Evolving Thoughts

What is “life”, again?

Now we turn to the modern accounts of life.

In 1828, Friedrich W÷hler produced uric acid without using ?kidney of man or dog?. Prior to that time, there was considered to be something different between organic chemistry and inorganic chemistry. Living things had some ?vital fluid? that other things lacked. Most often this was expressed in Aristotelian terms even if, like Buffon, they were very anti-Aristotelian. But still life was not fully explicable in chemical terms.

Vitalism, as this idea was termed, did not die with W÷hler, though. In fact, we can find instances of it until the middle of the 20th century, particularly on the Continent. The final blow was delivered, not by the discovery of the structure of DNA, as might be expected, but with the final elucidation of the Krebs citric acid cycle and similar metabolic processes.

But what chemists understood had little effect on ordinary biologists, and it was developmental biology that persisted in vitalism longest. So the first general attempt at a ?materialistic? explanation of life was done by a physicist. Erwin Schr÷dinger, living in Ireland during the war, in 1944 produced an influential little book entitled What Is Life? in which he argued that life is a matter of thermodynamics – it feeds on free energy, and thus reduces local entropy. Schr÷dinger called this “negentropy”. Entropy is the tendency of systems to become homogenous in their energy; that is, reach an energetic equilibrium. Life requires a difference in energy levels – this is a metabolic definition of life

This view is not wrong, I think. Life is, as one paper expressed it, a function of the Second Law of Thermodynamics – which states that entropy cannot decrease in a closed system. Life uses the fact that no living thing is closed to ensure that the entropy is increased somewhere else.

But this doesn?t define only life. A good many physical systems are like this, like refrigerators or air conditioners. However, this fact about life has been extended to a larger discussion of ?cosmic evolution? as the local decrease of thermodynamic entropy in parts of the universe, recently by Eric J. Chaisson.

So we need to move on past energetics alone.

The discovery that organic chemistry had a basis in inorganic chemistry was still a major shock, in the early years of the 20th century, and two researchers, Alexander Oparin and J B S Haldane (whose name I have never seen used in full – it is as if he was born with the initials only) both proposed a view that ordinary chemistry could be expected to have given rise to living things somehow.

In the 1950s, a graduate student named Stanley Miller tested the ideas of his advisor, Harold Urey, on the nature of the early atmosphere of earth, and synthesised the basic building blocks of life from a mixture of gases and water. Although the atmosphere Urey hypothesised is not now thought to be the right mix historically, Miller?s experiment showed that organic compounds might be formed through inorganic processes with some ease. A great many other chemistries have been shown to create organic compounds – some of quite complex structure.

William J. Schopf?s book takes the chemical tradition as a definition of life – life is that which is constructed of a half dozen elements in particular forms and compounds. Schopf?s term for it is CHON(SP) – life in composed of Carbon, Hydrogen, Oxygen and Nitrogen (plus Sulphur and Phosphorus).

Schopf?s view is historically true, although we would not be shocked to find a terrestrial organism that, say, replaced some carbon with silicon. Remember Hull?s Rule: there is nothing so absurd that some organism or other doesn’t have it.

The CHON(SP) account is post hoc. It takes life as we see it and makes these the conditions without which something is not alive. This is only partially useful – it points to life as we do know it, but doesn?t help us either delimit life from non-life that happens to be made from the same elements, and it doesn?t tell us what all other life, say on Mars, might be like. It is not, therefore a definition for a ?universal biology? as Kim Sterelny and Paul E. Griffiths put it.

Then there’s Mathematical life – Information and Alife. John von Neumann proposed an idea of “self-replicating robots“, which, being mathematical entities can be given a mathematical definition; life is what replicates its information or program. A number of people have tried to follow up John von Neumann’s suggestion that we might one day build robots that could construct copies of themselves, and which would therefore be subjected to evolution if they sometimes made mistakes (“mutations”). To this end they have proposed formal criteria for life, usually with a mathematical foundation.

Alan Turing, the father of the computer, worked out a mathematics of diffusion gradients that would generate patterns like a zebra’s stripes. When asked if he could therefore explain a zebra mathematically, Turing is reputed to have said, “the stripes, yes, but the whole horse is harder”. Still, a tradition known as process structuralism in biology attempts to describe life as a mathematical pattern.

Gregory Chaitin at IBM published a suggestion in the early 70s that life was a process of information-production. Life generated complexity, which can be understood as something that needs an algorithm of a certain length to describe. Living things were therefore computer programs, or something very like them. This of course ties nicely into the idea of development as a program.

This has flowered over the past two decades into the program known as Alife, or Artificial Life. A number of such programs are available – Thomas Ray’s Tierra is one, in which “animats” evolve through genetic algorithms. Another is Avida. In each case, a living thing in these “toy worlds” is something that can generate copies of itself, and which more or less satisfies a fitness function.

It is very tempting, in these cases, to call these things actual life, rather than simulations of life, and some do just that. I don?t – they are mathematical models that exist in a virtual world. They are abstractions. Life is concrete. But they may identify some general properties of living things?

And this is what Leslie Orgel proposed. For him, the dynamics of things are as important or more than the physical components they are constructed of. Orgel proposes a universal biology. He includes the Chaitin elements: complexity, and information. He makes them concrete objects, and he has them evolve, and evolve by natural selection.

Orgel calls these CITROENS:

  • Complex
  • Information-producing
  • Transforming
  • Objects, that
  • Evolve by
  • Natural Selection

This is a universal biology approach. Orgel specifically says that the elements in our own biota need not apply on a hot planet like Mercury. It is sufficient that objects that reproduce with a high information content through natural selection are alive. The motivation here is clearly the notion of evolution by natural selection, conjoined with the notion of information.

Again, though, some terms are left undefined. What is ?complexity?? He defines information as ?genetic information?, again without telling us how to measure it. When we come to look at this, we will find that it is not so easy to define information in a genetic context, at least, not in any way that addresses the sort of problem Orgel is addressing.

Manfred Eigen, a Nobel laureate physicist, addresses the origins of life as the outcome of what he calls “Hypercycles”. These are chemical reactions that catalyse the reagents needed for the next step, until the last step catalyses the reagents needed for the first step. Hypercycles are chemical merry-go-rounds, and since they are catalytic, that is, since their parts acts as templates for the synthesis of the molecules needed for the next step, they multiply exponentially.

Eigen brings all the traditions together. Life is a dynamic state of matter. It is organised. Information is produced by natural selection. It has a metabolism. This is all the necessary and sufficient conditions for something to be life:

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Unlike many of the others, Eigen treats information as a function of the physical structure of the catalysts in his process. DNA is a kind of catalyst – its products, via tRNA or mRNA, themselves catalyse protein assembly. There is no hard and fast ?information-metabolism? divide here.

Again, in contrast to Orgel, Eigen does not make information a prerequisite for life, but instead a product of natural selection. In his account, the thermodynamic, mathematical and chemical aspects of life are combined.

Comments

  1. #1 Bob O'H
    September 8, 2007

    (before anyone else does it)

    Orgel calls these CITROENS:

    Ah, so life is a 2CV. That might explain a lot.

    Bob

  2. #2 Thony C.
    September 8, 2007

    Alan Turing, the father of the computer

    More and more in my work I find myself fighting against the expressions “so an so is the father of Y” or “so an so is the founder of X” in the history of science and technology. I think that their use leads to a distorted picture of how science or technology progresses and promote an incorrect historiography of science and by association an incorrect philosophy of science. I agree with Lakatos’ claim that the two disciplines are in a complex way interdependent.

    I belong to a group called the Cauchy Forum that organises ten public lectures every autumn on a theme chosen from the mathematical sciences. Over a period of two years we held twenty lectures under the title From the Abacus to the Quantum Computer, my lecture which came almost at the end of the series was George Boole Father of the Computer? whereby the question mark was the most important aspect of the title. I started my lecture by recapping how many of the lecturers had argued that their subject was the “Father of the Computer”. We had had Turing, Horst Zuse on his father Konrad Zuse, Charles Babbage, Atanasoff and Berry contra Eckert and Mauchly and last but not least von Neumann. Each speaker had argued a good case for his candidate but I argued that Boole predated them all and although he had never even conceived of a computer, because all computers use Boolean Logic as the fundament of both their hard ware and their soft ware (not to mention its use as the fundament of all internet search engines) so he should be regarded as the true father of the computer. (As a small historical footnote I should point out that Boolean logic was actually invented by Stanley Jevons who changed Boole’s original exclusive “or” into an inclusive one, a small by highly significant change!) Now the list above of potential fathers is by no means complete, one can equally well argue for Aiken (the Mark I), Vannevar Bush (all three American teams, Aiken, Atanasoff and Berry, Eckert and Mauchly, set out specifically to create an improved version of Bush’s purely mechanical differential machine) or even for Wilhelm Schickard the inventor of the first mechanical adding machine. As soon as you include Schickard then both Pascal and Leibniz come into the frame. As you can see deciding paternity suits in science is not an easy task.

    For this years Cauchy Forum lectures we have chosen Optics as our theme and I will be holding a lecture with the title Johannes Kepler: Not just the Laws of Planetary Motion the blurb for which says that Kepler is also called the Founder of Modern Optics. In my lecture, on which I should be working instead of writing this, I shall explain why Kepler is given this title by many historians of science and just exactly what he did to earn it. I shall however close my lecture by pointing out that this title is also awarded by other historians to Al-Haythem, Descartes and Newton all of whom do so with good and convincing arguments. One could also offer good but slightly weaker arguments for Maurolico, Della Porta, Willebrord Snell and James Gregory.

    I have gone into some detail above because I wanted to illustrate what I consider to be an important point in the evolution of science. New disciplines are not created by individuals but by large groups of well known and not so well known investigators who are all interested in a particular area of thought. Science progresses not by strokes of individual genius but by the collective effort of many minds, some contribution are greater than others but all of them are needed to create the mosaic of a given discipline. Going back to Mr Wilkins’ fairly harmless comment about Alan Turing, his claim to the title of father of the computer is based less on the Colossus and more on his ground breaking theoretical work in meta-mathematics. This work was one part of the work done by a whole group of meta-mathematicians in this period including Goedel, Church, Post, Kleene, Ross and others on the problems of Entscheidbarkeit and Berechenbarkeit both of which had been thrown up by Hilbert’s Programme. All of this work played a significant role in the theoretical development of computing and to single out anyone of the contributors and to say he is The One leads, in my opinion, to a distortion of our understanding of the evolution of science.

    With the usual appologies to our host the Australian Silverback for ranting on his patch.

  3. #3 Thony C.
    September 8, 2007

    so life is a 2CV

    In German the 2CV is called Die Ente which is the German for “The Duck” and is so definitely a form of live!

  4. #4 Ian H Spedding FCD
    September 8, 2007

    French engineering had a reputation of being both innovative and – how shall we say – idiosyncratic, so CITROEN is an appropriate acronym.

    I have fond memories of my Xsara Picasso (who else would name a car after an artist?)

  5. #5 Antoni Jaume
    September 8, 2007

    Life is, as one paper expressed it, a function of the Second Law of Thermodynamics – which states that entropy cannot DEcrease in a closed system. Life uses the fact that no living thing is closed to ensure that the entropy is INcreased somewhere else.

    DSW

  6. #6 John Pieret
    September 8, 2007

    So, the purpose of life is to ensure that entropy is decreased somewhere else?

    I think I have a new motto!

  7. #7 John Wilkins
    September 8, 2007

    Thony, this was once a lecture to undergraduates. They had to know something about what the significance of Turing was. But I agree with you – history is not a succession of Great Men, and the historical roots of any advance involves a complex causal chain of antecedents.

    Antoni, thanks for picking up my error. I’ll fix that. There’s another, little known, law of thermodynamics: whenever a nonphysicist talks about it, there is a high probability they will screw it up.

  8. #8 A R
    September 8, 2007

    This is a very interesting topic to spin ones mental wheels on. Like everyone else I’ve got an opinion on what life is. I say that life can be defined as any replicant that processes raw energy or bonded energy (molecules for organic life, structured information for artificial) to increment the sum of information present in its constituents. ‘death’/time reverses this process in a way that the 2nd law is preserved.

  9. #9 A R
    September 8, 2007

    clarification: information contained in an entity = least amount of energy required to convert an entity from its most basic constituents to its current state

  10. #10 John Pieret
    September 8, 2007

    There’s another, little known, law of thermodynamics: whenever a nonphysicist talks about it, there is a high probability they will screw it up.

    There is some ambiguity in how even physicists and chemists use the term:

    When a system receives an amount of energy q at a constant temperature, T, the entropy increase [delta]S is defined by the following equation.
    [delta]S = q / T

    I still think there is a motto in there somewhere.

  11. #11 A R
    September 8, 2007

    Rewritten: I say that life can be defined as any process that uses energy (excited states for autotrophs, ordered energy/molecules for parasitic life, structured information for artificial) to increment the sum of information present in its constituents.

    Information contained in an entity is the least amount of energy required to convert an entity from its most basic constituents to its current state.

    Any difference in the information content of the environment (external to the process being ‘measured’) should also be added or subtracted from the initial ‘measurement’ to evaluate if a process constitutes life, because a living system will probably have to increment information if it is to replicate successfully.

    death’/time reverses this process in a way that the 2nd law is preserved….

  12. #12 Torbj÷rn Larsson, OM
    September 9, 2007

    Thony C.:

    Science progresses not by strokes of individual genius but by the collective effort of many minds,

    So you say that such framing is problematic? I think you have to call Nisbet out on this one. ;-)

    FWIW, I think noting key individuals and key results is useful in the same way as science programs. They label concepts to make them organized, with the mutual (scientists vs public) understanding that it is incorrect.

    Science programs/fads means rather unconnected research tries to capture grants; publication means dead ends and mistakes are suppressed. (Which btw seems to change now since you can publish negative results in special magazines.)

    The question in my mind is when the distortion becomes more harmful than useful. As you imply, this can happen.

  13. #13 Torbj´┐Żrn Larsson, OM
    September 9, 2007

    John Pieret:

    There is some ambiguity in how even physicists and chemists use the term

    As my old text book aptly notes, most thermodynamic laws expresses universal negatives, which makes positive expression (and verification) difficult. For example, the first law is really saying that energy can’t be destroyed (is conserved).

    So these laws can be given in a number of equivalent positive forms. The popular formulation on closed systems doesn’t mean that entropy can’t be observed or can’t increase in open systems, but that it defines the law. IIRC Wikipedia makes a mess of this point.

    Btw, your definition is “wrong” in the same way, it is incomplete. The equality describes only reversible processes. (Isothermal, but also adiabatic, processes.)

    If you read the footnote you can see that they note this on general processes with temperature changes: “However, the changes are supposedly take place slowly over a long period of time, or in an almost equilibrium or reversible condition. If the change takes place quickly in an irreversible manner, the entropy is greater than what is evaluated [by the equality], because the temperature increase is not uniform.”

  14. #14 Torbj´┐Żrn Larsson, OM
    September 9, 2007

    John Pieret:

    John Pieret:

    Isothermal, but also adiabatic, processes.

    Btw, just for kicks:

    The trick to remember this follows from the equality and the footnote that it only applies on quasistatic processes. Then the improper differentials are close to proper, so either ΔT = 0 (isothermal) or ΔQ = 0 (adiabatic) trivially satisfies T*ΔS = Q.

  15. #15 Torbj÷rn Larsson, OM
    September 9, 2007

    Sorry, read “only applies on” as “applies on”.

  16. #16 jeff
    September 9, 2007

    It is very tempting, in these cases, to call these things actual life, rather than simulations of life, and some do just that. I don´┐Żt – they are mathematical models that exist in a virtual world. They are abstractions. Life is concrete.

    Certainly they are models, but they are not math. They are instantiated in the real world, running on a “real” substrate, just as biological life does. Their behavior can be modeled mathematically just like biological systems (perhaps more accurately), but they are more than a mathematical abstraction. Software does indeed have concrete effects in the real world, otherwise it would be useless – i.e. the infamous WOM chip (write-only-memory).

  17. #17 Daryl McCullough
    September 9, 2007

    John Pieret writes:

    So, the purpose of life is to ensure that entropy is decreased somewhere else?

    Did you intend to say “increased somewhere else”?

    Although it is hard to predict the details of how evolution will proceed, there is a general trend that is pretty certain: The ecosphere as a whole evolves so as to increase the rate of consumption of resources. I’m not going to try to give an exact definition of “resource”, other than “stuff that can be used to do things, and is used up in the process”.

  18. #18 Karmen
    September 9, 2007

    Eigen’s definition seems to exclude viruses. They don’t exactly perform their own metabolism, but I’d rather not consider them non-life. I rather like Orgel’s definition… but wouldn’t it apply just as easily to a mountain as a mole?

  19. #19 John Pieret
    September 9, 2007

    Did you intend to say “increased somewhere else”?

    It was Wilkins! It was all his fault! He’s the one who passed the bad thermosdynamics! I told hin not to fool around with that stuff! You thermo cops ain’t got nothin’ on me!

    It is possible that my years of experience on talk.origins has triggered an over-response . . .

  20. #20 John Wilkins
    September 9, 2007

    Nu uh, Pieret. If I get caught out so do you. Take responsibility for your own actions. What are you, a lawyer or something?

  21. #21 Ian H Spedding FCD
    September 10, 2007

    I was wondering, if the model is not the ame as the thing modelled, are the ‘entities’ in those computer programs that model evolution living?

  22. #22 John Wilkins
    September 10, 2007

    Again, it depends on what criteria you use. Animats in computers lack metabolism. They have something programmed in sometimes (usually just a generalised fitness function) but they are abstract entities, abstracta. So on the presumption, which is not a bad one, I think, that living things have to be conrete entities, no they aren’t.

    A computer that could reproduce itself, on the other hand, might be.

  23. #23 jeff
    September 10, 2007

    they are abstract entities, abstracta. So on the presumption, which is not a bad one, I think, that living things have to be conrete entities, no they aren’t.

    Gotta disagree. They’re abstract when they’re not running (on disk or in memory or in someone’s imagination), but when executing in hardware, they become actual real processes happening in this universe – electrons instead of chemicals, but quite real nonetheless. And the more complex and self-modifying the software becomes, the more difficult it is to model (just as in biological systems).

  24. #24 Andre
    September 10, 2007
  25. #25 Thony C.
    September 11, 2007

    Torbjorn wrote:

    FWIW, I think noting key individuals and key results is useful in the same way as science programs. They label concepts to make them organized, with the mutual (scientists vs public) understanding that it is incorrect.

    I do not see what advantages such labelling might have but I do see the disadvantages, let us take the label “Galileo father of telescopic astronomy”

    Consider the following, the standard version usually goes something like this:

    The telescope was invented in Holland in 1608, we don’t actually know who invented…(but that’s another story!). Already in 1609 the great Galileo turned the telescope towards the heavens and through his discoveries revolutionised astronomy.

    A more realistic version would be something like this:

    The telescope was invented in Holland in 1608, we don’t actually know who invented… Within a year astronomers throughout Europe, Thomas Harriot in England and his pupil William Lower in Wales, father and son David and Johannes Fabricius in Friesland, Christoph Scheiner in Ingolstadt, Simon Marius in Ansbach, Christian Longomontanus and Cort Aslaksson two former assistants of Tycho Brahe in Copenhagen and the professor for mathematics in Padua Galileo Galilei had all acquired or constructed their own telescopes and begun to make scientific observations of the heavens. The relatively unknown Galileo was the first to publish the results of his observation, a move that him made famous throughout whole of the then scientific community.

    The first version is a good “sound bite” that as well as being misleading does not convey very much information at all. The second although somewhat longer actually only require a couple of minutes to read and digest and conveys a great deal of information. As well as the direct facts stated in the few lines, it manages to give an impression of the very rapid spread of the telescope through Europe and also that there were many working astronomers who were able to understand, utilise and exploit the advantages of this new instrument for the astronomy.

  26. #26 Heresiarch
    September 11, 2007

    A more thorough going analysis of what life is can be found at http://www.starlarvae.org. The author finds a way to break through the organic/inorganic barrier.

  27. #27 Nurturing Life
    April 4, 2008

    Life on this planet is diversified and this single word means different thing to different people. I have been to so many sites on life and now it seems life is a subject which is under study in every field. Life is biology, its philosopy, its chemisty and even career to some.

    Even life cycle of objects is also understood to be a meaning of life.