• [deleted]

Sara,

It will not be possible to develop a "universal communications language," based upon DNA, until we have a full understanding of the DNA coding algorithm. It seems we do not. Junk DNA

The scientific community doesn't learn from its past mistakes, probably because they do not "bother" telling new students about past mistakes.

I read an article some years back about the statements the Germans made about the content of the ancient Egyptian medical papyrus that came into their possession. The German physicians that participated in the translation used the term "sewer medicine" when the translation revealed that crocodile "dung" was used to cover open wounds. It was not revealed until 1951, after the antibiotic discoveries preceding that date, that crocodile "dung" had very strong antibiotic properties.

I think Georgina Parry should have been somewhat less diplomatic in her essay, topic 1316, when she used the term " incomplete information," as there are many instances where the term "ignorance" should be used.

The statement made by the eminent scientists that declared most of DNA is "Junk DNA" is no less ignorant than that made by the German physicians. Are the esteemed scientists so narcissistic that they cannot say, "We do not know."?

  • [deleted]

Hello,

I have several ideas, I like this topic :)

If the serie of uniqueness is inserted, so we can have a specific spherical architecture with the volumes.

The amino acids and their combinations of HCNO are incredible.The ionic links can be correlated with the number for the quantization, the volumes are essential at my humble opinion considering a good taxonomy for the exchange of informations. The atomic links and the hydrogen bridge also are under this logic. Like the interactions of London that I find very relevant personally.

The ARN this acid ribonucleic is so an interesting link for the encoding.If the bosonic fields and the gravitational stabilities are analyzed with the serie of uniqueness, and its number of spheres, finite.So it is relevant considering the rule of H and its serie of uniqueness. This quantum number is the same than our cosmological number.So the volumes of this serie are important.If the light is differenciated of the mass with a different sense of rotation, so we see the links with the singularities. The two roads are far of us, The informations and their complexity are there in the two senses.

Regards

    Hi Sara,

    "I am not yet convinced that information control would be nearly as robust in a purely analog chemical system, and therefore its capacity for reliable network switching should be limited as compared to an analog digital chemical system. I'd be very interested in any examples to the contrary."

    I see any self organized system as fundamentally analog, because it must be bounded and continuous. What I mean by that, is that the network node switching continuum examined on varying time scales reveals that the discrete effects of multi-scale variety (Bar-Yam) can vary widely as measured at short time intervals, though the system shows little change over the long term. The Braha--Bar-Yam approach to dynamic link utilization sheds light, I think, on why self organized systems -- whether organic or inorganic and by definition both self similar and self limiting -- are metastable. Even considering any multicellular organism as a corporation of cooperating cells that are constantly communicating, we see varying centers (hubs) of activity at short local intervals and stable coherence globally.

    Where is the boundary between the inorganic chemical self organization, and the organic? System-wide, they are interactive. We can always prescribe arbitrary boundaries among systems when we isolate characteristics, though we inevitably regress to systems of systems, when we deal with the deepest foundational questions.

    Yaneer Bar-Yam advanced the idea of " ... scale of response and the effect of coordinated versus uncoordinated response as a key attribute of complex systems ..." that integrates hierarchical control with distributed control in a compellingly rigorous fashion, in my opinion.

    I'm not disagreeing with you. I'm just questioning the idea that we may make any non-arbitrary distinction between life and non-life in the context of complex system self organization. If not, a logical entailment tells us that we can make no non-arbitrary distinction between consciousness and non-consciousness. *Then* from this continuum, digitsl schemata and thinking processes can be derived. The analog function is primary.

    You write, " ... somewhere in that potential continuum a major shift in the way information is handled and processed does occur and ... this is a constructive way of thinking about life's origins." Yes, I strongly agree -- that's the way that self organized criticality (Per Bak) works, and which supports the Gould-Eldredge model of punctuated equilibria in evolutionary biology.

    All best,

    Tom

    • [deleted]

    Semantic of the life

    I think that the life can have had the evolution from self-replicating rna, viroid, virus with capsid (the simplest membrane), macrovirus and bacteria.

    The passage from a low level life to high level is identified by closed system (capsid membrane): the chemical reaction chains must be in a closed system (no dispersion of the chemical products), so that multiple chemical process are possible.

    The chemical reaction are equivalent to a logic, where the word are the chemical compound, and the rna is the logic program (A +B=C is equivalent to: if A and B then C ): the chemical reaction in a closed system are a language (logic, programming or brain), this remember me the De Arte Combinatoria of Leibniz.

    The self-replicating rna is a semantic "I" (existence : the egocentricest being), there are not information processes.

    The simplest virus is "I think", where there is a chemical process that from two inner word produce a sentence: this is the life start, the consciousness.

    A colony of virus is a complex slow thought (years for a complete sentence): there are logical chemical sentences, where only the more intelligent (in the environment) virus is the winning idea (is it a brain thought a chemical process?).

    Saluti

    Domenico

    Frank,

    I do not know enough to comment on how the specific form of ionizing radiation might affect chiral biomolecules, although I do know that a lot of work has been done investigating the effects of UV circularly polarized light. It might be worth looking into that literature.

    I agree "junk" is a very big misnomer. My impression is that most the junk serves a purpose - either as noncoding RNAs or as instructions for excising nonfunctional bits but the details are far from clear at present. The story is far from complete!

    Best,

    Sara

    Steve, I am familiar with the early pioneering work of Oparin. Very interesting stuff, especially from a historical perspective.

    Best,

    Sara

    S Halayka,

    In principle I think something like this is certainly possible. In practice I am sure it would be very difficult. The life-detection on Viking was to similar effect (put organics and water in a closed chamber with Martian soil and see what happens metabolically), but has since been interpreted as being too ambiguous by much of the community to positively identify life.

    Best,

    Sara

    Tom, thank you for the Bar-Yam reference. Looks like a very interesting paper and very relevant to the discussion here!

    It is extremely difficult to draw any kind of line at the "origin of life". I am not convinced that there is a sharp transition. I personally also go back and forth "questioning the idea that we may make any non-arbitrary distinction between life and non-life in the context of complex system self organization." I don't doubt at all that the process scales all the way up through the biosphere - but I have yet to see an example of the kind we've been discussing here that isn't biological or derivative of biological organization, so it is interesting to consider how these systems arise naturally within the context of the origin of life (e.g. despite the "complexity" I don't think anyone has observed these kinds of dynamics in geochemical cycles, maybe no one has looked - but it would be fascinating if they did find something!).

    This is a very very tough question! Thanks for sharing your thoughts on it.

    Best,

    Sara

    Domenico,

    Thanks for sharing your thoughts. There is a problem with the scenario of naked RNA molecules in a hydrothermal setting - RNA is very unstable under aqueous conditions and it is difficult even to form dinucleotides abiotically. I don't think that this is the best way to start the whole process. However, there has been some work done in the direction you suggest that may be of interest to you http://www.pnas.org/content/104/22/9105.full

    One must be careful in identifying a possible ancestral phase of RNA-based life with modern viruses. Modern viruses are highly-evolved and survive by co-opting the machinery of cellular organisms. It is entirely possibly that viruses evolved with cellular life (or possibly came later), and that they enhanced the capacity for early populations of cells to undergo rapid information transfer and therefore increased their evolvability.

    I agree that a single self-replicating molecule has no information processing in the manner we've discussed here. To me the most interesting question in origins is a what level this comes in.

    Best,

    Sara

    Hello again Steve,

    I am not sure what you mean by a "series of uniqueness" and that we have a "specific spherical architecture". But I do think hierarchical organization is important in living systems - it allows information to be coarse-grained and processed on multiple levels in structural hierarchies.

    Best,

    Sara

    Hi Frank, I agree to an extent - science cannot be disentangled from the presence of an observer/measurer. This is especially interesting of course for quantum mechanics. I am not sure about the gravity bit - why is gravity singled out from the other forces?

    Best,

    Sara

    • [deleted]

    Hello Ms Walker,

    The number of cosmological spheres for example or an atom of H for example, see that this number is the same.Finte and precise, it permits to quantize the mass. The volumes of this entanglement are relevant when the central spheres,the singularities are the most important volumes. So the stabilities of evolution appears considering the polarization spherization between m and hv. The mass polarises this light in fact Ms Walker.

    The spheres inside the sphere are the answer.

    Best Regards

    Dear Sara,

    I've no doubt that life cannot completely be reduced to physical and chemical terms. There is something beyond of that. But it seems highly difficult to get in touch with this entity whatever it may be.

    Some people are calling it consciousness, other mind etc.

    In the past the scientific inquiry of this entity was simply a taboo, but now a paradigm shift is taken place and a purely materialist view of the universe including life does no longer dominate science.

    A good example is the research of Dr. Pim van Lommel, a renowned cardiologist, who has studied in a systematic way near-death experiences (NDEs). As a cardiologist, he was struck by the number of his patients who claimed to have near-death experiences as a result of their heart attacks. As a scientist, this was difficult for him to accept: Wouldn't it be scientifically irresponsible of him to ignore the evidence of these stories? Faced with this dilemma, van Lommel decided to design a research study to investigate the phenomenon under the controlled environment of a cluster of hospitals with a medically trained staff. For more than twenty years van Lommel systematically studied such near-death experiences in a wide variety of hospital patients who survived a cardiac arrest. In 2001, he and his fellow researchers published his study on near-death experiences in the renowned medical journal The Lancet. The article caused an international sensation as it was the first scientifically rigorous study of this phenomenon.

    His work proves that life is not restricted to a composed physical and chemical object like the body, but something different beyond space and time; something that can obviously be experienced separate from the body. Van Lommel himself has come to the conclusion that most likely the brain must have a facilitating and not a producing function to experience consciousness. By making a scientific case for consciousness as a nonlocal and thus ubiquitous phenomenon he has questioned a purely materialist paradigm in science.

    Hence, your paper resp. your thesis is touching a serious topic of future science.

    Good luck for your paper

    Helmut

      • [deleted]

      :) Oparine with a e Mr Walker.

      I was fascinated by the expermiment creating amino acids with methan,amoniac,water,acetylen.....more E under different forms like hv or heat or acids bases or this or that,it is fascinating to see the amino acids appearing . Our evolution, biological, mineral...is fascinating.The mass increases and the complexification is incredible in its adaptation.It is there that the spherical volumes of the serie of uniqueness take all their universal meaning.

      The spheres evolve in fact.

      Best Regards

      Thanks, Sara. Discussions I had with Dan Braha in 2007 convinced me that this result deserves more attention than it has gotten then or since. Translating bounded data sets into topological maps evolving in time suggests to me that much more lies beneath self-organizing phenomena than we have yet explored. Bar-Yam's theory of multi-scale variety (which he developed as a theorem from Ashby's law of requisite variety) is a very powerful tool for all kinds of systems function and analysis, whether biological or otherwise.

      I strongly agree on the origin of life question. You're right that examples are lacking of "life" phenomena that aren't " ... biological or derivative of biological organization ..." though my penchant for pushing boundaries and barriers tells me that a general definition of "organization" -- as order with feedback -- applies both top down and bottom up.

      Best,

      Tom

      • [deleted]

      Hi Sara, I read your essay with great interest. You've done a fantastic job challenging an assumption that reductionists would likely consider untouchable. I was delighted that you stressed the role of information, and particularly information-in-context -- this is the focus of my essay "Toward an Informational Mechanics", and I would love to get your thoughts on it.

      The main assumption I challenge is that information is underlain by objects. I argue that matter and spacetime may emerge out of information content, which can only arise in the relational context of other information. This is where the possible fundamental nature of life comes in: If we consider living organisms (and their technology) to be complex fundamentally informational systems, whose complexity has evolved in the context of other evolving informational complexity, then informational complexity *in the universe* may be a function of the informational complexity of the observer -- the biological or technological system doing the observing. I suspect that this or some other purely relational picture is what's keeping us from seeing the big picture, and how life fits into it.

      A purely chemical conception of life is deeply problematic, as you point out so clearly; but I go further by hypothesizing that the chemistry itself emerges from information-in-context (which may be where I lost some readers!).

      Thanks for the great read and best of luck.

        Dear Helmut,

        Thank you for the well wishes and your interest in the paper. I had not heard of the work of Dr. Pim van Lommel previously, but I've just pulled up the Lancet paper and it does look interesting. Thank you for sharing the reference.

        Best,

        Sara

        Hello Karl,

        The idea of all of reality emerging from "information-in-context" is intriguing, and I agree it definitely puts the phenomenon of life in a new perspective! I've just downloaded your essay and look forward to reading it.

        Best,

        Sara

        • [deleted]

        Heaven Breasts and Heaven Calculus

        http://vixra.org/abs/1209.0072

        Since the birth of mankind, human beings have been looking for the origin of life. The fact that human history is the history of warfare and cannibalism proves that humans have not identified their origin. Humanity is still in the dark phase of lower animals. Humans can see the phenomenon of life only on Earth, and humans' vision does not exceed the one of lower animals. However, it is a fact that human beings have inherited the most advanced gene of life. Humans should be able to answer the following questions: Is the Universe hierarchical? What is Heaven? Is Heaven the origin of life? Is Heaven a higher order of life? For more than a decade, I have done an in-depth study on barred galaxy structure. Today (September 17, 2012) I suddenly discovered that the characteristic structure of barred spiral galaxies resembles the breasts of human female essentially. If the rational structure conjecture presented in the article is proved then Sun must be a mirror of the universe, and mankind is exactly the image on earth of the Heaven.

        http://galaxyanatomy.com

        Dear Sara Imari Walker

        Your essay provided me a fresh reading on biology in a contest virtually devoted only to pure physical questions, including mine!

        My own position on the main theme of your essay is somehow in the middle betwen the vitalist and the reductionist. This is what the Nobel winner Jean Marie Lehn calls integrationism: the integration of upper levels with lower levels.

        Integrationism is at the very foundation of the observed hierarchical structure of matter and is the main paradigm used in supramolecular chemistry for the study of the frontier between living and non-living matter.

        The answer to your question is "yes". A theory of life is so fundamental as general relativity or quantum field theory in their respective fields, because none of those (neither highly speculative approaches as superstring theory) can explain the rich phenomena observed in living systems. The limits of physics have been debated in the recent XXI Solvay Conference on Physics. The proceedings have been published in the volume 122 of Advances In Chemical Physics (2002).

        You must find interesting the work "From Coupled Dynamical Systems To Biological Irreversibility" (pages 53-75 of the above volume) by Kunihiko Kaneko. You can find in part four, "Extension Of Quantum Theory And Field Theory", of the proceedings several works on generalizations of quantum field theory devoted to explain the fundamental irreversibilities observed in living systems. My own work must be considered a generalization of the dynamics of correlations developed by the Brussels-Austin School (pages 261-276).

        Regards