Musings from the mind of a mouse

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Casey Luskin is such a great gift to the scientific community. The public spokesman for the Discovery Institute has a law degree and a Masters degree (in Science! Earth Science, that is) and thinks he is qualified to analyze papers in genetics and molecular biology, fields in which he hasn't the slightest smattering of background, and he keeps falling flat on his face. It's hilarious! The Discovery Institute is so hard up for competent talent, though, that they keep letting him make a spectacle of his ignorance.

I really, really hope Luskin lives a long time and keeps his job as a frontman for Intelligent Design creationism. He just makes me so happy.

His latest tirade is inspired by the New York Times, which ran an article on highlights from the coelacanth genome. Luskin doesn't think very deeply, so he keeps making these arguments that he thinks are terribly damaging to evolution because he doesn't comprehend the significance of what he's saying. For instance, he sneers at the fact that we keep finding conserved elements in the genome, because as we all know, there are lots of conserved elements.

Hox genes are known to be widely conserved among vertebrates, so the fact that homology was found between Hox-gene-associated DNA across these organisms isn't very surprising.

Stop, Casey, and think. Here's this fascinating observation, that we keep finding conserved genes and conserved regulatory regions between mice and fish, which ought to tell you something, and your argument against a specific example is that it isn't rare? It really tells you something when your critics' rebuttal to a piece of evidence is that you've got so much evidence for your position that they're tuning out whenever you talk about the detais.

This is Luskin's approach to every example given in the NY Times article: 'Yeah? So? There are homologous genes all over the place!' I think Luskin might just live forever, which thrills me to pieces. He could get into a running gun battle with a mob from Answers in Genesis, be riddled with bullets, and he'll just point to a nick in his ear and say, "Yeah, so? This one didn't kill me!" and then dismiss all the other wounds because they're so common that no one should care any more. It is truly the logic of immortals.

The specific example he's addressing in his dismissal of Hox conservation, though, is a region of DNA that may play a role in mammals in the formation of the placenta. Luskin pooh-poohs the relevance of this observation by highlighting what we don't know, rather than the evidence at hand.

The authors aren't sure exactly what this particular segment of DNA does, though it's probably a promoter region. In mice the corresponding homologous region is associated with Hox genes that are important for forming the placenta. Ergo, we've solved the mystery of how the placenta evolved. Right?

Not really. Again, all that was found was a little homologous promoter region in Hox-gene related DNA in these two types of organisms. Given that we don't even understand exactly what these genes do or how they work, obviously the study offered no discussion of what mutations might have provided an evolutionary advantage. No evolutionary pathway was proposed, or even discussed. So there's not much meat to this story, other than a nice little region of homology between two shared, functional pieces of Hox-gene-related DNA. But of course, such shared functional DNA could be the result of common design and need not indicate common descent or Darwinian evolution.

He's right that this genetic sequence does not "solve the mystery" of the placenta, but then the authors of the original sequence analysis paper do not claim that it does. There's a lot that we don't know about the translation of any genetic sequence into a morphological feature, but that doesn't mean we know nothing — the paper is talking about stuff that we actually learned from comparing the genomes of different organisms.

We have identified a region of the coelacanth HOX-A cluster that may have been involved in the evolution of extra-embryonic structures in tetrapods, including the eutherian placenta. Global alignment of the coelacanth Hoxa14-Hoxa13 region with the homologous regions of the horn shark, chicken, human and mouse revealed a CNE just upstream of the coelacanth Hoxa14 gene. This conserved stretch is not found in teleost fishes but is highly conserved among horn shark, chicken, human and mouse despite the fact that the chicken, human and mouse have no Hoxa14 orthologues, and that the horn shark Hoxa14 gene has become a pseudogene. This CNE, HA14E1, corresponds to the proximal promoter-enhancer region of the Hoxa14 gene in Latimeria. HA14E1 is more than 99% identical between mouse, human and all other sequenced mammals, and would therefore be considered to be an ultra-conserved element. The high level of conservation suggests that this element, which already possessed promoter activity, may have been coopted for other functions despite the loss of the Hoxa14 gene in amniotes

What they are saying is that they found a region of DNA that is remarkably highly conserved between coelacanths and humans, and that among them are Conserved Non-coding Elements (CNEs), DNA that is not translated into proteins but instead is likely to be important in switching genes off and on. What they found is that this switch is linked to a particular gene, Hoxa14, in the coelacanth which is completely absent in mammals…but the switch still exists, but is now coupled to a gene associated with the formation of extra-embryonic membranes, like the placenta.

The key point is the known information: this snippet of DNA is highly conserved across all vertebrates, but the gene it is associated with has decayed in sharks and disappeared entirely in tetrapods. The question is how the switch has persisted: Luskin's preferred explanation is that God spliced this particular piece of DNA into every vertebrate species; the scientific explanation is that it shows a pattern of shared history, and that its role is conserved in tetrapods because it has found a novel function in regulating a different gene.

So far, this is nothing but Luskin-levels of ignorance and incomprehension. Let us now dive deep into Luskin-levels of outright stupidity and dishonesty.

The paper includes this diagram of the evolutionary relationships of various vertebrate species.

vertebrate phylogeny diagram

These are the relationships determined by comparisons of large portions of the entire genomes of these organisms — it's a phylogeny based on a large amount of data. Luskin obligingly simplifies it for us:

vertebratephylogeny_simplified

The closest relative to us tetrapods are lungfish, with coelacanths more distant, and teleosts further still. This is the consensus. It's supported by many comparisons.

But brace yourself: here's where Luskin proves that he's an idiot. He sets aside the synthesis of large data sets, and instead explains that if we look at single genes, evolution is proven wrong!

He read the paper and found a couple of examples interesting genes that were highlighted by the authors themselves. In particular, they cite examples of gene losses. All other vertebrates have a component of the immune system, a gene called immunoglobulin M (IgM), but coelacanths are unusual in lacking this particular gene. There's another immune system component, IgW, which seems to be a relatively primitive or ancestral immunoglobulin, which we tetrapods lack, and which is also missing in teleosts, but is found in coelacanths and sharks.

So what does Luskin do? He redraws the whole vertebrate phylogeny based on a single gene. He throws away almost the entire data set, and focuses on a single character.

vertebratephylogeny_igw

But in an IgW-based tree, tetrapods should be much more closely related to goldfish than to the coelocanth or the lungfish. That's startling and unexpected -- if you're a proponent of common descent.

Holy crap. That's simply a lie. No: if you look at individual genes, this is exactly what we expect to see, and we're completely unsurprised. Every single gene is not expected to change in lockstep with speciation events, and each lineage can experience the loss of subsets of genes independently of the larger clade. What Luskin is claiming is utterly contrary to everything any evolutionary biologist will tell you.

Here's the original phylogeny from the Amemiya paper. I've just added a couple of arrows to indicate simple events in the history of the IgM and IgW genes.

phylogeny with IgW, IgM highlighted

The simplest, most parsimonious explanation is that IgM and IgW were present in the last common ancestor of all of these organisms. The IgW distribution in extant forms is explained by two independent gene losses, one in the ancestor of all tetrapods and another in the ancestor of all teleosts. The IgM distribution is explained by a unique loss in the ancestor of the two modern species of coelacanths. This is trivial and totally unsurprising, requiring no magic, no all-powerful designer, and no processes other than known natural mechanisms of mutation.

Luskin, however, finds this improbable.

Of course this requires some extremely unparsimonious and unlikely events. Since IgW is found in vertebrates as diverse as lungfish and cartilaginous fish (e.g., sharks), a Darwinian evolutionary view would infer that the gene for IgW was present in the ancestor of all jawed vertebrates. If so, then IgW must have stuck around in vertebrates long enough to end up in the sarcopterygian line. But somehow evolutionary theory must explain why tetrapods and all teleosts lack this gene.

"Unparsimonious"? You keep using that word. I don't think it means what you think it means.

The evolutionary explanation requires three mundane events, the simple loss of a gene in an ancestral population.

The Intelligent Design creationist explanation requires that every extant species was specifically and intentionally stocked with a set of genes hand-chosen by a designer. God magically inserted IgM into each vertebrate species, except that he missed the coelacanths, and he magically inserted IgW into each and every shark, ray, coelacanth, and lungfish, but he intentionally left them out of every tetrapod and teleost.

And Luskin chooses to lecture biologists on the meaning of "parsimonious"? That's startling, but entirely expected from the frauds at the Discovery Institute.

117 Comments

Thanks Casey for once again proving that you are either a dishonest charlatan or an ignorant know nothing science wanna be, or both.

Once again, exaptation proves to be a major evolutionary mechanism. Once again, the evolution of a new function for an existing sequence is uncovered. Once again cladistics and parsimony provide a consistent phylogenetic perspective. Once again, GODDIDIT fails completely to explain the pattern seen in nature.

Don’t you just love the age of comparative genomics?

“He could get into a running gun battle with a mob from Answers in Genesis, be riddled with bullets, and he’ll just point to a nick in his ear and say, “Yeah, so? This one didn’t kill me!” and then dismiss all the other wounds because they’re so common that no one should care any more. It is truly the logic of immortals.”

Great!

“He could get into a running gun battle with a mob from Answers in Genesis, be riddled with bullets, and he’ll just point to a nick in his ear and say, “Yeah, so? This one didn’t kill me!” and then dismiss all the other wounds because they’re so common that no one should care any more. It is truly the logic of immortals.”

“‘Tis but a scratch… It’s just a flesh wound!” (The Black Knight, Monty Python and the Holy Grail)

Tirade?

You mean that squeaking?

Glen Davidson

Paul Burnett said:

“He could get into a running gun battle with a mob from Answers in Genesis, be riddled with bullets, and he’ll just point to a nick in his ear and say, “Yeah, so? This one didn’t kill me!” and then dismiss all the other wounds because they’re so common that no one should care any more. It is truly the logic of immortals.”

“‘Tis but a scratch… It’s just a flesh wound!” (The Black Knight, Monty Python and the Holy Grail)

Yes. I have often thought arguing with creationists is exactly like dueling the Black Knight.

Maybe, since ID proponents don’t like being called “creationists”, we should call them Black Knights.

The public spokesman for the Discovery Institute has a law degree and a Masters degree (in Science! Earth Science, that is) and thinks he is qualified to analyze papers in genetics and molecular biology, fields in which he hasn’t the slightest smattering of background, and he keeps falling flat on his face. It’s hilarious!

Par for the course amongst young Earth creationists.

Some don’t even have any scientific background whatsoever.

I find it amazing that so many of them are dentists, medical doctors, and mechanical/electrical engineers.

If Luskin doesn’t know what he’s talking about, then why don’t his comrades-in-arms come to his aid, e.g., Sternberg, Behe, Witt, Wells, Meyer, et. al and correct his errors, show him where he’s wrong? Oh, wait, they’re all stupid, sorry.

Aside: I still recall when Luskin posted his class notes from college to try to prove that he actually attended class!

Paul Burnett said:

“He could get into a running gun battle with a mob from Answers in Genesis, be riddled with bullets, and he’ll just point to a nick in his ear and say, “Yeah, so? This one didn’t kill me!” and then dismiss all the other wounds because they’re so common that no one should care any more. It is truly the logic of immortals.”

“‘Tis but a scratch… It’s just a flesh wound!” (The Black Knight, Monty Python and the Holy Grail)

Long before Monty Python brought us the Black Knight, there was Al Capp’s wonderful character Fearless Fosdick who was a parody of the square-jawed and utterly humorless cartoon detective Dick Tracy.

And before Fearless Fosdick there was the father of them all, Dr. Pangloss.

Hey! The image in that cladogram bears a strong resemblance to Luskin. Do you see it? It’s the one below and to the right of the Homo sapiens.

Mr Luskin is famous and a great asset to all of creationismdom because he does a great job of analysis of evolutionary biology. Mr Myers says he is not knowledgable in biological fields because he just got a degree in earthy sciences. First let this rule RULE in all origin discussions. How many times are creationists told scientists, in their billions, agree with evolution and that should persuade the rest of us! Indeed evolutionists should only score actual researchers/degree holders when asserting authority.

Yet independent people can study these things too. Mr Luskin is a intelligent man and so easily can understand the principals here of biological evolutionary claims. These are weighty subjects. lets all play by the same rules.

Go play somewhere else Robert. Leave the science to the professionals. Let this rule RULE.

Robert Byers said:

Mr Luskin is famous and a great asset to all of creationismdom because he does a great job of analysis of evolutionary biology. Mr Myers says he is not knowledgable in biological fields because he just got a degree in earthy sciences. First let this rule RULE in all origin discussions. How many times are creationists told scientists, in their billions, agree with evolution and that should persuade the rest of us! Indeed evolutionists should only score actual researchers/degree holders when asserting authority.

Yet independent people can study these things too. Mr Luskin is a intelligent man and so easily can understand the principals here of biological evolutionary claims. These are weighty subjects. lets all play by the same rules.

Can you (PZ) send Booby Byer’s inane babblings to the BW (along with the rest of his poop-stains), before the rest of this informative thread gets train wrecked? Please.

Honestly, I don’t want Byers to be banned or sent to the BW. He’s golden.

Byers says the things that creationists really think, but that most of them are too cunning and dishonest to say out loud.

But Byers just blurts it out. Like Casey Luskin has spent eight years of his life whining, “ID is not creationism!”

But Byers blurts out what creationists really know:

Byers wrote:

Mr Luskin is famous and a great asset to all of creationismdom because he does a great job of analysis of evolutionary biology.

Golden. That stuff is worth a lot to our side.

He’s like a Zen master of creationists. He writes these little Zen koans of anti-science.

Think, P.Z., think!!! “Cooption” and “switches” are intelligent tools. Darwinism doesn’t switch anything on and off and it doesn’t coopt anything. It can’t. It possesses no ‘abilities’. It has no goals. Mutations are random in relation to function, remember? (tell that to those starving lizards).

Darwinism is all about performing a self-lobotomy. It only works when you stop thinking. Only Darwinism can speak from both sides of its mouth, at once denying intelligence yet in the same breath, utilizes intelligent concepts to get the job done.

Evolution coopted? Evolution switches hox genes on and off? Well, I’ll be damned. Evolution is intelligent after all!!!!

P.Z., it’s a brave new world where intelligence is not about having a brain stem. Could you possibly wrap your intelligence around that idea?

Steve P. said: Darwinism is all about performing a self-lobotomy. It only works when you stop thinking. Only Darwinism can speak from both sides of its mouth, at once denying intelligence yet in the same breath, utilizes intelligent concepts to get the job done.

And yet

Net contribution of creationism to science = 0

Net contribution of intelligent design to science = 0

Net contribution of goddidit to curing disease, increasing crop yields, inventing the internet, reaching the moon, finding the higgs boson, developing the iphone, reducing emissions from automobiles, or explaining why the sky is blue = 0

Net scientific comprehension of Steve P. = 0

RPST said:

Steve P. said: Darwinism is all about performing a self-lobotomy. It only works when you stop thinking. Only Darwinism can speak from both sides of its mouth, at once denying intelligence yet in the same breath, utilizes intelligent concepts to get the job done.

And yet

Net contribution of creationism to science = 0

Net contribution of intelligent design to science = 0

Net contribution of goddidit to curing disease, increasing crop yields, inventing the internet, reaching the moon, finding the higgs boson, developing the iphone, reducing emissions from automobiles, or explaining why the sky is blue = 0

Well actually far less than zero for those things, owing to thousands of year of neanderthal thinkers like Steve P not only hating science, but actively working to obstruct and discredit it.

I’m currently marking Political Science essays from a group of my Chinese students; Robert, I’m sorry to have to be the one to tell you this, but I think they could be more persuasive in constructing a defense of creationism than you.

“because he just got a dgree in earthy sciences.” Please see me!

“Please see me, so you too can spell ‘degree’.” Boy is my face red.

Stevie PP the mindless troll blurts a self refuting piece of crapulence:

“Think, P.Z., think!!! “Cooption” and “switches” are intelligent tools. Darwinism doesn’t switch anything on and off and it doesn’t coopt anything. It can’t. It possesses no ‘abilities’. It has no goals. Mutations are random in relation to function, remember? (tell that to those starving lizards).”

Think Stevie, think!!! INtelligence doesn’t need to coopt anything, it can start from scratch. Only evolution is constrained to use what is already there.

How in the world can something that is “random” never switch anything on or off? If it’s “random” this would have to happen some of the time. Indeed, the only way to avoid it would be for some “intelligence” to actively prevent this from happening. And of course you have no answer whatsoever for all of the observations that it actually has happened, such as cecal valves in lizards. You just close your eyes, put your hands over your ears and shout “intelligence” at the top of your lungs, all the while showing a distinct lack of intelligence yourself.

How about poker Stevie? Can you get a royal flush from the deal alone without having to draw any cards? What “intelligence” was involved in that? There is clear molecular evidence that the promoter was coopted by random mutation and took on a novel function. If you want to argue differently you will have to read the paper and come up with a better explanation for the evidence. And of course, as usual, you will have to explain why your “interpretation” is better than the one that the writers, reviewers and editors proposed and why an untrained science illiterate knows better. Until you do, your uninformed opinion is, as usual, completely worthless. Good luck.

Time for another dump to the bathroom wall. It’s best to keep Stevie and Bobby isolated from decent society.

Robert, you are right, of course, that PZ is or would be mistaken, in so far as his (counter-)argument was or would be based on an argument from authority. And you are also right, naturally, that laymen can grasp the principles at issue here, and that Luskin’s lack of a degree in evolutionary biology consitutes no grounds for a dismissal of his claims. This argument from authority, however, insofar as one could claim that it was one, was not an essential element of PZ’s discussion, it was merely a rhetorical introduction with a few fireworks, fit (or not) for a web discussion. It would serve your cause much better if you would substantially confront and refute PZ’s arguments, showing them to be insufficient in the face of the available evidence and as compared with Luskin’s argumentation. This is surely why you are confronted with the admitedly unfortunately crass reception here on the Thumb.

Think Stevie, think!!! INtelligence doesn’t need to coopt anything, it can start from scratch. Only evolution is constrained to use what is already there.

Does “Intelligent Design” have anything to say about the creatures which preceded the ones with the “intelligently designed” features?

How did the pre-design creatures manage to survive without the design features? Where did those pre-design creatures come from: Were they created in a form in which they needed some added design?

RPST said:

Net contribution of creationism to science = 0

Net contribution of intelligent design to science = 0

Net contribution of goddidit to curing disease, increasing crop yields, inventing the internet, reaching the moon, finding the higgs boson, developing the iphone, reducing emissions from automobiles, or explaining why the sky is blue = 0

Net scientific comprehension of Steve P. = 0

I developed the concept of negative knowledge shortly after my first exposure to high school students in a particularly benighted area of the country: You’re better off NOT knowing something, and knowing that you don’t know it. You’re worse off if what you know is WRONG. Then you have to UNLEARN the wrong things, or learn that they are wrong.

That can be psychologically traumatizing if the wrong ‘facts’ were ‘learned’ from trusted parents or other authority figures–or if the ‘facts’ are seen as foundational to your religion.

If you’re ignorant of something, all you have to do learn the facts. If you’re WRONG about something, you first have to be convinced that you’re wrong (if that’s even possible), then learn the actual facts.

In developing facility in speaking, and particularly in writing, the English language, I always found that a student from a foreign country, with NO English background, was much easier to teach (and usually ended up way ahead of) a monolingual English student who had grown up learning “bad” (or nonstandard) English. The new immigrant only had to learn standard English. The native had to unlearn all ingrained bad habits before he could replace them with ‘proper English’.

Creationism is the most pernicious of negative knowledge. It’s not just wrong or harmful only to the individual creationist. In its proselytizing and activism it harms others.

A more basic misunderstanding than creationism is the idea that common sense is sufficient to understand science. Most modern scientific advances involve abstract concepts. Creationism employs “common sense” notions as substitutes for the abstractions required to fully grasp evolution.

Those who rely on “common sense” are gullible to pseudoscientific ideas in general of which creationism is a specific example.

Les Lane said:

A more basic misunderstanding than creationism is the idea that common sense is sufficient to understand science. Most modern scientific advances involve abstract concepts. Creationism employs “common sense” notions as substitutes for the abstractions required to fully grasp evolution.

Those who rely on “common sense” are gullible to pseudoscientific ideas in general of which creationism is a specific example.

On the other hand, why would it be “common sense” to have the assumption that one knows more about science than the scientists, themselves?

Why would people assume they know more than scientists?

From the standpoint of those of us who are fluent with at least some of the abstractions this is an obvious violation of common sense. From the standpoint of those who don’t deal with abstractions they’ll tell you right upfront (examples in this comment train) - scientists are ignoring common sense. There’s a divide which can’t be crossed w/o basic understanding of science.

Steve P. said:

Think, P.Z., think!!! “Cooption” and “switches” are intelligent tools. Darwinism doesn’t switch anything on and off and it doesn’t coopt anything. It can’t. It possesses no ‘abilities’. It has no goals. Mutations are random in relation to function, remember? (tell that to those starving lizards).

Darwinism is all about performing a self-lobotomy. It only works when you stop thinking. Only Darwinism can speak from both sides of its mouth, at once denying intelligence yet in the same breath, utilizes intelligent concepts to get the job done.

Evolution coopted? Evolution switches hox genes on and off? Well, I’ll be damned. Evolution is intelligent after all!!!!

P.Z., it’s a brave new world where intelligence is not about having a brain stem. Could you possibly wrap your intelligence around that idea?

Perhaps Steve P. would like to explain the Old Faithful geyser. It “switches” on and off in a relatively predictable pattern. Since “switches” are intelligent tools, then some intelligence must have created Old Faithful, and continues to switch it on, and off. Or tornados. They “switch” on, then off again. Certainly tornados are intelligently designed. Or lightening. Lightening certainly “switches” on, then off, quite suddenly and unpredictably. Prior to Ben Franklin (or thereabouts), people knew with 100% certainty (by faith alone), that gods caused lightening to “switch” on. Lightening was known to be of intelligent origin. Or stars. Stars “switch” on and off at night, sometimes quite rapidly. Certainly there must be an intelligent winker at work most nights. Or planets. Planets “switch” directions from prograde to retrograde in the night sky on a regular basis. Certainly there must be an intelligence moving the planets around the sky, especially in such predictable ways.

Anywhere there is a “switch”, there must be an intelligent Switcher.

Right Steve?

Les Lane said:

A more basic misunderstanding than creationism is the idea that common sense is sufficient to understand science. Most modern scientific advances involve abstract concepts. Creationism employs “common sense” notions as substitutes for the abstractions required to fully grasp evolution.

Those who rely on “common sense” are gullible to pseudoscientific ideas in general of which creationism is a specific example.

I would disagree to some extent, at least to the extent that Creationism has anything to say about reality. I think the difficulty has more to do with Just Bob’s comment prior to yours. The basic concepts of Evolution (in particular) really aren’t that difficult to understand; “Common Sense” really does suffice; IF you haven’t started with the “negative knowledge” of Creationism.

Now, understanding the details of Evolution (or of any science) certainly requires “abstract concepts.” Discovering new things in science certainly requires “abstract concepts.”

But the beauty of most science is that it makes sense. There’s a consistency and logic to it. (Outside of Quantum Mechanics, of course. :-) If someone can explain the basics to you, in most cases “common sense” is good enough to get the gist of what’s going on, and to understand the next piece of evidence in the chain of reasoning; even to predict the next link in the chain. The Scientific “common sense” tells us that all things are connected, that we can predict things from prior knowledge, that the world is knowable.

Take plate tectonics, for example. Once you’ve accepted the idea that rock is ductile and can move over great spans of time, the rest just makes “common sense”. Well, of course that’s how mountains are made. Duh! Of course that’s where earthquakes come from. Of course that’s why layered rocks look all wavy and folded. Once you see the big picture, it becomes “obvious”.

As Just Bob so cogently observes, the problem with the “negative knowledge” of Creationism, is that its basic “common sense” is wrong in the first place, and has to be unlearned. The problem with Creationism is that it doesn’t have any consistency or logic to it. Why is something the way it is? Because that’s how God wanted to make it. Or because of the Fall. Or because I told you so, that’s why. There’s no way to reason from one bit of Creationist “knowledge” to another. “Common sense” in the Creationist sense is useless, except to recognize everything as God’s handiwork, and (as such) as something mysterious and essentially unknowable. Creationist “common sense” tells us that the world is a bunch of unconnected “facts”, that nothing can be predicted from prior knowledge, and that reality is what some authority figure tells us is true. Back to Les Lane’s point, for the Creationist “common sense”, any crackpot pseudo-science is as good as any other.

That seems to be the “negative knowledge” of Creationism. The “common sense” of Creationism is that the world is mysterious and random and ultimately unknowable, and so why do you even bother trying to understand it? Why do you keep asking me “why”? Maybe that’s one reason why Creationism envies the trappings of Science. At some basic gut level Science just “makes sense”. Creationism only wishes it had that level of consistency and explanatory and predictive power.

And this bears repeating:

RPST said: Net contribution of creationism to science = 0 Net contribution of intelligent design to science = 0 Net contribution of goddidit to curing disease, increasing crop yields, inventing the internet, reaching the moon, finding the higgs boson, developing the iphone, reducing emissions from automobiles, or explaining why the sky is blue = 0

I’ve said the same myself, but RPST’s is beautifully concise. I might suggest a further equation:

Net POTENTIAL contribution of intelligent design to science (even if we accepted it) = 0.

I think we’re dealing with stage 1 of the 4 stages of competence (otherwise known as the Dunning-Kruger effect.) At this stage of competence (prescientific outlook) one accepts what one’s told (often negative knowledge) and is confident that other ideas are wrong.

joaozinho666 said:

John Harshman said: I think I can safely say that nobody here gets your point.

I’m having trouble believing you. I think that you are more intelligent than that. Doc Bill, not so much…

Start believing. Even after all your explanations, I still don’t understand your complaint, which seems to be morphing. You should consider the possibility that nobody here is stupid and that the problem is that you’re ironically (in view of your complaints about PZ) very bad at communicating your ideas.

Are you perhaps some kind of transformed cladist?

No, I’m a molecular geneticist who finds that PZ sucks at educating the public. Your hypersensitivity and evasions suggest that you agree to at least some extent.

No hypersensitivity, no evasions, and certainly no agreement. It’s just that you suck at educating the public. Again, I still don’t know what you’re trying to say. I don’t think you have any idea how to go about educating the public.

How is calling Fig. 1 a phylogeny helping IDiots?

Because it’s a perfect tool for educating the public about the sequence evidence, and the IDiots have chosen to fix their attention on it, serving it up on a platter. It’s a hanging curve ball and you’re whiffing at it.

It’s completely unclear what you want PZ to do and what errors he’s made.

How do assumptions about the nature of evolutionary transitions fit a design hypothesis,

I didn’t claim that they did, and I think you know that. I pointed out that none of the analytical tools that were applied to the data–the basis of your silly claim that Fig. 1 is an interpretation–preclude the use of the graphed data in Fig. 1 to test any sort of IDcreationist hypothesis.

Please stop accusing me implicitly of lying. None of my uncertainty is feigned. You have failed repeatedly to make your point clear. One could of course use the data to test other hypotheses. But that has nothing to do with what PZ is talking about. You apparently wish he had taken the opportunity to argue against separate creation. (I say “apparently” because you still haven’t managed to say anything clearly.) But that isn’t what the DI is talking about, it wasn’t what the original paper was about, and it wasn’t what PZ’s complaint was about. Why should every post be about creationism?

Further, calling the tree in Figure 1 “graphed data” is just absurd. The tree is an estimate of phylogeny given various assumptions about the evolutionary process. It was produced by testing a variety of possible trees and accepting the one that made the observed data most likely to have been observed. (Or, in a Bayesian MCMC framework, accepting the tree around which the search spent the most time.) This can in no way be characterized as a graph of the data. While I’m not quite sure what you mean by “an interpretation”, the tree is an inference from the data. It happens to be much more strongly supported than other potential inferences from the data. If you wanted to test some hypothesis of separate creation, you could easily do so as long as you had first created a model of separate creation and thus had some way of determining the fit of that model to the data. But nobody did that and it isn’t a matter in immediate contention.

…except to the extent that any possible data fit a design hypothesis given an omnipotent and capricious designer? And if that’s the case, what empirical predictions can their hypotheses possibly make?

Precisely! But PZ and you are pissing away this perfect tool for a public political debate by calling the data interpretation, which is precisely what they want you to do.

I don’t recall anyone calling the data interpretation, so you are complaining about a nonexistent error. Perhaps you will explain what you mean at some point, but I’m not sanguine. I think you may be incapable of it.

Go back and look at the figure from a didactic POV. It includes ONLY the organisms an uneducated layperson (the target of the IDiots) is concerned about. There’s nothing superfluous. It’s an absolutely perfect point of entry to the sequence evidence, and Luskin has already called attention to it. I don’t think I could find a better example, and here it is being served up on a platter.

But you and Doc Bill seem to put your tender egos far above thinking about public education strategies.

Again, no idea what you think ought to be done or what the problem is. I hypothesize that you may be saying we ought to be hyping this tree as evidence for common descent. Is that it? But why must every discussion be for the purpose of convincing creationists that there is common descent?

dalehusband said:

Ray Martinez said:

I am a Paleyan Creationist who has read Luskin extensively. The first and only thing I notice about his Discovery Institute apologetics is the fact that they are literally filled with cheap lawyer rhetoric from top to bottom. Said rhetoric, of course, insults intelligence. Of course Luskin has a law degree and is a lawyer. His writings will never stand up to scrutiny. Luskin, like all illegitimate axe-grinding revisionists, only understands the temporary here-and-now “success.” I predict future historians and scholars will dismiss and disregard everything he writes.

You are right. But ALL Creationist claims and the writings based on those claims are much the same way, including most of your lame comments around here. If you had any sense of integrity you would not be a “Paleyan Creationist” (what does that even mean?) because there is simply no reason to be one. But you clearly do not. You are an extremist who backstabs even people like Casey Luskin who would make great allies of yours. And that means no one should trust or respect you on any level.

A backstabbing charge presupposes that I and Luskin are on the same side. We are not on the same side. I am a Paleyan Creationist/IDist and he is a Discovery Institute IDist. The latter does not base its claims on Paley 1802, but mainly on the claims of Behe and Dembski. Both Dembski and Behe accept Darwin’s main claim (natural selection) to exist in nature, as well as microevolution and conceptual existence of macroevolution and common descent. I, like Paley, reject the concept of evolution existing in nature; species remain immutable because Naturalism assumptions, interpretive philosophy, and Darwinian evolution are completely false.

So, Luskin and company are on your side and in your bed, not mine in any way, shape or form. Just be glad that you’re on top.

snaxalotl said:

luskin has been down this path before on the issue of the human/chimp/gorilla tree, where his wordy arguments ultimately relied on a subtle insistence that ANY genes that disagreed with the calculated phylogeny rendered that phylogeny impossible. although it represents a refusal to acknowledge the obvious mechanisms by which genes can defy the larger pattern, this seems to have become a very useful crutch in terms of the ratio of what he can claim compared to how much integrity he needs to concede. clinging to that one plausible-sounding tool of the impossible single gene relationship doesn’t seem to require much reality-suppressing mental anguish, compared to the number of “winning” claims he is able to generate from it

However, in this case Luskin is NOT constructing a phylogeny by aligning a single gene. I don’t know what that would produce. Rather, he is arguing that the PRESENCE or ABSENCE of a single gene should be used to form a phylogeny. PRESENCE or ABSENCE of a single gene is basically one bit of information, YES or NOW– perhaps 1,000 or 1,500 times less information that you would get by aligning a single gene.

His argument is analogous to saying: the pika has no tail. Humans have no tail. If you form a phylogenetic tree based on the PRESENCE OR ABSENCE of a tail, yes or no, then humans are closer relatives to pikas than to monkeys. That’s his logic.

Luskin has on many occasions argued that phylogenies must only be based on single genes, because if they’re based on just one gene, you sometimes construct slightly different trees.

Lawyer Luskin’s argument is to stand in the laboratory door and order the scientists: “Stop looking at so much data, you guys! Use less data! Use less data!”

Ray Martinez said:

dalehusband said:

Ray Martinez said:

I am a Paleyan Creationist who has read Luskin extensively. The first and only thing I notice about his Discovery Institute apologetics is the fact that they are literally filled with cheap lawyer rhetoric from top to bottom. Said rhetoric, of course, insults intelligence. Of course Luskin has a law degree and is a lawyer. His writings will never stand up to scrutiny. Luskin, like all illegitimate axe-grinding revisionists, only understands the temporary here-and-now “success.” I predict future historians and scholars will dismiss and disregard everything he writes.

You are right. But ALL Creationist claims and the writings based on those claims are much the same way, including most of your lame comments around here. If you had any sense of integrity you would not be a “Paleyan Creationist” (what does that even mean?) because there is simply no reason to be one. But you clearly do not. You are an extremist who backstabs even people like Casey Luskin who would make great allies of yours. And that means no one should trust or respect you on any level.

A backstabbing charge presupposes that I and Luskin are on the same side.

Let’s see - Luskin’s masters want to replace reality-based science and evolution with willful ignorance and endless bleatings about the Xtian Magical Sky Pixie;

YOU want to replace reality-based evolution and science with willful ignorance and different endless bleatings about the SAME Xtian Magical Sky Pixie.

You, the IDiots and creationuts are on the same side, Ray; you are merely on different teams.

Since you have the same goal, differences in rhetoric and approach are irrelevant. You and the IDiots are like two rabid dogs after the same bone - you spend as much time biting and scratching at each other as you pursuing your goal.

Loons can always recognize how silly and ridiculous the rantings of OTHER loons are, but are unable to recognize how stupid and ridiculous they themselves are.

We are not on the same side. I am a Paleyan Creationist/IDist and he is a Discovery Institute IDist. The latter does not base its claims on Paley 1802, but mainly on the claims of Behe and Dembski. Both Dembski and Behe accept Darwin’s main claim (natural selection) to exist in nature, as well as microevolution and conceptual existence of macroevolution and common descent. I, like Paley, reject the concept of evolution existing in nature; species remain immutable because Naturalism assumptions, interpretive philosophy, and Darwinian evolution are completely false.

In other words, you are all deranged f*ckwits, but they accept a bit more of reality than you do.

One reason Dembski and Behe accept natural selection to exist in nature is BECAUSE IT EXISTS IN NATURE; one would have to be mind-numbingly STUPID to claim it doesn’t exist. The claim is so ludicrous that it would drive most of their paying imbeciles away.

Another reason is by accepting the reality of natural selection they have more things to misrepresent and lie about. All the sciency-sounding terms they throw around can sound impressive to anyone ignorant of the last half century of biological discoveries.

Reality-based folk have known that species are mutable for centuries Ray. If you weren’t so willfully stupid, you’d realize that immutability has testable effects.

IF living things were truly immutable, there would be no birth defects (caused by mutations). No drug resistant bacteria. No herbicide resistant plants. No insecticide resistant bugs. No new variations in anything. There would be no such thing as mutagens, and radiation would have no long term effects.

Examination of REALITY shows that birth defects and variations occur. Bacteria evolve drug resistance at an alarming rate. Weeds become immune to herbicides, and new pesticides have to be developed because all the old ones stop working because the insects evolved resistance. Many chemicals are known mutagens, and radiation causes mutations.

Now Ray farts out one of his homophobic parting insults before he runs away, screaming of his victory :

So, Luskin and company are on your side and in your bed, not mine in any way, shape or form. Just be glad that you’re on top.

No Ray - creationuts, IDiots and theoloons like yourself are all in the same cesspit, and all of you are pretending that it is the OTHER guy that stinks.

John Harshman said: No hypersensitivity, no evasions, and certainly no agreement.

It’s crystal clear that you tacitly conceded my point about the graph in Fig. 1 being analogous to claiming that a Michaelis-Menten graph isn’t data because it doesn’t include the spec readings.

It’s just that you suck at educating the public.

That could be, but I was under the impression that I was discussing this with people who view themselves as sophisticated enough to educate the public here.

It’s completely unclear what you want PZ to do and what errors he’s made.

Accepting an opponent’s dishonest framing for starters.

But that has nothing to do with what PZ is talking about.

PZ isn’t talking about the right thing.

But that isn’t what the DI is talking about, it wasn’t what the original paper was about, and it wasn’t what PZ’s complaint was about. Why should every post be about creationism?

Why should any intelligent person who purports to educate the public accept the framing of a liar like Luskin?

Further, calling the tree in Figure 1 “graphed data” is just absurd.

Yet you tacitly conceded that my analogy was correct. Or is a Michaelis-Menten plot not “graphed data” because it involves various assumptions about enzymology?

The tree is an estimate of phylogeny given various assumptions about the evolutionary process.

If you insist on calling it a phylogeny, it’s also a phylogeny in the mind of any intelligent Designer. It’s still a graph of the data either way.

While I’m not quite sure what you mean by “an interpretation”, the tree is an inference from the data.

No, your calling it a phylogeny of ORGANISMS is the inference. At best it’s a phylogeny of a limited sample of sequences, and still just data. You might recall that there are professional disagreements about whether the length of the branch leading to the coelacanth (the data) was properly interpreted by the authors. But I think your ego is clouding your memory.

I don’t recall anyone calling the data interpretation, so you are complaining about a nonexistent error.

The data are sequences. You called it a phylogeny of ORGANISMS. That’s interpretation. You can’t teach laypeople about this if you can’t grasp this distinction, man!

Again, no idea what you think ought to be done or what the problem is. I hypothesize that you may be saying we ought to be hyping this tree as evidence for common descent. Is that it?

Yes, but note that your hypothesis means that you were indeed lying when you claimed to have NO idea, Dr. Pedantic.

But why must every discussion be for the purpose of convincing creationists that there is common descent?

It’s not about every discussion, it’s about this one, because scientists have utterly failed to spotlight the sequence evidence to date. Here, Casey Luskin is spotlighting it for you but falsely reframing it, and you and PZ are accepting Luskin’s false framing.

PA Poland said:

Ray Martinez said:

dalehusband said:

Ray Martinez said:

I am a Paleyan Creationist who has read Luskin extensively. The first and only thing I notice about his Discovery Institute apologetics is the fact that they are literally filled with cheap lawyer rhetoric from top to bottom. Said rhetoric, of course, insults intelligence. Of course Luskin has a law degree and is a lawyer. His writings will never stand up to scrutiny. Luskin, like all illegitimate axe-grinding revisionists, only understands the temporary here-and-now “success.” I predict future historians and scholars will dismiss and disregard everything he writes.

You are right. But ALL Creationist claims and the writings based on those claims are much the same way, including most of your lame comments around here. If you had any sense of integrity you would not be a “Paleyan Creationist” (what does that even mean?) because there is simply no reason to be one. But you clearly do not. You are an extremist who backstabs even people like Casey Luskin who would make great allies of yours. And that means no one should trust or respect you on any level.

A backstabbing charge presupposes that I and Luskin are on the same side.

Let’s see - Luskin’s masters want to replace reality-based science and evolution with willful ignorance and endless bleatings about the Xtian Magical Sky Pixie;

YOU want to replace reality-based evolution and science with willful ignorance and different endless bleatings about the SAME Xtian Magical Sky Pixie.

You, the IDiots and creationuts are on the same side, Ray; you are merely on different teams.

Since you have the same goal, differences in rhetoric and approach are irrelevant. You and the IDiots are like two rabid dogs after the same bone - you spend as much time biting and scratching at each other as you pursuing your goal.

Loons can always recognize how silly and ridiculous the rantings of OTHER loons are, but are unable to recognize how stupid and ridiculous they themselves are.

We are not on the same side; the lawyer (and the rhetoric he uses to defend Dembski) is on Darwin’s side. ALL of his efforts presuppose Darwinian concepts to account for a majority of phenomena EXCEPT IC systems and other ultra-complex contrivances. By your logic “a Creationist is a person who readily accepts Darwin’s main conceptual claims.” It can’t get anymore absurd. Creationists reject said claims, they do not accept.

Sound logic says A cannot be A and not -A at the same time. Like yourself and ALL other Atheist-Evolutionists, I accept causation mutual exclusivity. Since the lawyer and Dembski reject mutual exclusivity.…guess what?

PA Poland said:

We are not on the same side. I am a Paleyan Creationist/IDist and he is a Discovery Institute IDist. The latter does not base its claims on Paley 1802, but mainly on the claims of Behe and Dembski. Both Dembski and Behe accept Darwin’s main claim (natural selection) to exist in nature, as well as microevolution and conceptual existence of macroevolution and common descent. I, like Paley, reject the concept of evolution existing in nature; species remain immutable because Naturalism assumptions, interpretive philosophy, and Darwinian evolution are completely false.

In other words, you are all deranged f*ckwits, but they accept a bit more of reality than you do.

One reason Dembski and Behe accept natural selection to exist in nature is BECAUSE IT EXISTS IN NATURE; one would have to be mind-numbingly STUPID to claim it doesn’t exist. The claim is so ludicrous that it would drive most of their paying imbeciles away.

Another reason is by accepting the reality of natural selection they have more things to misrepresent and lie about. All the sciency-sounding terms they throw around can sound impressive to anyone ignorant of the last half century of biological discoveries.

Said comments admit the lawyer and Dembski accept natural selection (Darwin’s main theoretical claim). These persons, therefore, CANNOT be real Creationists—which, of course, makes them happy. They’re quite satisfied to be in bed with Darwin and Dawkins. The fact shows just how deluded these “scholars” actually are. They’d rather be seen with Darwin and Dawkins than ArchDeacon Paley.

Reality-based folk have known that species are mutable for centuries Ray. If you weren’t so willfully stupid, you’d realize that immutability has testable effects.

IF living things were truly immutable, there would be no birth defects (caused by mutations). No drug resistant bacteria. No herbicide resistant plants. No insecticide resistant bugs. No new variations in anything. There would be no such thing as mutagens, and radiation would have no long term effects.

Examination of REALITY shows that birth defects and variations occur. Bacteria evolve drug resistance at an alarming rate. Weeds become immune to herbicides, and new pesticides have to be developed because all the old ones stop working because the insects evolved resistance. Many chemicals are known mutagens, and radiation causes mutations.

Note that our Evolutionist invokes phenomena that is NOT the main object of explanation in the Creation/Evolution debate. That main object is sexually reproducing animal species, not bacteria or antibiotic resistance. Natural selection is a short list of truisms explained to act as causing evolutionary change and eventually to have produced new species. Theobald calls the same an “explanatory mechanism.” The explanation of these truisms defies reality, sound logic and common sense. No such phenomenon exists in nature producing adaptation or species to exist.

PA Poland said:

Now Ray farts out one of his homophobic parting insults before he runs away, screaming of his victory :

So, Luskin and company are on your side and in your bed, not mine in any way, shape or form. Just be glad that you’re on top.

No Ray - creationuts, IDiots and theoloons like yourself are all in the same cesspit, and all of you are pretending that it is the OTHER guy that stinks.

The sexual metaphor employed perfectly depicts the situation that the lawyer and Dembski are in. Two “Christian/IDists” who accept Atheist-Materialist Darwin’s main claim are in that exact position.

RM (Old Earth, Paleyan Creationist, species immutabilist)

PA Poland said:

No Ray - creationuts, IDiots and theoloons like yourself are all in the same cesspit, and all of you are pretending that it is the OTHER guy that stinks.

Now there’s a line I’ll be stealing sometime soon ;)

diogeneslamp0 said: However, in this case Luskin is NOT constructing a phylogeny by aligning a single gene. I don’t know what that would produce.

It’s usually pretty good. You can try it yourself easily from BLAST.

Rather, he is arguing that the PRESENCE or ABSENCE of a single gene should be used to form a phylogeny. PRESENCE or ABSENCE of a single gene is basically one bit of information, YES or NOW– perhaps 1,000 or 1,500 times less information that you would get by aligning a single gene.

Correct, and here they’ve aligned 150 including the species creationists care most about–very little extra to cloud the issues. If I were choosing one to show to laypeople, I would choose a sample like this.

Lawyer Luskin’s argument is to stand in the laboratory door and order the scientists: “Stop looking at so much data, you guys! Use less data! Use less data!”

And the response should be, “Screw the coelacanth for now–let’s look at what all those other data mean and predict!”

Ray Martinez said:

Sound logic says A cannot be A and not -A at the same time.

Factually wrong, Ray. Fuzzy logic explicitly permits a variable to take on values of true and not-true at the same time.

Sorry, buddy, but you don’t know what you’re talking about.

joaozinho666 said:

It’s crystal clear that you tacitly conceded my point about the graph in Fig. 1 being analogous to claiming that a Michaelis-Menten graph isn’t data because it doesn’t include the spec readings.

No, you can’t take absence of comment as agreement. No, a Michaelis-Menton graph isn’t data, though it may contain data. Any curve fit to the data is certainly not data. Figure 1 contains no data.

That could be, but I was under the impression that I was discussing this with people who view themselves as sophisticated enough to educate the public here.

So you agree that you are very poor at communicating? I’m sure you can learn, and I suspect a big part of it is that you aren’t really trying to communicate but are mainly interested in scoring cheap rhetorical points.

It’s completely unclear what you want PZ to do and what errors he’s made.

Accepting an opponent’s dishonest framing for starters.

What dishonest framing?

PZ isn’t talking about the right thing.

Who are you to decide what PZ should be talking about?

Why should any intelligent person who purports to educate the public accept the framing of a liar like Luskin?

What framing did PZ accept? You still, after all this time, haven’t made that clear.

If you insist on calling it a phylogeny, it’s also a phylogeny in the mind of any intelligent Designer. It’s still a graph of the data either way.

It isn’t a graph of the data. I insist on calling it a phylogeny because that’s what it is; ask any systematist. (You could ask me, for example.) But phylogenies aren’t in the minds of intelligent designers; phylogenies are by definition hypotheses of evolutionary relationships.

No, your calling it a phylogeny of ORGANISMS is the inference. At best it’s a phylogeny of a limited sample of sequences, and still just data. You might recall that there are professional disagreements about whether the length of the branch leading to the coelacanth (the data) was properly interpreted by the authors. But I think your ego is clouding your memory.

You keep introducing new claims without making sense of the old ones. Yes, there’s a limited sample of sequences. Is there a reason to believe that the phylogenies of these sequences are not representative of the phylogeny of the organisms? If not, you are making empty objections. Yes, the disagreement is about the lengths of the branches, and it’s the first time you’ve mentioned that either. It’s well known in systematics that estimates of topology are more robust than estimates of branch length. What is your point?

The data are sequences. You called it a phylogeny of ORGANISMS. That’s interpretation. You can’t teach laypeople about this if you can’t grasp this distinction, man!

Is that what you were complaining about? It’s the first time you’ve mentioned it. And yes, it’s a phylogeny of species; it’s common practice to take individuals as exemplars of species and sequences as exemplars of genomes. Again, you seem only to be attempting to score a cheap point in some imagined game.

Again, no idea what you think ought to be done or what the problem is. I hypothesize that you may be saying we ought to be hyping this tree as evidence for common descent. Is that it?

Yes, but note that your hypothesis means that you were indeed lying when you claimed to have NO idea, Dr. Pedantic.

Again you accuse me of lying. And you don’t even tell me whether my hypothesis was right.

But why must every discussion be for the purpose of convincing creationists that there is common descent?

It’s not about every discussion, it’s about this one, because scientists have utterly failed to spotlight the sequence evidence to date. Here, Casey Luskin is spotlighting it for you but falsely reframing it, and you and PZ are accepting Luskin’s false framing.

You really need to explain what you’re talking about. What have scientists not done that they should have? How is it relevant to the point PZ was trying to make? Or why was his point the wrong point? You need to do much better. I have a few guesses about what you might be talking about, but no more than that. And it’s your fault for being unwilling or unable to make sense.

Ray Martinez said:

A backstabbing charge presupposes that I and Luskin are on the same side. We are not on the same side. I am a Paleyan Creationist/IDist and he is a Discovery Institute IDist.

A distinction without a difference, which is yet another lie of yours.

The latter does not base its claims on Paley 1802, but mainly on the claims of Behe and Dembski. Both Dembski and Behe accept Darwin’s main claim (natural selection) to exist in nature, as well as microevolution and conceptual existence of macroevolution and common descent.

They have to accept them because they are nothing less than factual, as much as the Earth being round and orbiting the Sun.

I, like Paley, reject the concept of evolution existing in nature; species remain immutable because Naturalism assumptions, interpretive philosophy, and Darwinian evolution are completely false.

Paley’s position was credible in his time because he lived at least a generation before Darwin and was unaware of the evidence for evolution that Darwin and others after him would discover. Thus, I can respect Paley even while disagreeing with him. You, on the other hand, I have nothing but contempt for because you flatly deny the truth that any rational and honest person would see and state clearly in the present day.

So, Luskin and company are on your side and in your bed, not mine in any way, shape or form. Just be glad that you’re on top.

There is only one way that claim can be supported. Do you assume the Earth is flat and at the center of the universe with everything orbiting it too?

Ray Martinez said:

PA Poland said:

Ray Martinez said:

dalehusband said:

Ray Martinez said:

I am a Paleyan Creationist who has read Luskin extensively. The first and only thing I notice about his Discovery Institute apologetics is the fact that they are literally filled with cheap lawyer rhetoric from top to bottom. Said rhetoric, of course, insults intelligence. Of course Luskin has a law degree and is a lawyer. His writings will never stand up to scrutiny. Luskin, like all illegitimate axe-grinding revisionists, only understands the temporary here-and-now “success.” I predict future historians and scholars will dismiss and disregard everything he writes.

You are right. But ALL Creationist claims and the writings based on those claims are much the same way, including most of your lame comments around here. If you had any sense of integrity you would not be a “Paleyan Creationist” (what does that even mean?) because there is simply no reason to be one. But you clearly do not. You are an extremist who backstabs even people like Casey Luskin who would make great allies of yours. And that means no one should trust or respect you on any level.

A backstabbing charge presupposes that I and Luskin are on the same side.

Let’s see - Luskin’s masters want to replace reality-based science and evolution with willful ignorance and endless bleatings about the Xtian Magical Sky Pixie;

YOU want to replace reality-based evolution and science with willful ignorance and different endless bleatings about the SAME Xtian Magical Sky Pixie.

You, the IDiots and creationuts are on the same side, Ray; you are merely on different teams.

Since you have the same goal, differences in rhetoric and approach are irrelevant. You and the IDiots are like two rabid dogs after the same bone - you spend as much time biting and scratching at each other as you pursuing your goal.

Loons can always recognize how silly and ridiculous the rantings of OTHER loons are, but are unable to recognize how stupid and ridiculous they themselves are.

We are not on the same side; the lawyer (and the rhetoric he uses to defend Dembski) is on Darwin’s side. ALL of his efforts presuppose Darwinian concepts to account for a majority of phenomena EXCEPT IC systems and other ultra-complex contrivances. By your logic “a Creationist is a person who readily accepts Darwin’s main conceptual claims.” It can’t get anymore absurd. Creationists reject said claims, they do not accept.

Then WHY does Mighty Mouse Luskin constantly squeak that “evolution CAN’T do it, therefore Xtian Magical Sky Pixie DIDIT !!!!” ?

By reality-based logic, a creationist is a person who claims Magical Sky Pixies somehow did something because evolution (supposedly) can’t do it.

Again, twit : IDiots are creationuts just like you; they just accept a touch more of reality than you do.

Sound logic says A cannot be A and not -A at the same time. Like yourself and ALL other Atheist-Evolutionists, I accept causation mutual exclusivity. Since the lawyer and Dembski reject mutual exclusivity.…guess what?

You are a blithering, self-absorbed imbecile under the delusion that your f*ckwitted rhetorical gymnastics magically absolves you of being significantly different than those OTHER blithering, self-absorbed imbeciles ?

PA Poland said:

We are not on the same side. I am a Paleyan Creationist/IDist and he is a Discovery Institute IDist. The latter does not base its claims on Paley 1802, but mainly on the claims of Behe and Dembski. Both Dembski and Behe accept Darwin’s main claim (natural selection) to exist in nature, as well as microevolution and conceptual existence of macroevolution and common descent. I, like Paley, reject the concept of evolution existing in nature; species remain immutable because Naturalism assumptions, interpretive philosophy, and Darwinian evolution are completely false.

In other words, you are all deranged f*ckwits, but they accept a bit more of reality than you do.

One reason Dembski and Behe accept natural selection to exist in nature is BECAUSE IT EXISTS IN NATURE; one would have to be mind-numbingly STUPID to claim it doesn’t exist. The claim is so ludicrous that it would drive most of their paying imbeciles away.

Another reason is by accepting the reality of natural selection they have more things to misrepresent and lie about. All the sciency-sounding terms they throw around can sound impressive to anyone ignorant of the last half century of biological discoveries.

Said comments admit the lawyer and Dembski accept natural selection (Darwin’s main theoretical claim). These persons, therefore, CANNOT be real Creationists—which, of course, makes them happy. They’re quite satisfied to be in bed with Darwin and Dawkins. The fact shows just how deluded these “scholars” actually are. They’d rather be seen with Darwin and Dawkins than ArchDeacon Paley.

So not only are you the world’s ONLY “TRUE XTIAN”, you are the world’s only “TRUE CREATIONUT” as well ?

They are creationuts Ray, much like you. No matter how much you squeal and whine. They just happen to accept a touch more reality than you do - generally so they have more to lie about and misrepresent.

Natural selection occurs, and only a willfully stupid imbecile would bellow otherwise.

Reality-based folk have known that species are mutable for centuries Ray. If you weren’t so willfully stupid, you’d realize that immutability has testable effects.

IF living things were truly immutable, there would be no birth defects (caused by mutations). No drug resistant bacteria. No herbicide resistant plants. No insecticide resistant bugs. No new variations in anything. There would be no such thing as mutagens, and radiation would have no long term effects.

Examination of REALITY shows that birth defects and variations occur. Bacteria evolve drug resistance at an alarming rate. Weeds become immune to herbicides, and new pesticides have to be developed because all the old ones stop working because the insects evolved resistance. Many chemicals are known mutagens, and radiation causes mutations.

Ray attempts a flaccid sidestep :

Note that our Evolutionist invokes phenomena that is NOT the main object of explanation in the Creation/Evolution debate. That main object is sexually reproducing animal species, not bacteria or antibiotic resistance. Natural selection is a short list of truisms explained to act as causing evolutionary change and eventually to have produced new species. Theobald calls the same an “explanatory mechanism.” The explanation of these truisms defies reality, sound logic and common sense. No such phenomenon exists in nature producing adaptation or species to exist.

PLANTS reproduce sexually. So do insects. So do people.

According to the reality-based community, evolution is a change in allele frequencies in a population - THERE IS NO REQUIREMENT THAT THE POPULATION BE SEXUALLY REPRODUCING !

Natural selection has been OBSERVED. It does not defy reality, sound logic, or common sense. It acts in ACCORDANCE to them !

But, then again, you are too willfully stupid to know such things.

Observations of REALITY show that variations (mutations) arise. Some of these variations may have an easier time living long enough to reproduce than others. Sane and rational folk realize that those variants will tend to become more common in a population.

Thus natural selection exists in reality, and can be deduced from sound logic and common sense - qualities you expunged from your ‘mind’ when you became a creationut.

Speciation occurs when a subpopulation cannot (or will not) produce offspring with the original population, generally via accumulation of changes that don’t necessarily need to be due to selection. THIS HAS BEEN OBSERVED.

PA Poland said:

Now Ray farts out one of his homophobic parting insults before he runs away, screaming of his victory :

So, Luskin and company are on your side and in your bed, not mine in any way, shape or form. Just be glad that you’re on top.

No Ray - creationuts, IDiots and theoloons like yourself are all in the same cesspit, and all of you are pretending that it is the OTHER guy that stinks.

The sexual metaphor employed perfectly depicts the situation that the lawyer and Dembski are in. Two “Christian/IDists” who accept Atheist-Materialist Darwin’s main claim are in that exact position.

RM (Old Earth, Paleyan Creationist, species immutabilist)

Then why are they trying to REPLACE EVOLUTION WITH MAGICAL SKYMANISM ?

THE EXACT SAME THING THAT YOU ARE TRYING TO DO ?

John Harshman said: No, a Michaelis-Menton graph isn’t data, though it may contain data.

You’re not making any sense. On the off chance that you are, what data might it contain? When wouldn’t it contain data? Limit yourself to the primary literature.

Any curve fit to the data is certainly not data.

You’re reaching, as no one to my knowledge publishes the curve fit without the data points in the primary literature.

Figure 1 contains no data.

So graphs aren’t data?

So you agree that you are very poor at communicating?

No.

I’m sure you can learn, and I suspect a big part of it is that you aren’t really trying to communicate but are mainly interested in scoring cheap rhetorical points.

You mean like your “So you agree that you are very poor at communicating?” above? Or should I reply to a snide “I’m sure you can learn” with “So that I can be unemployed as a scientist like you?” I wouldn’t go that low.

Who are you to decide what PZ should be talking about?

It was a direct response to your question.

What framing did PZ accept?

That points about the coelacanth would invalidate the whole phylogeny.

It isn’t a graph of the data. I insist on calling it a phylogeny because that’s what it is; ask any systematist. (You could ask me, for example.) But phylogenies aren’t in the minds of intelligent designers; phylogenies are by definition hypotheses of evolutionary relationships.

There’s nothing hypothetical about Figure 1.

Yes, there’s a limited sample of sequences.

Then any claim that it is a phylogeny of taxa is an interpretation.

Is there a reason to believe that the phylogenies of these sequences are not representative of the phylogeny of the organisms?

I don’t have one, nor does Luskin.

If not, you are making empty objections.

My objection is that you are mistaking the label for the thing.

Yes, the disagreement is about the lengths of the branches, and it’s the first time you’ve mentioned that either. It’s well known in systematics that estimates of topology are more robust than estimates of branch length. What is your point?

That you’ve lost sight of the difference between data (the length of the branch in Fig. 1) and interpretation.

Yes, but note that your hypothesis means that you were indeed lying when you claimed to have NO idea, Dr. Pedantic.

Again you accuse me of lying.

Well, “I hypothesise that you mean…” is a direct contradiction of, “I have no idea what you mean,” is it not?

And you don’t even tell me whether my hypothesis was right.

Now you’re delusional. You asked, “I hypothesize that you may be saying we ought to be hyping this tree as evidence for common descent. Is that it?” and I replied, “Yes, but note…” and you don’t understand that “Yes” was a direct reply to “Is that it?”

phhht said:

Ray Martinez said:

Sound logic says A cannot be A and not -A at the same time.

Factually wrong, Ray. Fuzzy logic explicitly permits a variable to take on values of true and not-true at the same time.

Sorry, buddy, but you don’t know what you’re talking about.

Oh, now you’re just going all Schrodinger on him.

joaozinho666:

Your complaint is simply bizarre. That is a diagram illustrating the phylogenetic relationships between the illustrated species. It shows much more, as well, but I’m not addressing the details here, only the broad notion that a single measure of the presence or absence of a single gene could supercede the conclusions derived from a larger data set.

Going off at length on the other issues in the diagram would not improve the discussion at all, but would instead distract from the point I was making. I can tell you as an educator and as someone who argues with creationists all the time that adding an assortment of tangents is NOT helpful at all.

joaozinho666 said:

John Harshman said: No, a Michaelis-Menton graph isn’t data, though it may contain data.

You’re not making any sense. On the off chance that you are, what data might it contain? When wouldn’t it contain data? Limit yourself to the primary literature.

The points on the plot are data. Figure 1 contains nothing analogous to such points. The closest analogy to Figure 1 would be a curve fit to the points. That curve isn’t data.

Any curve fit to the data is certainly not data.

You’re reaching, as no one to my knowledge publishes the curve fit without the data points in the primary literature.

And that’s why a M-M plot isn’t a good analogy to Figure 1. Figure 1 contains no data. It’s analogous to a curve fit to data.

Figure 1 contains no data.

So graphs aren’t data?

Several problems here. First, graphs aren’t data. They may contain data, depending on the graph. Second, Figure 1 isn’t a graph in the ordinary sense of the word, as a plot of data. Figure 1 is a graph only in the topological sense, i.e. a collection of nodes and lines. Third, Figure 1 is a phylogenetic tree, the result of analysis of data. It’s an inference from the data.

So you agree that you are very poor at communicating?

No.

Pity. I had thought to see a moment of self-realization.

I’m sure you can learn, and I suspect a big part of it is that you aren’t really trying to communicate but are mainly interested in scoring cheap rhetorical points.

You mean like your “So you agree that you are very poor at communicating?” above? Or should I reply to a snide “I’m sure you can learn” with “So that I can be unemployed as a scientist like you?” I wouldn’t go that low.

I believe you just did. Do I know you, perhaps under another name?

Who are you to decide what PZ should be talking about?

It was a direct response to your question.

Yes, and that was a question in response to your response. Could you answer?

What framing did PZ accept?

That points about the coelacanth would invalidate the whole phylogeny.

Where did he say anything of the sort?

It isn’t a graph of the data. I insist on calling it a phylogeny because that’s what it is; ask any systematist. (You could ask me, for example.) But phylogenies aren’t in the minds of intelligent designers; phylogenies are by definition hypotheses of evolutionary relationships.

There’s nothing hypothetical about Figure 1.

Now you’re playing with words. Figure 1 is a hypothesis of relationships. That’s what a phylogenetic tree is. It happens to be a very strongly supported hypothesis, to the point that we should be willing to accept it as true for all practical purposes. But it’s still a hypothesis.

Yes, there’s a limited sample of sequences.

Then any claim that it is a phylogeny of taxa is an interpretation.

If by “interpretation” you mean “inference”, then yes, of course. Everything we know is an inference. That happens, again, to be a very strong inference. I find it difficult to integrate your various objections into any coherent position. Perhaps you can explain with more than a cryptic sentence or two.

Is there a reason to believe that the phylogenies of these sequences are not representative of the phylogeny of the organisms?

I don’t have one, nor does Luskin.

If you don’t have one, why the complaint?

If not, you are making empty objections.

My objection is that you are mistaking the label for the thing.

I’m totally confused. What is the label? What is the thing? Again, more than a couple of cryptic phrases would be helpful.

Yes, the disagreement is about the lengths of the branches, and it’s the first time you’ve mentioned that either. It’s well known in systematics that estimates of topology are more robust than estimates of branch length. What is your point?

That you’ve lost sight of the difference between data (the length of the branch in Fig. 1) and interpretation.

You have no idea what you’re talking about. The branch lengths are not data. Sequences are data. The branch length is an inference from the sequences. (I’m not quite sure what you mean by “interpretation”.) There is some question about whether that branch length is accurate; that is, it’s intended to represent the total number of substitutions occurring in those sequences between the ancestral node and the living coelacanth. It may not accurately represent those substitutions, and in addition the substitutions in the chosen sequences may not accurately represent the average over the genome. The branch length in fact represents the mean of a distribution of branch lengths over a likelihood surface, as explored by a Bayesian MCMC algorithm.

Well, “I hypothesise that you mean…” is a direct contradiction of, “I have no idea what you mean,” is it not?

Only if you aren’t a native English speaker. I don’t know what you mean. I came up with a hypothesis. Is that hypothesis correct?

And you don’t even tell me whether my hypothesis was right.

Now you’re delusional. You asked, “I hypothesize that you may be saying we ought to be hyping this tree as evidence for common descent. Is that it?” and I replied, “Yes, but note…” and you don’t understand that “Yes” was a direct reply to “Is that it?”

Ah, I missed the significance. So now you say that your point is that we should all be hyping this tree as evidence of common descent. I don’t see how that point is consistent with all the other things you have said.

phhht said:

Ray Martinez said:

Sound logic says A cannot be A and not -A at the same time.

Factually wrong, Ray. Fuzzy logic explicitly permits a variable to take on values of true and not-true at the same time.

Sorry, buddy, but you don’t know what you’re talking about.

Imagine that; a totally ignorant evo makes the most stupid comment imaginable proving that he is totally ignorant and uneducated and his fellow evos remain completely silent!

Ray Martinez said:

phhht said:

Ray Martinez said:

Sound logic says A cannot be A and not -A at the same time.

Factually wrong, Ray. Fuzzy logic explicitly permits a variable to take on values of true and not-true at the same time.

Sorry, buddy, but you don’t know what you’re talking about.

Imagine that; a totally ignorant evo makes the most stupid comment imaginable proving that he is totally ignorant and uneducated and his fellow evos remain completely silent!

Scott F responded. Scott F is correct that there is an analogy between fuzzy logic and Schrodinger’s uncertainty principle.

Ray Martinez said:

phhht said:

Ray Martinez said:

Sound logic says A cannot be A and not -A at the same time.

Factually wrong, Ray. Fuzzy logic explicitly permits a variable to take on values of true and not-true at the same time.

Sorry, buddy, but you don’t know what you’re talking about.

Imagine that; a totally ignorant evo makes the most stupid comment imaginable proving that he is totally ignorant and uneducated and his fellow evos remain completely silent!

Well, regardless of the accuracy of what phhht said, it couldn’t possibly be considered “the most stupid comment imaginable” (because I can easily imagine stupider ones–or just refer to a whole slew of far stupider things you have said here), nor could it be proof “that he is totally ignorant and uneducated,” because there are obviously things about which he is not ignorant, and he clearly has some level of education.

Do you ever say anything that’s not inept?

You’ve got sticks and stones and bile and bluster.

I’ve got the truth.

You don’t know what you’re talking about with regard to logic, Ray.

Ray Martinez said:

phhht said:

Ray Martinez said:

Sound logic says A cannot be A and not -A at the same time.

Factually wrong, Ray. Fuzzy logic explicitly permits a variable to take on values of true and not-true at the same time.

Sorry, buddy, but you don’t know what you’re talking about.

Imagine that; a totally ignorant evo makes the most stupid comment imaginable proving that he is totally ignorant and uneducated and his fellow evos remain completely silent!

Ray Martinez said:

phhht said:

Ray Martinez said:

Sound logic says A cannot be A and not -A at the same time.

Factually wrong, Ray. Fuzzy logic explicitly permits a variable to take on values of true and not-true at the same time.

Sorry, buddy, but you don’t know what you’re talking about.

Imagine that; a totally ignorant evo makes the most stupid comment imaginable proving that he is totally ignorant and uneducated and his fellow evos remain completely silent!

I was strolling through Macy’s department store last year and came upon a strange object that looked quite out of place. On close examination, for the life of me, I couldn’t readily discern it’s use but it clearly had the hallmarks of design. Upon further examination I discovered the box from whence this device originated and read the following: Zojirushi 10-cup Fuzzy Logic Rice Cooker.

After a brief transaction with the appliances cashier, I traveled back to my residence and commenced cooking rice by the most extraordinary means imaginable. I placed into a container an amount of rice and water, closed the lid and pressed the pink button labeled “cook.” And that was it. Some time later the rice cooker, without any prompting by me, played a little tune, the light on the pink button went out and the light on the green button labeled “ready” came on. Sure enough, the rice was cooked perfectly. And so it has each and every time. Without fail.

Having lived with the Zojirushi fuzzy logic rice cooker for a while, now, I’ve come to believe it has a mind of its own. I don’t have to tell it how much rice I have put in nor what kind. All by itself it cooks long grain, short grain, basmati, jasmine, expensive or cheap rice. It cooks rice perfectly in cold weather, hot weather and in all degrees of humidity or condition of stored rice. Clearly, the rice cooker has free will. I know this because as a former rice cooker, myself, I am well acquainted with the various and myriad adjustments, calculations, weighings and measuring, stirring and tending that must occur in proper sequence and nature to expertly prepare rice.

Also, I have taken the time to investigate this “Zojirushi” company and have discovered that they are responsible for the design and creation of vacuum flasks, bread machines, electric kettles, hot water dispensers and refrigerators with each product appearing whole and fully-formed without ancestor in the corporate record: kettles with spouts, flasks with lids and refrigerators with coils.

Therefore, I must be a free-will Paley creationist intelligent design advocate, at least when it comes to rice cookers. It’s the best explanation, really.

Pz Myers said: Your complaint is simply bizarre. That is a diagram illustrating the phylogenetic relationships between the illustrated species.

No, the diagram illustrates the relationships between a set of only 150 sequences from each species. We both agree on the inferred relationships between species, but the diagram is derived from this subset of sequences only. Please don’t embarrass yourself by pointing to the title, as we know that the rule of thumb is that conclusions are OK in the title of the figure, while one sticks to a strict description in the remainder of the legend.

It shows much more, as well, but I’m not addressing the details here, only the broad notion that a single measure of the presence or absence of a single gene could supercede the conclusions derived from a larger data set.

Which is irrelevant to an ignorant layperson who might be on the fence about “believing” evolutionary theory.

Going off at length on the other issues in the diagram would not improve the discussion at all,

Discussion? There’s no discussing anything with Luskin!

…but would instead distract from the point I was making. I can tell you as an educator and as someone who argues with creationists all the time that adding an assortment of tangents is NOT helpful at all.

I can tell you as a scientist (only included in response to your pompous “as an educator”) that my complaint is that you are letting Luskin take YOU off on a tangent. YOU are failing to focus on the fact that he chose to argue about a beautiful, fundamental compilation of data that are important to laypeople on the fence.

Let me repeat that for you in another way so that you and Harshman can’t feign misunderstanding: I am criticizing your lack of focus–you are chasing tangents by responding to Luskin’s IDiocy instead of leveraging his spotlight to educate.

joaozinho666 said:

I can tell you as a scientist (only included in response to your pompous “as an educator”) that my complaint is that you are letting Luskin take YOU off on a tangent. YOU are failing to focus on the fact that he chose to argue about a beautiful, fundamental compilation of data that are important to laypeople on the fence.

Let me repeat that for you in another way so that you and Harshman can’t feign misunderstanding: I am criticizing your lack of focus–you are chasing tangents by responding to Luskin’s IDiocy instead of leveraging his spotlight to educate.

Feel free to post the response you think PZ should have made to Luskin. It would be an education for us all, and might even tell us just what your point is supposed to be.

John Harshman said: Feel free to post the response you think PZ should have made to Luskin. It would be an education for us all, and might even tell us just what your point is supposed to be.

It’s fine up through “immortals.” From there I would write,

We can deal with the specific case Luskin misrepresents later. We are more interested in this bit about the bigger picture:

“Once again, such similarities of sequence and function could be explained by common design and don’t necessarily tell us much about common descent.”

We hereby cordially invite Casey Luskin to offer his common design explanations for the DIFFERENCES shown in Figure 1, which he conveniently includes in his tirade.

Luskin also writes, “…let’s first look at the standard vertebrate phylogeny, shown in the Nature paper:”

Yes, let’s look.

Unfortunately for Luskin, even the scale bar shows us that it’s not simply a “standard vertebrate phylogeny.” The scale bar tells us that the lengths of the horizontal lines represent actual data that Luskin can’t explain: the lengths are shown on a scale of “substitutions per site,” that is, differences. In other words, this is a representation of the data.

While Luskin might whine that some of the assumptions made in processing the data are based on evolutionary parameters, every one of those parameters should have some counterpart in his common design hypothesis, explaining when, why, and how his Common Designer changed them. Vague blubbering about “similarity” is a cowardly dodge. How does Luskin explain the differences that are quantitated in Figure 1?

Luckily, the program to which the data were fed (PhyloBayes) is extremely customisable, so we welcome Casey’s detailing of which parameters should be adjusted and why, so that we may test the same sequence data against his hypothesis.

Or could it be that Luskin is tacitly conceding common descent of all the vertebrates? In that case, we welcome him to the side of sanity and request that he allows us to watch and eat popcorn while he explains this to his fans and bosses at the DI.

joaozinho666 said: It’s fine up through “immortals.” From there I would write,

We can deal with the specific case Luskin misrepresents later. We are more interested in this bit about the bigger picture:

“Once again, such similarities of sequence and function could be explained by common design and don’t necessarily tell us much about common descent.”

We hereby cordially invite Casey Luskin to offer his common design explanations for the DIFFERENCES shown in Figure 1, which he conveniently includes in his tirade.

Luskin also writes, “…let’s first look at the standard vertebrate phylogeny, shown in the Nature paper:”

Yes, let’s look.

Unfortunately for Luskin, even the scale bar shows us that it’s not simply a “standard vertebrate phylogeny.” The scale bar tells us that the lengths of the horizontal lines represent actual data that Luskin can’t explain: the lengths are shown on a scale of “substitutions per site,” that is, differences. In other words, this is a representation of the data.

While Luskin might whine that some of the assumptions made in processing the data are based on evolutionary parameters, every one of those parameters should have some counterpart in his common design hypothesis, explaining when, why, and how his Common Designer changed them. Vague blubbering about “similarity” is a cowardly dodge. How does Luskin explain the differences that are quantitated in Figure 1?

Luckily, the program to which the data were fed (PhyloBayes) is extremely customisable, so we welcome Casey’s detailing of which parameters should be adjusted and why, so that we may test the same sequence data against his hypothesis.

Or could it be that Luskin is tacitly conceding common descent of all the vertebrates? In that case, we welcome him to the side of sanity and request that he allows us to watch and eat popcorn while he explains this to his fans and bosses at the DI.

That isn’t altogether bad. The thought, though clumsily stated, is reasonable. The only paragraph I find altogether cringeworthy is the one beginning “Unfortunately…”, for reasons we have discussed already. I do not, however, see why this is a better point than the one PZ did make. What you perhaps should have done would be to note that there were other points that could have been made about Luskin’s post, and then make them yourself, rather than simply using your post to say “PZ, you suck”.

In case it wasn’t clear already, that was me.

Doc Bill said:

Jedidiah said:

“What more do you need, J-Boy?”

I’d start with not calling me J-Boy.

Fortunately, I’m not you, J-Boy.

Doc, stop trolling. You asked what I wanted, and I told you. Don’t play Creationist-style mind games by attacking me because I answered you. And your vaguely anti-Semitic slurs make me increasingly uncomfortable. Just because my name is Hebrew doesn’t mean you should use words that have been used to denigrate Jews.

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This page contains a single entry by PZ Myers published on April 27, 2013 7:26 AM.

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