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Bit by Bit: The Darwinian Basis of Life

  • Gerald F. Joyce mail

    gjoyce@scripps.edu

    Affiliations: Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America, Department of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America

    X
  • Published: May 08, 2012
  • DOI: 10.1371/journal.pbio.1001323
  • Featured in PLOS Collections

Reader Comments (3)

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How many bits and how to count them?

Posted by hkatcher on 12 May 2012 at 23:30 GMT

I think that any idea that the informational content of an organism is contained in its DNA is naive. If you were to take all the genes of that organism (in terms of DNA stretches that produced RNA) and transcribed and translated them (or no, if they're meant to be RNAs), into all their final products, threw that mix into a bowl of growth media - you would not have an organisms. Every organism came from a cell, and any multi-celled organism is not a bunch of components but the result of an organized process, one we call its 'development'. The organism is a structure ordered in both space and time, to think that a list of the twenty-five thousand different types of components, (its genome), is the same understanding the living organism is incorrect - I would like someone to build an advanced fighter jet from a list of its components - and a fighter jet is simplicity itself compared with a living cell. The codes for this four dimensional structure are not contained within DNA, the code for the sequence of amino acids constituting p53, the tumor suppressor protein doesn't tell us what other proteins it will interact with, doesn't tell the effects different phosphorylations will have on it and how it will interact with other proteins. The information content of the cell that makes all of the activities dependent on the transfer of genetic material (the chromatin code, the epigenetic code that controls development of organisms, something about which we know next to nothing, and then finally the simple genetic code). What the coding provided by the phosphorylation and other modifications of proteins by proteins, that change their behavior and how they interact with still other proteins - what about those interconnected webs of signaling molecules and transcription factors and DNA and how modifications affect them? How is that information coded in DNA? The interactions between chromatin, and chomosomal territories in interphase nuclei are of primal importance in cell differentiation, where is that carried in the DNA? A stem cell divides assymetrically, the chromatin of one daughter now different from the others', where is that coded in DNA and how do you measure it's informational content? So imagine that all that information about the interactions of proteins, DNAs, RNAs etc. with each other, the transcription factors, the kinases (some of which phosphorylate hundreds of different proteins, changing their activities, the, phospatases, acetylases, all that change the components of the cell. Those components now differ from their DNA representations (and alternate splicing extends still further the departure of a static list from the living process) , so that they are in a particular state (and what is the informational content of a 'state' of a living cell?)wherein the activities of one of it's proteins could no longer, even theoretically be predicted by the 100,000 letters in its name (nucleotides in it's DNA representation) if simply because modifications changed its properties. Does it seem credible that all of this information could be contained within the three billion nucleotides of its genome? It is simply not possible.

No competing interests declared.

RE: How many bits and how to count them?

TheMatrixDNA replied to hkatcher on 16 May 2012 at 22:24 GMT

That's great, wonderful, Mr. Hkatcher! Then we have a problem: where are those informations encoded inside an organism? What else has an organism that we still not know it?! As a naturalist philosopher living and observing the biosphere of Amazon jungle I have no Biology knowledge like you but I usually search knowledge in all scientifc fields trying to understanding the whole and my currently theory is suggesting the answer for this question. So, from now I will describe the theory. The key are five words: photons, software, cosmological evolution, systems, light. First of all, the DNA is not a code of something existing other than itself as a system. DNA is merely a pile of sub-systems called "lateral/horizontal pair of nucleotides". We call this pair as "bit" or fundamental unit of information. A kind of universal matrix. Why? Because the configuration of this bit is the same configuration of a primordial galactic system... So, there is a natural universal formula for organizing matter into systems, from atoms, to galaxies, to cell systems, to human beings. Well, I think that everybody will stop reading this here: this guy is away off the beam. But...

A electromagnetic spectrum of light going from X-ray to radio is the code for any life cycle when imprinted inside matter. We need do experiment for testing this strong hypothesis, which arose when in the jungle my eyes were going from the Earth surface to the Sun's surface radiating light and this light is presents at every step of life in its biosphere. Light is broken into photons, which each one is a copy of the whole wave. Photons are like atoms in the sense that they can have their behavior changed by the system who they belongs, but they can transfer the organization of this system when they fall into atoms belonging to other environment. This could be the principles of memory transference. At a new environment photons has the tendency to re-combination mimicking the configuration of their prior system. The result is a kind of software inside atoms/organisms composed by photons, performing a system that has informations not transferred to those atoms/organisms, which are the hardware. So, maybe here are hidden those informations that you, with good reason, are not seeing in the hardware DNA.

Each nucleotide bit is a kind of fractal, a copy of a prior system which is the last universal common ancestor (LUCA) of all biological systems. The problem is that LUCA does not lives at Earth surface, he is the astronomical galactic system. LUCA is half-mechanical/half-biological, since that we can get a biological sexual reproductive process in a mechanistic fashion only aligning astronomic bodies like planets, stars, pulsars, quasars, black holes and comets into a circuit performing a system. These semi-biological kind of matter organization is transferred to terrestrial atoms belonging to rocks and oceans through photons from stars/planetary nucleus radiation. But in the new earth environment there are no exactly copy of the astronomical system, then, each nucleotide is a copy with a detail of variation. So, the sum of all nucleotides performs a new system, RNA or DNA, which has more informations than we can find at each part. These informations is the identity of an emerging system.

Now, we need to consider that the sum of DNA's of any organism performs a new emerging system that is the organism itself. The organism as a whole must have more informations than the contained in each DNA. But, this excess of information, which arises from the fuzzy logic produced by DNA's connections and interactions, are hidden where? Again the aspect hardware/software. And we know that organisms are composed by a nervous system that obeys a command of instructions. At human brain this "command"are well expressed in which we call "thoughts" or "mind". Now I am studying the brain searching how the synapses are building the mind as a new shape of the universal matrix formula. The final conclusion is that we need to re-build ours laboratories, the new ones based in the search for effects of natural light. Over atoms that composes life forms. And how is the interaction of a plan belonging to the mind of Bill Gates, transcripted into diagrams of softwares with the hardware of a computer. At my website there are suggestions about the matrix/DNA formula, the picture of astronomical bodies performing a system like nucleotides, the division of light spectrum into the shapes produced by life cycles, etc. Certainly it is not complete, it is not a theory of everything, our brain never will be able to do that, I believe. certainly there are a lot of errors in the models. But it suggest a new perspective, full of food for thoughts. Cheers...

No competing interests declared.