Archive for the 'Science' Category

Doing a PhD

These are some notes on deciding to do a PhD, notes I wrote some years ago after completing my own PhD.

Choosing a PhD program is one of the hardest decisions we can make. For a start, most of us only make this decision once in our lives, and so we have no prior personal experience to go on.

Second, the success or otherwise of a PhD depends a great deal on factors about which we have little advanced knowledge or control, including, for example:

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Research funding myopia

The British Government, through its higher education funding council, is currently considering the use of socio-economic impact factors when deciding the relative rankings of university departments in terms of their research quality, the Research Assessment Exercise (RAE), held about every five years.   These impact factors are intended to measure the social or economic impact of research activities in the period of the RAE (ie, within 5 years). Since the RAE is used to allocate funds for research infrastructure to British universities these impact factors, if implemented, will thus indirectly decide which research groups and which research will be funded.    Some academic reactions to these proposals are here and here.

From the perspective of the national economy and technological progress, these proposals are extremely misguided, and should be opposed by us all.    They demonstrate a profound ignorance of where important ideas come from, of when and where and how they are applied, and of where they end up.  In particular, they demonstrate great ignorance of the multi-disciplinary nature of most socio-economically-impactful research.

One example will demonstrate this vividly.  As more human activities move online, more tasks can be automated or semi-automated.    To enable this, autonomous computers and other machines need to be able to communicate with one using shared languages and protocols, and thus much research effort in Computer Science and Artificial Intelligence these last three decades has focused on designing languages and protocols for computer-to-computer communications.  These protocols are used in various computer systems already and are likely to be used in future-generation mobile communications and e-commerce systems. 

Despite its deep technological nature, research in this area draws fundamentally on past research and ideas from the Humanities, including: 

  • Speech Act Theory in the Philosophy of Language (ideas due originally to Adolf Reinach 1913, John Austin 1955, John Searle 1969 and Jurgen Habermas 1981, among others)
  • Formal Logic (George Boole 1854, Clarence Lewis 1910, Ludwig Wittgenstein 1922, Alfred Tarski 1933, Saul Kripke 1959, Jaakko Hintikka 1962, etc), and
  • Argumentation Theory (Aristotle c. 350 BC, Stephen Toulmin 1958, Charles Hamblin 1970, etc). 

Assessment of the impacts of research over five years is laughable when Aristotle’s work on rhetoric has taken 2300 years to find technological application.   Even Boole’s algebra took 84 years from its creation to its application in the design of electronic circuits (by Claude Shannon in 1938).  None of the humanities scholars responsible were doing their research to promote technologies for computer interaction or to support e-commerce, and most would not have even understood what these terms mean.  Of the people I have listed, only John Searle (who contributed to the theory of AI), and Charles Hamblin (who created one of the first computer languages, GEORGE, and who made major contributions to the architecture of early computers, including invention of the memory stack), had any direct connection to computing.   Only Hamblin was afforded an obituary by a computer journal (Allen 1985).

None of the applications of these ideas to computer science were predicted, or even predictable.  If we do not fund pure research across all academic disciplines without regard to its potential socio-economic impacts, we risk destroying the very source of the ideas upon which our modern society and our technological progress depend. 

Reference:

M. W. Allen [1985]: “Charles Hamblin (1922-1985)”. The Australian Computer Journal, 17(4): 194-195.

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Can the obese now expect an apology from the medical profession?

Western medicine has a long history of blaming the victims of illness for their illness, attributing moral and character defects to the ill – eg, those suffering from cholera (before the mid 19th century), from physical addictions (until the mid 20th century), and from stomach ulcers (until the discovery of Helicobacter Pylori in 1982).   The most recent morality campaign waged by the medical profession has been against the obese, who are assumed by many medical practitioners to be lazy, weak-willed, or worse.  The medical professions urge the over-weight to diet and to exercise, and they even restrict treatment in some cases to people who are not obese.  Never mind that the scientific evidence for the relationship between regular exercise and appetite is weak, and suggests in any case that the former increases the latter: so that, if anything, more exercise is likely to lead to increased weight, not to reduce it.  

Now, science tells us that appetite – and hence obesity – may also be a function of one’s genes, as this article in tomorrow’s SMH reports

SOME of the children were so fat they had been listed on the British social services ”at risk” register because it was assumed their parents were abusing them with deliberate overfeeding.

”In one case, one of the children had been taken into care,” said Stephen O’Rahilly, a world expert on the genetics of obesity at the University of Cambridge.

But then his research team discovered the problem. The obese children had a section of DNA missing in their genetic code – a fault that produced a very strong drive to eat.

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The websearch-industrial complex

I think it is now well-known that the creation of Internet was sponsored by the US Government, through its military research funding agencies, ARPA (later DARPA).   It is perhaps less well-known that Google arose from a $4.5 million research project sponsored also by the US Government, through the National Science Foundation.   Let no one say that the USA has an economic system involving “free” enterprise.

In the primordial ooze of Internet content several hundred million seconds ago (1993), fewer than 100 Web sites inhabited the planet. Early clans of information seekers hunted for data among the far larger populations of text-only Gopher sites and FTP file-sharing servers. This was the world in the years before Google.

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Know-all

Terry Eagleton has been a strong defender of religious belief, religious practice, and theology against the attacks of the neo-classical atheists, as in this interview here.  I have a great deal of sympathy with Eagleton’s aims, but he seems confused about performative acts, actions which may or may not imply propositions, and, when they do, certainly rarely imply propositions reasonable people can agree on.   Normblog, here first and then here,  attacks Eagleton’s account of religious practice.  In his second post, Norm is responding to a post by Chris at Stumbling and Mumbling, a post which defends Eagleton by discussing tacit knowledge and coming-to-know-something-through-experiencing-it.

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Evil intentions

A commentator on Andrew Sullivan’s blog asks:  Where is the Darwinian theory of evil?   Because  modern biologists this last century or so have been very concerned to avoid teleological arguments, modern biology has still only an impoverished theory of intentionality.   Living organisms are focused, in the standard evolutionary account, on surviving themselves in the here-and-now, apparently going through these daily motions unwittingly to ensure  those diaphonous creatures, genes, can achieve THEIR memetic goals.  Without a rich and subtle theory of intentionality, I don’t believe one can explain complex, abstract human phenomena such as evil or altruism or art or religion very compellingly.   

Asking for a theory of intentions and intentionality does not a creationist one make, despite the vitriol often deployed by supporters of evolution.  One non-creationist evolutionary biologist who has long been a critic of this absence of a subtle theory of intentionality in biology is J. Scott Turner, whose theories are derived from homeostasis he has observed in natural ecologies.   I previously discussed some of his ideas here.

References:

Alfred Gell [1998]:  Art and Agency:  An Anthropological Theory.  Oxford, UK: Clarendon Press.

J. Scott Turner [2007]: The Tinkerer’s Accomplice: How Design Emerges from Life Itself. Cambridge, MA, USA:  Harvard University Press.

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Thinkers of renown

The recent death of mathematician Jim Wiegold (1934-2009), whom I once knew, has led me to ponder the nature of intellectual influence.  Written matter – initially, hand-copied books, then printed books, and now the Web – has been the main conduit of influence.   For those of us with a formal education, lectures and tutorials are another means of influence, more direct than written materials.   Yet despite these broadcast methods, we still seek out individual contact with others.  Speaking for myself, it is almost never the knowledge or facts of others, per se, that I have sought or seek in making personal contact, but rather their various different ways of looking at the world.   In mathematical terminology, the ideas that have influenced me have not been the solutions that certain people have for particular problems, but rather the methods and perspectives they use for approaching and tackling problems, even when these methods are not always successful. 

To express my gratitude, I thought I would list some of the people whose ideas have influenced me, either directly through their lectures, or indirectly through their books and other writings.   In the second category, I have not included those whose ideas have come to me mediated through the books or lectures of others, which therefore excludes many mathematicians whose work has influenced me (in particular:  Newton, Leibniz, Cauchy, Weierstrauss, Cantor, Frege, Poincare, Hilbert, Lebesque, Godel, and Kolmogorov).  I have also not included the many writers of poetry, fiction, history and biography whose work has had great impact on me.  These two categories also exclude people whose intellectual influence has been manifest in non-verbal forms, such as through visual arts or music, or via working together, since those categories need posts of their own.

Teachers & lecturers I have had who have influenced my thinking includeLeo Birsen (1902-1992), Sr. Claver Butler RSM (d. 2009), Burgess Cameron, Sr. Clare Castle RSM,  John Coates, Dot Crowe, James Cutt, Bro. Clive Davis FMS, Tom Donaldson (1945-2006), Sol Encel, Richard Gill, Rachel Harland, Chip HeathcoteAlec Hope (1907-2000),  John Hutchinson, Marg Keetles, Joe Lynch, Robert Marks, John McBurney (1932-1998), David Midgley, Terry O’Neill, Jim Penberthy* (1917-1999), Malcolm Rennie (1940-1980), John Roberts, Gisela Soares, Brian Stacey (1946-1996), Frank Torpie, Myrtle Torrens (1909-1984), Neil Trudinger, David Urquhart-Jones, Frederick Wedd (1890-1972), Gary Whale, Ted Wheelwright (1921-2007), and John Woods.

People whose writings have influenced my thinking includeJohn BaezOle Barndorff-Nielsen, Charlotte Joko Beck, Johan van Bentham, Mark Evan Bonds, John Cage (1912-1992), Albert Camus (1913-1960), John Miller Chernoff, Sam Eilenberg (1913-1998), Paul Feyerabend (1924-1994), Kyle Gann, Alfred Gell (1945-1997), Herb Gintis, Jurgen Habermas, Charles Hamblin (1922-1985), Vaclav Havel,  Jaakko Hintikka, Eric von Hippel, Wilfrid Hodges, Christmas Humphreys (1901-1983), Jon Kabat-Zinn, Herman Kahn (1922-1983), Maynard Keynes (1883-1946), Paul Krugman, Imre Lakatos (1922-1974), Trevor Leggett (1914-2000), George Leonard (1923-2010), Brad de Long, Donald MacKenzie,  Saunders Mac Lane, Karl Marx (1818-1883), Grant McCracken, Henry Mintzberg, Philip Mirowski, Michel de Montaigne (1533-1592), Michael Porter, Charles Reich, Jean-Francois Revel (1924-2006), Bertrand Russell (1872-1970), Pierre Ryckmans (Simon Leys), Oliver Sacks, George Shackle (1903-1992), Cosma Shalizi, Raymond SmullyanRory Stewart, Anne Sweeney (d. 2007), Nassim Taleb, Stephen Toulmin (1922-2009), Scott Turner, Roy Weintraub, Geoffrey Vickers (1894-1982), and Richard Wilson.

FOOTNOTES: 

* Which makes me a grand-pupil of Nadia Boulanger (1887-1979).

** Of course, this being the World-Wide-Web, I need to explicitly say that nothing in what I have written here should be taken to mean that I agree with anything in particular which any of the people mentioned here have said or written.




Newton and scientific publication

While on the subject of Isaac Newton, here are several statements by historian Scott Mandelbrote on Newton’s attitude to the public dissemination of his work.  The more we know of Newton, the less we should consider him a scientist in the modern meaning of the word.

His [theological investigation] was a voyage of personal discovery; even the Principia required Halley’s exertions as a midwife to bring them to light.  Newton might share his religious opinions with other members of the remnant, as he did in his letters to Locke, but he worried about the consequences of their wider dissemination:  ‘I was of opinion my papers had lain still & am sorry to heare there is news about them.  Let me entreat you to stop their translation & impression so soon as  you can for I designe to suppress them.‘  Newton’s concern may have reflected fear of being discovered to hold unorthodox  opinions, but it was also the product of religious motives.  Not everyone could be expected to comprehend ’strong meat’, which was  intended for personal consumption, and which might be wasted on others.” (p.299)

His [Newton's] theology pervaded his alchemy, in his analysis of the Emerald Tablets of Hermes Trismegistus, and in turn  his alchemy suggested to him how matter might be understood physically.  A true understanding of the uses of language enabled  Newton to introduce astronomical calculation into his chronological writings, and to complete his mathematical arguments with theological references:

[pagebreak]
. . . .  

Mathematics was God’s language; the language of the prophets communicated God’s purposes and ‘times’ to men.  Newton felt it was his duty to understand and to reconcile the two, to decipher the hieroglyphs which corrupted religion and learning had obscured.   The problems of mathematics ended in the solutions of divine majesty, and mathematical language solved the theological problem of describing Newton’s Arian interpretation of the relations within the Trinity:

. . . 

Newton’s natural philosophical and theological discoveries removed the obscurities from divine language, in the books of nature and of scripture.  In the life of the true believer, the two could not be separated.  But most had to be content with the milk for babes, because Newton’s own language was beyond them.” (pp. 300-301).

Reference:

Scott Mandelbrote [1993]:  ‘A dute of the greatest moment’: Isaac Newton and the writing of biblical criticism. British Journal of the History of Science, 26:  281-302.




Chasing the sources: a Newtonian mystery

As is well-known to historians (although less so among scientists), Isaac Newton was a devout religious believer, an alchemist, and a seeker after ancient wisdom about God and the cosmos.   He was a Unitarian, a belief not permitted at the time, and so he kept his religious views very, very close to himself and to a small circle of intimates.  When his friend and fellow FRS, Nicolas Fatio de Duiller, publicly supported the millenarian French Protestant sect, the Camisards (aka The French Prophets), in London in the first decade of the 18th century, Newton kept in touch with him to learn of their prophecies, and came close to publicly supporting them also.  

So when an historian writes the following it is very plausible, at least to people aware of Newton’s religious beliefs and interests:

Isaac Newton (1642-1727) was also enamored of Egyptian wisdom, as we shall see in the next chapter, even if it is not clear that he accepted the Hermetic tradition.  It was essential for his theory of gravitation to have an accurate measure of the world’s circumference, and for that he needed to calculate exactly a single degree of latitude.  Newton was convinced that there was no need to send a team of surveyors to plot distances on the ground, as the French were doing.  It was rather easier to determine the exact length of an Egyptian cubit, which ancient authors insisted was directly related to a degree of latitude.   This information could be obtained from the dimensions of the Great Pyramid, which was always believed (perhaps rightly) to enshrine perfect units of length, area and volume, as well as pi.  Sadly, the results of the Pyramid experiment did not fit Newton’s calculations, but, instead of scrapping the theory, the great scientist blamed the surveyors instead.   As luck would have it, the French astronomer Jean Picard (1620-82) succeeded in 1671 in measuring perfectly a degree of latitude in Sweden, so Newton could prove his theory of gravitation without the Egyptians.” (Katz 2005, page 31)

The reference the author David Katz cites for this story is Shalev 2002.  But consulting that reference, we do not see mentioned the story Katz relates here.  Instead, we find this sentence (on page 574): 

As Robert Palter has argued in his critique on Bernal’s  Black Athena, there is no evidence to show that Newton related his interest in the Egyptian cubit to his physics and geodesy.”

with the reference being to Palter 1993, pages 245 and following.

What is going on here?  Has Katz mistakenly cited the wrong source for the story above, something easy enough to do in academic writing?   Perhaps Katz could tell us.  I hope it is a simple mistake in citation, and not something more sinister.

References:

David S. Katz [2005]: The Occult Tradition:  From the Renaissance to the Present Day.  (London, UK: Jonathan Cape).

Robert Palter [1993]:  Black Athena, Afro-Centrism, and the history of science. History of Science, 31: 227-287.

Zur Shalev [2002]:  Measurer of all things: John Greaves (1602-1652), the Great Pyramid and early modern metrology. Journal of the History of Ideas, 63: 555-575.

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Argumentation in public health policy

While on the subject of public health policy making under conditions of ignorance, linguist Louise Cummings has recently published an interesting article about the logical fallacies used in the UK debate about possible human variants of mad-cow disease just over a decade ago (Cummings 2009).   Two fallacies were common in the scientific and public debates of the time (italics in orginal):

An Argument from Ignorance:

FROM: There is no evidence that BSE in cattle causes CJD in humans.
CONCLUDE:  BSE in cattle does not cause CJD in humans.

An Argument from Analogy:

FROM:  BSE is similar to scrapie in certain respects.
AND: Scrapie has not transmitted to humans.
CONCLUDE:   BSE will not transmit to humans.

Cummings argues that such arguments were justified for science policy, since the two presumptive conclusions adopted acted to guide the direction and prioritisation of subsequent scientific research efforts.  These presumptive conclusions did so despite both being defeasible, and despite, in fact, both being subsequently defeated by the scientific research they invoked.   This is a very interesting viewpoint, with much to commend it as a way to construe (and to reconstrue) the dynamics of scientific epistemology using argumentation.  It would be nice to combine such an approach with Marcello Pera’s 3-person model of scientific progress (Pera 1994), the persons being:  the Investigator, the Scientific Community, and Nature.

Some might be tempted to also believe that these arguments were justified in public health policy terms – for example,  in calming a nervous public over fears regarding possible BSE in humans.   However, because British public policy makers did in fact do just this and because the presumptive conclusions were subsequently defeated (ie, shown to be false), the long-term effect has been to make the great British public extremely suspicious of any similar official pronouncements.   The rise in parents refusing the triple MMR vaccine for their children is a direct consequence of the false assurances we were given by British health ministers about the safety of eating beef.   An argumentation-based  theory of dynamic epistemology in public policy would therefore need to include some game theory.    There’s also a close connection to be made to the analysis of the effects of propaganda and counter-propaganda (as in George 1959), and of intelligence and counter-intelligence.

References:

Louise Cummings [2009]: Emerging infectious diseases: coping with uncertaintyArgumentation, 23 (2): 171-188.

Alexander L. George [1959]: Propaganda Analysis:  A Study of Inferences Made from Nazi Propaganda in World War II.  (Evanston, IL, USA: Row, Peterson and Company).

Marcello Pera [1994]: The Discourses of Science. (Chicago, IL, USA: University of Chicago Press).

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