From: crb7q@kelvin.seas.Virginia.EDU (Cameron Randale Bass)
Subject: Re: Physics News Update #92 (8/19)
Keywords: physics news interesting cherry
Organization: University of Virginia
Distribution: usa
Date: Thu, 20 Aug 1992 05:40:59 GMT

In article <1992Aug19.205526.13923@midway.uchicago.edu> revu@midway.uchicago.edu writes:

>**********************************************************************
>
>PHYSICS NEWS UPDATE
>A digest of physics news items prepared by Phillip F. Schewe, AIP
>Public Information
>Number 92   August 19, 1992
>
>THE LANDSCAPE OF DNA MAY BE FRACTAL.  Several studies of DNA reveal
>unexplained relationships between nucleotides distant from each other.
>A Rockefeller/Tokyo team of scientists found such correlations in the
>genes regulating blood coagulation (Europhysics Letters, 7 Feb).
>Researchers at Boston University transformed sequences of nucleotide
>into a series of "random walks" and discovered correlations over many
>scales--- 1000, 10000, and 100000 nucleotide---suggesting a fractal
>pattern (Nature, 12 Mar.).  Self-similarity on a scale of 50 million
>nucleotides has showed up in a study at IBM (Phys. Rev. Lett., 22
>June).  Long-range correlations did not appear in DNA sequences where
>introns, little-understood intervals of apparently noncoding DNA, were
>absent, a fact which had frustrated earlier attempts to find
>correlations in bacterial DNA which did not contain introns.
>(Science, 7 August 1992.)

     Observation 1), the nuclide sequence is not random.
     Observation 2), as stated above, introns are not well understood.
     Observation 3), sequences that are similar are strongly correlated.
            Comment: their 'test' of whether this was what was
                     happening was to divide up the sequence into
                     segments of length 100 and then randomize the base
                     pairs within this segment and perform the same
                     random walk to see if they got the same long
                     range order.  Surprise, they did.  No shock actually,
                     since it seems to me that the long range behavior of 
                     the random walk may not be greatly affected
                     by sufficiently local base pair randomization.
                     A better test might have been to keep segments
                     of L=100 intact and randomize them globally to see if 
                     the long range order is 'thermalized'.  If it
                     is not, I think they're in real poo poo.
     Observation 4), the sentence that most sent alarm bells going was
                     "we find the most robust fits to power laws
                     scaling by computing the DNA walk for nucleotide
                     class (purine vs. pyrimadine) rather than for
                     any specific nucleide."
     Observation 5), long range correlations are quoted to 10^5 base pairs for 
                     a sequence of ~70,000 base pairs.
     Observation 6), the vast majority of the sequences in which they 
                     found correlations were comprised of over 50% introns
                     (see observation 2)).
     Observation 7), 60% of the data presented are from sequences 
                     of less than 12,000 base pairs
     Observation 8), their comparison of this 'long range order' with 
                     scaling behavior in nonequilibrium dynamical processes
                     seems to be a reach (to put it mildly). 

     If they found anything, it may have been that introns are strongly
     correlated at long range.  However, even this seems a bit uncertain.
     I also note that it might be easy to replicate using Genbank sequences 
     listed to investigate this in a more critical light,
     a cheap easy letter to Nature.  I blew my last one when I did not
     put out a quick response to the idiot that noticed in those hallowed pages
     that military campaigns seem to be correlated with time of 
     year.  Apparently, he had never thought of the obvious explanation
     that it is cold in winter.

                               dale bass
-- 
C. R. Bass                                           crb7q@virginia.edu
Department of Mechanical and Aerospace Engineering
University of Virginia
Charlottesville, Virginia                            (804) 924-7926