Wednesday, March 30, 2016

Evolving Adapatibility

Adaptability is a sophisticated form of intelligence. Ergo, rats are intelligent!
I've criticized  de-facto IDist Cornelius Hunter  on at least a couple of occasions in this blog (See here and here), although I have conceded that he brings up some robust challenges to conventional evolution.  Along the latter lines I found his latest post very interesting. Quoting the first part of his post: 

Organisms adapt to environmental challenges. In fact, many different organisms adapt in non-homologous ways to many different, unforeseen, environments. This contradicts evolution. For we are not talking about random changes occurring by chance, occasionally getting luck enough to confer an adaptation, and then propagating throughout the population. We’re not talking about an evolutionary process of random mutations and natural selection. That would take a long time. What we’re talking about are adaptations that specifically address environmental challenges, and occur in a good fraction of the population, over a few generations, or perhaps within a generation. Such directed adaptation occurs quickly.

That contradicts evolution because random mutations are not going to create such a complicated adaptation capability. Furthermore, they are not going to do this over and over, in so many different species, for so many different environments. And even if, by some miracle, this did occur, it would not be selected. That is because the adaptation capability is not for the current environment the organism faces, but for an unforeseen, hypothetical, future environment. The moment it arises, the adaptation capability is of no use, and would not be selected for.

Hunter goes on to claim that these rapid adaptations also appear to be passed on to future generations whilst they are needed.  Unless the observational claims about an apparently inherent rapid ability to adapt (and pass it on for the duration) are false then this poses problems for conventional evolution, a process whose "look-ahead" ability is nil. 

Measuring Nth order differentials across time in the parameters of real situations is always  tricky because one needs to take samples that are increasingly separated as the order of the differential increases.  That is, Nth order differentials compromise the paradigm of locality, because an Nth order differential can not be calculated from data taken at a single point.  This is related to the questions Hunter is raising about the evolution adaptability: Adaptability suggests we have an inkling of what's ahead; either that or the change has been seen before. If it's the latter then using very local trial and error random changes requires huge numbers of trials. So unless the spongeam is extremely constrained the evolution of adaptability is a pretty problem for random trial and error. 

I find the following remark by Hunter particularly interesting:

What we’re talking about are adaptations that specifically address environmental challenges, and occur in a good fraction of the population, over a few generations, or perhaps within a generation. Such directed adaptation occurs quickly.

On the face of it this seems to be saying that organisms have been observed to adapt but this adaptation is not sufficiently explained by real time trial and error selection. If organisms do have an ability to adapt very quickly in way that can not be justified by resort to random trial and error process, then what is the source of this ability? Is it some built in mechanism that has, in effect, been learnt from many trial and error events in the past? If the latter then it would mean that the current situation, or something like it, has seen before. The alternative, however, is extraordinary and involves immanent intelligence: Namely, that some look-ahead mechanism is in operation. Is this evidence of backloading?

But if adaptability is a high level form of intelligence then is evolution itself intelligence in operation? 

Tuesday, March 15, 2016

Denis Alexander at Norwich Cathedral.

The following are some notes I made after my visit to Norwich Cathedral to hear Christian Biologist DenisAlexander.  (8 March)

Denis Alexander: a man who deserves to be in the spot light rather than in the shadows!

Denis Alexander is very much a part of the scientific establishment – in fact part of tax payer funded public domain academia, a culture much despised by fundamentalists and the right wingers of the de-facto “IntelligentDesign” community. Unfortunately the latter have had the effect of blighting the term “Intelligent Design”, for although it is clear that Christians like Alexander would ultimately claim the universe to be the product of divine intelligence they are not likely to want to associate themselves with de-facto ID; perhaps because de-facto ID is too close to the cranko-fundamentalist fringe and the politics of the extreme right wing. Moreover, de-facto IDists have effectively hi-jacked the appellation “Intelligent Design” and rather presumptuously see the term as exclusively applying to themselves. No surprise then that Christians like Alexander are coy about identifying themselves with the rubric “Intelligent Design” (See also John Polkinghorne). It’s a classic case of community polarisation. Contrast this with the statement by Alexander that he attends a church in Cambridge where different views on the creation question are tolerated (as one would expect of a moderate and intelligent evangelical ethos).

Talk Notes.
The talk was titled Evolution & Adam: Reality, Myth & Symbolism
These notes are not comprehensive but really represent salient issues that stood out for me.

Alexander started with an overview of human evolution. He said that the first humans emerged around 200,000 years ago. Evidence supporting this data is a human skull radiometrically dated as around 195,000. (My comment: This date appears to be fairly well established in academic circles as I’ve heard it for several years now).

Migrations of humans to the rest of the world started out from Africa around 60,000 years ago. 50,000 years ago humans reached Australia and Europe 43,000 years ago (However, a human tooth has recently been found in China which could be 80,000 years old throwing doubt on these dates). African populations are more genetically diverse than non-African – this is evidence that makes sense if a relatively small human migration came out of Africa with a correspondingly narrower gene pool. Further support for the “out-of-Africa” theory comes from the presence of Neanderthal DNA in non-Africans caused by interbreeding.

After this introduction Alexander switched to theology which was his main concern given the title of the talk. Moreover, in his book “Creation or Evolution: do we have to choose?” Alexander says that he believes “the Bible to be the inspired word of God from cover to cover”, so clearly Christian theology will interest him deeply.

Alexander regards Genesis as a set of theological essays and quoted Philo who said Genesis is symbolic rather than literal, Origen who said the Bible was figurative, Augustine who believed the creation story wasn’t literal because he thought creation was instantaneous, and Calvin who said you can’t learn astronomy from Genesis. Alexander summed up by saying that there is no science in the Bible. He said that the Genesis reference to man as the image of God compares to the language used by the monarchs of the day who were claimed to be the image of God on Earth, In effect the Bible democratises the idea of all humans, both male and female, being made in the image of God on Earth. Hence, all humans have special status and this was contrary to the infanticide practices and slavery carried out in ancient times. There is ongoing infanticide (& slavery) in the world today (My Comment: However Alexander didn’t mention abortion which would have been a natural reference here)

The word “Adam” translates as a generalised type for man. Woman is the “helper” to man, a title also used of God himself. NT references to Adam are in the context of the origin of Sin.

Alexander said he regarded Evolution and Theology to be two complementary narratives.

At what point did people become responsible to God and when did sin begin? At what point did a community of faith start?  There are some speculative answers: 
Model A: Gradual awareness of God as humanity has evolved. Then there was a fall and rejection of God.
Model B: (Favoured by Alexander) God selected a community or a couple for revelation.  They become the federal “parent” of the race, just as Ataturk become the “father” of Turkey although not literally. The fall followed this revelation. (Note: I have found that fundamentalists seldom have the imagination to appreciate that old Earth narratives introduce so many degrees of freedom that the ways of integrating the fall and death into those narratives are myriad)


See here for a complimentary set of notes on Network Norwich and Norfolk. Either I missed it or there seems to have been quite a lot of interpretation inserted into the NN&N account, although not unreasonable interpretation: These interpretations emphasize the Genesis story as “a radical theological and political text” subversive of the politics and religion of the day, and also of modern times as well.

Question Time
The question time started with the chairman reading the riot act: People wanting to make lectures or engage in arguments would not be tolerated. The first “questioners” tried to do just this! I was rather puzzled as in my previous attendance to the talks of John Polkinghorne and Simon Conway Morris no warning was issued and the question time was good tempered. Had troublemakers been spotted coming in? The points of the “troublemakers” were too incoherent to record here

Q: (from a “Creationist”): How can a “good” creation be reconciled with death?  Should we expect death to reign in heaven?
A:  “Good” did not mean perfect but “fit for purpose”. “Good” doesn’t imply no death. Eating from the Tree of life lead to spiritual alienation not death.  You can’t have life without death biologically speaking,  cf. the huge thicknesses of chalk speak of death. Is there death in heaven? No Jesus had a radically changed resurrection body.  He had gone beyond death.  

Q: There are two discontinuities in this world: 1. Spontaneous complexity and OOL. 2. The discontinuity of consciousness. What sense can we make of these?
A:  Another century might fix the OOL problem. cf RNA world etc.  Lots of progress has been made.   Consciousness is an emergent phenomenon.  You see it emerging in children and in the animal world.  It’s a process and is complexity related.

Q: Is there life on other planets? 
A: Alexander would love to see life discovered elsewhere. Life is probably out there, but perhaps not intelligent life (Moot).  Convergent evolution suggests that life can be “discovered” many times. Very complex molecules have been discovered in space like fullerenes.


My general comment
The subliminal and sometimes not-so-subliminal theme underlying events like the above is the “science vs theology” dichotomy. This dichotomy has, in my view, been reinforced by fundamentalists (and also, might I add, by the “Intelligent Design” community who generally have a poor view of the immanence of God and what it entails). In fundamentalism the “science” of academia tends to be thought of as the “natural” profane human way of knowing, a way of knowing to be contrasted against the “supernatural” godly ways of knowing found in a blend of holy texts and gnostic revelations. Moreover, fundamentalism has a knack of distorting the epistemology of science in such a way that it potentially emasculates its epistemic potency.

And yet it is clear that so-called “holy texts” cannot be interpreted without a huge hinterland of background innate understanding, culture and non-biblical texts. Holy texts, so-called, are organically joined to their “natural contexts”. Perhaps as a way of attempting to bypass this inseparable union of holy-text and profane context there is sometimes a last resort to gnosto-fideism, a philosophy which claims to eschew reason and observation. This is the way of sublime inner light, the way which attempts to disconnect epistemology from profanity by affecting to rise above “natural” textual contamination through the pure revelations of irreducibly intuitive experiences of the divine. This, I theorise, is the religionist’s reaction to the epistemic pressure on Christianity that has built up since the Copernican revolution. The outcome has been a drift either toward text based Biblicalism or the existentialism of a gnosto-fideist rendition of Christianity.  It’s alright for bright guys like Alexander who can see their way through the epistemic jungle, but the average Christian often find themselves thrown into the arms of fundamentalists who pronounce bald certainties.

In the science vs. theology debate there is a great irony which I have noted before. Both subjects are empirical to a greater or lesser extent. This is a conclusion which will surprise many, but we only need observe Alexander’s methods to support it. Alexander is using his (presumably God given) gifts and talents to try to make sense of his observations on the human predicament, on society, on science, on holy texts and so on. Yes he’s doing a good job of it given its difficulty, but generalised empirical protocols actually form the basis of his theoretical synthesis; Viz: observations on life, observations on history, scientific observations, observations on scripture etc. These observations are the dots which are then joined into a unity by the overall textual synthesis Alexander has constructed.  In short sense is made of the human predicament through observation and synthesis of those observations by theoretical reflection. Ergo, theology is empirical, although it has to be added not in the highly controlled, standardised, formal and mechanically testable sense of spring extending and test-tube precipitating science.  But then it is arguable that the science of string theory has a more post-facto sense making role than it does as a testable theory.

The contrast couldn't be greater. When this wonderful vaulted ceiling was built the Ptolemaic cosmos, where man's abode was at the centre of special creation, still held sway. Man was confident about his position in the cosmos. Like the vault of the cathedral the vault of the heavens was clearly made to house man. But today with Denis Alexander's help we, as Christians, were trying to come to terms with a very, very different universe! Just how successful these attempts will ultimately prove to be remains to be seen. Time will tell.

Sunday, March 13, 2016

Tribal Rabble Rouser

Hair raising, absolutely hair raising. 

The above video on Donald Trump's presidential candidacy campaign has many disturbing aspects. Picking out one comment on the video:

The election process is finding people to blame for your problems .....and Trump is really, really good at it!"

A picture is painted not of a competent politician but a demagogue and "reality show" virtuoso skilled in creating what is in actual fact a fictional reality (if you get my meaning) and who knows how to connect to the crowds - or at least certain sorts of crowds who are angry and looking for targets of their anger. 

This article on the BBC news website is about the anger and polarization that is current in America at the moment. I think they ought to add "fear, insecurity and paranoia" to that - in fact the latter may explain the former. It is perhaps an irony that I became more aware of American politics when I moved into the intelligent design question and sensed the anger of IDists about publicly funded liberal-left academia. 

Trump appears to attract the right wing Christian evangelico-fundamentalists. Some evangelicals are anxious to show that Trump isn't a genuine Christian and that his embracing Christianity is just part of his theatre and spectacle. That's probably true, but it misses the point. Christian or not Trump connects with something in the evangelico-fundamentalist psyche and that is a little worrying because they clearly have a lot of common ground with Trump - they want what Trump wants. Like Trump they are intrinsically certain and insistent about what they believe. 

It's probably a an alarmist cliche to draw the comparison but without doubt there are parallels here with Hitler's Germany and those facist rallies of hi-emotion which stirred up fear, anger, paranoia and the identification of "sub-humans" who had lost the right to freedom.  Hilary Clinton had better win that election or else. Or else what? Liberals and Lefties getting knocks on their doors at night by enthusiastic and well armed thought vigilantes? The last thing we want is for the most powerful nuclear armed nation in the world to be run by these sorts of people.  But perhaps I'm getting paranoid myself; for such is the social ambiance of suspicion generated by the Trumps of this world.  

Wednesday, March 09, 2016

Gravity from Quantum Non-Linearity: Edition 3

The third edition of "Gravity from Quantum Non-Linearity" can be downloaded from here,  Below I publish the preface:


Preface to third edition
Gravity from quantum non-linearity contains a shortened and more direct treatment of gravity than I presented in my book Gravity and Quantum Non-Linearity. However, the latter does attend to some details that need airing and which are not found in this current paper; in particular in the book there was a lot more attention given to the matter of conceiving a version of quantum mechanics based on a computer simulation of it, although the approximate nature of the resulting theory is also mentioned in this paper.

The changes in this edition are as follows:

1.   Numerous small changes have been made to the text.

2.  A section has been inserted (See section 3) which examines the role played by the second term on the right hand of equation (2.8.1)

3.  In the previous version of this paper and also in my book I referred to the space-time metric expressed in (6.17.1) as the Schwarzschild metric. However, I’ve since realized that my space-time metric, unlike the Schwarzschild metric, is isotropic and I have made the appropriate long-overdue changes to the text. This, of course, implies further differences between the theory I am proposing and the ideas behind the standard Einstein equation.

4.  I have, I hope, improved the clarity of the discussion which surrounds the gravitational metric.

Finally my usual disclaimer: This paper is entirely speculative and makes no heavy claims about being the solution to the gravity vs. quantum mechanics problem. As a hobbyist I do this sort of work for its own sake and don’t necessarily expect a successful outcome. As I always say; one must endeavor to enjoy the journey because the destination may not be up to much. At least one can come out of it with some interesting explorations achieved.  

Sunday, March 06, 2016

Caution: IDist in Action

The process of intelligence involves trial and error?. 

In a post dated 6 March with the heading "Intelligent Design in Action" we can read the following on the "Intelligent Design" web site Uncommon Descent:

See if you can spot the pattern [William Dembski] highlights in the introduction to [No Free Lunch] and elsewhere: 
. . . (1) A designer conceives a purpose. (2) To accomplish that purpose, the designer forms a plan. (3) To execute the plan, the designer specifies building materials and assembly instructions. (4) Finally, the designer or some surrogate applies the assembly instructions to the building materials. (No Free Lunch, p. xi. HT: ENV.)
Are we getting a feel for what design as process and as artifact looks like?

Is it reasonable to argue that functionally specific, complex organisation and/or linked information (FSCO/I) is credibly produced by blind chance and/or mechanical necessity?

Is this authoritarian vision of plan formation and imposition really how intelligence works? I hope to comment briefly on this a little later.  In the meantime see if you can spot the pattern of misconceptions.

7/3/16 Further Notes
The above suffers from the usual defacto ID false dichotomies. Even if we assume intelligence as a "black box" it doesn't work in the manner of the simplified model above. Even "purpose" might have to be discovered. and a product of seemingly chance encounters. And once purpose is discovered intelligence doesn't then go on to form and execute foregone plans which are then imposed on "nature" to create "artifacts". There is a lot of trial and error with feedback from experiments and searches of the environment having a crucial role in the process of intelligence. "Blackboxing" intelligence is itself naive. Intelligence is not analytically indivisible and is decomposable: There are likely to be parts of the brain which are given to "thought" experiments and therefore have a role not dissimilar to the role environmental objects have in searches and experiments. In short there is, as I always maintain, no clear cut demarcation between intelligence and "natural forces" as the de facto ID community habitually assume.

As I have oft repeated many of the problems with defacto-ID can traced back to the explanatory filter

Tuesday, March 01, 2016

The Mathematics of the Spongeam.

The Spomgeam: An object full of holes
The following is a mathematical impressionist’s sketch of evolution and in particular of that enigmatic object I keep talking about, the “spongeam”; an object that is a necessary condition for evolution. As usual I make known my caution about claiming the existence of this object (See here for example), but in this post I am proceeding under the assumption that it exists.

When it comes to writing an all embracing mathematical equation for an object like evolution we are likely to remain in the land of make believe for a long while; the mathematics, at least my mathematics, is never going to be anywhere near complex enough. Moreover, there is one aspect of this affair I have found difficult to render and that is what is very probably the non-linear nature of evolution. Non-linearity arises because organic forms influence and create environments and therefore this in turn will affect evolution, very likely with non-linear feedback. (More about this later) 

But not to be out done….. as the saying goes: If you can’t solve a difficult problem try solving a simple problem like it. Well that’s what I’m doing here; in fact I’ve simplified things to the point of it really only being a metaphor that helps us to picture evolution in a very abstract way. So what’s below can’t be taken too seriously; it’s still very much a toy town model and is likely to remain so. Even so, I find the model below does help me think about conventional evolution abstractedly and perhaps may even pave the way for more sophisticated metaphors sharpening the focus further.

My starting assumption is that when living configurations breed their offspring vary randomly and by this I understand that each generation shifts a little in configuration space in a way that at least approximates to random walk. In using this mathematical abstraction we abstract away all the exact details of genetics and inheritance; all we assume is that a breeding organism is surrounded by a probabilistic halo in configuration space, a halo which means it can only generate offspring that on average are within a relatively short distance of its own form. One important reason for abstracting away all the conventional microbiological mechanisms of variation is that it is entirely conceivable these details are contingencies which are not a necessary condition for more general models of evolution.

If we start by assuming that a complex of causes result in variation and imply at least a pseudo random walk, then it follows that the distributions of offspring in configuration space will approximately obey diffusional laws. So let’s start with the multidimensional diffusion equation:

Equation 1

The symbol Y represents the distribution of living things in configuration space. Because configuration space has n-dimensions I’ve used the “house”2 symbol rather than the “Del”2 symbol of three dimensional diffusion. The diffusion coefficient resolves into three factors e, w and v. These symbols represent the typical step distance, the step probability and step velocity of random walk respectively (See my book Gravity and Quantum Non-Linearity for a proof of this). I’ve also thrown in the variable A to absorb any other factors we might think necessary.

In this model we imagine that living things replicate themselves with slight differences due to a multiplicity of causes (or perhaps  even acausal changes), a difference typified by the value e with a probability of w. I’m making another simplifying assumption here by assuming  w is not positionally or directionally dependent; that is, the probability of an organism generating any variant is the same for all variants within a typical distance of e. The rate at which an organism generates offspring is measured by the step velocity, v. In ordinary random walk we usually imagine a single agent walking around and generating a distribution graph that is in fact a probability curve, but in the random walk we are dealing with here the agent “walks” by replicating incremental variants in the surrounding space; in fact the parent doesn’t step at all but stays at the original position: it’s the production of offspring which does the stepping. 

So, from this model it is clear that if Y is integrated over configuration space the resultant value changes in time as it represents a changing population number; this contrasts with ordinary random walk where the distribution normalizes to unity when integrated. But we must also  remember that organisms die.  There is therefore a term missing from the right-hand side of equation 1. Viz:

Equation 2

The second term on the RHS caters for the combined effect of organism death and reproduction. The term reflects the assumption that in a population both the death rate and birth rate are proportional to population which in turn is proportional to Y. Hence the net result is the difference between a birth rate proportionality constant R and the death rate proportionality constant D. Simplifying by putting V = R – D gives:

Equation 3
Although this equation is relatively simple it hides many potential complexities in its variables. Leaving aside possible variation in e, w and v which could in fact make them vector fields, much complexity can potentially reside in the scalar field variable V, so let’s see what we can get out of V alone.

If an organism varies randomly then the destructive nature of randomness will ensure that the (overwhelming?) majority of variations are likely to be disadvantaged when it comes to reproduction and survival. Hence we expect most random variants to display a high value of D, so much so that we expect them to lead into (eventual) extinction (Hence the black holes in the picture of the spongeam). However, evolution, as we well know, depends on the conjecture that there are some walks where populations are maintained or even grow; it is along these pathways, if they exist, that it becomes possible for a population to “evolve”; that is, diffuse into new regions. These pathways must be both broad enough and traverse great enough distances in configuration space if they are to facilitate macro-evolution. It is this network of paths in configuration space that constitutes the spongeam.

Equation 3 has a form that is clearly related to the Schroedinger equation; in fact one only need insert “i” into the diffusion coefficient to get an equation with quantum behavior. In the Schrodinger equation analogue V constitutes the potential field and in equation 3 V would have a similar role. In particular, where V has a gradient it acts as kind of force which tends to drive the random walk in a particular direction. Thus I interpret the locations in configuration space where V has a gradient to be those places where a kind of “natural selection” is operating. But let’s note that natural selection is not a necessary condition for the general kind of evolution equation 3 allows. Provided V is positive in sufficiently extensive regions the diffusion of random walk gives rise to evolution even when V has no gradient. 

Each living configuration can only survive and replicate if it has the right construction and since it is the laws of physics which ultimately determine whether a configuration survives or dies then it follows that the value of V is implicit in the physical regime. Thus, if the spongeam exists to provide evolution with the requisite information then it follows that this information is implicit in physics, perhaps even physics we have yet to understand.  Hence conventional evolution depends on frontloaded physical information and this naturally raises questions about the origins of that information.

Non-Linearity: Non linearity arises in equation 3 because V is influenced by the very existence of life; that is, life is itself a significant part of the environment in which configurations survive and replicate. Mathematically this means that V is likely to be a nonlinear function of Y. Moreover, V is not going to be just a function of the local value of Y, but also the value of V elsewhere in configuration space. This is because widely diverse living configurations influence the environment of one another.  It is this complex feed-back feature, very dependent on the twists and turns of the history of life, which make it difficult to write an all embracing succinct evolution equation.

Let’s face it, equation 3 is even worse than the Drake equation: Too many unknowns make it all but insoluble, but at least it gives us a conversation piece....that is, something to talk about.