The ignorant miracle-workers

Cornelis_Pietersz._Bega_-_De_AlchemistIs science the surest way of arriving at truth? Can we validate its worth beyond anyone’s doubt? Surely, the limits of knowledge have been discussed ad nauseum by the ancients. Aristotle did not approve of Platonic metaphysics, but ask any string theorist what she thinks about the laws of nature and she will tell you maths. Where is maths? Where does it reside, before expressing itself in the motion of bodies or the flow of fluids? Where does music go when the instruments stop their play? Historians of science tell us that once upon the Middle Ages science and magic were twin sisters, Siamese twins living together side by side and forcefully separating not before the time of Descartes. His definition of res extensa was followed by logical positivism a few centuries later; but no one would have given a toss if it wasn’t for the Industrial Revolution. I stand firmly behind this argument: if it wasn’t for the engineering miracles that were produced as a result of scientific discovery, science would have been little more than a pastime for gentlemen and gentle ladies of plenty means and time to spare. Everyone had to bow to the miracles of science because the damn thing worked – and it did so better than prayer. Planes fly after all, not by well-wishing (although I often see many fellow passengers pray during take off) but by engines roaring and good wing design. But do we really know why they fly? I would argue that we do not, not really. We do have a good set of equations available, and a sound theory of aerodynamics that we teach to college students, but this corpus of descriptions sits uncomfortably on top of vast, unwavering void of stark ignorance. At the end of the scientists’ day what remains in the Petri dish, or the computer printout, or the spectrum of a far away galaxy, are unanswered questions followed by more unanswered questions. Some call this a virtue. And why not: there is certainly something alluding to heroism in a person willing to face mysteries whilst remaining agnostic. Heroics apart, however, the bottom line is that working the miracles of science was, and still remains, the biggest mystery of all. The body of knowledge is riddled with holes, curious singularities where our notions precariously stand. I would like to give three ready examples of such “singularities”. First, the Big Bang; and of course all that follows it, which is the whole of physics. Our descriptions of the universe, mathematical as they are, should not be confused with knowledge. Secondly: Life, the origin of. How did it come about? Thirdly: the mind. If you have doubts about those three examples, let me put them in another way. The litmus test of true knowledge is the power of reproduction. If I know something – truly know it, not suppose it – then I can reproduce it, nominally or otherwise. If we knew, or came to know, the nature of the Universe, of Life and of the Mind, we could easily reproduce all three of them. We do not (not “yet” some will say, but I dispute that). What we do (re)produce are similes; or simulations of. Scientists are ignorant miracle-workers performing in the circus of history while the rest of world watches in amazement. How long more will the show last? A good answer would be “when the miracles run out”. And then what? What will follow science? A retro-religious era perhaps?

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Aristotle on a chip

The reemergence of ancient notions in the modern field of bioinformatics

Aristotle, in his zoological opus Historia Animalium (The history of animals), launches into his analysis of the animal kingdom by observing differences and similarities between the species. For example, he observes that bats and birds both have wings, so he surmises that they must be grouped together; like fish and dolphins should. By examining animal anatomy and by comparing features such as number or shape of legs (or absence of legs), wings, types of skin, habitats, etc., Aristotle put together a logically coherent taxonomy of animal life that remained virtually unchallenged until Linnaeus. This idea of comparative anatomy, as systematized by Aristotle, is essentially the study of homology (from the Greek word “hómoios”: “similar”) – i.e. of similarities. The idea flowed naturally from Aristotelian Logic and in particular his theory of syllogisms: is A equals B and C equals B, then A equals C. If one replaces “equal” with “similar”, then homology is the logical corollary of equality.

Ancient Greek, and by consequence Medieval European, homology was explained by ideal archetypes, by timeless blueprints designed by a heavenly architect, and into which the objects of perceived reality were molded. Darwin’s revolutionary idea was to provide a naturalistic explanation to animal homology, thus ushering in the era of the scientific study of life.

One and a half centuries after the publication of Darwin’s Origin of Species the modern brethren of his Victorian genius spend much of their time, alas not aboard adventurous sailing yachts roaming the southern seas, but in front of computer monitors applying an ever-expanding arsenal of mathematical and computational techniques in the analysis of living organisms.

One of the most significant application areas of bioinformatics – as this contemporary fusion of biology, computer science and mathematics is termed – is in the study of complex molecules, such as proteins.

Proteins, the building blocks of cells, have structures made up from their particular sequence of aminoacids (which are, in turn, the building blocks of proteins); the way these amino acid molecules unfold in three-dimensional space is what determines the function of a protein. So it is very important for biologists to be able to predict the structure of proteins. What we know is that a protein structure is generally determined by the sequence of the gene that codes for it. And here is where the notion of homology reemerges. It is used to predict the function of a gene. If the function of gene A, whose function is known, is homologous to the sequence of gene B, whose function is unknown, one could infer that B may share A’s function. In a technique called homology modeling, this information is used to predict the structure of a protein once the structure of a homologous protein is known.

Caveat Lector: biologists beware! Meddling with mathematicians who are, secretly, Platonic devotees, may one day lead you to the defense of positivist naturalism against subversive philosophical attacks from the musical spheres of perfect, ideal, proteins-out-there. Ancient ideas, as you should know, are very hard to beat.

The book of the universe

Modern science is a hypertext narrative describing the birth and evolution of the Universe. Its chapters interconnect in multifarious ways with the many branches of scientific enquiry – and this includes the humanities – and many of the chapters are being written even today. Many important details are still missing, but arguably most of the work has already been done. Some, the “Platonists” (see “Spontaneous dichotomy in scientific debate”), would argue that the Scientific Corpus may be totally revised in the future and that indeed we may be very near that tipping point in history. I will argue that this could conceivably happen but it will only affect a small part of the Book of the Universe. It will revise the understanding we have for its beginning, it might even revise the understanding that we have about the origins of life; but it will not re-write the Book of the Universe. The narrative has been written and delivered, what is left to do is editorial work.

It is not therefore surprising that many contemporary philosophers and scientists, notably Richard Dawkins, Daniel Dennet and others, argue that science has already given to the world an excellent explanation of just about everything. They argue, in the name of universal peace and brotherhood that the Book of the Universe is taught across the globe, to everyone, to children of all nations, so that scientific understanding replaces religious belief. Their argument, which I happen to approve, is that religion and irrational belief systems in general, are too dangerous ideas to permeate the nations of a technologically advanced, nuclear-armed world like ours. On the contrary Science, as narrated in the Book of the Universe, unites in a rational and wondrous way all races of the planet, in the common appreciation and respect of nature, so instrumental in establishing some kind of peaceful co-existence and, ultimately, survival.

What interests me about their argument is that I find in it a fine example of the interplay between literature, science and the society of the future. But I will have to return to this point that I am making and expand it further.