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Monday, November 23, 2009

Reading List: Signature in the Cell

Meyer, Stephen C. Signature in the Cell. New York: HarperCollins, 2009. ISBN 978-0-06-147278-7.
At last we have a book which squarely takes on the central puzzle of the supposedly blind, purposeless universe to which so many scientists presently ascribe the origin of life on Earth. There's hardly any point debating evolution: it can be demonstrated in the laboratory. (Some may argue that Spiegelman's monster is an example of devolution, but recall that evolutionists must obligately eschew teleology, so selection in the direction of simplicity and rapid replication is perfectly valid, and evidenced by any number of examples in bacteria.)

No, the puzzle—indeed, the enigma— is the origin of the first replicator. Once you have a self-replicating organism and a means of variation (of which many are known to exist), natural selection can kick in and, driven by the environment and eventually competition with other organisms, select for more complexity when it confers an adaptive advantage. But how did the first replicator come to be?

In the time of Darwin, the great puzzle of biology was the origin of the apparently designed structures in organisms and the diversity of life, not the origin of the first cell. For much of Darwin's life, spontaneous generation was a respectable scientific theory, and the cell was thought to be an amorphous globule of a substance dubbed “protoplasm”, which one could imagine as originating at random through chemical reactions among naturally occurring precursor molecules.

The molecular biology revolution in the latter half of the twentieth century put the focus squarely upon the origin of life. In particular, the discovery of the extraordinarily complex digital code of the genome in DNA, the supremely complex nanomachinery of gene expression (more than a hundred proteins are involved in the translation of DNA to proteins, even in the simplest of bacteria), and the seemingly intractable chicken and egg problem posed by the fact that DNA cannot replicate its information without the proteins of the transcription mechanism, while those proteins cannot be assembled without the precise sequence information provided in the DNA, definitively excluded all scenarios for the origin of life through random chemical reactions in a “warm pond”.

As early as the 1960s, those who approached the problem of the origin of life from the standpoint of information theory and combinatorics observed that something was terribly amiss. Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created. Now of course, elementary particles aren't chemical laboratories, nor does peptide synthesis take place where most of the baryonic mass of the universe resides: in stars or interstellar and intergalactic clouds. If you look at the chemistry, it gets even worse—almost indescribably so: the precursor molecules of many of these macromolecular structures cannot form under the same prebiotic conditions—they must be catalysed by enzymes created only by preexisting living cells, and the reactions required to assemble them into the molecules of biology will only go when mediated by other enzymes, assembled in the cell by precisely specified information in the genome.

So, it comes down to this: Where did that information come from? The simplest known free living organisms (although you may quibble about this, given that it's a parasite) has a genome of 582,970 base pairs, or about one megabit (assuming two bits of information for each nucleotide, of which there are four possibilities). Now, if you go back to the universe of elementary particle Planck time chemical labs and work the numbers, you find that in the finite time our universe has existed, you could have produced about 500 bits of structured, functional information by random search. Yet here we have a minimal information string which is (if you understand combinatorics) so indescribably improbable to have originated by chance that adjectives fail.

What do I mean by “functional information”? Just information which has a meaning expressed in a separate domain than its raw components. For example, the information theoretic entropy of a typical mountainside is as great (and, in fact, probably greater) than that of Mount Rushmore, but the latter encodes functional (or specified) information from a separate domain: that of representations of U.S. presidents known from other sources. Similarly, a DNA sequence which encodes a protein which folds into a form which performs a specific enzymatic function is vanishingly improbable to have originated by chance, and this has been demonstrated by experiment. Without the enzymes in the cell, in fact, even if you had a primordial soup containing all of the ingredients of functional proteins, they would just cross-link into non-functional goo, as nothing would prevent their side chains from bonding to one another. Biochemists know this, which is why they're so sceptical of the glib theories of physicists and computer scientists who expound upon the origin of life.

Ever since Lyell, most scientists have accepted the principle of uniformitarianism, which holds that any phenomenon we observe in nature today must have been produced by causes we observe in action at the present time. Well, at the present time, we observe many instances of complex, structured, functional encoded data with information content in excess of 500 bits: books, music, sculpture, paintings, integrated circuits, machines, and even this book review. And to what cause would the doctrinaire uniformitarian attribute all of this complex, structured information? Well, obviously, the action of an intelligent agent: intelligent design.

Once you learn to recognise it, the signatures are relatively easy to distinguish. When you have a large amount of Shannon information, but no function (for example, the contour of a natural mountainside, or a random bit string generated by radioactive decay), then chance is the probable cause. When you have great regularity (the orbits of planets, or the behaviour of elementary particles), then natural law is likely to govern. As Jacques Monod observed, most processes in nature can be attributed to Chance and Necessity, but there remain those which do not, with which archæologists, anthropologists, and forensic scientists, among others, deal with every day.

Beyond the dichotomy of chance and necessity (or a linear combination of the two), there's the trichotomy which admits intelligent design as a cause. An Egyptologist who argued that plate tectonics was responsible for the Great Sphinx of Giza would be laughed out of the profession. And yet, when those who observe information content in the minimal self-replicating organism hundreds of orders of magnitude less likely than the Sphinx having been extruded from a volcanic vent infer evidence of intelligent design of that first replicator, they are derided and excluded from scientific discourse.

What is going on here? I would suggest there is a dogma being enforced with the same kind of rigour as the Darwinists impute to their fundamentalist opponents. In every single instance in the known universe, with the sole exception of the genome of the minimal self-replicating cell and the protein machinery which allows it to replicate, when we see 500 bits or more of functional complexity, we attribute it to the action of an intelligent agent. You aren't likely to see a CSI episode where one of the taxpayer-funded sleuths attributes the murder to a gun spontaneously assembling due to quantum fluctuations and shooting “the vic” through the heart. And yet such a Boltzmann gun is thousands of orders of magnitude more probable than a minimal genetic code and transcription apparatus assembling by chance in proximity to one another in order to reproduce.

Opponents of intelligent design hearts' go all pitty-pat because they consider it (gasp) religion. Nothing could be more absurd. Francis Crick (co-discoverer of the structure of DNA) concluded that the origin of life on Earth was sufficiently improbable that the best hypothesis was that it had been seeded here deliberately by intelligent alien lifeforms. These creatures, whatever their own origins, would have engineered their life spores to best take root in promising environments, and hence we shouldn't be surprised to discover our ancestors to have been optimised for our own environment. One possibility (of which I am fond) is that our form of life is the present one in a “chain of life” which began much closer to the Big Bang. One can imagine life, originating at the quark-gluon plasma phase or in the radiation dominated universe, and seeing the end of their dominion approaching, planting the seeds of the next form of life among their embers. Dyson, Tipler, and others have envisioned the distant descendants of humanity passing on the baton of life to other lifeforms adapted to the universe of the far future. Apply the Copernican principle: what about our predecessors?

Or consider my own favourite hypothesis of origin, that we're living in a simulation. I like to think of our Creator as a 13 year old superbeing who designed our universe as a science fair project. I have written before about the clear signs accessible to experiment which might falsify this hypothesis but which, so far, are entirely consistent with it. In addition, I've written about how the multiverse model is less parsimonious than the design hypothesis.

In addition to the arguments in that paper, I would suggest that evidence we're living in a simulation is that we find, living within it, complex structured information which we cannot explain as having originated by the physical processes we discover within the simulation. In other words, we find there has been input of information by the intelligent designer of the simulation, either explicitly as genetic information, or implicitly in terms of fine-tuning of free parameters of the simulated universe so as to favour the evolution of complexity. If you were creating such a simulation (or designing a video game), wouldn't you fine tune such parameters and pre-specify such information in order to make it “interesting”?

Look at it this way. Imagine you were a sentient character in a video game. You would observe that the “game physics” of your universe was finely tuned both in the interest of computability but also to maximise the complexity of the interactions of the simulated objects. You would discover that your own complexity and that of the agents with which you interact could not be explained by the regularities of the simulation and the laws you'd deduced from them, and hence appeared to have been put in from the outside by an intelligent designer bent on winning the science fair by making the most interesting simulation. Being intensely rationalistic, you'd dismiss the anecdotal evidence for the occasional miracle as the pimple-faced Creator tweaked this or that detail to make things more interesting and thus justify an A in Miss O'Neill's Creative Cosmology class. And you'd be wrong.

Once we have discovered we're living in a simulation and inferred, from design arguments, that we're far from the top level, all of this will be obvious, but hey, if you're reading it here for the first time, welcome to the revelation of what's going on. Opponents of intelligent design claim it's “not science” or “not testable”. Poppycock—here's a science fiction story about how conclusive evidence for design might be discovered. Heck, you can go looking for it yourself!

This is an essential book for anybody interested in the origin of life on Earth. The author is a supporter of the hypothesis of intelligent design (as am I, although I doubt we would agree on any of the details). Regardless of what you think about the issue of origins, if you're interested in the question, you really need to know the biochemical details discussed here, and the combinatorial impossibility of chance assembly of even a single functionally folded protein in our universe in the time since the Big Bang.

I challenge you to read this and reject the hypothesis of intelligent design. If you reject it, then show how your alternative is more probable. I fully accept the hypothesis of intelligent design and have since I concluded more than a decade ago it's more probable than not that we're living in a simulation. We owe our existence to the Intelligent Designer who made us to be amusing. Let's hope she wins the Science Fair and doesn't turn it off!

Posted at November 23, 2009 17:56