my blog on stuff I like

The Igs

2005-10-09T19:01:00.000-07:00

The 2005 Ig Nobel prizes were awarded on th 6th of October in a ceremony at Harvard University. There were some pure gold winners, my favorite was for Literature.

The Internet entrepreneurs of Nigeria, for creating and then using e-mail to distribute a bold series of short stories, thus introducing millions of readers to a cast of rich characters -- General Sani Abacha, Mrs. Mariam Sanni Abacha, Barrister Jon A Mbeki Esq., and others -- each of whom requires just a small amount of expense money so as to obtain access to the great wealth to which they are entitled and which they would like to share with the kind person who assists them.

There were a few Australian winners, such as for physics, showing that pitch really does drip:

John Mainstone and the late Thomas Parnell of the University of Queensland, Australia, for patiently conducting an experiment that began in the year 1927 -- in which a glob of congealed black tar has been slowly, slowly dripping through a funnel, at a rate of approximately one drop every nine years.
REFERENCE: "The Pitch Drop Experiment," R. Edgeworth, B.J. Dalton and T. Parnell, European Journal of Physics, 1984, pp. 198-200.

...and for Biology, showing that frog odours repel mozzies:

Benjamin Smith of the University of Adelaide, Australia and the University of Toronto, Canada and the Firmenich perfume company, Geneva, Switzerland, and ChemComm Enterprises, Archamps, France; Craig Williams of James Cook University and the University of South Australia; Michael Tyler of the University of Adelaide; Brian Williams of the University of Adelaide; and Yoji Hayasaka of the Australian Wine Research Institute; for painstakingly smelling and cataloging the peculiar odors produced by 131 different species of frogs when the frogs were feeling stressed.
REFERENCE: "A Survey of Frog Odorous Secretions, Their Possible Functions and Phylogenetic Significance," Benjamin P.C. Smith, Craig R. Williams, Michael J. Tyler, and Brian D. Williams, Applied Herpetology, vol. 2, no. 1-2, February 1, 2004, pp. 47-82.
REFERENCE: "Chemical and Olfactory Characterization of Odorous Compounds and Their Precursors in the Parotoid Gland Secretion of the Green Tree Frog, Litoria caerulea," Benjamin P.C. Smith, Michael J. Tyler, Brian D. Williams, and Yoji Hayasaka, Journal of Chemical Ecology, vol. 29, no. 9, September 2003.

Unfortunately the kiwis were given an award, probably out of sympathy, for 'Agricultural History':

James Watson of Massey University, New Zealand, for his scholarly study, "The Significance of Mr. Richard Buckley’s Exploding Trousers."
REFERENCE: "The Significance of Mr. Richard Buckley’s Exploding Trousers: Reflections on an Aspect of Technological Change in New Zealand Dairy-Farming between the World Wars," James Watson, Agricultural History, vol. 78, no. 3, Summer 2004, pp. 346-60.

I thought the Economics award was hilarious too, bringing cartoons to life:

Gauri Nanda of the Massachusetts Institute of Technology, for inventing an alarm clock that runs away and hides, repeatedly, thus ensuring that people DO get out of bed, and thus theoretically adding many productive hours to the workday.

Almost matching the longevity of the pitch experiment, and showing the kind of commitment to science that borders on the insane, was a Japanese guy who photographed every meal he ate for the last 34 years:

Dr. Yoshiro Nakamats of Tokyo, Japan, for photographing and retrospectively analyzing every meal he has consumed during a period of 34 years (and counting).

No, wait that guy is really just crazy.

There was some controversy that ElBaradei won the Nobel peace prize, but the Ig Nobel Peace prize didn't even make sense. Maybe that's part of the wacky zanyness of it all.

Claire Rind and Peter Simmons of Newcastle University, in the U.K., for electrically monitoring the activity of a brain cell in a locust while that locust was watching selected highlights from the movie "Star Wars."
REFERENCE: "Orthopteran DCMD Neuron: A Reevaluation of Responses to Moving Objects. I. Selective Responses to Approaching Objects," F.C. Rind and P.J. Simmons, Journal of Neurophysiology, vol. 68, no. 5, November 1992, pp. 1654-66.

How would you like to have your genitals removed? Think about how dogs feel. This guy did:

Gregg A. Miller of Oak Grove, Missouri, for inventing Neuticles -- artificial replacement testicles for dogs, which are available in three sizes, and three degrees of firmness.
REFERENCES: US Patent #5868140, and the book Going Going NUTS!, by Gregg A. Miller, PublishAmerica, 2004, ISBN 1413753167.

I'd just like to get the large ones fitted to a Chihuahua, 'it's not the size of the dog in the fight, it's the size of the..' Yeah.

And finally, two pieces of research that both could fit into fluid dynamics, the first is funny:

Edward Cussler of the University of Minnesota and Brian Gettelfinger of the University of Minnesota and the University of Wisconsin, for conducting a careful experiment to settle the longstanding scientific question: can people swim faster in syrup or in water?
REFERENCE: "Will Humans Swim Faster or Slower in Syrup?" American Institute of Chemical Engineers Journal, Brian Gettelfinger and E. L. Cussler, vol. 50, no. 11, October 2004, pp. 2646-7.

The second is just disturbing:

Victor Benno Meyer-Rochow of International University Bremen, Germany and the University of Oulu , Finland; and Jozsef Gal of Loránd Eötvös University, Hungary, for using basic principles of physics to calculate the pressure that builds up inside a penguin, as detailed in their report "Pressures Produced When Penguins Pooh -- Calculations on Avian Defaecation."
PUBLISHED IN: Polar Biology, vol. 27, 2003, pp. 56-8.

'He's always being stupid'

2005-10-03T16:04:00.000-07:00

This years Nobel prize for Physiology or Medicine has been given to Barry Marshall and Robin Warren, for figuring out that the bacteria Helicobacter pylori was responsible for many stomach ulcers (link). Warren found the bacteria in the stomach of many people who had ulcers. In order to test whether the bacteria caused the disease, Marshall swallowed the bacteria, and duly suffered gastritis. The Times reports that his wife says,

That’s a very Barry thing to have done... He’s always being stupid, bad jokes, puns, that sort of thing.

Potholes on the highway of the brain

2005-09-19T14:17:00.000-07:00

A few weeks ago a neurobiologist was talking to me about a former student of his that was doing a project on microtubules. Microtubules are large structural proteins made up of tubulin subunits. They form a spiderweb-like network in cells, and proteins can be transported along it by another protein called kinesin. Molecular Biology of the Cell videos of microtubules. One example is the transport of neurotransmitters along the axons of neurons. The stability of neurons means that these proteins can stay in place for years. Consequently, there can be degradation of the protein over this time. This guy was studying how sugars reacted with the protein over long periods of time and how it affected the microtubules.

A press release for another project on Science Daily shows why this might be important.

Microtubules are hollow cylinders made up of polymers of the protein tubulin. Agents that break up, or depolymerize, microtubules disrupt the railway, stop the traffic and reduce the number of cargoes that get delivered to the neuronal surface. Defects in neuronal transport are involved in many neurological diseases.
-Eunice Yuen

The research indicated that the serotonin receptor signals the cell to depolymerise microtubules. This results in the glutamate receptor not being transported to the cell surface by these microtubules. As glutamate is involved in memory and learning the hypothesis is that dysfunction in the regulation of the glutamate receptor by serotonin could lead to mental disorders.

Bacterial speech surprisingly sophisticated

2005-09-18T19:21:00.000-07:00

Picture: My messy interpretation of the PQS molecule embedded in a vesicle.

The bacteria Pseudomonas aeruginosa communicates to others of its species by releasing small molecules that the others can detect. When there are many of the species in the same area, the concentration of these molecules increases. This increase acts as a signal to turn on genes involved in transfering DNA, bioluminescence, producing pigments and infecting animals and plants.

One of these is called the Pseudomonas Quinolone Signal (PQS), which is a small hydrophobic molecule. Because it isn't very soluble in water it doesn't diffuse well, and it is also broken down by other bacteria. The bacteria solves this problem by using vesicles that were known to carry toxins to attack other cells. The PQS molecules nestle in the membrane of the vesicles and are carried to other cells.

PQS also seems to cause the formation of these vesicles. It diffuses into a membrane, such as a cell membrane, and destablises it. The membrane then rolls into little balls that form the vesicle. The vesicles probably also contain the toxins that attack other cells. Since Pseudomonas is a opportunistic human pathogen blocking the formation of the vesicles could be a means to prevent the bacteria from invading and attacking our cells.

Mashburn, L. M. & Whiteley, M. Nature 437, 422–425 (2005).

New rocks for molecular clocks

2005-09-18T16:31:00.000-07:00

In the sixties Linus Pauling and Emile Zuckerkandl noticed that hemoglobin amino acid sequences varied in a way that was proportional to the divergence of species. So they figured that such differences could be used to as a kind of clock to tell how long ago that two protein sequences diverged. The technique was gradually developed by other people over time, and is now most often applied to DNA sequences. In order to calibrate the clock, corresponding sequences of two species for which the date of divergence is known from the fossil record are compared.

A recent BioEssay paper argues that the commonly used calibration date, where mammals and birds diverged, is not known with enough certainty to be used, because:

(a) there are not enough fossil localities from the early Late Carboniferous that predate the earliest known evidence of the split,
(b) the same is true for the number of fossil localities immediately after the first appearance of amniotes and
(c) there are still several long ghost lineages in the phylogeny of early amniotes and their sister taxa. Thus, the fossil record simply does not have the required resolution for bracketing with confidence the evolutionary event associated with the mammal-bird split, as there is currently no closely related fossil taxon that provides a reasonable maximum age.

They also feel that multiple dates should be used, and have selected four dates for calibrating the molecular clocks:

Lungfish-Tetrapods 419-408 Ma
Bird-Lizard 257-252 Ma
Crocodile-Bird 251-243 Ma
Alligator-Caiman 71-66 Ma

The main problem, which they admit, is that the primary reason why the mammal-bird split is used is because of the large amount of genetic data that is available for birds and mammals. Until genomic sequence data is available for representatives of the different phylogenic groups, the scheme will be difficult to use. Once that data is available it will be interesting to see whether the new data causes any changes to the family tree.

Miller, J. & Reisz, R. BioEssays. 27:1069-1075. (2005)

End is nigher than ever

2005-09-16T12:57:00.000-07:00

The number of tropical cyclones in categories 4 and 5 (the highest two categories) has steadily increased over the last thirty years, the number per five year period doubling in that time. The number of storms and their duration also increased, but I personally didn't find these data as convincing. Whether this is linked to increasing global temperatures is a matter of speculation, and it may be part of a longer term oscillation. In any event, it looks the like the End Is Nigh placard business is set for some solid growth.

Webster, P.J., et al. Science. 309, 1844. (2005)

The price of life

2005-09-16T10:16:00.000-07:00

Science republished an interesting article by Kurosu et al. that showed a relationship between lifespan and fertility.

The Klotho protein was discovered in mice that appeared to age rapidly. A mutation that inactivated Klotho was to blame. Small variations in the human version of the gene are known to affect lifespan, and the risks of heart disease, osteoporosis and stroke. In the study mice were created that over-expressed the Klotho protein to determine whether more of the protein would have the opposite effect, causing them to live longer. The transgenic mice lived about 20% longer than wildtype controls. They ate much the same amount as the controls and were similar in bodyweight. The big difference was in the number of offspring produced, the wildtype producing nearly fifty pups per pair per year, the transgenics producing about thirty. From the paper:

As expected from the evolutionary theory of longevity, maximum fitness of the organism is a trade-off between life span and fertility. These data indicate that Klotho systemically modulates aging through mechanisms independent of food intake and growth, but potentially in association with reproduction.

I think it would be interesting to see whether the expression of this gene is affected by the environment.

Kurosu, H., et al. Science. 309, 5742 (2005)

Without your flaws, you'd be unable to resist yourself

2005-09-14T12:31:00.000-07:00

Theoretical modelling of the immune system predicts that if it were more effective at binding to pathogenic epitopes it would also be also more effective at binding to self epitopes, and would probably lead to a greater incidence of autoimmune disease. With theoretical modelling, the devil will be in the details, so it will be interesting to see if this gets accepted by those in the know.

Link

This is not a trip

2005-09-14T12:02:00.000-07:00

Here's some more on how people are using ants as inspiration.

No one else has really built a thousand robots on a millimetre scale that can do something useful and interesting and [are] fully autonomous.
-Lynne Parker

No, I guess they haven't.

Sun may shine on blue sky drug

2005-09-13T22:42:00.001-07:00

Sunlight leads to cancers, the high energy UV wavelengths being absorbed by DNA to cause mutations that then lead to a breakdown in cell regulation. One of the main muations is the formation of thymine-thymine dimers, where one thymine absorbs a photon and is promoted to a high energy state that allows it to react with an adjacent thymine.

Photolyase is an enzyme that repairs this damage. Unfortunately placental mammals don't have the enzyme, it was lost some time in the past, so we are more vulnerable to UV light.

The enzyme is interesting because of the way it repairs the damaged DNA. It binds to the thymine dimer, then absorbs a photon in the visible spectrum, which provides the energy to break the dimer apart by donating an electron, which is returned to the enzyme after the reaction. Some of research on the pysical process has been done by this group. One of the recent finding was that the DNA melts to allow the dimer to be exposed to the photolyase enzyme.

The new news though is that water regulates the time the electron spends within the dimer, which prevents the electron flowing back into the enzyme until after the catalysis has been performed.

Alot of the research is motivated by the interesting electronic mechnism of the enzyme, but there's also interest in producing a drug that could repair UV damage to DNA (JACS paper, pdf). It could be a lucrative product, as skin cancer can be a major killer.

Space ants conquer NASA

2005-09-12T22:59:00.000-07:00

I've been interested in ant behaviour for a few years, just a casual interest. Ants are clever little guys, at least collectively. They can organise themselves to do all kinds of tasks and build complex little nests. This organisation is built on each ant interacting with other ants, with very little in the way of a hierachy. It's sort of similar to how cells work to create a multicellular organism, in some ways. How they do this has been studied fairly intensely for a while now, the idea that it will give us ideas on how to develop similar systems, say with nanorobots or whatever.

New Scientist is reporting how one of those ideas has been to use this kind of system on spacecraft so that each part can do a variety of tasks. If one part gets damaged then the other parts will be capable of repairing it. NASA and CSIRO are developing one of these systems to make a kind of skin. Ageless Aerospace Vehicle concept demonstrator at CSIRO The test system at the moment seems to be designed to simply determine the location of a impact on the surface of a series of plates. Each plate has sensors attached to a PC, and communicates only with surrounding plates, like ants communicate with each other. The benefit of this system is that if one part of the skin is hit, the little computers in all the other sections can operate without it. This prevents a single hit resulting in catastrophic failure.

This is more highly developed by the folks doing the software for the system. From that site:

Single cells may make fast and automatic responses to sudden damage, while collections of cells may solve more complex tasks. For example, they may form impact boundaries that enclose the damaged areas - analogous to the initial clotting of a wound on a mammal. It is highly desirable that such boundaries form a continuously connected closed contour, and are robust to fluctuations caused by proximity to the impact.

Another important task is the formation of a flexible network (a minimum spanning tree) connecting cells that detected impacts. The obtained impact networks can facilitate fast inspections of impact areas, identification of high densities of impacts (e.g., meteor shower), and routing of repair resources.

It's fascinating stuff.

How many parents do you have?

2005-09-09T19:02:00.000-07:00

There's been a bit of controversy in the UK over removing a ban on the 'three parent embryo' (Link). It led to this comment:

The HFEA are relentlessly imposing their libertarian agenda on the people of this country against their wishes: the government must act to disband it immediately.
-Matthew O'Gorman, from the charity LIFE.

I think it is a little strange to say that a government body is imposing a lack of regulation on you.

Anyway, the process involves removing the pronucleus of a zygote and placing it in an egg produced by another woman. So the nucleic material is contributed by one woman and a man and the rest is contributed by a second woman. This means that the mitochondrial DNA is inherited from the second woman. This is important if the mitochondrial genome of the first woman contains a genetic disease.

A previous technique was the 'mitochondrial transplant' (Link). Here the mitochondria from a second woman are placed in the zygote, along with the the first mothers mitochondria. The link reported that this results in 'heteroplasmy', where both donor and recipient mitochondrial DNA is present in the child. Obviously if the recipient mtDNA has some disease it would be preferred if this wasn't carried by the children.

Much-maligned methane made by ancient Amazonian agriculturists

2005-09-09T05:28:00.000-07:00

You hear alot about anthropogenic carbon leading to global warming these days, but it seems that people in past were doing it too. An analysis of methane in antarctic ice cores found that twice as much methane was produced from burning biomass between 1000 and 2000 years ago than had been estimated. The researchers pin the blame on people burning forests such as the Amazon.

Link

"Liquid magnets"

2005-09-09T02:27:00.000-07:00

The material is nickel gallium sulphide (NiGa2S4), and it appears to be a "liquid magnet" when at very low temperatures link. What liquid means here is that the magnetic spins of the electrons in the crystal are not aligned as in a normal crystalline magnetic material, instead they are moving around all over the place, producing no net magnetic force.

Picture courtesy of S. Nakatsuji et al., Science, 9/9/2005

Noggin still loggin' changes

2005-09-09T01:28:00.000-07:00

A recent paper indicates that the brain has undergone genetic changes during the history of modern humans. The researchers worked on two genes that cause microcephalopathy when inactivated by mutation, and tracked polymorphisms of each gene in study groups. They found that, for each gene, a particular goup of polymorphisms had been positively selected for. The actual function of the genes isn't known with certainty, and the authors are keen to avoid any ubermensch talk.

Link