Re: A glossary of Pitmanese

On Feb 20, 2:35 pm, Seanpit <seanpitnos...@naturalselection.
0catch.com> wrote:
On Feb 20, 1:53 pm, Scooter the Mighty <Greyg...@xxxxxxxxxxx> wrote:



I'm not sure how one would "look this up."  Who exactly observed
this?  Can you link to their paper, or provide a reference?  How do
you tell how many amino acids are "fairly specified?"

You "look it up" by checking the literature dealing with examples of
evolution in action to see if any of the known examples that we have
produce any novel systems of function that require a minimum
structural threshold of at least 1000aa to work.  If you can find just
one example at this level or beyond, you will falsify my position.
Plain and simple.

Now hold on a second here!  You started this bit of thread with a
positive claim- that 1000 "fairly specified" amino acids was an
observed threshold beyond which nothing could evolve.

Not quite.  It is an observed threshold beyond which nothing has been
observed to evolve.  There's a difference.

So link me up with this observation please.

  I ask for
details about the observation (and you were the one who claimed there
was one) and now all of a sudden I have to search through the
literature and try to disprove it?  

The observation is a negative observation that is indeed falsifiable
by a single example of a positive.  You do understand that negative
hypotheses are quite useful in science?

Sure, but they involve someone specifically looking for something and
not being able to find it. Can you link me up with a paper in which
someone has looked for evolving fairly specified 1000aa protiens and
not found them?

How does that work? Is this in
fact an observation, or is it something that you made up that no one
has yet disproven, possibly because few people if anyone actually try
to determine how many amino acids in a protein are "fairly
specified"?

The lack of an event is just as much an observation as the
demonstration of an event.  For example, I observe that none of the
cows that I have ever seen have ever jumped as high as my house.  I
therefore hypothesize that no cow can jump as high as my house.
That's a hypothesis based on an observation of a negative - which is
quite a valid observation.


But what I'm having a hard time believing is that people actually
measure how many "fairly specified" amino acids occur in proteins. If
no one actually looks at the cows then you can't say how high they can
jump. Now I could easily be wrong, because I don't even know what you
mean by "fairly specified amino acid," so if you could link me up with
a paper in which this is measured I'd appreciate it.

Should be easy to do if in fact any such examples are known to exist.  Good
luck . . .

Yeah, it should be easy if scientists actually go through the work of
determing how many "fairly specified" amino acids are in the proteins
they study.  Can you link me up with a paper where the number of
"fairly specified" amino acids are determined in a protein? For that
matter, can you link me up with a paper that shows that a protein with
1000 "fairly specified" amino acids actually exists? What is the
definition of "fairly specified?"  It isn't a term that google scholar
seems to be familar with.

I've explained these terms extensively in this forum and on my website
if you care to look in those places.

OK, so I tried a google search and got someone complaining about the
vagueness of your definition of "fairly specified amino acids." You
recommended a google search for your name and Cytochrome C. I
performed that search and got this-

"...So, what does this mean? Well, take the minimum length of a
protein
with a cytochrome c function for example. It seems that this minimum
falls around the 80aa mark. Not only is this the minimum, but these
80aa are relatively specified. For example, the total one
dimensional/linear sequence space of 80aa is around 10^104 sequences.
Based on experimental work with cytochrome c sequence variability,
several have suggested to me that the total number of cytochrome c
sequences in sequence space ranges anywhere from 10^60 to 10^90. My
own calculations, based on the variability limits at each position
(can be found by a simple Google search), are in fair agreement with
the 10^60 calculation. But, even taking 10^90 are the actual number
of cytochrome c sequences in sequence space, the ratio is just 1 in
100 trillion."

I'm not finding this too helpful. In the first place, I don't see how
you determined anything here. How do we know that the minimum size
for Cytochrome C is 80aa? I can believe that, I just don't see how
you derived that. I also don't see how these "someones" are able to
suggest to you some wild-assed guess as to how many sequences have
cytochrome c function. I'm trying to learn how to make a calculation
here, what am I supposed to do, ask a bunch of guys who can't narrow
their answer down below 30 orders of magnitude and then pretend like
that number is gold?

And your calculation assumes that each of these amino acids has the
same level of "specification" which is a batch of jumping cow
muffins.

If there is going to be the possibility of a paper that invalidates
your argument then you are going to have to be able to spell out a
methodology that measures the fair specifity of amino acids so that
researchers other than yourself can do it. Right now, I don't have
enough details to even know if the paper I'm reading is agreeing with
you or not. Let's say I'm studying a 1000 aa protein right now, and
want to see if the amino acids are fairly specified- how do I go about
determing how many other sequences there are that would provide the
same function (or whatever the heck I need to know)?

.

Relevant Pages

  • Re: Harshman vs. Hershey
    ... functionally beneficial CytoC protein cannot be produced with any ... Do you not remember the many times I've listed the papers by Yockey, ... sequences in sequence space via phylogenetic sequence comparisons and ... research of substituting the 20 different types amino acids in two ...
    (talk.origins)
  • Re: Experimental basis for the Non-Beneficial Gap Problem
    ... Do you not remember the many times I've listed the papers by Yockey, ... sequences in sequence space via phylogenetic sequence comparisons and ... research of substituting the 20 different types amino acids in two ... After each substitution, the protein sequence was ...
    (talk.origins)
  • Re: Experimental basis for the Non-Beneficial Gap Problem
    ... Do you not remember the many times I've listed the papers by Yockey, ... sequences in sequence space via phylogenetic sequence comparisons and ... research of substituting the 20 different types amino acids in two ... After each substitution, the protein sequence was ...
    (talk.origins)
  • Re: Harshman vs. Hershey
    ... evolution is that one starts from some random sequence (or, ... of functional cytc to non-cytc sequences and that value can be used to ... research of substituting the 20 different types amino acids in two ... After each substitution, the protein sequence was ...
    (talk.origins)
  • Experimental basis for the Non-Beneficial Gap Problem
    ... Do you not remember the many times I've listed the papers by Yockey, ... sequences in sequence space via phylogenetic sequence comparisons and ... research of substituting the 20 different types amino acids in two ... After each substitution, the protein sequence was ...
    (talk.origins)
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