Monday, 5 September 2011



  • toluene -> water = approximation to gas phase -> water
  • based on the idea of dielectric
  • neglects specific interactions - e.g. pi stacking and entropy


  • separating electrostatic and solvation effects
  • what is solvation?
  • organisation of solvent molecules about a solute
  • initially a crude "Ewald" alignment - more detailed with time
  • alignment controlled by electrostatics, driven by entropy - halts when entropy is maximum

Monday, 13 June 2011

Why Sex is Fun - Jared Diamond.

"Becoming a male is a prolonged, uneasy and risky venture; it is a kind of struggle against inherent trends toward femaleness." A. Jost quote p46 WSIF
Chauvinists might go further and hail becoming a man as heroic and becoming a woman as the easy fallback position. Conversely, one might regard womanhood as the natural state of humanity, with men just a pathological aberration that regrettably must be tolerated as the price for making more women. I prefer merely to acknowledge at a Y chromosome switches gonad development from the ovarian path to the testicular path, and to draw no metaphysical conclusions. ibid p46
from evolution of mating systems amongst the primates he concludes;

"We thus conclude that promiscuity or harems, not monogamy, is the mating system that leads to concealed ovulation. This is the conclusion predicted by the many fathers theory. It doesn't agree with the daddy-at-home theory." p89
What about mixed strategies aren't these even better? Many fathers and daddy-at-home. Convince many that they may be the father and ye give one the strong belief that he can maintain monogamy by remaining at home in close proximity The necessary falsehood of monogamy is the most useful strategy as both parties have their cake and eat it. They both pretend monogamy is good while cheating like mad. The problem is the difference between perceived strategy as sensed amongst a populace or at least assumed and the real strategy which need not be the same.
Last year I received a remarkable letter from a professor at a university in a distant city, inviting me to an academic conference. I did not know the writer, and I couldn't even figure out from the name whether the writer was a man or a woman . The conference would involve long plane flights and a week from home. However, the letter of  invitation was beautifully written. If the conference was going to be as beautifully organized, it might be exceptionally interesting. With some ambivalence because of the time commitment, I accepted.
My ambivalence vanished when I arrived at the conference, which turned out to be every bit as interesting as I had anticipated. In addition, much effort had been made to arrange outside activities for me, including shopping, bird watching, banquets, and tours of archaelogical sites. The professor behind this masterpiece of organization and the original virtuoso letter proved to be a woman. In addition to giving a brilliant lecture at the conference and being a very pleasant person, she was among the most stunningly beautiful women I ever met.
 On one of the shopping trips that my hostess arranged, I bought several presents for my wife. The student who had been sent along as my guide evidently reported these purchases to my hostess, because she commented on them when I sat next to her at the conference banquet. To my astonishment, she told me, "My husband  never buys me any presents!" She had formerly bought presents for him but eventually stopped hen he never reciprocated,
 Someone across the table then asked me about my fieldwork on birds of paradise in New Guinea. I explained that male birds of paradise provide no help in rearing the nestlings but instead devote their time to trying to seduce as many females as possible. Surprising me again, my hostess burst out, "Just like men!" She explained that her 0wn husband was much better than most men, because he encouraged her career aspirations. However, he spent most evenings with other men from his office, watched television while at home on the weekend, and avoided helping with the household and their two children. She had repeatedly ask him to help: she finally gave up and hired a housekeeper.

There is, of course, nothing unusual a about this story. It stands out in my mind only because this woman was so beautiful, nice, and talented that one might naively have expected the man who chose to marry her to have remained interested in spending time with her. ibid p95-96
This is so sad she should ditch the fool it is annoying when brilliant women are wasted on neanderthal man.
Now compare the reproductive outputs of men pursuing the two different hunting strategies that Hawkes terms the 'provider' strategy d the 'show-off' strategy. The provider hunts for foods yielding moderately high returns with hi predictability, such as palm starch and rats. The show-off hunts for big animals; by scoring only 0ccasional bonanzas amid many more days of empty bags, his mean return is lower. The provider brings home on the average the most food for his' wife and kids, although he never acquires enough of a surplus to feed anyone else. The show-off on the' average brings less food to his wife and kids but does occasionally have lots of meat to share with others.
 Obviously, if a woman gauges her genetic interests by the number of children whom she can rear to maturity, that's a function of how much food she can provide them, so she is best off marrying a provider. But she is further well served b having show-offs as neighbours, with whom she can trade occasional adulterous sex for extra meat supplies for herself and her kids. The whole tribe also likes a show-off because of the occasional bonanzas that he brings home for sharing. p105
Physiology and molecular biology can do no more than identify proximate mechanisms; only evolutionary biology can provide ultimate causal explanations. As one simple example, the proximate reason why so called poison-dart frogs e poisonous is that they secrete a lethal chemical named batrachotoxin. But the molecular biological mechanism for the frog's poisonousness could be considered an unimportant detail because many other poisonous chemicals could have worked equally well. The ultimate causal explanation is that poison-dart frogs evolved poisonous chemicals because they are small, otherwise defenceless animal that would be easy prey for predators if they were not protected by poison p 116-117.

Consider SJ Gould and nipples the clitoris etc. and also Plato on levels of causes in  mol. biol. = material level and evo. biol. gives another level of cause but probably not the level of final cause. 

Sunday, 12 June 2011

Chance and Necessity - Jacques Monod II

The curve showing the variation of activity as dependent upon concentration of an effector (including the substrate) is almost always S-shaped. In other words the effect of the ligand at first increases faster than its concentration. This behaviour is the more remarkable in that it appears to be characteristic of allosteric enzymes.In ordinary "classic" enzymes, on the contrary, the effect increases more slowly than the concentration p68.
Foundation of the S-systems idea of Voit.

 For example: in state R the protein will be able to recognize and therefore to bind compound alpha at one site (but not compound beta), whereas in state T it will recognize and bind compound beta but not alpha. It follows that either compound will have the effect of stabilizing the protein in this or that of its two states, R or T, at the expense of the other; and that alpha and beta will be mutually antagonistic, since their respective interactions with the protein are mutually exclusive p70.
This might be a way of getting an XOR relationship.
There is no chemically necessary relationship between the fact that beta-galactosidase hydrolyzes beta-galatosides, and the fact that its biosynthesis is induced by the same compounds. Physiologically useful or "rational" this relationship is chemically arbitrary - "gratuitous" one might say. This fundamental concept of gratuity i.e. the independence, chemically speaking, between the function itself and the nature of the chemical systems controlling it  - applies to allosteric enzymes... enabling an interaction, positive or negative, to come about between compounds without chemical affinity, and thereby eventually subordinating any reaction to the intervention of compounds that are chemically foreign and indifferent to this reaction. p77.
This implies the generation of a hierarchy of levels of cybernetic control. It also suggests lots of possibilities for co-evolution of processes and regulation.
only failure awaits attempts to reduce the properties of a very complex organisation to the "sum" of the properties of its parts. A most foolish and wrongheaded quarrel it is, merely testifying to the "holists" profound misappreciation of scientific method and of the crucial role analysis plays in it. If a Martian engineer were trying to understand one of our earthling computers, how far could he conceivably get were he, on principle, to refuse to dissect the basic electronic components which in the machine execute the operations of propositional algebra? If any one branch of molecular biology illustrates better than others the sterility of holist theses as against the cogency of analytical method, it is indeed the study of these microscopic cybernetic systems.. p 79.
Monod is partly right and partly wrong the point is that the arrangement of the microscopic components is not embedded in the components themselves.
And even though these analyses are not yet near to furnishing us with a complete description of the cybernetic system of the simplest cell, they tell us that, without exception, all the activities that contribute to the growth and multiplication of that cell are interconnected and intercontrolled directly or otherwise. On such a basis, but not that of a vague "general theory of systems," does it become possible for us to grasp in what very real sense the organism does effectively transcend physical laws - even while obeying them - this achieving at once the pursuit and fulfilment of its own purpose.   
This is just an attack on Bertalanffy who is referenced for General Systems Theory. It is not actually presenting any kind of alternative framework and it is also contradictory.

Saturday, 11 June 2011

Chance and Necessity - Jacques Monod I

In the book he makes arguments for distinguishing signs of life from crystalline growth and other ways of creating order. A simpler approach is that of Lotka who said it was just a matter of definition and avoided the question all together. This is based on the idea of Paley and the watch-maker, showing that there must be design,

The cornerstone of the scientific method is the postulate that nature is objective. In other words, the systematic denial that "true" knowledge can be got at by interpreting phenomena in terms of final causes - that is to say, of "purpose" ...

Objectivity nevertheless obliges us to recognize the telenomic character of living organisms, to admit that in their structure and performance they act projectively - realize and pursue a purpose. p21-22.
Is this true? Do we need purpose? It is indirect because selection requires the purpose of being able to deal with the environment.
that invariance necessarily precedes teleonomy. Or, to be more explicit the Darwinian idea that the initial appearance, evolution, and steady refinement of ever more teleonomic structures are due to perturbations occurring in a structure which already possesses the property of invariance - hence is capable of preserving the effects of chance and thereby submitting them to the play of natural selection. p23-24.
This is the point that the genome is separate and "invariant" as in it allows the random changes to be passed between generations. But this also echoes the ideas of Claude Bernard and that complex organisms carry their environment around with them and so are more robust to environmental changes. He accuses Elsasser and Polanyi of scientific vitalism which is unfair.Teilhard de Chardin is intellectually spineless (this is the use of the personal fallacy - attack the person and not the idea). Teilhard has evolution act on all components not just living things. This agrees with Lotka's definition of evolution but there is a genotype in living things.

Living things are robust, plastic and evolvable. So they have a balance between  a defined shape/function and flexibility. They respond to the environment, yet they are separable pools of information. They are homeostatic but not closed.

We know however (contrary to what Laplace believed, and after him the science and "materialist" philosophy of the 19th century) that these predictions could be no more than statistical.
In a general manner the theory would anticipate the existence, the properties, the interrelations of  certain classes of objects or events, but would obviously not be able to foresee the existence or the distinctive character of any particular object or event. p43.
This is the point about biology being a phenomenological subject and that it might not have an fundamental predictive laws.
Plainly enough, the functional coherence of so complex a chemical machine, which is autonomous as well calls for a cybernetic system governing and controlling the chemical activity at numerous points. p45.
This specificity is two-fold:
  1. Each enzyme catalyses but one type of reaction.
  2. Among the sometimes very numerous compounds in the organism susceptible of undergoing that type of reaction, the enzyme, as a general rule, is active in regard to only one.
Nonsense - they are not so specific and there is a lot of kinetic control.