Why is science so sloooow 2

05/08/2010

Updating Magic Universe

WHY IS SCIENCE SO SloooOW? — continued

The modest output of major discoveries compared with a century ago, despite the huge increase in the scientific workforce, was the theme of an earlier post on this subject, which you can see here https://calderup.wordpress.com/2010/05/06/why-is-science-so-sloooow/ . A relevant extract  from the Magic Universe story on “Discovery” included this paragraph about the use of peer review to resist the funding and publication of novel research.

As a self-employed, independent researcher, the British chemist James Lovelock was able to speak his mind, and explain how the system discourages creativity. ‘Before a scientist can be funded to do a research, and before he can publish the results of his work, it must be examined and approved by an anonymous group of so-called peers. This inquisition can’t hang or burn heretics yet, but it can deny them the ability to publish their research, or to receive grants to pay for it. It has the full power to destroy the career of any scientist who rebels.’

Lovelock made those remarks in a lecture in 1989, but the situation remains grim. This month the life sciences magazine The Scientist has interesting articles on peer review.

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Mirror image molecules in Orion

31/07/2010

Pick of the Pics and Updating Magic Universe

Mirror-image molecules sorted in the Orion Nebula

But Pasteur’s hope for a cosmic driver comes true only locally

A predominance of either left-handed or right-handed versions of molecules is likely within huge dust clouds imaged by Japanese astronomers. The electric field of light rays coming from the clouds corkscrews to the left or corkscrews to the right, with “circular polarization”. The different kinds of clouds are clearly distinguishable in a massive star-forming region within the Orion Nebula, called BN/KL. Yellow denotes left-handed light, and red, right-handed. The largest yellow and red features are about 100 times wider than the Solar System, and the astronomers suggest that the polarized light will favour the formation of left-handed or right-handed molecules. The conspicuous dots left of centre near the bottom are bright young stars of the Trapezium group — strong winds  from which have helped the astronomers by blowing away dust that otherwise would obscure the BN/KL region of interest. Credit: Near-infrared (2.14 μm) image with the SIRPOL polarization instrument, NAOJ.

On seeing this report by Tsubasa Fukue and Motohide Tamura of the National Astronomical Observatory of Japan (with colleagues in Japan, UK, Australia and USA) my mind went straight back to Louis Pasteur.

Alanine, an amino acid, has mirror-image forms. L (laevo) rotates the electric field of light to the left and and D (dextro) to the right. Image NAOJ.

Although immortalized for the germ theory of disease, Pasteur’s initial claim to fame came from a discovery he made as a young student – namely that molecules from living sources have effects on the polarization of light, but the same molecules made synthetically do not. This is the phenomenon of chirality, or handedness. Chemists had to learn to think three-dimensionally about versions of molecules that are mirror images of each other. In the example shown here, every amino acid molecule in living things on Earth is of the left-handed (L) kind.

Molecular handedness is a fundamental feature of life and Pasteur suspected that some fundamental feature of the Universe was responsible for it. The phenomenon has been both a puzzle and a spur for investigators of the origin of life. The fact that carbon compounds in meteorites show the same bias in handedness as that seen on Earth suggests that some physical process was at work throughout the Solar System, at least.

The astronomers now offer an answer. Circularly polarized light pervading the dust cloud in which the Sun and its planets were born would have prompted our molecular bias. The scenario is made convincing by the sheer size of the clouds in Orion possessing one polarity or the other. But it ‘s not the Universe-wide mechanism that Pasteur expected. It seems that if the Solar System had originated in a cloud with the opposite kind of circularly polarized light, all our amino acids would be dextro.

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Planck’s whole sky

05/07/2010

Pick of the pics

Planck’s first overview of the cosmos

Credit: ESA / LFI and HFI Consortia

Microwaves from the entire sky, surveyed by Europe’s Planck spacecraft since August 2009, are here mapped in galactic coordinates. The centre of the Milky Way Galaxy, in Sagittarius, is in the middle. The ribbon of the Milky Way (the flat disc of the Galaxy) extends horizontally across the map, with Cygnus conspicuous towards the left and Orion towards the right. Streamers above and below the disc are regions of star formation. The more subtle mottled regions top and bottom show the cosmic microwave background, from the formation of the first atoms 400,000 years after the Big Bang. The strong microwaves from the Galaxy will have to be gauged and subtracted to reveal hidden parts of that background. Crucial for making the distinction is Planck’s range of nine different microwave frequencies, 30 to 850 Ghz, and its ability to measure the temperature of the sky to one-sixth of a degree.

In Magic Universe I call it “looking for the pattern on the cosmic wallpaper”. Named after the quantum theory pioneer, Planck is the successor to NASA’s WMAP mission. In 2003 WMAP returned wonderful information about the cosmic microwave background but did not quite pin down the theory of the Big Bang that best fits the facts. Maybe Planck will do that, and there seems little point in updating Magic Universe about the cosmic wallpaper until the full Planck results are in, after four surveys of the whole sky, in 2012.

George Efstathiou of Cambridge, the Planck Survey Scientist, says “It has taken sixteen years of hard work by many scientists in Europe, the USA and Canada, to produce this new image of the early Universe. Planck is working brilliantly and we expect to learn a lot about the Big Bang and the creation of our Universe.”

Reference for Efstathiou quote: UK Space Agency press release 5 July 2010.


How long you’ll live

02/07/2010

Updating Magic Universe

No, they can’t predict how long you’ll live

Excitement today in the media about the discovery of human genetic peculiarities associated with living to an exceptional old age leaves me sniffy. At the close of the story in Magic Universe called “Immortality: should we be satisfied with 100 years?” I recall:

On the day of his assassination, at what was then the ripe old age of 55, Julius Caesar declared, according to Shakespeare:

Of all the wonders that I yet have heard, / It seems to me most strange that men should fear; / Seeing that death, a necessary end, / Will come when it will come.

The veteran soldier would be bemused by 21st-Century hypochondria. In defiance of common sense and medical economics, the generation with the best life expectancy in history is obsessed with longevity.

Although overpopulation is said to be a great global problem, health educators insist that it is one’s duty to abjure motorbikes and butter and to live as long as possible. Yes, even though longevity may bring physical or mental incompetence so severe that it will cost more to keep you zimmering than to feed an entire African orphanage. As for the fear of death, if Christopher Columbus had been as bridled by cautious officials as astronauts are, his flotilla would not have quit the mouth of Spain’s Rio Tinto.

In the absence of significant disease, ageing sets a natural limit to the human lifespan. According to [Leonard] Hayflick it is about 125 years. Very few people lived past 75 until the 20th Century. But by 2000, 75 per cent of the inhabitants of the most affluent countries were doing so. The greying of the populations took actuaries and the medical profession by surprise.

The increase in human longevity slowed down in the closing decades of the 20th Century. Life expectancy at birth in affluent countries may level out at 80-90 years by the mid-21st Century. As the ageing process makes everyone more vulnerable to disease and gross degeneration, further prolongation of life may require medications yet to be invented.

They are not necessarily a good idea. Foreseeable problems range from tyrants who refuse to die to simply losing the carefree pleasures of retirement if young earners should decline to carry the economic burden of the elderly. Hayflick asked, ‘Would the least imperfect scenario be a future society in which everyone lived to their 100th birthday in good physical and mental health, then to die on the stroke of midnight?’

As Magic Universe relates earlier, Hayflick is the US microbiologist who around 1960 falsified a 30-year-old assertion by a French Nobel prizewinner that ordinary animal cells grown in a lab culture would thrive indefinitely. The natural lifespan of cells in culture, through a few dozen divisions at most, came to be called the Hayflick limit. In 1971, Alexey Olovnikov in Moscow speculated that every time a cell divides the telomeres, the DNA tie-strings at the very ends of the chromosomes, get slightly shorter, and this conjecture was fully verified 20 years later by the Canadian-born biochemist Calvin Harley and his colleagues.

Meanwhile, Thomas Kirkwood at Newcastle pointed out that burdening an animal with the genetic resources that might delay ageing is pointless if it is going to die young, because of the hazards of life. There is a trade-off between youthful vigour and provision for later life. Kirkwood called his idea the disposable soma theory, and evidence in its favour accumulated in the decades that followed.

Any update belongs before the closing section that I’ve quoted, because that still represents Hayflick’s opinion and my own.

Today’s update

Long life runs in families, and the genetics began to emerge in 2010. After comparing DNA from more than a thousand centenarians with a similar sample from the general population, Thomas Perls and his and colleagues at Boston University reported that they had found “genetic signatures” of exceptional longevity. These took the form of clusters of misprints in the DNA called “single-nucleotide polymorphisms” or snips, and 90% of centenarians could be grouped into one or another of 19 different clusters. Besides predicting exceptional longevity with 77% accuracy, using 150 snips, the team found variations between the clusters in the onset of age-associated diseases.

About these results from Boston, Kirkwood at Newcastle commented:

They are not suggesting that they can screen the genes of you and me, for example, and tell us the chance we will live to 100. This would be a tall order indeed, given that only a quarter of what determines the length of human life is genetic. … From what we know already, it is rather unlikely that genetic screens will ever be able to forecast how long an individual will live.”

References for the Update

N. Calder, Magic Universe, pp. 423-428, Oxford UP 2003

Perls ref.: Paola Sebastiani et al., “Genetic Signatures of Exceptional Longevity in Humans”, Science Express, 1 July 2010.

Tom Kirkwood, The Independent (London), 2 July 2010

ADDITION 3 July. I really should take the opportunity to put in a brief but more significant update, about the role of telomerase. It also gives me a diagram for the blog, and it reassures me in my lifelong self-imposed task of reporting Nobel-prizewinning discoveries long before the prizes are handed out.


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Freeze and evolve

01/07/2010

Updating The Chilling Stars and Magic Universe

When cosmic rays freeze the world, you’d better evolve

2100 million year-old multicellular fossil found in Gabon. Image: Kaksonen CNRS

Transforming the story of life on the Earth is a report in Nature today about multicellular creatures more than 2 billion years old, at a time when single-celled bacteria supposedly reigned supreme. Fossils you can pick up with your fingers, found in Gabon, West Africa, are far, far older than the multicellular animals that become detectable about 600 million years ago (Ediacaran period) and conspicuous 542 million years in the “Cambrian explosion”. The age is fixed with remarkable precision at 2070 to 2130 million years.

Exterior and interior of a fossil imaged by micro-tomography. Image: El Albani & Mazurier, CNRS

A team of 21 experts from France, Sweden, Denmark, Canada, Germany and Belgium make the report. The lead author is Abderrazak El Albani, at the University of Poitiers, France. He tells Agence France Press that “More than 250 specimens have been found so far. They have different body shapes, and vary in size from one to 12 centimetres.”

What excites me about the discovery is that here was a far-reaching evolutionary response to the rise of oxygen in the Earth’s atmosphere beginning more than 2000 million years ago. It occurred in the aftermath of a planet-wide freeze for which there is a cosmic explanation.

Chapter 6 in The Chilling Stars includes the story of “Snowball Earth” events. Here are some extracts.

In 1986, George Williams and Brian Embleton in Australia used the magnetism in grains of iron oxide dropped from ancient ice to show that they were released within a few degrees of the Equator. A few years later, Joseph Kirschvink of the California Institute of Technology confirmed this result in magnetism associated with other rock formations in Australia produced by ice action, and well dated as 700 million years old. He called it ‘bullet-proof evidence’.

It now seems clear that these extensive, sea-level deposits … were formed by widespread continental glaciers which were within a few degrees of the equator. The data are difficult to interpret in any fashion other than that of a widespread, equatorial glaciation.”

Kirschvink invented the name Snowball Earth for that dire climatic state. You have to visualise ice sheets, glaciers and frozen seas even at the Equator itself. The degree of ocean freezing is still debated. Some investigators imagine vistas of ice a kilometre thick or more, others prefer a ‘slushball’picture with drifting sea ice and icebergs. Either way the impact on life was severe.

Evidence from all the world’s continents unpacks into about three separate snowball episodes in the interval 750 to 580 million years ago. Worms that survived by scavenging the sea-bed detritus evolved the body-plans that made possible the explosion of animal life mentioned in the previous chapter, when the world became reliably warmer again in the Cambrian Period that started 542 million years ago.

Those cold Neo-Proterozoic times, as geologists call them, were not the only occasion of such radical events involving ice and evolution. By the end of the 20th century, geologists had amassed evidence from South Africa, Canada and Finland that confirmed two Snowball Earth episodes between 2,400 and 2,200 million years ago, in Palaeo-Proterozoic times. Our planet was then only half its present age.

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Better Remedy for Jet Lag?

26/06/2010

Updating Magic Universe

A Better Remedy for Jet Lag?

The word from the Max-Planck-Institut für biophysikalische Chemie in Göttingen is that the biological clocks associated with different organs in the body adapt to a new time zone at different rates — but the consequent physiological confusion of jet lag can be reduced, at least in mice, by attending to the adrenal glands, on the kidneys.

Coordinated bioclocks. Image: MPIBPC

A pacemaker in the brain’s hypothalamus, a group of cells called the suprachiasmatic nuclei (SCN), is supposed to synchronize all the other circadian [about a day] clocks. But the adrenal clocks are tasked to prevent over-rapid responses to changes in daylight, for example due to storm clouds. When the researchers either switch off the adrenal clocks or manipulate the synthesis of the hormone corticosterone by the adrenal glands, with the help of the drug metyrapone, the mice adapt more quickly to a new simulated time zone.

Most relevant in Magic Universe is the following passage in the story “Biological clocks: molecular machinery that governs life’s routines”. Read the rest of this entry »


Wisdom of Kilgore Trout

25/06/2010

Predictions Revisited, Updating Magic Universe, and Climate Change: News & Comments

The Wisdom of Kilgore Trout

While checking a reference for yesterday’s posting I came across an epigram concerning human behaviour that I declared, back in 1983, should rank with Einstein’s E=mc2 in physics. I quoted it in 1984 and After, but it really ought to be written on every blackboard in the world.

Who said so? None other than Kilgore Trout, the imaginary science fiction writer invented by the real-life science fiction writer, Kurt Vonnegut. In Breakfast of Champions, Vonnegut re-caps a Trout story called Plague on Wheels.

A space traveller called Kago told the Earthlings about the self-reproducing automobiles on a dying planet named Lingo-Three.

Kago did not know that human beings could be as easily felled by a single idea as by cholera or the bubonic plague. There was no immunity to cuckoo ideas on Earth.” Within a century of Kago’s arrival the Earth was dying too, littered with the shells of automobiles.

Getting an interview with Vonnegut was never easy, but when I managed it my key question was whether Kilgore Trout’s epigram expressed his own opinion. He said, Yes it did.

Before this accidental prompt, I wasn’t going to bother to comment on a paper published this week in the Proceedings of the National Academy of Sciences, no less. Anderegg et al. claim that scientists convinced about man-made global warming are cleverer and better respected, as well as much more numerous, than scientists who are unconvinced.

Now I’ll say that it’s scary but not surprising that the National Academy of Sciences should permit a division of experts into an ingroup and an outgroup, and an evaluation of them by arbitrary tests that have nothing whatever to do with the inherent substance or merit of their research. Unsurprising because it accords with Kilgore Trout’s insight into human behaviour, which has been well verified in psychological experiments.

Alec Nisbett of BBC-TV filmed one experiment called Klee-Kandinsky, executed for real with unsuspecting schoolboys, for our documentary “The Human Conspiracy” (1975).  I also summarize the experiment in Magic Universe, in the story “Altruism and aggression: looking for the origins of those human alternatives”.

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Self-organizing colours of butterflies

17/06/2010

Updating Magic Universe

Self-organizing colours of butterflies

The papilionid Emerald-patched Cattleheart, Parides sesostris. Source: Richard Prum

A multi-disciplinary study at Yale, by evolutionary biologists, physicists and various kinds of engineers, aided by X-ray scattering specialists at the Argonne National Laboratory, has clarified the way in which butterfly wings generate shimmering colours. The wings employ a physical trick of the light that’s more influential than any chemical pigments. The team, led by biologist Richard Prum, has published the findings in this week’s on-line issue of the Proceedings of the National Academy of Sciences.

A gyroid, as visualized by Alan Schoen. Image from NASA

Complex curved assemblies of molecules called gyroids do the trick, by scattering light in distinctive ways that depend on the dimensions of the gyroids, the slant of incoming light, and the angle of view. Digging a little, I find that a mathematician, Alan Schoen, discovered gyroids as possible shapes, long before their biological role was known. In 1970, while at the Electronics Research Center in Cambridge, Massachusetts, Schoen wrote a paper for NASA that began: “A preliminary account of a study of the partitioning of three-dimensional Euclidean space into two interpenetrating labyrinths by intersection-free infinite periodic minimal surfaces …” Key words there are “labyrinths” and “periodic”.

But how does a butterfly, however mathematically astute, set about building its gyroids?  According to Prum and his chums, the outer membrane of a cell in the butterfly’s wing folds into the cell’s interior from above and below to make a double gyroid. Then starchy chitin forms on the outer gyroid to solidify it before the cell dies – leaving the colour-generating crystal form on the surface of the wing.

Here’s the most relevant story in Magic Universe. It’s called “Molecular partners: letting natural processes do the chemist’s work”.

Strasbourg or Strassburg lies in the rift valley between the Vosges and the Schwarzwald, down which the Rhin or Rhein pours. The city is closer to Munich than to Paris, and repeated exchanges of territory between the French and the Germans aggravated an identity problem of the people of Alsace. It was not resolved until, after restoration to France in 1945, Strasbourg became a favoured locale for Europe-wide institutions. But history left the Alsatians better able than most to resist the brain drain to Paris, and to pursue their own ideas, whether with dogs, pottery or science.

As a 28-year-old postdoc in Strasbourg, Jean-Marie Lehn embarked in 1967 on a new kind of chemistry that was destined to become a core theme of 21st-Century research worldwide. It would straddle biology, physics and engineering. As it concerned not individual molecules, made by bonding atoms together, but the looser associations and interactions between two or more molecules, he called the innovation supramolecular chemistry.

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Conundrum about neutrinos

14/06/2010

Updating Magic Universe

A new conundrum about neutrinos

Billions of them are passing through your body right now. With no electric charge and very little mass, neutrinos are the most penetrating of the commonplace particles of the Universe – and the shyest. Detecting them calls for experiments on a monumental scale. To figure out their properties requires immense patience too, and big steps forward are few and far between. But, as announced today at the Neutrino 2010 meeting in Athens, a multinational team is 95% sure that there’s a greater contrast between the masses of different kinds of anti-neutrinos, than between different kinds of neutrinos.

The MINOS far detector in the Soudan Underground Laboratory consists of 486 octagonal steel sheets weighing 6000 tons altogether. Although billions of accelerated particles generate neutrinos every two seconds, the MINOS collaboration records only about 1000 neutrinos per year.

The work’s being done in the MINOS experiment (Main Injector Neutrino Oscillation Search) wherein a beam of muon neutrinos travels below the ground for 735 km, from Fermilab in Illinois to detectors deep in the Soudan mine in Minnesota. On the way, some of the muon neutrinos νμ change their “flavour” to become tau neutrinos ντ or, more rarely, electron neutrinos νe. Ditto for muon anti-neutrinos, when the Main Injector is set to create those instead.

Jenny Thomas of University College London, MINOS co-spokesperson, is quoted as saying:

We do know that a difference of this size in the behaviour of neutrinos and anti-neutrinos could not be explained by current theory. While the neutrinos and anti-neutrinos do behave differently on their journey through the Earth, the Standard Model [of particle physics] predicts the effect is immeasurably small in the MINOS experiment. Clearly, more anti-neutrino running is essential to clarify whether this effect is just due to a statistical fluctuation or the first hint of new physics.

The red dot and uncertainty rings are for anti-neutrinos and the blue curve for neutrinos.

If confirmed, this will be an important update for the story in Magic Universe called “Neutrino oscillations: when ghostly particles play hide-and-seek”. It tells the tale of Raymond Davis’s failure to detect the expected number of neutrinos from solar nuclear reactions, with a pioneering experiment in Homestake Mine in the Black Hills of Dakota. It led to the joky question, “Is the Sun still burning?”.

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Are earthquakes predictable?

09/06/2010

Updating Magic Universe

Are earthquakes predictable? Frankly, no.

News that seven Italian geophysicists may face manslaughter charges for not telling people to leave their homes before last year’s earthquake in L’Aquila brings seismic forecasting into forensic focus. And it prompts me to look again at what I say about it in Magic Universe, to see if it needs updating.

You can read the news here: http://www.lifeinitaly.com/content/prosecutors-probe-experts-who-said-laquila-quake-unlikely

On 31 March 2009, the experts now under investigation said that six months of low-intensity seismic activity in the Abruzzo region did not foretell a major event. At 2.32 am on 6 April a 6.3 magnitude earthquake killed many people in their beds. With a 5.5 aftershock on 7 April, the total death toll was 308.

The most pointed remarks in the news report, from both sides of the argument, are these:

L’Aquila Mayor Massimo Cialente recalled his frustration at receiving no clear reply to his repeated questions and the apparent lack of concern on the part of some present.

“I well remember the words of Enzo Boschi who said, ‘What do you expect? An earthquake in L’Aquila is bound to happen at some point’,” said Cialente, who said he had been angered and worried by the answer.

Boschi is president of Italy’s Istituto Nazionale di Geofisica e Vulcanologia, and what he said was measured and honest. If it ever comes to trial, he and his colleagues can point out that far more deadly earthquakes of recent years weren’t predicted either: 2004 in the Indian Ocean near Sumatra (causing the Boxing Day tsunami), 2005 in Kashmir, 2008 in Sichuan, China, or 2010 in Haiti.

Hiroo Kanamori Photo Caltech

And they can call on expert witnesses from around the world – starting perhaps with my favourite seismologist, Hiroo Kanamori of Caltech. What people call the Richter scale of earthquake magnitudes is really the Kanamori scale nowadays. Thanks to him and his fellow geophysicists world-wide, the causes of earthquakes are well understood. But after decades of intense personal effort, Kanamori concluded in 1997 that the timing of earthquakes is probably impossible to predict.

Here’s a passage that explains his verdict, from the story in Magic Universe called “Earthquakes: Why they may never be accurately predicted, or prevented”.

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