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  • Post #21

I am thinking, in this days, to a possible chemical reaction (similar to gene-protein reaction) for a self-replication of the starting structure.

If a complex structure (like a gene) produce a single protein equal to the gene, then this minimal structure (with start, produce and end chemical message) is a self-replication structure.

If the chemical structure is minimal (the simplest chemical structure, with only an RNA-virus gene, with no other function further the replication) then I think that is possible in each environment (in the Universe) the starting of the life (if there is noise like radiaction, there is evolution): is it possible to obtain a minimal self-replicating chemical structure?

If the self-replicating structure is not in organic chemistry, then there are life forms different from Earth life.

Saluti

Domenico

Thank you for a very interesting, thought provoking essay. My background is in computers and for a long time, reading about the developments in biology, genome in particular, I thought that life only appeared similar to information systems. Later on I took on biology and physiology; and the more I studied it, the more I became convinced that life does not just appear but is indeed programmed. After the years, this led me to begin questioning my believes. Born and raised as an atheist in the former Soviet Union, I suddenly started to entertain ideas that life was made (my intimate knowledge of information systems precludes me from believing that it could have organized spontaneously). This led to a curious development. I now believe that true evolution of life is not a simple emergence of new species but emergence of species capable of creating new worlds. We have recently created such a world and it is the Internet. The organization of its space (a world always starts with the space and follows its specifics) is already set in the sense that the underlying technology will undoubtedly change in the future, yet its organizing principle will stay the same. Even though the Internet is still very young, developing, and is entirely dependent on humanity, with years its maintenance will be more and more automated. What's more, it will never be turned off. Think about it. Humanity may perish, but the Internet will outlive it, even if for a short while. And should we continue long enough, the Internet may just evolve as an independent... no, not being, but a world populated by intelligent beings.

With time it occurred to me that our world was made in the same manner and for the same purpose, which is mainly entertainment. This fits very well with the biblical notion of Eden, which was defined as the Garden of Delights. Translated into the 20th century parlance, it means an amusement park, and in the current parlance, a virtual reality game. But I got carried away... sorry.

In this context, life is a desire for novelty of experience and its evolution is evolution of worlds.

Again, thank you for your stimulating essay!

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    • Post #23

    In an attempt to obtain the minimum length (entropy or information) replicating structure I try to obtain this information from the 33 viroids genoma (rna-virus without capsid, with near 10.000 atoms, but with many functions further the replication).

    If it is possible the rna sequencing (the dna sequencing is so simple, now, that it is possible in some hours with low cost), then can be possible to calculate a common ancestral viroid, and then can be possible to obtain the minimum replicating rna.

    Saluti

    Domenico

    Hi Conrad,

    You've hit on one of the important issues in this discussion. I completely agree that evolution is a central part of the story and of course some kind of evolution must have driven the first self-organizing chemical systems that eventually gave rise to life. However, while it may be a necessary to the process, I don't think it is sufficient to define life. As I stated above, it is too broad a criteria. It applies to too many physical systems (e.g. for purposes of this discussion, both those where only the physical structures evolve in a very limited capacity, and where both the physical structures and the 'virtual' machine evolve in tandem).

    At present there is no restriction imposed that the early evolution of a chemical soup must have been a Darwinian process, other than that the problem is simplest and most convenient to think about in these terms (mostly because we know Darwinian evolution so well from studying modern life). So usually we use it as a constructive starting but I think it is more likely that the early evolution of life didn't look much like a canonical Darwinian replicator. In fact, there is a lot of evidence that early life was dominated by collective modes of evolution (e.g. horizontal gene transfer) rather than the traditional notion of vertical Darwinian descent. Vertical descent may have taken over as the dominant mode of evolution only after the translational machinery became fixed in the last universal common ancestor (although many argue that even today collective modes dominate, being the most prominent driving force of microbial evolution). Some excellent discussion on collective evolution and early life may be found in the recent papers of Goldenfeld and Woese. My feeling is therefore that in general we have to be very careful using evolution as a definition for life, it is both too general, and there are potentially many classes of evolutionary processes that we don't typically include in our application of this criteria.

    I like your idea about life's ancestry where you state that "if such systems were something like bags of complex molecules that catalyzed each other's construction, all the molecules would have been part of the control-mechanism." I agree. In fact I think this is still true, with much of modern biochemistry being part of very elaborate control mechanisms. Even today the control is primarily NOT in the DNA, but in proteins and RNAs whose function is to modulate the activity of other components of the system, including blocking or enabling transcription of DNA. There are also essential parts of the cellular-machinery which are not explicitly contained in the inventory of information stored in DNA and instead are guided by self-assembly processes (e.g. lipids). When we discuss a "cellular program" these must be included. It is entirely possible that control emerged first, and reliable storage of certain parts of the program in inert digital polymers (DNA) came later. The notion of heredity in the earlier systems could have been very different.

    I will look for your essay, and thank you very much for the engaging discussion!

    Best,

    Sara

    Dominco,

    You've suggested some systems that community has been striving to build for quiet some time. There are a lot of models for 'minimal' replicators. The chemoton is a particularly elegant one aiming to capture those functions which are viewed as most essential to modern life, which sounds similar to your first proposal, but also includes metabolism.

    You seem to however be more interested in the idea of a minimal RNA self-replicator. This is certainly something many people are striving to engineer in the laboratory. Probably the closest we've come to it is the cross-replicating RNA enzymes studied in Gerald Joyce's lab (Lincoln and Joyce, 2009).

    While building such systems is a very useful and constructive exercise, I don't think it tells us much about the early evolution of life. These are highly engineered systems - for example consider the 'miracle' of the Bartel ligase - a RNA ribozyme capable of polymerase activity, whose discovery was likely as much attributable to the brillance of the researchers involved as just pure luck, since the polymerase inhabits a very small region of sequence space. The activity of the ligase is best under conditions that are not friendly to RNA - leading to rapid degradation. Conditions on the primitive Earth were likely even less friendly to RNA. It is extremely difficult to even get RNA nucleotides under prebiotic conditions, let alone any kind of oligomer. This probably emphasizes the necessity of a modular or gradual accumulation of catalytic activities, e.g. attempts to select for polymerase activity for the Bartel ligase directly from a completely random sequence pool were unsuccessful (ingenuity of the experimenters here paid off). And, this is not even a RNA replicase! So far, the goal of engineering a RNA replicase has not met with success.

    But despite these difficulties let's say that a RNA self-replicator could emerge under prebiotically plausible conditions. What then? Could we ever expect to get modern life from it? I am not convinced we could. Take for example the case of the of the Qbeta replicase (also more colloquially known as Spielgman's monster), an early example of the in vitro evolution of a RNA virus. Subjected to in vitro Darwinian evolution this virus decreased its complexity with time, by evolving toward shorter and shorter lengths. Why? Because a shorter sequence is faster to replicate, and selection favors fast replicators. Therefore, even if a RNA self-replicator could emerge de novo from a prebiotic soup it would likely not get us very far - there had to be a lot of other stuff going on. So while I think studying such minimal systems is fascinating in the context of understanding the minimal requirements for self-replication, it may therefore not tell us much about the origin of life on its own. There was a whole mess of chemistry going on in that period that contributed to the gradual complexification of living systems.

    Hope this clarifies some of the issues involved, and thanks for the comments!!

    Best,

    Sara

    Dear M.V. Vasilyeva,

    Thank you for contributing your though-provoking post to the discussion. While I agree with the validity of your argument, I don't think we have any evidence to draw the strong conclusion you've made. One does not even need to invoke the structure of living systems to make the argument. If simulated realities do in fact exist, which we believe they do (i.e. your example of the internet), the number of simulated realities should vastly outnumber the number of possible physical ones. One could therefore conclude that we are living in a simulation since it is much more probable. This is a standard argument. However, I've never heard a compelling argument that we are definitively living in a simulation.

    My question is where would the first intelligent designers come from in your particular example? It just pushes the solving problem to somebody else's reality and therefore doesn't get you very far.

    Best,

    Sara

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    • Post #27

    Thank you for the reply: I read, and learn, a new vast world of knowledge.

    I close my intervention (I don't want annoy and other bloggers that can say different things) in this interesting blog with a thought: I think that in an hostile environment, like a primordial Earth (with radiations, thermal activity, acidity, lightning,etc.), only gradually more complex rna-replicator can survive because a loss of an information in a simple rna lead to the destruction of the self-replicator: the evolution adapt the rna to the environment, so that complex environment give complex life (I think that this is true in general).

    I don't know the environment conditions of the Spiegelman Monster, so this is only an hypothesis.

    Saluti

    Domenico

    Oh Sara, you speak like a scientist and I am a wild visionary in search of entertaining ideas. I try to make sense of the world and the vision above makes perfect sense. More than any other idea I've heard. Especially, the Internet, how it evolved, the viruses and worms... It makes you wonder how did real viruses evolve? They cannot exist, unless there is already in existence a cell (and not just one!) with all its machinery running so that they can take over and make copies of themselves. It would seem that the widespread hypothesis that viruses are protolife from which a primitive cell eventually evolved is illogical. Some rightfully doubt that viruses can even be considered alive! The same is with the computer viruses. These little programs can exist and function only when a sophisticated system is in place and it is used often exchanging information with other systems (and the vector is a memory key, lol). But again I got carried away... You Sara, just get my brain going.

    But, returning to your question "where would the first intelligent designers come from in your particular example?"

    Ah! This is actually easy. Here we have to invoke the most ancient of myths and envision something like this: imagine a god, the one and only, alpha and omega, beginning and the end. And he is oh so lonely. There is nothing but him in the whole world. He is the world. With infinite time on his hands. And so it came to pass that God got bored. And he created a mirror. His image kept him entertained for an infinite while, as he kept company with himself. But then this too was no longer enough. God was overcome with terrible longing, longing for something he could not name. And so in a fit of frustration he smashed the mirror and it shattered into a myriad of pieces. That's how the first world was made.

    You have other questions?

    I had fun :)

    PS

    Or take the topic of many essays here, like Does nature have faithful mathematical representation? (by Roger Schlafly). Roger argues againts the prevailing notion of modern theoretical physics that the true nature of reality is mathematics. But why not? If our world is someone's computer, this would make perfect sense. After all, before computers were linked into a world wide network and became the main source of entertainment, their first designation was to compute. They are highly logically organized. And the stuff they can do! My last job was in LA, in a special effects studio. Already then the quality was such that you can hardly tell what's the real footage and what is rendered. Hey, the rendered stuff is usually better! Have you ever wondered, what goes on in between those blocks of 1's and 0's through which processes crunch for days on end? That's logically organized space represents a virtual world modeled on ours.

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    • Post #29

    Hi Sara,

    Having had the advantage (and pleasure) of reading your preprint "The Algorithmic Origins of Life," that George Ellis kindly linked on his site, I would like to reproduce here part of my reaction, as it applies to your current essay:

    "Take the statement, "To say that information is 'instructional' (or algorithmic) and 'coded' represents a crucial conceptual leap -- separating the biological from the non-biological realm -- implying that a gene is 'for' something."

    Even though I strongly subscribe to the view -- as I believe both Ellis and Davies also do -- that the universe is suffused with meaning and consciousness, I just can't get my mind around what the statement above logically entails: that ' ... coded instructions are useless unless there is a system that can decode. interpret, and act on those instructions.'

    In fact, we don't have a warrant to believe that the world is algorithmically compressible. If it isn't, there is no posssible non-arbitrary demarcation between organic and inorganic life. Self-replicating systems, demonstrably, are sustained on the concept of adaptation alone. In my local ecosystem, a mosquito is useless to me, while globally, my continued existence may depend on the mosquito larvae on which the fish feed and on which I in turn feed. I agree with the authors that analog systems are less adaptable than digital-switching memory processing, such as a CNS-endowed creature possesses; however, analog processes in complex systems allow robust network switching of useful resources for required task performance. So I have to disagree that ' ... in informational terms ... analog systems are not as versatile or as stable as digital systems and as such likely have very limited evolutionary capacity.' In fact, the evolutionary capacity of the complex system is measured in variety and redundance of resources. Nature trades efficiency for creativity, and those created products are manifestly analog systems which provide new input for creating more novel digital mechanical systems producing new analog creations.

    I don't know how -- with this piece -- Davies escapes joining the side of biological determinism (The "gene machine" of Dawkins) which in *The Matter Myth* he and John Gribbin criticized: 'Many people have rejected scientific values because they regard materialsm as a sterile and bleak philosophy, which reduces human beings to automatons and leaves no room for free will or creativity.' Personally, I still regard myself as a materialist and reductionist, though like Gell-Mann, I find no conflict between a continuum of consciousness (quarks to jaguars) and free will. If one refrains from drawing boundaries between life and non-life, algorithmic subroutines that define life and imbue its creatures with free will are not discontinuous with the complex system by which such life is sustained, though which itself is not demonstrably algorithmically compressible.

    I support the 'information narrative.' I think I'm more prone, though, to accept an approach that treats the narrative *itself* as an evolutionary continuum, such as Gregory Chaitin's newly published *Proving Darwin: Making Biology Mathematical.*"

    Having said that, though -- I appreciate the meticulous care that you have invested in identifying and demarcating non-trivial properties of biological life from the inorganic. I agree up to the point that coded instructions are useless without a decoder -- after all, just as genes contain a great number of "switched off" or undecoded potential functions, I find no reason to think that the rest of nature might not be so endowed -- i.e., assume infinite creativity, and infinite variety and redundancy must follow. This subverts biological determinism -- because we do not have to efficiently match codes to decoders -- without sacrificing the idea that life is emergent. Subsystems can just as well re-program themselves for adaptability. Life can just as well emerge from the quantum vacuum.

    If all reality is information-theoretic as Wheeler proposed, and all life is problem solving as Karl Popper proposed, the reality of life is sustained evolution, dependent on an infinitely varied potential of both used and unused resources in any time interval.

    Thanks for a great read and best wishes in the contest. I do hope you have a chance to visit my essay ("The Perfect First Question").

    Tom

      Sorry, lost my log-in. The above is mine.

      Tom

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      • Post #31

      My guess, in terms of causation, is that in non-life the feeding process (including the gathering) is a matter of bottom-up causation and in life it is a top-down causation. I mean, the photons emitted from a tasty piece of food are hardly enough to make us reach out and eat the food, but this is what happens nonetheless.

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      • Post #32

      I start to think a chemical reaction to obtain a self-replicating rna.

      The chemical composition of the rna is a trace of the creation zone: I wish to obtain a zone on the Earth where we had concurrently sulfur, phosphorous, oxygen, carbon, nitrogen and hydrogen.

      I think that only hydrothermal vent can transport in a zone all these element, from the inner layers of the Earth (I read a similar idea of Wachtershauser): only a transport phenomenon can melt different molecules.

      The hot hydrothermal vent in deep see, with high temperature, can form chaotic toroidal flux (close flux of water, enriched with chemical component), that cook the chemical soup, breaking the weak covalent bond, and recombining (cold phases far away from the hydrothermal vent) the break molecule in a complex way (hot stage, cold stage) in a chaotic way (the path of each molecule is different for chaotic vortex, so that each reaction time is obtained casually): the chemical deposition is a proof of the close path (that can be slow).

      It is an idea similar to Miller-Urey, using thermal energy instead of lightining, this can be simulated for high pressure and temperatue (I don't know, when I write, what is the critical thermodynamical point for the life, and if this point exist).

      The rna far away the hydrothermal vent have not feeding, the rna near the hot zone is favorite, but it is necessary a more complex life form (for a robust hot environment life), then the evolution start.

      Saluti

      Domenico

        Domenico, good point! The environment is certainly an essential feature (completely absent in the "speigelman's monster" experiment) and I agree that complex environments are more likely to foster the development of complex life.

        Thanks again for your interest!

        Best,

        Sara

        I do think like a scientist, how could you tell? ;-)

        I don't think its widely accepted that viruses came first. In fact, Freeman Dyson has a very nice model for the early evolution of life, where self-organized primitive lifeforms based on metabolic cycles became infected with digital sequences that later were integrated as the genetic material (i.e. viruses invaded an already extant biome and eventually transitioned to a symbiotic relationship). The model is outlined in his short book "The Origins of Life" which is a very good read. I highly recommend it.

        Best,

        Sara

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        • Post #36

        It's hard for me to say how such behaviour can be quantified, but I'm sure that it might have something to do with what's being investigated here.

        If I draw a fictitious spherical boundary around a region of space and then send in some blackbody radiation, I will reach the conclusion that absolutely nothing special is going on within the sphere if the blackbody radiation exits without delay (beyond that given by the finite speed of light) and without a change in the number of or frequency of the photons. If there is a delay, or change in the light's makeup, then I know that there is some kind of buffer inside the sphere that is allowing for the imbalance of input versus output power.

        So, I am wondering if we can somehow draw a distinction between life and non-life by analyzing the input vs output power over long periods of time. Surely there is information to be gained from this "holographic" analysis, if specific patterns in interaction are a hallmark of living matter.

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        • Post #37

        I am not an expert in organic chemistry, but at first sight these remember me the cracking process.

        In the cracking process (600 kpa or 7000 kpa, a column of water of 60m or 700m, and less of 900°C) there are obtained aromatic intermediate product (I think to the rna nucleobases), and a vast class of intermediate chemical compound.

        The interesting thing is that the cracking in the hydrothermal vent (if it is true) work like the crossing over, deletions and translocation (a thermal evolution before a genetic evolution): if this is true, the genes learned the method from the environment!

        Saluti

        Domenico

        Thomas, thank you for the thoughtful comments!

        I don't think that there is anything in our assessment that precludes the possibility of the evolutionary continuum that you suggest. It is entirely possible that there exists a gradation of states somewhere between what we might call 'living' and what we would call definitely 'not living'. The primary point is that somewhere in that potential continuum a major shift in the way information is handled and processed does occur and that this is a constructive way of thinking about life's origins because it gives you a guidepost beyond just looking at the evolutionary continuum (which doesn't exactly give you any intuition about whether you can expect the kind of information processing we see in biology to emerge or not - in some sense the continuum should be defined by a shift in informational efficacy).

        You've brought up some nice points about analog systems. I agree they can be much more robust than digital in complex networks, but ultimately this robustness requires some level of information control. In modern biology control is dominated by digitization (usually associated with sequence recognition, but also with concentration dependent binary control switches that enable orthogonality between potentially antagonistic sets of chemical reactions), so digitization seems critically important to the story of the emergence of information control. 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.

        Best,

        Sara

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        • Post #39

        You are welcome,

        Ps do you know the works of Oparine about the amino acids in a kind of primordial mixture ?

        Regards

        Steve D.

        We are all scientists here, each in our own way ;)

        I am glad that the majority no longer thinks that viruses came first. I stopped following this issue long ago, when I settled it for myself. I am afraid it will be a while before I could recommend you a book of mine, but something tells me you will read it anyway.

        I feel like perhaps I need to apologize for my playful posts above and hope to be forgiven on the grounds that everyone could use a moment of levity in a discussion as serious as ours.

        All the best to you!