Biocurious

/ a biophysics blog

(Frequency) Double or nothing?

Posted 18 February 2008 by PhilipJ under

Celebrating 50 years of the journal Physical Review Letters, the editors at PRL have begun collecting hightlights of the past 50 years. They’re only a few years into things, but there’s already a paper that caught my eye: Generation of Optical Harmonics by Franken et al., PRL 7, 118 (1961) (link, seemingly freely accessible).

Shortly after the invention of the ruby laser (and before that the maser), it was discovered that a harmonic of the laser’s natural frequency was being emitted from dielectrics when incident beam was sufficiently intense. This has become a commonly used property, in that many of the lasers today (particularly emitting in the green, like YAG lasers) all use frequency doubling to produce visible output, as the diodes naturally output in the near IR.

To find out how it works, I recommend reading the paper, but I suspect you might not be convinced. Here’s why:



No doubled light as far as I can tell! Maybe they didn’t have peer review back in those days.

(I actually suspect it is the manner in which the digital copies were created. I’m going to check the library’s paper copy tomorrow.)

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Biology is harder than physics?

Posted 2 January 2008 by PhilipJ under &

Just before the new year, Rosie Redfield (at RRTeaching) blogged about biology being more difficult than physics. Why?

Biological processes of course are consequences of physics and chemistry, which is why we require our biology students to study the physical sciences. But organisms are also historical entities, and that’s where the complexities arise. The facts of physics and chemistry are constant across time and space. Any one carbon atom is the same as any other, and today’s carbon atoms are the same as those of a billion years ago. But each organism is different. That’s not just a statement that fruit flies are different from house flies. Rather, each fruit fly is different from every other fruit fly alive today, and from every other fruit fly that ever lived, and it’s the differences that make biology both thrilling and hard.

No disagreements from me here. The laws which govern physics and chemistry are contant across the universe (though there is some debate as to their constancy in time). Without the strict adherence to the laws we observe, physics and chemistry would be near impossible to understand. It is lucky for biology that this is how the world works, because, as Rosie notes, biology depends on it!

Skipping ahead, here’s where I get confused:

Even genetically identical cells are not functionally identical. When a cell divides its molecules are randomly distributed between the two daughters; because ‘randomly’ does not mean ‘evenly’, these daughters will have inherited different sets of the proteins and RNAs that carry out their functions. And even if the two cells had identical contents, these contents would still have different interactions – repressors bump into cofactors at different times, DNA polymerase slips or doesn’t slip at different points in its progress along a chromosome. Understanding the how and why of biological phenomena thus requires us to consider historical and ecological factors that are many orders of magnitude more complex than those of physical systems.

When trying to understand biological systems (nay, any kind of system, be it a crystal or a batch of cells), much ultimately depends on the type of measurement. Every measurement does not need to take into account the histories and ecological factors that make up every individual cell – it is impossible to know them to the required resolution that such data would be useful. When and where a DNA polymerase may stall on the chromosome in a particular cell of a mL culture containing billions upon billions of cells is effectively irrelevant for a huge number of interesting experiments I might want to do with those cells — say, the study of expression of a particular gene with a gene chip.

Continuing,

The critical word is probably ‘population’. Biologists rarely try to define it, but they use the term everywhere to refer to similar but not identical organisms or cells (or even molecules) that interact in some way. ‘Population thinking’, the realization that species are populations, not pure types, is said to have been key to Darwin’s insight that members of a species undergo natural selection. And population thinking is probably what makes biology so much more complex than the physical sciences.

Here’s where I think my ultimate displeasure with the post lies. That biology is more complex than physics (though what exactly is limited to the realm of physics is now very much in question) is a reasonable statement: the most common biological molecules are much too complicated to apply something like the Schroedinger Equation and expect to understand anything about them, but “complex” and “difficult” are not the same thing. That physics has traditionally been confined to the well-defined and “simple” systems like infinite lattices of identical carbon atoms, doesn’t make it “easier” to study than biology. I don’t even know what it could mean for one field of science to be “easier” than another, given that everyone studying a science is different, like, as Rosie mentions above, how each fruit fly is different from every other fruit fly. Some people find the mathematics required to understand physical systems extremely difficult, while others don’t have the required attention to detail to perform a successful experiment in a biology lab. To do any kind of science, however, it is the same: you require critical thinking and quantitative analysis of experiments to make any sense of your results. This is true from particle physics all the way up to ecology.

Rosie’s opening paragraph ends with the following:

[I]n reality biology is much more complex than the physical sciences, and understanding it requires more, not less, brain work.

I hope someone in the social sciences gets wind of this and belittles biologists. Sociology is obviously more complex than biology, so it cleary requires more brainpower to be a social scientist than a biologist, right? Rutherford’s famous statement that all science save physics is mere stamp collecting wasn’t a useful thing to say, and this isn’t much better.

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Crayon Physics Deluxe

Posted 19 November 2007 by Andre under

Via Bill Tozier, comes this wondrous looking game (presumably more enjoyable with a tablet PC and stylus than with a mouse):

Both meditative and educational. Check out the creator’s blog here.

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Too Simple for Chemotaxis?

Posted 6 November 2007 by Andre under &

Chemotaxis in biological cells is a relatively complex process that requires a sensing apparatus that talks to a locomotion apparatus. This most famous of movies shows a neutrophil streaming after a bacterium and as you can imagine, there must be some pretty intricate chemistry behind this kind of behaviour:

That’s one of the reasons that scientists haven’t replicated this in an artificial system. Recently though, as you can read in my inaugural physicsworld.com news story, the Ayusman and Velegol groups from Penn State have come up with an alternative:

The team made a large number of tiny metal rods that were 2 µm long. Each rod was gold along one half of its length and platinum along the other. The rods were placed in a dish containing pure water and a piece of gel that contained hydrogen peroxide. The hydrogen peroxide slowly leached from the gel into the water, creating a concentration gradient in the surrounding water.

After about 110 hours, the team noticed that more than 70% of the rods had accumulated next to the gel. According to the researchers, this movement occurred because hydrogen peroxide undergoes different chemical reactions at the gold and platinum ends of the rods. This they say, drives fluid along the rod causing it to move. The particles’ speed increases with the local concentration of hydrogen peroxide and so on average the rods are “attracted” to the gel – a simple realization of chemotaxis.

A movie of the rods swarming towards the gel is available on the Ayusman lab website here.

In a previous paper in JACS, the Ayusman group showed (I think quite convincingly) that the force driving the locomotion is due to the electrochemical decomposition of H2O2 on the platinum surface and the reduction of H2O2 on the gold half resulting in an ion flux that drives fluid along the rods and causes them to move. That’s not the only possibility though. The Golestanian and Jones groups at the University of Sheffield have shown that non-conductive particles half-coated with platinum are also motile in H2O2 suggesting that a simpler mechanism is also possible. For these simpler particles, it seems that the motility is caused by the osmotic pressure that is built up when the H2O2 is broken down (resulting in more numerous products than there were reactants) on one side of the particle only. But you can get that story straight from one of the authors because Richard Jones has his own blog!

A professor of mine once told us that Purcell had shown that nanoswimmers were impossible because “life at low Reynolds number" is so different. It is very different, but he misread Purcell and if swimming bacteria weren’t convincing enough, surely swimming rods are.

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Space Station Science: Play time!

Posted 2 October 2007 by Andre under

Bob Park is no fan of the space station and while it seems that some science is being done there this comes at the expense of other projects:

The House Space Subcommittee told NASA to cover the latest $200M shortfall from existing accounts. But not just any existing accounts; Dana Rohrabacher (R-CA), the Subcommittee chair, told Wilbur Trafton, NASA’s space station chief, that he wants the money taken from Mission to Planet Earth, the environmental monitoring program Rohrabacher hates. NASA has already transferred $462M from space science to keep the space station on schedule.

The total cost of the space station is over $100 billion although it seems difficult to estimate the exact cost. Keep that in mind when enjoying this really neat demonstration:

Playing with bubbles is fun, but the American Physical Society wasn’t (and isn’t) convinced:

It is the view of the Council of the American Physical Society that scientific justification is lacking for a permanently manned space station in earth orbit. We are concerned that the potential contributions of a manned space station to the physical sciences have been greatly overstated and that many of the scientific objectives currently planned for the space station could be accomplished more effectively and at a much lower cost on earth, on unmanned robotic platforms, or on the shuttle.

Biophysics also has a role to play here. It has been claimed that there will be significant advances made in protein crystallography as a result of experiments in microgravity but an NRC study found that

The results so far are inconclusive, and the impact of microgravity crystallization on structural biology as a whole has been extremely limited. At this time, one cannot point to a single case where a space-based crystallization effort was the crucial step in achieving a landmark scientific result.

This is sad. I’ve always been enamored with space exploration and I find Carl Sagan’s arguments about both the allure and necessity of a mature space program for humanity compelling, but so much potential seems to have been squandered on the shuttle program (meant to be a cheaper way of getting stuff into space) and the space station. Now there’s Moon-Mars. What’s going on?

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Pierre-Gilles de Gennes, 1932-2007

Posted 23 May 2007 by PhilipJ under &

I just read (via some complicated series of links that started with the Bourbaphy seminar page) that Pierre-Gilles de Gennes passed away on the 18th.

He was a true giant in the field of soft condensed matter physics, and was the sole person awarded the 1991 Nobel Prize in physics for “discovering that methods developed for studying order phenomena in simple systems can be generalized to more complex forms of matter, in particular to liquid crystals and polymers”.

Le Monde has a nice writeup (for those who can read French), here.

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