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Mailing List complex-science@necsi.org Message #9675 | |
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| John, >Corrected: "are DNA molecules embedded in a 'dead' bio - organization >still storing (bio)'usable' reserves of energy?" I would say no. DNA in a 'dead' bio-organization would not store any useful energy but still can carry biological information that can be deciphered in the lab. Sung > Dear Sung, > thanks for the comprehensive reply. It is in "your" world, not "mine". > 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. > (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)). > 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. > Corrected: "are DNA molecules embedded in a 'dead' bio - organization > still storing (bio)'usable' reserves of energy?" > > <Live? should we restrict this quale to the terrestrial biology - i.e. the > C-etc.-Water based complex contraptions - subject to the so far > poorly/partially discovered 'bio'-related sciences? Or is it extendable to > anything at all responding to information? (as in (my) generalized > 'consciousness' of > thing, function, ideation)?> > > Words...words..., > Regards > > John M > > ----- Original Message ----- > From: Sungchul Ji > To: complex-science@necsi.org > 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. > 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 > 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 |
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