Wednesday, March 7, 2012

An apt description for how life works is: Slop! Part I

From Darwin's time to the present, theories advanced to explain the nature and evolution of life have generally attempted something that is law-like, precise, mathematical, and universal.  But they all have essentially failed--not as apt descriptions of aspects of life or instances of evolution, but as generalizations with the kind of precision expected of 'science'.

Genetics, being molecular, strikes many as the underlying domain where the precise laws of life occur.  If molecules and energy are the fundamental constituents of all of existence, then this must be so about life as well.  It seems to many to be a reasonable deduction that whole organisms must therefore be complex embodiments of the diktats of their genomes.  What is written in the DNA is often treated, even despite some casual caveats to the contrary, as written in stone: your fixed destiny!

But upon close examination this is just not how things generally are.  The causal aspects of life comprise a spectrum, a panorama ranging from very strong causation that largely fits the dreams of simple theoretical biology, to a large amount (we would say certainly the majority) of causation that is aggregative, cooperative, weak, statistical and hence probabilistic, and for which we do not have rigorous theory of the kind that chemists do.

In fact, since life began just as some sort of bubbling chemical reaction in the primeval 'soup', it has become 'life' rather than just a chemical reaction, because it developed sequestered regions (that eventually became cells, organs, organisms, and species) that internally had various interactions but became both isolated and different from other such regions.  The patterns of difference were generated by the evolutionary processes whose key characteristics include that it has no plan, and no pre-set direction.  There is no theory for what will evolve, only some generic processes.

At the level of individual molecules, molecule A interacts with molecule B just as is taught in chemistry class.  There is no violation, that we know of, of the laws of chemistry just because the molecules are found in a living cell.  Molecules are molecules.  The same individual biochemical reactions can in fact be produced in the proverbial test tube, and those of us in life science research achieve such miracles routinely every day.  But there are so many different types of molecules, at different concentrations, times, and locations even within a single cell, that the net results are not so simple.  They don't just add up like the sums of the prices on your grocery list.

For one thing, there are always chance aspects to whether two molecules will bump into each other or interact (as taught in chem class).   But things are not uniformly distributed even within a cell, the way they are in class.  Unlike a soup, there's nobody to stir them to make them mix evenly.  Life is in a sense about not mixing evenly.  So a very large number of probabilistic aspects of chemistry are relevant to the net result.

The overall result is different from a simple sloshing solution for very key reasons that go beyond just differences in concentration of ingredients.  This is that living reactions are hierarchical: what happens now depends on what happened just before, which depends on what happened just before that, in a chain that goes back 3.8 billion years of continuous contingencies!  Some individual reactions are, again as they teach in chem class, reversible.  But the hierarchy from conception to death, or differentiation of cells from one state to the next, is typically not reversible (for example, making stem cells from other types of cells is a form of such reversal, but engineered from the outside, not by the cell itself).

Any major biological function is a mix of such hierarchies with their own complexities, time relationships, and contingencies.  In some situations there are ways of going back, but in many this is not the case.  In particular, it's generally not the case with evolution: commitments get made, hierarchies get established, and they are too interwoven for Nature to do much backpedaling.  But the origin of these complex, hierarchical wefts and warps was haphazard in that, unlike a human weaver, it had no pattern or future use in mind (it had no mind!).  Hierarchies build up over time, that become too complex to be viable if they were to 'try' to reverse course.

Then why do things seem so orderly -- so tempting to develop nice, neat equations for life the way Einstein had a ridiculously simple equation for the entire universe (e=mc^2)?  Or the simple formula for water (H2O), so simple that we can tell where in the vastness of space water may exist just by knowing the formula?  The reason, in a phrase, is that while life is sloppy in the above ways, it is divided into units with enough members, and the members are closely related enough, that there are what can be called 'central tendencies'.  Individuals who are each a mix of huge numbers of components, like molecules of a certain kind, or copies of a protein coded by some gene, each variable but only up to an extent, can themselves vary among each other, but only up to an extent.  Humans vary, but not enough to ever be confused with rabbits.  Body temperature varies but only within a recognizable mammalian range (and when too far off, we can understand why it is a 'disease').

So, orderly slop is the order of the day for much of life.  The orderliness is rather loose, not at all like the orderliness of water molecules, the speed of light, or the pull of gravity.  It follows general principles generally, and at various levels follows basic physical and chemical principles rigidly.  But life is an evolutionary phenomenon based on divergence and difference.  It is not like a crystal that may grow, but only within very constrained bounds.

This is why, unsatisfying as it may seem to someone suffering from physics envy, the laws of life are frustratingly elusive--even if there are such 'laws'.  And yet, if one stops expecting and starts understanding, life is very orderly and understandable, taken on its own terms.  That's what makes it life!

What one would expect, and what one sees very clearly, is that the soup became slop:  very organized in some ways, wholly consistent with the laws of physics and chemistry, but not orderly and rule-following in the way of the physical sciences.  Tomorrow we'll offer some general principles, that we think go a long way toward explaining -- and predicting -- the orderliness as well as the slop in life.


caynazzo said...

Could you provide some example of "living reactions"?

Do genetic drift and natural selection belong? Is one hierarchical to another?

Ken Weiss said...

Drift and selection are not necessarily hierarchical relative to each other. An individual's reproductive success depends on its 'fit' to the risks and opportunities in its circumstances, plus luck (the chance aspects of reproduction).

In some situations selection could be a strong effect that over-rides the effect of drift, and by definition selection is non-drift so statistically that's what 'selection' means. But the relative impacts could be nearly the same when selection is very weak, as seems typical.

As to 'living reactions' what we meant, perhaps badly phrased, is that interactions in life can have consequences and hierarchical effects (a genetic variant once lost from the population can't arise from the crypt), and developmental and other results of complex interactions generally don't really reverse (see upcoming post on Dollo's law). Life is a branching (hierarchical) pattern, not like the ideal gas law or gravity etc.

Unknown said...

While the rules of physics can seem neat and linear, on paper, they are not, at least while in action. There are too many variables and possibilities and slop is the general result.

It was Newton's mathematical + reductionist genius that cut through most of the mush, setting a tone of abstraction that others could follow.

Today when most of the rules have been delineated, physics looks neater on paper than in reality. Like in engineering, for instance, where the lean, mean rules are wrapped in multiple layers of comfort clothing. They call them safety factors, which is slop by another name.

In chemistry and biology, with the number of variables simply greater, and the comparative absence of reductionist geniuses getting attracted to it, (tough work) it is reasonable to expect the job to be a trifle tougher.

Darwin, for instance, so much a real observation oriented biologist, yet one swayed by the easy success of reductionist geological and physics ideas, eager to see if they would apply. Which makes his "origin of species" book more scrumptious dialogue than sparse scientific treatise.

Take heart, one of these days we will exit the slop, the geniuses of biology are yet to be.