Is Life Fundamental? by Sara Imari Walker

Thomas Ray

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

Tom

[deleted]

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.

[deleted]

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

[deleted]

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

[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

Sara Walker

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

Sara Walker

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

Sara Walker

Interesting thought!

Best,

Sara

Sara Walker

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

[deleted]

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.

Sara Walker

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

[deleted]

You are welcome,

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

Regards

Steve D.

M. Vasilyeva

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!

[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

Sara Walker

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

[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

Thomas Ray

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

Sara Walker

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

Sara Walker

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

Best,

Sara

Sara Walker

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

Sara Walker

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

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