Friday, April 17, 2015

Biology is Not a Materialistic Science



In the two essays by Evelyn Fox Keller and John Dupré that I commented on in my last post, both authors describe themselves as materialists.  Keller says that she is an “unambivalent materialist” and Dupré says
Like Keller, I am a materialist.  That is to say, I do not believe that there is any kind of stuff in the world other than the stuff described by physics and chemistry.  There are no immaterial minds, vital forces, or extra-temporal deities.
It is hard not to read these statements as other than prophylactic confessions. They are nervous that any distance from a reductionist position might be taken for a belief in magic. 
I would argue that neither of them are in fact materialists because any materialism worthy of that name is untenable.  I suggest that the promiscuous use of the term arouses unnecessary opposition to science and especially to Darwinian biology and worse, it is misleading.  Materialism means nothing if it does not mean an account of something that reduces that thing to the properties of its material constituents.  So what does it mean when two philosophers of biology feel obliged to profess materialism and then deny that such reductionism is possible? 
To understand what materialism might mean it is best to begin with a simple materialist explanation.  Consider an iron bar.  It has color, weight, solidity, and other properties such as magnetism and electrical conductivity.  The bar is made out of small bits of iron, which we may then see as its material.  The properties of the whole result from the addition of the properties of the uniform parts and thus the one is explained by and therefore reducible to the other. 
Now suppose that we heat the bar.  What explains the new properties of the object‑its capacity to warm, turn red, and liquefy?  One explanation is that by heating it we have added new material to the existing material‑particles of heat to particles of iron.  The new material we may call caloric or phlogiston.  As water softens soil and makes it flow, so caloric softens iron and, additionally, makes it red hot.  It’s not an implausible suggestion at first glance.  It explains why the hot iron will warm a surface that it rests on.  The caloric is leaking out into the surface, just as water leaks from a sponge into a table cloth.  The caloric theory of heat is what a genuinely materialist explanation looks like. 
By contrast, the molecular theory of heat denies that heat is something material.  It is instead the energy with which the molecules of a substance collide against each other.  Heating the iron bar does not, as such, introduce a new material into the object.  Instead, it changes the state of the same material.  That is a non-materialist explanation precisely because it does not require belief in “any other kind of stuff” than the stuff of iron. 
Genuinely materialist explanations must work like the caloric theory of heat.  Any property of something would have to be explained by reference to the properties of its material constituents alone and any change in properties would have to be explained by the addition or subtraction of material constituents.  A genuine materialism would have to restrict itself to materialist explanations.  It is not as if such a materialism has not be attempted.  Anaxagoras may have been one of the few genuine materialists in the history of philosophy.  Aristotle made short work of him. 
I return to Dupré.  When he says that “there are no immaterial minds, vital forces, or extra-temporal deities”, in addition to confessing atheism he is in fact rejecting materialist explanations for biological phenomena.  The reference to “vital forces” indicates the idea that there is some kind of stuff in living things that animates them.  That explanation of life was, at least originally, a thoroughly materialist doctrine.  According to the ancient atomists (Lucretius being a good example) the soul was a kind of substance present in living bodies.  When a living body was cut open (say, by a sword) the soul particles leaked out, causing death.  That is what a materialist biology would look like!
Much the same is true of “immaterial minds”.  The reference here, I presume, is to substance dualism.  While dualists attempted to explain consciousness by the supposition of an “immaterial substance”, they are, almost always, positing a division in the kinds of material.  Physical substance forms physical things while mental substance forms ideas, impressions, etc.  This is why conman spiritualists in the 19th century had themselves photographed covered with cotton candy like “ectoplasm”. 
What is wrong with vitalism in biology and dualism in philosophy of mind is the same thing that wrong with the caloric theory of heat: they posit material substances that do not exist and propose materialistic explanations for phenomena which cannot be explained in material terms. 
To see that modern biology cannot be a materialistic science, one only has to compare it with Aristotle’s biology.  Aristotle believed in spontaneous generation.  Under certain conditions of heat, moisture, etc., material constituents spontaneously generate simple living organisms.  This happens, as Aristotle thought, frequently in swamps and perhaps dead bodies.  If that were true, then biology would be a much reductionist science that it is.  Aristotle was one of the most vociferous opponents of reductionism and, while he certainly incorporated materialist explanations in his biology, he was no materialist.  Yet he was more materialist than modern biologists.  The latter hold that all living organisms are the offspring of pre-existing organisms. 
Spontaneous generation must have happened at the very beginning of life on earth, but what was added to existing materials was not some new material but form‑a certain primitive structure and the process of self-generation and autonomous action.  Like the molecular theory of heat, any viable understanding of living organisms is non-materialistic.  Magical explanations are to be rejected precisely because they invent mythical materials and rely on inappropriately materialistic devices. 
As Aristotle recognized, materialist explanations are often appropriate in science.  Red paint is red because somebody added red powder to water.  Snowflakes take their amazing shapes because water molecules crystalize in certain patterns.  A baby comes to be because it comes to be out of something.  A materialistic biology is impossible because babies come to be something and come to be towards something and come to be because a process of ontogeny is pushing it out of its original state, to survey Aristotle’s four causes.  It is high time that philosophers and scientists stop calling themselves materialists when they are nothing of the sort. 

Contra Reductionism in Biology



I just finished reading two excellent essays in Contemporary Debates in Philosophy of Biology.  The book, edited by Francisco J. Ayala and Robert Arp, consists of a series of duets: essays taking opposite positions on basic questions in that domain.  The first essay was by Evelyn Fox Keller, who I had the pleasure of meeting in the mid-nineties during a six week seminar at Dartmouth College, led by Roger Masters and Ron Perlman. 
Keller’s essay is entitled “It is Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics”.  It is a very good introduction to the basic problem of reductionism in biology.  It is followed by an essay by John Dupré.  Dupré adds the word “not” to Keller’s title. 
It tells almost all that Keller begins by largely conceding the point.  She notes that in physics and chemistry, the fundamental principles are common denominators and they are coextensive, or equated, with the simple.  To provide my own example, the periodic table of the elements, so basic to chemistry, is literally a poster for simplicity.  By contrast, “whatever the meaning of fundamental in biology, it clearly cannot be equated with simple, nor is it at all obvious that it is common to all biological entities”.  Physical principles are simple and apply to everything in their domain.  Biological principles are rather few if any, and they are very complex.  The best of them admit to exceptions.  So how can we hope to reduce the one to the other? 
Keller goes on to do an admirable job of lubricating the track between the hard sciences of chemistry and physics and the flaccid science of biology by introducing a non-biological, simplified version of function.  In this view, if I understand it, a river functions as part of a system whereby water leaves the ocean for the sky, the sky for the mountains, and the mountains to get back to the sea.  The river is functional because “it contributes to the self-regulation of some entity of which it is a part.”  I note that she was quoting William Wimsatt here, who I also met in Dartmouth.  Pardon my name dropping, but this is taking me down memory lane. 
That simple version of function is fully compatible with physics.  However, while the river functions to get water down it doesn’t function to maintain some internal state of equilibrium (or more accurately, specified disequilibrium).  It doesn’t function to maintain a certain level of water or to keep the water within a specified range of temperatures.  That kind of function seems unique to living organisms, the organization of which functions precisely to keep the internal state within certain parameters by resisting and exploiting external conditions.  It occurs to me at this moment that this description of function neatly explains the difference between a virus, for example, which functions in the first sense, and its bacterial prey which functions in the second. 
As I suggested, the gap between the two kinds of function largely concedes the resolved point.  Chemistry and physics can explain the one kind of function but not the other. 
John Dupré makes the case against reductionism by arguing in favor of “strong emergence”.  He makes the distinction between the whole (a lynx, for example) and the parts (organs, cells, subcellular machinery, etc.).  He denies that “the behavior of the whole is fully determined by the behavior of, and interactions between, the parts.”  My own version of his argument goes like this: precisely because the organism works to maintain its own internal states from succumbing to equilibrium with its surroundings and does so by resisting and exploiting the conditions it finds itself in, its behavior is determined in part by those external conditions.  Those external conditions are determined not only by the physical nature of the molecular components but by a very wide range of accidents.  The same air can be bitterly cold or blisteringly hot.  At the very least, biology has to consider those accidents and among them is the accidental arrangement of molecules into living organisms. 
The unavoidable conclusion is that biology cannot be reduced to chemistry and physics.  Keller is at least open to the possibility that the one might be reduced to the other and suggests some avenues by which that possibility might be explored.  I do not think she succeeds in making it look likely. 
Since I am of the tribe of Plato and Aristotle, I am allergic to reductionism in all its forms.  So I am pretty happy with this outcome.  One thing that both authors profess to believe in, however, is materialism.  I am not a materialist.  Moreover, I don’t think that Keller or Dupré are either.  I intend to demonstrate that in the next post. 

Saturday, April 4, 2015

Borges, Plato, & Natural Selection



Tomas Luis Borges had an astonishing genius for channeling vast currents in the history of ideas into the narrow stream of a compelling story.  One of his most frequently mentioned stories was “The Library of Babel”.  It begins with these words:
The universe (which others call the Library) is composed of an indefinite and perhaps infinite number of hexagonal galleries, with vast air shafts between, surrounded by very low railings. From any of the hexagons one can see, interminably, the upper and lower floors. The distribution of the galleries is invariable. Twenty shelves, five long shelves per side, cover all the sides except two; their height, which is the distance from floor to ceiling, scarcely exceeds that of a normal bookcase. One of the free sides leads to a narrow hallway which opens onto another gallery, identical to the first and to all the rest. 
If you haven’t read the story, I am about to do you the terrible disservice of spoiling the end.  I can only offer the defense that many more people have read about the story than have actually read the story. 
The library consists of a vast but not infinite set of books. 
There are five shelves for each of the hexagon's walls; each shelf contains thirty-five books of uniform format; each book is of four hundred and ten pages; each page, of forty lines, each line, of some eighty letters which are black in color. There are also letters on the spine of each book; these letters do not indicate or prefigure what the pages will say… Second: The orthographical symbols are twenty-five in number.
The library consists of all the books that are logically possible, given the parameters just listed.  To say that this library would be vast is meaningful only in the strictest mathematical sense.  It would be, to say the least, astronomical in extent.  Consider that in this library somewhere is a perfect copy of Shakespeare’s Richard III.  There is also a copy of Dickey Three with alternative endings, including one in which the villain is rescued by the Mighty Morphin’ Power Rangers.  There are perfectly accurate histories of the life of every single human being and indeed every single organism along with alternative histories.  In one of them I am married to two Victoria’s Secret models. 
Of course, all of the coherent reads will be only a drop in the bucket.  Most of the books will be incoherent jumbles of nonsense.  One of the books will consist of nothing but the word “word” over and over again. 
This brilliant thought problem, in the form of a librarian’s musings on the bizarre world that he inhabits, is another version of the infamous infinite monkey theorem.  Could a set of monkeys (say 100), typing randomly, eventually produce a copy of Richard III?  According to the theorem, which I believe to be logically sound, the answer is “yes, given enough time”.  However, the time required is unimaginably vast.  Even to produce “Now is the winter of our discontent” would require more time, I recently calculated, than the age of the Kosmos itself.  Along the way you would get a vast number of half finished, garbled, and alternative versions. 
Darwin’s great idea was to explain how you could get Shakespeare himself out of processes just as random as our team of monkeys or Borges’ library.  All you need is some device that persistently steers the primates in the right direction.  If the monkeys keep typing now is the winter over and over again until they get the next letter right and then keep typing that…  That is what natural selection does. 
These reflections were set in motion by wonderful essay in Aeon.  Andreas Wagner, professor in the Institute of Evolutionary Biology and Environmental Studies at the University of Zurich and at the Santa Fe Institute in New Mexico, argues that Darwinian evolution could not work without “nature’s library of Platonic forms.” 
How do random DNA changes lead to innovation? Darwin’s concept of natural selection, although crucial to understand evolution, doesn’t help much. The thing is, selection can only spread innovations that already exist. The botanist Hugo de Vries said it best in 1905: ‘Natural selection can explain the survival of the fittest, but it cannot explain the arrival of the fittest.’…
A metaphor might help to clarify the problem. Imagine a giant library of books containing all possible sequences of letters in the alphabet. Such a library would be huge beyond imagination, and most of its texts would of course be pure gibberish. But some would contain islands of intelligibility – a word here, a Haiku there – in a sea of random letters. Still others would tell all stories real and imagined: not only Dickens’s Oliver Twist or Goethe’s Faust, but all possible novels and dramas, the biography of every single human, true and false histories of the world, of other worlds as yet unseen, and so on. Some texts would include descriptions of countless technological innovations, from the wheel to the steam engine to the transistor – including countless innovations yet to be imagined. But the chances of choosing such a valuable tome by chance are minuscule.
That giant library is, of course, Borges’ library, though Wagner doesn’t give credit here.  He does present the same problem. 
A protein is a volume in a library just like this, written in a 20-letter alphabet of amino acids. And while protein texts might not be as long as Tolstoy’s War and Peace, their total number is still astonishing. For example, a library of every possible amino acid string that is 500 letters long would contain more than 10600 texts – a one with 600 trailing zeros. That vastly outnumbers the atoms in the visible universe.
The library is a giant space of the possible, encoding all the proteins that could be useful to life. But here’s the thing: evolution can’t simply look up the chemicals it needs in a giant catalogue. No, it has to inch its way painstakingly along the stacks.
So how does natural selection find the next viable protein sequence?  How does this mindless process find the path that arrives at viable minds? 
For more than a decade, this endeavour has been a focus of my research at the University of Zurich and at the Santa Fe Institute in the US. We evolve molecules in the laboratory and record their journey through these libraries, together with any new and useful texts they find. We also map the locations of millions of molecules that nature’s populations have discovered in their billion-year journey. We use powerful computer simulations to explore those parts of a library that nature has not yet discovered. Through these efforts, we and others have found a system of organisation in these libraries that is as strange as it is perfect for guideless exploration.
One of its features is easily explained once we observe that neighbouring texts in nature’s library have similar letter sequences, and the closest texts – immediate neighbours – differ in just a single letter.
If natural selection had to pick at random from the possible protein sequences, no conceivable time would suffice for evolutionary processes.  But it didn’t have to do that.  The basic molecules on which natural selection works (at the molecular level) open up a large but not vast number of pathways.  Many different directions are open, but only so many.  A library of possible forms is on the same shelf and it is a big shelf, but manageable.  Certain pathways prove very fruitful, and natural selection moves up and down them again and again.  Many different combinations of genes work the same outcomes along a viable pathway. 
The remarkable thing is, having so many different ways to say the same thing means that there are many more possible slips of the tongue. And with each slip of the tongue comes the possibility of saying something different. Just as the word GOLD emerges from a single letter change in MOLD, some neighbours of a text express new meanings. And as the browsers work their way through each synonym for some original text, different innovations become accessible. By creating safe paths through the library, genotype networks create the very possibility of innovation.
Let me put this point as strongly as I can. Without these pathways of synonymous texts, these sets of genes that express precisely the same function in ever-shifting sequences of letters, it would not be possible to keep finding new innovations via random mutation. Evolution would not work.
What Wagner thinks, if I read him right, is that the molecular material that natural selection began to work on from the very beginning of life on earth already contained a large but manageable set of forms.  If it hadn’t, evolution could not have been possible.  He recognizes this library of viable forms to be Platonic.  That makes two of us.