Sunday, January 27, 2013

A major paradigm change in biological science

The great Denis Noble emails that his brilliant lecture which "shows that we now know that all the central assumptions of the modern synthesis (neo-darwinism) have now been broken", is now being adopted and publicised internationally by one academic society and institute after another, and that he has been asked to write a major review article. I agree with him when he says "we are privileged to live at a time of a major paradigm change in biological science."
Fig 4 from Nelson et al.
Indeed since he gave his lecture (as Denis points out) further evidence continues to emerge. For example this paper in PNAS (Vicki Nelson et al, "Transgenerational epigenetic effects of the Apobec1 cytidine deaminase deficiency on testicular germ cell tumor susceptibility and embryonic viability") conclusively demonstrates epigenetic maternal inheritence over several generations. The accompanying coment paper makes the point that "the belief that the soma and germline do not communicate is patently incorrect" (citing as an example this paper).

It is interesting BTW that so many of the key figures in overturning the ridiculous dogmas of "Neo-Darwinism" are women. "we achieve immortality through spreading our genes" is a particularly appealing view to a certain type of male - indeed I have been told that fathering illegitimate children (and activities conducive to this) with students was a major factor in the break-up of the marriage of at least one prominent advocate of Neo-Darwinism.  I can't find much about Vicki Nelson on the web except that she was a graduate of the HHMI Exceptional Research Opportunities program and is still as CWRU.  It's scandalous that this paper has only been cited once so far - adherence to dogma in the face of evidence is rife in biology departments.

Meanwhile I gather that Dawkins will be trying to debate against Rowan Williams at the Cambridge Union on Thursday.  Williams is so much brighter than Dawkins that from an intellectual PoV it will be a turkey shoot (Rowan speaks or reads 10 languages and was elected FBA at 40 - Dawkins scraped into the RS as a "general candidate", not for any particular scientific contribution, when he was 60.)  However whether Cambridge Union attendees will recognise this remains to be seen.

PS it's worth noting that:
  1. The idea that "DNA determines your body" was disproved in 2005 when it was shown that fish growing from enucleated goldfish eggs with carp DNA had 27 vertebrae compared to 33 for carp and  26 for goldfish. (Carp and Goldfish are not merely different species but from different genuses).
  2. Experimental confirmation of the fact (established by Nowak, Tarnita and Wilson) that kin selection/inclusive fitness was not the correct explanation of altruism comes in this paper in Naturwissenschaften which described mixed colonies of two different species of spider which live together in shared colonies and care for each others’ young indiscriminately.
  3. One of the mechanisms of epigenetic inheritance has been elucidated in a new Science paper (Hackett et al), though of course it doesn't explain the observation in (1) above.

Friday, January 25, 2013

Janie Dee, and Miranda


Went last night to Janie Dee's wonderful Cabaret at Brasserie Zedel just off Piccadilly Circus.  She was on terrific form, with an all-new programme (ie songs I haven't heard her sing before) which was an absolute delight. Flirting outrageously with the audience and performing the songs with such mastery as a great actress.  Twiggy was in the audience which was fun for everyone.

Most of the songs I didn't know - and there was one especially striking one which the web thinks is by Liza Minnelli (but surely she just sings it?).

Yes, Say yes
Life keeps happenin' every day
Say yes

When opportunity comes your way
You can't start wonderin' what to say
You'll never win if you never play
Say yes


Not wise advice universally of course, but within reason...

Also may I just say how much we are enjoying the 3rd series of Miranda (thank you kindly).  The episode this week was sheer comic genius and is going to be a classic for years and years.  She has this knack of writing contrapuntal comedy in that she will put in a joke which is really funny and then refer back to it rather unexpectedly later on which is really really funny. There were several moments like that (eg Gary and the geese).  Also by having set up a situation where she and Stevie consult a random man in their shop about Mirdanda's problems they can have him reliably blurt out exactly the wrong thing becasue he has no idea who the other people who come in are.

It's also becoming clear to people through watching her in Call the Midwife that she really is a great actress. Her ability to get the audience laughing by a single look isn't just becasue she is funny.  The moment when she makes a declaration of love (to the wrong person) is a bit like "kill Claudio" in Much Ado. And although the studio audience would all have seen the joke which on the TV you can't see until the close-up pans away, no-one was laughing becasue she got the emotional temperature just right.

Apparently the show had slighly lower viewing figures (6.8M) - probably becasue there was a Comic Relief show on BBC2 scheduled against it. It's perfectly obvious that a lot of BBC media types don't like Mirdanda's clean winsome fun humour, so the BBC runs a "foul mouthed" comedy immediately afterwards. Ah well. Changing a dreadful culture takes time.



Tuesday, January 22, 2013

More from Monopolizing Knowledge

I'm continuing to read Monopolizing Knowledge with pleasure and profit. There are some thinks I disagree with but a great deal to admire. Here are a few more gems:
  • "It is a mere presumption, not based on scientific results, to suppose that a scientific description 'explains away' personality."
  • "The scientistic dehumanization of history and the portrayal of society as subject to inevitable laws of dynamics became the ... base material from which could be fasioned political rationalizations bearing the spurious honorific of 'scientific'."
  • "It was Descartes, not Newton, who sought to reduce all nature to mechanism...In fact Newton's achievement was precisely not to reduce the celestial motions to mechanics, not to the material... but rather to model it with mathematics."
  • "For Darmin, and evolutionary theorists since, the nature of explanation is taken not to be to demonstrate that the phenomena observed are a necessary consequence of the laws or principles...[but] to set forth a plausible history of how the observed phenomena could have beena consequence of natural selection."
  • "Scientism might well be comfortable simply not asking [questions about where the laws of physics come from]... but it offers no logical reason for not doing so."
He also quotes some dolt called William Provine who writes "Modern science directly implies that there are no inherent moral or ethical laws...[and].. free will ... simply doesn't exist... There is no way that the evolutionary process as cuirrently conceived can produce a being that is totally free to make moral choices."   This statement is so ridiculous on so many levels that it is almost not worth unpacking. But:
  1. There is no conceivable scientific experiment that could show that "there are no inherent moral or ethical laws."  Of course you could show that particular moral laws are not always followed, or that there was disagreement about what moral laws were, but that's completely different!
  2. To say "I do not see how X could have evolved therefore X cannot have evolved" is a terrible argument rightly ridiculed by evolutionists. And in fact it is perfectly obvious how and why free will could have evolved. To survive and thrive in social situations with intelligent beings there is enormous selective advantage in being able, when the need arises, to make decisions that cannot be reliably predicted by others and free will also provides enormous advantages in creativity and problem solving (see Questions of Truth p133 for a brief discussion). 
He astutely points out that "social Darwinism" has a long history and was used to 'justify' eugenics, unbridled greed ("the struggle for life and the survival of the fittest must be left to work out their effects without mitigation" wrote Spencer) Nazism and so forth.  I think he's a little unfair on EO Wilson in using the present tense in some of his 1970s views, but he rightly quotes Wilson who concedes that "scientific materialism is itself a mythology...addressed with precise and deliberate affective appeal to the deepest needs of human nature."  He concludes:
  • "It seems significant to me that evolutionary metaphysicians of adjacent generations have drawn practically opposite conclusions about ethics and social policy, from essentially the same scientific theory" (p127)

Sunday, January 20, 2013

There is no such thing as a gene for any kind of behaviour

Interesting review in Science by Johan Bolhuis of The Nature-Nurture Debates by Dale Goldhaber. In it he rightly criticises:
"evolutionary psychologists and other scientists who cling to a reductionist nativist view of development and, most important, the general public. Unfortunately, the truth about development as a dynamic process cannot be captured in simple sound bites. It is so much easier to boldly state that a particular human trait lies “in our genes”—which is why the media continue to use such outmoded terminology. I share the frustration of many colleagues when our students continue to talk about “innate behavior” despite our attempts to provide them with a nuanced view of development. This sorry state of affairs often forces developmental scientists to fight ever-popular notions of nature and nurture."
and he makes the very clear point that:
In fact, there is no such thing as a gene for any kind of behavior or cognitive mechanism.
This needs to be stated and re-stated lound and clear in the face of ridiculous popularisers of reductionist tosh - not just Dawkins but a whole crew of simplistic nth-raters.

Of course this is not at all to say that genetic and biological mechnaisms are unimportant in behaviour, far from it, but that as serious biologists realised in the 1960s. As Bolhuis says "development is a complex process involving continual interaction between the individual and its environment. Because the environment changes all the time, the nature of the interaction itself changes during development".  He has a long-ish 2011 article in PLoS One setting out his critique of the standard tenets of Evolutionary Psychology which is well worth reading.  This concludes:
The key concepts of EP have led to a series of widely held assumptions (e.g., that human behaviour is unlikely to be adaptive in modern environments, that cognition is domain-specific, that there is a universal human nature), which with the benefit of hindsight we now know to be questionable. A modern EP would embrace a broader, more open, and multi-disciplinary theoretical framework, drawing on, rather than being isolated from, the full repertoire of knowledge and tools available in adjacent disciplines. Such a field would embrace the challenge of exploring empirically, for instance, to what extent human cognition is domain-general or domain specific, under what circumstances human behaviour is adaptive, how best to explain variation in human behaviour and cognition. The evidence from adjacent disciplines suggests that, if EP can reconsider its basic tenets, it will flourish as a scientific discipline.
(The fact that this article is only cited by 17 other suggests that the EP crew are closing their ears - what a surprise!)

Saturday, January 19, 2013

Back, Bill Gates, and Ian Hutchinson

Back from an amazing week in Beijing - many very productive meetings none of which are bloggable alas.

Very sad news about the hostage crisis in Algeria.

Interesting that Bill Gates is prepared to say "God’s work" about at least some aspects of the work of his foundation: "...the women who are doing God’s work and getting out to these children and delivering the vaccine.”  The article continues:
Gates does not usually speak in religious terms, and has traditionally danced around the issue of God. His wife, a Roman Catholic, is less defensive on that topic but ploughs her own furrow, encouraging contraception when necessary, in contradiction to teaching from Rome....

So, is it about some new-found faith, all this giving? “It doesn’t relate to any particular religion; it’s about human dignity and equality,” he says. “The golden rule that all lives have equal value and we should treat people as we would like to be treated.”
I did get some time to read more of Monopolizing Knowledge and there are many choice quotes it would be good to share.  It also prompts further musing on the sense in which science "knows" things about the world.  There is the ridiculous Cargo Cult "Argument" for Scientism which says that we have to accept Scientism because we use "the fruits of science" which are taken to mean any beneficial technology that human beings have devised over the last few hundred years (aeroplanes are a prime example).

First of all, even if it were true that all beneficial technology were developed entirely by people who believed in Scientism this doesn't impose a logical or moral obligation to share such a belief upon people who use this technology - though perhaps it does impose some form of obligation to treat the belief with a certain level of respect.   Secondly it is not true that all scientists believe in Scientism, indeed in practice almost none of them really do.  And of course much of the science and technology on which we depend for our daily lives was developed by Christians.  Thirdly, science and technology can be applied for evil ends as well as beneficial ones - if humanity does become extinct in the next few hundred years it will probably be because of the mis-application of technology.

But more interestingly (perhaps) it's worth pointing out that "Science" does not actually make any of the beneficial goods on which society depends.  To the extent that these goods are machines then it's Engineers that can claim this honour - and no-one AFAIK has been so transparently idiotic as to propose a creed of Engineerism whereby "all knowledge is Engineering".  Of course it's true that some Engineers have a scientific background or training and that engineers will, where relevant, use scientific knowledge to help them in their work.  But all that says is that Engineers are practical and will use whatever is conveniently available to achieve their goals.  Engineers use mathematics far more than they use science. If we took a half-way reasonable list of the greatest engineers of all time (eg this one has: Leonardo, Edison, Ford, Wright Bros, Hero of Alexandria, Archimedes, Tesla, Otto and Turing - clearly done by an American and highly disputable but will illustrate the point) we'd find that remarkably few were even trained as scientists let along practicing ones (that list has only two graduates: Tesla in Engineering and Turing in Mathematics).

There is of course a lot more that can be said about all this - in what sense can we say that scientific theories are true for example.  But that's well beyond the scope of this post!

Saturday, January 12, 2013

More support for MaxHELP

Fi 7 from Fressin et al.
My MaxHELP conjecture (that the fundamental constants of the universe might be such as to maximise the expected number of Habitable Earthlike Planets) is looking increasingly plausible:
  • David Spiegel in the IAS review has an interesting article on "Life on other planets". I've reached out to him because he'd be a very good person to explore this conjecture with.
  • Tuomi et al's paper “Periodic variations in the Tau-Ceti velocities” suggests that there are earth-like planets in stars quite close to earth.
  • Fressin et al's “The False Positive Rate of KEPLER and the Occurrence of Planets” suggests that about 16% of main-sequence FGKM stars have planets whose mass is appx the same as that of Earth (85-125%). Of course these are not necessarily "Habitable Earth-like planets" since this require stable solar systems over a period of c.4bn years, which almost certainly needs a Jupiter, a very large moon, and certainly needs the star to be reasonably well-behaved and far enough away from other stars and black holes.
  • Now Bagdonaite et al in Science find "A Stringent Limit on a Drifting Proton-to-Electron Mass Ratio from Alcohol in the Early Universe" basically showing that this particular fundamental constant hasn't changed by more than 1 part in 10^7 over a period of 8 bn years.
I wonder whether the mass of the Higgs will turn out to be a fundamental constant?  This would deal with the "need" to invoke supersymmetry to "explain" it. If so we should find that d(EHelp)/d(mHiggs) = 0.  Another fascinating and testable-in-principle consequence of the MaxHelp conjecture.

Sunday, January 06, 2013

Higgs and Dyson papers

From PNAS commentary on Dyson paper
Catching up on some scientific reading:

  • Iterated Prisoner’s Dilemma contains strategies that dominate any evolutionary opponent is a paper by William H. Press and Freeman Dyson in PNAS that, remarkably, discovers a fundamental new property of Iterated Prisoner's Dilemma games. It turns out that there are strategies whereby "a player X ...can (i) deterministically set her opponent Y’s score, independently of his strategy or response, or (ii) enforce an extortionate linear relation between her and his scores. Against such a player, an evolutionary player’s best response is to accede to the extortion. Only a player with a theory of mind about his opponent can do better, in which case Iterated Prisoner’s Dilemma is an Ultimatum Game." (see also commentary here).

    This point about "Theory of Mind" is very interesting and important.  It's a demonstration in microcosm of why the evolution of a Theory of Mind is so important. Similar considerations also push for the evolution of freewill if defined as "the ability to make decisions that cannot be reliably predicted by other creatures with which you interact".

    And of course it's pretty impressive to make a major contribution to a new field when you are 88 - this may be a record and I'd be interested to know who has published a Nature/Science/PNAS paper at a more advanced age.  He is one of the last working scientists to remember Einstein well, they overlapped at the IAS from 1953 to 1955.
  • The Higgs Bosons paper in Science. I hadn't appreciated just how intricate and indirect the observation of the Higgs is. The authors all make the point in different ways that the Higgs points to Supersymmetry,  ("Without new phenomena, quantum loop processes would drive the predicted Higgs boson mass far above the highest energy scale at which the SM is valid." (ATLAS) "It is known that quantum corrections make the mass of a fundamental scalar particle float up to the next highest physical mass scale currently known, which, in the absence of extensions to the SM, is as high as 1015 GeV...In the minimal supersymmetry model, five types of Higgs bosons are predicted to exist. Furthermore, the lightest stable neutral particle of this new family...could be the particle constituting dark matter. If, as conjectured, such particles are light enough, they ought to reveal themselves at the LHC." (summary article). 

    As readers of this blog will know I'm very sceptical about string theory as physics (it's clearly very deep and interesting mathematics) and I can't help feeling that the idea of QM corrections making a mass "float up" almost 12 orders of magnitude is extrapolating ridiculously far. It seems more likely that there will be an adjustment to the corrections, based perhaps on  information-theoretic considerations limiting the number of iterations of correction or maybe from quantisation of space.  But I'm not competent to go into the mathematics. (I do know that Supersymmetry doesn't necessarily imply String Theory, but they are close relatives).

Saturday, January 05, 2013

More from Hutchinson on Monopolising Knowledge

Very much enjoying Ian Hutchinson's Monopolising Knowledge which certainly deserves to be more widely known and read. Here are a few gems:
  • He contrasts Kepler's "My aim is to show that the machine of the universe is not similar to a divine animated being, but similar to a clock" with Newton's "hypotheses non fingo" explicitly declining to propose a mechanism for gravity.
  • "in the middle of thinking what I might say about [reductionism]... I began picking up books [about history and philosophy of science] and looking into their indices....In none of them did the word reductionism appear...Reductionism has come to the fore largely through the debate about ... science and religion" He makes the point that abstraction rather than reductionism is really a characteristic move of science. (I must introduce him, at least intellectually, to Denis Noble) and that the notion of explaining away is completely fallacious.
  • "to believe or imply that science is all of real knowledge and that matters outside science are not matters of knowledge is analagous to denying that justice exists or is a useful concept simply becasue courts focus instead on legality."
He is on very strong ground pointing out that there is no satisfactory single account of what constitutes science and the scientific method, and that various attempts like "logical positivism" and "falisification" have collapsed. I hadn't reaslied the absurd way in which Compte and others tried to make a Religion of Humanity or that George Eliot was one of his adherents.

However I'm less convinced than he is that Phyiscs and Chemistry are the exclusive paradigms of science. When he says that science rules out on principle explanations involving agency and purpose this seems to me to depend on deciding that Computer Science, Psychology etc.. are not, after all, sciences. It's perfectly clear that, for any engineered or designed object, it is entirely reasonable to ask "what is the purpose of feature X" and it is possible to investigate this question scientifically.

I will continue to read - I'd urge you to get the book if you are interested in these topics.

Wednesday, January 02, 2013

Happy New Year

Happy New Year!

The last of our grandchildren departed this morning - it was wonderful having everyone staying.

Fascinating article by Freeman Dyson in Science, comparing Khunian paradigm-shifts and the approach studied by Peter Galison in Image and Logic, suggesting the much scientific progress is driven by improved tools.  Dyson concludes that "We are standing now as we stood in the 1950s, between a Kuhnian dream of sudden illumination and a Galisonian reality of laborious exploring. On one side are string theory and speculations about multiverses; on the other are all-sky surveys and observations of real black holes. The balance today is more even than it was in the 1950s. String theory is a far more promising venture than Einstein's unified field theory. Kuhn and Galison are running neck and neck in the race for glory. We are lucky to live in a time when both are going strong."

Delighted that Miranda was the most watched TV show in the UK over the Christmas period. It is tremendous how she has transformed the culture of comedy trumping the dreadfully negative tone of most of them. Her book has also been selling excellently.

Let us hope and pray that 2013 will be a year of great progress, spiritually (I have very high hopes of Justin Welby) and scientifically.

PS: I see that Miranda came 3rd in a YouGov poll of who was the best Actress on TV in 2012, and this was taken before the Christmas Call the Midwife and Mirdanda episodes. She "lost out" to Dame Maggie Smith and Dame Judi Dench, and indeed in the 25-39 age range she narrowly beat them!

It's also encouraging to see this exchange with Steven Hill on the Comment section of the Telegraph.