Saturday, March 18, 2006

Below-50-IQ Simulator of the Month (Nov. 1998)

In  I read this message from Peter Nyikos <>:

Gee, you had a computer problem. You have my sympathy.

[snip] For the n'th time, Peter, Vince did troll. Trolling is a form of dishonesty. When I said Vince was "dishonest" I referred to his trolling. Trolling, btw, he has admitted. Sheesh.

[emailed now and when Peter returns]

Matt Silberstein ------------------------------------------------------- In the old days, it was not called the Holiday Season; the Christians called it "Christmas" and went to church; the Jews called it "Hanukka" and went to synagogue; the atheists went to parties and drank. People passing each other on the street would say "Merry Christmas!" or "Happy Hanukka!" or (to the atheists) "Look out for the wall!"

 [Dave Barry, "Christmas Shopping: A ! Survivor's Guide"]


Anonymous Anonymous said...


Maybe it was because of your flouting of netiquette.

[400+ lines of netiquette-flouting deleted]


8:38 PM

Anonymous Anonymous said...

In article <199812212347.SAA05@milo.Math.Sc.Edu>,   Peter Nyikos <> wrote:


I don't understand what you're referring to, here.

Well, the fact that they're professional biochemists, and they've never heard of such a thing is evidence in itself. Another thing is, if you admit that there's no evidence that anyone has every considered them disqualifiers, what is it that's causing you to think they are disqualifiers? All of this, of course, is besides the fact that people have given you examples of polypeptides containing iron (e.g., Wade's siderophores). In fact, Kevin recently described it so explicitly to you that you developed some new interpretation of your claims involving the chemical formula of heme which, frankly, may be a loophole out of this for you. It depends on what the exact wording of your previous claims was.

You're not claiming this? What's the controversy about, then?

Then why do you seem so insincere? Maybe it's just your style of writing.

What about the similarities in your views? (E.g., intelligent design)

No, it's more like your claims make utterly no sense. How is it that you came to be aware of this disqualifier? Why has no one else heard of it? You need to present evidence, or your position doesn't even have a coherent history (since, in the absence of evidence for your claim, you have no reason to want to make it in the first place). The only way this could make sense is if you were claiming that you had heard this somewhere, but forgot exactly where; is this what you're claiming?

No, that's like trolling, which I don't do anymore.

The fact is, no one was claiming that the baseball analogy was logically wrong, only that it wasn't applicable to heme. But you seemed to be implying that some people couldn't comprehend the basic point of the analogy, i.e. that their conclusions about heme followed from the sort of logical error found in the analogy, rather than from the specific facts of biochemistry.

What am I taking?

Obfuscatory word games, yes.

Neither do I; it's just a question of general useage, not a logical error or anything.

If they're doing it unconciously, what could be causing this psychological phenomomenon to happen to them?

Why would they be interested in flaunting this? That is, why is it significant that I allow them get away with simulating low IQs, while being famous for taking too much delight in pointing out their other problems? And why is simulation of low IQ the sort of thing one would feel a burden to point out? Are you calling them trolls? Or do you feel that there's some deeper, perhaps sinister motive for adopting this facade of mental retardation?

I don't think anyone was trying to depict this about you. I mean, we all know that you know hemoglobin, for example, is a protein.  But I'm interested in whether or not we can close this loophole I was talking about: your statement here seems to imply that you think polypeptides can't "contain" metal atoms. But let's go back to Kevin's description of polypeptides "folding around" metal atoms, which you seemed to accept as valid (and even tried to turn into an argument in your favor): isn't "wrapping around" a metal atom the same thing as "containing" it?

Okay, right. Why is it, in your view, that biochemists have created this dichotomy between protein and polypeptide nomenclatures? Why are the latter allowed to have metal atoms, but not the former?

I still don't understand how this relates to your present claims.


9:08 PM

Anonymous Anonymous said...

No one ever said there was an amino acid with Fe *in* it.  OTOH, there are amino acids that ionically associate with Fe in the same way that Fe ionically associates with the porphyrin ring of heme.  I think I know where you got confused.  The picture you saw of heme had two solid lines attaching to Fe and two dotted lines.  You took that to mean that there were two different types of bonds from the Ns of the porphyrin ring to the Fe.  That is not the case.  A picture is a picture, not reality Peter, and I know you have some trouble making the leap between pictures and reality.  The bonds attaching Fe to the ring structure are all equivalent bonds which are pictured in pairs for the same reason that the ring structured of aromatic carbon rings are pictured with alternating double and single bonds in two different ways. [snip]

No, Peter.  An R-group is individual specifier.  What determines that a compound is an amino acid is that it have the following structure:

    H H2N-C-COOH     R

That is the primary structure of all amino acids.  The R can literally be anything or bind to anything.  As Wade would point out, proline is considered an 'honorary' amino acid.


I saw Peter saying that the presence of Fe associated with the R group rules out the structure from being called a peptide.  Isn't that what this has been about?


To be precise, your words made *me* think that you thought that Kevin was a loon who thought that Fe could be an amino acid because he claimed that the presence of Fe does not prevent a polypeptide from being a polypeptide.  And, since, in your twisted little mind which is capable of misreading anything, Fe could only be a *part of* or *associated with* a polypeptide by *becoming* an amino acid, Kevin must be the crazy loon.  Thus, in Nyikosworld, anyone who says that Fe does not prevent a macromolecule from being a polypeptide is essentially saying that polypeptides can have Fe as an amino acid (which *is* crazy).  Weird from a chemistry point of view, but strangely mathematically logical.

Perhaps I just did as well.  But I am trying to come up with some explanation that makes sense of the nonsense you stated initially that got this rolling, namely that the presence of Fe would rule out heme as a polypeptide *even if it were a macromolecule composed of a polypeptide chain*.  And your continued insistance that that statement is correct. The only explanation that I can give is that you somehow think that your 'opponents' are proposing that Fe can *become* an amino acid.  Nothing else makes the slightest sense.

Yes.  He sequences the amino acids.  The sequence is determined by the linear order of the R groups and not the polypeptide backbone, which has no information content.  The R groups include such rare ones as the one that binds to heme.  That is an unusual R group, but that is all it is.

This is what I *suspect* you think the structure of any polypeptide that contains iron would look like - only replacing sulfur with iron introduced somehow as a replacement for the peptide bond linking two amino acids (not by linking two R groups).  *If* that were the case, one might reasonably say that a polypeptide with iron has a break in the polypeptide chain (with iron acting as an amino acid) and shouldn't be called a polypeptide.  But the idea is pretty weird chemically, so that none of those who know some chemistry would have suspected that this is what you were thinking.

No.  You have not made it clear.  Perhaps you could draw a structure showing where you think that the Fe would be introduced into the polypeptide in such a way as to prevent it from being a polypeptide?  I have drawn pictures showing how Fe can be associated with a polypeptide in the same way that Fe is associated with the porphyrin ring and shown that this association has no effect on the polypeptide bonds linking the amino acids.

12:38 AM


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