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Life And Energy; Synthetic Biology ?

February 22, 2006

From: henis dov

Sent: 30 July 2007

To: Synthetic Biology , The Royal Society

Subject: Synthetic Biology ?

Life Is Wholistic Until Decomplexed To Energy

A. Cells Are Not Organisms

It irritates me again and again when unscientific science editors allow reference to cells as organisms. Cells are the spaceships, the edifices, that house the genome, the organism. Scientifically Cells are NOT organisms.

A possible explanation of this scientific ignorance is our still incomplete knowledge of the nature of the constituents of the cells' contents coupled with misty comprehension of the nature of life.

B. Genomes Are Earth's Organisms

http://blog.360.yahoo.com/blog-P81pQcU1dLBbHgtjQjxG_Q–?cq=1&p=179

Again and again I re-explain the meaning and consequences of Darwin's observations, i.e. that the extent of the relative stability of compositions of genomes, genomes being Earth's live organisms, is proportional to their survival's dependence on physiological adaptation. The more the genome, the organism, depends on physiological adaptation for survival the more its composition changes. On the other hand the further complexed is the culture of the genome, of the organism, the smaller is the number of its genes that change for survival and simultanously the greater is the number of variations-changes in its genes involved in its culture. Its culture serves it for survival in lieu of physiological adaptation. It modifies its environment instead of adapting to its environments.

C. ENCODE's Updated Gene Definition

http://www.genome.org/cgi/content/full/17/6/669

The ENCODE consortium is engaged in characterizing the human genome by various high-throughput experimental and computational techniques designed to characterize functional elements (The ENCODE Project Consortium 2007). While the landmark human genome sequencing surprised many with the small number (relative to simpler organisms) of protein-coding genes that sequence annotators could identify (21,000, according to the latest estimate), ENCODE highlights the number and complexity of the RNA transcripts that the genome produces. ENCODE suggests that it has changed our view of "what is a gene" considerably more than the sequencing of the Haemophilus influenza and human genomes did (Fleischmann et al. 1995; Lander et al. 2001; Venter et al. 2001). The discrepancy between previous protein-centric view of the gene and one that is revealed by the extensive transcriptional activity of the genome prompts a reconsideration of what a gene is and made ENCODE propose a new tentative updated gene definition:

"The gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products".

D. Genes Were Primordial Life's Organisms

Repeating again and again:

It is the "lifehood" of genes that makes us and all other forms of life on Earth living organisms, and evolution has been the route of Life's ever more complexing progress since the first replication of the first gene(s).

Early independent peptides, primordial genes, have entered into symbiotic associations in which eventually each of the ever increasing host of functions/tasks vital for the evolving associations is taken up by the member most efficient at it, leading to gene speciation and to gene specialization.

The history of life begins with independent genes, cascading fractally from single independent genes to agregate of genes, then to agregate of agregate of genes. Cooperative association is an inherent feature of life throughout all its evolution and at all its levels, in pre-cell and in mono-cell life and in mono-cell communities and in multi-cell life-forms and in communities of multi-cell life forms.

E. Today's Genes Are Yesterday's Genomes

Today's genes are pre-today's-genomes'-genomes. Keep decomplexing today's genomes and you get, fractally, sub-genomes until you reach the primordial independent genes. However, evolution complexing have rendered all the fractal base elements completely interdependent. There's no going back to independent genes.

D. Genetics Is Wholistic Until It Arrives At Energy

The farthest we go in reductionism in Life we shall still end up with wholism, until we arrive at energy. Energy is the base element of everything and of all in the universe. The universe and evrything in it are continuously evolving and all the evolutions are intertwined.

end

Dov Henis

===============================

March 15 1999, PalPasych forum, "Getting and spending"

(1)

– Quote from the subject posting:

"These < orderly > structures can only maintain themselves while energy is flowing into them in the right amounts. Once the energy–whether it's heat or light or some other form–disappears, so does the pattern.Sally's insight is that life has the ability to store energy–to warehouse enough of it so that when the light or heat stops, the self-organizing form can survive. Not only can life-forms maintain their self-organized shapes, but they can seek out another source of the energy which has disappeared and thus survive to see another day. (Sally's observations are in her book "After The Clockwork Universe", published May 1999)"

( PS: From my July 1997 posting "Origin and Nature of Life":

" We do not yet know if the Earthly PNs are the only compositions/configurations organized into life in the universe. It seems, though, that the origin and drive of life is energy and as material is a form of energy then life is a manifestation or evelation of energy. This opens the awful question "what is energy", reminding us that as far back and as deep down we learn to observe and as much as we think we comprehend , the Unknown is still there infinitely ahead of us".)

DH remark:

Seems we are back to basics, to enthalpy and entropy. You need an input of energy to affect order, be it in a classroom or in an inanimate or in a living system. And relaxing the input leads to dispersion and release of the system's energy content.

—————————

– Quote from the subject posting :

"Surplus and the ability to seek resources thus show up as basics of life on a level so elementary it's astonishing…"

DH remark :

Surplus energy and spending of it is a common physical occurance all around us when input of energy shifts electrons into a next orbit and when the energy is released as the electron returns to its normal energy level. Intake of energy and expending it is a common occurance in many forms all around us. Therefore please slow down and ponder: what is so astonishing that the seeking of resources is a common feature to living organisms ? This feature after all is a RESULT of life, not a CAUSE of birth of life.

And an additional DH remark :

I urge you to TRY to apply my concept of the "Origin and Nature of Earth Life" to each and every described/reported biological process/occurance you meet and to ask yourself if they can or cannot be explained based on this concept…. And I suggest that neither now nor 100 years from now will we have "found" the ultimate final explanation of the nature of life. We can only hope and succeed to make progress in this quest.

DH

(2)

From Sally J. Goerner To Dov Henis, re "Getting and spending":

DH: " Surplus energy and spending of it is a common physical occurance all around us when input of energy sh
ifts electrons into a next orbit and when the energy is released as the electron returns to its normal energy level. Intake of energy and expending it is a common occurance in many forms all around us."

SJG: You should make a stronger statement here. As far as we know, energy is in ALL forms around us. It is what makes matter move.

DH: "Therefore please slow down and ponder : what is so astonishing that the seeking of resources is a common feature to living organisms? This feature after all is a RESULT of life, not of birth of life."

SJG: "Seeking" implies following "information" (in its energy form). Following information too is a result of natural energy reactions but it is pretty special in that it amounts to the first perceiving-acting systems (as the ecological psychologists call them) or the early stirring of mind (as other folks say). This is a whole lot more interesting that earlier energy cycles which, as you say, are completely ubiquitous. How do you KNOW that this feature does not constitute the "birth of life"? Neo-Darwinists take reproduction and genes as the crucial element of life but that is a historical bias–it is simplistic and lacks appreciation of the larger web which gave birth to life and in which all organisms are still embedded. I think that, in the emerging web/Integral view, life is a unique blend of elements. Of these, the mind element (which had to exist for life to exist) is probably more crucial than the lesson storage mechanism of genes. Life that cannot eat is not life. Life that cannot pass its life lessons down might still be life.

S.J.

————-

(3)

DH: Re our exchange I do not have anything near similar background and knowledge that you have in this subject yet I feel that somehow you keep seeing the PRODUCTS of life as the SEEDS of life…

This is a guts feeling, of course, not based on any bibliography.

Dov

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