"Transition from Inorganic to Organic Life was Based on Information, Not Chemistry"
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October 21, 2013

"Transition from Inorganic to Organic Life was Based on Information, Not Chemistry"

 

Originoflife 3 (1)


In December of 2012, a radical new approach to the question of life's origin was proposed by two Arizona State University scientists that attempts to dramatically redefine the problem. The researchers – Paul Davies, an ASU Regents' Professor and director of the Beyond Center for Fundamental Concepts in Science, and Sara Walker, a NASA post-doctoral fellow at the Beyond Center. "We propose that the transition from non-life to life is unique and definable," added Davies. "We suggest that life may be characterized by its distinctive and active use of information, thus providing a roadmap to identify rigorous criteria for the emergence of life. This is in sharp contrast to a century of thought in which the transition to life has been cast as a problem of chemistry, with the goal of identifying a plausible reaction pathway from chemical mixtures to a living entity."

In a nutshell, the authors shift attention from the "hardware" – the chemical basis of life – to the "software" – its information content. To use a computer analogy, chemistry explains the material substance of the machine, but it won't function without a program and data. Davies and Walker suggest that the crucial distinction between non-life and life is the way that living organisms manage the information flowing through the system.
"When we describe biological processes we typically use informational narratives – cells send out signals, developmental programs are run, coded instructions are read, genomic data are transmitted between generations and so forth," Walker said. "So identifying life's origin in the way information is processed and managed can open up new avenues for research."

One of the great mysteries of life is how it began. What physical process transformed a nonliving mix of chemicals into something as complex as a living cell? For more than a century, scientists have struggled to reconstruct the key first steps on the road to life. Until recently, their focus has been trained on how the simple building blocks of life might have been synthesized on the early Earth, or perhaps in space. But because it happened so long ago, all chemical traces have long been obliterated, leaving plenty of scope for speculation and disagreement. Focusing on informational development helps move away from some of the inherent disadvantages of trying to pin down the beginnings of chemical life.

"Chemical based approaches," Walker said, "have stalled at a very early stage of chemical complexity – very far from anything we would consider 'alive.' More seriously they suffer from conceptual shortcomings in that they fail to distinguish between chemistry and biology."

"To a physicist or chemist life seems like 'magic matter,'" Davies explained. "It behaves in extraordinary ways that are unmatched in any other complex physical or chemical system. Such lifelike properties include autonomy, adaptability and goal-oriented behavior – the ability to harness chemical reactions to enact a pre-programmed agenda, rather than being a slave to those reactions."

"We believe the transition in the informational architecture of chemical networks is akin to a phase transition in physics, and we place special emphasis on the top-down information flow in which the system as a whole gains causal purchase over its components," Davies added. "This approach will reveal how the logical organization of biological replicators differs crucially from trivial replication associated with crystals (non-life). By addressing the causal role of information directly, many of the baffling qualities of life are explained."

The authors expect that, by re-shaping the conceptual landscape in this fundamental way, not just the origin of life, but other major transitions will be explained, for example, the leap from single cells to multi-cellularity.*In addition to being a post-doctoral Fellow at the Beyond Center, Walker is affiliated with the NASA Astrobiology Institute in Mountain View, Calif., and the Blue Marble Space Institute, Seattle.

The Daily Galaxy via Arizona State University

Image Credit: With thanks to http://originslectures.uga.edu/lectures/origin-life

Comments

IMHO, this article partly makes sense. Certainly, at the chemical level, it appears the ‘chemistry’ of life is a natural outcome of the post-Bang, generation of simple to more complex atoms and molecules, including peptide segments which seem to float in a space ’soup’ waiting to combine further. It’s not unexpected therefore to see that after several billions of years, what we know as RNA could arise from the natural valence-structural ‘fit’ of these segments. But this is all standard chemistry.

The issue for this commenter is not that bio-systems (chemical species and higher order chemical morphologies such as RNA and DNA) evolve (like tossing lego pieces in a bag) but HOW (and WHY?) such chemical structures then somehow began to store organized and useful INFORMATION. One suspects that the core question is not as this article posits that life USES information (a given) but how information was acquired/manufactured to begin with. And then, WHAT IS BIO-INFORMATION? Shouldn’t we define bio-information as not simply a structure but as the whole (holistic) PROCESS that creates 'meaningful' structures from the contextual experience (survival in the environment) of the ‘organism’. ‘Meaningful’ in this sense means structure-experience correlations essential to survival of the individual and type (species). The link between an organism’s experience and changes in its bio-information structures seems to be the core definition of ‘life’. ‘Epi-genetic pathways’ come to mind. One might have missed something but it seems there has existed a gap in theory on the subject of HOW an admittedly complex structure like RNA somehow becomes information - until ‘information’ is acquired RNA is still just a curious chemical morphology.

Re-examining the question of bio-informaton, a computer systems picture might be - we know the hardware, and the software (gene segments), and the output (replicated traits). We even have recently acquired the ability to repair ‘errors’ (diseases). So we know how to use and repair this machine, but we don’t know yet how this nice shiny machine transitioned from a box of circuit elements to a functioning information system with inputs, outputs, software and logic! What/who/how wrote the software?

Using this hardware/software approach is interesting, the question becomes how few primitives are needed to support the programming language for the software, given that the primitives are necessarily hardware constructs. For the Lisp programming that minimum number of primitives is 7-9. I think I got that range from Paul Graham's works, and it certainly feels right.

Identifying even one possible primitive could lessen the search space for the physical chemistry people. One way to identify such primitives is to start with a set of highly conserved genes, from archaea to zebra. Nice work.

Yet, another attempt to bring religion and creationism into the picture in the long run.

Look, the human is not a computer to have software and hardware, was not built overnight in the final form, was not designed and created with a purpose in mind. DNA is not a computer code nor created information, although we can represent and interpret it as one. It evolved from simple to complex, as life, from molecules to cells to organisms, for 3.5 billion years on 5 billion billions of centimeters of earth's surface and thousand billion billions of water liters in oceans.

Considering that new cells generations are born only in 20 minutes and that they multiply exponentially we can estimate that existed trillions of trillions generations and trillions of trillions of trillions members. They had to die so we can be here, so this DNA "Information" was filter end enhanced by evolution into what we see today.

To find the truth must go from complex to simple, brake down the problem in smaller pieces, all the way to chemistry origins; if you make things more complex then you'll never be able to solve a puzzle. The "Information" (structure) of the DNA we currently see represent only the final step(status) in the process, completed altered over time by mutations(even non-coding genes), does not cover the full process, and deffinilty cannot be used to derive the first step; unless that's what you want, to move the discussion towards the idea: is all too complex to be explained therefore somebody did it

There is no experimental evidence of mutation-initiated natural selection. However,in: "The epigenome and top-down causation" Davies wrote: "Epigenetics provides striking examples of how bottom-up genetic and top-down epigenetic causation intermingle." [sans mutations theory]

In: "Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors," I detailed the molecular epigenetics of cause and effect from bottom-up nutrient uptake to top-down pheromone-controlled physiology of reproduction.[sans mutations theory]

In: "Nutrient-dependent/pheromone-controlled adaptive evolution: a model," I provided examples of cause and effect in model organisms from microbes to man.[sans mutations theory] http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553

This is not a new model of cause and effect [sans mutations theory], however. The conserved molecular mechanisms in species from yeasts to mammals were addressed in our section on molecular epigenetics in a 1996 Hormones and Behavior review article: From Fertilization to Adult Sexual Behavior. http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html

"Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes.... Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans.... That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes." [sans mutations theory]

Clearly, if you cannot get to sex differences via mutation-initiated natural selection, you cannot go further with claims of mutation-driven evolution without beginning to look more and more foolish. If it's epigenetics in one species, it's epigenetics in all species.[sans mutations theory]


This is excellent. I have often pondered this question myself.

@James: "mutation-initiated natural selection" not observed?
Probably because there's correlation but not causality. Mutations do not trigger natural selection, they are two separate phenomenon/process but put together make up the evolution: one provide change the other provide selection of the change.

The evolution goes only one way, if the animal with mutation manage to survive and procreate, the new trade get stagnant or enhanced in next generations not dimmed (different genealogy might dim it) As Richard Dawkings put it: you can only climb up on Mount Probable.
http://www.dailygalaxy.com/my_weblog/2009/09/evolutions-mutation-screening-process-discovered-oneway-upgrades-only.html

The separation from asexual to sexual indeed pose a tough problem: even there was a mutation that will create male you will not have exactly in the same time a female considering the mutation rates.

As for why, few experiments have shown the survival benefits of sexual breeding comparing to asexual in fish ( variety, resistance to viruses, etc).

However there are two mechanisms that i know of, that could maybe make it possible: Sex Reversal (in Zebrafish) or environment temperature driven sex determination (on frog embryos). Zebra fish produced hundreds of eggs every 5 days, if a mutated fish produced only females there was a chance some eggs changed sex and managed to mate. As for the frog, all it takes is different incubation area across temperature threshold.

Wouldnb't it be nice to identify first what we mean when uttering " L I F E "? Is it the C-O-H-N-etc. based 'BIO'-life of OUR Terrestrial Earth surface, or is it a wider concept (into what?)
It is currently customary to base the term on the past reductionist 'model'-view of our "WORLD" concept (in conventional sciences, explaining everything WITHIN the framework of knowledge as of yesterday, the figments of a 'physical world' with chem, human logid MATH and phenomena learned by primitive instruments over millennia of development in the past).
THEN we can think about theorizing how THAT 'LIFE' originated and how it works. In my opinion: MORE than we think of today.

Another great explanation that explains nothing and that is utterly uncorroborated. great science.
This kind of researches either need a vacation or to ban the verb "explain" from their vocabulary: they use it too frequently, they do not appear to know its meaning.

Hypothesis non fingo.

In my previous post, the "tetractys" did not get displayed properly and, besides, one important element was missing. Hence it should be replaced by the following:


Life/Information = Matter/Energy = Complementarity (1)

In words, Equation (1) reads as follows:

"Life is to information what matter is to energy,
and both these relations are in turn related by
the principle of complementarity."

That is, Eq. (1) represents what has been referred to as the liformation-mattergy complementarity in "Molecular Theory of the Living Cell" (http:www.conformon.net).


In an astrobiology course I took at the beginning of this year I learned about what evolutionary biologists refer to as LUCA or the Last Universal Common Ancestor. I think LUCA contained that information replicating and metabolizing life via RNA and DNA. DNA the code.

@Jennifer: "The separation from asexual to sexual indeed pose a tough problem:..."

It poses no problem at all in the context of the nutrient-dependent pheromone-controlled alternative splicings we detailed in the section on molecular epigenetics in our 1996 Hormones and Behavior review article. At the advent of sexual reproduction in yeasts, morphogenesis of sexually differentiated cell types is obviously nutrient-dependent. The physiology of reproduction is controlled by the metabolism of nutrients to species-specific 'sex' pheromones that enable self vs non-self identification in species from microbes to man.

The only problems that arise come from attempts to introduce mutations as the cause of something that must clearly involve controlled feedback loops. You then introduce the nonsense typical of those who think in terms of predatory control of reproduction (e.g., in moths) instead of acknowledging the fact that reproduction is nutrient-dependent and pheromone-controlled in all species.

@James: Agree, nutrient-dependent(e.g. moths), pheromone-dependent, temperature-dependent(e.g. frogs), population-dependent, in short environment-dependent, but there is no controlled feedback loop just survival and growth of the fittest DNA chain: which includes not only predatory control but more important virus and infection resistance selection(stronger in sexual organism), more rapid evolution changes (more combinations, more mutations) and together with sexual selection of the stronger/healthier/better males/females boosted evolution speed providing a net benefit and faster progress of sexual organisms over asexual organisms

My personal opinion is that there were 2 major milestones which changed evolution speed to exponential levels:

- First was the irreversibility of mutations in offspring, which transformed random mutations into non-random natural selection one way street. This random step took 1-3 billion years to happen, and before it life only produced huge quantities of prokaryotic and perhaps eukaryotic cells. After this step, cells and microorganism evolved exponentially.

- Second milestone was sexual spit, which allowed genes diversity instead of self cloning organisms, which perhaps caused the Cambrian explosion.

The DNA chains started very small and grew big over trillions of trillions of trillions of trial and errors; nature discarded those unsuitable DNA combinations then kept successful ones and enhanced them in future generations new trials.


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