Showing posts with label life. Show all posts
Showing posts with label life. Show all posts

Friday, August 11, 2017

Fire and Life

Recently a colleague in the history department at Northern stumped me.  I am ashamed to admit this, as his question went directly to the matters I have been thinking about for years.  The question was this: is fire alive
It is a very good and obvious question.  Fire must breathe.  It consumes fuel and turns it into energy, just as living organisms do.  It also produces waste.  Is there an essential difference between a campfire and a living organism? 
I didn’t think about this seriously until I was actually looking at a fire, after backpacking up into the Wind River Range in Wyoming.  By then, the answer had occurred to me.  I think that this is one of those questions that is a key to understanding.  So here is my reply.  Fire is almost the opposite of a living organism.
A fire begins, necessarily, with a situation of low entropy.  Consider a glass of water with an ice cube floating in it on the dining room table.  If I isolate the glass as a system in thought I note that the system is in a state of low entropy.  All the cold stuff is in the ice cube; all the lukewarm stuff is in the liquid surrounding it.  This is a highly ordered system. 
As the ice begins to melt, the system becomes gradually less and less ordered.  The water locked in ice warms up and releases its energy into the surrounding liquid.  Eventually, the system is at equilibrium.  All the water is at roughly the same temperature: a disordered state.  The system has gone from a state of low entropy to a state of high entropy. 
Fires follow a similar trajectory.  I pile a bunch of firewood in the pit and set it alight.  At that moment, the system is highly ordered.  All the energy is in the wood and much less in the pit and the surrounding air (good thing, that!).  As the wood burns it moves steadily toward a system of high entropy, which is why I have to keep adding more wood.  Fire moves always in that direction: from low to higher states of entropy. 
Entropic processes can be exploited to resist entropic processes.  If I have a pot of water at the same temperature as the surrounding air (high entropy) and I put it on the fire, it will heat up.  Now all the hot stuff is in the pot and the surrounding air is cooler (low entropy).  Boiling water exploits entropic processes to resist entropy. 
Living organisms do precisely that in order to continually recreate themselves.  The sun is constantly bleeding its stored energy into space.  The tree takes that energy and uses it to build its trunk and branches.  I use its bones to build my fire.  I pour the boiling water into a bag of freeze dried food, full of organically sequestered energy, and eat it.  Being a warm-blooded creature, this allows me to resist equilibrium with the steadily cooling air around me. 
Fire is a purely entropic process, as much as an ice cube melting in water.  Living organisms exploit such processes in order to resist such processes.  That is why I am alive and my campfire is not.  I would add one other thing.  Living organisms are always part of a lineage.  I have a mommy and a daddy.  A single celled organism has its predecessor.  My campfire had none of the above.  That seems to me to be more important that it looks. 
I finish with a final, rather depressing note.  My high school physics teacher said that the universe is dying a heat death.  He meant that the cosmos as a whole is basically a campfire.  We living organisms and all the bright lights in the sky will eventually burn out.  All the energy in creation will be evenly distributed and nothing more will ever be done. 

This is not something to be worried about.  The earth will be uninhabitable long before that happens.  It is a reminder to be astounded and grateful that such as ourselves should stand under this canopy of stars.  

Thursday, May 26, 2016

How do you say "physics" in the tongue of biology?

Okay, so we have our chimpanzee banging away at typewriters.  Each keystroke is assumed to be random (this is a thought problem, not a hiring problem).  Let’s limit the keys to the twenty six letters of the alphabet so I don’t have to count the keys on my laptop.  How long does it take our pan troglodytes to produce Shakespeare’s Richard the Third
Well, our hairy scribe will produce one “n” about every twenty-six strokes.  Multiply 26 by 26 and that is how many strokes will be needed to produce the first two letters “no”.  Assuming that Bonzo types 260 letters a minute, how long will it take him to turn out Now is the Winter of Our Discontent Made Glorious Summer by this Son of York?
I once actually calculated this out and quickly determined that it would take more time than the kosmos has existed for our chimp or indeed a whole army of chimps to get even halfway through that first line. 
I like to use this popular thought problem to test my philosophy students.  Could chimpanzees produce a Shakespeare play by random typing?  The answer is that not only could they do so but they would inevitably do so, given enough resources including time.  The problem is that the requirements are so vast as to be, for all practical purposes, impossible.  She who agrees with what I have just said is capable of thinking logically.  He who refuses to acknowledge even the contingent possibility is not. 
One might say that Darwin explained how it was not only possible but actual that that random typing produced chimpanzees.  What you need is some means of saving the good letters.  If every good letter survives and every bad letter perishes, then every twenty six strokes will get you one letter closer to My Kingdom for a Horse! 
Darwin can explain how you get from the simplest replicating organisms to certified public accountants because replicating organisms, by definition, have a means of saving and compiling the good letters in the DNA (or RNA) script.  But how do you get from inorganic chemistry to those UR organisms? 
Physicist Jeremy England has an intriguing guess.  His work is discussed in “How do you say “life” in Physics” by Alison Eck in Nautilus.  England addresses the problem that life presents to physicists. 
To the physicist steeped in statistical mechanics, life can, in this sense, appear miraculous. The second law of thermodynamics demands that for a closed system—like a gas in a box, or the universe as a whole—disorder must increase over time. Snow melts into a puddle, but a puddle does not (on its own) spontaneously take the shape of a snowflake. Were you to see a puddle do this, you’d assume you were watching a movie in reverse, as if time were moving backward. The second law imposes an irreversibility on the behavior of large groups of particles, allowing us to play with words like “past,” “present,” and “future.”
The arrow of time points in the direction of disorder. The arrow of life, however, points the opposite way. From a simple, dull seed grows an intricately structured flower, and from the lifeless Earth, forests and jungles. How is it that the rules governing those atoms we call “life” could be so drastically different from those that govern the rest of the atoms in the universe?
England’s guess is that the solution turns on irreversible shifts in states of atoms.  Here is my version, which mixes the metaphors in the Nautilus articles.  Someone jumping a fence with a pogo can jump back, given that she has enough energy to do so.  That’s a reversible change in state.  Someone being shot out of a canon cannot return.  His flight is irreversible. 
How does this work at the atomic level? 
A group of atoms could take a burst of external energy and use it to transform itself into a new configuration—jumping the fence, so to speak. If the atoms dissipate the energy while they transform, the change could be irreversible. They could always use the next burst of energy that comes along to transition back, and often they will. But sometimes they won’t. Sometimes they’ll use that next burst to transition into yet another new state, dissipating their energy once again, transforming themselves step by step. In this way, dissipation doesn’t ensure irreversibility, but irreversibility requires dissipation.
Now, if I understand the argument, a shift in a configuration of atoms that dissipates the energy required to effect it is a means of saving information.  If the configuration acquires more energy and then jumps to yet another new configuration, then information is in effect compiled.  The third configuration has a history.  To really understand what it is, you would have to know the steps that led up to it.  To the extent that that is true, the history involves the compiling of information.  The gaggle of atoms is saving the good letters. 
This is a very long way from explaining how genuine organisms emerge out of the inorganic soup.  It doesn’t give us any idea of the chimpanzee typing odds.  It does give us an idea of how the simplest mechanics might have produced a selection pressure that tilted inorganic processes towards the emergence of life. 

The origin of life is one of the major mysteries.  The fact that life did emerge on planet Earth tells us that inorganic nature contained within it the seeds of life.  I like that idea.  England may be onto an important clue as to where those seeds lay and how they germinated.  

Friday, August 29, 2014

Living Organisms, Autonomy, & Lineages



Miranda: you are better than any student I have ever known at seeing what the next question is.  That is the single most important element in philosophy. 
Aristotle considered metabolism (the ability of a living organism to nourish itself and consequently produce waste) as a sufficient condition for life.  He referred to this as "nutritive soul."  Plants have this alone, whereas animals have additional layers (mobility, perception at a distance) and human beings have still others.  These are the elements that define various levels of autonomy.  I don't think that this makes autonomy just another word for life.  The word life points to what we are trying to understand whereas the word autonomy helps us to understand what life is. 
However, I smuggled in an element that does not seem to belong to autonomy so much: the production of babies.  Some philosophers of biology argue that, in addition to autonomy, living organisms have to be part of a lineage.  Every living organism is the offspring of a line of successful replicators. 
I am not certain, but I think that the addition of the lineage as an essential element of life is an attempt to head off the kind of objection that Scott James raises against me.  A political community, for example, seems to display autonomy or something very close to it.  It seems to struggle to maintain itself and it has to feed and produce waste.  Aristotle himself argued that the political community is precisely that human association that works enough dynamic cycles that it is "self-sufficient".  Well, if political communities are self-sufficient are they not autonomous?  And if they are autonomous, are they not alive? 
I think that the self-sufficient human community is a much stronger challenge to my view of autonomy than are refrigerators or thermostats.  It is tempting to talk about the evolution of political institutions and to see, for example, the United States as, perhaps, an example of political speciation.  The American regime broke off from the British regime in much the same way as homosapiens broke off from the common ancestor with pan troglodyte. 
This is misleading.  Political communities do not form lineages.  The Second Continental Congress formed spontaneously, as relations between the continent and the mother country worsened; it had no mommy or daddy.  Regimes form spontaneously all the time.  By contrast, living organisms do not form spontaneously.  They always have at least one biological parent. 
It is a very interesting question (and one that did not occur to me until your latest comment) whether the biological lineage is an element of life distinct from autonomy or whether it is another element of autonomy.  The cells and organs of my body (with the exception of my reproductive organs) have sacrificed any opportunity to reproduce.  Like sterile castes among the ants, they can have offspring only through the reproductive activity of something else (my gonads in the one case, the queen in the other).  Does this compromise their autonomy?  Every cell in my body is robustly alive as is the sister forager feeding on my picnic lunch.  I will have to ponder this one. 

Saturday, July 20, 2013

Metabolism & Replication



In Chapter 5 of What is Life? Addy Pross considers theories of the origin of life on earth.  There is a lot in here to chew on, but I will focus on a couple of themes.  One is the relationship between historical and ahistorical explanations. 
Historical explanations of abiotic genesis concern the question of how life actually did emerge from inorganic matter.  Ahistorical explanations concern how organically complex systems could have emerged, given some propitious set of circumstances.  If we knew how life did emerge, it would obviously help us understand the physical processes that made such an event possible.  Likewise, if we understood how life could have emerged it would help us determine what to look for in the geological record.  Unfortunately, we don’t have plausible answers to either question.  This reminds me of an old joke.  There are two ways for a man to deal with a woman.  Nobody knows either one of them. 
The second theme is the dichotomy involving metabolism first accounts of the origin of life and replicator first accounts.  Metabolism is the regulation of chemical reactions that makes all organic processes possible.  Materials have to be exchanged with the environment and transformed within cells.  Energy must be acquired and expended for this to happen. 
Metabolism first explanations of life’s origin hold that it begins with a holistic, autocatalytic reaction among inorganic chemicals.  Suppose that molecule A catalyzes molecule B; B catalyzes C; C, D; and D in turn catalyzes A.  You know have a potentially self-sustaining cycle.  Perhaps that’s how life got started: digestion precedes reproduction. 
Replicator first accounts look to molecules that can replicate themselves.  Chain A-B-C can catch an additional A, which catches a B, which catches a C.  At that point the C-A connection breaks, and we have two A-B-C molecules. 
In existing organisms, metabolism and replication support one another.  It is very unclear how either could get going by itself, let alone both of them independently.  If Pross’ survey is fair, no one knows how either could climb “uphill” against the second law in order to produce even the simplest organisms. 
I keep waiting for some sign of how a reductionist account of life might be possible, as Pross promised.  I haven’t got to the end yet, but I am getting rather near it.  Meanwhile, I am sticking with Aristotle.  Life looks to me as if it were ontologically irreducible to the same laws that seem to govern inorganic matter.  I am not arguing for some deus ex machina.  I think, rather, that the appearance of life tells us something about inorganic matter that we could not possibly guess were life not in evidence. 

Wednesday, December 19, 2012

Roger White on Origin of Life Explanations 2



Roger White distinguishes three types of phenomena, illustrated by “pebble patterns.” 
The Chancy Explanation: Pebbles scattered randomly on a sidewalk require no other explanation than chance. 
Unintentional Biasing: Pebbles arranged in order of diminishing size as they a near the shoreline. 
Intentional Biasing: Pebbles arranged in the shape of a fish (without legs). 
I altered the last one in a way that I hope will be amusing.  According to White, all but a few of those who write with expertise on the problem of the origin of life believe this phenomenon must fall into the second category.  Some natural forces must bias the Kosmos toward the emergence of life, just as the tides bias the pebbles toward a coherent pattern. 
The third explanation is ruled out as unscientific.  The first is ruled out because it is wildly implausible that the conditions upon which the emergence of self-replicators depends should have come about, in the time allotted, merely by chance.  Unintentional biasing must therefore be true by default. 
White argues that the reason that the origin of life is not at all like the unintentional biasing of pebbles by size on the beach. 
The numerous steps required for life to exist are quite unlike this. It is not a matter of the same event-type or property being instantiated many times without exception. The conditions required for the emergence of life have little at all in common.
Adding a bit to what White says, the emergence of life on earth seems to have been a single event (however long it took), not a repeated pattern. 
Why then are most scientists so reluctant to allow too much chance into their accounts of life’s emergence? I will offer a speculative diagnosis. The conviction that life couldn’t have arisen by chance is typically a gut reaction to the data, not a conclusion arrived at on the basis of a theory about when it is plausible to ascribe something to the work of chance.
What makes this event seem so implausible to so many is that it seems to suggest unmistakable evidence of design. 
Again adding to White, I would contrast the origin of life problem with the problem that Darwin addressed.  Why do so many different organisms exist, all of them more or less well adapted to their respective ecological niches?  That is a pattern that is persistent historically and geographically.  Natural selection then can be seen as the unintentional biasing mechanism analogous to the motion of water acting on the pebbles. 
Interestingly, unintentional biasing would be a much more likely explanation for the origin of self-replicators if Aristotle had been right about spontaneous generation.  If the emergence of living organisms from non-living matter under predictable conditions were a persistent feature of nature, as Aristotle, for understandable reasons, believed that it was, then unintentional biasing toward the emergence of life would be very likely indeed.  Of course, this is not the case. 
White makes a strong case that unintentional biasing in nature is not a well-grounded explanation for the origin of life.  That leaves chance and intentional (or intelligent) design.  I would suggest, however, that his dismissal of the gut reactions of so many scientists is premature.  To use one of his analogies, if a tornado picked up a pile of spare parts and assembled it into a working 747 airliner, no one would interpret this was the work of mere chance.  If even the simplest molecular self-replicators as well-designed as the airplane (which may be the case) and unintentional biasing is not a plausible interpretation of the former, then…
I am not making an argument for intelligent design here.  I am not particularly interested in it only because I don’t know what to do with it when thinking philosophically and scientifically about the phenomenon of life.  I do think that White’s argument could be turned almost as easily (perhaps just as easily) into an argument for intelligent design as for the origin of life by chance.  That fact may tell us something about the phenomenon.  If so, it would be unscientific to ignore it.