From: (JohnM) Sender: (Yaneer Bar-Yam) To: complex-science Date: Mon, 18 Aug 2008 01:32:40 -0400 Message-ID: X-Original-Return-Path: Received: from smtp107.sbc.mail.re2.yahoo.com ([68.142.229.98] verified) by necsi.org (CommuniGate Pro SMTP 4.0.6) with SMTP id 22508525 for complex-science@necsi.org; Wed, 06 Aug 2008 11:16:42 -0400 Received: (qmail 75876 invoked from network); 6 Aug 2008 15:16:40 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=prodigy.net; h=Received:X-YMail-OSG:X-Yahoo-Newman-Property:Message-ID:Reply-To:From:To:References:Subject:Date:MIME-Version:Content-Type:X-Priority:X-MSMail-Priority:X-Mailer:X-MimeOLE; b=B7Yjrt5vgTLSg7yKuKsn9dltTCJFhjo1HbO3Vx4KTe0LoozViABi3C+9FGSR3mhy0e481C8JpcBB0TW/QYvdPXMHteUa1ZPpABN1x3cxXB/OqoE6Gc+o+q0zdUuI1677wTgxcefhE3OCM0QJeWkRlVi+gPbbBgEjPNFstvwugjc= ; Received: from unknown (HELO JohnCompaq) (jamikes@prodigy.net@12.75.197.18 with login) by smtp107.sbc.mail.re2.yahoo.com with SMTP; 6 Aug 2008 15:16:27 -0000 X-YMail-OSG: VhG2zjsVM1nHvGcyxfBbhUNMNOHkqwT9tMcQntuxnMP62wUYqHmZ3NrMWY2xrs6ZrSX_DTyOMS1gl1Z3norQzjriGXGrl8ZfaYnhuvL.IGQvAUVmVrgxi_cocQ.ZbPIxLwc3qNe8Tteu3LFVVoB9jU4G X-Yahoo-Newman-Property: ymail-3 X-Original-Message-ID: <000c01c8f7d7$633c88c0$12c54b0c@JohnCompaq> Reply-To: "JohnM" X-Original-To: References: Subject: Re: What is a gene? A dynamic & triadic definition of a gene X-Original-Date: Wed, 6 Aug 2008 10:45:48 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0010_01C8F7B1.96B14090" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.3138 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.3198 This is a multi-part message in MIME format. ------=_NextPart_000_0010_01C8F7B1.96B14090 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Sung, thanks for the comprehensive reply. It is in "your" world, not "mine".=20 SJ: ">...DEAD or ALIVE do not apply to molecules in my opinion, because the = smallest living entity is the cell. So a cell can be living or dead, = but the molecular components of a cell are neither alive nor dead, = regardless of whether or not they are a part of a living cell or dead = cell....< JM: My mistake: I used 'live' without acceptable ID of the term.=20 (Dead I identified with the lack of such.) In my views there is much = more to anything than identified in conventional science views ('your = world') - even a 'cell' is unrestrictedly(?) connected and influenced by = factors 'outside' such cell (besides its connections to = in-organizational partners) and I thought of 2 different such outside = 'networking' - when callable live or dead. All circumstances are not = (yet?) knowable, some are disclosed in our present level of the = epistemic process. ((one helps proliferation and biological functioning, = the other rather oxidative etc. decomposition)).=20 However we use of the *organization* of cells the different terms 'live' = and 'dead' and my question referred to the latter when the "assipative" = factors are different from maintaining the (live??) biology-processes of = the cell-built organization.=20 Corrected: "are DNA molecules embedded in a 'dead' bio - organization = still storing (bio)'usable' reserves of energy?" Words...words...,=20 Regards John M =20 ----- Original Message -----=20 From: Sungchul Ji=20 To: complex-science@necsi.org=20 Sent: Wednesday, August 06, 2008 12:02 AM Subject: Re: What is a gene? A dynamic & triadic definition of a gene John, Thanks for your comments. > Sung, > your post is commendable, an advanced treatise to extend the = narrowness of > the limited model-view even in the 'more advanced' version of the = obsolete > views (definitions). > > As usual: I have 2 questions. > > 1. Isn't there a chance for a 'reversed' Prigogine effect: to > 'assipate'(!!) factors INTO the process from the ambience, maybe at = least > not not yet recognised, or even discovered? Are you referring to the opposite of "dissipate"? Perhaps plant = leaves can be said to "assipate" free energy through their photosynthesis.=20 Leaves are open systems, and they must receive more free energy from = its environment than dissipate free energy into its environment, so that = they can store free energy in the form of carbohydrates. Since every term must have its antonym, "dissipate" must also, and "assipate" sounds to me like a good candidate. > > 2. If there is 'mechanically' stored energy in the (unassigned?) DNA > stretches, is such energy capable of being put to use from DEAD = tissue? DEAD or ALIVE do not apply to molecules in my opinion, because the smallest living entity is the cell. So a cell can be living or dead, = but the molecular compoents of a cell are neither alive nor dead, = regardless of whether or not they are a part of a living cell or dead cell. There are experimental evidence that the mechanical energy stored in = DNA molecules play an important role in gene expression, especillay in chromatin remodeling (i.e., the opening or closing of chromatin = segments=20 to expose the appropriate DNA sequences for transcription or = replication as required by the need of the cell). There are many ATP-dependent chromatin remodeling enzymes that have been discovered during the past decade or so. One article lists 49 of them [A. Traverse and T. Owen-Hughes, "Nucleosome remodeling", in: Chromatin Strcutre amnd Dynamics: State-of-the-Art (J. Zlatanova and S. H. Leuba, eds., = Elsevier, 2004, pp. 421-465]. (I > think of some answers: "dead" may mean that it lost such capability > together with other transformations, the other is the fact that > transplantations are feasible. I may be lay-wrong.) > > Respects > > John M > ----- Original Message ----- > From: sji > To: complex-science@necsi.org > Sent: Wednesday, July 09, 2008 11:54 PM > Subject: What is a gene? A dynamic & triadic definition of a gene > > > (Yaneer, if it is not too late, please replace my previous post = with > this > one. Thanks. Sung) > > The most widely accepted definition of a gene during the past four > decades > has been a stretch of DNA that codes for a protein. Although this = simple > definition of a gene served well for the 20th-century molecular = biology > and genetics, the new data that have been emerging since the = mid-1990's > (when DNA microarrays were invented) have made the = protein-centered > definition of a gene obsolete [1,2,3]. A new definition proposed = by > Gerstein and his coworkers at Yale now includes as a gene those = DNA > regions that code for RNA as well [2]: > > "A gene is a union of genomic sequences encoding a > coherent set of potentially overlapping functional > products." . . . . = . (1) > > The important phrase here is "functional products", by which the = authors > mean proteins and RNA molecules that are biologically active. > > The new definition of a gene given in (1) was motivated by the = recent > unexpected finding [1,3] that a large portion of the human genome = (about > 30% of the DNA mass), although not coding for any proteins, = nevertheless > code for RNA molecules whose functions have not yet all been > characterized. > > There are two aspects to the definition of a gene given in (1) = that I > believe require revisions: > > i) It is too static, being based solely on gene "products", = i.e., > proteins and RNA, which are "equilibrium structures". According = to > Prigogine (917-2003)[4], there are two fundamental classes of > structures in nature -- equilibrium (e.g., rocks, chairs, DNA = double > helix, nucleotide or amino acid sequences) and dissipative = structures > (e.g., the flame of a candle, all sorts of gradients, action = potentials, > gene expression profiles). One convenient way to distinguish = dissipative > structures from equilibrium structures is to remember that, when = energy > input is stopped, the former disappears but the latter remains. > For example, when a computer is turned off, the primary memory (a > dissipative structure) in CPU disappears but the secondary memory = (an > equilibrium structure) in the hard disk remains. > > ii) It excludes those DNA regions that regulate gene expression > (called > promoters, enhancers, silencers, etc.) without producing any = proteins or > RNA. In other words, Gerstein et al's definition of a gene = excludes > "dissipative structures" which would include all regulatory = processes in > the living cell. This is what Gerstein et al state [2]: > > "Although regulatory regions are important for gene > expression, we suggest that they should not be > considered in deciding whether multiple products > belong to the same gene. . . . " . . . . . . . . . . . = (2) > > To remedy these perceived shortcomings, I suggest that the concept = of > "dissipative structures" [4] be incorporated into the definition = of a > gene > itself. One way to do this is as follows: > > "A gene is a DISSIPATIVE STRUCTURE that embodies (or > stores) not only genetic information (in the form of a > nucleotide sequence of DNA regions) but also mechanical > energy (in the form of conformationally strained DNA > regions) generated from chemical reactions catalyzed > by enzymes." . . . . . . . . . . . . . . . . . . . = (3) > > The fact that active regions of DNA carry mechanical energy, for > example, > in the form of DNA supercoils, has been well established [5]. = Such > mechanical energy stored in DNA has been variously referred to as > conformons [6] and "Stress-Induced Duplex Destabilizations" or = SIDDS > [5]. > > The definition of a gene given in (3) is tantamount to postulating = that > a > gene is a molecular machine composed of DNA segments and = associated > proteins that stores mechanical energy generated from chemical = reactions > and uses this energy to transcribe its sequence information into = RNA > molecules whenever and wherever needed in the cell for a right = duration > of > time. > > The definition of a gene given by (1) can be made compatible with = the > definition given by (3) if we make the following two postulates: > > "The whole DNA carries three kinds of genes -- p-genes > coding for proteins, r-genes coding for RNA, and > d-genes coding for DNA molecules." . . . . . . (4) > > The existence of d-genes is self-evident, since DNA serves as the > template > for its own replication and this ability of DNA is heritable from = one > cell > generation to the next. > > "DNA carries not only genetic/sequence information but > also the mechanical energy (called conformons or SIDDS) > to power gene expression. . . . . . . . . . . . . . . = (5) > > In other words, by combining the dissipative structure concept of > Prigogine [4] and the conformon concept introduced in molecular = biology > more than three decades ago (reviewed in [6]), a new definition of = a > gene > can be > formulated in two parts as follows: > > i) "DNA carries three kinds of genes, each coding > for proteins (p-genes), RNA molecules (r-genes), > and DNA molecules (d-genes)." . . . . . . . . . . . . . . . = .(6) > > ii) "DNA stores mechanical energy in the form of > conformons or SIDDS that powers the > spatiotemporally organized motions of chromatins > in order to express p-, r- and d-genes in > response to the signals received from the > cytosol." . . . . . . . . . . = . (7) > > Statement (6) can be regarded as a definition of terms that are > compatible > with facts, and what is original in the proposed 'triadic' = definition of > a > gene is contained in Statement (7) in the concept of conformons = [6] or > SIDDS [5]. Conformons are defined as the sequence-specific > conformational > strains of biopolymers that carry 'ordered energy' to power > goal-directed > molecular motions [6]. The first direct experimental evidence for > conformons in DNA was provided by DNA supercoils [5] and for = conformons > in > proteins by the single-molecule measurements of myosin motions = along > actin > filament [7]. Also, Statement (6) deals with the informational = aspects > of > a gene, while Statement (7) is concerned primarily with the = energetic > aspect of a gene, consistent with the information-energy = complementarity > principle believed to underlie all self-orgnaizng processes in = nature > [8]. > > With all the best. > > Sung > > ___________________________________________ > Sungchul Ji, Ph.D. > Department of Pharmacology and Toxicology > Rutgers University > Piscataway, N.J., 08855 > > > References: > [1] Pearson, H. (20056). Genetics: What is a gene? Nature > 441:398-401. > [2] Gerstein, M. B. et al. (2007). What is a gene, post-ENCODE? > History > and updated definition. Genome Research 17:669-681. > [3] Greally, J. M. (2007). Genomics: Encyclopedia of human DNA. > Nature > 447: 782-783. > [4] Prigogine, I. (1977). Dissipative Structures and = Biological > Order. > Adv. Biol. Med. Phys. 16:99-113. > [5] Benham, C. J. (1996). Duplex Destabilization in Supercoiled = DNA > is > Predicted to Occur at Specific Transcriptional Regulatory Regions. = J. > Mol. Biol. 255:425-434. > [6] Ji, S. (2000). Free energy and information content of = Conformons > in proteins and DNA. BioSystems 54: 107-130. > [7] Ishijima, A., Kojima, H., Higuchi, H., Harada, Y., Funatsu, = T. > and > Yanagida, T. (1998). Simultaneous measurement of chemical and > mechanical reaction. Cell 70:161-171. > [8] Ji, S. (2002). The Bhopalator: An Information/Energy Dual = Model > of > the Living Cell (II). Fundamenta Informaticae 49(1-3), 147-165. > > > -------------------------------------------------- > For information about this discussion group visit > http://necsi.org/discuss/discuss.html -------------------------------------------------- For information about this discussion group visit http://necsi.org/discuss/discuss.html ------=_NextPart_000_0010_01C8F7B1.96B14090 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Sung,
 thanks for the comprehensive reply. It is in "your" world, = not=20 "mine".
SJ:
">...DEAD or ALIVE do not apply to molecules in my opinion, = because the=20 smallest living entity is the cell.  So a cell can be living or = dead, but=20 the molecular components of a cell are neither alive nor = dead, regardless=20 of whether or not they are a part of a living cell or dead = cell....<
JM:
My mistake: I used 'live' without acceptable ID of the term.
(Dead I identified with the lack of such.) In my views there is = much more=20 to anything than identified in conventional science views ('your world') = - even=20 a 'cell' is unrestrictedly(?) connected and influenced by factors = 'outside' such=20 cell (besides its connections to in-organizational partners) and I = thought of 2=20 different such outside 'networking' - when callable live or dead. All=20 circumstances are not (yet?) knowable, some  are disclosed in = our=20 present level of the epistemic process. ((one helps proliferation and = biological=20 functioning, the other rather oxidative etc. decomposition)).
However we use of the *organization* of cells the different terms = 'live'=20 and 'dead' and my question referred to the latter when the "assipative" = factors=20 are different from maintaining the (live??) biology-processes of = the=20 cell-built organization.
Corrected: "are DNA molecules embedded in a 'dead' bio - = organization still=20 storing (bio)'usable' reserves of energy?"
 
<Live? should we restrict this quale to the = terrestrial=20 biology - i.e. the C-etc.-Water based complex contraptions - subject to = the so=20 far poorly/partially discovered 'bio'-related sciences? Or is it = extendable to=20 anything at all responding to information? (as in = (my) generalized=20 'consciousness' of
thing, function, ideation)?>
 
Words...words...,
Regards
 
John M
 
----- Original Message -----
From:=20 Sungchul Ji
Sent: Wednesday, August 06, = 2008 12:02=20 AM
Subject: Re: What is a gene? A = dynamic=20 & triadic definition of a gene

John,

Thanks for your comments.

>=20 Sung,
> your post is commendable, an advanced treatise to extend = the=20 narrowness of
> the limited model-view even in the 'more = advanced'=20 version of the obsolete
> views (definitions).
>
> = As usual:=20 I have 2 questions.
>
> 1. Isn't there a chance for a = 'reversed'=20 Prigogine effect: to
> 'assipate'(!!) factors INTO the process = from the=20 ambience, maybe at least
> not not yet recognised, or even=20 discovered?

Are you referring to the opposite of = "dissipate"? =20 Perhaps plant leaves
can be said to "assipate" free energy through = their=20 photosynthesis.
Leaves are open systems, and they must receive = more free=20 energy from its
environment than dissipate free energy into its=20 environment, so that they
can store free energy in the form of=20 carbohydrates.

Since every term must have its antonym, = "dissipate" must=20 also, and
"assipate" sounds to me like a good=20 candidate.

>
> 2. If there is 'mechanically' stored = energy in=20 the (unassigned?) DNA
> stretches, is such energy capable of = being put=20 to use from DEAD tissue?

DEAD or ALIVE do not apply to = molecules in my=20 opinion, because the
smallest living entity is the cell.  So a = cell=20 can be living or dead, but
the molecular compoents of a cell are = neither=20 alive nor dead, regardless
of whether or not they are a part of a = living=20 cell or dead cell.

There are experimental evidence that the = mechanical=20 energy stored in DNA
molecules play an important role in gene = expression,=20 especillay in
chromatin remodeling (i.e., the opening or closing of = chromatin segments
to expose the appropriate DNA sequences for=20 transcription or replication
as required by the need of the cell). = There=20 are many ATP-dependent
chromatin remodeling enzymes that have been=20 discovered during the past
decade or so.  One article lists 49 = of them=20 [A. Traverse and T.
Owen-Hughes, "Nucleosome remodeling", in: = Chromatin=20 Strcutre amnd
Dynamics: State-of-the-Art (J. Zlatanova and S. H. = Leuba,=20 eds., Elsevier,
2004, pp. 421-465].


(I
> think of = some=20 answers: "dead" may mean that it lost such capability
> together = with=20 other transformations, the other is the fact that
> = transplantations are=20 feasible. I may be lay-wrong.)
>
> = Respects
>
> John=20 M
>   ----- Original Message -----
>   = From:=20 sji
>   To: complex-science@necsi.org>  =20 Sent: Wednesday, July 09, 2008 11:54 PM
>   Subject: = What is a=20 gene? A dynamic & triadic definition of a=20 gene
>
>
>   (Yaneer, if it is not too = late,=20 please replace my previous post with
> this
>  =20 one.  Thanks.  Sung)
>
>   The most = widely=20 accepted definition of a gene during the past four
>=20 decades
>   has been a stretch of DNA that codes for a = protein. Although this simple
>   definition of a gene = served=20 well for the 20th-century molecular biology
>   and = genetics,=20 the new data that have been emerging since the = mid-1990's
>  =20 (when DNA microarrays were invented) have made the=20 protein-centered
>   definition of a gene obsolete = [1,2,3]. A=20 new definition proposed by
>   Gerstein and his = coworkers at=20 Yale now includes as a gene those DNA
>   regions that = code=20 for RNA as well = [2]:
>
>       =20 "A gene is a union of genomic sequences encoding=20 a
>         coherent set = of=20 potentially overlapping=20 functional
>        =20 = products."          &nb= sp;           &nbs= p;            = ;       =20 . . . . . (1)
>
>   The important phrase here is = "functional products", by which the authors
>   mean = proteins=20 and RNA molecules that are biologically = active.
>
>  =20 The new definition of a gene given in (1) was motivated by the=20 recent
>   unexpected finding [1,3] that a large = portion of=20 the human genome (about
>   30% of the DNA mass), = although not=20 coding for any proteins, nevertheless
>   code for RNA = molecules whose functions have not yet all been
>=20 characterized.
>
>   There are two aspects to = the=20 definition of a gene given in (1) that I
>   believe = require=20 revisions:
>
>     i)  It is too = static,=20 being based solely on gene "products", i.e.,
>   = proteins and=20 RNA, which are "equilibrium structures".  According=20 to
>   Prigogine (917-2003)[4], there are two = fundamental=20 classes of
>   structures in nature -- equilibrium = (e.g.,=20 rocks, chairs, DNA double
>   helix, nucleotide or = amino acid=20 sequences) and dissipative structures
>   (e.g., the = flame of=20 a candle, all sorts of gradients, action = potentials,
>   gene=20 expression profiles). One convenient way to distinguish=20 dissipative
>   structures from equilibrium structures = is to=20 remember that, when energy
>   input is stopped, the = former=20 disappears but the latter remains.
>   For example, = when a=20 computer is turned off, the primary memory (a
>   = dissipative=20 structure) in CPU disappears but the secondary memory = (an
>  =20 equilibrium structure) in the hard disk=20 remains.
>
>     ii) It excludes those = DNA=20 regions that regulate gene expression
> = (called
>  =20 promoters, enhancers, silencers, etc.) without producing any proteins=20 or
>   RNA. In other words, Gerstein et al's = definition of a=20 gene excludes
>   "dissipative structures" which would = include=20 all regulatory processes in
>   the living cell. This = is what=20 Gerstein et al state = [2]:
>
>     =20 "Although regulatory regions are important for=20 gene
>       expression, we = suggest that=20 they should not be
>       = considered in=20 deciding whether multiple = products
>      =20 belong to the same gene. . . . "      . . . . = . . . .=20 . . .  (2)
>
>   To remedy these perceived=20 shortcomings, I suggest that the concept of
>   = "dissipative=20 structures" [4] be incorporated into the definition of a
>=20 gene
>   itself. One way to do this is as=20 follows:
>
>       "A gene = is a=20 DISSIPATIVE STRUCTURE that embodies=20 (or
>        stores) not only = genetic=20 information (in the form of=20 a
>        nucleotide = sequence of DNA=20 regions) but also = mechanical
>       =20 energy (in the form of conformationally strained=20 DNA
>        regions) = generated from=20 chemical reactions = catalyzed
>       =20 by = enzymes."           . = . .=20 . . . . . . . . . . . . . . . . (3)
>
>   The = fact that=20 active regions of DNA carry mechanical energy, for
>=20 example,
>   in the form of DNA supercoils, has been = well=20 established [5].  Such
>   mechanical energy = stored in=20 DNA has been variously referred to as
>   conformons = [6] and=20 "Stress-Induced Duplex Destabilizations" or SIDDS
>=20 [5].
>
>   The definition of a gene given in (3) = is=20 tantamount to postulating that
> a
>   gene is a = molecular machine composed of DNA segments and = associated
>  =20 proteins that stores mechanical energy generated from chemical=20 reactions
>   and uses this energy to transcribe its = sequence=20 information into RNA
>   molecules whenever and = wherever=20 needed in the cell for a right duration
> of
>   = time.
>
>   The definition of a gene given by = (1) can be=20 made compatible with the
>   definition given by (3) = if we=20 make the following two=20 = postulates:
>
>       &nbs= p;=20 "The whole DNA carries three kinds of genes --=20 p-genes
>         coding = for=20 proteins, r-genes coding for RNA,=20 and
>         d-genes = coding for=20 DNA molecules."  . . . . . . (4)
>
>   The=20 existence of d-genes is self-evident, since DNA serves as the
>=20 template
>   for its own replication and this ability = of DNA=20 is heritable from one
> cell
>   generation to = the=20 next.
>
>         = "DNA=20 carries not only genetic/sequence information=20 but
>          also = the=20 mechanical energy (called conformons or=20 SIDDS)
>          = to power=20 gene expression.       . . . . . . . . . = . . . .=20 .  (5)
>
>   In other words, by combining = the=20 dissipative structure concept of
>   Prigogine [4] and = the=20 conformon concept introduced in molecular biology
>   = more=20 than three decades ago (reviewed in [6]), a new definition of = a
>=20 gene
>   can be
>   formulated in two = parts as=20 follows:
>
>       i) "DNA = carries=20 three kinds of genes, each=20 coding
>          = for=20 proteins (p-genes), RNA molecules=20 = (r-genes),
>          = and=20 DNA molecules (d-genes)." . . . . . . . . . . . . . . .=20 .(6)
>
>      ii) "DNA stores = mechanical=20 energy in the form=20 of
>           = conformons or SIDDS that powers=20 = the
>          =20 spatiotemporally organized motions of=20 = chromatins
>         &= nbsp;=20 in order to express p-, r- and d-genes=20 in
>           = response to the signals received from=20 = the
>          =20 = cytosol."          &nbs= p;            = ;      =20 . . . . . . . . . . . (7)
>
>   Statement (6) = can be=20 regarded as a definition of terms that are
>=20 compatible
>   with facts, and what is original in the = proposed 'triadic' definition of
> a
>   gene is = contained in Statement (7) in the concept of conformons [6]=20 or
>   SIDDS [5]. Conformons are defined as the=20 sequence-specific
> conformational
>   strains = of=20 biopolymers that carry 'ordered energy' to power
>=20 goal-directed
>   molecular motions [6].  The = first=20 direct experimental evidence for
>   conformons in DNA = was=20 provided by DNA supercoils [5] and for conformons
>=20 in
>   proteins by the single-molecule measurements of = myosin=20 motions along
> actin
>   filament [7]. Also, = Statement=20 (6) deals with the informational aspects
> = of
>   a=20 gene, while Statement (7) is concerned primarily with the=20 energetic
>   aspect of a gene, consistent with the=20 information-energy complementarity
>   principle = believed to=20 underlie all self-orgnaizng processes in nature
>=20 [8].
>
>   With all the=20 best.
>
>   Sung
>
>  =20 ___________________________________________
>   = Sungchul Ji,=20 Ph.D.
>   Department of Pharmacology and=20 Toxicology
>   Rutgers University
>  =20 Piscataway, N.J., 08855
>
>
>  =20 References:
>      [1] Pearson, H. = (20056).=20 Genetics: What is a gene? Nature
>=20 441:398-401.
>      [2] Gerstein, M. B. = et al.=20 (2007). What is a gene, post-ENCODE?
> = History
>   and=20 updated definition. Genome Research=20 17:669-681.
>      [3] Greally, J. M. = (2007).=20 Genomics: Encyclopedia of human DNA.
> = Nature
>   447:=20 782-783.
>      [4] Prigogine, I. = (1977). =20 Dissipative Structures and Biological
> = Order.
>   =20 Adv. Biol. Med. Phys. 16:99-113.
>      = [5]=20 Benham, C. J. (1996). Duplex Destabilization in Supercoiled = DNA
>=20 is
>   Predicted to Occur at Specific Transcriptional=20 Regulatory Regions.  J.
>   Mol. Biol.=20 255:425-434.
>      [6] Ji, S. = (2000). =20 Free energy and information content of Conformons
>   = in=20 proteins and DNA. BioSystems 54:=20 107-130.
>      [7] Ishijima, A., = Kojima, H.,=20 Higuchi, H., Harada, Y., Funatsu, T.
> and
>   = Yanagida,=20 T. (1998).  Simultaneous measurement of chemical = and
>  =20 mechanical reaction.  Cell=20 70:161-171.
>      [8] Ji, S. (2002). = The=20 Bhopalator: An Information/Energy Dual Model
> = of
>  =20 the Living Cell (II). Fundamenta Informaticae 49(1-3),=20 147-165.
>
>
>  =20 --------------------------------------------------
>   = For=20 information about this discussion group visit
>   http://necsi.org/discuss/d= iscuss.html




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