Edwin, thanks for adding to the discussion here. I look forward to reading your comments on my essay!
Is Life Fundamental? by Sara Imari Walker
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You got top community rating from the very beginning but then my reaction prompted some prudent administrator to sort things out? I should have reacted earlier when other favorites instantly occupied top positions (and are still there). What a fair contest!
Pentcho Valev pvalev@yahoo.com
Hi Sarah,
nice essay.
"I stressed top-down causation in the essay, implicitly it is always a combination of causal factors, and could never be just top-down. So 'mutual causation' is always the case. The interesting thing in biology is that something which is nonphysical or virtual (but must of course be instantiated in physical structures) appears to have causal efficacy."
Nicely stated - I agree fully!
best wishes
George
Dear Sara
It is refreshing to leave the world of photons, Relativity and Quantum conundrums for a while, to read your very well written and thought-out essay about a related area of science. It reminded me again that I have not yet read Schrödinger's "What Is Life?" if only for historical reasons. I think I understood your thesis here, but do not agree with it - that studying the origin of life life requires a new physical paradigm to explain the process why some molecules started self-reproducing.
Perhaps the reason I stick to my reductionist approach is that in a model of the universe I have cooked up Beautiful Universe Theory (BU) the causal and local self-assembly of universal building blocks is the only interaction possible. Moreover this BU only exists in one universal 'now' state - ie the concept of time, of past and future future, does not exist as a physical dimension. State A affects and changes the next State B, but not vice-versa. Therefore I do not agree - in pure physical terms - to the 'vice-versa' in your statement ' It is the information encoded in the current state that determines the dynamics and hence the future state (s) and vice versa."
But because a living organism has a definite set of cyclic states , say ABCDEFG ABCDEFG ABCDEFG that repeat themselves it can seem that the G state appears before and is the cause of the A state, so your 'vice-versa' makes biological sense. Yet it it does not require any new physics to implement the process.
The other thing I had a problem with is 'top-bottom causation' since you yourself in footnote 5 say it is difficult to define the concept.
Someone said my BU theory can be classified as a sort of cellular automata, and since you have studied artificial life you may accept the idea that the universe as a whole is always 'living' because it changes dynamically all the time (that word is inescapable!) , but that in certain clusters of molecules this 'living' becomes cyclic and can be called Life?
If you feel like an easy-to-read fqxi essay check out my colorfully illustrated my fqxi essay Fix Physics!
With best wishes
Vladimir
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Sara,
An earlier essay, topic 1416, "Topological solitons of ellipsoid field - particle menagerie correspondence", presented material on "spin". Also, this is the first essay that contains substantive information on solitons.
I made the following comment on "Aug. 24, 2012 @ 00:59 GMT ":
"Do you realize that you are presenting material as to why ionizing radiation is so destructive to biological tissue, the rotational form of the energy field allows it to efficiently couple to DNA and other helical structures within the body."
The only thing I ever read about ionizing radiation is its energy level and nothing about the structural form of the energy. I realized last year that a helical type energy field would efficiently couple its energy to helical type structures within biological material. I had submitted a paper to an IEEE publications describing the helical structure. It did not fare well with peer review, as there were no experiments to "prove" that the helical field structures exist. I had included the Whyte "Chirality" reference, but that did not satisfy peer review.
Someone with a good background in biology needs to write an article about how ionizing radiation with "spin" can efficiently couple its energy to biological structures. I have a paper that describes a basic helical energy structure, but it does not mention frequency or intensity, which would have to be considered as factors in how it would effect biological material.
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What a fascinating essay. I agree with Vladimir that it was a great escape from the low-level reality. Thank you for sharing it.
Another essay here about cosmic engineering might relate to what you are saying. I think their essay is trying to say that living material often doesn't take the path of least resistance like non-living material would (ie. refraction of light by a material, deflection of light in a vacuum by a gravitational field).
So, I guess one question that might be useful is "at what stage does this difference emerge"? My guess is the feeding stage. Living cells feed themselves, but the Voronoi cells that form in rocks do not. Then again, maybe this has nothing to do with finding the answer. I'm not sure.
Thank you George, I very much enjoyed reading your essay as well!
Best,
Sara
Hi Vladimir,
Thank you for your kind comments. The central thesis is not quite "that studying the origin of life life requires a new physical paradigm to explain the process why some molecules started self-reproducing" as you state it. I completely agree that this particular aspect of the problem doesn't necessitate invoking any new physics. But, I think one much be very careful to distinguish trivially self-replicating systems from non-trivial self-replication. For an example of the former, one could look at Penrose blocks (Penrose & Penrose Nature 1958) - replication of a given seed structure (blocks aligned in one orientation or the other) is completely determined by local physics and chemistry. Contrast this with the logical structure of something like a von Neumann self-replicating automata (a very rough approximation to the way cells do business), which requires an algorithm to specify how the machine will replicate. In this scenario replication is explicitly programmed in the machine. The machine may therefore be programed to construct specific objects, and does so in some sense independent of direction by the implicit physics and chemistry (although of course adhering to the constraints imposed by physical law). Evolution is distinguished between these two possibilities since for trivial replicators only the physical structure evolves, while for nontrivial replicators you must evolve both the physical structures and the algorithms (e.g. one may loosely think of the dichotomy between genotype and phenotype in living systems and how they cannot be disentangled, leading to highly nontrivial evolutionary dynamics). So life is very different because it has explicit programming. That is the central thesis - we do not see this anywhere outside of the biosphere (computers here are included in the biosphere since they are derivative of it). So the critical question in the origin of life is how does this state of affairs arise in nature? My intuition is that it has everything to do with information transiting to an active cause in the system.
You mention that organisms can have a definite cycle of states and I completely agree! But one trick in biology is that in your example, if you remove G say, which is a cause for A, another element in the system might take over for G. More interesting is that it is not a simple case of a cyclic process, but those states are tightly regulated, you would need information control with reliable protocols interfacing between elements of the system in your example to more accurately capture what biology is actually doing. That makes the situation both much more complicated but also more interesting.
The information control issue is what is critically interesting to me. Top-down causation is a useful concept in this framework because you can more easily articulate the fact that the algorithm(s) play a distinctive role in the dynamics of the system. Everything about the way information is implemented in biology is context-dependent suggesting that these nonphysical or virtual aspects of the systems operation are changing with the states and vice versa and actively influencing the dynamics. To me that suggests that information is a cause in its own right - that is the radical departure from more traditional ways of doing business in physics and indicates that biology is much closer to to the realm of Turing than to the realm of traditional physics. Causation is not the difficult part to define however - so it is not the 'top-down' that is difficult. The difficult part is defining what are the 'levels' and what are the protocols/algorithms? So this is what I meant about difficulty with defining the concept - its a challenge for practical application. I think we are only at the beginning stages of trying to grasp at concrete answers to these questions as molecular biologists are now embarking on mapping regulatory networks in the cell (e.g. just this week with the ENCODE project).
Thank you for the engaging discussion, and I will be sure to look into your BU theory.
Best,
Sara
Hello S Halayka.
Interesting observation! I am not sure the feeding stage is a satisfactory criteria in of itself though - in some sense certain chemical reactions are capable of "feeding" in the sense that they act like a rudimentary metabolism - catabolizing other chemical species. So you'd have to come up with a rigorous criteria for how feeding by living organisms is different than for these much simpler processes, which could be an interesting question to explore. Perhaps it has something to do with behavior?
Best,
Sara
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As I skimmed through your very interesting essay, I thought, "emergentism and panpsychism" are explanations for life to originate where ALL things have a "memory" and an "awareness". Humans are a bit arrogant, to view something as simple as water, H2O, having such properties.. Yet, it would be awful lonely if it did not have a crucial role in nurturing "life".
To Seek Unknown Shores
聽聽 http://fqxi.org/community/forum/topic/1409
presents a model in End Notes, that satisfies a 6.25% possibility for any life to originate..
Your essay was good!! Good luck.
Ted, thank you for your kind note!
Hi Sara,
Your essay presents your case very nicely. I agree that "informational efficacy" identifies something unique about living things, that certainly deserves more thought. But I tend to imagine this as resulting from the evolution of life, rather than as the defining feature of the process.
You distinguish above between "trivial" and "non-trivial" kinds of self-replication, where the latter involves "explicit programming". More typically, I think biologists (going back to Darwin) say that what makes biological replication non-trivial is that it produces inheritable variations, which subjects the process to natural selection. What you emphasize - the informational control over the chemistry - is made possible by this selective process.
The primitive self-replicating systems that eventually gave rise to life would not yet have shown this distinction between the programming and the chemistry it controls. For example, 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'm not clear through what stages the control-function might have become segregated into a specialized sub-system, eventually leading to the actual encoding of programmatic instructions in stable DNA molecules, with mechanisms for translating that information out into the protein-chemistry. But I can imagine many reasons why this would be advantageous - supporting a remarkably accurate/reliable replication process while including mechanisms that produce and control variation.
I think you're right that this discussion is relevant to fundamental physics, though I would make the connection a little differently. I suggested at the end of my essay that there might be an evolutionary process in physics analogous to the biological process, but based on the functionality of communication rather than self-replication. Then we might think of the "laws of physics" as having a role similar to the function of DNA in biology... as a controlling information-structure that evolved to support the structure of interaction that makes things observable.
In any case, thanks for your contribution -- this definitely brings a different perspective to the question of how information works in the physical world.
Conrad
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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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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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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.