Archive for the ‘Biology’ Category

A few interesting pieces from BMC

April 15, 2010

[1] A personal view on autism — you can either watch the video or read the edited transcript.

[2] When and whether to model — in molecular biology

[3] When it comes to scientific publishing, bigger is better?

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Mathematisation of …

March 30, 2010

Sexual attraction; here is the abstract:

Pollen tubes follow attractants secreted by the ovules. In a recent paper in BMC Plant Biology, Stewman and colleagues have quantified the parameters of this attraction and used them to calibrate a mathematical model that reproduces the process and enables predictions on the nature of the female attractant and the mechanisms of the male response.

Here is the last paragraph of the piece:

As with many other mathematical approaches to complex biological behavior, this new model from Stewman et al. [3] raises more questions than answers. But the fact that new approaches are contributing to a precise experimental description of the system [2,11,12] may make mathematical modeling an important tool for testing and selecting candidate molecules that may fit the in vivo biological profile of the final step of plant sexual attraction.

Here are the references in question:

[2] Dresselhaus T, Márton ML: Micropylar pollen tube guidance and burst: adapted from defense mechanisms? Curr Opin Plant Biol 2009, 12:773-780.

[3] Stewman SF, Jones-Rhoades M, Bhimalapuram P, Tchernookov M, Preuss D, Dinner AR: Mechanistic insights from a quantitative analysis of pollen tube guidance.

BMC Plant Biol 2010, 10:32.

[11] Márton M, Dresselhaus T: A comparison of early molecular fertilization mechanisms in animals and flowering plants. Sex Plant Reprod 2008, 21:37-52.

[12] Okuda S, Tsutsui H, Shiina K, Sprunck S, Takeuchi H, Yui R, Kasahara RD, Hamamura Y, Mizukami A, Susaki D, Kawano N, Sakakibara T, Namiki S, Itoh K, Otsuka K, Matsuzaki M, Nozaki H, Kuroiwa T, Nakano A, Kanaoka MM, Dresselhaus T, Sasaki N, Higashiyama T: Defensin-like polypeptide LUREs are pollen tube attractants secreted from synergid cells.

Nature 2009, 458:357-361.

Here is Reference 3. Have fun!

Smoking: in or out?

March 16, 2010

Yesterday in a restaurant in Tokyo, someone at the table next to us lit up a cigarette. I asked my Japanese host if no one ever asked smokers to go outside. His answer took me by surprise: one is not allowed to smoke on the street. Inside is fine, outside is wrong. It’s the opposite of what we are used to in the West.

The point is not so much the reason for the Japanese rule (which is that a walking smoker often holds his or her cigarette at children’s eye level, hence may accidently blind a child – apparently, this has happened!), but the fact that cultural differences often baffle us. This is because we assume our own perspective to be the only one that matters or makes sense. The same applies very much to my field of primatology, which owes much to Japanese pioneers.

Thus begins a piece by Frans de Wall in 3quarksdaily. Link via Swarup.

Have fun!

What can microfluidics do for stem-cell research

February 12, 2010

An interesting Q&A.

Shape of a long leaf

December 30, 2009

An interesting one from H Liang and L Mahadeavan:

Long leaves in terrestrial plants and their submarine counterparts, algal blades, have a typical, saddle-like midsurface and rippled edges. To understand the origin of these morphologies, we dissect leaves and differentially stretch foam ribbons to show that these shapes arise from a simple cause, the elastic relaxation via bending that follows either differential growth (in leaves) or differential stretching past the yield point (in ribbons). We quantify these different modalities in terms of a mathematical model for the shape of an initially flat elastic sheet with lateral gradients in longitudinal growth. By using a combination of scaling concepts, stability analysis, and numerical simulations, we map out the shape space for these growing ribbons and find that as the relative growth strain is increased, a long flat lamina deforms to a saddle shape and/or develops undulations that may lead to strongly localized ripples as the growth strain is localized to the edge of the leaf. Our theory delineates the geometric and growth control parameters that determine the shape space of finite laminae and thus allows for a comparative study of elongated leaf morphology.

Take a look!

Numbers in biology: estimated and measured

December 23, 2009

An interesting paper from the latest PNAS:

A feeling for the numbers in biology

Rob Phillips and Ron Milo

Although the quantitative description of biological systems has been going on for centuries, recent advances in the measurement of phenomena ranging from metabolism to gene expression to signal transduction have resulted in a new emphasis on biological numeracy. This article describes the confluence of two different approaches to biological numbers. First, an impressive array of quantitative measurements make it possible to develop intuition about biological numbers ranging from how many gigatons of atmospheric carbon are fixed every year in the process of photosynthesis to the number of membrane transporters needed to provide sugars to rapidly dividing Escherichia coli cells. As a result of the vast array of such quantitative data, the BioNumbers web site has recently been developed as a repository for biology by the numbers. Second, a complementary and powerful tradition of numerical estimates familiar from the physical sciences and canonized in the so-called “Fermi problems” calls for efforts to estimate key biological quantities on the basis of a few foundational facts and simple ideas from physics and chemistry. In this article, we describe these two approaches and illustrate their synergism in several particularly appealing case studies. These case studies reveal the impact that an emphasis on numbers can have on important biological questions.

Eusocial insects

December 3, 2009

A piece by D Balasubramanian in The Hindu. I am disappointed though that there are no references either to the works of Raghavendra Gadagkar or to his classic Survival strategies.

The broom of Ockham

October 20, 2009

Although it is increasingly difficult to gauge what people can be expected to know, it is probably safe to assume that most readers are familiar with Ockham’s razor – roughly, the principle whereby gratuitous suppositions are shaved from the interpretation of facts – enunciated by a Franciscan monk, William of Ockham, in the fourteenth century. Ockham’s broom is a somewhat more recent conceit, attributable to Sydney Brenner, and embodies the principle whereby inconvenient facts are swept under the carpet in the interests of a clear interpretation of a messy reality. (Or, some – possibly including Sydney Brenner – might say, in order to generate a publishable paper.)

In due course, the edge of the carpet must be lifted and the untidy reality confronted, and in this issue of Journal of Biology we are launching an occasional series of Opinions in which contributors inspect the sweepings and discuss their implications.


Thus begins an editorial of Miranda Robertson in the Journal of Biology
. A nice concept that is worthy of emulation by other journals too!

Quantum coherence and photosynethsis

October 14, 2009

An interesting paper:

Theoretical examination of quantum coherence in a photosynthetic system at physiological temperature

A Ishizaki and G R Fleming

The observation of long-lived electronic coherence in a photosynthetic pigment–protein complex, the Fenna–Matthews–Olson (FMO) complex, is suggestive that quantum coherence might play a significant role in achieving the remarkable efficiency of photosynthetic electronic energy transfer (EET), although the data were acquired at cryogenic temperature [Engel GS, et al. (2007) Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Nature 446:782–786]. In this paper, the spatial and temporal dynamics of EET through the FMO complex at physiological temperature are investigated theoretically. The numerical results reveal that quantum wave-like motion persists for several hundred femtoseconds even at physiological temperature, and suggest that the FMO complex may work as a rectifier for unidirectional energy flow from the peripheral light-harvesting antenna to the reaction center complex by taking advantage of quantum coherence and the energy landscape of pigments tuned by the protein scaffold. A potential role of quantum coherence is to overcome local energetic traps and aid efficient trapping of electronic energy by the pigments facing the reaction center complex.

Here is a commentary on the paper:

Some quantum weirdness in physiology

P G Wolynes

Quantum mechanics seems alien to physiology. Alarm bells go off in our heads when we hear even people of such genius as Sir Roger Penrose (1) invoke the weird coherence of quantum mechanical wave functions to explain biological function. Of course, it is only some of the “weirder” parts of quantum mechanics that bother us. Structural biochemistry is founded on the rigid geometrical relationships involved in chemical bonding that arise from quantum mechanics; the α-helix could only have been discovered by Pauling by acknowledging the power of quantum mechanical resonance to flatten the peptide bonding unit (2). Nevertheless, most modern biomolecular scientists view quantum mechanics much as deists view their God; it merely sets the stage for action and then classically understandable, largely deterministic, pictures take over. In this issue of PNAS Ishizaki and Fleming (3), by combining experimental and theoretical investigations, demonstrate that quantum coherence effects play a big role in light energy transport in photosynthetic green sulfur bacteria under physiological conditions. Quantum coherence allows a nonclassical simultaneous exploration of many paths of energy flow through the many chromophores of a light-harvesting complex, thereby significantly increasing the efficiency of the energy capture process, presumably helping the bacteria to survive in low light.

World´s foremost expert on R Marginata

July 2, 2009

Prof. Gadagkar gets profiled at PNAS! The same issue also carries the inaugural piece by Prof. Gadagkar. Have fun!