Tuesday, December 27, 2011

The Wrong Sort of Scratching

(Click to enlarge)

The above illustration was posted by Prof Larry Moran in a blog post where he makes special note of the Cambrian Conundrum. What is the Cambrian Conundrum? Let me explain:

The blue profile in the illustration plots the graph of the very sudden rise in the diversity of phyla at the start of the Cambrian era (Phylum: a category of organisms with the same basic body plan). This sudden diversification was also accompanied by a parallel prolific diversification of classes (a class is a subdivision within a phylum) as shown by the yellow profile.

Shown as an overlay on the two aforementioned graphs is the “tree of life” as deduced from genetic molecular sequence analysis together with an assumed rate of mutation. Larry points out that the molecular tree of life fits in very well with the tree of life as determined from morphological analysis. But there is one big and obvious problem here: The molecular tree of life appears to show no obvious relation to the phyla and class profiles, profiles that are determined by observation on the fossil record. Why doesn’t the fossil record concur with the tree of life as constructed from molecular sequence analysis? How is it that this tree of life extends for hundreds of millions of years before the Cambrian and yet there is little in the way of fossil evidence prior to the Cambrian?

As a diehard evolutionist Larry is a good sport in being candid about this problem as he well knows that anti-evolutionists are attracted to this sort of thing like flies to an open wound. A couple of his correspondents give a stab at trying to explain this apparent inconsistency in evolutionary theory: One (schenk) suggests that chemical conditions prior to the Cambrian didn’t favour preservation: The other (nwrickert) submits the very interesting idea that the gene pool had developed to a point where the potential for sequence crossovers constituted a kind of “recombinant DNA laboratory” paving the way for a combinatorial explosion that gave organisms the DNA language needed to match a rapidly changing environment. I must admit I find this latter idea very appealing; it’s a special case of the more general idea that some “non-linear” bio-tech threshold was crossed at the start of the Cambrian ushering in a tremendous potential for change and development – in fact we see something similar with human society; farming, writing, industry, microchips and other technological changes entailed the crossing of thresholds that opened up huge vistas of possibility once the initial invention had made an appearance; these vistas were then rapidly explored resulting in rapid change.

But be that as it may, the fact is that there is an important lesson here for evolutionary theory. Evolution is a theory of a very complex object – namely, the history life. As such it has many degrees of freedom and adjustable variables. This implicit flexibility helps “rescue” evolution in the face of the sort of conundrum we have just looked at by allowing an adjustment of its many degrees of freedom until a fit to the dots of observation is achieved. But evolution’s strength in theoretical flexibility is also its weakness: Like some sprawling battle front evolution is vulnerable to myriad different kinds of attack on its many varied claims. In fact evolution is interdisciplinary and high level enough an object to be tantamount to a world view perspective. With byzantine objects like evolution there exists a constant tension between their vulnerability to criticism and the measure of latitude that comes of realizing that their complex ontology is never going to return the standard of observational “verification” we might expect of simple objects like Hooke’s springs and Newton’s gravity. The balancing act needed here is not easy to keep in the polarized North American environment where anti-evilutionists and atheist zealots are clawing one another’s eyes out in order to win their noetic battles. If with an eye on fair play one endeavors to be generous to either side one is then in danger of having one’s eyes scratched out by the other side.

In this connection I was fascinated by this post on PZ Myers’ blog where he tells his readers about theologian Alister Mcgrath’s comparison between the sense making facility of the conjectured Higgs boson and the theist positing Deity as a world view level sense making object. PZ Myers agrees that the Higgs boson is a valid theoretical sense making construction, but he takes Mcgrath to task for not taking the next scientific step; namely, that of proposing a test for deity; after all, says PZ, a lot of money was spent in order to test for the existence of the Higgs Boson; shouldn’t theists do the same for God?

Well yes, I’ll concede the admirable sentiment behind PZ’s remark, but in doing so I make all due allowance for the ontology of the objects we are proposing to test; that ontology may make these objects less than voluntarily accessible and/or give them a complex of adjustable variables that compromises the value of any number of tests; this in turn will impact the epistemological standards we employ. You see, whilst we may accept that PZ Myers' demand for a test is fair enough, we nevertheless should acknowledge that voluntary high standard testing at will is not an option with many real objects of study; historical objects are a notorious case in point; in particular evolution.

After all, it is clear that an object like evolution cannot be tested at will; as we have seen the fossil data needed to test for the existence of the conjectured evolutionary cladogram beyond the Cambrian is not forthcoming; it might, of course, come to light at some future date but that is not something over which we have control. Moreover, the conjectured extended cladogram may in fact not exist at all, and its absence explained by adjusting the parameters of history’s many degrees of freedom. (As a couple of Larry’s correspondents do; feasibly and plausibly in my view). In doing so, however, we are not using evolutionary theory predictively but instead invoking its flexibility to make post facto sense of the observed situation. Provided this is carried out with all due caution and awareness this post hoc practice is in my view perfectly legitimate science in the face of an absence of other choices. (See here for more comment along these lines: http://quantumnonlinearity.blogspot.com/2011/11/science-and-imagination.html )

It would be nice, of course, if we could test at will, or be lucky enough to have the necessary test data involuntarily fall into our laps, but unfortunately life is not always like that, particularly when the objects we desire to test shade over into the high level objects that are the stuff of world views. On balance, then, I would say that Mcgrath’s treatment of theism as a post facto sense making construct is rational enough given the ontological nature of deity; although having said that many Christians would claim that the ultimate (anecdotal) test of theism is in the tasting (Ps 34:8).

World view construction is largely a post facto activity that sometimes boarders on myth construction not because this is a rational ideal, but simply because force of epistemic circumstances make it so. Toy town science practitioners might find difficulty in accepting this inconvenient fact and may even be inclined to scratch our eyes out for breaching their narrow jot and tittle view of rationality. But then the purveyors of toy scientism are not the only ones unprepared to give leeway in the face of epistemic challenges. The zealous anti-evolutionists are in no mood to give all due allowance to evolution’s measure of post-facto sense making science. This is particularly ironic given that many anti-evolutionists are theists and that theism itself is not exactly the epitome of readily testable science!

The Right kind of scatching: If you scratch my back I'll scratch yours.

Friday, December 23, 2011

Don’t Play this at Home:

The obscenities in this video tear through the sentimental and schmaltzy fabric of Xmas with the sound of a low flying jet over a soft Kincaidian landscape. The message is that Santa gets all the accolades (and gets to look charitable to boot) whilst the beasts of burden (the reindeer) and the small men (elves, pixies and dwarfs) do all the work. Given that Santa is patron saint of Xmas capitalism, the video reminded me very sharply of the days when I used to read the stridently Marxist newspaper “Socialist Worker”. The video expresses that paper’s vision of society to a tee: In raucous and harsh tones it forever condemned middle class capitalist acquisitiveness at the expense of working class wealth producers. “Stuff the Bosses”, “Stuff the Tories!”, “Stuff the Royals!” were the kind of headlines that often graced the front page.

I myself, however, was as cynical toward this Marxist message as the Socialist “Workers” were to the society that sustained them in sufficient freedom to express their opinions. Theirs was a materialist version of an archetypical eschatology that promised worker salvation on the great and terrible day of Revolution. Thence on the workers would own the means of production ushering in a supposedly classless society where everyone’s interests coincided and therefore all would live in peace.

But as the video says: “What a croc of ****”. A successful society depends on differentiation and specialization, thus implying classes, thereby setting the scene for potential conflicts of interest. Potential conflicts of interest are a fundamental feature of social existence. The so-called “dictatorship of the proletariat” is a cloud cuckoo land concept that in practice leads to an elite ruling class who stifle all debate and dissention under the pretext that in a (fictitious) “classeless” society no conflict would exist and therefore by definition dissenters are reactionaries.

How many times have we seen the failure of this sort of cloud cuckoo land social philosophy? The Christian cults and sects do exactly the same: They are so sure they have found the secret to a social and spiritual utopia where (wo)man is at one with fellow (wo)man. But they fail to get the right balance between positive and negative democracy; accordingly their uncompromising effort to usher in a new unified and free Christian community has exactly the opposite effect. Their zeal, conviction and misplaced confidence in the rightness of their proprietary vision of community betrays them and they end up creating a social nexus ten times more oppressive than what they aim to replace; a nexus where censorship and compulsion are the norm and imposed by a (self) righteous elite. As the video says: “What a croc of ****”.  Oh the pathetic irony of it all!

No social restructuring of community and society will ever relieve us of the basic challenge we face day by day; namely, that of finding the strength of moral character to meet the demands of gainsaying self in favour of our neighbor. There is no uptopian society so structured that the moral choices we should make come effortlessly and naturally. This age old challenge is as much with us today as it always has been:

And what does the LORD require of you? To act justly and to love mercy and to walk humbly with your God. (Micah 6:8)

Whether you believe the Christmas story is a myth or signifies deep ontological realities, the values and challenges it embodies are timeless and for all: It is a story of a double condescension by Deity: One: That of giving our contingent and suffering world the power to allow its emergence out of the platonic realm of possibility into reality. Two: Of that Deity giving up all to visit this graciously reified world and identifying with it to the point of death:

1 In the beginning was the Word, and the Word was with God, and the Word was God. 2 He was with God in the beginning. 3 Through him all things were made; without him nothing was made that has been made. 4 In him was life, and that life was the light of all mankind. 5 The light shines in the darkness, and the darkness has not overcome[a] it.
9 The true light that gives light to everyone was coming into the world. 10 He was in the world, and though the world was made through him, the world did not recognize him. 11 He came to that which was his own, but his own did not receive him. 12 Yet to all who did receive him, to those who believed in his name, he gave the right to become children of God— 13 children born not of natural descent, nor of human decision or a husband’s will, but born of God.
14 The Word became flesh and made his dwelling among us. We have seen his glory, the glory of the one and only Son, who came from the Father, full of grace and truth.

Whether as a myth or as an “in fact” reality the Christmas story, in beauty, meaning, depth and grace, surpasses all.

Friday, December 09, 2011

Free Lunch: But Who's Paying?

In a blog post dated 6th December and entitled “Adaptation by Directed Modification Rather than Selection” anti-evolutionist Cornelius Hunter, tells us about an interesting recent scientific paper (Feb 2010). This paper publishes evidence that breeding populations of cells very rapidly adapt to changes in environmental stress and then pass on the adaptations to descendents. Hunter interprets this rapid “learning” to be evidence of the presence of some kind of Lamarckian mechanism built into to cells.

(Aside: I’m not going to evaluate the paper Hunter refers to, or his opinion of it as I’m not a biologist. However, assuming for the moment that the paper Hunter quotes is evidence of the presence of Lamarckian or epigenetic mechanisms then the following question is prompted : Are these mechanisms reified in the form of some sophisticated molecular machinery or is there some transcendent law that acts on molecular matter to produce these effects and thus effectively adds to the canon of physics? )

Hunter is arguing, I think, that this evidence suggests the existence of some sophisticated biological mechanisms, currently unrecognised by the  academic establishment, and these mechanisms explain natural history; in short these mechanisms explain evolution rather than are explained by it. That may (or may not) be the case as far as my knowledge of biology is concerned. I'm of the opinion, however, that even if evolution happened just like the academic establishment maintains, it nonetheless must be resourced by high sophistication in the transcendent physical canon that governs our universe. (Which is something I have said repeatedly on this blog). The choice is this: Either the mechanisms guiding evolution are reified in given molecular engineering (Hunter's suggestion, I think) or they are to be found in the transcendent physical canon in terms of the constants and laws that govern our universe.

In the polarized impassioned disputes that Hunter and other anti-evolutionists get themselves into with zealous atheists I find myself a rather disinterested party. It’s not that I’m disinterested in the engine of natural history - I’m very interested in fact; my disinterest is in the high stakes that some theists (particularly fundamentalists) and atheist zealots have vested in particular hoped for outcomes to the evolution debate. The basis for the rejection of standard evolution by theists like Hunter is that it appears to threaten God’s role as a homunculus intervener in natural history and therefore threatens faith; this, I suspect, drives the rationale for the vehement anti-evolutionism of many “Intelligent Design” supporters. They have taken to heart the atheist zealot billing of evolution as the unguided “blind watch maker”, an idea that takes no cognizance of the sophistication required  to select the physical canon needed to service evolution and make it work; zealous atheists treat that canon as if it were a mathematical trivialism. In response anti-evolutionists have allowed through this portrayal of the physical canon as the blind direction-less director. In this vein Hunter talks about “undirected mutations” (see referenced post) and Jonathan McLatchie in this post on “Evolution News” is even clearer; he talks about:

“....the common scientific view that all life is explicable by mechanisms of unguided chance and necessity… The key point is that the mechanisms undergirding the evolution of life, according to Darwinism, are non-intelligent”.

This fanciful idea of “undirected chance & necessity” is at once the bogy of the God fearing anti-evolutionists and the darling of atheist zealots. On the one hand McLatchie’s fancied “necessity” threatens the role of a homunculus Intelligent Designer, but on the other hand atheist zealots appear to see no threat from a sophisticated logical contingency in the physical regime, a very particular form of contingency, in fact, that is required to give a realistic probability to evolution. This contingency raises unsettling questions for atheist zealots. (But the convoluted physical logic needed to drive evolution seems to have the effect of obscuring the presence of this contingency from the human mind; conditional necessity is easily conflated with absolute necessity) Because both sides have put down huge stakes on the table, the disinterested party such as myself  has to factor this in when considering their arguments; frankly, this contentious polarised context is not conducive to trust.

However we try to cut it, one mathematical truism remains: If evolution has occurred, even in the manner maintained by the scientific establishment, then the algorithms able to generate our natural history are likely to be extraordinarily rare mathematical classes in the space of all possibilities. In which case the inappropriately named "necessity" that McLatchie fears is no necessity at all but instead exceedingly unique and contingent circumstances on which evolution is conditioned.

Humanly speaking it is not possible to purge our mathematical models of the rare & peculiar preconditions needed to confer on evolution a realistic probability; all sensible outcomes, it seems, eventually trace back to the startlingly unique conditions that, as far as we are concerned, constitute a free lunch from nowhere – and that’s true even in a universe generating multiverse (See here: http://quantumnonlinearity.blogspot.com/2011/05/middlebrow-atheism-part-5-final-part.html). Necessity and aseity are destined to ever elude our science. It is an irony that the anti-evolutionists, like the atheist zealots, do not make much of this fact.

STOP PRESS 14/12/2011
I found this cartoon on PZ Myers blog. Given the above material and a little modification it's perfect:

Two reasons to feel superior: What would life be like without the Schadenfreude of looking down on someone?

Sunday, December 04, 2011

Not such a geeky waste of time after all.

The above is a picture of a contraption I built in 1980 in order to amuse myself and at the same time make use of my old redundant Meccano set, a set that included electrical parts such as solenoids. I decided to build something that would generate a disordered binary sequence. More views of the machine, including the output results, can be seen on my facebook album here.

So how does it work? The lower story of the machine consists of an assembly of cogs and band drives which periodically operate various switches. These switches interact electrically to produce a complex combined sequence of 1s and 0s. This sequence is stored in 8 bit chunks in the one byte solenoid memory occupying the upper story. A long sequence of 1s and 0s is therefore generated byte by byte; these bytes have to be marked up one at a time by hand on graph paper in order to build up a long sequence.

Yes, it’s nineteenth century technology, but it worked and moreover there is a moral in the tale.

If we represent the nth switch in the machine by the binary variable “Sn” and imagine that this variable switches between 1 and 0 with a particular periodicity, then the whole machine carries out the following logical operation:

(S1 + S2 + S3) . S4

Where “+” designates an “OR” operation and “.” designates an “AND” operation. For example, if switches 1 & 2 are “on”, switch 3 is “off” and switch 4 is “on” we get:

(1 + 1 + 0) .1 = 1

One way of thinking about this operation is to think of the combined result of S1, S2, and S3 to effectively select or “gate” the result of S4; that is, if (S1 + S2 + S3) generates a 1 then it allows through the binary pulses from S4.

If S1, S2 , S3 and S4 all have different switching periods then the logical expression above results in a quite complex (i.e. disordered) sequence in itself, especially if the periodicities of the switches are expressed in real numbers with lots of decimal places. These inherent real number constants have the effect of helping to generate chaotic sequences, although under these circumstances alone the sequences generated would nevertheless still display a measure of periodicity and therefore would be far from maximum disorder. However, the secret of the machine’s ability to disrupt periodicity and generate high disorder doesn’t just depend on the use of “real numbers” but in fact resides in three features:

1) "Analogue" band drives were employed and their non integral ratios produced real number periodicities; this entails the likelihood that the differing periodicities of S1, S2, S3 are not fully resolvable; that is in absolute terms the sequenced product of these three switches is a-periodic.

2) The other important feature of analogue band drives is that they have inevitable accuracy tolerances - unlike "digital" cogs which only produce exact integral ratios.

3) Compared to the other switches Switch 4 is made to switch on and off rapidly.

The result of these features means that the gating switches S1, S2, S3 force a sampling of S4 that is both chaotic and inaccurate. The inherent inaccuracy in the periods of the gating switches is of comparable size to the distance between the pulses delivered by the rapid switching of S4, giving rise to a probabilitistic hit or miss situation. The result; a very non-periodic disordered sequence. The “disordered” results can be seen in my facebook album.

Moral of the Tale.
The way disorder is generated in the above model reminds me very much of an idea mooted by Michael Frayn in his book “The Human Touch”. He suggests that quantum uncertainty is a result of the muddled and chaotic macroscopic world attempting to sample the precise periodicities of the microscopic world. In my model the macroscopic world is represented by the logical operation (S1 + S2 + S3) which is chaotic and inaccurate. The microscopic world is represented by the high frequency pulsing of S4 with its implied small “wavenumber”.

Frayn’s idea is a very neat idea and it is reminiscent of the quantum decoherence interpretation of the random jumps of the state vector, which as I have said here, is also a very neat idea. I must admit I’m very tempted by both ideas and they shouldn’t be discarded lightly. But, and here’s the inevitable “But"; as Roger Penrose points out decoherence does not easily explain the jumps of the state vector entailed by null results, (if indeed the state vector does jump under these circumstances) Secondly – and this is my own idea – the quantum wave calculus looks too much like an imaginary number version of probability calculus for us to discard the notion that those random jumps are actually absolute and not just a product of deterministic chaos. No wonder, then, that I gave my high frequency switch its own uncertainty; a static commutator with an electric current picked up by a rotating flailing sprung head. (See below)
High frequency switching is  achieved by a  static commutator and a rotating sprung pick up head.