Re: Lack of evolution in computers and living things

On Jun 18, 10:44 am, Gene Poole <gene.po...@xxxxxxxxxxxxxxxxx> wrote:

Even with the distribution of systems with relative few residues
(<400) the linear expansion of the average gap distance is obvious.
Consider the following 3D illustration of hyperdimensional sequence
space and the location of smaller and larger protein-based systems
within that space relative to each other:

http://www.pnas.org/content/vol103/issue38/images/large/zpq0370634700...

What is this? It is completely void of context. "Hyperdimensional?"
What are the dimensions?

Protein sequence space dimensionality depends upon the size of the
protein sequence in question.

"The dissimilarity matrix then was subject to the classical
multidimensional scaling (MDS) procedure (26) to find the positional
coordinates in a multidimensional (1,898 dimension) space of the
protein structure universe. We used s99.95 to prevent a few extremely
large similarity scores from dominating the distribution feature of
the structural space map. To capture and visualize the major features
of the high dimensional space, we represent the protein structure
space in three dimensions (Fig. 1) by using the three components with
highest eigenvalues, which are substantially greater than the rest."

What are these graphs supposed to represent?

A projection of 1898 dimensional space onto 3 dimensions (bottom-left
graph in the jpg).

I assume they were attached to an article (the PNAS URL). What is the
article?

http://www.pnas.org/cgi/content/full/103/38/14056

Do the authors support your conclusions?

They don't discuss the gap problem in the article, even though their
data demonstrates that the average gap distances do in fact increase
linearly as a function of size.

Notice that the larger the sequences the farther apart they are on
average in sequence space. Smaller sequences are more closely
clustered together and have a significantly smaller average distance
between themselves compared to larger sequences. This is a linear
function that increases in a linear manner as the size of the minimum
sequence requirement increases.

I don't see that at all. The parent article please.

Do you not see an increase in the average size between the 370aa
proteins (red dots) in comparison to the 30aa proteins (dark blue
dots)?

Now, consider that a linear increase in the gap distance translates
into an exponential in crease in the average number of random
mutations needed (of any kind) to find a novel beneficial sequence.
This problem only gets exponentially worse and worse, statistically,
as one approaches and moves beyond the 1000aa level of functional
complexity.

In other words, the answer to my questions above is, "I have no data to
support my assertions." HTH.

Only if you are blind to the obvious. Another way you can disprove my
position is by showing two 1000aa+ systems that are functionally
unique but that are within 5 or 6 residue difference of each other.

Sean Pitman
www.DetectingDesign.com

.

Relevant Pages

  • Re: Hyperdimensional Sequence/Structural Space - for Howard Hershey
    ... the clear relationship between beneficial structure and sequence. ... of aa's in a protein and claiming that that number represents ... than having 172 dimensions. ... character difference is just one step away from its closest neighbor. ...
    (talk.origins)
  • Re: Hyperdimensional Sequence/Structural Space - for Howard Hershey
    ... the clear relationship between beneficial structure and sequence. ... of aa's in a protein and claiming that that number represents ... than having 172 dimensions. ... character difference is just one step away from its closest neighbor. ...
    (talk.origins)
  • Re: Sean Pitman: definitions wanted
    ... >> protein sequences were far smaller than they are now. ... > in a sequence without a complete loss of function as long as it is done ... as well as minimum size and specificity requirements ... The mathematical properties of the specific random walk on the ...
    (talk.origins)
  • Re: Experimental basis for the Non-Beneficial Gap Problem
    ... It suggests that the particular protein we happen to have ... If you disagree, attack my reasoning. ... sequences in sequence space via phylogenetic sequence comparisons and ... Evolution is observed all the time, in real time, when it comes to ...
    (talk.origins)
  • Re: Non-beneficial Gaps
    ... majority of possible protein sequences are "non-viable". ... selection simply excludes such sequences from being searched. ... certainly can search regions of non-viable protein sequence space. ... sequence space can be reached by a single mutation from some pre- ...
    (talk.origins)