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Friday, May 28, 2021

Watson, Crick, Franklin, Wilkins & Scientific Wisdom.

DNA Pioneers: James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin. 


I recently re-watched a video I had recorded way back in the March of 2003. It was recorded from the UK's Channel 4 and was entitled DNA: The secret of life. It told the story of the discovery of the structure of DNA. James Watson, Francis Crick and Maurice Wilkins appeared on the programme. Also appearing was Raymond Gosling who at the time was a PhD student and lab assistant to Rosalind Franklin. According to the program Franklin and Wilkins of King's College were the experimentalists who generated the X-Ray diffraction patterns which so helped Crick and Watson to successfully theorise about the structure of DNA. It's not that the King's College team weren't theorists themselves, but they also did the hard work of getting the necessary experimental data about DNA. It is very easy to put Crick and Watson into the role of the "lazy lads" who just theorised together down at the pub and let others do the hands-on science. That they appeared to be riding on the backs of others was the cause of tension. But whatever, they were clearly very bright guys who can rightly claim credit for making the right inferences from the data. It didn't help the King's College team that Franklin and Wilkins had a poor relationship; in contrast it seems that Watson and Crick worked well together (and drank well together!). Also, that Franklin was a pretty woman in a largely man's world may have introduced frustrating pressures and detrimentally affected her attitudes. Or perhaps she was just a awkward personality.

The programme tells us of Watson and Crick's first attempt at a model. The King's College team came to have a look at this model. But when Rosalind Franklin saw it she laughed out loud; in the light of the experimental data the King's team had accumulated the model was clearly wrong. Watson & Crick were suffering from their working in a too rarified experimental semi-vacuum. Then one day Wilkins, who seems to have been an obliging sort of character, showed Watson an X shaped diffraction pattern that the King's team had obtained. Watson and Crick knew immediately that this implied DNA was a double helix and they went on to develop the correct model we are all familiar with.  Lab assistant Ray Gosling takes up the story:

Wilkins undoubtedly (and I think if you ask him he will say he did), if there are any cats to be let out of any bags, he had done it.

To which Wilkins responded:

Well I suppose it's perfectly true, but science isn't supposed to be kept in bags, no more than cats. I mean, I don't know what he means but I don't like as a scientist working away and sort of "Oh no! I mustn't tell the other scientists". I don't think it's the way to be working. Science ought to be an open activity, so you can work as a community. 

Well yes, in theory, that's the ideal world: that's wisdom we should aspire to, take home and act on: But no, we aren't in that kind of world; we're in a human world. Human beings can't be so detached and dispassionate. Competition, reputations, making a name for yourself, not to mention wealth & fame are at stake and have a strong tendency to trump the cooperation and community effort thing. The consequent mutual distrust means that people keep their cards close to their chests. Competition vs community effort! It's all very reminiscent of the capitalist conundrum of free market vs community.  And yet again I'm reminded of Philippians 2:1-11 which seems to be the key to community living

During the program, Maurice Wilkins also came out with another pearl of Wisdom. As we've seen Crick and Watson's first model was laughed off stage by Rosalind Franklin. But of this failed attempt Wilkins comments wisely as follows:

One might say but why not? It's an exploration to make a model. You make a model and if you make a bit of a fool of yourself in the process why worry? ....you might get lucky!

A big lesson there for all blue sky theorists: Its any exploration and there's no telling whether you are going to  make a fool of yourself or win the jackpot - most likely the former,. So enjoy he ride while it lasts; you may not be the chosen one after all!

Useful Link:

https://www.theguardian.com/science/2015/jun/23/sexism-in-science-did-watson-and-crick-really-steal-rosalind-franklins-data

Wednesday, May 19, 2021

Make it IDist proof and along comes a better IDist

                                 

In a Panda's Thumb post dated 5th May Evolutionary Mathematician Joe Felsenstein criticises Intelligent Design aficionado Granville Sewell for making the claim that the following problem is unsolvable: According to Sewell that problem is, how do we...

#3 Explain how life could have originated and evolved into intelligent humans, through entirely natural (unintelligent) processes.

Felsenstein quotes Sewell where Sewell explains why he thinks the foregoing problem is unsolvable (Emphases are mine):

Well, I have a very simple proof  [*GASP!*] that the biological problem #3 posed above is also impossible to solve, that does fit in the margin of this document. All one needs to do is realize that if a solution were found, we would have proved something obviously false, that a few (four, apparently) fundamental, unintelligent forces of physics alone could have rearranged the fundamental particles of physics into libraries full of science texts and encyclopedias, computers connected to monitors, keyboards, laser printers and the Internet, cars, trucks, airplanes, nuclear power plants and Apple iPhones.

Is this really a valid proof? It seems perfectly valid to me, as I cannot think of anything in all of science that can be stated with more confidence than that a few unintelligent forces of physics alone could not have rearranged the basic particles of physics into Apple iPhones.

The irony is that the chief weakness of Sewell's argument is due to potential internal inconsistency in his world view; for presumably Sewell's a Christian theist who like myself believes in a created cosmos; all of it & not just some bits that God did! That means as far as we know those so-called "unintelligent natural forces" and their constants might have been intelligently selected to ensure that the evolution of life somewhere in the universe has a high probability given the size of the cosmos. If you are a Christian you are not supposed to be a dualist who sees the "natural world" as somehow, well.... natural and therefore inferior in some way; it is after all the creation of an omniscient omnipotence. 

Now, although many respected evangelical Christians are not at all adverse to evolution in terms of the proposed mechanisms of change (e.g. Tom Wright, Francis Collins, Denis Alexander, Simon Conway-Morris, John Polkinghorne)  I myself do entertain considerable doubts about those mechanisms (But I accept the story of natural history - an important distinction there). My issue with evolution revolves around whether a structure I call the spongeam exists in configuration space (See links at end). But having said that I probably have more in common with these evangelicals than I do the de facto Intelligent Designers like Sewell who see the world through polarising filters, in this case  a natural forces vs God did it intelligent agency dichotomy. The logical outcome of this subliminally dualist world view is the kind of crass argumentation we get from Sewell which he then presents as a perfectly valid "proof". 

Given my doubts about standard evolutionary mechanisms and my I belief that Divine intelligence has acted and continues to proactively act in creation, particularly the creation of life, one might think I would find common cause with people like Sewell in spite of their dualism. But no, there is no chance of that; Politics has seen off that possibility. The de facto ID culture along along with its ugly fundamentalist sisters (Like Answers in Genesis) has gravitated toward the extreme right-wing even in some cases voicing the conspiracy theories of a "stolen" 2020 US election. Rejected by the academic establishment the de facto ID movement have fallen into the arms of right-wing "drain-the-swamp" fantasists whose liar-in-chief is Donald Trump, a man who seeks to overthrow the necessarily  argumentative, factionalism  & fractiousness of democracy with the illusion of a bucolic volk-libertarianism.*. To this far-right community the middle ground politics of Joe Biden looks like the far left! 
 

On the Spongeam

https://quantumnonlinearity.blogspot.com/2019/09/evolution-naked-chance.html

https://quantumnonlinearity.blogspot.com/2016/03/the-mathematics-of-spongeam.html

https://quantumnonlinearity.blogspot.com/2016/02/on-structuralism-and-spongeam.html

https://quantumnonlinearity.blogspot.com/2015/11/intelligent-designs-2001-space-odyssey.html

http://quantumnonlinearity.blogspot.com/2015/06/algorithms-searches-dualism-and_13.html


Footnote

* The wealth making and innovating energy of the market is without doubt, but unfortunately that energy sometimes thrashes uncontrollably: The non-linear instabilities of the market and its power law wealth spectrum, often perceived as unjust, are liable to fuel alienation and far left socialism.  Community identification & the highly localised "serve yourself" operation of the market often find themselves at odds. Somehow the best of the free market and the best of community values have to be reconciled - the alternative is volk-libertarianism which will  generate a counter culture of alienation and extreme socialism. See here: https://quantumnonlinearity.blogspot.com/2020/07/marx-vs-smith_30.html

Sunday, May 09, 2021

Freewill and Determinism (Again)


Correspondence of formal structure isn't the same as correspondence of quality.


The first person perspective of conscious cognition is barely recognised as a reality in some cognitive science circles, perhaps even denied a real existence altogether in some cases. The reason for this, I propose, is because science is necessarily almost exclusively framed in third person narratives. The third person, by definition, takes the perspective of an observer external to the person who is the subject of observation and study. That external perspective 
is only ever going to return the subject person’s experience in terms of what the external perspective can only ever hope to observe (baring a "mind meld"); namely, ostensible patterns of the human presence; in the first instance human behaviour of which a closer look only yields the dynamical patterns of cells, neurons, fields, charges, currents, molecular chemistry etc. 

This latter fact seems to confound some people: It’s as if they expect consciousness, if it exists, should be discovered lurking like some mysterious but observable quintessence inside the brain. Since this hasn’t been found (and at my guess will never be found) then a naïve conclusion is that consciousness doesn’t exist. But in the highly focused third person account of human and neuron dynamics the equivalent of a magicians redirection trick readily comes into play and the obvious location of conscious cognition has been missed; that location is found not by looking at brain behaviours, no matter how close or detailed that look, but by looking back down the line of sight of the third person observer who in the final analysis is of course also the centre of another first person conscious perspective; the very act of observing, theorising, knowing and creating a third person narrative is an implicit acknowledgment of the existence of another first person perspective doing the observing and theorising. Third person narratives are meaningless apart from the implicit assumption that the first person observer and theoriser exists in the first place, for whom the narrative is meaningful.

Since the enlightenment formal third person narratives, as descriptions of the world, have undoubtedly proved to be overwhelmingly successful: They have identified the deeply organised wonder of creation and given us science, technology, and industry. Those narratives can be expressed in communicable formal terms of quantifiable “weights & measures” and dynamic geometry. The third person’s perspective on another person can be encapsulated in information that is transmissible & translatable between agents.  That information tells of a common underlying ontology that is the medium by which first persons perspectives can communicate and understand one another. 

The ontology of this common medium, an ontology which has a level of organisation which makes it amenable to being rendered in formal theoretical terms, reminds me of those industry standard page description languages (PDLs) like Postscript and PDF which make the world of document description portable and shareable between printing machines. A page description language isn’t an end in itself: Such “third person” narratives as PDLs are there to provide printing machines with the basis for supplying the rich colourful experience of printed output. The formal terms of PDLs are very different in quality to the printed page itself but they nevertheless have a very close functional relationship with one another.  PDLs are to the printed page as third person narratives are to human experience.

The formal third person narratives describing the ontology of the physical patterns of brain dynamics need make no reference to how this formal account of human beings breaks down into the qualia of conscious cognition; the human system appears to take care of that translation, thus betraying a close functional relationship between formal third person theories and the first person experience of conscious cognition. In the context of a potentially successful formal language description of human cognition (and the cosmos as a whole), it is very easy to lose sight of the fact that these formal third person narratives are a kind of page description language for human consciousness. The consequence is that in science and technology there is frequently a loss of connection between formality and feeling and when this has happened it has caused alienation. As I theorize in this blog post the misdirection which has lead to a loss of cognizance of the importance of consciousness as a central cosmic reality has led to the romantic reaction against what is perceived as the dehumanisation & deconsecration of the cosmos.


***

It is against the foregoing background that the “Free will vs Predestination/Determinism” contention must be discussed. I have already discussed this question in these posts:

http://quantumnonlinearity.blogspot.com/2018/12/the-unintelligible-notions-of-free-will.html

http://quantumnonlinearity.blogspot.com/2019/01/the-incoherent-notions-of-free-will-and.html

http://quantumnonlinearity.blogspot.com/2019/02/the-incoherent-notions-of-free-will-and.html

I have to say that I’ve lost a certain amount of patience with those who bandy about the term “free will” without first giving us any notion as to what they mean by it. In the above posts I strongly criticise Christian Justin Brierley who launches into the topic determined to defend the notion of "free will" and attempts to smuggle past us his undisclosed understanding of “free will” (whatever that is) without ever examining whether he is dealing in an intelligible concept.

Actually, from the point of view from someone like Brierley it may well look as though I've come down on the side of determinism. In fact I came to the opinion that in a crude sense even a computer flowing through a deterministic program has “free will”, depending on how you define it. But of course human beings are just a little more complex and a little more mysterious that even the most complex computer algorithm. For a start it is quite likely that the human brain is capable of mathematically chaotic behaviour (It has non-linear feedback) which in turn would mean it is sensitive to the apparent indeterminism of quantum fluctuation: This may give humanity its unpredictable creative edge as it seeks to satisfy declarative goals with novel solutions. So, even from the third person narrative point of view, humanity is a very different kettle of fish to Turin computers. Much of my own view on the subject depends very much on my take on the nature of Disorder and Randomness; without the understandings embodied in my "book" on Disorder and Randomness I don’t think I could make much progress.

Really, whether or not human beings are mathematically deterministic, it actually has no effect on my understanding of “free will”: As I've already said even the execution of a deterministic algorithm can have “free will” after a fashion. But there is one aspect true of humans (and probably also true of parts of the animal kingdom such as chimps, dogs, cats, dolphins, octopus etc) that is not true of computers, even those computers running AI simulations: Viz: that is, it is probably meaningless to ask “What does it feel like to be a computer?”. Computers are not using the created physical regime in a way that “prints out” conscious thought and feeling. In contrast the complexities of biological architecture, as we know from our own first person perspective, generates conscious cognition. As such, human beings know what it feels like to be who they are and what it means to make “free choices”; that's true even if those free choices are mathematically determined in the abstract sense of having some complex deterministic algorithm capable of describing the events of consciousness in formal terms. Those who launch into this debate arguing in favour of, or against, some incoherent notion of freewill often do so with philosophical vested interests; either in order to maintain a Christian gnosto-dualism which contrasts "spirit" against matter, or because a thoroughgoing secularist philosophy prefers Christian dualism and believes the work of refuting a gnostic notion of "spirit" to be like shooting fish in a barrel (which actually may be true). But in subliminal fear of the mysteries of the numinous some secularists have fought shy of the idea that our physical regime is the medium which supports the first person perspective of conscious cognition * 

Footnote: 

* It would be very wrong to claim that all those who believe in a purely secular worldview deny the existence of the conscious perspective. Philosopher John Searle has made a strong case for the conscious first person perspective being an irreducible feature of our "material" world. However, unfortunately Searle has queered his pitch by being involved in sexual misconduct. 


ADDENDUM 18/05/21 & 3/06/21

18/05/21 The following addendum appeared on my post of  12/02/19: It concerns the rear view mirror perspective of history:

All our decisions, whether labelled as "determined" by determinists or "free-will" by "free-willists", eventually take their place in the fixed and "determined" resin block of history. In one sense we can look back on our decisions with a kind "God's eye view" on them with the potential of knowing those decisions and their results in full. The question then is this; does this perfect hindsight render what at the time were thought of as "free-will" decisions as no longer a case of "free-will" but somehow determined?  Or if we go back in time before the decisions were made does the fact that those decisions are, from a divine omniscient perspective, seen in a kind of hindsight, make them "determined"?  That is, does the mere existence of the omniscient render what would otherwise be "free-will" no longer "free will"?  I think that questions like this are an reductio ad absurdum for the whole "free-will vs determinism" contrived dichotomy. 

3/06/21 Here's another addition that came out of an email discussion. These notes concern the nature of the ontology on which our cosmos runs. 

As you know I've attempted to express the idealist philosophy several times. I think I can trace my idealism back to my dabbling in positivism at university. But strong positivism can go too far and almost become solipsist. Somewhere a balance needs to kept. Strong materialism has trouble defining what "materialism" means in the absence of experiencing and thinking observers and strong idealism has a problem with the reality of all that ontology that goes unobserved and unthought about. As Berkley realised however the idealist problems are well addressed once one brings in a sentient God whose mind can underwrite all that ontology beyond the human sphere. 

 I attempted to express my idealism in the introduction to my "book" Gravity and Quantum Non-Linearity -. Another recent foray was in my blog entry on Freewill and determinism where I use the metaphor of a page description language. 

 But I think we are struggling here to express the true essence of the noumena; it's probably bound up with the stuff of God's mind on which the cosmic "simulation" is running and what chance do we have of understanding the essence of God?.  All we can do is describe the regular patterns of our experience and assume they are rooted in some kind of God given ontology. 

I tend to opt for circular logic: Viz The regular "material" world explains mind and mind gives meaning to materialism. That's why in my book "Gravity &* Quantum Non-linearity" I used the metaphor of a computer language compiler that is written in the very language it compile

***

Mathematics provides what I refer to as the formal structure of reality. But a formal structure without its translation into experience is meaningless:  Take for example the simulation of car in computer memory: if it's a good simulation it will have a one-to-one relationship with the parts of an actual car and also the dynamic relations between moving parts. This example is not so far fetched as I believe Babbage's analytical engine has been simulated in a computer before now in order to illustrate its workings. Now, a good simulation may mathematically, that is formally, be completely correct. But it lacks one thing: A simulated car isn't a car; you can't get in it and get the car experience; In order to get the experience of a car you have to translate all that formal structure via transduces, servo motors, converters and what not, all of which provide the on screen and inertial experience of driving. Ergo, formal structure only has meaning if it is translated into experience. 

 This is why I used the "page description language" metaphor in this post. Postscript is a formal mathematical language but it makes little sense unless it is there to provided the richness of the printed output experience. 

Monday, May 03, 2021

Science Ignoramus

The following letter sent to Norfolk & Norwich's Eastern Evening News is a priceless gem of science illiteracy. I don't have the date of the paper: I just happened to stumble across the letter  recently already in clipped form. 


As is the way with this kind of thing I did at first wonder if the letter originated from some mischievous journalist wanting to stir up a big mail bag for the letters page, but that we appear to have a name and address counts against that.

I'm sure 1930s schooling couldn't have been that bad, so it's likely that Fred has forgotten some very basic lessons and is also failing to put 2 and 2 together: "CO2 is most definitely not emitted from vehicle or aircraft exhausts et alia....." *GASP*!

The above letter isn't worth critiquing. In any case I'm sure the Evening News got their big post bag (& email box) of intelligent critics teaching Fred a thing or two about elementary science - at least I hope they did; it would restore my faith in Norwich people's grasp of reality! 

In spite of picking up at least some (if not enough!) lessons from the educational establishment in the 1930s Fred now effectively dismisses that establishment and writes them off as "learned" pundits telling us "squit". Paranoid delusions about a government plot to make money have filled in the spaces of his ignorance. If he's still alive today and a web user then he would be fertile ground for covid 19 conspiracy theorism!

Certainly, the establishment isn't exactly angelic (one need only think of Boris Johnson); that establishment is, after all, populated with sinners like the rest of us. But those who perceive the machinations of Machiavellian motives driving a baroque Agatha Christie style plot behind every government move are a nutritious seed bed for conspiracy stories. When the intuitions and feelings tell one that something is wrong and that one is otherwise unable to discover or articulate what is wrong, the "left brain", or what Steven Pinker has called the "baloney generator", gets to work to rationalise one's fears and invents an explanatory story; perhaps a story of conspiracy. Failure to see that one could be part of the problem need not enter into this story, for one may well be suffering from what Kenneth Clark calls that most fatal of delusions - one sees oneself as virtuous! This is what far-right popularism looks like at grass roots level. If exploited by a would-be-dictator self-righteous popularism is a ready tool for an opportunist to attempt to overthrow the argumentative, messy & factious democratic status quo. It's ironic that establishment overthrow is exactly what the far left also seeks. Marx, however, did correctly perceive that alienation is an aspect of even democratic societies and in fact are part and parcel with a democratic society; that's because democracy must (by definition) give space to dissention.