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  Topic: From "LUCA" thread, Paley's Ghost can back up his assertions< Next Oldest | Next Newest >  
The Ghost of Paley



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(Permalink) Posted: Nov. 03 2005,14:29   

Quote
Wow. Without even figuring out the right equation to use, my bone-stupid estimate (i.e., "wild-ass guess") was around 1 E 50 Kg. Does that get me within a couple of orders of magnitude? I think so.

Yep. My calculated mass is 55 times higher. Pretty good agreement, I'd say.
Quote
But I'm going to assume that coming up with a figure that is probably heavy for a galactic supercluster doesn't change Bill's mind about his geocentrism. Am I right?

Right again. More to come. Cue the narrator, please.

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Dey can't 'andle my riddim.

  
ericmurphy



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(Permalink) Posted: Nov. 03 2005,15:00   

Quote (The Ghost of Paley @ Nov. 03 2005,20:29)
Quote
But I'm going to assume that coming up with a figure that is probably heavy for a galactic supercluster doesn't change Bill's mind about his geocentrism. Am I right?

Right again. More to come. Cue the narrator, please.

Okay, I admit it. You've piqued my interest. I await next week's episode with bated breath....

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2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
ericmurphy



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(Permalink) Posted: Nov. 04 2005,13:00   

I'm a little hung over right now, so I might not be thinking clearly. But it's occurred to me that Bill's figure for the mass of the earth, 5.5 E 51 Kg, might compare with the mass of the observable universe (at least the visible, non-"dark" part of it). I wonder if that's where he's going with this...

(Oops...am I giving the game away?)

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2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
The Ghost of Paley



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(Permalink) Posted: Nov. 05 2005,05:50   

Quote
I'm a little hung over right now, so I might not be thinking clearly. But it's occurred to me that Bill's figure for the mass of the earth, 5.5 E 51 Kg, might compare with the mass of the observable universe (at least the visible, non-"dark" part of it). I wonder if that's where he's going with this...

(Oops...am I giving the game away?)

 Patience, my son. I will unveil the model when I get some free time: after all, one can't interweave art and science, unify and explain cosmological mysteries, and awe the human mind on demand. Slather on a little more Devon cream and order another latte in the meanwhile..........

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Dey can't 'andle my riddim.

  
C.J.O'Brien



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(Permalink) Posted: Nov. 05 2005,09:38   

Who/What-ever the heck this guy is, he's something else isn't he?

Yes, GoP (hmmm...), I'm stll lurking about, and I haven't forgotten about The Master, either. But my optics is a little rusty, haha.

Awaiting the ummm, "unveilling."

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The is the beauty of being me- anything that any man does I can understand.
--Joe G

  
ericmurphy



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(Permalink) Posted: Nov. 05 2005,13:36   

Quote (The Ghost of Paley @ Nov. 05 2005,11:50)
 Patience, my son. I will unveil the model when I get some free time: after all, one can't interweave art and science, unify and explain cosmological mysteries, and awe the human mind on demand. Slather on a little more Devon cream and order another latte in the meanwhile..........

Well, given the task I've set you (i.e., overturning 500 years of settled natural law, as it were), I'm not expecting an answer any time soon (unless you've already been working on this for a decade or two, in which case…).

But would you care to estimate a time frame? Another couple of years, maybe? Just so I don't have to keep checking back.

P.S. I'm actually not much of a latte lover.

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2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
The Ghost of Paley



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(Permalink) Posted: Nov. 07 2005,06:33   

Quote
But would you care to estimate a time frame? Another couple of years, maybe? Just so I don't have to keep checking back.

 Worst case scenario: A week from this upcoming Friday (Nov. 18, I believe)

 Best case: This Thursday (Nov. 10)

 I hope this helps.

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Dey can't 'andle my riddim.

  
MDPotter



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(Permalink) Posted: Nov. 07 2005,09:03   

Ya right, you're arguing for geocentrism and I'M the one slobbering.
Hysterical.

  
ericmurphy



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(Permalink) Posted: Nov. 07 2005,09:04   

Quote (The Ghost of Paley @ Nov. 07 2005,12:33)
Worst case scenario: A week from this upcoming Friday (Nov. 18, I believe)

 Best case: This Thursday (Nov. 10)

 I hope this helps.

Will you booking your hotel room in Stokholm, then? :-)

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2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
Steverino



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(Permalink) Posted: Nov. 07 2005,09:09   

I'm sorry but, how can anyone who is still convinced that the Lunar Landings were a hoax, be taken seriously?

He chooses to ingore first hand account, eye witness...which is his/their major reason for not recognizing Evolution...."cause no one was there to witnes it.

It's hypocritical at best.

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- Born right the first time.
- Asking questions is NOT the same as providing answers.
- It's all fun and games until the flying monkeys show up!

   
The Ghost of Paley



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(Permalink) Posted: Nov. 07 2005,09:10   

Quote
Well, given the task I've set you (i.e., overturning 500 years of settled natural law, as it were), I'm not expecting an answer any time soon (unless you've already been working on this for a decade or two, in which case…).

 You have the time frame now. And I'll make this promise: if I don't deliver at least the rough draft of my geocentric model by November 18, I will personally fly to Clichy-sous-Bois, walk to the nearest mosque, and do a spirited Ait Bogar for the residents clad in a Crusader Rabbit diaper and a t-shirt emblazoned with the phrase " Paley a le beguin pour Sarkozy!"

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Dey can't 'andle my riddim.

  
ericmurphy



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(Permalink) Posted: Nov. 07 2005,11:38   

Quote (Steverino @ Nov. 07 2005,15<!--emo&:0)
I'm sorry but, how can anyone who is still convinced that the Lunar Landings were a hoax, be taken seriously?

I can't say I'm taking this guy seriously, but he has demonstrated some knowledge of orbital mechanics and Newtonian physics (more than mine, anyway), so he's not a complete half-wit.

But I'm interested to see how he wriggles out of this particular box.

(And when I say I'm not taking this guy seriously, I mean I don't think he really believes anything he says he believes.)

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2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
The Ghost of Paley



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(Permalink) Posted: Nov. 07 2005,14:24   

Quote
He chooses to ingore first hand account, eye witness...which is his/their major reason for not recognizing Evolution...."cause no one was there to witnes it.

It's hypocritical at best.

 I don't know why people think that this argument is mine, when I've tried to make it clear all along that I'll accept circumstantial evidence so long as it converges on a single conclusion. If someone would present consistent, independent evidence for a particular lineage, I would buy the evo account, but what I receive are a plethora of crazy and flatly contradictory trees that reflect nothing so much as the insanity of the brainpans that generated them in the first place. I think people don't read what I write so much as what they think I would write if I was the slack-jaw that they assume I must be, given the certitude of their assumptions.

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Dey can't 'andle my riddim.

  
Steverino



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(Permalink) Posted: Nov. 08 2005,03:14   

Quote (ericmurphy @ Nov. 07 2005,17:38)
[quote=Steverino,Nov. 07 2005,15<!--emo&:0]I'm sorry but, how can anyone who is still convinced that the Lunar Landings were a hoax, be taken seriously?

I can't say I'm taking this guy seriously, but he has demonstrated some knowledge of orbital mechanics and Newtonian physics (more than mine, anyway), so he's not a complete half-wit.

But I'm interested to see how he wriggles out of this particular box.

(And when I say I'm not taking this guy seriously, I mean I don't think he really believes anything he says he believes.)[/quote]
My point is that while he may be very intelligent, which I believe he is, he also finds it very easy and convenient to discard, ignore documented fact to form a belief.

I believe this practice makes his other arguments less credible.

--------------
- Born right the first time.
- Asking questions is NOT the same as providing answers.
- It's all fun and games until the flying monkeys show up!

   
The Ghost of Paley



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(Permalink) Posted: Nov. 08 2005,05:52   

Quote
My point is that while he may be very intelligent, which I believe he is, he also finds it very easy and convenient to discard, ignore documented fact to form a belief.

I believe this practice makes his other arguments less credible.

 Let's assume that you've got my character nailed: I'm a hopelessly baffled person whose scientific judgement can't be trusted, and my arguments reflect this flaw. Or I'm an incorrigible troll. Great.
 Then why can't anyone refute my arguments? And what does this imply about your character? Or about your positions? In any case, I'm willing to focus strictly on the evidence; how about you?
 By the way, how does my stance on some issues detract from my advocacy of others? What kind of ontological voodoo are you proposing? Either I have good arguments or I don't; please focus on rebutting, rather than psychoanalysing, me. The fact that you rely on the latter makes me suspect you can't do the former.
 I don't see a bunch of free-thinkers here - merely religious apologists with their minds rusted shut. Prove me wrong, boys.

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ericmurphy



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(Permalink) Posted: Nov. 08 2005,06:04   

Quote (The Ghost of Paley @ Nov. 07 2005,20:24)
...I'll accept circumstantial evidence so long as it converges on a single conclusion. If someone would present consistent, independent evidence for a particular lineage, I would buy the evo account, but what I receive are a plethora of crazy and flatly contradictory trees that reflect nothing so much as the insanity of the brainpans that generated them in the first place.

But Bill, the tree I've presented to you is supported by exactly the kind of evidence you say you want. Now, granted, certain groupings of certain organisms using certain types of evidence will result in different trees. But that's to be expected, if for no other reason than the truly astronomical number of possible trees. And there are a lot of organisms for which the phylogenetic relationships are controversial, as you'll note if you poke around on the Tree of Life site. But large portions of the tree are well-established using multiple, independent lines of evidence from very different areas of the life sciences (e.g., genalysis, the fossil record, stratigraphy, geology, morphological studies). The tree on Theobald's site is well-established, well-supported, and non-controversial, which is why it's called the "consensus tree."

Granted, the phylogenetic relationships of, say, lungfish and coelacanths can be hard to figure out, but I don't think anyone denies the phylogenetic relationships between tuna and chicken, or between starfish and spiders.

Details, controversial. General structure of the tree, not. But your position seems to be that the entire tree is wrong. That's not true. It just isn't.

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2006 MVD award for most dogged defense of scientific sanity

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Steverino



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(Permalink) Posted: Nov. 08 2005,09:35   

Bingo!...My point is you filter out what you information goes against what you believe or want to believe.  Even though that information is proven.

The Lunar Landings are proven but, fact, they happened but, those you cannot choose not to recognize that.

So, what is the point in debating fact with you when you can just offer as a defense.."No thats wrong"?

--------------
- Born right the first time.
- Asking questions is NOT the same as providing answers.
- It's all fun and games until the flying monkeys show up!

   
The Ghost of Paley



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(Permalink) Posted: Nov. 08 2005,13:18   

Quote
But Bill, the tree I've presented to you is supported by exactly the kind of evidence you say you want. Now, granted, certain groupings of certain organisms using certain types of evidence will result in different trees. But that's to be expected, if for no other reason than the truly astronomical number of possible trees.

 You do realise that this "astronomical number of possible trees" business is derived solely from Hubert Yockey's cytochrome c analysis, which does not account for alternative splicing? And without Yockey's crutch, we're back to the puzzle of weirdly discordant molecular trees which don't match each other, let alone the phylogenies derived from morphology. Therefore, no consilience.
Quote
So, what is the point in debating fact with you when you can just offer as a defense.."No thats wrong"?

 And still you don't get it. I always back up my arguments with evidence. Which is why they get ignored, of course.

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ericmurphy



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(Permalink) Posted: Nov. 08 2005,16:05   

Quote (The Ghost of Paley @ Nov. 08 2005,19:18)
 You do realise that this "astronomical number of possible trees" business is derived solely from Hubert Yockey's cytochrome c analysis...

This is wrong. The "astronomical number of possible trees" has nothing to do with cytochrome c analysis, or any analysis at all. It has to do with mathematics.

I know you said you've read Theobald closely, Bill, but you keep providing me evidence to the contrary. As Theobald points out, as the number of taxa (or, for that matter, any kind of object -- cars, asteroids, library books) that you're trying to relate to each other increases, the number of possible genealogical "trees" you can construct goes up geometrically. Theobald presents a handy little chart (Table 1.3.1). I'll excerpt a few entries so you can get the general flavor of what we're talking about:

2 taxa: 1 relationship
4: 15
7: 10,395
11: 34,459,425
20: 8,200,794,532,637,891,559,375
30: 4.95 E 38

This has nothing to do with how you analyze the objects you're trying to relate to each other. It's a matter of pure mathematics.


Which brings me way, way back to what I said in this thread about six or seven pages ago. The consensus phylogenetic tree that Theobald depicts is based on, not a few proteins, not a few genes, and not a lot of proteins or a lot of genes. It's based on genetics, protein analysis, the fossil record, morphological studies, developmental evolution, geology, and other lines of inquiry. All of these lines of evidence converge on the tree as Theobald shows it.

Now, you've pointed out that different individual lines of evidence can show discordant trees. You won't get an argument from me there. But you're talking about individual lines of evidence showing weird relationships between two different species. There are tons of organisms, as I stated a couple of messages ago, which are problematic in terms of what their exact phylogeny is. But for the 30 major taxa in Theobald's tree (note there are no species mentioned, or genera, or families, for that matter), there is an overwhelming consensus opinion that the phylogenetic tree as pictured is correct.

The tree shows that fungi are more closely related to animals than either are to plants. It shows that birds are more closely related to mammals than either are to insects. Surely you don't deny phylogenies at this level of detail, do you, Bill? When you get down either to the level of genera, or conversely to the base of the tree (are archae more closely related to eubacteria, or to eukaryotes?) things get murky. But the worst you can say about the consensus tree is that it's a solid beginning, supported by solid independent lines of evidence. And the fact that a dozen or more lines of evidence all converge on the same tree, out of ~5 E 38 possibilities, is pretty persuasive evidence for common descent, don't you think? Even if cladistic analysis could get the number of trees down to only a million different ones, isn't that an unbelievable level of precision? How many physical constants are known to 32 decimal places? The mass of the electron is known to seven places. G, the universal gravitation constant, is known to three places.

I think you greatly overestimate the problems with phylogeny, Mr. Paley.

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2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
ericmurphy



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(Permalink) Posted: Nov. 08 2005,17:45   

Quote (The Ghost of Paley @ Nov. 08 2005,19:18)
Quote
So, what is the point in debating fact with you when you can just offer as a defense.."No thats wrong"?

 And still you don't get it. I always back up my arguments with evidence. Which is why they get ignored, of course.

Well...not always. I once asked you why you thought the consensus phylogenetic tree is wrong. Your reply: "Why not?"

Don't mean to be persnickety, but I just couldn't resist...

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2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
The Ghost of Paley



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(Permalink) Posted: Nov. 09 2005,07:15   

Quote
I know you said you've read Theobald closely, Bill, but you keep providing me evidence to the contrary. As Theobald points out, as the number of taxa (or, for that matter, any kind of object -- cars, asteroids, library books) that you're trying to relate to each other increases, the number of possible genealogical "trees" you can construct goes up geometrically.

 Yes, I forgot about this aspect of his argument. Theobald's claim resembles an argument Sean Pitman once made about the relationship between the number of amino acids and the potential sequence space. He essentially stated that the ratio between useful sequence space and potential sequence space decreases at an exponential rate as you add more residues, and that this large target prohibits certain types of neutral evolution, thus rendering some types of evolution (those requiring fortuitous double and triple mutations, for example) impossible. Sean's math was sound, as was his conclusion. The problem, of course, was that Sean did not account for the existence of protein families that cluster together in sequence space, thus destroying his initial assumption of even distribution of potential function throughout the search area.
 This brings us to Theobald's argument. Theobald asserts that the potential number of branches in any tree increase at a factorial rate as the number of organisms increase, rendering an astronomically large "tree space". Therfore, we should embrace any theory that winnows this number down. But without biological facts to back it up, this argument suffers from the same defects as Pitman's: it assumes a uniform bodyplan distribution throughout morphological space. This is not true, as I'll demonstrate. (Hint: compare placental mammals to marsupials. Do you see any animals with similar features?). More later.

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The Ghost of Paley



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(Permalink) Posted: Nov. 09 2005,07:51   

Quote
Will you booking your hotel room in Stokholm, then? :-)

 A zif. :angry:

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The Ghost of Paley



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(Permalink) Posted: Nov. 09 2005,08:15   

Quote
More later.

 Here's the problem: morphological characters do not have to be, and in fact are not, uniformly distributed throughout the sample space of all potential body types. We see this in many cases of "convergent evolution" between marsupial and placental mammals. No matter how the similarities came to be, the fact remains that God- or nature - is not as adventurous as Theobald implies. This suggests that there is a natural grouping of "kinds" that can be investigated in different ways, none of them requiring the notion of common descent. In other words, I have no need for that hypothesis.  :)
 
Quote
Well...not always. I once asked you why you thought the consensus phylogenetic tree is wrong. Your reply: "Why not?"

 I hope this addresses your question.

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ericmurphy



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(Permalink) Posted: Nov. 09 2005,08:40   

Quote (The Ghost of Paley @ Nov. 09 2005,14:15)
Quote
More later.

 Here's the problem: morphological characters do not have to be, and in fact are not, uniformly distributed throughout the sample space of all potential body types. We see this in many cases of "convergent evolution" between marsupial and placental mammals. No matter how the similarities came to be, the fact remains that God- or nature - is not as adventurous as Theobald implies. This suggests that there is a natural grouping of "kinds" that can be investigated in different ways, none of them requiring the notion of common descent. In other words, I have no need for that hypothesis.  :)
 
Quote
Well...not always. I once asked you why you thought the consensus phylogenetic tree is wrong. Your reply: "Why not?"

 I hope this addresses your question.

I still think you're misinterpreting Theobald's point. The number of potential trees has nothing to do with whether there's a uniform distribution of body plans, or protein conformations, or anything whatsoever. It's exclusively dependent on the number of taxa to be classified.

Someone gives you a group of 30 names of people. He tells you they're all related, but doesn't tell you how. The letters of the names have all been scrambled, so you can't use surnames as a clue. Now, he tells you to come up with all possible relationships between this group of 30 individuals. How many possible trees can you come up with? ~5 E 38. The same would be true of natural languages, or computer languages, or anything. The number of possible phylogenetic trees has nothing whatsoever to do with morphological characteristics, or indeed any characteristics. It is purely dependent on the number of taxa, and nothing else.

Now. Why do biologists think that the tree, as depicted, is accurate? For the reasons I've given you. You keep saying there's no biological evidence that the tree is correct, but I have to insist you're simply wrong there. And in any event, whether the tree is in fact correct (or could even be attempted) is only part of the argument for common descent. The other part of the equation is the nested hierarcies that all life forms fall into. There are no protostomes with feathers. There are no bacteria with mitochondira. There are no vertebrates with exoskeletons. The only known (and maybe the only possible) explanation for such nested hierarchies is common descent with modification. Therefore, whether you believe that neodarwinian evolution is the cause of common descent with modification, you simply cannot escape the fact of common descent with modification. It is simply a fact that needs explanation.

You asked me once how science knows which morphological features are the important ones. It comes down to which ones allow us to trace out a phylogenetic tree. Bats and birds both have wings, right? So they should be grouped together, right? Wrong. Because the wings don't fall into the other groupings or morphological features that birds and bats naturally fall into. Birds have feathers, avian lungs, hard-shelled eggs, etc., which group them all together. Bats have fur, placentas, mammalian inner ears, etc., which group them all together. This is why phylogenetic relationships need to be traced out using large numbers of characteristics from different independent lines of inquiry. It's the only way to develop well-supported phylogenies, and it's why it takes decades, if not centuries, to figure out the taxonomic relationships among organisms.

But again, common descent is a fact. Nested hierarchies are a fact. They are both facts wanting explanation. You simply cannot plausibly deny they exist. Now, whether God made it all happen, or unguided evolution, that's a separate matter. But you simply cannot get away with claiming there are no relationships among organisms.

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2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
The Ghost of Paley



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(Permalink) Posted: Nov. 09 2005,10:12   

Quote
I still think you're misinterpreting Theobald's point. The number of potential trees has nothing to do with whether there's a uniform distribution of body plans, or protein conformations, or anything whatsoever. It's exclusively dependent on the number of taxa to be classified.

 Certainly. But this is mathematically trivial; what makes the argument potentially relevant to biology is whether or not the classification process itself is truly arbitrary, absent common descent. And this depends on the distribution of morphological characters. Which is decidedly nonrandom in any working ecosystem.
Quote
Nested hierarchies are a fact.

They are if you use a tree-like scheme in the first place. But the methodology had better not force the conclusion.

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ericmurphy



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(Permalink) Posted: Nov. 09 2005,12:37   

Quote (The Ghost of Paley @ Nov. 09 2005,16:12)
Quote
Nested hierarchies are a fact.

They are if you use a tree-like scheme in the first place. But the methodology had better not force the conclusion.

Actually, this is what I should have said: "Nested hierarchies" is not a hypothesis; it's an observation. There are no known exceptions to the observation of nested hierarchies, when one looks at the totality of the evidence.

Common descent with modification was originally a hypothesis put forth to explain nested hierarchies. But common descent with modification is so overwhelmingly supported by the evidence that it has achieved the status of a fact in need of an explanation, rather than a hypothesis in need of verification.

One possible explantion for common descent with modification is directed evolution, i.e., evolution directed by some sort of supernatural intelligence. Another possible explanation is embodied by neodarwinian evolution. But in either event, it is long past the point where it is possible to deny either nested hierarchies or common descent with modification.

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2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
The Ghost of Paley



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(Permalink) Posted: Nov. 09 2005,13:05   

Quote
Common descent with modification was originally a hypothesis put forth to explain nested hierarchies. But common descent with modification is so overwhelmingly supported by the evidence that it has achieved the status of a fact in need of an explanation, rather than a hypothesis in need of verification.

 And this is where we disagree. You seem to be saying that large groups of morphological characters can triangulate a tree, and thereby make it factual (at least on some branches). If so, then why do genetic phylogenies? Any discordant result must be tossed out, given the previously established tree. And if the genes do count, the morphological tree must still in some sense function as a hypothesis that needs testing. Remember, genetic testing wasn't established until the sixties. Are you saying common descent wasn't a fact until then? Or did the phenotypic characters make it factual?
 I'm not being deliberately obtuse; I'm really confused about this.
(Paley braces for the inevitable witticism......)

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ericmurphy



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(Permalink) Posted: Nov. 09 2005,14:03   

Quote (The Ghost of Paley @ Nov. 09 2005,19<!--emo&:0)
And this is where we disagree. You seem to be saying that large groups of morphological characters can triangulate a tree, and thereby make it factual (at least on some branches). If so, then why do genetic phylogenies? Any discordant result must be tossed out, given the previously established tree. And if the genes do count, the morphological tree must still in some sense function as a hypothesis that needs testing. Remember, genetic testing wasn't established until the sixties. Are you saying common descent wasn't a fact until then? Or did the phenotypic characters make it factual?
 I'm not being deliberately obtuse; I'm really confused about this.
(Paley braces for the inevitable witticism......)

Nope, no witticisms (at least, none at your expense).

Well, you probably need an expert opinion on this question, but I think you need to look at it this way: for some phylogenetic questions, morphological analysis provides the answer. For others, genetics is the way to go. For still others, the fossil record gives brighter illumination.

It's like any large accumulation of data. Imagine you're trying to determine the weight of the electron. Most of your test results are going to converge on 500 keV. But an occasional result might give a ridiculous answer, like 3.5 geV. Another might give you 1,200 eV. You have to toss those anwers, even if, for the moment, you're not sure why they're wrong.

There are a lot of things about genetics and molecular biology that are only approximately understood. How accurate is the molecular clock when it comes to mutation rates? Well, one way you could calibrate the clock is by comparing the results to what you see in the fossil record. Or what about mutation loci and frequencies in protein analysis? You might need to confirm your results by comparison to morphological studies.

You used an example earlier of a particular protein analysis (might have been cytochrome c, I can't remember) that showed that kangaroos diverged from humans before they diverged from other mammals. Well, we know from lots of other evidence that this isn't true. So we need to find out why the protein evidence is discordant. But since we have, at this stage of the game, a really good idea of approximately when kangaroos and humans diverged, we can use evidence from other areas to try to figure out why the protein evidence gives unexpected answers.

The point is, you have to use huge datasets, coming from indpendent lines of research, to trace out lines of descent. You're looking for confirmation of evidence from as many different areas as possible. I pointed out earlier that guinea pigs and humans have the same mutation that makes the gene for producing ascorbic acid inoperative. Looking at just the genes, you might be forgiven for assuming that guinea pigs are more closely related to humans than, say, macaques are. But you'd be wrong, because it's certainly not impossible that humans and guinea pigs have the same mutation for reasons that have nothing to do with common descent; i.e., sheer bad luck.

Also, I should probably make what might seem like a fine distinction. That there is, in fact, "one true tree," at this point must be regarded as a fact in need of explanation. But a particular tree is still, necessarily, a hypothesis in need of verification. However, as I said, the large-scale structure of the tree is for the most part sufficiently supported to be considered well-settled. But again, as I said earlier, there are definitely regions of the tree that are still controversial. Given past successes, it's to be expected that the same lines of evidence, including genetic evidence, will eventually illuminate the true structure of the tree.

At any rate, Bill, people who actually do evolutionary biology are not concerned with the overall structure of the phylogenetic tree (although there are certainly spirited disagreements on the details). There's just too much evidence to support it. I'm wondering if the problems you have with accepting the accuracy of the tree aren't partly a matter of missing the forest for the trees. Or, maybe you're missing the "tree" for the "leaves." :-)

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2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
The Ghost of Paley



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Joined: Oct. 2005

(Permalink) Posted: Nov. 11 2005,06:03   

Quote
Well, you probably need an expert opinion on this question, but I think you need to look at it this way: for some phylogenetic questions, morphological analysis provides the answer. For others, genetics is the way to go. For still others, the fossil record gives brighter illumination.

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Quote
Also, I should probably make what might seem like a fine distinction. That there is, in fact, "one true tree," at this point must be regarded as a fact in need of explanation. But a particular tree is still, necessarily, a hypothesis in need of verification. However, as I said, the large-scale structure of the tree is for the most part sufficiently supported to be considered well-settled. But again, as I said earlier, there are definitely regions of the tree that are still controversial. Given past successes, it's to be expected that the same lines of evidence, including genetic evidence, will eventually illuminate the true structure of the tree.

 Fair enough. I think part of our problem is we have different definitions of consilience. My definition stresses the independence of differing lines of evidence, while yours emphasises the unity of knowledge. It's like the baseball Hall of Fame: much of the controversy revolves around differing ideas about what makes a man a hall of famer. Is it the excellence of his play, his notoriety, or his contribution to winning teams that should be given the most weight? Problem is, people don't attempt to define the basic issues; they project their presuppositions instead and wonder why others can't see things their way.

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Dey can't 'andle my riddim.

  
ericmurphy



Posts: 2460
Joined: Oct. 2005

(Permalink) Posted: Nov. 11 2005,19:33   

Quote (The Ghost of Paley @ Nov. 11 2005,12<!--emo&:0)
 Fair enough. I think part of our problem is we have different definitions of consilience. My definition stresses the independence of differing lines of evidence, while yours emphasises the unity of knowledge.

Here's how I picture things, if you could travel back in time (I don't know if many evolutionary biologists would agree with me here, but I think Dawkins would). The "one true phylogenetic tree," as it applies to me personally, is simply a genealogical tracing all the way back, until we reach the point where we're not talking about life anymore. Go back, say, 5,000 generations, and we're still talking humans. Go back further than that, and we're not talking exactly humans anymore. Go back 15 million years, and we're talking about lower primates. 150 million years, we're talking ancestors who are probably indistinguishable from tree shrews. A billion and a half years, we might be talking about bacteria, or maybe simple eukaryotes. And amazingly, against all odds, every single one of those ancestors, without exception, left descendants. Every one of them, in evolutionary terms, was a success.

The point, Bill, is that unless you believe in some sort of special creation, that has to be the way it happened (let me know if you can think of some alternative story). If you assume life evolved without direct intervention of a creator (or maybe even if you do assume a creator), there's an unbroken chain of living organisms extending backwards in time from me to the simplest forms of life.

And for me personally, I'm actually at one end of that chain (I'm not having children). All you have to do is assume that the world is as it appears to be (i.e., a few billion years old), and that there is no special creation. So you can trace my genes back from today, all the way back almost four billion years ago. That's a third of the lifetime of the universe! Isn't that kind of, well…cool?

I'll grant that none of this is very scientific. (But then, I'm not a scientist--or a lawyer, for that matter :) ) But for me, at least, it's an appealing concept. If you think of your own existence that way, extending backwards in time in some very real fashion almost four billion years ago, your genes coursing through uncounted generations of ancestors, I think it gives you a palpable sense of your place in the universe, and your connectedness to all life. How's that for unity?

Gives me kind of a warm feeling.

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2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
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