64205

Posted by Steviepinhead on December 22, 2005 4:25 PM (e)

Gosh, Ghosty, it seems like you don’t quite grasp the concept of falsification either.

A theory that can and must adjust to new facts around its fringes is a robust theory that can be falsified, i.e., it’s science.

It’s the “theory” that never has to adapt to the evidence because it never adduces any evidence, couldn’t care less about the evidence, and desperately prefers to ignore all evidence that can’t be falsified, and is, therefore neither science nor a theory.

Do any candidates for the latter category jump to mind?

Comment #64208

Posted by PZ Myers on December 22, 2005 4:34 PM (e)

I don’t think he understands the cladogram, either. Look again: it doesn’t say we evolved from lungfish.

Comment #64214

Posted by Russell on December 22, 2005 4:49 PM (e)

I don’t think he understands the cladogram, either. Look again: it doesn’t say we evolved from lungfish.

Well, you’re probably right. But he’s saying that the cladogram doesn’t represent the consensus of evolutionary opinion on the subject. And I’m eagerly awaiting his references to substantiate that claim.

Comment #64215

Posted by Steviepinhead on December 22, 2005 5:02 PM (e)

And, PZ, I think that all we’re saying is that–even if Ghosty had a point (concededly a dubious proposition)–it still wouldn’t support his claim about the falsifiability vel non of evolution.

Another nice science article, by the way, and thanks!

Comment #64225

Posted by Martin Brazeau on December 22, 2005 6:01 PM (e)

I’d like to wade in here since this particular bit of research was done in my lab.

Let’s take it from the top:

Interesting fossil, as is the immaculately preserved Acanthostega. Just one problem: Morphological studies of lungfish, including analyses of their skull characteristics, preclude their direct ancestry to tetrapods.

This demonstrates a failure to understand that evolution is a branching phenomenon. Two taxa can be close ‘cousins’ without one being descended directly from the other. Certainly, lungfishes are not the direct ancestor of tetrapods. Since the widespread acceptance and use of cladistics by palaeontologists, few (if any) have ever proposed lungfishes as the direct ancestor of tetrapods.

The lungfish-tetrapod split is rather well documented. In the Early-Middle Devonian, we find a number of generalized fishes collectively known as “rhipidistians”. On the one hand, we see progressively more lungfish-like characteristics in forms such as porolepiforms, Powichthys, Youngolepis, and Diabolepis. We can see: the fusion of the intracranial joint as well as the transformation of the palate into massive tooth plates. On the tetrapod-side of the equation, we have forms such as Kenichthys that demonstrate the transformation of the earliest tetrapod synapomorphy: the internal nostril. Kenichthys is followed by various osteolepiforms such as Osteolepis, known in considerable abundance from the Middle Devonian of Scotland.

Thus, biologists proposed the coelacanth - like Eusthenopteron as the direct ancestor instead.

This is so terribly wrong. You seem to think that all lobe-finned fishes are the same for some reason. Coelacanths and Eusthenopteron belong to two separate groups of Sarcopterygii: Actinistia and Osteolepiformes, respectively. The morphological consensus looks as follows: (Coelacanths(Lungfishes(Eusthenopteron(Panderichthys;Tetrapoda))))

With Jenny Clack’s discoveries, it all seemed to fit together: Coelacanth->Eusthenopteron->Acanthostega->Ichthyostega, a relatively smooth transition.

Sorry, but that was never a hypothesis that was considered since Jenny’s discoveries. Please, refresh your history on this matter. Providing some references that suggest such ancestor-descendent relationships would be greatly appreciated.

And Panderichthys added further support to this story.

Panderichthys provides incontrovertible evidence of a transitional form between osteolepiform fishes and tetrapods. Consider the following characters exhibited by Panderichthys:

Paired frontals,
Flattened head
Internal nostrils
Ventrally expanded scapulocoracoid
Absence of dorsal and anal fins

I will be adding to this list shortly, but the paper is currently embargoed.

The last piece: a genetic test of some sort. Good news! Modern Coelacanths and lungfish were available to check this yarn. And that’s when all hell broke loose. It seems the genes don’t support the fishy tale. Some studies did group the Coelacanths with the tetrapods. Others preferred placing them with bichir. Still others were all mixed up. Poor, poor, fishies. Where will you go now that Darwin has tossed you back into the sea?

I’ll agree, there is disagreement among molecular trees about the tetrapod, lungfish, coelacanth trichotomy. However, Hell has not broken loose. There is a well-understood phenomenon here called long-branch attraction. There are biases in molecular estimates of phylogeny because deeply-branching phylogenies have long histories and thus higher probabilities of convergence. It is not surprising to find this kind of disagreement. The fossils, however, are unequivocal: lungfish are the extant sister taxon to tetrapods.

I saw the cladogram, but this does not represent the majority point of view, morphology-wise. I think a careful reading of Zimmer’s book will highlight the difficulty in the Lungfish/Amphibian transition; in fact, I think he makes the same point about lungfish skulls that my source does. In any case, check out the evo predictions prior to the molecular studies - it’s a classic case of an ad hoc adjustment to avoid falsification.

Morphology-wise, as you say, this is precisely the consensus. In the diagram in Zimmer’s book he has left out all the stem-dipnomorphs (the transitionals at the node between lungfish and tetrapods) because if he had included them all, each taxon would have been represented by a blob of ink about the size of a match head. Zimmer’s book was about the origin of tetrapods, not the origin of lungfishes.

Comment #64229

Posted by RBH on December 22, 2005 6:08 PM (e)

Thanks, Martin. One of the attractions of the Thumb is that people who actually know their stuff post here. (So when is the embargo lifted, hm?)

RBH

Comment #64235

Posted by Russell on December 22, 2005 6:25 PM (e)

Thanks, Martin!

Looks like another one of those “Marshall McLuhan in Annie Hall” moments we’re often treated to here at The Thumb.

(Or are you going to set the good doctor straight, GoPpy?)

Comment #64237

Posted by Martin Brazeau on December 22, 2005 6:37 PM (e)

RBH, I only wish I knew when the embargo will be lifted. That paper above (Catherin Boisvert’s) was accepted for publication only a few weeks before mine. So, hopefully in a few weeks. As far as I know, the journal is plugged with papers at the moment.

Comment #64271

Posted by 'Rev Dr' Lenny Flank on December 22, 2005 8:43 PM (e)

this does not represent the majority point of view, morphology-wise.

Hey Paley, why isn’t *ID* the majority point of view, morphology-wise?

Oh, wait — it’s because scientists are all atheistic god-hating devil-worshippers, right? (snicker) (giggle)

How about telling all of us the, uh, scientific explanation offered on the matter by intelligent design, uh, “theory” …. .

Oh, wait — you don’t HAVE any, do you?

What did the designer do to produce tetrapods, Paley? What mechanisms did the designer use to do whatever the heck you think it did? Where can we see the desigenr using these mechanisms to do … well . . anything?

Or is “POOF! God – er, I mean, The Unknown Intelligent Designer – dunnit!” the best, uh, “science” that ID can come up with?

Comment #64277

Posted by The Rev. Schmitt. on December 22, 2005 9:12 PM (e)

Cracking comment Dr Brazeau. One of my favourite things about the Thumb is the propensity for genuine experts to pop up now-and-then to absolutely demolish twaddle with reality.

And on that note - thanks to both Dr Myers and Dr Brazeau for discussing several of our ancestors which are rarely sensationalised. Solid science makes a nice break from crushing creationism - as amusing as the past few days have been.

Comment #64490

Posted by The Ghost of Paley on December 23, 2005 3:20 PM (e)

I’ve been distracted lately, so I don’t have time for a long rebuttal, but I have four questions for Dr. Brazeau:

1) Based on the fossil evidence alone, are lungfish or coelacanths closer relatives to Eusthenopteron?
2) What is the independent evidence for the long-branch attaction artifact in this specific phylogeny?
3) Are the Devonian Coelacanth skull roofs as prism-like as the fossil lungfish’s?
4) Do the coelacanths possess the lungfish ball and socket arrangement, or the tetrapod one?

Comment #64513

Posted by Martin Brazeau on December 23, 2005 4:35 PM (e)

I’ve been distracted lately, so I don’t have time for a long rebuttal, but I have four questions for Dr. Brazeau:

Very flattering, but I’m only a Ph.D. student. So, you’ll have to refrain from calling me “Dr.” for the next two and a half years.

I’ll now answer your questions as best as I can, however all of these can be addressed by spending a few hours doing some research.

1) Based on the fossil evidence alone, are lungfish or coelacanths closer relatives to Eusthenopteron?

My first post already answered this. Lungfishes are closer to Eusthenopteron than either is to a coelacanth. This is based on the fact that stem-lungfishes and Eusthenopteron share a number of unique similarities in common: three coronoids in the lower jaw, a sqaured dorsal margin of the cleithrum (the major dermal element of the shoulder), the posterior nostril placed close to the margin of the mouth, to name a few.

2) What is the independent evidence for the long-branch attaction artifact in this specific phylogeny?

Which specific phylogeny? It depends on whose phylogeny and the methods used by the authors. The issue at hand here is that it is not uncommon for morphological and molecular trees (or for multiple molecular trees) to disagree when the branches are long. It’s straight-up probability theory.

It is false to assume that molecular trees are constructed without bias, especially when dealing with such divergent lineages, the use of informative sequences and the proper alignment of those sequences can be problematic and have an element of subjectivity.

Furthermore, lungfishes have enormous polyploid genomes about 30 times larger than our own. Thus, their molecular biology can be quite complex, strange, and highly divergent. It is therefore quite difficult to probe truly homologous sequences in the lungfish genome when compared with ‘simpler’ genomes of coelacanths.

If you care to do any of your own research into this question, you can start here: url href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15545497&query_hl=2&itool=pubmed_docsum> and here: url href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15037746&query_hl=4&itool=pubmed_docsum>

3) Are the Devonian Coelacanth skull roofs as prism-like as the fossil lungfish’s?

What do you mean by “prism-like”? The skull roof of Devonian coelacanths present an arrangement not entirely unlike the generalized bony fish condition. The unique condition of lungfish skull roof bones (with a pattern difficult to homologize with other sarcopterygians) can bee traced through Porolepis and Powichthys. More lungfish-like forms such as Youngolepis and Diabolepis have markedly more lungfish-like skull roofs and have a fused intracranial joint. However, other aspects of their braincases reflect a more generalized condition shared with the aforementioned taxa and osteolepiforms (denticulated parapshenoid, palates not fused to the braincase etc.).

4) Do the coelacanths possess the lungfish ball and socket arrangement, or the tetrapod one?

What anatomy are you referring to?

Comment #64525

Posted by 'Rev Dr' Lenny Flank on December 23, 2005 5:00 PM (e)

however all of these can be addressed by spending a few hours doing some research.

IDers don’t do research. They don’t need to. God has already told them they’re correct. (shrug)

Comment #64526

Posted by 'Rev Dr' Lenny Flank on December 23, 2005 5:02 PM (e)

I’ve been distracted lately, so I don’t have time for a long rebuttal

Why is it that ID/creationists ALWAYS have the time to POST their baloney, but NEVER seem to have the time to DEFEND any of it …?

Comment #65369

Posted by The Ghost of Paley on December 28, 2005 9:51 AM (e)

Mr. Brazeau:

1)The “cracked eggshell” patterning of the dermal skull bones of the modern lungfish, as well as its concave humerus/convex shoulder joint arrangement, is hard to reconcile with its role as a tetrapod ancestor.

2)Earlier researchers dispute the Dialepis/dipnoan link (1), while others would displace Youngolepis from its rhipsidian crown position (2) to a more basal sarcopterygian one. Still others (3) would divorce modern lungfish from porolepiforms proper, which renders your synapomorphies moot, and Kenichthys irrelevant. Also see (5) for a critique of modern guesswork such as Chang’s

3) your argument about the lung fish genome isn’t relevant because it’s the coelacanth that is getting pushed around the molecular tree (4).

Please excuse the terrible formatting, citing, and spelling; I’m working with the best computer available…..
(1)Google “Characteristics of Dipnoi, a monophyletic group”
(2)Google “Synapomorphies and Scenarios-more characteristics of Youngolepis”
(3)google “Dipnoans as Sarcopterygians”, and see the last two sentences of the abstract
(4)Google “whole genome mitochondrial phylogeny” and “Comprehensive vector phylogeny” for the study.
(5)Google “Diabolepis and its relationship to dipnoi”

I apologise for the lack of links, but this computer won’t let me hyperlink. The badly cited papers should be familiar to you anyway, I hope.

Rev. Jim: Shouldn’t you be working on a critique of the latest Wizard monographs, or at least give an evidenced, specific reasson as to why they’re irrelevant? As opposed to moving your shoulders up and down…..

Yenta: Look for a new rebuttal soon…..

Comment #65662

Posted by sir_toejam on December 29, 2005 2:51 PM (e)

Paley sure sounds more and more like Blast, doesn’t he?

Comment #68285

Posted by Martin Brazeau on January 6, 2006 10:07 AM (e)

There are a lot of fallacies and misconceptions in Ghost’s last post. I apologize for the delay, but I had to prepare my response in a text-editor because it was very difficult to untanlge the mess!

1)The “cracked eggshell” patterning of the dermal skull bones of the modern lungfish, as well as its concave humerus/convex shoulder joint arrangement, is hard to reconcile with its role as a tetrapod ancestor.

I’ve already pointed out in my first post that there is not one palaeontologist who holds this view. Please find me one reference (preferably from the past 25 years) where a scientist suggests that dipnoans (lungfishes) are ancestral to tetrapods.

Again, the “cracked eggshell”, down to the topological pattern can be seen to emerge in forms such as Diabolepis.

2)Earlier researchers dispute the Dialepis[sic]/dipnoan link (1),

Yes, and some continue to. See my response to (5) below. They are a minority opinion and their work has been subject to much criticism or has been contradicted by the most recent analyses, most notably: Ahlberg (1991), Chang (1995, 2004), Zhu and Yu (2002), and Zhu et al. (2001).

The fact that Diabolepis is difficult to classify as either a “rhipidistian” or a lungfish does not play very well in your favour. As a creationist, you tend to focus on the fact that there exists some contention on this matter. As you wallow in the crapulent joy of the moment, you fail to realize that you must then admit that there exist fossils of an animal that represents a combination of both derived dipnoan features and basal ‘rhipidistian’ features all while denying that there are any ‘transitional forms’. How you can try to make this a problem for me is rather perplexing.

while others would displace Youngolepis from its rhipsidian crown position (2)

Quite possibly, but this doesn’t help you at all: if there were no stem-group sarcopterygians then you could point to a gap there.

Nevertheless, if we pluck out Youngolepis you still have porolepiforms, Powichthys, Diabolepis, and a host of basal Devonian lungfishes to contend with. That’s at least four more transitional forms than you’re prepared to deal with.

to a more basal sarcopterygian one. Still others (3) would divorce modern lungfish from porolepiforms proper, which renders your synapomorphies moot, and Kenichthys irrelevant.

Those are some pretty bold words, my friend! Some would divorce them, but most would not. For example, the fin morphology of lungfishes and porolepiforms is uniquely shared among bony fishes url href=http://www.usm.maine.edu/bio/courses/bio205/sarcop_fins.jpg> . Yes, the morphology of the dipnoan skull is very peculiar, but aspects of the postcranial anatomy of Devonian lungfishes are still pretty conserved.

How can you say that the synapomorphies I raise are moot? Any piece of circumstantial evidence is open to dispute, but that hardly makes them ineffectual. What has really happened is that you found some sources (which I doubt you’ve read or criticized yourself) that disagree with the prevailing view on sarcopterygian phylogeny. You’ve chosen to rely on these because they are at odds with what I have presented above. Nevertheless the value of particular synapomorphies is a function of the test of congruence: a phylogenetic (parsimony) analysis.

Which leads me to this:

Also see (5) for a critique of modern guesswork such as Chang’s

Cambell and Barwick (2001) rely on rather specious argumentation in dealing with Chang’s characters. Moreover, they never submit their changes to the test of congruence and therefore fail to test the value of their own synapomorphies. Instead, they’re relying on considerably more biased information in placing a preferred weight on particular synapomorphies. This, in fact, renders their analysis moot.

You selective citation is an example of the “Defeat my paradigm in order to trash yours” fallacy. You can’t accept the criticisms of Campbell and Barwick while calling Chang’s “guesswork” (again, discussing papers you probably haven’t even read!). Both are evolutionary. Both accept that sarcopterygians share a single common ancestor and that tetrapods are descended from them. As I remember correctly, that was the original contention here.

3) your argument about the lung fish genome isn’t relevant because it’s the coelacanth that is getting pushed around the molecular tree (4).

This is a common fallacy that undergraduates make in their introduction to systematics. It often goes undiagnosed and untreated unfortunately, so don’t feel bad. In a cladogram all topologies are relative. It makes no sense to talk about a particular taxon “getting pushed around”. The coelacanth is getting ‘pushed around’ because that’s the one you’re paying attention to! The lungfish/coelacanth/tetrapod molecular phylogeny has gone through all three of the possible topologies of any three-taxon statement:

a) (T(L;C))
b) (L(C;T))
c) (C(T;L))

Where C is coelacanth, L is lungfish, and T is tetrapods.
[Note: (A(B;C))=(A(C;B))=((B;C)A)=((C;B)A) and (A(B;C)) does not equal ((A;B)C) etc.]

Taxa are not “being pushed around”. Each taxon placement is dependent upon the weight of synapomorphies that supports a particular monophyletic grouping (i.e. any tier of brackets or common node in a tree).

More importantly you ignore the fact that the most recent and up-to-date analysis (linked to in my previous post) resolves the preferred topology of palaeontologists: (C(L;T)). This is very important because molecular biology and methods in molecular systematics advance at an alarmingly rapid pace. We ignore the most recent work at our peril.

Please excuse the terrible formatting, citing, and spelling; I’m working with the best computer available…..
(1)Google “Characteristics of Dipnoi, a monophyletic group”
(2)Google “Synapomorphies and Scenarios-more characteristics of Youngolepis”
(3)google “Dipnoans as Sarcopterygians”, and see the last two sentences of the abstract
(4)Google “whole genome mitochondrial phylogeny” and “Comprehensive vector phylogeny” for the study.
(5)Google “Diabolepis and its relationship to dipnoi”

Please refrain from this sort of selective citation. The most recent and up-to-date analyses support a Diabolepis+Dipnoi sister group relationship (Including your reference 2, actually. You ought to read the paper before commenting on it or trying to use it to support your case). Again the “Defeat my paradigm in order to trash yours” fallacy surfaces.

The other, and possibly most important point, is that if we dig into the history of any science we will find a variety of contradictory, dissenting, and discredited viewpoints. In fact, it’s guaranteed that we will. What you are looking at is the history of scientific progress - something which creationism is completely immune to. Because creationists have no evidence to support their own case and fail to even grasp how science is done, they (ironically enough) point to healthy and spirited scientific discourse (while Chang Mee-Mann and Ken Campbell might disagree on dipnoan phylogeny, that never stopped her from naming Kenichthys cambelli).

Nevertheless, this is a sharp derailment from the actual topic of this post: tetrapod origins. Were you to contest that tetrapods are descended from fish, the evidence is hopelessly against you. There is no dispute among palaeontologists that tetrapods are descended from osteolepiform fishes: this is born out by the thousands of specimens of Devonian osteolepiforms and the hundreds of specimens of Devonian tetrapods and the dozens and growing number of ‘elpistostegalians’ (i.e Panderichthys & co.) that show an even finer scale of transformation between them. If Panderichthys and Elpistostege are not enough to convince you, just wait a few months. Some new and highly anticipated data are going to have creationists scrambling!

Hint: Little piggies that swim.

Comment #68307

Posted by k.e. on January 6, 2006 11:28 AM (e)

Hmmmm
I’m guessing, but here goes “So long and thanks for all the fish” ?

Comment #68606

Posted by The Ghost of Paley on January 7, 2006 2:48 PM (e)

Whoops-just saw your reply. Thanks for wading through the wretched spelling and all. I need to post a physics paper Monday, and then I’ll get back with a proper response late Monday or Tuesday. Once again, I was working under severe time constraints so please keep that in mind. My Monday/Tuesday rebuttal will be much better, I promise. :>). I just can’t stand crappy technology!

Comment #68612

Posted by Arden Chatfield on January 7, 2006 3:28 PM (e)

I don’t think he understands the cladogram, either. Look again: it doesn’t say we evolved from lungfish.

It’s a good thing – ‘cuz otherwise, why do we still have lungfish???

Ziiiinnnnng!!!!!

Comment #68626

Posted by Martin Brazeau on January 7, 2006 6:50 PM (e)

My Monday/Tuesday rebuttal will be much better, I promise.

I’ll wait for it. Don’t worry about delays. After Sunday, I won’t be able to respond until the following Tuesday/Wednesday.

Comment #68629

Posted by Martin Brazeau on January 7, 2006 7:12 PM (e)

Correction: I won’t be able to respond until a week from Tuesday/Wednesday

Comment #71837

Posted by The Ghost of Paley on January 14, 2006 3:43 PM (e)

Mr. Brazeau wrote:

Please find me one reference (preferably from the past 25 years) where a scientist suggests that dipnoans (lungfishes) are ancestral to tetrapods.

I suppose you mean directly ancestral. Well of course not, partly due to the reasons alluded to above. But there’s always the “indirect” ancestor thingie to fall back on.

Mr. Brazeau wrote:

[The lungfish naysayers] are a minority opinion and their work has been subject to much criticism or has been contradicted by the most recent analyses, most notably: Ahlberg (1991), Chang (1995, 2004), Zhu and Yu (2002), and Zhu et al. (2001).

Perhaps so, but scientific opinion isn’t subject to majority vote. I realise that some synapomorphies group Dipnoids with tetrapods, but my contention has always been that other groupings can be, and have been, defended. To get a taste of how large the minority opinion is, let’s look at this recent molecular study:

Among the traditionalists, the view prevailed ultimately that coelacanths were the
closest living relatives of tetrapods (Romer 1966). Similarly, although the cladistic
approach has produced a prevailing view [i.e., that lungfishes are the closest extant
relatives of the tetrapods (Tree 1); see Rosen et al. (1981), Gardiner (1984), Maisey
(1986), Panchen and Smithson (1987), and Ahlberg (1991)], alternative views
continue to draw staunch support: the coelacanth-tetrapod sister group relationship
(Tree 2) is advocated by Fritzsch (1987), Long (1989), Young et al. (1992), and Zhu
and Schultze (1997) among others, whereas the coelacanth-lungfish sister group (Tree
3) is favored by Northcutt (1986), Chang (1991), and Forey, Gardiner, and Patterson
(1991), for example. The reasons for the different conclusions reached by these
authors seem to be the choice of taxa included in the analysis, the selection of
characters and the interpretation of character polarity, as well as the use of different
variants of the cladistic method. The use of molecular markers has not resolved the
controversy either.

Now why would anyone support alternative ancestral relationships? This paper lists some reasons:

The hypothesis that Latimeria is the sister group of amphibians is the least corroborated, as only a single possible synapomorphy, presence of cervical and lumbar enlargements of the spinal cord, supports this hypothesis. The hypothesis that lungfishes are the sister group of amphibians is supported by two possible synapomorphies: loss of a saccus vasculosus and the presence of neurocranial endolymphatic sacs. The hypothesis that actinistians are the sister group of lungfishes is the most corroborated, based on five possible synapomorphies: presence of a superficial isthmal nucleus, a laminated dorsal thalamus with marked protrusion into the third ventricle, olfactory peduncles, evaginated cerebral hemispheres with pronounced septum ependymale, and electroreceptive rostral organs. However, all five characters may be plesiomorphic for bony fishes. The nervous systems of Latimeria and Neoceratodus are very similar to each other, as are the nervous systems of lepidosirenid lungfishes, caecilians, and salamanders. If Neoceratodus is the most plesiomorphic species of living lungfishes, then lepidosirenid apomorphies may have arisen by paedomorphosis. Our inability to examine the neural characters of a relevant outgroup (rhipidistians) may result in many sarcopterygian plesiomorphic characters being interpreted as apomorphic characters, due to the wide distribution of paedomorphic characters among living sarcopterygians and their possible resemblance to plesiomorphic characters present in living outgroups that can be examined.

Three-Dimensional analyses of palatal bones also link the modern coelacanth to rhipidistians, although the researchers defer to Diabolepis for a definitive answer. Originally, scientists even considered the coelacanth inner ear transitional between fish and amphibians.

So why the change? Mr. Brazeau argues that the fossils made ‘em do it, but I have another idea.

Comment #71841

Posted by The Ghost of Paley on January 14, 2006 3:49 PM (e)

To find out Paley’s hypothesis, tune in tomorrow at the regularly scheduled time….…….

Comment #72234

Posted by The Ghost of Paley on January 15, 2006 4:50 PM (e)

So why the change? There are several factors at work. One involves hedging. That is, Darwin-science constructs several mutually exclusive hypotheses, waits for one to triumph, and then adduces empirical support for the nebulous theory underwriting the contradictory speculation. In this case, evos claimed that the fossils supported:
1) Tetrapods closer to coelacanths
2) Tetrapods closer to lungfish
3) Tetrapods equidistant from the two groups.

When the molecular evidence started trickling in during the early nineties, Darwinists began placing their bets on claim 2):

The use of molecular markers has not resolved the controversy, either. Mitochondrial DNA sequences of individual genes (Meyer and Wilson 1990; Meyer and Dolven 1992; Yokobori et al. 1994), gene fragments, or whole genomes (Hedges, Hass, and Maxson 1993; Cao et al. 1998; Zardoya et al. 1998) generally support a sister group relationship between lungfishes and tetrapods (Tree 1), although at least one gene (Yokobori et al. 1994) and the maximum-parsimony analysis of the whole genome (Zardoya et al. 1998) favor the coelacanth-lungfish sister group relationship (Tree 3). Various nuclear genes, on the other hand, supports Tree 1, 2, or 3, depending on the gene. Thus, Tree 1 is supported by DM20/PLP (Tohyama et al. 2000), RAG1, RAG2, POMC, and DM20/PLP (Venkatesh, Erdmann, and Brenner 2001) markers; Tree 2 is supported by the hemoglobin genes (Gorr, Kleinschmidt, and Fricke [1991]; but for criticism see, Forey [1991], Sharp and Lloyd [1991], Stock and Swofford [1991], Meyer and Wilson [1991], Meyer [1995]) and the 18S ribosomal RNA gene (Stock et al. 1991); and Tree 3 is supported by the 28S ribosomal RNA gene (Zardoya and Meyer 1996).

Was this a conscious decision? Not necessarily. As a group, evolutionists are probably as honest as other scientists; unfortunately, their cladistic tools don’t allow firm predictions. This difficulty renders them vulnerable to subliminal cueing, and like Clever Hans tapping out the square root of 36, cladistic analysis is harmonised with the molecules. The trick lies in knowing the answer ahead of time. Worse, this principle compromises the original morphological analysis itself:

Rosen et al. (1981) proposed the novel hypotheses that lungfishes (dipnoans) are the
nearest relatives (sister-group) of tetrapods, and that all other sarcopterygians such as
osteolepiforms and coelacanths are more distantly related (Fig. 4). On their cladogram,
extant lungfishes and tetrapods share the following synapomorphies, which are absent
in the living coelacanth (genus Latimeria) and other living vertebrates: (1) presence of
glottis and epiglottis in the oral cavity, (2) separation of pulmonary (lung) and systemic
blood circulation in heart and aortic arches, (3) atrium and ventricle of heart partly or
fully divided, (4) ventral aorta developed as a truncus arteriosus. All four features
function in air-breathing in extant lungfishes and tetrapods (Panchen & Smithson,
1987, 1988) : the first is employed during inhalation (‘gulping’ air) while the other three
serve to convey blood to and from the lungs. All are features of soft anatomy, usually
not preserved in fossils. Rosen et al.’s (1981) cladogram, however, presents them as
lungfish±tetrapod synapomorphies and thus implies that they were present in the
earliest (fossil) tetrapods, and the earliest (fossil) lungfishes.
However, biological considerations are inconsistent with this view. Campbell &
Barwick (1988) have reviewed in detail the palaeoecology of all the early, primitive
lungfishes. All these lungfishes are found in marine sediments, and many articulated
skeletons demonstrate that this distribution is not an artefact of post mortem transport.
Furthermore, lungfishes are invariably absent from contemporaneous, non-marinedeposits. Geological analysis of the preservational environments indicates that the
lungfishes inhabited depths of over 100 m in the open ocean, and morphological and
palaeoecological observations indicate that they were bottom dwellers. They possessed
large gill chambers and well-developed, stable gill arch supports with grooves for blood
vessels, similar to those of extant fish that rely entirely on gill respiration. They show
none of the osteological features found in recent lungfishes which are necessary for airbreathing
(e.g. large buccal cavity, slot between toothplates for tongue pad, highly
mobile ceratohyal and pectoral girdle). Clearly, the morphology, taphonomy and
environment of early lungfishes suggests strongly that they did not engage in airbreathing.
The cladogram of Rosen et al. (1981), however, implies that they nevertheless
possessed the soft-anatomical adaptations for air-breathing noted above (Panchen &
Smithson, 1987, 1988; Campbell & Barwick, 1988). As with the haematotherm
example, there are two solutions. It might be possible to explain this unusual cooccurrence
of traits by resorting to special pleading. Alternatively, it could be assumed
that early dipnoans did not have the soft anatomical adaptations associated with airbreathing,
which would mean that these apparent lungfish±tetrapod synapomorphies
are convergences. However, this would remove much of the support for Rosen et al.’s
(1981) cladogram in the first place.
Thus, the evolutionary principles here appear to be strong: primitive lungfishes
could not have possessed soft anatomical adaptations associated with lung breathing.
However, the cladogram of Rosen et al. (1981), which implies that they possessed such
structures, is very weak. Panchen & Smithson (1987), Edwards (1989) and others have
comprehensively re-examined the evidence and have shown that the homologies and
distribution of many of the supporting synapomorphies were incorrectly interpreted.
Thus, in this case, it appears prudent to accept tentatively the biological generalizations,
which imply that certain aspects of Rosen et al.’s (1981) cladogram are wrong. Either
the topology is wrong, and lungfishes are not the nearest relatives of tetrapods, or some
of the supporting synapomorphies have been incorrectly interpreted (e.g. the soft
anatomical adaptations for air-breathing are not synapomorphies of lungfishes and
tetrapods). Panchen (1992) has already suggested that this is a possible example of a
scenario refuting a cladogram.

So whether the claims involve ancestry or the identification of transitional species, the educated layman is justified in treating Darwin with suspicion.

Comment #72238

Posted by Sir_Toejam on January 15, 2006 5:01 PM (e)

Is Darwin still making new theories?

If so, yeah, i would be suspicious as well.

Comment #72241

Posted by Russell on January 15, 2006 5:08 PM (e)

So whether the claims involve ancestry or the identification of transitional species, the educated layman is justified in treating Darwin with suspicion.

Oh? What did Darwin say about it?

Comment #72260

Posted by Arden Chatfield on January 15, 2006 6:04 PM (e)

So whether the claims involve ancestry or the identification of transitional species, the educated layman is justified in treating Darwin with suspicion.

Charles Darwin rises from the grave, hungry for HUMAN BRAINS!!!!

Comment #72263

Posted by steve s on January 15, 2006 6:18 PM (e)

whereupon a witness justifiably says “I’m skeptical of you, Zombie Darwin!”

Comment #72267

Posted by Russell on January 15, 2006 6:27 PM (e)

Just in case anyone feels the need to spend a lot of time on Paley’s ruminations, trying to figure out whether or not there’s a ghost of a point in there somewhere, let me just share with you this gem he posted over at After The Bar Closes:

Lynn Margulis (wife of Satan…..err….Sagan) has proposed the endosymbiotic theory to account for new genes/functions. This a just one germ digesting another. My theory, which proposes RNA transfer from digestive enzymes to germ cells via RAG recombination, is merely an extention of Margulis’s concept. Granted, there are some minor details to be worked out, but that’s why ID research is so crucial for the progress of science.
My application of her concept to multicellular organisms reveals my willingness to seek truth wherever it might be - even from the wife of a Marxist.

Um, need I say more?

Comment #72268

Posted by Sir_Toejam on January 15, 2006 6:31 PM (e)

I’d like to get back to zombie darwin…

are we sure this is a real undead, not live, rotting flesh walking type zombie darwin?

or could it be a serpent and the rainbow style zombie darwin, created with pyschotropic drugs that cause temporary paralysis?

inquiring minds want to know!

Comment #72270

Posted by Arden Chatfield on January 15, 2006 6:36 PM (e)

Lynn Margulis (wife of Satan…..err….Sagan)

Yet another datum in the growing body of evidence that ID has nothing whatsoever to do with religious apologetics.

Granted, there are some minor details to be worked out, but that’s why ID research is so crucial for the progress of science.

And we’re just waiting on pins and needles for you guys to get started!

My application of her concept to multicellular organisms reveals my willingness to seek truth wherever it might be - even from the wife of a Marxist.

Both a woman and a commie! Mighty broad-minded of ya there, Paley.

Comment #72272

Posted by Arden Chatfield on January 15, 2006 6:40 PM (e)

or could it be a serpent and the rainbow style zombie darwin, created with pyschotropic drugs that cause temporary paralysis?

Well, we thought for a while that Charles’s bite paralyzed people merely due to the bacteria in his saliva, but now scientists are starting to think that there really is a low level of actual venom in his teeth.

Comment #72275

Posted by Dean Morrison on January 15, 2006 6:51 PM (e)

‘Ghost of Paley’ is the only zombie I can see around here. And a Google cut and paste merchant to boot - how come he’s always busy ‘working on a paper’ - yet we never get to see one?

The real scientists on PT are happy to use their real names - under what name does ‘Paley’ intend to publish his papers? Since he touts himself as a future ‘Fields’ and ‘Nobel’ prize winner, does he really expect to turn up in Stockholm with a white sheet over his head?

Comment #72278

Posted by Arden Chatfield on January 15, 2006 7:00 PM (e)

The real scientists on PT are happy to use their real names - under what name does ‘Paley’ intend to publish his papers? Since he touts himself as a future ‘Fields’ and ‘Nobel’ prize winner, does he really expect to turn up in Stockholm with a white sheet over his head?

I guess Paley’s setting himself up to be the Thomas Pynchon of evolutionary biology.

Comment #72279

Posted by steve s on January 15, 2006 7:18 PM (e)

meaning he’s got big buck teeth?

Comment #72281

Posted by Arden Chatfield on January 15, 2006 7:45 PM (e)

Since he touts himself as a future ‘Fields’ and ‘Nobel’ prize winner,

Has Paley literally said he’s going to win a Nobel prize someday? Do you have a link to him saying this somewhere?

Has Paley ever revealed what training or degrees, if any, he has?

Comment #72283

Posted by Sir_Toejam on January 15, 2006 7:52 PM (e)

Has Paley ever revealed what training or degrees, if any, he has?

lol. does it matter?

Comment #72284

Posted by Sir_Toejam on January 15, 2006 7:54 PM (e)

…but now scientists are starting to think that there really is a low level of actual venom in his teeth.

hey! you should tell this to Blast from the Past! I’m sure he will consider that supports his pant-loading theory.

*snicker*

Comment #72286

Posted by Arden Chatfield on January 15, 2006 8:26 PM (e)

Since he touts himself as a future ‘Fields’ and ‘Nobel’ prize winner, does he really expect to turn up in Stockholm with a white sheet over his head?

Maybe he’ll unmask himself and reveal his true identity when he steps up to the stage to receive his trophy. You know, sort of a ‘Superman’ thing.

Comment #72287

Posted by cogzoid on January 15, 2006 8:29 PM (e)

“Paradigm-shattering, nobel-level physics (with a Fields medal on the side) doesn’t come easily, even for ectoplasmic folk.” is what Dean was referring to. (The quote is halfway down.)

Comment #72290

Posted by Flint on January 15, 2006 9:03 PM (e)

After slogging through this thread, I admit I don’t yet see Ghost’s point, at least not beyond Brazeau’s comment that science necessarily works by trial and error, and that disputes are useful vehicles for focusing informative tests and studies. But is Ghost trying to say that because there always have been, are today, and always will be disputes, new data, and improvement (or outright abandonment)of existing theories, that creationism is a better model?

Is it important to what theological preconceptions one attributes a good testable idea? Or is it only important that the idea proposes a useful test from which genuine knowledge emerges?

Cladograms always seem to be at some level debatable; different cladograms might be (and often are, if I read this correctly) reasonably supported by different emphases placed on the available evidence. I wouldn’t be bothered if the cladogram being argued about here were “wrong” (again, if I read this correctly, there are sincere disagreements and so *somebody must* be wrong.)

But is Ghost trying to argue that because cladograms are often not knowable in great detail without possibility of doubt, therefore evolution didn’t happen? This strikes me as arguing that Shakespeare’s plays don’t exist because there is debate about who actually wrote them. Or is Ghost trying to argue that God wrote those plays, and our uncertainties about authorship only serve to illustrate that our false assumption (that they were written by one or more people) is *guaranteed* to produce the wrong answer?

Does anyone have a clear Ghost translator?

Comment #72295

Posted by k.e. on January 15, 2006 10:01 PM (e)

Ghosty’s premise
500 monkeys on typewriters could not write Shakespeare’s plays
same old same old
uninspired nonsense
haunted musings of men driven mad by trying to make a square peg fit in a round hole (and we all know what that means)
I’m surprised he is back after his brush with Marcel Duchamp’s “The Large Glass”

Comment #72296

Posted by Flint on January 15, 2006 10:06 PM (e)

OK, I think I get it now:

Premise: Evolution never happened.
Observation: Scientists often disagree about the exact course evolution took.
Conclusion: Evolution never happened.

I don’t understand Ghost’s concern with the details, though. Who needs them?

Comment #72297

Posted by k.e. on January 15, 2006 10:13 PM (e)

he wants to “share” his “Bliss”

Comment #73053

Posted by The Ghost of Paley on January 17, 2006 8:11 PM (e)

Flint wrote:

But is Ghost trying to argue that because cladograms are often not knowable in great detail without possibility of doubt, therefore evolution didn’t happen? This strikes me as arguing that Shakespeare’s plays don’t exist because there is debate about who actually wrote them. Or is Ghost trying to argue that God wrote those plays, and our uncertainties about authorship only serve to illustrate that our false assumption (that they were written by one or more people) is *guaranteed* to produce the wrong answer?

Does anyone have a clear Ghost translator?

Since everybody’s been silenced by the brilliance of my position, let me clarify.
Mr. Brazeau argues:
1) the (coelacanth(lungfish, tetrapod)) clade is the current consensus opinion
2) this consensus is overwhelmingly supported by the evidence
3) the fossils support common descent between tetrapods and fish.

I’ve responded by noting that:
1) there is more contention between battling hypotheses than Mr. Brazeau would like to admit
2) the majority opinion has been shaped by forcing a fit among different lines of evidence (with no fraud involved - just a whole mess of wishful thinkin’)
3) the fossils are an unreliable guide to ancestry, since molecules and “soft” morphology often conflict with them when they can be brought to bear on the issue

And you guys respond with wisecracks. Entertaining, but all too typical.

Comment #73059

Posted by Steviepinhead on January 17, 2006 8:18 PM (e)

Paley Aley:

Since everybody’s been silenced by the brilliance of my position

Uh, no, we were just politely looking away while you struggled to extricate one part of your anatomy from another part of your anatomy.

Since you have, evidently, not yet achieved success, by all means, please carry on.

Though a tad less grunting and straining would be appreciated.

Comment #73069

Posted by The Ghost of Paley on January 17, 2006 8:38 PM (e)

More wisecracks.

I just hope that Mr. Brazeau brings more to the table….….……

Comment #73071

Posted by Russell on January 17, 2006 8:45 PM (e)

I’m still waiting for GoP to tell us what Darwin has to say about any of this. Remember?

So whether the claims involve ancestry or the identification of transitional species, the educated layman is justified in treating Darwin with suspicion.

(By the way, wouldn’t that be Dr. Brazeau, to you, Paley?)

Comment #73080

Posted by Popper's ghost on January 17, 2006 9:52 PM (e)

And you guys respond with wisecracks. Entertaining, but all too typical.

It’s a typical response to cranks. Ergo, you are a crank.

Comment #73122

Posted by Martin Brazeau on January 18, 2006 3:12 AM (e)

Ghost, what is your point? I don’t see any evidence that you have actually read and understood anything I have written. You seem to be more intent on using my words to create an entangled morass of self-deluded fantasy. I’m not sure if it is your careless disregard for which issues are actually being discussed or your disregard for the actual history of this debate that makes your argument both difficult to follow and difficult to disentangle.

That being said, I think Flint has adequately responded to conceptual problems with what is (apparently) Ghost’s point. I’ll take up particulars that I find especially deceitful.

For starters, I consider this particularly dishonest and the subsequent and repeated use of this misquotation to further your pointless diatribe.

Mr. Brazeau wrote:

[The lungfish naysayers] are a minority opinion and their work has been subject to much criticism or has been contradicted by the most recent analyses, most notably: Ahlberg (1991), Chang (1995, 2004), Zhu and Yu (2002), and Zhu et al. (2001).

Perhaps so, but scientific opinion isn’t subject to majority vote. I realise that some synapomorphies group Dipnoids with tetrapods, but my contention has always been that other groupings can be, and have been, defended. To get a taste of how large the minority opinion is, let’s look at this recent molecular study

Note the substitution of “[lungfish naysayers]” ahead of my text, inserted as though Ghost is welcome to disassemble and reassemble my argument in a fashion that suits his purpose. This is particularly nefarious because my statements were with regards to Diabolepis+lungfish sistergroup relationships, not tetrapods, lungfishes, and coelacanth sistergroup relationships. However, this didn’t stop Ghost from altering my statement.

Ghost’s purpose appears to be to support this hypothetical scheme:

Since everybody’s been silenced by the brilliance of my position, let me clarify.
Mr. Brazeau argues:
1) the (coelacanth(lungfish, tetrapod)) clade is the current consensus opinion
2) this consensus is overwhelmingly supported by the evidence
3) the fossils support common descent between tetrapods and fish.

I’ve responded by noting that:
1) there is more contention between battling hypotheses than Mr. Brazeau would like to admit
2) the majority opinion has been shaped by forcing a fit among different lines of evidence (with no fraud involved - just a whole mess of wishful thinkin’)
3) the fossils are an unreliable guide to ancestry, since molecules and “soft” morphology often conflict with them when they can be brought to bear on the issue

And you guys respond with wisecracks. Entertaining, but all too typical.

Very nicely done, Ghost. I see you’re not averse to distorting this discussion at all levels.

For starters, I never failed to acknowledge that paleontologists and molecular biologists have, frequently produced conflicting results or that paleontologists themselves have come to conflicting results. Please do not continue to charicature my arguments.

The difference is that I am willing to defend the most recent and complete analyses only. I am also defending those that I think are based on the best and most complete analyses and have followed the most rigorous procedures and argumentation.

Ghost seems to be entertaining two conflicting notions that make his diatribe nearly impossible to decipher. On the one hand, we’re treated to lists of citations (which Ghost has never read) as some kind of evidence of methodological decay among vertebrate paleontologists. Then we’re treated to sweeping generalizations implying flock-like behaviour with respect establishing phylogenetic consensus.

Which is it, Ghost? Are we flocking or disagreeing? Maybe it’s neither. Maybe scientists are going about their business using clues provided by fossils, morphology, and molecules to try to reconstruc the past. Since this is always going to be an incomplete record, disagreements on particulars will always occur. With some luck and a lot of work, we’ll resolve some of them.

This is particularly telling [emphasis added]:

So why the change? There are several factors at work. One involves hedging. That is, Darwin-science constructs several mutually exclusive hypotheses, waits for one to triumph, and then adduces empirical support for the nebulous theory underwriting the contradictory speculation. In this case, evos claimed that the fossils supported:
1) Tetrapods closer to coelacanths
2) Tetrapods closer to lungfish
3) Tetrapods equidistant from the two groups.

When the molecular evidence started trickling in during the early nineties, Darwinists[sic] began placing their bets on claim 2):

For one, you’re adducing psychological explanations for why certain views have been held. However, you’re claims are unsupported. You cite numerous references, however fail to demonstrate that you’ve even read any of them. So, I don’t see your point. I find it unlikely that your hypothesis is true. Paleontologists are generally unafraid of their data conflicting with molecular workers’ and vice versa. Each frequently defending their phylogenies tooth and nail. So, your claims of flocking or forcing consensus are invalid.

This is not hedging if disagreeing evidence is disregarded. However, cladistic analyses permit the use of discretely conflicting data in order to test their phylogenetic signals. This is precisely why I said that Cambell and Barwick’s (2001) analyses was invalid. It failed to do this. Hedging is a question of a particular analysis and how those authors treat disagreeing data. Generally, the best analyses argue characters and methods thoroughly and account for conflicts. As we uncover new data, we can add this information to help rule between conflicting hypotheses. I see no problem with this.

Comment #73309

Posted by Steviepinhead on January 18, 2006 5:46 PM (e)

Thanks, Dr. Brazeau.

Here’s some more of interest regarding this fascinating transitional fossil:
http://www.nature.com/news/2006/060116/full/060116-8.html, courtesy of Baynesian Bouffant over on a Pharyngula thread.

And guess who the researcher is? You bet, Dr. B. Here’s the link to the Nature article itself:
http://www.nature.com/nature/journal/v439/n7074/abs/nature04196.html.

Comment #73310

Posted by Steviepinhead on January 18, 2006 5:48 PM (e)

Sorry, the second link leads to the abstract, not the article itself…

Comment #73311

Posted by Russell on January 18, 2006 6:05 PM (e)

Dr. Brazeau wrote:

Ghost, what is your point?

Well you might ask. And ask. And ask…

But all for naught! See, it’s the style of a common species of creationist to spout a lot of scientific sounding nonsense on some arcane subject, implying that he’s widely read and extremely knowledgeable, and just exude smugness, implying that somehow this poses grave problems for evolution. When challenged to explain how, he’ll attempt to drown out the question by smugly denigrating the questioner. The appearance on the scene of an actual, acknowledged expert on the subject is his worst nightmare.

Thank you, Dr. Brazeau.

Comment #73357

Posted by The Ghost of Paley on January 18, 2006 8:41 PM (e)

Mr. Brazeau wrote:

Note the substitution of “[lungfish naysayers]” ahead of my text, inserted as though Ghost is welcome to disassemble and reassemble my argument in a fashion that suits his purpose. This is particularly nefarious because my statements were with regards to Diabolepis+lungfish sistergroup relationships, not tetrapods, lungfishes, and coelacanth sistergroup relationships. However, this didn’t stop Ghost from altering my statement.

I admit I shouldn’t have used that particular quote and I apologise. But I thought your views on the trichotomy “consensus” were clear from the start:

Mr. Brazeau wrote:

This is so terribly wrong. You seem to think that all lobe-finned fishes are the same for some reason. Coelacanths and Eusthenopteron belong to two separate groups of Sarcopterygii: Actinistia and Osteolepiformes, respectively. The morphological consensus looks as follows: (Coelacanths(Lungfishes(Eusthenopteron(Panderichthys;Tetrapoda))))[Paley’s emphasis]

Was I mistaken? Are you arguing that there is a substantial controversy after all? If not, then how is the misquote a serious distortion?

The difference is that I am willing to defend the most recent and complete analyses only.

It’s true the molecules support the lungfish-tetrapod clade, but they don’t indicate a close relationship between coelacanths and lungfish. This latter result overturns the synapomorphies uniting sarcopterygians by inserting rayfins within that group. And I gave several arguments (with supporting papers) contesting your clade on morphological grounds. I don’t see what their publication date has to do with anything - the neurological, skeletal, and molecular characters exist just the same. And have the advantage of being recorded before the genetic tests were in, thus serving as an independent check. An inspection that evolution fails, as it so often does.

Which is it, Ghost? Are we flocking or disagreeing? Maybe it’s neither. Maybe scientists are going about their business using clues provided by fossils, morphology, and molecules to try to reconstruc the past. Since this is always going to be an incomplete record, disagreements on particulars will always occur.

Or maybe it’s both: evos disagreeing before the genetic tests were run, then trying to harmonise the results afterwards. Which, given the problems of gene trees, doesn’t exactly inspire confidence in either method.

However, cladistic analyses permit the use of discretely conflicting data in order to test their phylogenetic signals. This is precisely why I said that Cambell and Barwick’s (2001) analyses was invalid. It failed to do this.

From what I’ve seen, “conflicts with ‘known’ parts of Darwin tree” -> “bad phylogenetic signal”. This strikes me as circular reasoning at best.

As we uncover new data, we can add this information to help rule between conflicting hypotheses. I see no problem with this.

But the new information conflicts with the old. So why should we accept any of it?

Comment #73372

Posted by Sir_Toejam on January 18, 2006 9:09 PM (e)

So why should we accept any of it?

Indeed, why accept any science at all, ghost?

why accept both newtonian mechanics and relativistic mechanics? heck they contradict each other in spots, don’t they?

pretty ridiculous argument, like most of your arguments.

YOU don’t have to; nobody is forcing you to. but ignorance of the work cited, whether willfull or not, doesn’t make your opinion on the matter any more informed, or any of the rest of us care about your opinion one way or the other.

I’m kinda amazed that Dr. Brazeau even bothered to reply, to tell you the truth.

you should spend more time debating politics in the ATBC area. You don’t have any expertise there either, but at least there your gross mischaracterizations and generalizations can be considered humorous, and you are on equal footing with most of the rest of us.

bottom line; don’t quit your day job of pontification in ATBC; you haven’t made any good cases for any issue in evolutionary biology that you have attempted to address, regardless of how much (like Larry) you seem to value your own ill-formed opinions.

Comment #73373

Posted by Steviepinhead on January 18, 2006 9:13 PM (e)

And, Pale Guy, it still might help–even if only a little–if you’d stop hopping around on one foot long enough to get the other extremity out of that opening in which it seems to have become, um, wedged.

Comment #73381

Posted by The Ghost of Paley on January 18, 2006 9:48 PM (e)

Sir Wiggles wrote:

bottom line; don’t quit your day job of pontification in ATBC; you haven’t made any good cases for any issue in evolutionary biology that you have attempted to address, regardless of how much (like Larry) you seem to value your own ill-formed opinions.

Then why are you the one that’s sweating?

Comment #73431

Posted by Martin Brazeau on January 19, 2006 2:19 AM (e)

First, thanks all, but as I mentioned before I’m not a “Dr.” yet. I’m still in the second year of my Ph.D.

Ghost writes:
I admit I shouldn’t have used that particular quote and I apologise. But I thought your views on the trichotomy “consensus” were clear from the start:

[quotes me]

was I mistaken? Are you arguing that there is a substantial controversy after all? If not, then how is the misquote a serious distortion?

You apologize by following it up with blatant and repeated misuse of my quotes. I have already stated (as you point out) that the prevailing opinion regarding the sister-group relationships of the living sarcopterygians is that of (Coel(Lungf; 4Pod)). As I also mentioned, there is a controversy with some molecular systematists who obtain conflicting trees.

The misquote will always remain a serious distortion because the quote regarded the sister-group relationships of the fossil taxon Diabolepis and lungfishes. There prevailing view (which I think is pretty incontrovertible at this time) is that Diabolepis is the closest sister taxon to the lungfishes. A good place to start is: Chang and Yu (1983), Proc. Linn. Soc. N.S.W. 107: 171-184 and Chang 2004, which you cited in one of your previous posts as a purported example of dissent (which flew in your face as evidence that you don’t actually read these papers, much less even examine the figures and illustrations they provide).

It’s true the molecules support the lungfish-tetrapod clade, but they don’t indicate a close relationship between coelacanths and lungfish. This latter result overturns the synapomorphies uniting sarcopterygians by inserting rayfins within that group. And I gave several arguments (with supporting papers) contesting your clade on morphological grounds. I don’t see what their publication date has to do with anything - the neurological, skeletal, and molecular characters exist just the same. And have the advantage of being recorded before the genetic tests were in, thus serving as an independent check. An inspection that evolution fails, as it so often does.

I saw no evidence that cited any paper. But that is incidental. Which ray-fin was inserted? Polypterus bichir? It has long had an ambiguous history of classification - morphologically and molecularly (again, selective citation on your part). I doubt it is a sarcopterygian. However, in order for me to doubt that particular analysis (or choose, in turn, to doubt my own doubt) depends on my reading of the molecular analysis. What genes did they use? What gap penalty did they use in the sequence alignment? Which taxa did they choose? All of these are important points. There are ‘rules’ for a good analysis and certain things that set some aside as contentious or dubious without even looking at the tree. That is something you need to realize.

Also, you have to realize that the 2004 study in PNAS that I cited retrieved a (Coel(Lungf; 4Pod)) topology. However, I wouldn’t even place my bets on that analysis (even though it agrees with the paleontological view - yes, unlike you I’m open to having my preferred view challenged. Which is why I have continued to respond to your queries). The overall view is that the molecular systematic results are equivocal. It will only become accepted among molecular biologists once they start independently achieving the same results.

What you, Ghost, have done is to project the image of ‘flocking’ onto evolutionary biologists by using blanket terms and statements peppered with “they”. This reinforces your preconceived view that evolution cannot be true and that converging evidences are, in fact, not converging at all. Rather, there is a fabrication of convergence. Unfortunately, you’ve left out examples of the nearly vitriolic disputes that morphologists and molecular systematists have had in the past. There is anything but subconscious ‘flocking’ going on.

Furthermore I don’t see any of your “several arguments (with supporting papers) contesting your clade on morphological grounds”. You, in fact, gave no morphological arguments. Instead, you’ve wielded paper abstracts which you clearly hadn’t read. In the case of Chang (2004), the views expressed in the body of that paper and (the 109-character data matrix) disagree completely with your statements. I don’t see where you are going with any of this. You didn’t even read any of those papers or analyze them criticially yourself. You simply cited them because (you thought) they all agreed with you. Until you have read and critically evaluated any of those papers, I don’t think you’ve proffered any argument at all.

Or maybe it’s both: evos disagreeing before the genetic tests were run, then trying to harmonise the results afterwards. Which, given the problems of gene trees, doesn’t exactly inspire confidence in either method.

Except though the selective use of citation, you haven’t showed that this is happening.

From what I’ve seen, “conflicts with ‘known’ parts of Darwin tree” -> “bad phylogenetic signal”. This strikes me as circular reasoning at best.

Darwin had a tree? Bad phylogenetic signal can be determined objectively on a scale. On your end, there ought to be zero phylogenetic signal. On my end, it depends on the completeness of the data at hand. The ‘signal’ actually refers to the ability for data to resolve a phylogenetic tree. Without sufficient, non-conflicting data, a phylogenetic analysis will return multiple equally parsimonious trees. We consider this a lack of resolution. In a matrix with n taxa, the minimum number of characters that can fully resolve the tree is n -1. However, as real-world data tend to be noisy and have some statistical randomness, more than n -1 characters are usually required. Systematists use bootstrap analyses (among others) to resample data matrices and test whether or not the resolution of trees is random with respect to the data. This is not perfect, but it flies in the face of what you just said. Again, demonstrating that you don’t really understand what is actually being done when systematists do their work.

But the new information conflicts with the old. So why should we accept any of it?

No, the information does not. The total information is included in the analyses. It is the results that conflict. The reason why we accept it is that, by and large, the emerging picture is not one of conflict but of increased resolution. Historically, it was presumed that tetrapods descended from some fishes. Then, it was determined that it was the sarcopterygian fishes. Then, after some time, it was finally settled that it was from the osteolepiform fishes. All of these took some time, contention, and debate. In the end, the ones that one did so because as new information was collected it allowed us to discriminate between conflicting hypotheses.

Comment #73522

Posted by Anton Mates on January 19, 2006 11:10 AM (e)

While I greatly appreciate this lession in tetrapod evolution, hopefully-soon-to-be-Dr. Brazeau–I personally didn’t know much of anything about osteolepiform phylogeny–please don’t feel obligated to spend more of your time on GoP than you can easily afford. If he’s not going to bother reading about the studies he cites, I doubt he’s any more likely to read about the ones you mention. The rest of us worked out some time ago that, amazingly, the people worth listening to about an organism’s phylogeny are the ones who actually study it.

Comment #73537

Posted by Brandon on January 19, 2006 11:54 AM (e)

Some other creationist really needs to tag this Paley chap out. He’s punch-drunk. It’s really embarrassing for all involved. As children, we used to in trouble for beating up the neighborhood retard. Don’t you people have any shame? Any decency?

Comment #73544

Posted by KenL on January 19, 2006 12:05 PM (e)

An interesting point to consider. Since GoP seems capable of reading citations and abstracts at least, maybe this will help him/her, too:

Kruger, J and Dunning D (1999), “Unskilled and Unaware of It: Difficulties in Recognizing One’s Own Incompetence Lead to Inflated Self-Assessments”, Journal of Personality & Soc. Psych, Vol77#6, pp1121-1134.

Abstract: People tend to hold overly favorable views of their abilities in many social and intellectual domains. The authors suggest that this overestimation occurs, in part, because people who are unskilled in these domains suffer a dual burden: Not only do these people reach erroneous conclusions and make unfortunate choices, but their incompetence robs them of the metacognitive ability to realize it. Across 4 studies, the authors found that participants scoring in the bottom quartile on tests of humor, grammar, and logic grossly overestimated their test performance and ability. Although their test scores put them in the 12th percentile, they extimated themselves to be in the 62nd. Several analyses linked this miscalibration to deficits in metacognitive skills, or the capacity to distinguish accuracy from error. Paradoxically, improving the skills of participants, and thus increasing their metacognitive competence, helped them recognize the limitations of their abilities.

Sadly, some folks seem to be fundamentally, philosophically opposed to increasing their metacognitive competence, dooming them to continued incompetence (and concomitant blissful ignorance thereof).

Comment #73604

Posted by DJ on January 19, 2006 1:44 PM (e)

I just couldn’t pass this up. While reading Ghost of Paley’s comments I considered that at least he was studying or attempting to study the field(s) about which he was arguing.

But in one of his Jan 7 posts,

Ghost of Paley wrote:

“…I need to post a physics paper Monday, and then I’ll get back with a proper response…” emphasis mine

Of course. Another physics guy arguing against evolution. Makes sense.

Martin Brazeau, thank you for all the information you posted here. I am a complete (but passionate) amateur in anything resembling biology and I appreciate informed experts coming to PT and clearing the air fouled by the likes of Ghost of Paley.

Comment #73639

Posted by Frank Habets on January 19, 2006 2:42 PM (e)

Good work, Proto-doctor Brazeau!
It’s a tough slog having to ‘debate’ GoP –unlike most IDers you see posting in forums/blog comments, this dude seems to have a basic grasp of scientific jargon, giving his arguments a patina of quasi-crediblity. Thanks for putting the time and patience in ,er, ‘addressing’ him.

Comment #73651

Posted by The Ghost of Paley on January 19, 2006 3:02 PM (e)

First:
Congratulations on your recent find, Mr. Brazeau. How many interviews have you had?

Second:

Mr. Brazeau wrote:

I saw no evidence that cited any paper. But that is incidental. Which ray-fin was inserted? Polypterus bichir? It has long had an ambiguous history of classification - morphologically and molecularly (again, selective citation on your part). I doubt it is a sarcopterygian. However, in order for me to doubt that particular analysis (or choose, in turn, to doubt my own doubt) depends on my reading of the molecular analysis. What genes did they use? What gap penalty did they use in the sequence alignment? Which taxa did they choose? All of these are important points. There are ‘rules’ for a good analysis and certain things that set some aside as contentious or dubious without even looking at the tree. That is something you need to realize.

Was the link broken? See Figure 6, and look between “pdol” and “lcha”. The rest of the paper covers the methodology. We can discuss this paper further if you wish.

Third:

Furthermore I don’t see any of your “several arguments (with supporting papers) contesting your clade on morphological grounds”. You, in fact, gave no morphological arguments. Instead, you’ve wielded paper abstracts which you clearly hadn’t read. In the case of Chang (2004), the views expressed in the body of that paper and (the 109-character data matrix) disagree completely with your statements. I don’t see where you are going with any of this. You didn’t even read any of those papers or analyze them criticially yourself. You simply cited them because (you thought) they all agreed with you. Until you have read and critically evaluated any of those papers, I don’t think you’ve proffered any argument at all.

See this post for the neurological and skeletal evidence linking coelacanths with tetrapods and/or lungfish, which conflicts with Stuart et al’s taxon-rich whole mitochondrial genome analysis (just cited). The latter is the most comprehensive vertebrate phylogeny I can find, and it conflicts with both recent and traditional phylogeny in wrenching coelacanths apart from lungfish.
That’s all for now. More to come…..

Comment #73655

Posted by Sir_Toejam on January 19, 2006 3:10 PM (e)

More to come…..

you only have two kidneys, ghost, and both have already been deftly removed.

I think you should move on before Martin moves on to other organs.

Comment #73666

Posted by S. C. Hartman on January 19, 2006 3:34 PM (e)

Hey Ghost: about that physics paper. Let me guess: it’s your argument that since quantum mechanics and general relativity have not been reconciled, why should either one be believed?

To Martin Brazeau: many thanks for your patient, clear exposition of a difficult scientific topic. Perhaps the exercise will serve you in good stead come time to defend your dissertation. Of course, your committee won’t consist of a bunch of ineducables who know nothing about how science proceeds, which should be a relief.

Comment #73671

Posted by The Ghost of Paley on January 19, 2006 3:41 PM (e)

KenL wrote:

Abstract: People tend to hold overly favorable views of their abilities in many social and intellectual domains. The authors suggest that this overestimation occurs, in part, because people who are unskilled in these domains suffer a dual burden: Not only do these people reach erroneous conclusions and make unfortunate choices, but their incompetence robs them of the metacognitive ability to realize it. Across 4 studies, the authors found that participants scoring in the bottom quartile on tests of humor, grammar, and logic grossly overestimated their test performance and ability. Although their test scores put them in the 12th percentile, they extimated themselves to be in the 62nd. Several analyses linked this miscalibration to deficits in metacognitive skills, or the capacity to distinguish accuracy from error. Paradoxically, improving the skills of participants, and thus increasing their metacognitive competence, helped them recognize the limitations of their abilities.

Thanks for the paper. Any insight into the evo mind is always appreciated.

Sir Wiggles wrote:

you only have two kidneys, ghost, and both have already been deftly removed.
I think you should move on before Martin moves on to other organs.

So why are you the one that’s bleeding?

Brandon wrote:

Some other creationist really needs to tag this Paley chap out. He’s punch-drunk. It’s really embarrassing for all involved. As children, we used to in trouble for beating up the neighborhood retard. Don’t you people have any shame? Any decency?

Naah…I’m more like this guy. (note: you may have to click past an ad first)

Comment #73675

Posted by Arden Chatfield on January 19, 2006 3:49 PM (e)

you only have two kidneys, ghost, and both have already been deftly removed.
I think you should move on before Martin moves on to other organs.

So why are you the one that’s bleeding?

Translated:

“I know you are – but what am I?”

Comment #73679

Posted by Faidon on January 19, 2006 3:54 PM (e)

Hmm. Come on people, give the guy a break. Googling up “coelacanth lungfish tetrapod morphology taxonomy relation alternative dispute conflict disagree” and then also selecting what to link (not to mention pretending you have a clue what the hell it’s about), can be hard work, you know. What with the Physics project and all.

Also, um, hello!

Comment #73682

Posted by Sir_Toejam on January 19, 2006 3:58 PM (e)

welcome, Faidon.

Comment #73711

Posted by Stephen Bent on January 19, 2006 5:02 PM (e)

GoP: It is interesting to note in the Stuart paper that the branches in the consensus tree that support the interposition of ray-finned fishes between lungfish and coelacanth have about the same support (14/17 and 12/17) as the branch that places the elephant with the primates. Other nonsensical placements are also evident. Branch lengths would be helpful here, as well as some indication of what a given support value actually means statistically, and an analysis of possible artifacts in this methodology. It is important to incorporate new methodologies in determining the relationship between organisms, extant or otherwise, but no one method will get all the answers correct. In fact, the process you deride as hedging bets is the fundamental process by which science works. If you hate it so much, throw away your computer, it’s tainted by scientists hedging their bets about the properties of semiconductors.

OK, so if you want to quibble about conflicting trees, which topology do you believe to be accurate? Is is a baraminist polytomy of created kinds at the time of creation, with trajectories staying within kinds like kids bumper bowling, or would you rather not be nailed down on an answer to that, in typical ID “no model” fashion? Or are you just an open-minded “Ghost of the Gaps” concern troll…

Never mind.

Comment #73714

Posted by Lefty on January 19, 2006 5:15 PM (e)

Man, this has been going on for almost a month! I just finished reading through the thread and it’s not over yet….

What will be ‘more to come’?
Will GoP (uh oh) admit that he hasn’t read his sources?
Could Brazeau actually be an ID infiltrator, and there actually are no ‘little pigs that swim’?
Is it a prerequisite to be a complete loon to study physics?

This is better than ‘Lost.’

Comment #73720

Posted by Jan Theodore Galkowski on January 19, 2006 5:59 PM (e)

The Ghost of Paley wrote:

… doesn’t exactly inspire confidence in either method.

i know very little about Devonian anatomies, but i am very interested in scientific methodology. i wonder if Paley’s Ghost would care to opine about what constitutes a proper method in this respect? the Ghost seems quite sure of what the requirements for such methods are.

i am listening.

Comment #73729

Posted by Loris on January 19, 2006 6:14 PM (e)

Paley said,

It’s true the molecules support the lungfish-tetrapod clade, but they don’t indicate a close relationship between coelacanths and lungfish. This latter result overturns the synapomorphies uniting sarcopterygians by inserting rayfins within that group.

I’ve read several papers that examine the superorder Archonta (Primates, Scandetia, Chiroptera (depending on who you ask), Dermoptera). Of the papers that employ molecular data, a few have developed cladograms and maximum parsimony trees that break up the monophyly of Primates with Lagomorpha or other Orders (though unfortunately I cannot find the articles to which I am referring, oops I’ll look around at work tomorrow).

This goes against huge amounts of morphological evidence that Lemuroidea, Tarsioidea and Anthropoidea are all more closely related to each other than to other mammals (though there may be a basal trichotomy here, tarsiers are so darn problematic). The explanation I have come across repeatedly for the inclusion of Lagomorpha and certain members of Insectivora in a clade of primates is that primates, rabbits and hares and some insectivores have heavily conserved genomes. Because the genomes of these groups retain more of the ancestral sequences, it is more difficult to figure out the relationships. Add the time depth complication and the problem becomes very large indeed.

Is this the kind of thing that is going on with the rayfin insertion Paley refers to? I admit that my knowledge of fish phylogeny is very poor, but the time depth of the divergences that are being talked about here seems to be complicating the molecular picture.

Comment #73767

Posted by Arden Chatfield on January 19, 2006 7:49 PM (e)

This goes against huge amounts of morphological evidence that Lemuroidea, Tarsioidea and Anthropoidea are all more closely related to each other than to other mammals (though there may be a basal trichotomy here, tarsiers are so darn problematic). The explanation I have come across repeatedly for the inclusion of Lagomorpha and certain members of Insectivora in a clade of primates is that primates, rabbits and hares and some insectivores have heavily conserved genomes. Because the genomes of these groups retain more of the ancestral sequences, it is more difficult to figure out the relationships. Add the time depth complication and the problem becomes very large indeed.

Interesting, historical linguistics has almost the exact same problem. When comparing languages, especially in trying to prove relatedness or the depth of it, it sometimes happens that two languages that are not especially close can look deceptively similar if they both coincidentally happen to be very conservative, sharing a lot of archaic features. So the dictum in historical linguistics is that shared innovations count for more than shared archaisms. Tho of course, you have to be able to recognize when something is an innovation rather than a conservatism.

Comment #73776

Posted by Steviepinhead on January 19, 2006 7:57 PM (e)

So, Arden, is Haida a true isolate in your view, or just a very deeply-rooted member of Na-Dene? Or related to some other family entirely?

(Let’s see, I’m sure I can tie this in with ancient fish fossils somehow…)

Oh, yeah, did I mention that the Haida are great exploiters of the sea’s bounty?

Comment #73825

Posted by The Ghost of Paley on January 19, 2006 9:08 PM (e)

Emboldened by their leader Martin “The Ripper” Brazeau, Genie’s kids swarm over the enemy, and post:

Stephen Bent wrote:

GoP: It is interesting to note in the Stuart paper that the branches in the consensus tree that support the interposition of ray-finned fishes between lungfish and coelacanth have about the same support (14/17 and 12/17) as the branch that places the elephant with the primates. Other nonsensical placements are also evident.

Thanks for actually reading the paper. First, it’s important to remember that what’s poison for the morphologist is food for the molecular biologist. Molecules often group mammals by geography, while the fossils beg to differ. So Stuart’s phylogeny recapitulates most of the molecular hypotheses, including Laurasiatheria.

Branch lengths would be helpful here, as well as some indication of what a given support value actually means statistically, and an analysis of possible artifacts in this methodology.

Here’s the distance metric:

Vector definitions for all 832 mitochondrial proteins were retrieved from the SVD output and used to calculate pairwise cosine values, which were subsequently converted into a matrix of pairwise evolutionary distances using the formula dij = -ln [(1 + cos)/2]. This formula is derived from the standard distance formula d = -lnS and converts a similarity measure ranging from 0 to 1 into a distance measure potentially ranging from 0 to infinity. The corresponding species distances were estimated by summing the 13 vector definitions for each organism and then using the pairwise cosine values between the derived species vectors to estimate the evolutionary distance (Stuart et al. 2002 ).

And here’s a discussion of the singular value decomposition methodology. You’re welcome.

Jan Theodore Galkowski wrote:

i know very little about Devonian anatomies, but i am very interested in scientific methodology. i wonder if Paley’s Ghost would care to opine about what constitutes a proper method in this respect? the Ghost seems quite sure of what the requirements for such methods are.
i am listening.

For one thing, scientists should have clear mathematical/genetic criteria for selecting characters for analysis, and the weight placed on these characters should be derivable from preexisting theory. Each character’s independence should be established by reference to developmental biology in addition to statistical tests that do not assume common ancestry. I hope this helps.

Arden Chatfield wrote:

So the dictum in historical linguistics is that shared innovations count for more than shared archaisms. Tho of course, you have to be able to recognize when something is an innovation rather than a conservatism.

This is evolution’s central dilemma.

Comment #73836

Posted by Arden Chatfield on January 19, 2006 9:27 PM (e)

So, Arden, is Haida a true isolate in your view, or just a very deeply-rooted member of Na-Dene? Or related to some other family entirely?

Wow, really good question. Well, I am not a specialist in either Haida or Na Dene, so I have to tread very carefully in making a pronouncement on that.

The consensus on Haida has been swinging back and forth. Long ago, Edward Sapir thought it was related, but on quite skimpy evidence. Then with a good deal more evidence, much later, Na Dene specialists declared that the link between the two was bogus and based on misanalyzed evidence, and that Haida’s resemblance was purely a result of resemblances it had acquired from being next to Na Dene for millenia (another chonic problem). But now, the world’s leading expert on Haida (the first person to do fresh fieldwork and research on it in 50 years) has written an article saying Haida IS related to Na Dene. I read the article and I think he may be on to something, but I didn’t consider it conclusive. There’s massive borrowing back and forth between Haida and Tlingit, which obscures things. But like I said, that geographic area ain’t my specialization.

(No one has ever tried to link it to any family other than Na Dene.)

(Let’s see, I’m sure I can tie this in with ancient fish fossils somehow…)

Yeah, better be careful, don’t wanna get us bumped to the ‘Urinal’.

Oh, yeah, did I mention that the Haida are great exploiters of the sea’s bounty?

I hear they make a zesty stew out of Panderichthys broth.

Comment #73843

Posted by Steviepinhead on January 19, 2006 9:39 PM (e)

[Pointedly ignoring Whitebread…)

Arden, are you talking about John Enrico? Or someone else? I’d love to see the article, if you have a link, or to track it down, if you have a reference. I have invented an excuse for myself to be on the U. Wash. campus twice a week (to audit a Northwest Coast art history course), so I have easy access to a good library.

As I recall, Ruhlen and Greenberg have been critiqued–both on the Tlingit-“borrowing” ground and, more recently, on blood-group grounds, for supporting and extending Sapir. But–whatever else can be said about the dangers of the kinds of comparisons that Ruhlen and Greenberg make–it was my impression that they attempted to compare terms that (they argue) are resistant to change, even under strong borrowing pressure (like kin terms, personal pronouns, etc.), so I have never been sure how effective the “borrowing” critique (in and of itself) was…

Comment #73856

Posted by Arden Chatfield on January 19, 2006 10:11 PM (e)

Arden, are you talking about John Enrico?

Yup!

Or someone else? I’d love to see the article, if you have a link, or to track it down, if you have a reference.

See here:

http://www.indiana.edu/~anthling/v46-3.html

I have invented an excuse for myself to be on the U. Wash. campus twice a week (to audit a Northwest Coast art history course), so I have easy access to a good library.

As I recall, Ruhlen and Greenberg have been critiqued—both on the Tlingit-“borrowing” ground and, more recently, on blood-group grounds, for supporting and extending Sapir.

You really don’t want to hear what I think of Ruhlen and Greenberg’s work…

But—whatever else can be said about the dangers of the kinds of comparisons that Ruhlen and Greenberg make—it was my impression that they attempted to compare terms that (they argue) are resistant to change, even under strong borrowing pressure (like kin terms, personal pronouns, etc.), so I have never been sure how effective the “borrowing” critique (in and of itself) was…

The borrowing critique is very serious indeed. We know of many cases where languages change typologically utterly under the influence of unrelated languages. A classic example is Vietnamese, an Austro-Asiatic language that transformed itself to look a whole lot like Chinese and Thai (all unrelated), becoming a typical southeast Asian language with monosyllables and phonemic tone. (Which is not what typical Austro-Asiatic languages are like.) But in the case of Vietnamese, the depth of separation between it and the rest of Austro-Asiatic is not too great, so the connections are still detectible. The problem is tho, for languages where the genetic links are in the more distant past (like Haida & Na Dene), or where we lack the detailed background knowledge on the languages to make informed choices. Then the decisions become extremely difficult, and actual expert knowledge of the languages in question becomes very helpful.

Besides, it’s now starting to emerge that even the rule of comparing vocabulary that’s supposedly resistant to change isn’t totally reliable. Kin terms, numbers, body part terms, and pronouns are often put in this category, but we now know that those kinds of vocab items most assuredly can be borrowed, under the right circumstances. For example, almost every language in southeast and east Asia has borrowed numbers from Chinese. And moreover, there has been some recent research to indicate that pronominal systems naturally tend to phonetically differentiate their primary elements as much as possible (i.e., languages try to keep first, second, and third person markers sounding different). This tendency would greatly dilute the usefulness of using vague resemblances of pronominal systems as evidence of long-term genetic relatedness.

So, how about those Panderichthys, eh? Hell of a critter… :-)

Comment #73861

Posted by Steviepinhead on January 19, 2006 10:21 PM (e)

Yeah, gee whillickers, those Panderichthys are pretty phemomenal, especially when stewed in a bentwood bowl with hot rocks, and flavored with a little eulachon oil!

We’ve had so much fun with them here, maybe we should start calling them Panda-ichthys!

Seriously, I appreciated every word of your last post, and will try to comb through Enrico’s article tomorrow.

Comment #73862

Posted by Brandon on January 19, 2006 10:26 PM (e)

Are you kidding? You got slaughtered in there. I’m actually feeling sympathy pains.

Comment #73864

Posted by Lenny's Pizza Guy on January 19, 2006 10:31 PM (e)

Well, as long as we’re talking about, um, Pizza-icthys, I’d just like to point out that–within less than 15 minutes of my mentioning that Lenny had called in to order his nightly pizza–the good Rev went into mute-mode. And didn’t return for more than an hour! And I was gone, too.

What are my oh-so-topical points?

First, Lenny really does have a real pizza guy–when I tell you that he’s just ordered a pizza, you can take it to the bank (OK, just to stay in the rough area of the topic, the tangled bank).

Second, when we guarantee delivery in 15 minutes or less, that’s just exactly what we mean: durn good pizza, piping hot, from our oven to your table, on the dot!

Again, what’s this got to do with evo and ID? (You might well ask…) Just this, kiddies: there’s credible people in this world, who can back up their words with the evidence.

And then there’s the other kind.

Comment #73870

Posted by Sir_Toejam on January 19, 2006 10:41 PM (e)

dammmnn! that would make a great pizza commercial if you got Larry to wear his clown suit and read that aloud on videotape.

Comment #73871

Posted by Steviepinhead on January 19, 2006 10:42 PM (e)

Brandon wrote:

Are you kidding? You got slaughtered in there. I’m actually feeling sympathy pains.

Eh? If this was directed at my discussion with Arden, then I’m always happy to be pointed in the right direction by those who know more than I do.

But I have a sneaking suspicion that you’re talking about our Pale friend, in which case, truer words were never spoken.

Comment #73878

Posted by Charles Shelton on January 19, 2006 11:13 PM (e)

Ghost of Paley wrote:

1) there is more contention between battling hypotheses than Mr. Brazeau would like to admit
2) the majority opinion has been shaped by forcing a fit among different lines of evidence (with no fraud involved - just a whole mess of wishful thinkin’)
3) the fossils are an unreliable guide to ancestry, since molecules and “soft” morphology often conflict with them when they can be brought to bear on the issue

I’m a little confused about what you’re arguing. Based on the above statements from your earlier post, I’m guessing your point is:
1) Scientists don’t have a clear consensus agreement on the relationships among coelacanth, lungfish, and tetrapods. The different lines of evidence have conflicts.
2) The majority opinion is the result of scientists using subjective methods and forcing the data to fit a preconceived conclusion (evolution happens and all species are related by common descent).
3) Therefore evolution is wrong and all conclusions about common descent are wrong.

Is this your argument? If so, I’m not buying it. I confess I’m a layman when it comes to biology and physics, so please point out any errors in my reasoning. Allow me to present an analogous argument:

1) Scientists don’t have a clear consensus agreement on the value of the universal gravitational constant to 10 decimal places.
(see The Controversy over Newton’s Gravitational Constant )
2) The majority opinion is the result of scientists using imprecise measurement equipment and forcing the data to fit a preconceived conclusion (gravity happens uniformly throughout the universe and all matter is affected by gravitational forces)
3) Therefore gravitation is wrong and all conclusions about gravitational forces are wrong.

Of course, you’d be correct in pointing out that my argument ignores all the other evidence for the existence of gravity, and that the correctness of gravitational theory doesn’t depend on knowing the exact value of G.

Similarly, the correctness of evolutionary theory doesn’t depend on knowing the complete phylogenetic tree of life with 100% certainty. What about the fact that the trunk and major branches of the tree have not changed as new evidence has been collected? What about the fact that these fossils do have transitional characteristics between fish and tetrapods? Do you repudiate the “no transitional forms” canard?

Scientists never claim to know everything, and consensus hasn’t been reached on all aspects of any theory. But the evidence does seem to indicate that common descent via evolution is the best explanation we have for the diversity of life, given the incompleteness of the data. The fact that we don’t know everyhing seems to encourage scientists to continue to collect more data.

Can you provide a better explanation for the disagreements in the technical details? How is ID a better explanation than, “We don’t have enough data to make an airtight conclusion about all the details, but the overwhelming evidence points to evolution and common descent, despite our lack of knowledge of the complete history?”

What is the ID explanation for the diversity of life? Which species (if any, according to ID) really are related, and which just “look” related, but were separately designed? Are housecats, lions, tigers, cougars, panthers, and jaguars related by common descent, or are they just similarly designed? Are humans and apes (chimps, gorillas, orangutans, etc.) related by a common ancestor? If not, what explains the independent identical patterns of morphological and genetic similarities?

Comment #73892

Posted by Arden Chatfield on January 20, 2006 12:02 AM (e)

Yeah, gee whillickers, those Panderichthys are pretty phemomenal, especially when stewed in a bentwood bowl with hot rocks, and flavored with a little eulachon oil!

I read something recently about coelacanths being threatened by new netting practices. They get caught incidentally. Apparently, no one actually wants to eat coelacanths, tho – apparently they’re horribly oily and taste like shit.

Seriously, I appreciated every word of your last post,

Not a problem. It’s rare that I get an opportunity to bloviate about my actual specialization here.

and will try to comb through Enrico’s article tomorrow.

Brace yourself, it’s got a massive amount of data. But it will answer all your questions.

Comment #73954

Posted by Jaime Headden on January 20, 2006 6:22 AM (e)

Curious as I am in the matter, I recall a concern over the argumentation about particulars being expanded by some (GoP) to include innate quality disjunction, that the two perspectives are so inimical that they cannot be trusted. I am reminded of an episode of Star Trek (original series, mind), wherein two protagonists were at such conflicts that neighter cared to know why they fought, only that one fought the other to continue fighting. This episode was written largely to open eyes to the implicit problems of racism. There is an addage, perhaps very apt in this discussion, about cleaning one’s house before you attempt to clean anothers, which derives from a allegory in the Bible. Paley will be familiar. Which brings me to the point of this post:

If Ghost of Paley wishes us to focus on the nature of disagreement between certain groups of data sets (morphological criteria versus molecular sequencing) to disregard the nature of evolutionary change by the differing topologies they produce, should we also then apply this to topics of a more philosophical bend? Shall we, say, apply this theologically? If the nature of God is debated, does this mean we should discard God? If the Bible’s accuracy is so debated that there are whole denominations of Christians including Catholics who do not apply it literally, versus those that do (much of Protestantism in the USA), should we simply discard the Bible and its writers as delusional?

As a specialist who works on the field to which Ghost of Paley has applied criticisms by Google-trawling, Martin Brazeau has shown substantive resolve in putting up with arguments that never attempted to understand the critical difference between data choice and result through various forms of analysis. Brazeau has also shown himself competant to discuss the very papers GoP has not read, save for the few that are available online through web-crawling. If I were so inclined to do research in this fashion, in a manner that has been largely frowned upon by university professors as their students’ choice for collecting information they are supposed to be researching, but seems in keeping with High School study topics, I would disregard the whole point of reading papers and just read online summaries and abstracts as they might hold the grist and guts of the issue, and disregard the data. Science is, in all that I’ve understood it, the very nature of “why?” and “how?” and looking for means to answer those questions while making the fewest subjective assumptions. To do science, we must remove ourselves of bias, and to this end, I offer my tagline, from P. D. Medawar:

“Innocent, unbiased observation is a myth.”

So long as we keep this in mind, we will be as much critical of what comes out of OUR OWN MOUTHS as that which we hear from others. Indeed, to remove the plank from our own eyes before we pull it from that of another.

Comment #74458

Posted by The Ghost of Paley on January 21, 2006 4:37 PM (e)

Just a few questions:

1) Do the large conflicts between Chang (2004) and the latest molecular research pose problems for the Coelacanth-Lungfish-Tetrapod trichotomy? And how does this affect the placement of putative tetrapod ancestors? Which line of evidence should be given more weight, particularly if both approaches boast low p-values? This also applies to the Afrotheria hypothesis, which is supported by high bootstrap values and SINE insertions, yet clashes with the latest fossil evidence.

2) Why shouldn’t I rely on online research when it allows onlookers to verify my sources without making numerous trips to the library? Should I cite obscure papers instead?

3) Why should cladograms giving the highest tree resolution be preferred a priori, unless the goal is to verify common descent by assuming its existence?

Any assistance is appreciated.

Comment #75079

Posted by The Ghost of Paley on January 23, 2006 12:53 PM (e)

[chirp chirp chirp]

Well, I guess Mr. Brazeau has given up on me. I’m just glad he took time out of his busy schedule to address my earlier arguments. Can anyone else answer my questions, or have the hyenas fled the field?

Comment #75108

Posted by Steviepinhead on January 23, 2006 2:18 PM (e)

I can only get to the abstract of Enrico’s article by following the link, so I’ll try to track it down up at the UW library tomorrow, when I’ll be on and near campus anyway…

Comment #75110

Posted by steve s on January 23, 2006 2:33 PM (e)

Comment #75079

Posted by The Ghost of Paley on January 23, 2006 12:53 PM (e)

[chirp chirp chirp]

Well, I guess Mr. Brazeau has given up on me.

Maybe he got tired of an ignorant person calling him dishonest. Maybe he realized GOP was committed to his erroneous belief, and that hBrazeau’s refutation was sufficient for anyone who wasn’t, which is the best he can hope for.

Comment #75118

Posted by The Ghost of Paley on January 23, 2006 3:15 PM (e)

steve s wrote:

Maybe he got tired of an ignorant person calling him dishonest.

Well, if you find that person, tell him to cut it out. Good thing I specifically stated that he wasn’t dishonest, or you would have jumped on me as well. :>)

Maybe he realized GOP was committed to his erroneous belief, and that hBrazeau’s refutation was sufficient for anyone who wasn’t, which is the best he can hope for.

Oh, I missed the part where he explained the clashing results among the latest methods. He just noted that Chang’s cladogram resolved the trichotomy, and I pointed to recent, comprehensive molecular research that inserted an entire class within the sarcopterygii. But being a nonignorant person, you should have no problem resolving the dilemma.

Comment #75126

Posted by Sir_Toejam on January 23, 2006 3:46 PM (e)

Should I cite obscure papers instead?

yup, that’s how science works. aside from the fact that you set up a deliberate strawman by naming anything that likely disputes your idiotic claims as “obscure”, you also acutally need to be able to read, comprehend, and be able to understand where these “obscure” articles fit into the subject matter at hand.

That’s right; you can’t just read abstracts online and expect to understand the entire history and application of cladistics, and make grand pronouncements about what’s all wrong with evolutionary theory based on that.

that’s why we call you ignorant.

as you continue further and further down this track, we have come to the opinon you might be stupid as well. hence the ever decreasing level of response.

you can easily answer your own questions.

yeah, by getting off your arse and actually going to a library to read the primary literature firsthand.

Comment #75192

Posted by Stephen Bent on January 23, 2006 7:17 PM (e)

GoP wrote:

3) Why should cladograms giving the highest tree resolution be preferred a priori, unless the goal is to verify common descent by assuming its existence?

Your point 3 is particularly revealing. Common descent has been demonstrated on a wide range of divergence times, so your pointing to it as an assumption clearly illuminates what your goal is here. You want your baraminist polytomy and you want it now. Well, it’s a nice little gap for you to stick your God into, and it’d be a shame to see Him (or Her?) squeezed by more morphological and molecular evidence. Sorry, but if a bifurcating tree holds for “microevolution” (as you might refer to it), unless a mechanism can be proposed with support, there is no reason to believe that that pattern does not hold in the “macroevolutionary” relationships. Where do you draw that line between the trees we can see and the creation you see in the noisy data of the distant past?

I’m sorry we don’t have all of the answers to put you out of your misery, but I also want to call you on the thoroughly disingenuous nature of your questioning. You are clearly not asking questions because you want the answer, but you are posing questions to gleefully point out the things that scientific inquiry has not determined. Maybe God Did It, but we just want to know what happened given evidence we can look at. Each transitional fossil found will make your argument get more convoluted, with more hand-waving epicycle expostulation, until you take your God and retreat to the next gap. Not a very dignified position to put a deity in (or is it an alien?), methinks.

Comment #75212

Posted by The Ghost of Paley on January 23, 2006 8:56 PM (e)

Sir Wiggles wrote:

yup, that’s how science works. aside from the fact that you set up a deliberate strawman by naming anything that likely disputes your idiotic claims as “obscure”, you also acutally need to be able to read, comprehend, and be able to understand where these “obscure” articles fit into the subject matter at hand.

That’s right; you can’t just read abstracts online and expect to understand the entire history and application of cladistics, and make grand pronouncements about what’s all wrong with evolutionary theory based on that.

that’s why we call you ignorant.

Wow. You have no ability to read. None at all.

Here are my points. I’m going to make this as simple as possible, so please try to keep up:

1) When debating someone in hostile territory, I prefer to rely on as many online sources as possible, as this allows the skeptic to check my claims. If I use hard-to-find sources, I leave myself vulnerable to the charge that I quote-mined, misunderstood, lied, etc. Since I found plenty of good, reputable material online, I stuck with that.
2) Contrary to Mr. Brazeau’s claim, I do read the papers I cite. I realise that the researchers do not support my argument; this is part of the reason I cite them. I want to prove that even those predisposed to my opponent’s side agree with at least part of what I have to say. Do you really think Mr. Brazeau would listen to creationist sources?
3) Our debate covered many different claims. Mr. Brazeau established exactly one: based on recent cladograms, the majority opinion favors the (coelacanth(lungfish, tetrapod)) relation. My main point, however, remains uncontested: the traditional grouping of the big three is falsified by recent molecular evidence. Since the same cladograms that the good professor uses also accept this trichotomy, this indicates a problem with his evidence.
4) I still don’t see why the earlier studies don’t count. Notice that Brazeau doesn’t contest the characters - he just claims that the latest research refutes them. But it’s easy to create spurious trees with high levels of support; scientists do it frequently. So why discount so much evidence, especially when a minority of scientists consider this data important?
5) Despite repeated claims that my position is mistaken, no one can answer my latest questions. Here’s an example:

Stephen Bent wrote:

Your point 3 is particularly revealing. Common descent has been demonstrated on a wide range of divergence times, so your pointing to it as an assumption clearly illuminates what your goal is here. You want your baraminist polytomy and you want it now. Well, it’s a nice little gap for you to stick your God into, and it’d be a shame to see Him (or Her?) squeezed by more morphological and molecular evidence. Sorry, but if a bifurcating tree holds for “microevolution” (as you might refer to it), unless a mechanism can be proposed with support, there is no reason to believe that that pattern does not hold in the “macroevolutionary” relationships. Where do you draw that line between the trees we can see and the creation you see in the noisy data of the distant past?

Common Descent may rest on many evidences, but defining a “good” tree by how robustly it supports evolutionary relationships, and then using that tree as independent evidence for evolutionary relationships, is circular reasoning at its most transparent. What if “star” phylogenies represent reality better? How would a Darwinist know? Answer: he wouldn’t, because a tree full of long branches is tossed in the wastebasket.

I see consilience paraded in book titles, but rarely achieved in practice. And apparently, no one here can find it either.

Comment #75308

Posted by Ubernatural on January 24, 2006 9:01 AM (e)

Indeed, why not a seven-dimensional sphere of life! ;)

Comment #75395

Posted by Stephen Bent on January 24, 2006 1:27 PM (e)

Are there any Darwinists here?

I’m a Dobzhanskyist.

WRT your star topology, does each species get it’s own branch, going back to creation, or were the “created kinds” some other taxonomic level? From your link to the Springer paper in TREE, “Morphology and molecules agree on the monophyly of 16 out of 18 placental orders”. So that leaves your fallback gap as “God/Aliens/FSM created the placental orders, and they evolved into their current forms from there.” That sounds a bit weak to me, like “on the third day, The Designer designed Lagomorpha, and they were hoppy.”

Comment #75505

Posted by The Ghost of Paley on January 24, 2006 8:59 PM (e)

Stephen Bent wrote:

WRT your star topology, does each species get it’s own branch, going back to creation, or were the “created kinds” some other taxonomic level? From your link to the Springer paper in TREE, “Morphology and molecules agree on the monophyly of 16 out of 18 placental orders”.

Good question. Since the Bible doesn’t equate “kinds” with “orders”, the phylogenies are probably uncovering convergent insertions and rearrangements. Don’t laugh: these two papers verify this suspicion. And if you run a heat-map analysis to test Darwin’s bush against Dembski’s star, what do you find? Another victory for I.D. science!

We feel that our heat maps challenge the use of a tree-like pattern to describe molecular evolution. There was always more than one plausible topology retained (see Additional file 1 for a description of the diversity of these plausible topologies). Archaeal and eukaryotic markers favoured 60 and 92 topologies, respectively (Figures 1A and 1B), and alpha-proteobacterial markers (Figure 2A) favoured 12 different trees. Among those best topologies, none are supported by all the genes. Instead, a given topology is accepted by some markers and rejected by others, leading to multiple multicolour lines in mosaic heat maps. The absence of an entirely light line means that genes fail to agree on a single topology, even though they reject many of them and thus do contain some phylogenetic signal. This seems compatible with the redefined “weak” view of the tree. By contrast, the bacterial markers were apparently more discriminating and retained two plausible trees only (Figure 2B), one of which was supported by most of the actual markers. Furthermore, these two topologies are compatible. Could these results support an organismal tree? In fact, these trees consist of two star-phylogenies, which differ only in their ability to recover the monophyly of proteobacteria, and do not resolve any deep relationships between accepted monophyletic groups otherwise. The absence of basal resolution leaves all possibilities concerning the process of molecular evolution in bacteria open. Such a star-tree can be explained either by multiple ancient LGT events, a radiation, or the lack of ancient phylogenetic signal. [Paley’s emphasis]

To my knowledge, this method has only been applied to the root of the tree. But what happens when the root withers? The tree collapses. Especially when it’s been supported by rotten wood from the very beginning.

Wizard, is there anything you can’t do?

Comment #75507

Posted by Steviepinhead on January 24, 2006 9:17 PM (e)

That the passage of time and lateral gene transfer pose difficulties for resolving the origins of bacterial genes is not exactly news, and does nothing to support IDiocy.

Nor does it mean that we won’t eventually nibble away at the edges of the problem until we get it resolved.

Your first cite contains nothing that advances your argument. Retroviruses are a possible source of lateral gene transfers. Wow! This might have been startling news–quite some time ago.

Lay out for us, in your own words, how any of this provides positive evidence for ID.

Heck, while you’re at it, Paleface, why not just lay out for us–in anyone’s words–what the “theory” of ID is, what evidence supports it, and what this evidence tells us about how and when the “designer” did whatever you claim it did to bring about whatever you claim it brought about.

Why not shoot the moon, and identify any event, affecting any species, order, kind, phylum, etc., that you believe was a “design intervention” event, and then explain it for us, using evidence, from an ID perspective–what, when, how, and the all-important why–in a way that you think evolution can’t…

Obviously, I won’t be holding my breath. In fact, it’s pizza time, and I’ve got a long linguistics article by John Enrico to read.

Comment #75709

Posted by Steviepinhead on January 25, 2006 2:12 PM (e)

There’s definitely something fishy going on here:
http://seattlepi.nwsource.com/national/1501AP_Indonesia_Tiny_Fish.html.
But it’s a very small something…

Comment #75718

Posted by Arden Chatfield on January 25, 2006 2:28 PM (e)

There’s definitely something fishy going on here:
http://seattlepi.nwsource.com/national/1501AP_In….
But it’s a very small something…

Dang, yet another animal Noah had to fit on the ark!

At least it wouldn’t have taken up much room…

Comment #75719

Posted by The Ghost of Paley on January 25, 2006 2:30 PM (e)

Vic wrote:

That the passage of time and lateral gene transfer pose difficulties for resolving the origins of bacterial genes is not exactly news, and does nothing to support IDiocy.

Excuses: plentiful. Data: contradictory. Mood: sullen.

Heck, while you’re at it, Paleface, why not just lay out for us—in anyone’s words—what the “theory” of ID is, what evidence supports it, and what this evidence tells us about how and when the “designer” did whatever you claim it did to bring about whatever you claim it brought about.

But when I try, all I get are insults. Like now, for instance. Care to defend your model? Oh that’s right - you’re ignoring me…….

Comment #75726

Posted by Flint on January 25, 2006 2:47 PM (e)

Excuses: plentiful. Data: contradictory. Mood: sullen.

Support for ID: ignored.

But when I try, all I get are insults. Like now, for instance.

Note the subtle implication that he HAS tried to produce a theory of ID. Recently, Behe was asked (by a biology class) what tests he could apply to determine whether or not something was designed. His response: “I don’t know, but I know design when I see it.” Kinda like N-rays, I guess.

For the record: if Ghost or *anyone* had ever produced any method of testing for design whose results were NOT predetermined, the entire scientific world would take immediate and sincere notice. Huge budgets would follow, along with intensive research programs. It would be the scientific breakthrough of all time.

Comment #75728

Posted by Jim Harrison on January 25, 2006 2:58 PM (e)

If you are even a desultory reader of science journals, you’re aware that researchers, ever on the lookout for a project that can attract grant money, automatically subject received ideas to new tests and experiments. Come up with an assay for Intelligent Design and a host of labs will be running it next week. Doable experiments are almost as lovable to scientists as billable hours are to attorneys.

Comment #75731

Posted by Martin Brazeau on January 25, 2006 3:07 PM (e)

I was going to leave this thread for dead, but it appears as though GoP has taken my absence as a license to spew unchecked falsehoods and misinformation (as well as continue to distort the nature of this ‘discussion’, read: trainwreck). I’ll have to return.

I’m at a field school this week and most of next, I’ll try to draft some responses for when I get back to the office.

GoP makes one interesting and, I think, good point: the apparent circularity of phylogeny reconstruction. The clues to the answer to this question are: congruence and distribution.

Before I run off:

Ghost of Paley wrote:

Common Descent may rest on many evidences, but defining a “good” tree by how robustly it supports evolutionary relationships, and then using that tree as independent evidence for evolutionary relationships, is circular reasoning at its most transparent. What if “star” phylogenies represent reality better? How would a Darwinist know? Answer: he wouldn’t, because a tree full of long branches is tossed in the wastebasket.

Neat trick. The phrase “defining a “good” tree by how robustly it supports evolutionary relationships” is where you go wrong. A “good tree” has a solid nested character distribution (characters being observable data) with few incongruences and ambiguities. From that, we may provisionally assert corroboration for a phylogenetic hypothesis. However, your characterization of the methodology likens it to a ‘goodness of fit test’ for a preconceived view of phylogeny.

I don’t deny that work has actually been done in such a fallacious way, I agree. I can probably point to several examples. However, one must recognize that such results are often severely criticized. Browse some issues of Systematic Biology and see for yourself.

Also, this argument makes no sense to me:

Ghost of Paley wrote:

My main point, however, remains uncontested: the traditional grouping of the big three is falsified by recent molecular evidence. Since the same cladograms that the good professor uses also accept this trichotomy, this indicates a problem with his evidence.

What is the ‘traditional grouping of the big three’?. (LF(Coel;Tet))? That’s largely a pre-cladistic grouping that used a concept of ‘overall similarity’ as a basis for grouping coelacanths with osteolepiforms and porolepiforms. However, evidence from fossils such as Powichthys, Youngolepis, Diabolepis, and early lungfishes provide an excellent transformation series between porolepiforms and lungfishes. Coelacanths, as I pointed out before, retain a lot of more generalized bony fish characters and lack many of the key features shared among members of the lungfish+tetrapod clade.

Finally, this:

I still don’t see why the earlier studies don’t count. Notice that Brazeau doesn’t contest the characters - he just claims that the latest research refutes them.

Because from my understanding of this discussion, the isse was never about actual data. For the most part, you seem to be uninterested in actual data. It was in fact you who cited results as contradictory to the value of particular data:

Ghost of Paley wrote:

Still others (3) would divorce modern lungfish from porolepiforms proper, which renders your synapomorphies moot, and Kenichthys irrelevant.

You’ve here discounted data (synapomorphies) on the basis of alternative interpretations of phylogeny. I find it hilariously ironic.

Moreover, (3) (Paleontology, Systematics and Phylogeny Dipnoans as sarcopterygians by Hans-Peter Schultze) is a review not presenting new data. It’s Hans-Peter re-asserting his preferred hypothesis that he’s maintained for some 30 years or more!

Your earliest flurry of posts was mostly in an attempt to discredit me on the basis of a number of studies that didn’t agree with my preferred view of sarcopterygian interrelationships (which largely, with some here irrelevant exceptions, reflects the prevailing view amongst vertebrate paleontologists). I never engaged questions of data or relevance because my only goal was to establish that the view I held was considered well-supported among credible authors with relevant expertise. I have made no attempt here to either support my views or overturn those of others.

Must go! I’ll try to slap together an illustrated phylogeny of the sarcoptergii if I have time when I get back.

Comment #75741

Posted by The Ghost of Paley on January 25, 2006 3:44 PM (e)

Look for my response later tonight.

Comment #75744

Posted by Alan Fox on January 25, 2006 4:24 PM (e)

guts to gametes????????

Comment #75745

Posted by Steviepinhead on January 25, 2006 4:26 PM (e)

Ahhh, I’ve been “banned” to the Panderichthys thread!

Arden, thanks a bunch for the John Enrico reference.

A few thoughts, with vague application to the reconstruction of ancient forms in biology:

It does get increasingly difficult to recover old forms and old relationships the deeper one delves into the past. Errors may well occur, and require correction and re-correction. But that’s no reason not to make the effort. Nor does it render the attempts (which, ideally, will begin to converge on more-and-more correct reconstructions) unscientific (to the contrary, in fact, as several posters have attempted to inform the Pale Pest above–the self-corrective tendency is a critical aspect of why such endeavors are scientific).

While Pale Transparence has been mucking about, dredging up asserted difficulties and disagreements in the fossil and molecular reconstructions, Arden and I have been having a little “sidebar” fun with a mutual interest in the reconstruction of ancient linguistic forms (an area in which I am very much the dabbler, and in which Arden is the expert).

Like extant biological species, human languages are presumably related by common descent–and can likewise to some degree be grouped together in families and super-families, which can in turn be charted out on “cladograms” or branching trees. Some famous “isolates” around the world have long puzzled researchers (like Basque in Europe and Haida on the Queen Charlotte Islands off the Northwest Coast of North America). These languages are generally presumed to have “split” or speciated from related languages so deeply in the past that their connection with other living languages can no longer be reconstructed.

An alternate hypothesis–and one that bears at least a superficial resemblance to the “special creation” of biological kinds–might be that humanity dispersed at a time when the invention of language was imminent, so to speak, but not actual: in other words, language was invented separately by separate groups of people. Thus, arguably, some isolates might not just be “unrooted” due to the loss or lack of the information that would be needed to tie them into the “tree,” but might actually be separate “sprouts.”

(There is even a quasi-religious tie-in here: most human cultures have their own unique origin myths, and a culture that speaks an “isolate” language might even argue that this supports the validity of its unique origin story. Though most indigenous peoples are not quite so silly about this as the fundies and IDists are, hints of this kind of attitude sometimes emerge in the debate over the fate of very old human remains, with the currently-“resident” tribes arguing that the bones must be those of their immediate ancestors because “we have always lived here.”)

As noted above, the Haida language has been the subject of scholarly debate: is it a “true” isolate (either so deeply rooted that its precise connection can no longer be recovered, or even a language that was “separately” invented) or is it demonstably related to other languages still spoken today (or in recent times–since indegenous languages are suffering a wave of extinction in parallel to the current ecological crisis)?

Various famous (or infamous) anthropologists and linguists have suggested over the years that Haida is not a true isolate, but is instead a distant relative of a language family dubbed “Na-Dene” which assertedly includes Athabaskan (native languages of interior Alaska, interior western Canada, and the SW United States–including Navajo), Eyak (interior-coastal Alaska), and Tlingit (SW coastal Alaska). Navajo is still spoken by a large community, and Tlingit, though struggling, is still alive and relatively well.

Word lists were more-or-less carefully and comprehensively collected from “vanishing” or rapidly-acculturating peoples by better-or-worse trained explorers, priests, missionaries, folklorists, anthropogists, and linguists. The Haida language was first “excavated” in the last part of the 19th and the first part of the 20th centuries. For almost 3/4ths of a century, no further work was done, partly based on the assumption that ongoing acculturation had taken too much of a toll.

Meanwhile, based on the collection work that had already been done, scholars advanced various versions of what became the “Na-Dene” hypothesis. This hypothesis was also vigorously attacked–with some of the critiques bearing some resemblance to the similar attacks on evolutionary claims of species relationships: (1) what look like traits shared due to common ancestry may instead be due to “convergence” (lateral transfer, borrowing, diffusion, contamination–which with human languages may be due to cultural contact, trade, conquest, and so on); (2) there are too many “missing links” (too much time has gone by, so we’ll never have the evidence to resolve the claimed relationships one way or the other); etc.

In short, What some scholars saw as “genetic” relationship, others saw as mere borrowings or random resemblance.
The debate see-sawed back and forth, with some pointing to the contention and lack of resolution as reasons to abandon the effort (like Paleface here?).

The Haida case was a modest exemplar of a larger debate going on among linguists and other scholars. How far back, realistically, can languages, and proto-languages, and “Ur”-languages be reconstructed before the haze of the past obscures all?

As with evolution and paleontology, evidence of different kinds was ingeniously deployed (geological dating and molecular comparisons, as well as morphology of the bones themselves; blood groups, dental patterns, and DNA, as well as the forms of the words and syntaxes of the languages in issue), and just as ingeniously disputed.

Deeper relationships between languages separated by thousands of years are ordinarily validated by demonstrating that consistent sound shifts and other detailed comparisons can be made to “unwind” the changes wrought by time and distance. But certain Russian linguists, and the controversial American duo of anthropologist Greenberg and researcher Ruhlen, instead employed very broad comparisons of word-forms (“similar” sounding words in widely-dispersed languages with “similar” meanings) to arguably construct large linguistic families and super-families, going back perhaps tens of thousands of years into the history of the dispersion of humanity across the globe. These super-groupings were hotly disputed by scholars with more-intimate knowledge of the languages in question, who claimed insufficient information, false resemblances, and overly-elastic comparisons of meanings and sounds that “stretched” well beyond any significant similarity of meanings and sounds.

Ruhlen and Greenberg, and various allies (some found in strange places) defended themselves, asserting that more-detailed comparisons have to start somewhere, and resorting to overarching correlations with blood group and dental data. They also claimed that their comparisons were restricted to sets of words (numbers, body parts, kinship terms) that were more resistant to change than “ordinary” vocabulary items.

(See Arden’s 1/19/06 comments above–post # 73856–to get the flavor of some of the weaknesses and flaws in the Greenberg-Ruhlen approach.)

Then linguist John Enrico (Indiana University) came along and, over the last 15-20 years, went back to “the dig.” He actually went to the Queen Charlottes, located living informants who still spoke Haida (with no disrespect to the Haida matriarchs who served as his informants, this was a bit like unearthing magnificent new fossils), and spent years, not only compiling new “data,” but taking the time to cross-check, validate, and fill in the “gaps” in the Haida words and myths that had been collected by previous generations of scholars. Enrico has published scholarly articles, a collection of myth translations, and a dictionary of Haida.

Meanwhile, other scholars had begun detailed “reconstructions” (in the traditional, not the Greenberg-Ruhlen manner) of proto-Athabaskan. The Eyak language proved to be a revelatory “link” between Tlingit and the Athabaskan group of languages, so some work on reconstructing proto-Athabaskan/Eyak/Tlingit was begun.

Like Martin Brazeau here, in other words, Enrico was able to increase the data set of characters and features of a critical “fossil,” all against a background of advancing work in the immediately-surrounding field. On the basis of the enriched data (and a heck of a lot of hard and dedicated work), Enrico was able to make a much more detailed comparison between the languages in issue, and was also able to “control” much more carefully for “false positives” (borrowings and random resemblances). He pulls no puches in critiquing some of the rather sloppy, poorly-supported, and premature work by his predecessors.

Like Brazeau here, however, he doesn’t throw out the baby with the bathwater. While some of the earlier work was sketchy, and based on insufficient and poorly-controlled data, he also acknowledges that at least some of the previously-advanced comparisons were correct (if not always for the right reasons).

Enrico makes these interesting comments about Greenberg (“Toward Proto-Na-Dene,” Anthropological Linguistics, vol. 46, no. 3, Fall 2005, pp. 229-302, at p. 296, fn. 2):

Greenberg…defended the proposing of large numbers of etymologies (sets of resemblances or putative cognates) on the basis of poor data on the grounds that it gets the job done. That is true if the job consists, as it has in his case, of merely determining in a preliminary way in which languages are probably genetically related, but, of course, one would like to go beyond that, and for that one needs good data and careful choice of potential cognates. In particular, care must be taken to leave borrowings and probable borrowings out of the the picture…

One can of course push my “comparison” of the science of reconstruction (of Panderichthys and the origin of the tetrapod clade on the one hand and of Haida and proto Na-Dene on the other) too far. But I think there is a valuable lesson here: just because we don’t yet have all the data we would like to have is no reason not to get on with the job, in at least a preliminary way. But that, in turn, doesn’t mean that preliminary hypotheses, on the basis of insufficient or “contaminated” data, should not come in for criticism and refinement. (At the same time, there has to be some scientific hypothesis that can be tested with at least some data, and subjected to replication and review, unlike the scientifically-vacuous handwaving of ID.)Just because we don’t have it right yet (or even if we have it flat wrong) doesn’t mean we shouldn’t keep digging, looking for better fossils, surviving informants, and more valid reconstructions, whether linguistic or molecular.

And just because the hypotheses and data go through this robust process of validation and refinement does not mean we should abandon the effort, or that science is so error-prone that it is ultimately unproductive.

Absolutely au contraire, my Pale Non-Friend. That process of debate and discovery is precisely why science ultimately works as well as it does to enlarge our knowledge and understanding of the world. Science’s–and evolutions’s–self-correction is its strength, not its weakness.

Comment #75752

Posted by Martin Brazeau on January 25, 2006 4:47 PM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #75766

Posted by The Ghost of Paley on January 25, 2006 5:21 PM (e)

One quick point: The problems run deeper than the professor suggests. By divorcing coelacanths from lungfish, the molecules contest not only the branchings within the trichotomy, but the trichotomy’s very existence. This overturns the central predictions of evo biology. If the science can’t even get the basics correct, why trust the details?

Comment #75768

Posted by Martin Brazeau on January 25, 2006 5:27 PM (e)

Interesting note, the two papers that Paley cites fly in the face of his own assertions and do not back up the assertions of ID.

Recall that ID makes very few (if any) novel assertions (i.e. predictions). It also has no methodology other than trying to point out illogic or fallacies in evolutionary thinking. Paley has tried to point out that:

Ghost of Paley wrote:

Common Descent may rest on many evidences, but defining a “good” tree by how robustly it supports evolutionary relationships, and then using that tree as independent evidence for evolutionary relationships, is circular reasoning at its most transparent. What if “star” phylogenies represent reality better? How would a Darwinist know? Answer: he wouldn’t, because a tree full of long branches is tossed in the wastebasket.

They show scientists working under an evolutionary framework of biology determining that evolution needn’t always proceed according to a stochastic branching process, but may in fact be anastomosing. How can IDists maintain that we operate under circular reasoning while at the same time finding that many of our core assumptions are not supported? Still, how then can we even go on accepting evolution/common ancestry if this is the case?

None of these papers reflect “victories for ID”. Each of them specify very explicity how evolutionary models may not only accomodate but predict the data they provide. How can you make such profoundly dishonest claims?

There are many deeply mistaken aspects Paley’s assertions on these matters. In large part, these papers do much to damage Paley’s case and point out why molecular studies can go so horribly wrong when estimating phylogeny. These have virtually nothing to do with how morphology affects our interpretation of phylogeny (especially as these papers have very little to do with the developmental genes that control morphology).

We must also note that morphology is phenotypic and therefore subject to selection more directly than a lot of ‘background’ molecular happenings. Because some molecular changes (esp. where retroviruses are concerned) may be mirrored - especially where similar evolutionary processes are involved (San Mauro et al., 2006) - it does not logically follow that morphology will do the same thing. This is especially true where embryonic development is concerned.

Again, the studies relating to horizontal transfer relate to much ‘deeper’ levels of Life than the Vertebrata (which we are primarily concerned with). Still, I know of no mechanism that would permit the transfer of entire genetic pathways involved in skull morphogenesis that could be transferred from a coelacanth to a tetrapod (or vice versa) by means of a retroviral insertion.

What I see in Paley’s writing is a growing web of confusion and contradiction. This is becoming increasingly clear as he moves to single pieces of work to support individual claims. In the process the information provided in these works contradict other claims made about the nature of evolutionary biology. As Paley continues this, I’m sure we will find more of such contradiction.

Comment #75771

Posted by Alan Fox on January 25, 2006 5:31 PM (e)

Guts to gametes, Mr P?

Comment #75774

Posted by Russell on January 25, 2006 5:41 PM (e)

If the science can’t even get the basics correct, why trust the details?

And why spend so much time and effort digging up articles in field where you have no confidence in either the details or the foundation? To try to find “inconsistencies” to convince others they should share your lack of confidence? To try to bolster your own certitude that the experts are all wrong? Just doing your part on the science front of the culture war?

Comment #75777

Posted by Martin Brazeau on January 25, 2006 5:44 PM (e)

One quick point: The problems run deeper than the professor suggests. By divorcing coelacanths from lungfish, the molecules contest not only the branchings within the trichotomy, but the trichotomy’s very existence. This overturns the central predictions of evo biology. If the science can’t even get the basics correct, why trust the details?

This makes absolutely no sense. It does not translate into a meaningful statement about which a person can make a meaningful response. Please, if you’re going to use the term ‘trichotomy’ in the context of systematics, please use it properly. ‘Trichotomoy’ usually refers to an unresolved phylogenetic tree (that is, a dendrogram with three branches to a common node, rather than two to a node). What is this ‘trichotomy’ that you keep talking about?

The concept of ‘divorcing’ is also undefined here. What do you mean by ‘divorcing coelacanths from lungfish’? You mean not resolving them as sister taxa? Well, neither do morphological studies? Do you mean moving them away from all other Sarcopterygii? Well, what are the reasons for this? Most molecular analyses I’m familiar with support a sarcopterygian status for coelacanths. Why should we conclude that the data used to generate any result are to be the basis of any conclusion?

Certainly, this is a question I must answer as well as you. However, you seem wont to to use phylogenetic analysis in making conclusions with much more certainty than I ever would. You simply cherry-pick the phylogenetic result you want and use it as the basis of an argument claiming that evolutionary biologists are committing that very same fallacy.

Comment #75835

Posted by The Ghost of Paley on January 25, 2006 9:45 PM (e)

OK, the good professor has given me much to chew on, and I’ll only be able to address a sliver of it tonight. Here goes:

Please, if you’re going to use the term ‘trichotomy’ in the context of systematics, please use it properly. ‘Trichotomoy’ usually refers to an unresolved phylogenetic tree (that is, a dendrogram with three branches to a common node, rather than two to a node). What is this ‘trichotomy’ that you keep talking about?

Systematists often use “trichotomy” to refer to three closely related groups whose relationship is hard to resolve. For example, we have the human-chimp-gorilla trichotomy. Now imagine if a molecular study inserted fruit bats within this group: wouldn’t you find this a tad difficult to explain on evolutionary grounds? You wouldn’t just say, “Well, the exact branches elude us, and it’s a trichotomy after all, so anything goes!”. So why doesn’t the inclusion of ray fins within sarcopterygians bother you?

Most molecular analyses I’m familiar with support a sarcopterygian status for coelacanths. Why should we conclude that the data used to generate any result are to be the basis of any conclusion?

The reason more molecular studies don’t show Stuart’s result is because most molecular studies avoid including ray fins with both lungfish and coelacanths. Stuart et al didn’t, and got the surprise of a lifetime.

Certainly, this is a question I must answer as well as you. However, you seem wont to to use phylogenetic analysis in making conclusions with much more certainty than I ever would. You simply cherry-pick the phylogenetic result you want and use it as the basis of an argument claiming that evolutionary biologists are committing that very same fallacy.

I prefer molecular studies because they alone can rigorously define a character and subject it to independent statistical tests. Perhaps this explains why so few of them support evo wishful thinking. And as I’ve mentioned before, the Stuart study was the most comprehensive analysis available. No cherry-picking on my part. And why do you keep questioning my character anyway? The studies stand or fall independent of who cites them, or so I’ve been led to believe. More later.

Comment #75838

Posted by Stephen Elliott on January 25, 2006 9:58 PM (e)

GOP,
Why do you never clearly state your position, so that even somebody as ignorant as I am can see it?

You always seem to want to play things out as a game.

Why not simply give your hypothesis and back it up with evidence in a single post?

Comment #75845

Posted by 'Rev Dr' Lenny Flank on January 25, 2006 10:11 PM (e)

Why not simply give your hypothesis and back it up with evidence in a single post?

Because he can’t. (shrug)

ID simply has nothing scientific to offer. And he knows it just as well as we do.

Comment #75846

Posted by Stephen Elliott on January 25, 2006 10:15 PM (e)

Posted by ‘Rev Dr’ Lenny Flank on January 25, 2006 10:11 PM (e)
Because he can’t. (shrug)

ID simply has nothing scientific to offer. And he knows it just as well as we do.

Bah! Spoilsport.

Comment #75863

Posted by Martin Brazeau on January 26, 2006 2:42 AM (e)

Ghost of Paley wrote:

The reason more molecular studies don’t show Stuart’s result is because most molecular studies avoid including ray fins with both lungfish and coelacanths. Stuart et al didn’t, and got the surprise of a lifetime.

This is quite simply false. In fact, it’s either incredibly ignorant or a lie. Any analysis of sarcopterygian interrelationships generally includes ray-finned fishes. Usually Polypterus and or Polyodon where sequences are available. Certainly always Fugu and/or Danio.

As for Stuart et al., their analysis may be very complete but it has a number of problems. One is that they only a single method of three construction - Neighbor Joining (NJ). This is a phenetic distance measure and not a character-based method like parsimony, max. likelihood or bayesian. It is not surprising that it ‘clades’ what are widely regarded as the two most basal taxa of the sarcopterygii and actinopterygii - as their sequences would be most likely to exhibit overall similarity.

You referred to their results as ‘inserting an entire class withing the sarcopterygians’. Again, you commit this same error. Please explain the difference between ‘inserting actinopterygians’ into the sarcopterygii, or the ‘pushing of coelacanths’ to a basal osteichthyan position. The quotes refer not to direct quotes of you, but the use of your terminology.

Brinkmann et al. (2004) does in fact include a variety of ray fins (including Polypterus where sequences are available) and submits these to maximum likelihood analysis - a parametric character-based method.

I have to run, more later.

Comment #75873

Posted by Martin Brazeau on January 26, 2006 7:27 AM (e)

A few things to note about Stuart et al. 2002:

-The purpose of the investigation was not so much to resolve the vertebrata as it was to develop a method for interchanging gene trees (phylogenies focused on the evolution of genes) with species trees (phylogenies that might use genes but are interested in sorting out taxonomic relationships). They developed a new method for dealing with sequence data and tried it out and are admittedly cautious in their interpretation of this phylogeny:

Stuart et al. 2002 wrote:

The resolution of this particular analysis may be limited by the relatively small number of independent characteristics (64–80 copep motifs) extracted from the 13 gene families of mitochondria. Many more independent characteristics would likely be available from larger data sets containing whole bacterial or nuclear genomes.

-They used the Neighbor Joining (NJ) method only. This method, along with UPGMA, are distance-based methods and are among the most susceptible to long-branch attraction. In fact, most of the studies you cited early on were NJ trees. It’s probably the worst method and should be avoided where possible. It is, however, a lot faster than character-based methods because it ‘builds’ a tree rather than searching trees. That is, character-based phylogenies have to go through every possible tree combination and count character state changes until it finds the shortest one(s). As the number of taxa grows, the number of trees grows exponentially and the analysis will take more time than modern computing speeds can handle (or likely will every be able to handle). NJ is a heuristic method of getting around this problem (although it is not the only one) by ‘snapping’ branches together based on distance metrics. Distance measures only summarize overall similarity and not sequential character state changes. Because of this, taxa that are ‘primitive’ may well share a lot of states in common and thus snap together. However, the reality may be that they simply are reflecting the ancestral condition of much larger clades. The results are thus to be taken lightly.

-The ‘orthodox’ tree that Paley claims Stuart et al. refute looks like this: ((((actinopts)Polypterus):(coelacanth(lungfishes(tetrapods)))). Thus, if this is correct, coelacanth and Polypterus are the deepest, most basal lineages of their respective clades (Actinopterygii and Sarcopterygii).*

-They also represent very undiverse lineages of their own (there’s only one coelacanth genus and very few polypterids). In Stuart et al.’s analysis, polyperids were represented by only one species and (understandably) so were coelacanths. This is the very definition of long branches. There were no candidate sister taxa for these groups that could ‘break up’ these branches and thus these two taxa, we might predict from first principles alone, will clade together regardless of their actual phylogenetic relationships.

These factors considered together basically scream: ‘textbook case of long branch attraction’. You’ve got perfect candidate taxa and use a method (NJ) which is highly prone to this type of error. It should be no surprise that, in Stuart et al.’s tree, the most basal sarcopt and actinopt actually ‘snap together’ as a clade. This is what we might expect given the confounding factors in this analysis.

Ghost also mentions:

I prefer molecular studies because they alone can rigorously define a character and subject it to independent statistical tests. Perhaps this explains why so few of them support evo wishful thinking. And as I’ve mentioned before, the Stuart study was the most comprehensive analysis available. No cherry-picking on my part. And why do you keep questioning my character anyway? The studies stand or fall independent of who cites them, or so I’ve been led to believe. More later.

Rigorously defines what a character is? Really? This is a common fallacy regarding molecular analyses. Any molecular phylogeny requires that you align sequences. This means, looking at a computer readout of the data and shifting the frame of the sequence so that there is a minimum incongruence between sequences. This involves assigning a gap penalty, which is totally arbitrary, which is a parameter determining how many ad hoc gaps the alignment program can insert in order to align the sequences better. Also, alignments may frequently be corrected by eye to ensure better alignments. There can be as much or more subjectivity in a molecular analysis as in a morphological one.

*Paley might charge that my third point above assumes that the preferred topology is actually correct and is thus circular reasoning. This would be true if I were using it as evidence, but I am not. I am pointing out that if that were the true phylogeny, coelacanths and polypterids become the number-one candidates for long branch attraction to one another - they are thus ideal candidates for coming out as sister taxa in a NJ tree (not unlike the result of Stuart et al. Coincidence? I think not). Given the nature of the analysis, Stuart et al.’s result is not in fact inconsistent with the preferred ‘orthodox’ phylogeny.

Comment #75936

Posted by The Ghost of Paley on January 26, 2006 3:01 PM (e)

While criticisms of the NJ method may have merit, other tree-sorting methods don’t seem to fix the problem; oddly enough, more powerful techniques often make things worse. Although one molecular synapomorphy unites the coelacanth with his putative lungfish cousin, Maximum and log likelihood analyses argue that “Old four-legs” is a basal skate. For some reason, some scientists omit the coelacanth from their studies, relying solely on lungfishes as their representative sarcopterygian. I predict that a heat map analysis would recover a star phylogeny for fish, and that a comprehensive study of all shared insertions would muddy the phylogenetic waters. More later.

Comment #75937

Posted by The Ghost of Paley on January 26, 2006 3:05 PM (e)

Please remove the question mark from the web address on the second link if you want this paper to show up.

Comment #75947

Posted by Martin Brazeau on January 26, 2006 5:17 PM (e)

Quick reply before bedtime.

While criticisms of the NJ method may have merit, other tree-sorting methods don’t seem to fix the problem;

No kidding, but NJ is a hell of a lot worse than non-distance based methods. We have, in the phylogeny provided, a classic textbook case of long branch attraction. This renders your claims of falsification impotent and indeed highly exaggerated.

oddly enough, more powerful techniques often make things worse.

Garbage-in-garbage out. The value of your analysis can only be as good as your data.

Although one molecular synapomorphy unites the coelacanth with his putative lungfish cousin,

…from the data used in that study.

Maximum and log likelihood analyses argue that “Old four-legs” is a basal skate.

Good ol’ Arnason et al.

Two major problems are apparent here. For one, it’s clear that you don’t know how to read trees (this explains alot). Their result has coelacanths, chondrichthyans, and teleost fishes as an unresolved polytomy. The coelacanth is not resolved as a basal skate

More importantly and perhaps deeply embarrassing for you: A similar and more recent study by Brinkmann et al. 2005 (which still stands as a more recent study) does not find this. Unlike Arnason et al., Brinkmann et al. don’t completely ignore tetrapods! You know, in order to test the question of who is more closely related to tetrapods, actual tetrapods are likely to be an important source of data and should be included in the analysis!

Without tetrapods, there is no potential source of synapomorphies that would unite either coelacanths or lungfishes with them in the analysis.

For some reason, some scientists omit the coelacanth from their studies, relying solely on lungfishes as their representative sarcopterygian.

Yes, I agree that this should not be done. Just as I think analyses concerning the question of gnathostome interrelationships should not omit the second largest group of gnathostomes!

I predict that a heat map analysis would recover a star phylogeny for fish, and that a comprehensive study of all shared insertions would muddy the phylogenetic waters. More later.

Have fun with that. I think I’m done here.

Comment #75949

Posted by Steviepinhead on January 26, 2006 5:43 PM (e)

Again, Martin, the rest of us here at PT have very much appreciated your willingness to post and your doggedness in responding with accurate information, even to a dogged troll–definitely a free education for us all (though PaleThing will be smarting from his “education”).

Comment #75952

Posted by PZ Myers on January 26, 2006 6:14 PM (e)

Nah, GoP will continue to be oblivious. It was fun watching him get casually smacked around, though.

Comment #75979

Posted by The Ghost of Paley on January 26, 2006 9:40 PM (e)

P.Z. Myers wrote:

Nah, GoP will continue to be oblivious. It was fun watching him get casually smacked around, though.

Not so fast, sir. There’s still a healthy chunk of mystery to be had.

'Ripper' Brazeau wrote:

Good ol’ Arnason et al.
Two major problems are apparent here. For one, it’s clear that you don’t know how to read trees (this explains alot). Their result has coelacanths, chondrichthyans, and teleost fishes as an unresolved polytomy. The coelacanth is not resolved as a basal skate

True enough - but this doesn’t help you at all. The study clearly groups coelacanths, teleosts, and cartilaginous fishes in a tight trichotomy while moving lungfishes to a suspiciously basal position. No tetrapods needed, since coelacanths obviously wouldn’t cooperate in a mitochondrial analysis anyway. More importantly, the coelacanths occupy a crown position with skates. Could it get any more embarrassing for our poor little evos? A red-faced Arnason notes that:

Similarly, the crown position of Chondrichthyes in the piscine tree, rather than as the sister group of the bony fishes, negates the strict cladistic definition of the Osteichthyes as including all extant gnathostomous vertebrates except Chondrichthyes. The use of the name Sarcopterygii to describe both lobefinned fishes and terrestrial vertebrates is also unjustified [I’ll say! G.o.P.], as the jawed fishes and the amniotes form separate branches in the gnathostome tree (Rasmussen et al. 1998).

But with an assist from that famous sidekick, Senor Assumption, our authors regain their composure:

However, this does not imply that tetrapods do not have piscine ancestors. On the contrary, it is probable that extinct piscine taxa (such as Elpistostegalians, ‘Osteolepiforms’ and Rhizodontiforms) constitute the forerunners of the tetrapods, with the two groups forming the Tetrapodomorpha (see Janvier 1996; fig. 5.3, branch 5). This interpretation is consistent with Jarvik’s (1980) theory that the ‘osteolepiform’ Eusthenopteron was anatomically close to the hypothetical ancestral gnathostome.

When in doubt, let the paleontologists sort it out - with no contrarian DNA to muck things up.

'Ripper' Brazeau wrote:

More importantly and perhaps deeply embarrassing for you: A similar and more recent study by Brinkmann et al. 2005 (which still stands as a more recent study) does not find this. Unlike Arnason et al., Brinkmann et al. don’t completely ignore tetrapods! You know, in order to test the question of who is more closely related to tetrapods, actual tetrapods are likely to be an important source of data and should be included in the analysis!

Wu am I to question a phylogeny constructed from two whole genes? Especially when it has such rich taxon sampling!

Ghost of Paley wrote:

The reason more molecular studies don’t show Stuart’s result is because most molecular studies avoid including ray fins with both lungfish and coelacanths. Stuart et al didn’t, and got the surprise of a lifetime.

This is quite simply false. In fact, it’s either incredibly ignorant or a lie. Any analysis of sarcopterygian interrelationships generally includes ray-finned fishes. Usually Polypterus and or Polyodon where sequences are available. Certainly always Fugu and/or Danio.

But most relevant studies do not probe “sarcopterygian interrelationships”, preferring to dwell on that infamous trichotomy.

I think I’m done here.

Too bad. You were just getting interesting.

Comment #75982

Posted by Steviepinhead on January 26, 2006 9:52 PM (e)

The wingnuts are always at their most amusing when they blithely display not a clue as to how fast their little wings are spinning…

Comment #75985

Posted by Flint on January 26, 2006 10:31 PM (e)

I second the rather hopeless desire that Ghost make his position clear. I’m trying very hard, as a nonspecialist, to follow the discussion, but I’m having a lot of trouble extracting the underlying positions. Brazeau seems to be saying that different techniques produce different possible cladistic relationships, that these techniques each have strengths, dangers, and drawbacks, and that “best-fit” phylogenies are thus hard to pin down; there’s no slam-dunk surefire history.

Ghost, on the other hand, seems to basically agree that there are debates, ambiguities, and difficulties here. But rather than argue in favor of one particular interpretation of insufficient/ambiguous evidence over another, I guess Ghost is saying that if we don’t know what actually happened, somehow - what? -*nothing* happened? Magic happened? We shouldn’t bother to make the effort to resolve these questions? If we don’t know exactly what branched from what when, then branches didn’t happen?

Beats me. Is Ghost trying to use unresolved issues at the bleeding edge of biology as support for the position that evolution never happened at all? Or what?

Comment #75989

Posted by 'Rev Dr' Lenny Flank on January 26, 2006 11:07 PM (e)

Is Ghost trying to use unresolved issues at the bleeding edge of biology as support for the position that evolution never happened at all?

Yep.

After all, ID has nothing scientific to offer, itself. The best it can hope to do is exclaim “Evolution can’t explain X, Y or Z, therefore ID must be right !!!!!!!!”

Or, as DI co-founder George Gilder so eloquently and correctly put it:

“What’s being pushed is to have Darwinism critiqued, to teach there’s a controversy. Intelligent design itself does not have any content.”

Comment #75992

Posted by Anton Mates on January 27, 2006 12:15 AM (e)

For some bizarre reason, Ghost of Paley wrote:

More importantly, the coelacanths occupy a crown position with skates.

Why in Oannes’s name do you keep saying this? Mr. Brazeau already corrected you once, and we can all download the paper so we know you’re wrong. The coelacanths have jack to do with skates according to its tree. As Brazeau explained, “Their result has coelacanths, chondrichthyans, and teleost fishes as an unresolved polytomy.” Coelacanths aren’t even grouped with chondrichthyans, let alone skates in particular. Sure, their tree does not have coelacanths and lungfish as sister taxa, which I think would probably support your argument (if only slightly, given the problems Brazeau mentioned) if we knew what it actually was. So why not just report that fact faithfully and not embellish it with obvious errors?

You realize that your preferred “copy down paper names at random and claim that there’s a disagreement in there somewhere, therefore evolutionary biology is an evil lie mastermined by Zombie Darwin” rhetorical technique is somewhat weakened when virtually every paper anyone bothers to check turns out not to say what you claimed it says?

Comment #75996

Posted by Anton Mates on January 27, 2006 12:49 AM (e)

And here, again:

Ghost of Paley wrote:

Especially when it has such rich taxon sampling!

while linking to this, evidently intending to imply that the Brinkmann et al. paper didn’t look at enough taxa. Of course he somehow overlooked that this was only one of three trees the paper contains, and that the biggest one, which also supports their conclusion re: Everything Else(Coelacanths(Lungfish Tetrapods)), contains 22 species–as many species, in fact, as the Arnason et al. paper GoP was previously touting, and drawn from a far richer array of vertebrate taxa. Including, as Brazeau said, actual tetrapods, which is kinda helpful.

Honestly, if GoP tells you the Pope’s Catholic, you’d better call the guy up and ask.

Comment #75997

Posted by Martin Brazeau on January 27, 2006 3:04 AM (e)

Don’t worry, I wasn’t going to leave without reading your replies. I guess you took it as a license to continue to reach new levels of ridiculousness.

True enough - but this doesn’t help you at all. The study clearly groups coelacanths, teleosts, and cartilaginous fishes in a tight trichotomy while moving lungfishes to a suspiciously basal position. No tetrapods needed, since coelacanths obviously wouldn’t cooperate in a mitochondrial analysis anyway. More importantly, the coelacanths occupy a crown position with skates. Could it get any more embarrassing for our poor little evos?

For a start, I’m not looking for help. If you think you’re holding my on trial here, think again. Each post you make reveals your deep ignorance masked in a veneer of freshly dredged references. Branch statistics are only as good as the data distributions they represent. Change/add taxa (especially large, well-sampled groups) and the distributions will change. I should not have to tell you this

You can’t test/predict the behaviour of taxa in an analysis this way. You need to include them to test them! If tetrapods are added to the tree, what were apparent ‘synapomorphies’ causing the high support for coelacanth+chondrichthyans+teleosts may turn out to be generalized gnathostome characters. Either way, the exclusion of nearly half the gnathostomes is the exclusion of a rich source of data - in a phylogeny aimed at resolving gnathostomes.

It’s clear, once again, that you know absolutely nothing about phylogeny reconstruction or the behaviour of data in such analyses.

Comment #76000

Posted by k.e. on January 27, 2006 3:47 AM (e)

GoP of course can’t see the forest for the ‘trees’.
He doesn’t deny that there is a forest made up of trees he just wishes that the trees were …well…. not trees but magical trees.

He acknowledges there are branches and leaves he just wishes no one would tell him about the rest of the tree because the magical trees can have leaves and magically supported branches so he can continue his ‘day dream’ of Santa being real.

I call this the pubescent ‘Paris Hilton’ school of biology.

I thought Santa Claus was real until I was 17 until some mean person told me he didn’t exist.
Paris Hilton.

Comment #76022

Posted by The Ghost of Paley on January 27, 2006 11:11 AM (e)

Anton Mates wrote:

And here, again:

Ghost of Paley wrote:

Especially when it has such rich taxon sampling!

while linking to this, evidently intending to imply that the Brinkmann et al. paper didn’t look at enough taxa. Of course he somehow overlooked that this was only one of three trees the paper contains, and that the biggest one, which also supports their conclusion re: Everything Else(Coelacanths(Lungfish Tetrapods)), contains 22 species—as many species, in fact, as the Arnason et al. paper GoP was previously touting, and drawn from a far richer array of vertebrate taxa. Including, as Brazeau said, actual tetrapods, which is kinda helpful.

What’s funny about this complaint is that I was originally going to link to the first figure until I saw that it was based on only one gene. Fearing that some would accuse me of ignoring the tree drawn from the concatenated RAG 1/RAG 2 data, I chose the more comprehensive phylogeny instead, and still got flamed. But in any case, my point stands: the paper did not include many fish species, and this compromises its conclusions. And what about the other paper?

Comment #76035

Posted by Arden Chatfield on January 27, 2006 12:44 PM (e)

Steviepinhead:

Sorry for the delay in responding. I dont think we need to worry that this is off topic, since this thread is way off the front page anyway. If it wasn’t for GoP’s pointless bickering with Brazeau, this thread would have died long ago.

Anyway, I basically agree with your appraisal of the Enrico piece. Congrats on having made your way thru it – it’s extremely technical. If you dont mind my asking, what is your degree in? Have you had some ling classes? I was basically able to follow it, with the qualification that I don’t know much at all about Pacific Northwest languages.

My basic feeling about the Greenberg & Ruhlen show is that they seem to believe that the old ‘garbage in/garbage out’ rule is overridden if you put ENOUGH garbage in. That is, if you posit 1,000 etymologies, it doesn’t matter if 999 are shit, so long as one is valid – the one valid etymology proves the whole thing, and refutes all your opponents. It’s not too different from the ID modus operandi.

Another lesson from the Enrico article is just how vastly improved the results of the research are when the researcher has expert knowledge of at least one of the languages involved. (As Bloomfield once said, “if you are going to compare two languages, it helps to know one of them”.) This lack of deep expert knowledge in, well, anything, is another fatal flaw in the Greenberg/Ruhlen approach. And again, the analogies between that and the ID movement (indeed, elsewhere within this very thread!) aren’t hard to spot.

That said, my personal feeling is that Enrico has correctly revived the debate over the relationship between Haida and NaDene, but I still don’t see how several of his conclusions follow. He posits numerous historical scenarios to account for the current linguistic situation seen in the Alaska/NW British Columbia area, such as positing that the Tlingits were a ‘high status group’ of the Haidas once upon a time, but he doesn’t offer evidence for these notions. I think if you want to use historical explanation to buttress a linguistic argument, you have to have something more than linguistic evidence for it. So I feel that Enrico sort of slips a bit when he tries to be a historian.

Comment #76049

Posted by The Ghost of Paley on January 27, 2006 2:15 PM (e)

w

Comment #76053

Posted by The Ghost of Paley on January 27, 2006 2:36 PM (e)

Martin 'The Rippa' Brazeau wrote:

For a start, I’m not looking for help. If you think you’re holding my on trial here, think again. Each post you make reveals your deep ignorance masked in a veneer of freshly dredged references. Branch statistics are only as good as the data distributions they represent. Change/add taxa (especially large, well-sampled groups) and the distributions will change. I should not have to tell you this

Which is precisely my point. The lability of phylogenetic branches bedevils Darwinists, since even the sturdiest of branches may collapse at a taxon’s notice. That’s why the Arnason study prickles at the conscience: what would happen to Brinkmann’s delicate Bonsai if he allowed the addition of a few ray fins? No one knows, and few wish to try. The only recourse is to rely on the dreaded Neighbor-Joining algorithm, or narrow the study’s scope. One thing is certain: Brinkmann needs more genes to support his position.

Comment #76058

Posted by Steviepinhead on January 27, 2006 4:19 PM (e)

Yeesh! One thing I don’t like about the new comment format is the small box size. I guess I could go to Word, where I could see what I’m doing, then bring it back here, but that seems tedious.

Anyway, Arden, thanks for your response (and, again, for your willingness to discuss this offshoot and your cite to this new Enrico article). I think the easiest way to respond to your remarks is a paragraph at a time:

Arden Chatfield wrote:

I basically agree with your appraisal of the Enrico piece. Congrats on having made your way thru it — it’s extremely technical. If you dont mind my asking, what is your degree in? Have you had some ling classes? I was basically able to follow it, with the qualification that I don’t know much at all about Pacific Northwest languages.

Let’s see–my undergrad degree was in anthropology. I was an “undergrad TA” (kind of a weird hybrid, which drew some understandable but largely undeserved resentment from some grad students–I didn’t displace any of them, and got paid from a separate “projectionist’s” fund, heh heh) for both an introductory cultural anthro course and for a really cool course in “primate anthropology” which compared the behavioral traits of various species of primates, from lemurs up through baboons, macaques, and great apes. Anyway, I went skiing for a year and then went to law school. Aa a college kid away from home, I was fortunate enough to find older adult mentors of several kinds, including one woman who very kindly loaned me a book on IndoEuropean philology (I remember thinking that “cognate” was just the coolest word!).

My ex-wife was an anthro grad student (and ultimately Ph.D.). We moved to Seattle and her research focused on NWC native peoples. Bill Holm, the world expert on NWC art, was on her committee. At one point, she got a grant to research museum collections, and I got to tag along to the AMNH, Peabody, Smithsonian, British Museum! To facilitate her fieldwork, we lived with native people in B.C. for two years, were guests at ritual occasions, and so on.

I don’t know much about NWC languages either, but have amassed a bunch of art and anthro books on the culture, history of contact, and inevitably–both through native acquaintances and through reading–have been, um, exposed to the “look and feel” of some of them, particularly Wakashan and the northern groups (probably Haida the most).

So, your basic fascinated dabbler.

My basic feeling about the Greenberg & Ruhlen show is that they seem to believe that the old ‘garbage in/garbage out’ rule is overridden if you put ENOUGH garbage in. That is, if you posit 1,000 etymologies, it doesn’t matter if 999 are shit, so long as one is valid — the one valid etymology proves the whole thing, and refutes all your opponents. It’s not too different from the ID modus operandi.

Here, you know much more than I. I have read some of the popular treatments, and have been fascinated by the attempts (not just on linguistic fronts) to chronicle the dispersion of humans across the globe. Obviously, there’s a serious question how far back any sort of rigorous reconstructions of proto-languages can go (I seem to recall a relatively recent computer textual analysis approach which concluded that it might be possible to go back 9,000-11,000 years, but not much further). To the extent that G’n’R state their hypothesized connections, lay out their data and techniques and their methodologies to be critiqued or crucified, I think they’re a lot closer to trying to practice science than the IDers.

To this point, obviously, the knowledgeable critics have not been very kind to either their methodologies or to their results (Africa perhaps excepted), so I certainly understand your view that they may not be very good linguists. I did find it of some interest that Enrico was not as utterly dismissive as he easily could have been.

Another lesson from the Enrico article is just how vastly improved the results of the research are when the researcher has expert knowledge of at least one of the languages involved. (As Bloomfield once said, “if you are going to compare two languages, it helps to know one of them”.) This lack of deep expert knowledge in, well, anything, is another fatal flaw in the Greenberg/Ruhlen approach. And again, the analogies between that and the ID movement (indeed, elsewhere within this very thread!) aren’t hard to spot.

I totally agree that, to effectively “resolve” the question of whether any of the relationships posited by such as G’n’R (or anyone else) are correct in detail, workers with real expertise in the specific languages need to get involved. Clearly, you need good clean datasets of the kind that Enrico elicited, and then you need to carefully control for “false positives.” To the extent that G’n’R fail to do this, they open themselves up to charges of psuedoscience–charges of the same general kind that we levy against Dembski’s laughable “filter” and Behe’s “Ah knows it when Ah sees it” shtick.

At the same time, maybe to some degree it takes a “generalist,” rather than a specialist in a given language, using data that may be less than pristine, to at least begin to nibble away at the more overarching historical connections between families that split long ago. If this turns out to be a feasible project at all, which is concededly a humongous “if.” I’m reminded maybe of abiogenesis research–just because it may turn out that we simply won’t be able to roll back the mists of time beyond a certain point, is perhaps not a sufficient reason not to start processing the problem with whatever tools we currently have.

My lay impression at this point is that reconstuction of actual nuggets of “Proto-World” may never prove persuasive, but sketching in some plausible connections between super-families may be more realistic…

That said, my personal feeling is that Enrico has correctly revived the debate over the relationship between Haida and NaDene, but I still don’t see how several of his conclusions follow. He posits numerous historical scenarios to account for the current linguistic situation seen in the Alaska/NW British Columbia area, such as positing that the Tlingits were a ‘high status group’ of the Haidas once upon a time, but he doesn’t offer evidence for these notions. I think if you want to use historical explanation to buttress a linguistic argument, you have to have something more than linguistic evidence for it. So I feel that Enrico sort of slips a bit when he tries to be a historian.

I agree Enrico is at his weakest in this section, though he does cite some of the archaeological work by Fladmark and others. He does seem to have some evidence for an old layer of Haida-Tlingit (and, to a lesser extent, Haida-Eyak) contact. Whether this supports his “high class” or “opposite moiety” speculations is certainly open to question. There are, at least, good reasons to believe that there was a general movement of Tlingits northward (both on the mainland, with Tsmshians filling the void, and in the southmost Alaska islands, with Haida from the northmost Queen Charlottes filling the void–or driving the migration).

There are also some suggestions in recent years that the outlying islands may have become ice-free earlier than the continental landmass–or even stayed ice-free throughout the last glaciation, and that a southward movement people along the west coast of the Americas may not only have been possible, but may explain some of the dating conundrums currently bedeviling American archaeologists.

If so, Enrico may simply have his directions of movement wrong–the Haida may, for example, been the folks who stayed behind on the islands (which would have been an initial beach-head for occupation) as others moved onto the mainland and up the river valleys. In any event, I also read this section with a large dose of Morton’s–though I’m fairly sure that Enrico intended these thoughts to be quite tentative.

Lots more work to be done!–in stark contrast to the “Paley” it’s-all-contentious, so let’s-throw-up-our-hands approach.

Comment #76070

Posted by Lou FCD on January 27, 2006 6:30 PM (e)

So, for the layman here (me) the long and the short of this is that this little guy is a close cousin of four legged animals and is sort of half fish, half ground critter that might resemble that little darwin fish I want to put on the back of my car? Oh, the irony. I must apologize for the extreme over simplification, but I’m not a biologist, just a regular Joe. Wading through all the nonsense to get to the meat of the thread can really be distracting.

Martin Brazeau said

ID makes very few (if any) novel assertions…

Indeed, if they are still harping about Paley’s 200 year old argument about the watchmaker which was a theft of Cicero’s 2000 year old argument about a sundial maker it’s at least refreshing that Paley’s ghost has come up with something novel.

Correct me if I’m wrong, but I don’t ever recall hearing someone arguing that eating a steak will give you cow DNA before.

Comment #76079

Posted by Flint on January 27, 2006 6:55 PM (e)

I think I have it now. I live in a town of perhaps 200,000 people. 30 years ago, it was a town of 60,000 people or so. Growth has been pretty explosive, and it’s not easy to find people who were born and raised here. I certainly wasn’t. Now let’s imagine a study trying to determine how those not born here actually got here. We start at the physical level…

We look at Joe Blow. He doesn’t have much money, he doesn’t own a car. No passenger trains stop here. So we speculate that he arrived either by bus, or as a passenger in someone else’s car. It’s not a sure thing, but it seems most likely.

But wait! Here comes Ghost, pointing out that our speculations are dubious in some respects. Our basic problem, says Ghost, is that we are assuming Joe got here by some form of transportation, and we are presuming the existence of transportation because Joe is here. Us poor ‘transpos’ are using circular reasoning.

Now Martin points out that our analysis is the best we can do based on limited data. Yes, Joe *might* have flown in, he *might* have previously owned a car but has it no longer, but when we’re looking at tens of thousands of Joe Blows, we can make fairly accurate probabilistic analysis.

Ghost now counters that he has examined the alleged bus station and airport for milliseconds on end and seen no sign of the purported “transportation”. Which he finds entirely to his expectations. Instead, he has found a study showing that individuals are actually capable of walking great distances.

Martin replies that yes, walking is indeed possible and perhaps someone in the current population actually used that method, but studies examining the surrounding roads and countryside have found that pedestrians are nearly nonexistent. Certainly the are not present in anywhere near the numbers necessary to explain the population growth. These same studies find vast multitudes of highway traffic. Surely that traffic is strongly indicative of how people got here.

Ghost responds that he has found multiple studies showing that this can’t be the case. He has studies of vehicular reliability showing millions of failures, studies showing a ferocious traffic accident rate, studies of drunks and teenagers, all carefully linked and cited. So clearly the “highway traffic” tale is at the very least subject to multiple powerful countervailing evidence. Which of course ‘transpos’ choose to ignore, because it doesn’t fit their doctrine.

Martin now tries another tack. An increase in population by a factor of 3 over 30 years exceeds any rational human breeding rate. Studies of specific characteristics of individuals, especially speech characteristics, strongly suggests that only a small minority of the population could have been raised in Alabama.

Ghost replies with studies showing that speech is an unreliable indicator of origin. And another study showing breeding and population growth rates indeed DO show a tripling in 30 years in many places. It’s entirely unexceptional.

Martin says, well, speech is only one characteristic. We all have reliable data about age, dress, income, skill sets, etc.

Ghost produces a study showing the wide range of human variability.

Martin produces actual testimony from a sampling of individuals, who say they came by car (some by plane), and where they came from.

Ghost produces studies showing that people’s testimony is unreliable, along with a great many documented cases of mendacious claims. Taking testimony is evidence not of history, but of tester’s gullibility. But of course, gullibility is guaranteed when the alternative is for poor little dogmatic “transpos” to admit error.

So the battle goes back and forth. And it’s clear that Martin is trying to figure out how people got here. What Ghost is trying to say isn’t clear at all.

Comment #76103

Posted by Anton Mates on January 27, 2006 10:46 PM (e)

What’s funny about this complaint is that I was originally going to link to the first figure until I saw that it was based on only one gene. Fearing that some would accuse me of ignoring the tree drawn from the concatenated RAG 1/RAG 2 data, I chose the more comprehensive phylogeny instead, and still got flamed.

Ah, so you were misrepresenting it out of a spirit of charity. That would be slightly easier to believe if you hadn’t proceeded to complain about the small number of genes used and the paucity of species.

But in any case, my point stands: the paper did not include many fish species, and this compromises its conclusions.

How including relatively few fish species compromises a paper on this subject more than including no tetrapods at all, I’m not entirely sure.

And what about the other paper?

The Wu paper? Sure, more genes would be better to avoid the problem of segregation of ancient polymorphisms. However, the Wu paper itself notes that that problem is proportional in severity to the probability of such polymorphisms in the first place, and since the RAG1 & RAG2 genes are very highly conserved across tetrapods, their use is probably comparatively safe.

You’re welcome to do a followup study with a dozen genes and a hundred representative taxa, though–find us that star phylogeny you’re hoping for!

Comment #76113

Posted by Martin Brazeau on January 28, 2006 4:36 AM (e)

I guess this will die a slow death…

Ghost of Paley wrote:

Which is precisely my point. The lability of phylogenetic branches bedevils Darwinists, since even the sturdiest of branches may collapse at a taxon’s notice.

Right, but this is not what you’re showing. Basic analytical treatment of Arnason et al. shows the deep-cutting flaws. The fact that one can do this runs counter to your claims.

This isn’t about lability, but how character transformations are constructed and the basic analytical steps a person must take when trying to ask questions about such things as how gnathostomes (jawed vertebrates) are related to one another. Without a branch that draws together bony fishes with tetrapods, then characters that are actually primitive will be optimized as synapomorphies (unique novel characters).

That’s why the Arnason study prickles at the conscience:

LOL! My word, that’s hilarious. ‘Prickles at the conscience’? Are we seeing psychological projection here? There certainly is a form of projection going on when you talk like this and refer to ‘red-faced Arnason’. That’s just silliness and it reflects the lack of a genuinely substantive argument on Ghost’s part.

what would happen to Brinkmann’s delicate Bonsai if he allowed the addition of a few ray fins?

There are ray fins. Why don’t you download an alignment and phylogenetics package and try it yourself? I’ll do it when I get back to Uppsala.

No one knows, and few wish to try.

Well…

The only recourse is to rely on the dreaded Neighbor-Joining algorithm, or narrow the study’s scope. One thing is certain: Brinkmann needs more genes to support his position.

This just gets funnier. Somehow, Brinkmann et al. ‘need more taxa’, but it’s okay for Arnason et al. to exclude representatives of a clade accounting for nearly half of all gnathostomes.

I agree, actually, that Brinkmann et al. should include more taxa. I would never discount that (NJ needn’t be the only recourse, just that ML would take a lot more time/computing power - but there’s nothing stopping it). However, a straight-up analytical examination of Arnason et al. reveals severe problems with their analysis. Moreover, I am not placing stock in any particular molecular analysis until they start to agree among themselves.

Comment #76168

Posted by The Ghost of Paley on January 28, 2006 5:03 PM (e)

Time is limited, so this post will be a little crude.

Anton Mates:
You still miss my point. Brinkmann’s 22 species were distributed across a large phylogenetic space. This is entirely different from a more focused approach, because adding more taxon within a family often “breaks up” monophyletic groups and pushes some members of the old clades towards others. Also, his approach leaves him vulnerable to the charge of cherry-picking “well behaved” species that exhibit “tree-like” behavior, instead of including all sequenced organisms and letting the chips fall where they may.

Even slowly evolving genes have their problems, so no, one must always use whole genomes or multiple genes when testing a phylogeny. Read Theobald if you don’t believe me. If you wish, I’ll also throw some references your way.

Mr. Brazeau:
Sorry, but I’m still skeptical. If lungfish and coelacanths share a close relationship, this should be robust over different analyses, and shouldn’t crucially depend on including tetrapods. I plan on supporting this claim a little later.

More to come….

Comment #76174

Posted by Anton Matse on January 28, 2006 6:06 PM (e)

You still miss my point. Brinkmann’s 22 species were distributed across a large phylogenetic space. This is entirely different from a more focused approach, because adding more taxon within a family often “breaks up” monophyletic groups and pushes some members of the old clades towards others.

Circular reasoning. Leaving out tetrapods only results in a “more focused” or “within-family” approach if you already assume that tetrapods don’t fall into the clades in question. If you’re not sure, the only thing you can do is leave them in and see where they do end up. If they’re a true outgroup, they should pop out as basal, and you have a justification for leaving them out in further studies. But they didn’t.

Also, his approach leaves him vulnerable to the charge of cherry-picking “well behaved” species that exhibit “tree-like” behavior, instead of including all sequenced organisms and letting the chips fall where they may.

And Arnason et al. are equally vulnerable to such a charge, since they picked an equal number of species. Except Arnason et al. included only one lungfish species while Brinkmann et al. included all three extant species. Now I wouldn’t charge Arnason et al. with cherry picking because I’m not sure whether the other lungfish mtDNAs were available to them, nor do I think that clarifying the lungfish-coelacanth relationship was the main point of their study. But Brinkmann et al. clearly come out ahead on the score of relevant species inclusiveness.

Even slowly evolving genes have their problems, so no, one must always use whole genomes or multiple genes when testing a phylogeny. Read Theobald if you don’t believe me. If you wish, I’ll also throw some references your way.

Please don’t bother. I think we’ve established that none of them would say what you claim they say, and I have neither the time nor the expertise to check them all.

Comment #76181

Posted by 'Rev Dr' Lenny Flank on January 28, 2006 6:43 PM (e)

More to come….

How about a scientific theory of design, that isn’t empty of content, and can be tested using the scientific method. Is that “to come”? Or are y’all, uh, still working on that …?

When Luskin told us that there is a “positive case for design” that does NOT depend merely on “negative arguments against evolution”, was he just BS’ing us?

Comment #76213

Posted by Martin Brazeau on January 29, 2006 1:25 PM (e)

Sorry, but I’m still skeptical. If lungfish and coelacanths share a close relationship, this should be robust over different analyses, and shouldn’t crucially depend on including tetrapods. I plan on supporting this claim a little later.

If this is the case then that means you’re deeply mistaken about how phylogenies are constructed. You’re committing the types of errors that students often make in their introductory systematics courses. This is a fallacy of the form: ‘if the earth is moving then we should be able to feel it move’. It’s commonsensical, but wrong.

A coelcanth+lungfish clade should emerge. The nature of the taxa and the analysis dictate otherwise.

1) Tetrapods are lacking. A source of synapomorphies for either of the sarcopterygians included is lacking. This has already been discussed. It is far and beyond the most important point; by itself totally invalidating the results of Arnason et al. for this discussion. Nevertheless, we soldier on.

2) The ‘problematic’ taxa represent very disparate and undiverse lineages. They are thus unlikely to provide a rich source of ‘good synapomorphies’ linking them closely with any taxon. Notice how very diverse clades with lots of closely related sub-lineages (such as the teleosts and chondrichthyans) clump together rather nicely and form the monophyletic groups we expect. The taxa that always seem to ‘fly around’ from one analysis to the next tend to be these lonely and disparate taxa.

3) There is a large, unresolved clade of coelacanth, chondrichthyans (sharks, rays, and chimaeroids), and teleosts (advanced ray-fins). This suggests that the information in the preceding plesions (lungfish and bichir - what I’ll call the ‘immediate outgroup’) and the outgroup are insufficient to polarize this ingroup. There are many conflicting signals that are resulting in all three possible topologies emerging in the analysis. This is a problem that would be expected to emerge if, say, you had an inappropriate immediate outgroup!

The lungfish and coelacanth needn’t clump together because, in the absence of tetrapods, symplesiomorphies are probably being reconstructed as synapomorphies. With tetrapods, a ‘bushier’ branch is provided that could pull over coelacanths and lungfishes and reveal their synapomorphies which are currently getting swamped by a erroneous optimization.

It’s not so much the simple exclusion of a branch that includes tetrapods, but the fact that this probably upsets the entire optimization of the tree.

Comment #76232

Posted by steve s on January 29, 2006 5:26 PM (e)

Make sure you have an exit strategy here Martin. Don’t wait for “Ghost of Paley” to understand he’s wrong and concede.

Comment #76234

Posted by The Ghost of Paley on January 29, 2006 5:56 PM (e)

'Ripper' Brazeau wrote:

1) Tetrapods are lacking. A source of synapomorphies for either of the sarcopterygians included is lacking. This has already been discussed. It is far and beyond the most important point; by itself totally invalidating the results of Arnason et al. for this discussion. Nevertheless, we soldier on.

2) The ‘problematic’ taxa represent very disparate and undiverse lineages. They are thus unlikely to provide a rich source of ‘good synapomorphies’ linking them closely with any taxon. Notice how very diverse clades with lots of closely related sub-lineages (such as the teleosts and chondrichthyans) clump together rather nicely and form the monophyletic groups we expect. The taxa that always seem to ‘fly around’ from one analysis to the next tend to be these lonely and disparate taxa.

Sell it to the hillbillies at Florida State, whose intrafamily squirrel tree makes do with a mountain beaver outgroup. Seems mighty undiverse to me.

'Ripper' Brazeau wrote:

3) There is a large, unresolved clade of coelacanth, chondrichthyans (sharks, rays, and chimaeroids), and teleosts (advanced ray-fins). This suggests that the information in the preceding plesions (lungfish and bichir - what I’ll call the ‘immediate outgroup’) and the outgroup are insufficient to polarize this ingroup. There are many conflicting signals that are resulting in all three possible topologies emerging in the analysis. This is a problem that would be expected to emerge if, say, you had an inappropriate immediate outgroup!

The lungfish and coelacanth needn’t clump together because, in the absence of tetrapods, symplesiomorphies are probably being reconstructed as synapomorphies. With tetrapods, a ‘bushier’ branch is provided that could pull over coelacanths and lungfishes and reveal their synapomorphies which are currently getting swamped by a erroneous optimization.

I understand. I would find this explanation more convincing if there was a way to quantify this effect beforehand. Otherwise, the researchers can just fiddle with the outgroup and taxon density until they achieve the results they wish (not that I’m implying conscious cheating). But I’ll comment more on this later.

Comment #76244

Posted by Flint on January 29, 2006 7:07 PM (e)

Ghost:

I understand. I would find this explanation more convincing if there was a way to quantify this effect beforehand. Otherwise, the researchers can just fiddle with the outgroup and taxon density until they achieve the results they wish (not that I’m implying conscious cheating).

From what I’m reading and (perhaps not quite) understanding, it seems that multiple trees are at least possible, that there is at least some potentially real ambiguity in present data, and that given different techniques and different inputs, different trees can be constructed. Yes, perhaps some decent consensus can be reached as to which is currently considered most likely, but that consensus is always subject to change.

If this is what you’re saying, OK, I understand, but what point are you trying to make? If different results can be defended, and a “currently considered most likely” result can be selected, you still can’t conclude that the selected result was wished for ahead of time. My reading of the history of science is that there is *always* debate about new material, difference of opinion, plenty of scope for further testing and hypothesizing, and some particular “most likely” always exists, even if it’s in rapid flux.

How is this dishonest or inappropriate? It seems to me this is what you’d expect anytime the answer is not known before you start.

Comment #76252

Posted by Anton Mates on January 29, 2006 10:01 PM (e)

Ghost of Paley wrote:

Sell it to the hillbillies at Florida State, whose intrafamily squirrel tree makes do with a mountain beaver outgroup. Seems mighty undiverse to me.

I really shouldn’t be doing this now, but as usual, Ghost isn’t actually reading the papers he cites. That study used eleven outgroup species from the Muridae (true mice and rats), Dipodidae (jumping mice) and Aplodontidae (mountain beaver). The only outgroup they bothered to show on their tree was Aplodontia, because it turned out to be the most closely related:

“The single ML tree (Fig. 2; L¼)24,061.56 including outgroups) places Aplodontia as the outgroup to the Sciuridae, forming the Sciuroidea (note that, in all figures, muroid and dipodoid outgroups are removed for clarity).”

Comment #76255

Posted by Anton Mates on January 29, 2006 10:29 PM (e)

Not that, even if the FSU study had some horrible methodological flaw, that fact would somehow support Arnason et al. or refute the validity of phylogenetics or disprove common descent or cause Zombie Darwin to burst into flames or do whatever it is Ghost is aiming to do.

Flint:

If this is what you’re saying, OK, I understand, but what point are you trying to make? If different results can be defended, and a “currently considered most likely” result can be selected, you still can’t conclude that the selected result was wished for ahead of time. My reading of the history of science is that there is *always* debate about new material, difference of opinion, plenty of scope for further testing and hypothesizing, and some particular “most likely” always exists, even if it’s in rapid flux.

I believe he’s basically making a claim about convergence. Biologists–and of course scientists in general–expect their interpretations to converge over time as new data is found and old data analyzed more rigorously. As you say, there’s always debate, but one hopes that the bigger claims will one by one be settled, so that only the fine detail has to be resolved. GoP is arguing, I think, that the addition of new data has not and will not assist the convergence of biologists’ common descent models, because no such model is actually valid. Hence his prediction of star phylogenies–eventually biologists will be left saying, “Well, we don’t see any real relationships between any of these guys, and we can’t fit their similarities and differences into a hierarchical pattern, but we still assume they all descended from something.”

Of course even if that happened it would not provide positive evidence for the specific creation model provided by (interpretation X of translation Y of) the Bible, or whatever variant of that GoP supports. And the data he’s presented to support that claim are frequently misinterpreted or simply false. But to his credit, I think he is making a testable claim.

Comment #76267

Posted by Martin Brazeau on January 30, 2006 4:15 AM (e)

Ghost of Paley wrote:

I understand. I would find this explanation more convincing if there was a way to quantify this effect beforehand. Otherwise, the researchers can just fiddle with the outgroup and taxon density until they achieve the results they wish (not that I’m implying conscious cheating). But I’ll comment more on this later.

You chose to comment on my weakest point which was in fact only circumstantial. All it does is suggest a potential problem with the analysis, post hoc.

However, the lengthy plesions of lungfish, coelacanth, and bichir are predictably bad. They ‘fly solo’: unlike the other members of ‘bushier’ lineages, they’ve been evolving independently of their nearest sister taxa (no matter how you arrange the tree) for more than 400 million years.

The math behind this is pretty straight forward, the more taxa you have along a branch, the more state changes that can be reconstructed as ingroup transformations. The fewer taxa along a branch and the fewer changes you can interpret as novel to that particular branch. Wich 400 million years between lineages (each evolving independently for that time) the ability to detect convergence, divergence, and plesiomorphy become increasingly difficult. Most importantly, the amount of sequence divergence that can occur in that amount of time can erase synapomorphies.

That being said, I think rooting problems are probably inherent in the Arnason et al. study. I searched their coelacanth and lungfish sequences on the NCBI database. Appearing as highly significant alignments were, of course, coelacanths and lungfishes (generally preceded by only one or two odd ray fins). Tetrapods also ranked extremely high with frog and lizard sequences, ahead of any shark sequence (which never appeared on the first page). Such searches can help find very similar sequences and give you results suggesting taxa to include in your analysis - such as tetrapods.

Arnason et al. did not include tetrapods. I don’t know how many times I have to say it but that invalidates their study. This is not some arcane branch in the tree that may or may not affect the results. It is a large, diverse, well-sampled branch that will have important effects on the result.

Comment #76275

Posted by 'Rev Dr' Lenny Flank on January 30, 2006 7:52 AM (e)

How about a scientific theory of design, that isn’t empty of content, and can be tested using the scientific method. Is that “to come”? Or are y’all, uh, still working on that …?

When Luskin told us that there is a “positive case for design” that does NOT depend merely on “negative arguments against evolution”, was he just BS’ing us?

Still waiting, Ghost ….

(sound of crickets chirping)

Comment #76279

Posted by The Ghost of Paley on January 30, 2006 9:44 AM (e)

Anton Mates wrote:

I really shouldn’t be doing this now, but as usual, Ghost isn’t actually reading the papers he cites. That study used eleven outgroup species from the Muridae (true mice and rats), Dipodidae (jumping mice) and Aplodontidae (mountain beaver). The only outgroup they bothered to show on their tree was Aplodontia, because it turned out to be the most closely related:

I sure picked the wrong study to skim, didn’t I? Thanks for catching the mistake. My essential point stands: the authors stuck within one order (or even one suborder, by some rodent classification schemes). According to Mr. Brazeau, this should result in a funky tree. But the tree seems reliable enough. And yes, rodents are fecund and have quickly-evolving genomes. Doesn’t overturn my argument.

Comment #76302

Posted by Martin Brazeau on January 30, 2006 12:26 PM (e)

Ghost of Paley wrote:

I sure picked the wrong study to skim, didn’t I? Thanks for catching the mistake. My essential point stands: the authors stuck within one order (or even one suborder, by some rodent classification schemes). According to Mr. Brazeau, this should result in a funky tree.

How so? The FSU group had a decent outgroup size and few disparate ingroup taxa with deep independent lineages.

Comment #76306

Posted by Henry J on January 30, 2006 12:48 PM (e)

Re “(sound of crickets chirping)”

Yeah, but they’re still crickets!

(Ducking for cover.)

Comment #76311

Posted by The Ghost of Paley on January 30, 2006 1:24 PM (e)

Martin Brazeau wrote:

How so? The FSU group had a decent outgroup size and few disparate ingroup taxa with deep independent lineages.

So Arnason’s study (which used all three fish classes) was less diverse than the intraordinal squirrel study? How do you figure that? Or are you saying that the number of outgroups is the determining factor, even if the outgroups are closely related? If Arnason had sampled more lungfish, then would everything have been OK?

Comment #76317

Posted by The Ghost of Paley on January 30, 2006 2:27 PM (e)

Anton Mates wrote:

I believe he’s basically making a claim about convergence. Biologists—and of course scientists in general—expect their interpretations to converge over time as new data is found and old data analyzed more rigorously. As you say, there’s always debate, but one hopes that the bigger claims will one by one be settled, so that only the fine detail has to be resolved. GoP is arguing, I think, that the addition of new data has not and will not assist the convergence of biologists’ common descent models, because no such model is actually valid. Hence his prediction of star phylogenies—eventually biologists will be left saying, “Well, we don’t see any real relationships between any of these guys, and we can’t fit their similarities and differences into a hierarchical pattern, but we still assume they all descended from something.”

Yep, that’s pretty much what I’m saying.

Of course even if that happened it would not provide positive evidence for the specific creation model provided by (interpretation X of translation Y of) the Bible, or whatever variant of that GoP supports. And the data he’s presented to support that claim are frequently misinterpreted or simply false. But to his credit, I think he is making a testable claim.

Thanks for noticing. But wouldn’t star phylogenies provide positive evidence for multiple special creations?

Comment #76318

Posted by The Ghost of Paley on January 30, 2006 2:40 PM (e)

Reverend Jim wrote:

Still waiting, Ghost ….

(sound of crickets chirping)

Hey Lenny, didn’t you see my prediction earlier in this thread?

I predict that a heat map analysis would recover a star phylogeny for fish, and that a comprehensive study of all shared insertions would muddy the phylogenetic waters.

Let me guess: “I don’t see a prediction!”

Comment #76321

Posted by Anton Mates on January 30, 2006 3:52 PM (e)

Ghost of Paley wrote:

So Arnason’s study (which used all three fish classes) was less diverse than the intraordinal squirrel study? How do you figure that?

Diversity is relative. The FSU study mostly concerned relationships within the squirrel family, not the location of said family within the entire rodent order (although it did contribute some information towards that). No need to have highly unrelated outgroups like cats or alligators or something–indeed, they’d probably be less helpful because they wouldn’t give you a good idea of ancestral rodent characters.

And, as Mr. Brazeau said, the FSU study also had “few disparate ingroup taxa with deep independent lineages,” which is really an independent issue from the overall diversity of the entire taxon set.

Or are you saying that the number of outgroups is the determining factor, even if the outgroups are closely related? If Arnason had sampled more lungfish, then would everything have been OK?

? The lungfish weren’t the outgroup in the Arnason et al. study. Four species were–sea lamprey, lancelet, starfish and sea urchin. Outgroups are what you use to root the tree…you’re not usually expecting to get a reliable depiction of their internal patterns of descent, just using them to estimate the ancestral condition of your lineages of interest. You still need a decent number of them for the latter purpose, though.

But since the lungfish were a lineage of interest, yes, sampling more than one species as well as those of a diverse, well-stocked and probably closely-related clade–the tetrapods–is even more critical!

But wouldn’t star phylogenies provide positive evidence for multiple special creations?

Nope. Star phylogenies aren’t particularly strongly predicted under a multiple-creation model–presumably the Creator could poof new species into existence with a hierarchical pattern of similarities, or some other pattern, or none at all, as he/she/it pleased. Moreover there are alternate theories which could explain them even under a single-origin assumption–huge amounts of horizontal gene transfer in the past, for instance, or huge amounts of molecular evolution between speciation events. That’s already known to be a big problem when trying to make trees for prokaryotes, as mentioned in the Bapteste et al. study you cited; it’s not that biologists don’t believe their modern representatives got here by the usual evolutionary processes, but that those processes just don’t imply a nice tree-of-life in their case. Now of course we don’t think that’s as big a factor in, say, vertebrate evolution, but if everyone started getting star phylogenies they might have to reconsider.

If you wanted positive evidence for multiple creations, I think you’d probably have to find it in the fossil record and in geographical distributions of past and present taxa–just as Darwin used evidence from those same areas to support common descent in the first place.

Comment #76322

Posted by Martin Brazeau on January 30, 2006 3:54 PM (e)

Ghost of Paley wrote:

So Arnason’s study (which used all three fish classes) was less diverse than the intraordinal squirrel study? How do you figure that? Or are you saying that the number of outgroups is the determining factor, even if the outgroups are closely related?

Oh brother, the number of things wrong with this.

From the top:

First, I would think that the number of terminals in the analysis would be a better index of diversity, not the number of equally-ranked clades. Sampling from more higher level clades means more disparity, not necessarily more diversity. Of course, you already knew this because you’ve proven yourself to be such an expert thinker.

Secondly, the phrase ‘all three fish classes’ is simply Arnason et al.’s mistake re-stated. It assumes the correctness of the ‘fish typology’ as a natural group. However, there is ample evidence that tetrapods are descended from some ‘fish’ and that taxa of interest to us here belong along that branch.

No, I’m not saying that number of outgroups is the determining factor. Where do you get this from what I wrote? It was a comment on your bogus assertion that the FSU group used a single outgroup and that this was somehow relevant to my comments on the problems foreseeable in the use of an ancient and undiverse lineage as an ingroup taxon.

I think you still don’t understand what the problem is with Arnason et al. or with any molecular phylogeny that considers coelacanths, lungfishes, and bichirs. These lineages are undiverse. They’re disparate and they’re very ancient. By consequence they increase their probabilities of convergence, aquire deep degrees of dissimilarity (i.e. disparity - I never solely relied un the lack of diversity), and thus tend to have very few useful character states for phylogeny reconstruction.

Lungfishes compound this problem by having massive polyploid genomes that play havoc with our attempts to determine paralogous vs. orthologous sequences - truly orthologous genes are needed, when in fact there may be dozens of paralogs of any given gene in a lungfish genome. Huge genomes are also difficult to probe for good sequence material.

The analysis of the FSU team is nothing like the analysis of Arnason et al. and it is deeply misleading to compare them.

If Arnason had sampled more lungfish, then would everything have been OK?

If Arnason had more lungfishes or coelacanths from which they could sample, their problems would not have been as great. This is the point that you seem to miss time and again. We’re dealing with lineages that are not diverse (one genus of coelacanth, three lungfishes). We therefore cannot get better estimates of what the plesiomorphic state of the lineage was because we don’t have any ‘side branches’ of coelacanth or lungfishes. They have been evolving independently of each other for over 400 million years, that will add up to a lot of divergence. When dealing with sequence data the result can be considerable ‘overprinting’ of important characters.

Comment #76323

Posted by Martin Brazeau on January 30, 2006 3:57 PM (e)

Interesting but not surprising, Anton and I wrote pretty heavily overlapping responses.

By the way, I wanted to say this before, please call me Martin. “Mr. Brazeau” is way too formal.

Comment #76326

Posted by Anton Mates on January 30, 2006 4:49 PM (e)

Martin Brazeau wrote:

Interesting but not surprising, Anton and I wrote pretty heavily overlapping responses.

Heh, I wouldn’t have written if I’d known you were still bothering to respond. I’ve only ever taken a single cladistics course and have no plans to become an expert in the subject (although I’m dabbling in consensus algorithms). I just got on this thread in the first place to point out some inaccuracies in paper-citing! Of course since then there have been phylogenetic claims so badly wrong that even I can see the problem, and since I love to hear myself talk…

Incidentally, if you do ever have time to put together that “illustrated phylogeny of the sarcopterygii,” please drop a link on this thread. There are all sorts of lovely visuals for the dino-to-bird and ape-to-man transitional series in lay literature, but it seems to me that the lobefins get short shrift.

Comment #76329

Posted by Henry J on January 30, 2006 5:24 PM (e)

What’s a star phylogeny? Is that where several (more than two) lineages appear to have split off from their latest common ancestor at so close to the same time that we can’t distinguish the order of separation?

Henry

Comment #76338

Posted by The Ghost of Paley on January 30, 2006 6:12 PM (e)

Anton Mates wrote:

? The lungfish weren’t the outgroup in the Arnason et al. study. Four species were—sea lamprey, lancelet, starfish and sea urchin.

Yes, I know. I meant to say “lamprey” but had lungfish on the brain. But you guys know what I meant. My question remains, “Is there an objective way to determine the ideal outgroup a priori?” My argument will be, “No there isn’t.” I also intend to explore the latent circularity of the phylogenetic enterprise. Much more later.

Comment #76359

Posted by Steviepinhead on January 30, 2006 8:52 PM (e)

For those for whom this thread has gotten a little over-technical, or for those who would like some idea of what all the fuss is about, the December ‘05 issue of Scientific American had a good article on the fish ==> tetrapod transitional fossils, and the current phylogenies.

This appears to be a very active area of research, as well it should be. Scientists are learning more all the time about which environments were conducive to this kind of evolution, as well as refining the information available from already-retrieved specimens (several interesting fossils have been “discovered” in museum drawers, where they were languishing).

Both processes help bootstrap further research and fieldwork (knowing the kinds of environments these animals lived in helps to tighten up the not-yet-sampled locations and formations that might yield fossils; likewise, discovering a previously-unrecognized transitional fossil furnishes another clue, as the formation that produced it may be worth revisiting).

A mass of info has been uncovered in only the last decade or two–in the last year or two!–and there’s every reason to expect more exciting news about these critical critters!

Comment #76369

Posted by The Ghost of Paley on January 30, 2006 9:54 PM (e)

To see my latest response (it’s well worth the effort!), please go to the LUCA thread on “After the Bar Closes” (it’s on page 46). The software wouldn’t let me post here, so I had to transfer it. Sorry for the inconvenience, and obviously, leave all replies here.

Comment #76375

Posted by Anton Mates on January 31, 2006 1:25 AM (e)

Henry J wrote:

What’s a star phylogeny? Is that where several (more than two) lineages appear to have split off from their latest common ancestor at so close to the same time that we can’t distinguish the order of separation?

It’s basically the worst-case scenario of that, where we can’t say that any separation of lineages occurred before any other. It’s not formally a claim that they all diverged simultaneously–rather, it’s a statement that many wildly different possible patterns of divergence are judged equally likely or valid under your best-tree criteria (maximum likelihood, maximum parsimony, etc.)

As for what it actually implies–well, Martin can correct me on this. AFAIK it could mean they all did diverge simultaneously; or that you happened to pick uninformative characters or defined states badly; or that fast rates of molecular evolution between divergence events have rendered pretty much all characters uninformative; or that your best-tree criteria are ill-chosen. Or it could mean that the pattern of relationship among these lineages is not tree-like: maybe they were created separately, or maybe there was lots of horizontal gene flow. Phylogenetic trees are constructed under lots of assumptions, which makes them harder to trust without a lot of consensus and agreement with the fossil record–but the flip side of that is that when they look wacky, you’ve got a long way to go before you decide historical reality’s wacky too.

Comment #76386

Posted by Martin Brazeau on January 31, 2006 4:39 AM (e)

Anton Mates wrote:

Phylogenetic trees are constructed under lots of assumptions

Especially molecular ones. Methods such as Max. Likelihood, for instance, can correct for problems of long branch attraction, for instance. However, that depends greatly on selecting the correct model for your likelihood distribution. The wrong model will change the results dramatically.

Comment #76389

Posted by Martin Brazeau on January 31, 2006 5:53 AM (e)

I’ve got a test to write on Thursday. Will be back by the weekend. Sorry for the hiatus.

In the meantime…

Paley, explain for us why you are so confident in particular analyses. I don’t want to know why you prefer them. I want to know why you are so confident in the validity of their results.

For the record, please don’t synonymize my views on molecular phylogeny with Brinkmann et al. I don’t assert the same level of confidence in single analyses as you do.

Comment #76539

Posted by The Ghost of Paley on January 31, 2006 5:17 PM (e)

Here’s the link to my lost reply. It’s the third post down.

Martin wrote:

Paley, explain for us why you are so confident in particular analyses. I don’t want to know why you prefer them. I want to know why you are so confident in the validity of their results.

Eh? How can I explain my confidence in a particular study without outlining its strengths, i.e. stating a preference? I don’t understand the question. Perhaps Flint’s summary would help:

What Ghost is saying is, at the cutting edge of science, you would expect this sort of debate - very few of the results have come in yet, and those that have come in aren’t particularly reliable, so there’s lots of scope for debate.

Ghost’s point is that over the last decade or so, a very large amount of additional results have become available, adding a wealth of genetic and molecular analysis evidence to the existing morphological evidence. And yet these trees are NO CLOSER to resolved than they were before. Which lineages are included in the sample change the apparent relationships among other lineages. Different analytical techniques using the same data produce very different trees.

Ghost’s argument is that when a wealth of additional information becomes available, and when that information is a great deal more reliable, and we STILL can’t build trees any more robust than ever, maybe the problem is that our assumption of trees is wrong in the first place. We can’t produce good reliable trees because there are no trees to produce - the data stubbornly refuse to fit our wrong assumption.

Does this answer your question?

Comment #76675

Posted by Martin Brazeau on February 1, 2006 2:58 AM (e)

Ghost of Paley wrote:

Does this answer your question?

No, not at all. Re-read my question. I’ll get to your post on the weekend. I have a test tomorrow and I’m travelling back to Uppsala on Friday.

Comment #76689

Posted by Dean Morrison on February 1, 2006 4:21 AM (e)

Selective quotation from my good friend Flint only shows that you are sinking fast GOP. There is a hole in your Googletrawler perhaps?

Allow me to furnish this thread with the rest of what Flint had said, before GOP is allowed to sully Flint’s reputation:

..in continuation Flint wrote:

To which two counter-arguments have been presented over at PT. First, that there has indeed been a trend toward a solid consensus as more information comes in; the tree model seems to be working just fine. And second, that EVEN IF the tree model is wrong, this lends absolutely no positive support to the ‘poof’ model.

Ghost has at this point been reduced to claiming the consensus as to phylogenetic trees isn’t very solid, and for the good reason that God didn’t do it that way. Instead, God created ‘kinds’ that have been generally milling around their Platonic centers. And therefore attempts to find that one ‘kind’ evolved out of another is doomed to the kinds of problems cladists are suffering; they’re looking for what didn’t happen.

Now, if only we’d read the freepin’ BIBLE, we’d have known this all along and saved ourselves all this confusion and heartburn.

… puts a rather different light on Flint’s meaning don’t you think?

Comment #76797

Posted by The Ghost of Paley on February 1, 2006 1:49 PM (e)

The Yenta wrote:

Selective quotation from my good friend Flint only shows that you are sinking fast GOP. There is a hole in your Googletrawler perhaps?

Well it wouldn’t be a Paley thread without the Yenta throwing his considerable weight around. To answer the charge, the purpose of the quotation was to describe my position, not argue it. So Flint’s rebuttal was irrelevant. By the way, Mr. Martin, I really don’t understand your question. Could you please rephrase it? Thanks.

Comment #76813

Posted by k.e. on February 1, 2006 2:45 PM (e)

So Paley you don’t disagree with the rest of Flints quote? ….interesting

Comment #76841

Posted by Martin Brazeau on February 1, 2006 4:36 PM (e)

Ghost of Paley wrote:

By the way, Mr. Martin, I really don’t understand your question. Could you please rephrase it? Thanks.

I should have guessed that you wouldn’t. That seems to be the crux of the biscuit here.

You need to establish why you think a particular analysis ought to be a good estimate of phylogeny and why you think the conflicts actually amount to evidence against evolution. The effects of differential evolutionary rates, non-diverse taxa, disparate taxa, convergence, biased substitution models etc. have all been tested using models and can all lead to wildly varying estimates of phylogeny - even when the ‘true tree’ is known (because we modeled it). In short, our own methodologies are admittedly coarse and naive estimates of phylogeny that must always contend with an incomplete data set. Nobody expects them all to get the same answer all the time - especially where different data sets are used.

You need to determine why a particular analysis that you employ as evidence of internal contradiction is an unbiased estimate of phylogeny and why we ought to think of it as evidence of a true contradiction and not biases or the coarseness of our methodology.

For instance, you’ve cited taxon inclusiveness as a criterion, but the importance of the number of terminals tapers off when these added taxa belong to fairly stable monophyletic groups across analyses (i.e. tetrapods, teleosts, chondrichthyans). You can add as many tetrapods, teleosts, or chondrichthyans you want. It’s not going to change the reconstruction of character states at their basal nodes in the same way as it would if we had say 5 or 10 deep-branching lungfishes (that is lineages that came off during the Devonian or Carboniferous - which we don’t have).

You also need to judge the appropriateness of the data. Some types of molecules are used for higher-rank (i.e. phylum level) phylogenetic estimates while others are used for lower-rank (i.e. species or family level) estimates because of their degree of polymorphism. So, when a particular analysis sets out to test higher order interrelationships and uncovers lower order conflicts (or vice versa) are you taking such factors into account? If, given a particular data set, you equate the displacement of chondrichthyans with the displacement of an individual plesion such as a coelacanth you’re gravely mistaken.

There’s no rush in replying. I cannot write any lengthy responses to anything until the weekend.

Comment #77317

Posted by The Ghost of Paley on February 3, 2006 2:00 PM (e)

Martin wrote:

You need to establish why you think a particular analysis ought to be a good estimate of phylogeny and why you think the conflicts actually amount to evidence against evolution.

As you know, scientists screen genes for their reliability as phylogenetic markers before using them in a particular analysis; frequently used genes have already been certified kosher by Darwin. Researchers also use several stategies to combat varied mutation rates, hidden paralogy, and other problems. To no avail.

You also need to judge the appropriateness of the data. Some types of molecules are used for higher-rank (i.e. phylum level) phylogenetic estimates while others are used for lower-rank (i.e. species or family level) estimates because of their degree of polymorphism. So, when a particular analysis sets out to test higher order interrelationships and uncovers lower order conflicts (or vice versa) are you taking such factors into account? If, given a particular data set, you equate the displacement of chondrichthyans with the displacement of an individual plesion such as a coelacanth you’re gravely mistaken.

I still don’t think you understand my position. I realise that each molecule has its own strengths, weaknesses, and frame of reference. Highly conserved genes such as 18S rRNA wouldn’t be useful for resolving the chimp-human-gorilla trichotomy (although the squirrel study relies on heavily conserved c-myc exons and the N terminal variable regions of the RAG 1 gene to study intrafamily relationships! I guess any port in the storm of confusion known as Darwinism…..). Nevertheless, molecular studies do return highly significant values that clash with the body of knowledge accumulated by prior evo research, causing a net reduction of information. In this way science mirrors nature by demonstrating the implacability of God’s Second Law of Thermodynamics.

Comment #77325

Posted by Steviepinhead on February 3, 2006 2:32 PM (e)

Aaiiieee!,” shrieks The Thing Called Paley. “I’ve come to a curb! Measurements are inexact! It’s probably only six inches down, but how can we ever really know? And the far side of the street is, is, another inexact distance, one virtually unfathomable, given the multiple inexactitudes of measurement, the unreliability of instrumentation, the uncertainties of temperature, pressure, and the uncertain structural integrity of the untested materials that span the predatory void between this perilous curb and that other, possibly illusory mirage of an apparent curb, far over yon! Whatever is a poor pedestrian to do?”

Our knowledge about any situation is never going to be perfect, precise, or complete, Fading Fast. That doesn’t mean–to most of us–that we’re not entitled to do the best we can with what we’ve got.

But that’s okay, reality-wracked one! Stay at home with the cat ladies and the newspaper-collecting people.

While you wait for the firefighters to show up to pass you out your apartment window on a stretcher and take you away to a very safe place where you can be alone with the pristine forms that vibrate harmonically inside your head, the rest of us will just have to take our chances with that getting-somewhere-in-the-world-despite-reasonable-risks thing that we call life.

Comment #77328

Posted by k.e. on February 3, 2006 2:52 PM (e)

Stevepinhead
Paley is impervious to abstaction although I think he probably dreams of electric sheep. Good little robot.
I think the Grand Old Designer painted one of those bosons in the big bang with Paleys name just to remind everyonelse how lucky they were.
Oh thats right Paleys so smart that that silly boson could not have found life on earth I mean what if it ended up in a black hole ?
Soo he must have really got some dirt under his finger nails …….oh Calvin dinner now and don’t forget Hobbs!

Comment #77330

Posted by The Ghost of Paley on February 3, 2006 3:10 PM (e)

Vic wrote:

But that’s okay, reality-wracked one! Stay at home with the cat ladies and the newspaper-collecting people.

Good liberals, each and every one.

While you wait for the firefighters to show up to pass you out your apartment window on a stretcher and take you away to a very safe place where you can be alone with the pristine forms that vibrate harmonically inside your head, the rest of us will just have to take our chances with that getting-somewhere-in-the-world-despite-reasonable-risks thing that we call life.

Translation: Help me, Mr. Martin, the man with the big words and bad-talk is making my head hurt again! You pwomised to make him stop! :>)

k.e., how much if I add scones to my pumpkin spice latte?

Comment #77335

Posted by Steviepinhead on February 3, 2006 3:21 PM (e)

Attaboy, Paley! Though you’re still poised, paralyzed and trembling, above that perilous step, you’ve still got the cajones to launch your spittle at those walking by.

Who of course avert their heads, thinking, “Poor fellow! If only everyone had access to quality psychotherapy!”

Comment #77337

Posted by k.e. on February 3, 2006 3:22 PM (e)

Paley
How much? Oh 3 gods of the gaps …or bosons whatever you can’t imagine.
You know if you are having trouble with creation can I suggest the Kama Sutra?

Comment #77347

Posted by Henry J on February 3, 2006 3:58 PM (e)

Re “frequently used genes have already been certified kosher by Darwin”

And here I could’ve sworn that Darwin didn’t know about genes… ;)

Comment #77367

Posted by BWE on February 3, 2006 5:12 PM (e)

Ok, I you dragged me in again.

ghost wrote:
I saw the cladogram, but this does not represent the majority point of view, morphology-wise. I think a careful reading of Zimmer’s book will highlight the difficulty in the Lungfish/Amphibian transition; in fact, I think he makes the same point about lungfish skulls that my source does. In any case, check out the evo predictions prior to the molecular studies - it’s a classic case of an ad hoc adjustment to avoid falsification.

No. It’s a case of more evidence leading to more understanding. So, in the ID sciences, (I just made that up. I think I will continue to refer to the “ID sciences”) when you get more information (data) that leads to a better understanding of the flourishing field of Intelligent Design, you adjust your model until it gets better and better, right?

I’m pretty sure this is how it works. I mean, I really don’t contribute much to the “sciences” (although I do hope to someday collect my diaries into a book about how politics is related to research in my field) but I think I have a reasonable grasp of how it works in the universities: you look at empirical evidence- i.e. the universe is really, really big. You form a hypothesis- i.e. My dad is really big, so the universe must be like my dad. I want to name this new hypothosis after him but if I spell Dad backwards it doesn’t get me anywhere so I will use the next best thing: dog. I will name the concept after dog. I will spell it backward out of reverence to my dad who is really big too. So, now I have a new word, god, which means something like, “the universe is really really big like my dad.” I think the universe is like my dad.

So now I will look for evidence that would demonstrate that the universe is like my dad. ID. As I come up with more and more supporting data, I will refine my idea until I have either disproven my hypothesis or demonstrated that it seems to work. Let’s say that the evidence begins to point toward common descent of species (as the ID folks over at Uncommon descent are saying), then your hypothosis would now say that god includes common descent. So, you have refined your understanding of your hypothesis. Now, if your evidence showed that the universe is unequivically NOT like your dad, then you would have to abandon your hypothosis. But that is not what happened. The evidence does not disqualify your hypothesis so you can go on testing and refining away. In the case of this issue, the evidence does not disprove the hypothesis but it does refine our understanding of it.

Comment #77369

Posted by Arden Chatfield on February 3, 2006 5:18 PM (e)

frequently used genes have already been certified kosher by Darwin

I had no idea Darwin was Jewish

Comment #77373

Posted by Steviepinhead on February 3, 2006 5:28 PM (e)

Arden:

I had no idea Darwin was Jewish

…Only because you overlooked the part where Greenberg & Ruhlen placed Darwinism and Judaism together in the same super-family!

Comment #77391

Posted by Arden Chatfield on February 3, 2006 6:41 PM (e)

I had no idea Darwin was Jewish…

…Only because you overlooked the part where Greenberg & Ruhlen placed Darwinism and Judaism together in the same super-family!

You know, Ruhlen and Dembski are actually quite a lot alike, now that you mention it…

Comment #77678

Posted by The Ghost of Paley on February 5, 2006 3:33 PM (e)

To catch people up: my latest reply cites a fresh Arnason paper that sequences more lungfish in an effort to increase the Sarcopterygian diversity and thereby remove the spurious long branch attractions in the older study. He also includes plenty of tetrapods to create a potential source of synapomorphies for the modern sarcopterygians, while taking advantage of the phylogenetically friendly characteristics of entire mitochondrial DNA genomes. He even tosses in a few nuclear genes! Yet the results, as predicted, support Dembski’s ID model.

Comment #77682

Posted by Martin Brazeau on February 5, 2006 3:52 PM (e)

Ghost of Paley wrote:

Let’s review some complaints of the original Arnason study:

1) No tetrapods
2) Not enough lungfish/coelacanth species
3) Bad root, partly due to 1)

[…]

To address the first two points, let’s examine fresh studies. After making the very adjustments that Martin et al. demand, our dear Aranson finds that the results don’t improve

I’ll get to the tetrapods below. Let’s first address something that appears to be a bit of a repeated problem:

Without a time machine, you cannot correct #2. There are no more lungfishes or coelacanths. Three and one, that’s all we’ve got. Polypterids (bichirs and ropefish) are represented by similarly few lineages. There’s nothing you can do to add more of these, thus these long lineages will predictably have molecular sequences that are problematic for phylogenetic estimates.

As for #3, I never said anything about a bad root. You can’t have a bad root due to ingroup taxa. You’re spouting nonsense and once again making up arguments which I have not made. What I have said is that the lack of ingroup resolution is consonant with a series of plesions that do not properly polarize the major ingroup clade of coelacanths, teleosts, and chondrichthyans.

There is truth to the matter that agnathans are not a great ougroup (esp. where mtDNA is concerned), but there’s nothing we can really do about it. Unfortunately, the agnathans are a rather spindly lineage, like coelacanths and lungfishes. By consequence, they’re bound to create problems. Nevertheless, agnathans are the earliest lineage of vertebrates to appear in the fossil record. They are generalized in many aspects of their anatomy and they have a Hox complement that is intermediate between that of lancelets (indeed, almost any invertebrate if you wanted to get more general) and that of other vertebrates. They are, thus, the best outgroup we can rely on.

Finally, yes, they did include tetrapods. Certainly it does not acheive a result more consonant with the accepted gnathostome phylogeny. I will concede that the exclusion of tetrapods was not solely causing the strange result. But I never claimed that to be the sole cause of the problem, but a serious technical problem and one that invalidated the analysis for the purpose of our discussion.

Which leads to:

On the other hand, its nuclear DNA behaves better under the evolutionary whip. So should this organism be used? Depends on the researcher’s presuppositions.

Could you please define “the evolutionary whip”?

What happens with nuclear DNA, as opposed to mtDNA, is that it has less among site variation from one taxon to the next. This is suggestive of considerably less rate heterogeneity. This phenomenon is well known to cause conflicting results even with high bootstrap support.

By the way, Bichirs and ropefish were the basal piscines, leading to the oddly creationist mantra: “a tetrapod is a tetrapod, and a fish, a fish”.

Could you please tell me what a water-dwelling gnathostomous vertebrate with gills and fins is, if not a fish?

In case you didn’t notice (and I know that you did), they polarized against a agnathans - which are fish. Thus, this tree still optimizes the ancestor of tetrapods as a gnathostome fish.

As you know, scientists screen genes for their reliability as phylogenetic markers before using them in a particular analysis;

I didn’t ask if scientists did or did not do this. What I want to know is why you think that, at the end of an analysis, the only bias was our ‘evolutionary interpretation’. I want to know what makes you so sure that the authors have been so careful, that the data/methods do not share their own biases. All of this gets clarified below.

frequently used genes have already been certified kosher by Darwin.

Then how do you explain the fact that scientists publish these very same conflicting trees which you cite?

Researchers also use several stategies to combat varied mutation rates, hidden paralogy, and other problems. To no avail.

They do, and it is false to say that they are to no avail. The other thing you have to realize is that any type of compensatory model is is not always optimal in correcting for biases in the analysis. You should read Inferring Phylogenies by Joe Felsenstein to learn some more about how these methods actually work before assuming that they are even perfect representations of evolutionary theory, let alone as represntations of data. There are computational limits to how well these corrections can actually work. Many of them even assume prior knowledge of the correct model of evolutionary change - which we can seldom (if ever) know before hand.

The corrections certainly are not acheiving the standard that you would wish for them to acheive, but you still haven’t established an objective ground for that standard.

Your standard applies only if we’re dealing with the optimal and most complete data set. Unfortunately, we’re not dealing with such data. Even if I discount any assumptions about evolution, more taxa are extinct than are alive today. Our current sample is highly non-random. The current complement of organisms is not a random sample of all that has ever lived. It is, in fact, a heavily biased sample where selection and regional effects are involved. Then, if we even admit that evolution has happened, then we’re dealing with extremely long independent evolutionary histories, variation in rates, heterogeneity, saturation, and convergence. Then there are methodological and computational biases that I needn’t name here.

The methodologies are coarse and, by necessity, naïve in their approach to reconstructing phylogeny. Because they conflict here and there is hardly a strong argument. You can always find one tree that disagrees with another in the placement of anywhere from one to many taxa. But to use that as evidence of disasterous conflict requires that you ignore all other places where the topologies, in fact, agree.

To do this requires no great skill. As long as you’re only looking at conflicts (and not trying to explain the conflicts), you’re never going to notice how these trees in fact agree. You ignore countless other studies that are not published online but are covered in books (or, for that matter, you ignore the congruent clades and focus - rather uncrticially - on the conflicting nodes).

One fine example is the analysis of Zardoya and Meyer (1998, in Ahlberg, P.E. [ed.] Major Events in Early Vertebrate Evoltion, Taylor and Francis, pp. 135-155). Arnason et al. have largely ignored this study which demonstrates considerable among site variation in the mtDNA sets. Highly variable sites also corresponded with a high degree of ‘noise’ (i.e. conflicting signals) in the data set. As these highly variable sites were trimmed out, the resulting trees approached the more generally accepted tree. The high bootstrap values of Arnason et al is coming from sites with a low consistency index. That is, they are not coming from a clear signal in the data but by sites that are highly variable, calling into question the validity of that statistic in the analysis of mitochondrial DNA.

Arnason et al. may also encountering serious long branch problems. They did, however, use a variety of methods, including Maximum Likelihood which should correct for a lot of these problems (provided that they used the correct model - which we may never know).

In short: we know there are problems, we can diagnose those problems, and we in no way think that the task of phylogeny reconstruction is going to be problem free. The other point I’m trying to stress here is that there is no pretense (at least not on my part) that basal vertebrate interrelationships will not be problematic.

Comment #77687

Posted by Martin Brazeau on February 5, 2006 4:03 PM (e)

To catch people up: my latest reply cites a fresh Arnason paper that sequences more lungfish in an effort to increase the Sarcopterygian diversity and thereby remove the spurious long branch attractions in the older study. He also includes plenty of tetrapods to create a potential source of synapomorphies for the modern sarcopterygians, while taking advantage of the phylogenetically friendly characteristics of entire mitochondrial DNA genomes.

To catch up, I have a rather lengthy post that outlines why:

1) Three genera of (closely related) lungfishes cannot possibly undo the branch-length problems of lungfishes.

2) Indeed tetrapods were included, and I note that I had been wrong in diagnosing that as the major problem witht he analysis. To keep a balance, I should note here that Paley fails to note that they recovered consistent groupings of monophyly and paraphyly. Oh well! We can’t be bothered to cite results that disagree with our conclusions, can we?

3) Mitochondrial genomes are not ‘phylogenetically friendly’, but are rife with the sorts of characteristics that are predictably problematic. The clades and thier high bootstratp values in Arnason et al are supported by characters with low consistency index values and are thus highly contentious.

Comment #77689

Posted by steve s on February 5, 2006 4:12 PM (e)

Comment #77678

Posted by The Ghost of Paley on February 5, 2006 03:33 PM (e)

Yet the results, as predicted, support Dembski’s ID model.

If you’re ever in RTP, North Carolina, please stop by my apartment and give me a hit off that. You must have the really good stuff, like the Jamaican Blue Mountain of weed.

Comment #77690

Posted by BWE on February 5, 2006 4:24 PM (e)

http://www.dinofish.com/

martin wrote:
Without a time machine, you cannot correct #2. There are no more lungfishes or coelacanths.

Comment #77700

Posted by Russell on February 5, 2006 5:26 PM (e)

Yet the results, as predicted, support Dembski’s ID model.

Though I suspect GoP is a prankster playing the role of creationist-provocateur, I’ll bite. Where can I find “Dembski’s ID model” in sufficient detail to make any predictions at all?

Comment #77804

Posted by Martin Brazeau on February 6, 2006 3:33 AM (e)

BWE,

I meant in addition to the ones we’ve already got. I work on sarcopterygian fishes, I’m quite aware of what does/doesn’t live today. ;)

Comment #77849

Posted by The Ghost of Paley on February 6, 2006 10:37 AM (e)

Russell wrote:

Though I suspect GoP is a prankster playing the role of creationist-provocateur, I’ll bite. Where can I find “Dembski’s ID model” in sufficient detail to make any predictions at all?

Mind the mathematical thorns in this thicket and you’ll emerge with a firm grasp of Darwinism’s problems. Watch the Wizard skewer the jello of natural selection to the wall of disproof, leaving independent creation as the only viable alternative.

I’ll deal with Martin’s complaints a little later…

Comment #77853

Posted by Flint on February 6, 2006 11:06 AM (e)

Watch the Wizard skewer the jello of natural selection to the wall of disproof, leaving independent creation as the only viable alternative.

As usual, two errors here that cannot penetrate the creationist mindset. First, even if theory A is wrong, this doesn’t make theory B correct. Second, magic explains everything, without constraint, no matter what. As such, it’s not a ‘viable’ explanation of anything. It’s just another way of saying “I don’t know and I won’t admit it.”

This still leaves a question I don’t think I’ll ever be able to answer: To someone whose faith provides a one-size-fits-all answer to every possible question, WHY BOTHER trying to poke holes in competing explanations? Insecurity? Gamesmanship?

Comment #77863

Posted by k.e. on February 6, 2006 12:42 PM (e)

So Paley that ID Model of Dembski’s is the one where all of evolution and common descent is accepted, right? You should really catch up.

Dembski’s blog is saying that all living things are descended from living parents and no one has seen a living thing created from a non living thing.

Are you saying you have seen a living thing created from nothing ?
Or are you saying, you imagine a living thing created from nothing ?

Dembski supports neither of those arguments.

Comment #77870

Posted by Russell on February 6, 2006 12:59 PM (e)

GoP intimated that Dembski had some kind of “model” that made specific predictions about the phylogenetic relationships being discussed in this thread.

His response:

Mind the mathematical thorns in this thicket and you’ll emerge with a firm grasp of Darwinism’s problems. Watch the Wizard skewer the jello of natural selection to the wall of disproof, leaving independent creation as the only viable alternative.

First of all, I challenge anyone to extract any biological predictions at all from the cited papers, let alone specific predictions about phylogenies.

Second, I challenge anyone to find a single positive critique of those papers not written by a known creationist.

Give it up, GoP - you don’t really buy this crap any more than I do.

Comment #77881

Posted by The Ghost of Paley on February 6, 2006 2:04 PM (e)

The Wizard wrote:

To appreciate the significance of the No Free Lunch Regress in this latter sense, consider the case of evolutionary biology. Evolutionary biology holds that various (stochastic) evolutionary mechanisms operating in nature facilitate the formation of biological structures and functions. These include preeminently the Darwinian mechanism of natural selection and random variation, but also others (e.g., genetic drift, lateral gene transfer, and symbiogenesis). There is a growing debate whether the mechanisms currently proposed by evolutionary biology are adequate to account for biological structures and functions (see, for example, Depew and Weber 1995, Behe 1996, and Dembski and Ruse 2004). Suppose they are. Suppose the evolutionary searches taking place in the biological world are highly effective assisted searches qua stochastic mechanisms that successfully locate biological structures and functions. Regardless, that success says nothing about whether stochastic mechanisms are in turn responsible for bringing about those assisted searches. Evolving biological systems invariably reside in larger environments that subsume the search space in which those systems evolve. Moreover, these larger environments are capable of dramatically changing the probabilities associated with evolution as occurring in those search spaces. Take an evolving protein or an evolving strand of DNA. The search spaces for these are quite simple, comprising sequences that at each position select respectively from either twenty amino acids or four nucleotide bases. But these search spaces embed in incredibly complex cellular contexts. And the cells that supply these contexts themselves reside in still higher-level environments. As a consequence, the uniform probability on the search space almost never characterizes the system’s evolution. Rather, according to evolutionary biology, the larger environment bestows a nonuniform probability that brings the search (i.e., an assisted search) to a successful conclusion. This, in a nutshell, was Richard Dawkins’s (1996) argument in Climbing Mount Improbable: biological structures that at first blush seem vastly improbable (i.e., with respect to the uniform probability, blind search, pure randomness, call it what you will) become quite probable once the appropriate evolutionary mechanisms are factored in to reset the probabilities. Even if we accept the full efficacy of evolutionary mechanisms to evolve biological structures and functions, the challenge that displacement poses to evolutionary biology still stands. A larger environment bestows a nonuniform probability qua assisted search. Fine. Presumably this nonuniform probability, which is defined over the search space in question, splinters off from richer probabilistic
structures defined over the larger environment. We can, for instance,
imagine the search space being embedded in the larger environment, and such richer probabilistic structures inducing a nonuniform probability (qua assisted search) on this search space, perhaps by conditioning on a subspace or by factorizing product space. But, if the larger environment is capable of inducing such probabilities, what exactly are the structures of the larger environment that endow it with this capacity? Are any canonical probabilities defined over this larger environment (e.g., a uniform probability)? Do any of these higherlevel probabilities induce the nonuniform probability that characterizes effective search of the original search space? What stochastic mechanisms might induce such higher-level probabilities? For any interesting instances of biological evolution, we don’t know the answer to these questions. But suppose we could answer these questions. As soon as we could, the No Free Lunch Regress would kick in, applying to the larger environment once its probabilistic structure becomes evident. And so, this probabilistic structure would itself require explanation in terms of stochastic
mechanisms. On the other hand, lacking answers to these questions, we
lack a stochastic mechanism to explain the nonuniform probabilities (and corresponding assisted searches) that the larger environment is supposed to induce and that makes effective search of the original space possible. In either case, the No Free Lunch Regress blocks our attempts to account for assisted searches in terms of stochastic mechanisms. Evolutionary biologists at this point sometimes object that evolutionary mechanisms like Darwinian natural selection are indeed a free lunch because they are so simple, generating, as Richard Dawkins (1987: 316) puts it, biological complexity out of “primeval simplicity.” But ascribing simplicity to these mechanisms betrays wishful thinking. The information that assisted searches bring to otherwise blind searches is measurable and substantial, and discloses an underlying complexity (see section 4). Just because it’s possible to describe the mechanism that assists a search in simple terms does not mean that the mechanism, as actually operating in nature and subject to countless contingencies
(Michael Polanyi called them boundary conditions), is in fact simple.
A final question therefore presents itself, namely, Is it even reasonable, whether in biology or elsewhere, to think that the assisted searches that successfully locate small targets in large spaces should be conceived as purely the result of stochastic mechanisms? What if, additionally, they inevitably result from a
form of intelligence that is not reducible to stochastic mechanisms–a form of intelligence that transcends chance and necessity? The No Free Lunch Regress, by demonstrating the incompleteness of stochastic mechanisms to explain assisted searches, fundamentally challenges the materialist dogma that reduces all intelligence to chance and necessity.

This precludes evolution beyond the family level. More later.

Comment #77892

Posted by Russell on February 6, 2006 2:42 PM (e)

The Wizard wrote…

This is bull$#!t of such exquisite purity, I wouldn’t be surprised if it crystallized before my very eyes.

Two questions: (1) why the family level? What is there in that “argument” that would permit X amount of evolution, but not 2X? and (2) have you found any mathematicians or similarly qualified theoreticians - not known to be creationists - who have found any merit in Dembski’s ruminations?

Give it up Paley. You’re really Dave Cerrutti, prankster extraordinaire, aren’t you?

Comment #77901

Posted by k.e. on February 6, 2006 3:04 PM (e)

The Wizards wank
Blah blah all evolution is conjectural blah bla deny deny blah blah de Wizard don’t like it blah blah couldn’t happen because my mommy said so blah blah ….fundamentally challenges the materialist dogma that reduces all intelligence to chance and necessity.

7 out of 10 for ***sophism.
2 out of 10 for Sesquipedalian Obscurantism.: not nearly up to Denbski’s OR even Sal’s level.

Well Paley now we are getting somewhere.
If necessity is the mother of invention and hence intelligence and it came about by incremental change then why are you and wizard so damn dim ? You do realize sophism is just mental masturbation don’t you ? Have you any idea what circular reasoning IS ?

Oh that’s right you don’t know what IS is.

***
The essential claim of sophistry is that the actual logical validity of an argument is irrelevant (if not non-existent); it is only the ruling of the audience which ultimately determine whether a conclusion is considered “true” or not. By appealing to the prejudices and emotions of the judges, one can garner favorable treatment for one’s side of the argument and cause a factually false position to be ruled true.

The philosophical Sophist goes one step beyond that and claims that since it was traditionally accepted that the position ruled valid by the judges was literally true, any position ruled true by the judges must be considered literally true, even if it was arrived at by naked pandering to the judges’ prejudices — or even by bribery.

There is no hope for you Paley have you considered a career in ignorance? You have all the prerequisites.

Comment #77912

Posted by The Ghost of Paley on February 6, 2006 3:51 PM (e)

k.e. wrote:

7 out of 10 for ***sophism.
2 out of 10 for Sesquipedalian Obscurantism.: not nearly up to Denbski’s OR even Sal’s level.

So the second rating praises me, while acknowledging that even Dembski isn’t up to Dembski’s level.

Russell wrote:

Two questions: (1) why the family level? What is there in that “argument” that would permit X amount of evolution, but not 2X?

The huge environmental search space that natural selection must navigate in order to implement complex changes on multipart cellular systems. And since family-level evolution requires these multipart changes, this process is nearly impossible. Which, of course, prevents scientists from constructing consistently robust trees. Even Arnason would agree, although he would apparently draw a “kind” at higher taxonomic levels.

Comment #77942

Posted by Anton Mates on February 6, 2006 7:02 PM (e)

Martin Brazeau wrote:

Finally, yes, they did include tetrapods. Certainly it does not acheive a result more consonant with the accepted gnathostome phylogeny. I will concede that the exclusion of tetrapods was not solely causing the strange result. But I never claimed that to be the sole cause of the problem, but a serious technical problem and one that invalidated the analysis for the purpose of our discussion.

I’m actually not sure if they really did treat tetrapods properly in this later paper either. Before they worked on the data set for all taxa, they first found trees for tetrapods alone and for the paraphyletic “fish” alone; if they used those results to constrain their search on the total data set, wouldn’t that tend to bias their results toward that of the earlier study in which they ignored tetrapods completely?

I can’t tell whether they did use those results, though. They describe the final searches on the combined data set as “exhaustive,” but it seems to me a literal search of every possible tree topology and character state change placement is probably computationally out of the question here. More likely, I suspect, they swapped around large branches while keeping the internal topologies of those branches unchanged. What do you think?

Comment #77944

Posted by Anton Mates on February 6, 2006 7:07 PM (e)

The Ghost of Paley wrote:

The huge environmental search space that natural selection must navigate in order to implement complex changes on multipart cellular systems. And since family-level evolution requires these multipart changes, this process is nearly impossible.

Is “family-level evolution” your new name for “macroevolution” or something? Who told you “family” was a particularly significant taxonomic classification?

Comment #77965

Posted by Anton Mates on February 6, 2006 8:54 PM (e)

Well, thanks to GoP’s plug above I finally bothered to read some Dembski…and ouch. Elementary mathematical errors, the same old creationist “Isn’t it amazing that [a priori improbable event X from a huge space of similarly improbable events] occurred?” canard. No wonder other mathematicians pay no attention to this guy.

I mean, just look at this, from the “Searching Large Spaces” paper GoP linked to:

Intelligence acts by changing probabilities. Equivalently, intelligence acts by generating information. For instance, a slab of marble temporarily has a high probability of remaining unchanged. Then, without warning, Michelangelo decides to sculpt David, and the probability of that marble slab taking on a new form (i.e., receiving new information) now changes dramatically.

What in the world does that have to do with “intelligence”? You could remove Michelangelo and substitute a critical mass of uranium-235 and everything Dembski says would be equally true–that marble slab was going to sit aroud unchanged before, but hey, look, a nucleus just fissioned without warning and now the slab has a high probability of being vaporized shortly! Hell, the uranium nucleus is more intelligent than Michelangelo by Dembski’s definition–as far as we know the nucleus really does decay “without warning” and alter probabilities in a way we couldn’t have predicted beforehand, whereas an exhaustive analysis of Michelangelo’s brain might have let us predict his decision some time in advance.

As for mathematical errors, look at the following excerpt, from pages 5-6:

The prototypical example of an assisted search is an Easter egg hunt in which instead of saying
“yes” or “no” for each possible place where an egg might be hidden, one says “warmer” or “colder” depending on whether the distance to an egg is narrowing or widening.”

Later, he argues that for an assisted search to be more effective than a blind one, the set of responses (by the guy assisting you) should be mappable to the set {0,1}, where 0’s a miss and 1’s a hit–in other words, at minimum you should be able to determine from the response itself whether you’ve reached your target or not:

Since assisted search is supposed to augment the information inherent in blind search, the information function associated with an assisted search needs to contain strictly more information than is contained in the indicator function of the corresponding blind search. This strict increase in information can be characterized as follows: An information function j´strictly augments the information
in an indicator function j associated with a target T provided there is a function ϕ from Λ to {0, 1} such that ϕ ◦ j´= j and for any such ϕ there is no function ψ from {0, 1} back to Λ such that ψ ◦ ϕ ◦ j´= j

But this is trivially false in the very Easter egg hunt example he provided! Neither “Warmer” nor “Cooler” translates to a hit or a miss in itself…rather, you work out that you reached the target by moving a small distance in all possible directions and receiving the response “Cooler” every time. Of course that algorithm maps the “information function” (Dembski’s term for the function relating the location or sequence of location you suggested to your helper’s response) to the indicator function (the function relating the suggested location to {0,1} depending on whether it contains the target). But it does not map the range of one function into the other.

It’s really not hard to see why Dembski cut and ran from his scheduled appearance at the Dover trial. He would have been slaughtered.

Comment #77987

Posted by Henry J on February 6, 2006 10:54 PM (e)

Re [Dembski’s] “Intelligence acts by changing probabilities. Equivalently, intelligence acts by generating information.”

Really? Maybe his acts differently than mine, but my intelligence acts by causing my body parts to move in ways that produce the desire results, such as typing this sentence into the computer.

Henry

Comment #77996

Posted by Anton Mates on February 7, 2006 12:22 AM (e)

Flint wrote:

This still leaves a question I don’t think I’ll ever be able to answer: To someone whose faith provides a one-size-fits-all answer to every possible question, WHY BOTHER trying to poke holes in competing explanations? Insecurity? Gamesmanship?

Because, I think, no one lives that much by faith. If they did, they’d all sign up for the Omphalos argument–the universe looks like whatever it looks like, the scientists can say whatever they want, but it was really created six thousand years ago. But even the most die-hard Creationist recognizes deep down that the scientific method is just a formalization of how we all solve problems every day, and that its complete rejection leads not to religion but to nihilism.

Creationists want science. They just want to have the emergency option of disregarding bits of it if they’re too disturbing. I find that heartening, myself–there’s still hope for them.

Comment #78001

Posted by BWE on February 7, 2006 12:52 AM (e)

Dembski seems to have missed that there is a 100% probability of things ending up as they are.

Comment #78029

Posted by Martin Brazeau on February 7, 2006 4:22 AM (e)

Anton Mates wrote:

I’m actually not sure if they really did treat tetrapods properly in this later paper either. Before they worked on the data set for all taxa, they first found trees for tetrapods alone and for the paraphyletic “fish” alone; if they used those results to constrain their search on the total data set, wouldn’t that tend to bias their results toward that of the earlier study in which they ignored tetrapods completely?

I can’t tell whether they did use those results, though. They describe the final searches on the combined data set as “exhaustive,” but it seems to me a literal search of every possible tree topology and character state change placement is probably computationally out of the question here. More likely, I suspect, they swapped around large branches while keeping the internal topologies of those branches unchanged. What do you think?

Yes, their explanation of methods is a bit unclear. It is impossible to do exhaustive searches on data sets that large. They were, in fact, constraining topologies along the way. However, as far as I could tell, none of them were constraining a monophyletic Pisces. If they were constraining topologies, then a branch-swapping algorithm would be biased, but I don’t think it would be to the point of not recovering something closer to the preferred tree if the correct signal were there. You’d have to test it with a model.

There appears to be more than one problem with their analysis. It appears to be more of a problem with saturation, heterogeneity, and long branches. The highly heterogenous mitogenomic DNA doesn’t appear to be a very good candidate for resolving things interrelationships and the taxa we are dealing with are prone to causing problems. But Ghost still thinks that the addition of two lungfishes was the improvement I was looking for.

Indeed, there are problems with any phylogenetic analysis. The greatest difficulty is getting a rather coarse method to properly model evolution. This is computationally difficult. Perhaps impossible. The methods will always have problems and biases. It’s up to us to diagnose the potential problems and treat each analysis with caution and criticism (even when they support your preferred topology - the question is still ‘why?’). A tree diagram isn’t a phylogeny until we interpret it as such. Even then, that doesn’t make it true. We have to try to base our estimates of phylogeny on careful, analytical investigation. It must be done with a healthy respect for the potential biases and assumptions (as opposed to the “More! Bigger! Better! Bust!” approach of Ghost of Paley). Then, we are most justified in selecting our trees as phylogenies when they converge on independent data sets and are well-supported. Even this, however, must be provisional.

Comment #78069

Posted by Flint on February 7, 2006 10:05 AM (e)

ghost wrote:

The huge environmental search space that natural selection must navigate in order to implement complex changes on multipart cellular systems. And since family-level evolution requires these multipart changes, this process is nearly impossible.

Seems to me ghost is, unsurprisingly, assuming that the GOAL of all organisms was to reach the environmental space they now occupy. And the sheer unlikelihood of reaching those exact goals means it couldn’t have happened without Divine Assistance.

But ghost’s position evaporates as soon as we realize that ANY viable change, in ANY direction, is acceptable. Evolution doesn’t have any goal, it’s not constructing a search, change itself isn’t even required. He may as well argue that the “search space” available to water running downhill is so huge, the chances of rivers being exactly where they are and nowhere else shows it can’t possibly have happened without God’s help. And furthermore, if it’s so unlikely that any particular stream reached its “obvious goal” of being just where it is, imagine the odds against whole watersheds being just where THEY are. Nearly impossible.

It’s a boneheadedly silly error, but exactly the kind of error that’s almost unavoidable when you start with your conclusions and work backwards to make the evidence fit, especially when it does not.

Comment #78079

Posted by ben on February 7, 2006 10:29 AM (e)

The huge environmental search space that natural selection must navigate in order to implement complex changes on multipart cellular systems. And since family-level evolution requires these multipart changes, this process is nearly impossible.

It’s also “nearly impossible” for an individual photon to leave the sun, bounce off Jupiter, and land on my retina. But I look up, and there they are, photons that left the sun, having bounced off Jupiter, hitting my retina. From probability .0000000000000000000000001 to probability 1. The photon wasn’t trying to get to my retina…

Comment #78080

Posted by Wislu Plethora, FCD on February 7, 2006 10:50 AM (e)

Martin Brazeau:

You shouldn’t waste your time with GoP. Take a page from his book:

“Give not that which is holy unto the dogs, neither cast ye your pearls before swine, lest they trample them under their feet, and turn again and rend you.” Matthew 7:6

Comment #78085

Posted by BWE on February 7, 2006 11:20 AM (e)

Another look at intelligent design vs. evolution: In God’s book, the Bible, he says we can know him by his creation. At least 80 percent of scientists now believe in intelligent design, and some don’t even know the designer.

http://kennebecjournal.mainetoday.com/view/letters/2386085.shtml

Darn. And all this time I’ve been making fun of these guys. Seems the pendulum has shifted the other way. I’ll pack my bags and move over to the other camp now.

Comment #78115

Posted by k.e. on February 7, 2006 3:42 PM (e)

BWE ….and the Design Institute says ID has nothing to do with G-D …oh no 80% of Op Ed writers with the intelligence of a bee say so, so they must be right.

Well said Wislu Plethora;
Sucky science and sucky spirituality.
2 Things you won’t get from Creationists
The sermon on the mount, the plain and simple version of Christianity and plain common sense thought.
The bit they do get, and take to extreme, is the bit about ‘thou shalt not insult’ kind of fits right in with the Post Modernist concept of equal time for stupid ideas, not quite the same thing, but they don’t consider their ideas stupid.
Pity young JC didn’t have a sense of humor, but then when your on a radical and dangerous mission and so thin, there is little time for humor.

The dead hand of the irrational literalistic objectivist “The one true word of GodTM” and ass backwards thinking.

Anton you point out Creationists want science

Indeed at second glance the creationists ARE rational thinkers and more like “scientists” than we would care to admit. They realize that faith alone will never produce a live divine entity, that’s irrational right? And just what did their savior say ? Faith is just too subjective for them, they can’t compare it to any material thing. Faith MUST be material OR the language/law/consensus for describing reality must be changed to remove any firm significance for material nature itself. That is why they love Post Modernism.
Strange really, with the reliance feminism and pro choice had on PoMo one would think Creationism, a largely right wing political movement, would look askance at PoMo, but when one realizes that the fathers of PoMo were French Nazi collaborators who spent the rest of their lives rejecting any firm grip on reality (read conscience), it makes sense.
It used to be that 20% of the French believed in god and 60% in hell “la vie est merde”, the English translators completely missed the cultural context.
Sociologists like Steve Fuller, the token lefty riding shotgun for the Design Institute and Howard Ahmanson, gets a HEAP of free publicity to sell lots of books.
Fuller has come up with something even more ridiculous to get his moment of glory, some nonsense about denying sophism explained by….wait for it….pure sophism and science reality envy, stupidity never dies….. it just rents a new tuxedo.

Orwell would not have been the least bit surprised to see his Newspeak aped so perfectly by this current crop of obscurantists particularly the press who have no more idea than Paley and his fellow travelers, indulging in “Newspeak C Vocabulary” as though it were some fantasy foreign language from another planet, where not one thing is known about it in their own minds, even the color of the sky.

To them Myths are a LIE they just don’t,can’t,won’t do metaphor or even nuance. They deny it but they DO have metaphor, consider the the various wars on “nouns”.
And those Mythic tales echo the word wars and the people involved in them right to the present day not as a predictor of what will happen but as an insight into the mind of the actors. The Hydra is a perfect example complete with bad breath (that’s propaganda kids). Note that Hercules had to cut down an entire forest to cauterize the stump of each head he chopped off but even then the damn thing only retreated to the swamp (the collective human subconsciousness) to terrorize the villagers again at some future time. Those Greeks new a thing or two about human nature.

There is no subjective comparison that they are able to make between belief systems that carries any value since their life experience is so monotonous and devoid of historical meaning. I almost feel sorry for them.

The total beauty of the Fundamentalist mind set is to completely change reality in the believers minds and fix it on “The one true word of GodTM” they can then reject ANY authority that conflicts with their reality (and if you think I kid about their reality, get your heads around this, what they believe IS as REAL to them, as an actual ice-cream is to a kid)

To make their system work they MUST create a separate entity that removes their immediate responsibility to their own conscience and more importantly makes everyone else subservient to that divine entity. And guess what? THEY get to decide what that divine entity likes and dislikes, so all the dark little prejudices, irrational fears,pride,desire for power,desire for wealth and hubris get projected. The Greeks and Egytians had all this stuff mapped out and described in their underworlds, where do you think Dante got all his ideas from ?. He even recognised his friends in his version.

GoP and his little bunch each line up to take their place under Shiva’s foot AND they love it.

Each time they get rejected they repeat the age old martyrs glory, their humiliation CONFIRMS the Grand Old Designer is really there WAITING for them to give them each their eternal holiday at Club Med or 72 virgins, GUARANTEED rest and glory in the afterlife.

No different to that Easter Islander, who listening to the retelling of the one true word of whatever, hacked the last tree down to move his statue so it could watch over and ensure the return of his ancestors. A worldview completely unmoderated by any firm grasp of the consequences in the here and now because introspection is postponed, at least until your neighbor wants to eat you, because there is no wood left to make canoes for fishing.
Dembski postponed his own judgment at Dover because he knew what the outcome would be. He knows, as any sane person does, that there is nothing “over there” to recon with guilt, how can you be guilty after you are dead ? Better to have an ‘imaginary after life friend’ who as the good book says will redeem all those nasty doubts and inject…ah wash …er dip you in rapture after all the dirty work is done down here.
Those guys give rapture a bad name, its something you ‘get’ in the here and now.
The same old side show alley, roll up roll up get your rapture here, at gun point if necessary.

Oh by the way (giggle) what is the collective noun for sophists

A pride of sophists

Comment #78329

Posted by The Ghost of Paley on February 8, 2006 2:57 PM (e)

Martin wrote:

We have to try to base our estimates of phylogeny on careful, analytical investigation. It must be done with a healthy respect for the potential biases and assumptions (as opposed to the “More! Bigger! Better! Bust!” approach of Ghost of Paley). Then, we are most justified in selecting our trees as phylogenies when they converge on independent data sets and are well-supported. Even this, however, must be provisional.

And how do we weight these “potential biases”? Mitochondrial DNA was supposed to be an ideal molecule given its lack of recombination and the fact that it traces a matrilineal line of descent. To be sure, mitochondral mutation rates can be up to an order of magnitude higher than the average nuclear rate and also exhibit base pair bias, both factors contributing to saturation, but these problems aren’t intractable. The main problem seems to be mtDNA’s inability to derive the correct phylogeny.

Anton Mates: In the future, please don’t confuse analogies with math. The Wizard is not interested in hand-waving.

Comment #78413

Posted by The Ghost of Paley on February 8, 2006 8:08 PM (e)

Martin wrote:

Without a time machine, you cannot correct #2. There are no more lungfishes or coelacanths. Three and one, that’s all we’ve got. Polypterids (bichirs and ropefish) are represented by similarly few lineages. There’s nothing you can do to add more of these, thus these long lineages will predictably have molecular sequences that are problematic for phylogenetic estimates.

An untestable assertion, of course.

As for #3, I never said anything about a bad root. You can’t have a bad root due to ingroup taxa. You’re spouting nonsense and once again making up arguments which I have not made. What I have said is that the lack of ingroup resolution is consonant with a series of plesions that do not properly polarize the major ingroup clade of coelacanths, teleosts, and chondrichthyans.

But a bad root can sometimes distort ingroup relationships, so I thought you were fretting over this issue as well. It’s something to discuss at any rate.

Could you please define “the evolutionary whip”?

Just a cute way of saying that lamprey’s mitochondrial genomes have a way of jerking lungfish around.

Your standard applies only if we’re dealing with the optimal and most complete data set. Unfortunately, we’re not dealing with such data. Even if I discount any assumptions about evolution, more taxa are extinct than are alive today. Our current sample is highly non-random. The current complement of organisms is not a random sample of all that has ever lived. It is, in fact, a heavily biased sample where selection and regional effects are involved. Then, if we even admit that evolution has happened, then we’re dealing with extremely long independent evolutionary histories, variation in rates, heterogeneity, saturation, and convergence. Then there are methodological and computational biases that I needn’t name here.

The methodologies are coarse and, by necessity, naïve in their approach to reconstructing phylogeny. Because they conflict here and there is hardly a strong argument. You can always find one tree that disagrees with another in the placement of anywhere from one to many taxa. But to use that as evidence of disasterous conflict requires that you ignore all other places where the topologies, in fact, agree.

But then how can evos use these trees to check morphological analyses? Even when molecular trees don’t clash, they often contradict other lines of evidence (see the Afrotheria hypothesis v. recent fossil discoveries, for instance). Contra Theobald, we must discard molecular trees as potential evidences for common descent until we work out the kinks. Too bad - it looked promising there for a while….

Comment #78420

Posted by Steviepinhead on February 8, 2006 8:32 PM (e)

Sigh.

Pasty-Face, do the concepts “baby” and “bathwater” have any meaning in Bizarro World?

By now, the answer’s pretty obvious to both of us (though only one of us will admit it):

That every molecular tree can’t yet be confidently and consistently connected in deep time, due to the kinds of technical and evidential difficulties that Martin Brazeau has kindly explained and that EctoSpasm keeps trying to mangle and confuse, does not mean that hundreds and thousands of valid trees cannot be constructed, nor does it mean that these trees cannot be of immense assistance to us in working out any number of interesting issues in evolutionary biology.

Yeesh.

Comment #78423

Posted by Flint on February 8, 2006 8:51 PM (e)

Ghost’s line of argument sounds eerily familiar: It’s imperfect. Therefore it’s wrong. Therefore something devoid of any evidence whatsoever must be right. Which just happens to be what my religion teaches.

Still, I gotta admit that the extent Ghost is willing to go to convince himself that his evidence-free foregone conclusions are superior to 99.9% of the evidence is impressive. He digs awful hard to find a speck of verisimilitude here and there, tuning out all else, and living in a world barren of understanding, but finding it better than a world rich in *wrong* understanding. A shame some people can’t sue their parents for crippling them for life.

Comment #78448

Posted by Anton Mates on February 8, 2006 11:47 PM (e)

The Ghost of Paley wrote:

Anton Mates: In the future, please don’t confuse analogies with math. The Wizard is not interested in hand-waving.

Hey, don’t look at me…it’s Dembski that thinks his hand-waving analogies amount to actual mathematical research. Possibly more mathematicians would agree with him if not for undergraduate-level errors like the one I pointed out above.

Martin wrote:

Without a time machine, you cannot correct #2. There are no more lungfishes or coelacanths. Three and one, that’s all we’ve got. Polypterids (bichirs and ropefish) are represented by similarly few lineages. There’s nothing you can do to add more of these, thus these long lineages will predictably have molecular sequences that are problematic for phylogenetic estimates.

An untestable assertion, of course.

Not at all. It’s testable by modeling, by population genetics studies and by comparison to non-molecular data. That’s why Martin said “predictably.”

Contra Theobald, we must discard molecular trees as potential evidences for common descent until we work out the kinks. Too bad - it looked promising there for a while….

Dang! If only Zombie Darwin had known that those molecular trees he used to convince everybody of common descent were unreliable…

Comment #78571

Posted by Martin Brazeau on February 9, 2006 3:49 PM (e)

Ghost of Paley wrote:

The main problem seems to be mtDNA’s inability to derive the correct phylogeny.

Right, and when it doesn’t derive the correct phylogeny, we see that it is supported by noisy characters. Sorta what you’d expect when…

Ghost of Paley also wrote:

mitochondral mutation rates can be up to an order of magnitude higher than the average nuclear rate and also exhibit base pair bias, both factors contributing to saturation

The methods that can be used to ‘correct’ this also require assumptions about the correct model of substitution and the problems of applying the methodly uniformly to a whole tree that is supposed to, in fact, reflect heterogenous rates of evolution.

Okay, that’s it. Seriously. I’m done. Sorry, but I really don’t have time for this any more. I’ve got a course and I’ve got some major revisions to the direction of my thesis that I have to make (sorry GoP, I’m not including any ID ;-) )

Comment #78637

Posted by The Ghost of Paley on February 9, 2006 5:33 PM (e)

Martin wrote:

Okay, that’s it. Seriously. I’m done. Sorry, but I really don’t have time for this any more.

That’s OK, I need to focus on other things too. Maybe one day we’ll have time to discuss the fossils.