Archive for September 16th, 2008

The Giant’s Shoulders: third edition

September 16, 2008

This is, by far, the smallest Giant’s Shoulders blog carnival; and, I hope it will remain so in future too. The next edition of the carnival will be hosted by Doctor Silence at second order approximation on October 15, 2008. So, have fun with this one and be ready with your entries for the next one!

[1] 350 BC Aristotle on mayfly

John Wilkins at Evolving thoughts decides to read a bit of Aristotle and evaluate his writings, with specific reference to mayfly:

At any rate, the more I read Aristotle, and the more I understand both where things stood at his time and what he actually said, I find him to be an amazing natural historian, a good observer, and generally not a bad theoretician. Sure, his theories are wrong, and his overall philosophy of teleology in biological cases (not, I hasten to add, in his physics) is unnecessary now we have teleosemantic explanations (i.e., natural selection), but he is not the moron of popular history of biology; far from it.

Funnily enough, the EMBOR author of the canard, Katrin Weigmann, is trying to make the case that science is not infallible, while ignoring the very real actual achievements of the people she denigrates. Nobody thought science was infallible anyway, but trying to make out that errors were made where they weren’t doesn’t give one much confidence in any subsequent argument. And of course this is another case of scientists doing bad history for [scientific] political reasons.

[2] 1817 Defining Parkison’s disease

Scicurious at Neurotopia writes about a classic monograph by Parkinson on shaking  palsy:

I definitely recommend Parkinson’s monograph, partially because it’s always interesting to read the old lit, and also because his case descriptions are incredibly vivid and empathetic. Although his methods of treatment probably brought little real cure, he was a compassionate physician and a brilliant man of his time, who put together all the dots to define what we now call Parkinson’s Disease.

[3] 1958/59 Modelling spinodal decomposition

I write about a series of papers that laid the foundation for the Cahn-Hilliard equation for the study of microstructural evolution:

In a series of papers published in The Journal of Chemical Physics, Cahn and Hilliard (and Cahn, by himself) provide the context as well as formulation of the CH equation; the first of these papers, published by Cahn and Hilliard in 1958 [1] discusses the formulation of the free energy which takes into account the interfacial energies that result from composition gradients; the second, published by Cahn in 1959 [2] discusses the thermodynamic basis behind the free eenergy formulation; the third, published by Cahn and Hilliard in 1959 [3], the formulated free energy is used to study phase separation in immiscible liquid mixtures. In a paper published in Acta Metallurgica in 1961 [4], Cahn discusses the study of spinodal decomposition in solids (including the elastic stress effects due to the lattice parameter differences between the two phases). These four papers (sometimes along with another by Cahn and Allen [5] — which is a classic by itself and deserves a separate post for one of the future Giants’ shoulders carnival) forms the theoretical basis for almost all the diffuse interface studies on microstructural evolution in the metallurgical and materials science literature.

[4] 1963 Interference between different photons

Skullsinthestars writes about a clever and simple experiment that proved one of the most famous statements concerning the quantum mechanics of photons wrong:

One of the most famous statements concerning quantum mechanics, as it relates to the light particles known as photons, was made by the brilliant scientist Paul Dirac in his Quantum Mechanics book:

“each photon then interferes only with itself.  Interference between different photons never occurs.”

This statement is bold and unambiguous: in Dirac’s view, a photon only creates interference patterns by virtue of its own wave function, and wave functions of different photons do not interact.

The statement is bold, unambiguous, often quoted — and wrong!  In 1963, Leonard Mandel and G. Magyar of Imperial College disproved this statement with a clever and simple experiment and a two-page paper in Nature.

[5] 1973 Beginnings of Genetic Engineering

Evilutionary biologist writes about a classic which started the field of genetic engineering:

Cohen had previously determined how to make E. coli take in foreign DNA (a citation classic worthy feat in itself) when he transformed E. coli with a plasmid known as pSC101, that conferred resistance to the antibiotic tetracycline.

Boyer on the other hand had discovered EcoRI, a restriction enzyme that could snip open pSC101 while leaving “sticky ends“.

Like chocolate and peanut butter, the combination was unbeatable. Cohen and Boyer realized they could combine their techniques to create a new plasmid containing foreign DNA.

[6] 1977 Categorizing fundamental types of living beings

Epicanis at the Big room (and the little things in it) writes about a paper that forms the basis of the modern classification of fundamental types of living beings — the three groups in the phylogenetic tree of life:

The “plant” and “animal” distinction is pretty classic – until comparatively recently, bacteria were assumed to be “plants”, just as fungi (”plants” that lacked chlorophyll) were. Non-photosynthetic bacteria were referred to as “schizomycetes” (literally “fission” [splitting in two] fungi, because they reproduce by splitting from one cell into two rather than forming spores), while bacteria with chlorophyll (cyanobacteria or “blue-green” algae, and possibly the “green sulfur bacteria”) were designated “schizophyta” (”fission plants”).

Within the last fifty years or so, though, it’s become obvious that bacteria were a different type of life from fungi, chlorophyll-containing plants, or animals. The latter critters have cells that in turn contain “organelles”, which are more or less very specialized “mini-cells” within themselves. The nucleus, for example, is a compartment within the cell where the cell’s DNA is kept and processed. Bacteria, it turned out, don’t have any of these organelles (in fact there’s good evidence that at least some if not all organelles used to be bacteria, but this post’s long enough already so I won’t go into that), and life was re-organized into the bacterial “prokaryotes” (”before nucleus”) and the “eukaryotes” (having a “true nucleus” – i.e. everything that isn’t bacteria).

From this paper we get the the modern fundamental three groups we still use today: Eukaryotes, Eubacteria [“True” bacteria], and the Archaea (or “Archaebacteria” as this paper names it). The name comes from the idea that the environment in which methanogens thrives resembles what has often been assumed to be the atmosphere of the very early Earth.

Happy reading!