Thursday, December 24, 2009

Darwin Bicententary Part 30: The Mystery of Life’s Origin, Chapter 9

Continuing my consideration of the three online chapters of Thaxton, Bradley and Olsen’s book “The Mystery of Life’s Origin

Absence of Evidence…

In chapter 9 of the Mystery of Life’s origin Thaxton, Bradley & Olsen start by expressing the essential mystery of life’s origin:

In Chapter 7 we saw that the work necessary to polymerize DNA and protein molecules from simple biomonomers could potentially be accomplished by energy flow through the system. Still, we know that such energy flow is a necessary but not sufficient condition for polymerization of the macromolecules of life. Arranging a pile of bricks into the configuration of a house requires work. One would hardly expect to accomplish this work with dynamite, however. Not only must energy flow through the system, it must be coupled in some specific way to the work to be done.

What TB&O are saying here is that although the energy required to carry out the work of organizing atomic and molecular units into a living configuration may be available, that energy in itself is useless without some kind of information engine directing how it is to be used. An analogous situation arises if one has a large work force of men; this work force is all but useless unless they have the information on how to act.

In chapter 9 TB&O look at the crucial question of abiogenesis; that is, the question of whether disorganized elemental matter has the wherewithal to organize itself into complex living structures. They consider a variety of proposed mechanisms: Pure chance, natural selection, self ordering tendencies in matter, mineral catalysis, non-linearity in systems far from equilibrium and the direct production of proteins and DNA. Needless to say they are of the opinion that at the time of writing no substantive model of abiogenesis exists. I am not aware that the situation has improved substantially in favour of abiogenesis since TB&O’s book was written in the mid eighties.

TB&O’s main point comes out very clearly when they consider experimental attempts to directly form polypeptides. TB&O believe that most theories of abiogenesis founder in one important respect: Whilst they accept that under the right disequilibrium conditions organic polymers can be synthesised, they point out that these polymers are randomly configured, and thus by implication contain no useful information content. In TB&O’s opinion the chief challenge to theories of abiogenesis is the question of what supplies the necessary “configurational entropy work”. In their words:

Virtually no mechanism with any promise for coupling the random flow of energy through the system to do this very specific work has come to light. .

TB&O tender experimental results which suggest that the formation of polypeptides shows no bias in the frequency of connections:

The polymerization of protein is hypothesized to be a nonrandom process, the coding of the protein resulting from differences in the chemical bonding forces. For example, if amino acids A and B react chemically with one another more readily than with amino acids C, D, and E, we should expect to see a greater frequency of AB peptide bonds in protein than AC, AD, AE, or BC, BD, BE bonds.

Furthermore, the peptide bond frequencies for the twenty-five proteins approach a distribution predicted by random statistics rather than the dipeptide bond frequency measured by Steinman and Cole. This observation means that bonding preferences between various amino acids play no significant role in coding protein. Finally, if chemical bonding forces were influential in amino acid sequencing, one would expect to get a single sequence (as in ice crystals) or no more than a few sequences, instead of the large variety we observe in living systems. Yockey, with a different analysis, comes to essentially the same conclusion.

Coupling the energy flow through the system to do the chemical and thermal entropy work is much easier than doing the configurational entropy work. The uniform failure in literally thousands of experimental attempts to synthesize protein or DNA under even questionable prebiotic conditions is a monument to the difficulty in achieving a high degree of information content, or specified complexity from the undirected flow of energy through a system.

This kind of evidence supports TB&O’s belief that there is no natural information mechanism that can correctly configure an arrangement of atoms:

We have noted the need for some sort of coupling mechanism. Without it, there is no way to convert the negative entropy associated with energy flow into negative entropy associated with configurational entropy and the corresponding information. Is it reasonable to believe such a "hidden" coupling mechanism will be found in the future that can play this crucial role of a template, metabolic motor, etc., directing the flow of energy in such a way as to create new information?


My own reaction to TB&O’s rather negative assessment of abiogeneis is that if they are genuinely interested in the possibility of a natural route from inorganic matter to functioning organisms they are looking in the wrong place and therefore find what they expect: No evidence of abiogenesis. But if they do start looking in the right place there is a major epistemological snag: it likely to be in the nature of abiogenesis (and evolution as well) to be difficult to observe.

If natural abiogenesis has occurred on our planet then, as I have already mooted in this Darwin Bicentenary series, the coupling mechanism providing the information for abiogenesis is likely to be found in the arrangement of structures in morphospace; for abiogenesis to work there must exist a connected class of stable structures with complexities ranging from the very simple to the very complex; that is abiogenesis requires biological structures to be reducibly complex. This structured class is an object that is neither dynamic nor visible but instead is a static platonic structure that, if it exists, must be implicit in the laws of physics. The information for abiogenesis and evolution is not going to be found in chemistry that encodes the right information in biopolymers in a straight forward way. The information structures, if they exist, will be found in a mathematical object spanning morphospace, an object that has no material reification.

The scientific challenge faced by those committed to abiogenesis (and evolution too) should not be underestimated because abiogenesis may be a computationally irreducible processes. If this is true then it follows that there is no simpler analytical proof of the existence of abiogenesis other than to observe the actual processes that generate life. In this case the evidence of abiogenesis will rest less on theoretical analysis than it will on observation. Hence an absence of fossil evidence becomes a serious barrier to scientific progress in abiogenesis and will add plenty of fuel to the fire of anti-evolutionism. Another problem for theories of abiogenesis is that if there is a natural route from inorganic matter to living structures then fossil evidence is likely to largely comprise of unstructured chemical signatures of equivocal interpretation. Researchers are thus left with little choice but to propose very tentative and speculative chemical scenarios that might look as though they have the potential to generate life. But if TB&O have presented the evidence fairly then it is clear that no consensus theory of abiogenesis exists, let alone a theory with a robust observational base.

TB&O in common with other anti-evolutionists conflate information and complexity:

Regularity or order cannot serve to store the large amount of information required by living systems. A highly irregular, but specified, structure is required rather than an ordered structure.

Whilst I would give a qualified acceptance to the idea that information is conserved in that it requires prerequisite resources either in the form of highly improbable pre-conditions or the huge spaces of a multiverse, is it not true in general that structural complexity cannot be “created” from regularity in relatively short times. Fractals and pseudo random sequences are an example of a “free lunch” complexity derived from simple starting conditions in polynomial computation times. As yet I know of no principled reason why the complex arrangements in morphospace required by abiogenesis cannot also be generated relatively rapidly from the right physical regime of laws. ID theorists may tell us that “equations and equations don’t generate Complex Specified Information” but in spite of that assertion equations can A) be the depository of large amounts of information, B) create complexity in polynomial time, and C) therefore be used to specify complex static forms. (See my last post)

The anti-evolutionists appear to rule out abiogenesis on the basis of the methodological rule “absence of evidence is evidence of absence”. But ardent evolutionists may claim that the onus is on ID theorists to demonstrate that biological structures are irreducibly complex and therefore cannot be product of abiogenesis and evolution. See this post of mine for the ironies of this stand-off between evolutionists and anti-evolutionists. The irony is further compounded when one hears atheists attacking theism on the basis that there is no God because “absence of evidence is evidence of absence”. God and evolution are both very complex objects so perhaps it is not surprising that like abiogenesis it is in the nature of God to be difficult to observe!

Saturday, December 12, 2009

Darwin Bicentenary Part 29: Dembski and Marks’ Latest Paper.

My Unfinished Business with the Anti-Evolution ID Community

William Dembski and Robert Marks’ latest published paper can be found by following a link from this Uncommon Descent post. Its content is very reminiscent of this paper which I considered here here and here*. In this latest paper, however, Marks and Dembski shift the focus to what they call Bernoulli’s principle of insufficient reason, a principle that justifies their assuming equal a priori probabilities over a space of possibilities. It is likely that they feel the need to justify this principle further as their conclusions regarding the “conservation of information” stand on this assumption. I raised this very issue in this discussion on UD where I said:

Yet another issue is this: When one reaches the boundary of a system with “white spaces” beyond its borders how does one evaluate the probability of the systems options and therefore the system’s information? Is probability meaningful in this contextless system? I am inclined to follow Dembski’s approach here of using equal a priori probabilities, but I am sure this approach is not beyond critique.

The choice of using Bernoulli’s PrOIR arises when one is faced with a set of possible outcomes for which there is no known reason why one outcome should be preferred over another; on this basis Bernoulli’s PrOIR then assigns equal probabilities to these outcomes. However, probability (as I proposed in my paper on probability) is a quasi-subjective variable and thus varies from observer to observer and also varies as an observer’s knowledge changes. In particular probability estimates are liable to change if knowledge of the context in which the outcomes are embedded increases. For example consider a six sided die. Initially, if we know nothing about the die then using PrOIR we may assign an equal probability of 1/6 to each side. However, if after, say, examination of the die we find it to be biased, or find that it repeatedly returns lopsided frequencies when it is thrown, then these larger contexts of observation have the effect of weighting the probabilities of the 6 possible outcomes. Thus given this outer context of observation we find that we can no longer impute equal probabilities to the six possible outcomes. But, and this is Dembski and Marks’s essential point, the cost of buying better than PrOIR results on the die is paid for by an outer system that itself has improbable lopsided probabilities. From whence comes this improbable skew on the outer system? This skew can only itself come from a wider context that itself is improbably skewed and so on. According to Dembski and Marks it is not possible, in realistically sized systems, to destroy this improbable loading. Ergo, some kind of conservation law seems to be operating, a conservation law Dembski and Marks call the conservation of information.

I believe Dembski and Marks’ essential thesis to be unassailable. Bernoulli’s PrOIR can be used to set up a null hypothesis that leads one to conclude that the extremely remote probabilities of living structures point to a kind of loaded die in favour of life. Thus, evolution, if it has taken place, could not have happened without biasing its metaphorical die with what Dembski and Marks calls “active information”. In fact as I discussed in this post even atheist evolutionists, in response to one of Dembski and Marks’ earlier papers admit that evolution must be tapping into the resources of a physical regime loaded in favour of life, most likely by the laws of physics; but from whence came our particular physical laws? For these atheists, however, this is effectively a way of shelving the problem by projecting it onto the abstruse and esoteric realm of theoretical physics where it awaits solution by a later generation of scientists. Hiding up the mystery of the origins of living things in the ultimate genesis of the laws of physics allows atheists to get on with their day to day life without any worries that some unknown intelligence could be lurking out there.

It is ironic that multiverse theory is a backhanded acknowledgement of Dembski & Marks’ essential thesis. Speculative multiverse theory assumes that in an all but infinite outer context the butter of probability is spread very thinly and evenly. Hence, because no configuration is given a probabilistic bias over any others it seems unlikely that there is an intelligence out there fixing up the gambling game in favour of life. But if we are to conclude that we can shrug off life as “just one of those chance things” probability theory requires the multiverse to be truly huge. These immense dimensions are required to offset (or "pay for" in D&M's terms) the minute probability of our own apparently “rigged” cosmic environment. That the multiverse must be so extravagantly large in order to make our highly improbable context likely to come up in the long run so to speak, is eloquent testimony of just how active Dembski’s and Marks’ active information must be if our own cosmos should in fact prove to be a one-off case.

We must acknowledge of course that in the final analysis Dembski & Marks are anti-evolution ID theorists and therefore have their sights on “evilution”. They conclude that evolution, if is to work in realistic time, must be assisted by a large dollop of active information; that is, the die must be loaded in its favour. As I see it there is no disagreeing with this general conclusion, but the irony is that just as the multiverse theorists acknowledge the concept of active information in a backhanded way, Dembski & Marks provide us with the general conditions of the scenario that evolution needs in order to succeed.

For Dembski & Marks’ paper, as have all the papers on “active information” I am aware of, provides no killer argument against evolution. In fact if anything it points to the general criteria that must be fulfilled if evolution is to work. They tell us that if evolution has happened then somewhere there is a bias, an improbable skew hidden up in the system. The first port of call in the search for this bias is, of course, the laws of physics. But as a rule, anti-evolution ID theorists will try to tell us that simple equations can’t create information. Their argument, such as I recall it, seems to be roughly based on the following lines.

1. The laws of physics are to be associated with necessity

2. Anything that is necessary has probability of 1.

4. The information content of anything with probability of 1 is zero

5. Therefore equations have no information content

6. Information is conserved. (I give this point a qualified acceptance)

7. Therefore from 5 and 6 it follows that equations can’t create information

The main fault with the above argument is point 1. Christian anti-evolution ID theorists often seem to be subliminal dualists and this inclines them to contrast the so called “natural forces” over and against the superior creator God. These inferior "natural forces" they inappropriately refer to as “chance and necessity”. The so-called “necessity” here is identified with the laws of physics or succinct mathematical stipulations in general. But such mathematical stipulations are themselves an apparent contingency and, as far as we are concerned, don’t classify as necessity; therefore they can embody information.

To see how laws can be the depository of information, it helps to understand that the quantity “information”, as Dembski and Marks use it (= - log[p] ), can only pick up high improbabilities; it is not very sensitive to the exact details of the source of those improbabilities. This is because it lumps together a field of independent probabilities into a single quantity by summing up the logarithms of those probabilities. Therefore “information” as an index cannot distinguish the difference between single probabilities and complex fields of probability. In short information is not a good measure of configuration. Thus single items of probability, if they have sufficient improbability, can embody as much information as collections or configurations of probabilities. This means that although it is true that equations don’t create information, they may yet be the depository of information in their own right if they are themselves highly improbable items; and this can be the case if those equations have been selected from a huge space of possibility over which Bernoulli’s PrOIR is applied. Equations are far from what anti-evolutionist ID theorists call “necessity”. In fact irony is piled upon irony in that we need look no further than Dembski and Marks’ paper for evidence that relatively mathematical simple stipulations may be the depository of active information.

In Dembski and Marks’ latest paper we read this:

Co-evolutionary optimization uses evolutionary tournament play among agents to evolve winning strategies and has been used impressively to identify winning strategies in both checkers [25] and chess [26]. Although co-evolution has been identified as a potential source for an evolutionary free lunch [69], strict application of Benoulli’s PrOIR suggests otherwise.

Dembski and Marks then go on to rightly observe that such systems have a built in metric of gaming success and that this “loads the die” with active information:

Claims for a possible “free lunch” in co-evolution [69] assume prior knowledge of what constitutes a win. Detailed analysis of co-evolution under the constraint of Bernoulli’s PrOIR remains an open problem.

Once again I agree with Dembski and Marks; the co-evolutionary game must be suitably loaded for complex game winning strategies to evolve. But this is to miss the giveaway point here. It seems that all one needs do is to define some succinct game playing rules, then impose a constraint in the form of some relatively simple game wining metric and then given these two constraints the “thermal agitations” of randomness are able to find those complex game winning strategies in polynomial time. A presumed corollary here is that the space of gaming strategies is reducibly complex. Thus it follows that the stipulation of the rules of the game and the selection metric are sufficient to define this reducibly complex space of game wining strategies. These stipulations have the effect of so constraining the “search space” that the “random” agitations are no longer destructive but are the dynamic that seeks out the winning solutions.

The foregoing is an example of an issue I have repeatedly raised here and have even raised on Uncommon Descent. The issue concerns the question of whether in principle it is possible to define complex structures (such as living things and games playing strategies) using relatively simple reductionist specifications and then find these specified complex structures in polynomial time. The generation in polynomial time of complex fractals and pseudo random sequences are examples of a polynomial time map from reductionist mathematical specifications to complex outputs. In the checkers game example the reductionist specifications are the gaming rules and the metric that selects successful strategies and these together define a complex set of winning game strategies that can be arrived at in polynomial time using an algorithmic dynamic which uses random “thermal agitations”. Evolutionary algorithms that identify game playing strategies are an example where simple mathematical stipulations map to complex outputs via a polynomial time algorithm. Of course, because evolutionary algorithms work for games doesn’t necessarily mean that the case is proved for biological evolution given the laws of physics, but the precedent set here certainly raise questions for me against the anti-evolutionist ID theorists tacit assumption that evolution in general is unworkable. But at the very least it seems that evolution does have an abstract “in principle” mathematical existence.

It is over this matter that have I have unfinished business with the anti-evolution ID theorists. I have failed to get satisfaction from Uncommon Descent on this matter. I agree with the general lesson that barring appeal to very speculative multiverse scenarios information can’t be created from nothing – certainly not in polynomial time. But where I have an issue with the ID pundits of Uncommon Descent is over the question of whether or not it is possible to deposit the high information we observe in living structures in reductionist specifications such as the laws of physics. I suggest that in principle simple mathematical stipulations can carry high information content for the simple reason that maps which tie together simple algorithms to complex outputs via a polynomial time link are very rare in the huge space of mathematical possibility, and thus have a low probability (assuming PrIOR) and therefore a high information content. The confusion that I see present amongst Uncommon Descent contributors is the repeated conflation of high information content with complexity; as I have said, information as a measure lumps together a configuration's improbability into one index via a logarithmic addition over its field of probabilities and thus it cannot distinguish single high improbability items from complex configurations of independent probabilities. Elemental physics may therefore be the depository of high information.

As I look at the people at the top of anti-evolution ID community like Dembski and Marks, it seems to me that the implications of their work are not fully understood by the rank file ID supporter. For that supporter, it seems, leans on his academic heroes, quite convinced that these heroes provide an intellectual bulwark against the creeping "atheist conspiracy". The impressive array of academic qualifications that these top ID theorists possess is enough, it seems, to satisfy the average ID supporter and YEC that the battle against “evilution” has been won. The very human attributes of community identification, crowd allegiance, loyalty and trust loom large in this scientific debate.

* I originally (and perhaps wrongly) attributed this paper to Dembski; it has no author name although its URL has Marks’ name in the directory path.

Friday, December 04, 2009

University of Big Disappointments

This University of East Anglia “Climategate” business that William Dembski keeps banging on about is rather (too) close to home - literally almost within walking distance; a childhood stamping ground in fact. Fears, doubts, vulnerabilities come out in private emails; sometimes with a gloss of black humour, bluster and even superciliousness. Trouble is, nobody admits to having them, else they are exploited by opponents and easily misrepresented. But doubts, vulnerabilities and even fears are the stuff of genuine science, as I suggested in this post long before “Climategate” had blown up. There is such a thing as a “scientific attitude”. However, covering up, secrecy, self delusion, conceit, pride and above all epistemological arrogance are the antithesis of that attitude.

The Green House Effect at the University of East Anglia: Don’t cast the first stone if you live in a glass house like this.

Addendum 6/12/09. The Smith and Jones affair.

Below is a YouTube video that needs to be set beside the claims of those for whom this whole affair is a most wonderful windfall. Conspiracy theorist Alex Jones makes a brief and loud appearance on the video and is caught foaming at the mouth over the UEA emails. It's all very reminiscent of pentecostal evangelical Barry Smith's millennium bug conspiracy, which of course is now all but forgotten. Interestingly and ironically Smith's conspiracy theories implicated George Bush Senior in the new world order conspiracy; so are the religious right and the powerful environment poluting corporation bosses supposed to be part of the conspiracy or against the conspiracy? To add to the "we're all having a ball" feel about these e-mail revelations I am beginning to wonder when David Ike is going to make an appearance; in fact he's probably got a YouTube video out there already, but I just can't be bothered to look.

I wonder what William Dembski thinks of some of the company he is keeping?