Wednesday, March 15, 2006

The Misrepresentations of Richard Forrest

I could get huffy and take that as an insult, but I won't. But I am interested in why you are unwilling to defend your flood geology claims.

rf indicates amino acids

24 Comments:

Anonymous Anonymous said...

No idea. The same as 381 residues working together, I suppose.

No. Nor does it show any ignorance of it.

Sure. I'm making a very small point that has nothing to do with Sean's claims, which is just that attacking him for saying "amino acids" is just silly and only distracts from the real issues.

8:08 PM  
Anonymous Anonymous said...

Thank you.  Actually, I'm honored.

In another post you noted that you can't always get accurate information for Google.  But Pitman *could* have Googled for me and discovered that while I am *not* biochemist and *not* an organic chemist, I am in fact a chemist working at a fairly well-known university and have had a small bit of training.

I'm sorry to note that we do not use Larry's book.  I don't know if we are using Lehninger or not, but I will check just for the heck of it.

But I doubt if Pitman will get the humor of your post.  I love the fact that you invoke the written word to prove your point.  The written word cannot be denied.

So you quoted your own book.  ;-)

I doubt Pitman will be amused.

I'm waiting for him to present his probability argument against a given string of 1000 residues.  That has nothing to do with evolution, of course, but that sort of calculation is right up my alley.  That's *my* field.

    ----- Paul J. Gans

10:53 PM  
Anonymous Anonymous said...

Right.  Down in flames you go, Pitman.  I'll take that as a concession.

And I'll be rude enough to say again what I said before.

If you want to pretend to discuss scientific issues in detail, use the proper language.

As you may recall, when I first joined this little charade of yours, I specifically asked what you meant by 1000 amino acids acting together.  To me that's a meaningless statement. It isn't even wrong.  It is simply gibberish.

So I asked several times for you to clarify it.  You didn't. As I said, it gave you wiggle room.  Now you claim it is trivial.

I gather that your claim is then that nature never makes a change of a thousand residues in a protein all at once. If that is you claim, I will agree that it is most often true.

But of course it has nothing to do with evolution at all. Nobody working in the field (as several have tried to tell you) thinks that's the mechanism for protein change at all.

So your attacking it and claiming that it is impossible thus ID is the only answer is just silly.

It is like my crying that pigs can fly because oats don't grow on trees.  Well, oats *don't* grow on trees and pigs still don't fly.

And there is still no proof whatsoever for ID.  It doesn't fly either.

   ---- Paul J. Gans

12:08 AM  
Anonymous Anonymous said...

Not so.  I specifically asked him several times what he meant. The rest of what he wrote was so jumbled that it made no sense.

Your use above is quite different.  Your sentance "Cytochrome b contains 381 amino acids." makes it quite clear that you are talking about the components of a single molecule.  

I could not believe that Pitman was talking about the evolution of the system as requiring a more or less simulaneous change in 1000 residues spread out on one or more proteins.

He never said that.  And I asked several times.

Thanks to your posts I finally deduced that yes, he *was* talking about that.  Which is when I decided that his argument was based on *two* assumptions, not one.  And that the first one, the one about the 1000 residues, was clearly false.

I'm not in any way putting down the shorthand use of terms in conversation with collegues who know what you are talking about.  But if you were in a hostile area and trying to make a point understandable to non-experts, you'd doubtless use the right terminology and even explain it if you felt it necessary.

Pitman did not do that.  He kept it because it gave him wiggle room.  He never said how many proteins were involved nor did he ever say how long the changed sections had to be.  All he said was gibberish.

    ----- Paul J. Gans

9:08 AM  
Anonymous Anonymous said...

It is really impossible to tell what he does really think. His newest postings seem to be positing a quite different sort of thing than his earlier ones.  

Now he seems to want only 50 residues to change all at once.  And he specifically denies that one can have a significant change with only one changed residue.

So we are off into a different fog again.  Again it is not clear what he is talking about.  He's now using the term "residues" but the rest of it is still gibberish.

   ---- Paul J. Gans

10:53 PM  
Anonymous Anonymous said...

On Wed, 23 Feb 2005, Paul J Gans <g@panix.com> wrote:

Maybe he's going to, when he finishes the 200 or so in the queue before your request.

-- Bobby Bryant Austin, Texas

12:24 AM  
Anonymous Anonymous said...

peers.

I would agree.  From the perspective of a biological system, the environment (foot) is the template or basis on which functional (shoe) modifications over time are selected.  Improved functional complexes (fits to the environment), created via random changes in each generation, are preferentially selected for improved reproductive fitness over their less snug peers.

See, I can play meaningless semantic games too.  Why don't you apply your probability analysis and compute the expected time you would expect an antibody, of, say 870 residues would need to evolve.  I'll even start you off: the sequence space size is 20^870 or about 7.872e1131.  Please, continue...

[snip]

3:23 AM  
Anonymous Anonymous said...

Do we not see similar chromosomal differences amongst members of the same species?

And then there is fossil evidence to deal with. Skull morphology differences between ER3733 and modern Homo Sapiens is much greater than that between ER3733 and ER1813 (considered to be H. Habilis). Then you have D2700 stuck right about in the middle of ER3733 and and ER1813. I haven't seen any creationists classify D2700 as human or ape, but they typically consider ER3733 human, and it would be really tough to exclude D2700 if ER3733 is considered human. In light of the finds in Flores I suppose one could argue that ER1813 is a shrunk down variant of H. ergaster, but then you necessarily would have to rethink classifying STW53 and OH24 as apes.

I'm impressed that you even responded.

How about ERVs, do you consider them to be useful markers to determine relation by descent?

4:53 AM  
Anonymous Anonymous said...

Really? I thought it turned out to be 50. I presume you have no idea where he would get either number, so I also presume it doesn't matter which one you pick. I myself gave up trying to make sense of the whole neutral gap thing long ago, since it doesn't seem to have anything to do with actual biology. It makes him happy.

Perhaps I would, but in the particular case of "amino acids" vs. "residues" I would do so, if I did, which I doubt, only to avoid pedants making a big deal out of it. Pitman's real terminology problems are the ones that cause actual confusion to his listeners, not this "ha ha, you're wrong" crap.

Agreed. But "amino acids" vs. "residues" has nothing to do with it.

5:26 AM  
Anonymous Anonymous said...

Actually, there's plenty of such evidence. Sean just rejects all of it, using various lame excuses. For example, in Sean's world, any sequence under selection is invalid for phylogenetic analyses, and all sequences are under selection.

That was presumably the point of the horse/donkey comparison, but Sean hasn't noticed.

True. But so what? Why should that matter if the question is one of phylogenetic relationships? Sean adopts a common creationist tactic here: if we don't know everything, that means we know nothing. So any area of ignorance, no matter how irrelevant to the question at hand, is enough to render the question undecidable. Clever trick.



Note the introduction of the irrelevant matter of mutation and natural selection. The mechanism by which differences arise and become fixed is irrelevant. The important point is that they form a nested hierarchy, the sort of thing that only results from a tree of common descent. How the various changes got onto the tree doesn't matter. But Sean constantly confused pattern (tree) and process (selection etc.), thinking that evidence for or against one somehow affects the other.

I doubt it. My guess: they're functional, even though we think they aren't, and therefore they are useless for phylogenetic analysis.

3:23 PM  
Anonymous Anonymous said...

I think it's something to do with the holes in his claims, the ever growing gaps between his vocabulary and his definitions.

-- Bobby Bryant Austin, Texas

7:53 PM  
Anonymous Anonymous said...

Ah, but the problem with defining species arises naturally from the fact that speciation is a gradual process that happens over evolutionary time. If "kinds" were created distinct from the beginning, they should be easy to identify and define. But they aren't, are they? That's a strong argument against your position.

No, in fact it seems like a random number pulled out of thin air, attached to a definition so ambiguous that it's hard to figure out what you're talking about. Perhaps if you gave a real example of your definition in practice. What two species are different kinds based on your idea?

11:11 PM  
Anonymous Anonymous said...

Isn't this the one Sean reponded to? Something along the lines of "I've found some quotes on the internet which seem to support my position, therefore you don't know what you're talking about and I know more about amino acids/genes/sedimentary processes/geology/(add subject here if not listed)* than you do. I've explained it over and over again, and I can't believe that anyone can be so stupid as to fail to see that I have proved my case."

RF

*delete as appropriate.

1:23 AM  
Anonymous Anonymous said...

On Wed, 23 Feb 2005 05:29:43 GMT,

[snip]

I agree that it doesn't seem like a very important issue. Some of us care about the correct use of terms so we're pretty sensitive when biochemical language is misused - especially when it interferes with understanding.

Others have different priorities. I understand that there are some scientists who care about the definition of "species", for example. I've even heard of scientists who will object to the misuse of words like "macroevolution." To each his own.

I responded to Sean for another reason. Rather than just admit that he was using "amino acids" when the correct technical term was "resides," he went on the attack. He accussed Paul Gans of being stupid and he (Sean) claimed that the biochemistry textbooks supported his use of "amino acids." That was too tempting a target for me ...

This little episode shows one thing. It shows that Sean is quite incapable of learning on his own even when he is given mumerous hints. It indicates, once again, that Sean has his own personal agenda and he won't listen to anyone else until it becomes perfectly obvious that he is wrong.

Larry Moran

3:08 AM  
Anonymous Anonymous said...

Bobby D. Bryant <bdbry@mail.utexas.edu> wrote:

Well, I've learned something (or had my suspicions verified) from all this.

The first is that in the end, ID rests on personal incredulity. I live in New York where several million people *still* cannot believe that the Yankees, with a lead in the ninth inning of the fourth game of the World Series, leading three games to nothing, managed to *lose* the World Series, four games to three.

Now *that* is personal incredulity that is meaningful.  IDers are far behind.

Another thing I've learned is that ID is basically antithetic to Christian fundamentalism.  If the designer is not God, ID is unbiblical.  If the designer *is* God, then ID is blasphemous because, among many other things, God is revealed as a bumbler.

Case in point:  the flagellum arose twice and the two forms are derived from different starting materials.  Now if God is the designer He is clearly not omnescient, otherwise He would have chosen the *best* design and used it twice.

I've also had confirmed the notion that creationists in general seem incapable of understanding even simple things about proof, demonstration, and argument.

   ---- Paul J. Gans

5:08 AM  
Anonymous Anonymous said...

Well, OK.  But clearly Pitman saw that I (and others) were confused by his terminology and lack of precision.  His refusal to clear that up seems meaningful to me.

I'm also amused by his insistance that one has to produce a given active sequence in a protein _de nouveau_.  I gather that is where his odds against stringing 50 (or 500 or 1000 or whatever) proteins together come from.

I could use the same arguments to show that the odds against my existing are so very very much smaller -- so small as to be negligible.  Thus since I do exist I must have been created, either by Xordaxians or by God.  In either case I'm thus the product of superior knowlege and he really ought to listen to me.

    ----- Paul J. Gans

5:38 AM  
Anonymous Anonymous said...

Agreed.  Since I came in after the start of this, I really did not know how he was using the term.  I (initially) could not believe that he was talking about the sequential creation of a string of 1000 or so residues, one after the other, as being the way evolution operates.

So I assumed that his use of the phrase "amino acids acting in concert" meant something else entirely.

When others use the phrase "amino acids" in sentences such as "this protein has a highly conserved 30 amino acid region" I understand quite well what is being talked about.

As to Pitman's agenda, I never entertained any hope of changing his mind.  I know that there are many lurkers for every poster. And I think that it is important to dissect Pitman's arguments down to their basics and show where they are wrong.

His resultant squirming does not really interest me.

   ---- Paul J. Gans

7:23 AM  
Anonymous Anonymous said...

erm...I believe that was the ALCS. Boston went on to beat St Louis in the WS, 4 games to zero.

11:38 AM  
Anonymous Anonymous said...

by "Seanpit" <seanpitnos@naturalselection.0catch.com>:



Excuse me, but were not you the one who issued the challenge to go to a textbook to see the terminology used? Then, when someone actually does it, you go off in a huff and call *them* petty?

-- Ferrous Patella (Homo gerardii) T.A., Philosophy Lab University of Ediacara

"Nature as God's "reality" show  - what a concept!" --A t.o. poster who wishes to remain anonymous

12:08 PM  
Anonymous Anonymous said...

No wiggle room there. You are explicitly making a universal claim, so you can't claim that myosin is not relevant.

Yes, but your estimate of it is fatally flawed.

Not a very large sample.

You don't know what is required. You are only looking at existing sequences.

That's the type of residue that we mutated to one not found in nature without abolishing function.

Moreover, there are two important points to consider:

1) The tyrosine residue is in the active site; and 2) It is in contact (or close proximity to) the substrate itself.

Therefore, your claim that a survey of existing sequences tells you which aa residues are compatible with function is demolished.



We didn't mutate one of those in our myosins, so your attempt to portray our work as this type is dishonest and/or incompetent (I hypothesize both).

No, our results directly contradict your hypothesis, which you are dishonestly portraying as a fact.

You don't know that.

The picture is that you jump to conclusions and lack the integrity to admit it when you are caught.

As others noted, the specificity/length ratio is not constant.

That's not obvious at all.



What do you think that the facts we (and others, see Shokat for kinases) published do to one of your most fundamental assumptions, Sean?

---snip---

8:53 PM  
Anonymous Anonymous said...

On Wed, 23 Feb 2005 08:29:53 -0800,

[snip[

We're talking about New Yorkers! They've completely suppressed the fact that they didn't even get into the World Series! By next summer the typical New Yorker will believe that the umps stole the series from them.

Larry Moran

7:08 AM  
Anonymous Anonymous said...

Ferrous,

Textbooks also use the term "amino acids" in sequence to describe proteins.  The term "residues" is not always used nor is this term necessary to avoid confusion in this context - except when a creationist visits forums like this where people look for ways to be confused. I just couldn't believe that the lack of the term "residues" was a source of confusion, in this context, for anyone.  That is why I couldn't believe it when Paul Gans said I wasn't using the "correct" term.  What term could he possibly be talking about?  When he came back with "amino acid residues" I was quite shocked!  That's it?! The term "residues" was the source of his confusion?!  Come on now. . . I get accused of using "nonstandard" terminology all the time, and this is the best he can come up with? LOL - too much!

Sean Pitman www.DetectingDesign.com

12:53 PM  
Anonymous Anonymous said...

"Paul J Gans" <g@panix.com> wrote in message ...

LMAO! Hilarious but not incredulous.

3:23 PM  
Anonymous Anonymous said...

Actually, by then, they may have won the Series.

Joe

5:38 PM  

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