[Cz-biology] Requesting consideration of approval of[[Life/Draft]]to replace [[Life]]

Wed Jan 23 20:59:39 CST 2008

Biology Workgroup:

In the CZ-biology mailing list, David Goodman writes:  "Philosophy of
biology to me is less important than actual biology, but then I'm a
biologist not a philosopher. What life ultimately is and how life is exactly
defined cannot be intelligently discussed until you know what its physical
structure consists of.  I'd move all the philosophy to a separate article as
subsidiary. The main article on the subject should be about life as
biology."  

"This is too important an article to proceed without some time for thought
about it. "

I agree with David Goodman that "The main article on the subject 'Life'
should be about life as biology."  Since CZ has defined biology (in its
[[Biology]] article) as the "science of life", one might argue that that
biology article, and those related articles it links to, should cover the
subject of "life as biology" -- as they appear to do.

I believe we need, in addition, as emphasized in the [[Life]] article, an
article that focuses on life as the processes that enable the activity of
'living', with the theme, "''Life is what is common to all living beings''"
(Christian De Duve).  Namely, the theme what fundamental processes
characterize living things that distinguish them from non-living matter?

The discovery of those fundamental processes clearly have led to a deeper
understanding of the biology of life.  To take one example from the article:

a)    Living things sustain their biology in virtue of their location within
the downhill stream of a flowing energy gradient, whether that gradient
consists of photons emitted by the sun, electrons transferred from reduced
mineral compounds in hydrothermal vents, or energy-rich matter generated by
other livings.  We must understand that before we can make sense of the
"physical structure" comprising living things (on Earth).

b)    Living things build their physical structure in virtue of their
ability extract a portion of that energy flowing past them and to utilize it
to do the work of creating and re-creating the ordered (low-entropy) state
that constitutes their physical structure.

c)     Living things can accomplish that work of self-fabrication and
re-fabrication in virtue of their ability to maintain a state far from the
equilibrium (high-entropy) state of randomness.

d)    They accomplish the maintenance of a far from equilibrium state in
virtue of their ability to export into their surrounding a more degraded,
less usable form of energy than they extracted, in quantities that create
more disorder overall -- system plus surroundings - according to the
dictates of the Second Law of Thermodynamics.

e)    In doing that, they hasten the rate of dissipation of the energy
gradient they lie in, hastening its distribution toward maximal randomness,
a disposition that energy gradients possess  by nature.

Those considerations, of the driving force of energy gradients and the
constraints imposed by the Second Law of Thermodynamics, reveal fundamental
aspects of the commonalities of the biological basis of living things,
despite their diversity of physical structures.  They seem to me more
germane to a Science of Life than to a Philosophy of Life.

Nevertheless, the point of the request to replace the currently approved
version of [[Life]] with the nearly year-long redrafting, [[Life/Draft]],
resides in the fact that, though the theme of the article has not changed,
the development of the theme has proceeded to the point where the draft
version improves on the CZ approved version.

I personally would not know how to proceed with an article entitled,
[[Philosophy of Life]], but I doubt it would bear much resemblance to our
[[Life]] article.

On the Talk page of [[Life/Draft], David also comments as follows:

"::Yes it's [[Life/Draft]] an advance in some respects, but I think as
general observations:"

"1/the two sections on systems biology and on thermodynamics have been
enlarged disproportionately to the rest of the article."

A.S response:  Yes, I can see how the systems biology section could be
shortened.  Its main message is about a fundamental aspect of living
organisms, namely the 'emergence' of levels of organization with novel
properties not predictable from the parts.  I can see shortening the
section, possibly re-titling it to refer more specifically to emergence, and
reconsidering where I should be located in the article.  I will work on
that.

I will re-examine the length of thermodynamics section.  The concepts there
may be difficult for many readers and therefore may require a more lengthy
discussion than the other sections in the article.

"2/ The total absence of some sort of systematic discussion of what types of
living things there are is a little remarkable, both in the older version
and the present one. Life is about living organisms, after all. "

A.S response: Yes, I agree, "Life is about living organisms."  But, on a
deeper, more fundamental level, life is also about the commonalities of the
processes, shared by all living organisms (on Earth), that underpin the
activity of living itself.  We have taken that as our (stated) theme for the
article.  So the article is about living organisms after all.  Perhaps what
we need to do to get to the level of the taxonomy of living organisms is to
link to the appropriate articles in CZ that do that, or to write a separate
article that deals with the diversity of living organisms on Earth.

"3/the organic chemistry as informatics section at the end is not adequate
integrated in either version. Some of it is a simple duplication of the
section on molecules, some of it  probably goes up with informatics, to
explain the physical substrate that is actually being discussed "

A.S Response: I agree, and will rework the section in response to David's
observations.

"4/ "Identifying the different scientific perspectives seems a parallel
article, or an alternate way of arranging the article, but I think it was
intended as a summary.

A.S Response:  Yes, it was intended as a summary, but also one that arranges
the sequence of the article differently, to give the reader a reprise in a
novel way that hopefully encourages reflection.

Is the current version perhaps intended as an intermediary version until the
other portions can be expanded? If so, do we really want such a long article
as that would be? Instead of mainly adding to the original content, perhaps
we should be thinking of concision. "

A.S Response:  Naturally, some topics in CZ will require more text than
others.  With a topic as large as 'Life' (no pun intended), perhaps such is
the case.

Anthony.Sebastian

From: cz-biology-bounces at mail.citizendium.org
[mailto:cz-biology-bounces at mail.citizendium.org] On Behalf Of David Goodman
Sent: Sunday, January 20, 2008 5:49 PM
To: Biology Workgroup List
Subject: Re: [Cz-biology] Requesting consideration of approval
of[[Life/Draft]]to replace [[Life]]

Philosophy of biology to me is less important than actual biology, but then
I'm a biologist not a philosopher. What life ultimately is and how  life is
exactly  defined cannot be intelligently discussed until you know what its
physical structure consists of.  I'd move all the philosophy to a separate
article as subsidiary. The main article on the subject should be about life
as biology.  

This is too important an article to proceed without some time for thought
about it. 

On Jan 20, 2008 3:59 PM, John Moffett <john at factinista.org
<mailto:john at factinista.org> > wrote:

Hello All,

Yes, the article is much improved, and should replace the old one. Changes
and additions can be made later. By philosophy of biology I meant it
discussed ideas about what life is and how it is defined more than it
discusses the basics of how life works (membranes, metabolism, eukaryotes
vs. prokaryotes, ribosomes and the relation between genes and proteins, gene
regulation, evolution, etc).

John M.

  _____  

From: cz-biology-bounces at voltaire.citizendium.org
[mailto:cz-biology-bounces at voltaire.citizendium.org] On Behalf Of Anthony
Sebastian

Sent: Sunday, January 20, 2008 2:22 PM

To: 'Biology Workgroup List'
Subject: Re: [Cz-biology] Requesting consideration of approval
of[[Life/Draft]]to replace [[Life]]

Workgroup:

I agree with John that we need to include the commonalities of metabolism
and information processing in the article.  But that will take some time to
get right and succinct - universality of biochemistry.  We can do that in
the next draft.

I just think we have a much improved draft now compared with the approved
version, and should make the substitution now to show a better version.

I disagree the article discusses the philosophy of biology.  It tries to
discuss the shared characteristics of all living things, as much as we know
it today.

Thanks.

Anthony.Sebastian

From: cz-biology-bounces at mail.citizendium.org
[mailto:cz-biology-bounces at mail.citizendium.org] On Behalf Of John Moffett
Sent: Sunday, January 20, 2008 5:59 AM
To: 'Biology Workgroup List'
Subject: Re: [Cz-biology] Requesting consideration of approval of
[[Life/Draft]]to replace [[Life]]

Hello All,

It will take some time to go through all that to look for problems or
omissions. In general, it looks good, but from a biologist's perspective it
seems to discuss the philosophy of biology more than the substance of it.
For example, any discussion of life that leaves out ribosomes, and the
DNA-RNA-protein expression system is not really getting to the meat of the
subject of how life works.

John

  _____  

From: cz-biology-bounces at voltaire.citizendium.org
[mailto:cz-biology-bounces at voltaire.citizendium.org] On Behalf Of Anthony
Sebastian
Sent: Saturday, January 19, 2008 8:24 PM
To: cz-biology at voltaire.citizendium.org
Subject: [Cz-biology] Requesting consideration of approval of
[[Life/Draft]]to replace [[Life]]

Biology Workgroup:

Please review the draft version of the approved article, [[Life]], at
http://en.citizendium.org/wiki/Life/Draft.  Please consider it for approval
to replace the approved version, as it has been considerably reworked since
its April '07 approval, and may be an improvement over what we have now as
the approved version.

Thank you.

Anthony.Sebastian

.

-------------------------

Anthony Sebastian, MD

Professor of Medicine

University of California San Francisco

Postal Mail Address:

Anthony Sebastian, MD

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San Francisco, CA 94131

Anthony_Sebastian at msn.com [preferred email address]

415-648-0834 [tel]; 415-358-5953 [fax]

Faculty Affiliations:

Department of Medicine, Division of Nephrology

Clinical and Translational Science

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   --CTSI Strategic Opportunities

     Support Center

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sebastia at gcrc.ucsf.edu

Faculty Webpage:

http://medicine.ucsf.edu/nephrology/faculty/anthony_sebastian.html 

View/Download Selected Publications:

http://groups.msn.com/Anthony-Sebastian

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