Panderichthys rhombolepis

| 230 Comments
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)

230 Comments

Of Panderichthys and People!

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?

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?

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

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?

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.

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.

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?

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

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.

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!

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.

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

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?)

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.

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?

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.

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?

Syntax Error: not well-formed (invalid token) at line 19, column 93, byte 2093 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

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)

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 …?

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.….

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

Syntax Error: not well-formed (invalid token) at line 23, column 201, byte 2689 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

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

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!

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!!!!!

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.

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

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.

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.

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?

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?

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.

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

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.

Dembski seems to have missed that there is a 100% probability of things ending up as they are.

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.

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.

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…

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

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.c[…]386085.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.

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

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.

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.…

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.

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.

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…

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 ;-) )

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.

About this Entry

This page contains a single entry by PZ Myers published on December 22, 2005 10:49 AM.

KQED radio appearance at 9 am PST was the previous entry in this blog.

Boy, they *really* don’t get it is the next entry in this blog.

Find recent content on the main index or look in the archives to find all content.

Categories

Archives

Author Archives

Powered by Movable Type 4.361

Site Meter