HDTenEightyP/NetNews huggingface dataset:
From: gapdrr@gsusgi2.gsu.edu (Daniel R T Rothman)
Newsgroups: bionet.info-theory
Subject: Re: dspace question and relatedly, D
Date: 15 Apr 92 14:32:25 GMT
Organization: Georgia State University

toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes:

>In article <gapdrr.703287864@gsusgi1.gsu.edu> gapdrr@gsusgi2.gsu.edu
>(Daniel R T Rothman) writes:

>>	[Toms] paper states that the orientations of the components are not
>>    germaine, and thus may be ignored, yielding, by my calculations (6-3)n
>>    degrees of freedom. tom uses the formula 3n-6 for dspace.

>The formula is used in molecular spectroscopy.  Look up under vibrations of
>molecules also.  Suppose there are n atoms.  Then to define the location of the
>n atoms in a coordinate system, we need 3n numbers.  How a molecular machine
>works (usually) is not affected by its orientation (unless it is relative to
>some other object, a case we will ignore for simplicity).  There are 3 numbers
>that define the center of gravity of the molecule, and another three numbers
>for its rotational orientation in space.  So 6 of the 3n numbers are not
>important in a description of what the machine is doing, so we get 3n-6.  This
>is important in molecular spectroscopy because it determines the number of
>modes of vibration of the molecule.  The published version of the theory
>doesn't deal in molecular vibrations (directly) so the connection is not so
>clear.  (I mentioned my reason for not doing this in an earlier posting.)

these six numbers, the x-,y- and z- coords of the molecule, and the 
three orientation numbers are irrelevent in a coordinate system such as you
described in your paper. with the coordinate axis FIXED at the local cg,
there is no need to describe them. it has always been my experience that
degrees of freedom are measured in the local coordinate system. is it perhaps
true that the 3n-6 formula is appropriate for a global coord system, but not
in a natural one?

is it perhaps appropriate to say then that the number dspace is a measure of
modes of vibration, and not necesarily one of degrees of freedom? i have this
distinct feeling that we're trying to discuss using different definitions for
terms....
From: CFARMER1@UA1VM.BITNET ("Chet Farmer, Asst. Dir., Project IDEALS")
Newsgroups: bionet.info-theory
Subject: ANNOUNCEMENT OF SAGSET CONF
Date: 9 Apr 92 22:23:12 GMT
Distribution: bionet


  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* *                                                                 * *
*     ----------------------                                          *
*     Call for participation:  ---------------------                  *
*     ----------------------   Joint 1992 conference:  ///////////    *
*                              ---------------------   S A G S E T    *
*                                                       I S A G A     *
*   Society for the Advancement of Games and           \\\\\\\\\\\    *
*   Simulations in Education and Training                             *
*                   International Simulation and Gaming Association   *
*                                                                     *
*   Conference theme:        Developing transferable skills through   *
*   ----------------                          simulation and gaming   *
*                                                                     *
*   18-21 August, 1992       Napier University, Edinburgh, Scotland   *
*                                                                     *
*   For further information:                          Fred Percival   *
*   =======================       SAGSET/ISAGA Conference Secretary   *
*                                                 Napier University   *
*                                                 219 Colinton Road   *
*   Telephone:  44 / 31-455-4394                 Edinburgh EH14 1DJ   *
*   Facsimile:  44 / 31-455-7989                           Scotland   *
*                                                                     *
* *                                                                 * *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

+-----------------------------------------------------------------------+
|  Chet Farmer, Assistant Director   |   English / 103 Morgan           |
|  Project IDEALS -- FIPSE, DoE      |   Tuscaloosa, AL  35487-0244     |
|  University of Alabama             |   tel 205-348-9494               |
+-----------------------------------------------------------------------+
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: promoters for M. capricolum (was: Hyperplane separability)
Keywords: information theory, molecular machines, promoters, homosequences
Date: 14 Apr 92 20:16:17 GMT
Organization: NCI Supercomputer Facility, Frederick, MD

In article <gapdrr.703274125@gsusgi1.gsu.edu> gapdrr@gsusgi2.gsu.edu
(Daniel R T Rothman) writes:

>please no flames, i'm REAL new at this.
Have some chowder instead.

|toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes:
|
|>In article <brenner.702379747@husc10> brenner@husc10.harvard.edu (Steven Brenner)
|>writes:
|
|>|>So: how did you pick these out?  
|>|
|>|These promoters were *all* of those listed in GenBank for this
|>|organism.  The way all but two they got in there is that original authors
|>|used the "hmmm, it looks like there's a promoter here based
|>|upon what I think a promoter looks like, and because its
|>|just a little ways upstream of the first gene I found."  In fact, the
|>|group which found something like 80% of those I listed gave no method
|>|at all by which they picked putative promoters.  Further, they didn't
|>|pick some others which seemed just as good to me (based on E. coli
|>|data) but weren't where the group expected them to be.
|
|>So it's really a big guess, and I wouldn't trust the results very much!
|
|perhaps a silly question, but is it not possible to make a qualitative
|estimate by creating distribution histograms for a nmber of orgnisms for
|the range around the purported promoters and making a determination based
|on the site homogeneity? i realize it's really over the thumb, but it
|might be better than what you've currently got..

It's no good to make an estimate of any kind.  The trouble is that "out there"
in nature are the patterns to which Steve's protein binds.  He is attempting to
make a model of the patterns.  If he makes a model based on his own guesses,
it's circular reasoning.  His model would be based on nothing substantial!  To
avoid this, he must use pure experimental data which indicate the locations of
the binding sites.  There are lots of ways to do this in molecular biology, but
they may be difficult or impossible to do in a particular system.  Finding
promoters can be done by dropping random bits of the genome into a plasmid
(circle of DNA) such that if there is a promoter the organism becomes drug
resistant (or makes a stain turn blue, or glows or does your taxes for you...
:-)

Tom
From: gapdrr@gsusgi2.gsu.edu (Daniel R T Rothman)
Newsgroups: bionet.info-theory
Subject: Re: promoters for M. capricolum (was: Hyperplane separability)
Keywords: information theory, molecular machines, promoters, homosequences
Date: 14 Apr 92 17:55:25 GMT
Organization: Georgia State University

toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes:

>In article <brenner.702379747@husc10> brenner@husc10.harvard.edu (Steven Brenner)
>writes:

>|>So: how did you pick these out?  
>|
>|These promoters were *all* of those listed in GenBank for this
>|organism.  The way all but two they got in there is that original authors
>|used the "hmmm, it looks like there's a promoter here based
>|upon what I think a promoter looks like, and because its
>|just a little ways upstream of the first gene I found."  In fact, the
>|group which found something like 80% of those I listed gave no method
>|at all by which they picked putative promoters.  Further, they didn't
>|pick some others which seemed just as good to me (based on E. coli
>|data) but weren't where the group expected them to be.

>So it's really a big guess, and I wouldn't trust the results very much!

perhaps a silly question, but is it not possible to make a qualitative
estimate by creating distribution histograms for a nmber of orgnisms for
the range around the purported promoters and making a determination based
on the site homogeneity? i realize it's really over the thumb, but it
might be better than what you've currently got..

please no flames, i'm REAL new at this.


daniel rothman                        | gapdrr@gsusgi2.gsu.edu  Internet
computer specialist - GAP             | gapdrr%gsusgi2@gsuvm1   Bitnet
 - - funny quote thingy - - 
Newsgroups: bionet.info-theory
From: mroussel@alchemy.chem.utoronto.ca (Marc Roussel)
Subject: Re: dspace question and relatedly, D
Organization: Department of Chemistry, University of Toronto
Date: Thu, 16 Apr 1992 00:46:26 GMT

In article <gapdrr.703287864@gsusgi1.gsu.edu> gapdrr@gsusgi2.gsu.edu
(Daniel R T Rothman) writes:
>first: tom states that dspace represents the degrees of freedom available
>    to the components of a three-D system, where the coordinate origin is
>    established at the systems center of gravity (cg). 
>	normally, the degrees of freedom for this system would be calculated
>    as 6n (where n is the number of components), representing the 3 spatial
>    dimensions, and the 3 directions of orientation.

     This is wrong.  The position of each particle of a system embedded
in three-space is described by three coordinates; 6n coordinates are
required to construct a phase space since both the positions and momenta
are needed to describe the state of the system.  Particles don't have
"orientations".

>	the paper states that the orientations of the components are not
>    germaine, and thus may be ignored, yielding, by my calculations (6-3)n
>    degrees of freedom. tom uses the formula 3n-6 for dspace.

     Three coordinates describe the position of the centre of mass;
three more describe rigid rotations about the c.m.  In configuration
space, that leaves 3n-6 relevant coordinates.  In phase space, there are
6n-12 relevant coordinates (the 6 irrelevant configuration coordinates
and 6 associated generalized momenta).

>	this formula appears to break down for small n ie 1 or 2.

     Our discussion so far has involved some implicit assumptions.  If
the symmetry of the system under consideration is that of a sphere,
rotations about the c.m. are not defined; since a single particle has
the symmetry of a sphere, a single particle is described simply by three
translational coordinates.  If the symmetry of a system is that of a
cylinder, rotations about the axis of symmetry are undefined.  (After
all, how could you tell?)  There are only two well-defined rigid
rotation coordinates for such systems so the number of relevant
configurations is 3n-5.  Systems with only two particles clearly have
the symmetry of a cylinder (symmetry axis along the line of centres).

>second: it occured to me that the vectorization that is done to the
>    informational degrees of freedom was very similar to the vectorization done
>    in non-linear diff-eq's. i haven't done enough work with large non-linear
>    systems to be authoritative about this, but was wondering if someone could
>    offer more insights into this.

I happen to know something about nonlinear DE's, but I'm not sure I know
what you're getting at.  Perhaps you could refer to specific bits of
Tom's paper and I can comment.  I think this could be interesting.

                                Sincerely,

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: dspace question and relatedly, D
Date: 16 Apr 92 23:45:46 GMT
Article-I.D.: fcs280s.3012
Organization: NCI Supercomputer Facility, Frederick, MD

In article <gapdrr.703348345@gsusgi1.gsu.edu> gapdrr@gsusgi2.gsu.edu
(Daniel R T Rothman) writes:

>these six numbers, the x-,y- and z- coords of the molecule, and the 
>three orientation numbers are irrelevent in a coordinate system such as you
>described in your paper. with the coordinate axis FIXED at the local cg,
>there is no need to describe them. it has always been my experience that
>degrees of freedom are measured in the local coordinate system.

Note that the difference between 3n-6 and 3n doesn't matter much if the number
of atoms n is huge, as is usually the case in biology.

> [I]s it perhaps true that the 3n-6 formula is appropriate for a global coord
> system, but not in a natural one?

Hunh?

>[I}s it perhaps appropriate to say then that the number dspace is a measure of
>modes of vibration, and not necesarily one of degrees of freedom? i have this
>distinct feeling that we're trying to discuss using different definitions for
>terms....

The 3n-6 formula is well known in molecular spectroscopy.  It counts either the
number of positions and momenta of a system OR the number of modes of vibration
in a molecule.  That is, you need 3n-6 numbers to describe the state of the
system, no matter how you look at it.  3n-6 is the number of degrees of
freedom: it's the number of independent directions that things can move in.

dspace is now going one step further.  To connect these degrees of freedom to a
translation of Shannon's work into molecular biology, we have to find the
degrees of freedom that the molecular machine is USING.  But since the
discussion is very general, we can't just go out and count them.  (Actually,
nobody knows how to count them anyway!)  So I used 3n-6 as AN UPPER BOUND on
the number of degrees of freedom that the machine uses.  Think about pins in a
lock on your door.  Since there are huge numbers of atoms, n is huge.  So 3n-6
is enormous.  But the effective number of degrees of freedom in the lock (in
terms of how the lock works) is only the number of pins.  That is, atoms within
a pin are correlated.  So the number we want is dspace < 3n-6.  In general it
is probably much less than, so that is the origin of formula (2) in the paper,
dspace << 3n-6.

Later on in the paper I use the fact that n is huge in the case of rhodopsin so
that even if dspace is much less than 3n-6, the number of dimensions used by
rhodopsin could still be big enough to have sharp edged spheres.

For a long time I constructed the theory on the basis of harmonic modes.
Although this is possible, the math was tricky.  It is not clear to me whether
that will be a good way to look at things in the long run or not, we simply
don't know enough about how the machines do their thing.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: C749SCB@SEMOVM.SEMO.EDU (Walt Lilly)
Newsgroups: bionet.general
Subject: protease mutants in fungi, yet again
Date: 9 Apr 92 17:50:55 GMT
Distribution: bionet

I apparently had a problem with a message posted 04/07/92.  Let me try
again.  We are trying to isolate mutants for specific proteases from
a wood-decaying fungi.  Anyone have a suggestion for a selection scheme
that might work?  The problem is complicated by the fact that several
proteolytic activities are produced by the fungus including both exo-
and endo- proteases.  We can operate from spores using liquid or plate
culture.

Does anyone know of commercially available peptide substrates conjugated
to a toxin?  I'm thinking of some kind of fungal growth inhibitor,
perhaps as simple as CN, that might be released upon hydrolysis.
Any hot ideas?
************************************************************************
*  WALT LILLY                     *                                    *
*  DEPARTMENT OF BIOLOGY          *  INTERNET: C749SCB@SEMOVM.SEMO.EDU *
*  SOUTHEAST MISSOURI STATE UNIV. *  BITNET: C749SCB@SEMOVM            *
*  CAPE GIRARDEAU, MO 63701       *                                    *
************************************************************************
From: AJB@UK.AC.DARESBURY.DLVH
Newsgroups: bionet.general
Subject: Test 1 of 3  Ignore
Date: 14 Apr 92 16:51:00 GMT
Distribution: bionet
Organization: SERC Daresbury Lab., Warrington, U.K.
Original-To: BIOFORUM@UK.AC.DARESBURY
Via: UK.AC.DARESBURY.DLVH;  Tue, 14 Apr 92 16:55 WET (V40 at UK.AC.DARESBURY.DLGM)

Daresbury BIOSCI Test. Ignore
From: kab@WELCHGATE.WELCH.JHU.EDU (Kerryn Brandt)
Newsgroups: bionet.general
Subject: Re:  Question: What are the HGML numbers in MEDLINE?
Date: 14 Apr 92 19:13:00 GMT
Distribution: bionet

David Steffen asked about the HGML numbers in the MS field of MEDLINE
(actually the SI field in NLM's record):

HGML was the Human Gene Mapping Library; as David mentioned, all of the
data in HGML was moved to GDB (Genome Data Base) in August of 1990.  The
HGML number in MEDLINE's SI field is the accession number of the
citation in the former HGML database.  You can use these numbers to
retrieve the same citations in GDB's Source Manager (Specify ID Type: 
HGML Id; then enter the Id:), which contains all of the literature
references that were in HGML.  You might then find additional
information by calling one of the other data managers from the retrieved
source.  For example, H6936 is a paper by Law et al. on the hemopexin
gene.  If you call Locus Manager from this record, you will find
information on the HPX locus.  If you call Probe Manager from the HPX
locus, you will retrieve data for the lambdaHx5 probe.

Not all references from HGML that are in MEDLINE have the HGML Id
numbers in the SI field; we estimate perhaps 45% do.  Since GDB's
inception, every citation entered into the Source Manager has also been
assigned a unique GDB Id number.  This information does not appear in
the MEDLINE SI field.

Hope this helps.

Kerryn Brandt
Training Coordinator
Genome Data Base
The Johns Hopkins University School of Medicine and the 
William H. Welch Medical Library
1830 E. Monument St.
Baltimore, MD 21205

(410)-955-1307
FAX:  (410)-955-0054
Internet:  kab@library.welch.jhu.edu 
Newsgroups: bionet.general
From: young@sasquatch.serum.kodak.com (Rich Young (x37176))
Subject: Re: Mechanical stress and lignification
Organization: Clinical Products Division, Eastman Kodak Company
Date: Thu, 9 Apr 92 22:59:25 GMT

In article <1992Apr2.144844.20239@macc.wisc.edu> nmrdb@vms.macc.wisc.edu (BEVERLY SEAVEY) writes:
>In article <kljjkbn@lynx.unm.edu>, mwfolsom@hydra.unm.edu (Mike Folsom) writes...
>
>>>I only received one e-mail response to my question about the responses
>>>of plants to mechanical stress ...
>>>
>>>I'm interested in factors affecting the resistance of crop varieties to
>>>'lodging' damage and I wondered if anyone knows if mechanical stress
>>>can, itself, lead to lignification?  I know about 'stress' wood in
>>>trees but don't know if more subtle changes occur in response to
>>>mechanical stress such as the load from wind blowing on a canopy.
>>>
>
>Check out work by Janet Bramm. She had an article in cell showing that
>mechanical stimulation of Arabidopsis resulted in increased calmodulin
>production ( which I can imagine might be related to increased polysaccaride
>production and therefore cell wall stuff). The first article was in 
>Cell about 
>late 1989, I think
>> 


   I didn't think for a minute that I'd be able to contribute anything of
   use to this group, but I just happened to be reading through back issues
   of SCIENCE NEWS and remembered a reference to the Braam study.

   The summary is in SCIENCE NEWS, Vol. 137, No. 8, page 117; Feb. 24, 1990,
   and the published study is in CELL, Feb. 9, 1990.

   I hope this is of some use, even though it's a week late.


-Rich (young@serum.kodak.com)
From: AJB@DLVH.DL.AC.UK
Newsgroups: bionet.general
Subject: Test 3 of 3. Ignore
Date: 14 Apr 92 16:52:00 GMT
Distribution: bionet


IRLEARN BIOSCI Test. Ignore
From: Eric_S_Klien@cup.portal.com
Newsgroups: bionet.general
Subject: Alcor Nevada
Date: Sat, 11 Apr 92 18:46:16 PDT
Organization: The Portal System (TM)
Distribution: world

Alcor Nevada will be meeting Sunday April 12th at 5 PM at the 
Riverside Casino owned by Don Laughlin in Laughlin, Nevada.  Don 
Laughlin will be attending our meeting.  The use of Hydergine to slow 
down cerebral arteriosclerosis, and therefore to delay the day that 
you will need to be cryonically suspended will be discussed.  For more 
info call Eric Klien at (702) 255-1355.
 
Note that opinions of this discussion group do not necessarily 
reflect the views of the non profit organization Alcor.
From: young@sasquatch.serum.kodak.com (Rich Young (x37176))
Subject: Re: Image processing newsgroup under discussion
Organization: Clinical Products Division, Eastman Kodak Company
Distribution: bionet
Date: Thu, 16 Apr 92 16:55:12 GMT

ajt@uk.ac.sari.rri (Tony Travis) writes:

[...]

>I have just been active in promoting the creation of bionet.plants
>where, amongst other things, we are dicussing the application of image
>analysis to plant anatomy.

[...]

	Is bionet.plants live yet?  I remember the voting, but my newsreader
	hasn't yet asked me to subscribe.


-Rich (young@serum.kodak.com)
From: kristoff@GENBANK.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.general
Subject: IMPORTANT - new BIOSCI transatlantic distribution mechanism
Date: 10 Apr 92 20:34:53 GMT
Distribution: bionet


BIOFORUM/bionet.general readers,

Monday AM, UK (GMT) time, we will change our distribution mechanism on
this newsgroup between GenBank and Daresbury, the U.K. BIOSCI node.

Messages will be exchanged directly between the news systems at these
two sites instead of via the current mail distribution.  This will
ultimately add reliability and allow easy recovery from any prolonged
network interruptions because the news software will automatically
check the archives at each site after an interruption and retrieve any
messages which may have been missed.

Over the next few weeks we will be switching all of the newsgroups to
this new distribution mechanism, but first we are moving selected
groups as a test.  We will monitor the system closely and appreciate
your patience if any problems do develop.  We will do our best to
resolve them ASAP.

E-mail subscriptions will continue to be available from both sites.
The only difference is that currently GenBank and Daresbury exchange
messages by mail and then pass them on to e-mail subscribers.  Now the
exchange will be only via news and news postings will be extracted and
mailed to e-mail subscribers at each site.  Of course, we continue to
encourage all of you to drop e-mail as a means of participation and
make the switch to news software at your local sites.

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff@genbank.bio.net