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    What Is Life - Part 2
    By Gerhard Adam | February 7th 2013 11:10 PM | 11 comments | Print | E-mail | Track Comments
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    Almost two years ago, I wrote an article entitled "What is life - Part 1" describing various aspects of life that dealt with the issues of "intent" and "purpose".  These are obviously heavily loaded terms, and represent a tremendous difficulty in defining life and trying to come to terms with the obvious and yet inexplicable behaviors we see.

    Yet, we all recognize this type of behavior and biology even uses the term teleonomy to characterize this (1).

    Now, the problem faced in biology is that we have these "purposeful" systems called organisms, and yet we must simultaneously recognize that they originated from inanimate processes.  Often the phrase "emergent properties" is used to describe this, but this ultimately explains nothing.  Similarly concepts like "self-organization" may describe what we observe but it offers no explanation as to why we see the behaviors we do.

    In considering the transition from basic chemical processes to life, we are faced with the difficulty of having to explain the origin of life.  However, we can gain some insights and avoid the tangled problem of origins, if we can utilize an existing organic molecule [RNA enzyme] and establishing whether it might be subject to Darwinian selection and evolution.  The answers this would provide can handily sidestep the questions around the origin of life and leave that as a separate concern, while simultaneously establishing that chemical processes may actually be subject to the same kind of selection pressures [or something quite similar] we observe in organisms that are alive.

    One of the essential points here is that RNA is not alive.  So whatever "behaviors" one observes are simply a property of the chemistry involved and cannot be construed as anything more.  Similarly, by using an RNA enzyme, we don't have to address the question of how such a molecule formed, or deal with the historical process that might have produced such a molecule.  We simply take it as given, and attempt to see if its behavior is comparable to biological systems.  Finding such a link would strengthen the argument about an RNA world, or some such organic molecules achieving higher degrees of complexity, ultimately producing "life".

    In fact, precisely such experiments were performed, with some very interesting results.

    An autocatalytic RNA ribozyme was used as a replicator, but was only able to double, twice, over a period of 17 hours.  However, when two RNA ribozymes were employed using a cross-catalytic network, replication occurred within an hour and could be sustained indefinitely.  In effect, these cross-catalytic ribozymes demonstrated the equivalence of chemical "cooperation"
    The above results, though still limited in scope, suggests that cooperative behavior can emerge and manifest itself at the molecular level, that the drive toward more complex replicating systems appears to underlie chemical, and not just biological, replicators.
    http://www.jsystchem.com/content/pdf/1759-2208-2-1.pdf
    However, despite these results, it is important to recognize that one cannot arbitrarily extend the Darwinian theory into the realm of chemistry.  Darwin's theory is a biological theory and must be extended and refined if it is to include biological precursors in chemistry.
    The observation of Darwinian-like behavior at the chemical level is highly significant, not because it suggests that molecules behave in a biological fashion, but because it opens up the possibility of explaining biological behavior in chemical terms.
    http://www.jsystchem.com/content/pdf/1759-2208-2-1.pdf
    An additional biological concept that has a chemical corollary is the "competitive exclusion principle" where two absolute competitors cannot coexist in the same niche.  One will be driven to extinction.  In the chemical version, we find that two replicators that are dependent on the same resources will result in one of the replicators also being driven to "extinction".  
    Thus chemical natural selection appeared, the first step in the transition from inanimate to animate matter. It initiated the first animate property, fitness, i.e., the capacity to adapt to the environment and to survive.
    http://www.ncbi.nlm.nih.gov/pubmed/9010131
    ...one can therefore say that biological natural selection emulates chemical kinetic selection, i.e., biology reduces to chemistry for this most fundamental of biological phenomena
    http://www.jsystchem.com/content/pdf/1759-2208-2-1.pdf
    Perhaps one of the most striking results occurs when two RNA ribozymes competed for five substrates.  When they competed for the same resources, extinction was assured for the least efficient of the enzymes.  However, the availability of multiple substrates, comparable to multiple niches, resulted in mutations accumulating and each enzyme "evolving" to utilize available substrates without direct competition, thereby assuring the survival of both, by "adapting" to their own respective niches.  
    The competitive exclusion principle states that 2 species that compete for the exact same resource within the same environment cannot stably coexist.

    However, when the 2 enzymes were presented with 5 potential substrates, each enzyme adapted to use a different substrate, demonstrating what is termed ‘‘ecological character displacement’’. Once differentiated in this way, the 2 enzymes were capable of sustained coevolution, which in principle could be continued indefinitely.

    In the present study, those interactions were entirely competitive, but other types of interactions, such as commensalism or predation, might have emerged.
    http://www.pnas.org/content/early/2009/04/29/0903397106.full.pdf+html
    The upshot of all this is that these experiments strengthen the ideas that biology can be ultimately reduced to chemistry.  Given the constraints mentioned previously in not merely jumping to biological conclusions when there are chemical similarities, but rather to consider that when chemical systems can "behave" in comparable ways to the principles governing biology, then there is a reason to be optimistic in presuming that this scientific gap can be bridged.  

    ===========================

    (1) For more discussion regarding the teleonomic nature of biological systems [and possibly making sense of it].
    http://www.bgu.ac.il/~pross/PDF-5%20%28Teleonomy%29.pdf

    Comments

    Steve Davis
    Gerhard, from the paper you referred to; "The above results, though still limited in scope, suggests that cooperative behavior can emerge and manifest itself at the molecular level,..."
    It seems to me that artificial life was created there.
    What was observed was a cooperative process that was self-sustaining.
    If we are not going to call that life, then this question will remain unresolved forever, which is quite ridiculous.
    If we are not going to call this life, where will we draw a line in the sand?
    The cooperation view of life is applicable at all levels of life from molecules to groups, and has explanatory power in clarifying such issues as the origin of life and the ongoing dispute over group selection.
    It has so much to recommend it, and above all, it's simple.
    Gerhard Adam
    Where we draw such a line is certainly somewhat arbitrary at this point.  It is not unlike the debate over whether viruses are truly alive or not.  So you can see why RNA enzymes would be questionable.

    In my view, what recommends this paper is that it is cautious in making claims that are too sweeping or inclusive, by acknowledging that Darwin's theory is about "life" [as we currently define it] and we don't have a corresponding theory about how these principles and whatever limits might apply to chemistry.  Until such a theory is developed, it is probably prudent to gather this data and take these hints as indicators that it is a potentially promising path to pursue.

    You may want to check out some of the other links, because the paper by Addy Pross addresses many of these points quite specifically.
    Mundus vult decipi
    Steve Davis
    "...by acknowledging that Darwin's theory is about "life" [as we currently define it]..."
     But "life" is not defined Gerhard, that's the problem.
    What has been defined is "life forms", their features and activities.
    The essence or driver of those features has not been defined.
    Gerhard Adam
    OK, fair enough, but the point is that Darwin's theory only extends to those "life forms" as we know them to be.  Whether the theory needs to be extended or revised to deal with origin-type issues is still to be determined.

    There's little question at this point that gene-centricism is fundamentally dead.  No one can possibly suggest that it is definitive given all the additional information regarding epigenetics and the microbiome.  As I'd mentioned in the article, the existence of germ-free mice and all their attendant differences [and difficulties] is enough proof that the genes are insufficient to account for how things work. 

    In a discussion I've had elsewhere, it is my feeling that the objective in genes is to try and maintain stability within the species.  Mutational forces are too small to be significant, so the purpose of the genetic process is to supply "conserved" traits and to avoid changes.  Sexual selection and sexual reproduction seem [at least in part] to promote the idea of diluting traits, whereas it is common knowledge that inbreeding [or focusing on existing genes] tends to amplify undesirable traits and is detrimental to the species.

    Epigenetics and the microbiome appear to be counter-forces that act to accelerate changes, even within a single generation.  As a result, it stands to reason, that they would operate against the existing genes to express some and not others as circumstances dictate.  Again, the point is not to arbitrarily introduce large scale changes without a context, so the genes represent the context against which epigenetics can operate.

    If similar conditions prevail then it is likely that epigenetics will be more influential even without direct inheritance through the germ-line.  The more extreme conditions are, the greater the selection pressures to exploit the outer ranges of gene expression.  In that respect we would expect to see more rapid evolution through harsher selection and epigenetic markers.  If things are relatively stable, then one would expect to see the genes exert more influence [epigenetics being more "silent"], maintaining stability within the species and letting few changes through into the population.

    Of course, this ignores those aspects of the phenotype that are outside the purview of genes to influence, because the genome is "blind" to the requirement.  In this area the microbiota for a species will be more influential, since they will provide the necessary "trait" to increase fitness.  In effect, it is an external genome that provides the necessary development [i.e. consider protozoans and termites].

    Admittedly many of these relationships are described as symbiotic, but I feel that misses the point.  Symbiosis implies that these are beneficial relationships, but that things could progress without such a relationship.  That clearly isn't the case, when the maturation of our immune system absolutely depends on our microbiota, it is trite to consider our relationship to the microbes as purely symbiotic instead of essential.

    So, as you've stated before.  We have clear evidence that life is a process that involves the interactions of numerous elements and organisms, such that one can't readily find any particular dividing line between one entity and another.  Perhaps one of the issues in defining "life" is that we are behaving as if it is something that can be selectively applied to individuals rather than recognizing that "life" encompasses the entire suite of interactions and that it is their combination that represents what that is.
    Mundus vult decipi
    Steve Davis
    "Perhaps one of the issues in defining "life" is that we are behaving as if it is something that can be selectively applied to individuals rather than recognizing that "life" encompasses the entire suite of interactions and that it is their combination that represents what that is."
    Nicely put, Gerhard.
    And now that you're thinking that way I just need to nudge you in the right spot and you'll be with me all the way! :)
    If I was to say that cooperation adequately describes "the entire suite of interactions" would you accept that?

     
    Gerhard Adam
    This is where one has to be careful of definitions.  My point is that if "life" doesn't reflect individuals but is descriptive of the totality of those interactions.  Then it is meaningless to talk about any particular organism [as simply a part of that totality] as being alive without specifically implying that it is only within the context of the larger "picture".

    If that is the case, then we have a problem with the word "cooperation" since that reverts us back to considering organisms as individuals that can "choose" to cooperate or that are evolutionarily/developmentally "compelled" to cooperate.  In either case, it takes us back a level to considering individuals again.

    So, in that sense, we would have to define "cooperation" as the term that describes that interconnectedness that is the "glue" that holds our definition of life together.

    Does that make sense?
    Mundus vult decipi
    Steve Davis
    "If that is the case, then we have a problem with the word "cooperation" since that reverts us back to considering organisms as individuals that can "choose" to cooperate..."
    Only if we consider life to exist at the level of organisms, which is clearly not the case, as life most likely began at the level of molecules. Life must also include groups, I believe.
    "...can "choose" to cooperate..."
    If we accept that life can be seen at the levels of molecules, organisms, and groups, then the only level at which choice is a factor is that of groups, with individual organisms choosing to cooperate.
    At the molecular level the cooperation just happens as a product of the meeting of particular compounds. No choice involved.
    At the organism level, at the start of life there is no choice. Again, it just happens. An embryo, for example, has little choice.
    But the constant in all these levels is cooperation, whether that is between molecules, cells, or organisms. 

    "So, in that sense, we would have to define "cooperation" as the term that describes that interconnectedness that is the "glue" that holds our definition of life together."
    Not quite. But that's very close to how I would describe it. 
    I see cooperation as the interconnection between all levels of life, as well as that which holds a living entity together. If that is so then cooperation is life.

    Gerhard Adam
    If that is so then cooperation is life.
    That sounds unsatisfactory to me.  Cooperation is a trait, but it isn't a "thing" that one can use to define something else.  In other words, it would be like defining some quality called ABCD and then simply saying that ABCD is life.  It may be true, but it doesn't explain anything.  It's simply substituting another word for a difficult definition.

    For example, it might make more sense to say that life is defined as a series of interactions for resources that are marked by independent agents that are ultimately cooperative in their totality.  Cooperation in this sense should not be interpreted from the individual's perspective, but rather from the system as a whole where each organism is a constituent part. 

    In that way, cooperation really suggests that organisms interact to obtain and exchange resources with each other to perpetuate this thing called "life". 

    So, while someone might object to describing a predator/prey relationship as cooperative, when viewed as a whole, then we would recognize that all creatures are engaged in obtaining resources from each other to perpetuate each other.  In other words ... death is "nothing personal", it's just the means by which resources may be obtained from you, just as you might obtain resources from some other organism.  Now, some might argue that this isn't really cooperative if it is compelled, but I think as a general description it would still be cooperative.  In particular, my point is that if it were purely competitive, then there would be a remote possibility that someone could "win".  Yet, such a scenario would result in death, since without the presence of other organisms with which to exchange resources, then there can be no life.

    Since, in essence, it could be viewed as a kind of game, where we are part competitors, but we also cooperate by following the rules of that game.

    Sorry for the muddled response.  It's getting late here.
    Mundus vult decipi
    Steve Davis
    "...it might make more sense to say that life is defined as a series of interactions for resources that..." That's a process, and you're right to see life as a process, but a definition of life cannot be too detailed an account of that process because life exists at several levels.
    This means that the process will have different features at different levels because the physical and chemical constraints will be different.
    So we have to arrive at an explanation of life that accurately or adequately captures the process at all levels.
    And because it has to apply at all levels it will have to be worded in a very general way, which means that it may appear too simple.
    But I think it is simple.
    I think the easiest way to come to grips with it is to by-pass the origin of life issue as that will always be somewhat murky, and go straight to the life of a group or community - something that we can observe directly.
    When does a number of individuals become a group?
    When they decide to cooperate.
    As soon as they cooperate the group is alive, so the life of the group is the cooperation.
    That simple explanation holds true at all levels, even though the features of the cooperation vary at each level.
    It also provides a guide for those searching for extra-terrestrial life that might be based on unfamiliar chemistry.
    A better explanation of life might well exist, but it will have to be pretty special to cover all the aspects of life that are satisfactorily explained by cooperation.
    Gerhard Adam
    Part of the problem with "cooperation" is that any critic can immediately seize on it by pointing out areas of competition and conflict.  As a result, while it's certainly an important trait, isn't quite comprehensive enough for my tastes.

    I was thinking about it, and it seems that a better word might be "synergy".
    Mundus vult decipi
    Steve Davis
    "Part of the problem with "cooperation" is that any critic can immediately seize on it by pointing out areas of competition and conflict."
    Only if they are confused between "life" and "life forms." Life forms, living entities, can compete without that undermining the cooperation explanation of life at all.
    "I was thinking about it, and it seems that a better word might be "synergy". "
    Same meaning, different word. Here's a definition:
    1. The interaction of two or more agents or forces so that their combined effect is greater than the sum of their individual effects.
    2. Cooperative interaction among groups, especially among the acquired subsidiaries or merged parts of a corporation, that creates an enhanced combined effect.
    So I'm quite happy to accept your definition of life as synergy.
    Welcome aboard the good ship SYNERGY, shipmate! :)

    Actually, after thinking about it for a while I like "synergy" more and more.
    In my line of work it referred to the combined effects of toxins being greater than the sum of the individual effects, which is reflected in part 2 of the definition given above.
    That enhancement effect is true of the cooperation we see in life at all levels.
    When we consider the origin of life, the molecules, after combination, produced replication which is surely a synergistic outcome.