A green Christmas

My university is making a big push for the environment, with an environmental studies curriculum being added, an ongoing effort for energy independence with wind and biomass power, and conservation in the construction of a new green dorm, so this holiday project for everyone is particularly appropriate: apply sustainable building design practices to a gingerbread house. Get to work, you’ve got until 31 December to submit photos.

I’m thinking we need to take all that sugar and convert it to alcohol…

Never trust a creationist ellipsis — Hector Avalos on the Gonzalez emails

Hector Avalos sent me his response to the Discovery Institute’s ‘shocking’ revelation that people had been discussing Guillermo Gonzalez’s affiliation with Intelligent Design creationism before they denied him tenure. It’s a classic pointless objection: of course they were, and of course his openly expressed, unscientific beliefs which were stated as a representative of ISU were a serious consideration. It does not speak well of the Discovery Institute that they had to cobble together quote-mines from the email to try and make a non-case for a non-issue.

[Read more…]

Very pretty, but fundamentally wrong

This exercise in false equivalence, Duelity, is beautifully animated but promotes a poor idea. It’s basically two videos, one telling the Christian creation myth inaccurately and in the style of a scientific explanation, and another that inaccurately summarizes the evolution story as if it were holy writ. There’s a pretense that these are equally valid descriptions of the history of the world that is completely wrong, and that amplifies the errors throughout the individual stories from mere irritations to dishonest propaganda.

The comments there are largely positive. All I can assume from that is that a lot of people are easily swayed by good production values.

I hope it’s not a metaphor for the current situation

I have to consider this a rather dispiriting story:

In 1818, a whale oil dealer refused to pay a fish-product fine on whale oil, because a whale isn’t a fish. The inspector insisted on the tax, and a spirited court and public battle played out.

It’s dispiriting because you’d think the weight of scientific evidence (and if you prefer it, the testimony of no less an authority than Aristotle) would have settled this case easily, but no…the whale lost and was declared a fish.

Circadian Clock Neurons

Here’s another interesting question from our most recent neurobiology exam. With some luck PZ won’t get irritated that I keep recycling my work. This paper was a bit of a brain thumper but also very interesting after deciphering what it’s talking about.

3) Summarize this paper and describe both the neural circuit and the genes underlying this particular rhythm.
Stoleru D, Peng Y, Agosta J, Rosbash M (2004). Coupled oscillators control morning
and evening locomotor behavior of Drosophila. Nature 431:862-868

The roughly one hundred bilaterally arranged circadian clock neurons in adult fly brains occur in six groups: dorsal neurons (DN1, DN2, DN3), dorsal lateral neurons (LNdS), and the PDF neuropeptide expressing small and large ventral lateral neurons (LNvS). Extirpation via proapoptotic genes was used to assess that D.melanogaster lacking LNvS in natural light/dark conditions displayed little change however in continuously dark environments yield arrhythmicity. Time intervals in the light/dark experiment were determined using Zeitgeber time in which lights on (sunrise) corresponds with ZT0 and lights off (sunset) corresponds with ZT12. Although the two LNvS cell groups have an imperative role in rhythmic gene expression, neurons expressing circadian photoreceptor cyrptochrome (cry) genes were also found to assist rhythmicity in natural light/dark conditions.

Green fluorescent protein reporter was used to stain the six clock neuron groups, determining that the cry-GAL4 driver, which facilitates cry gene expression, is present in all dorsal and ventral lateral neurons (LNdS and LNvS) and in two dorsal neurons (DN1). The proapoptotic gene hid was used to excise the cry gene in LNdS and LNvS generating cry-GAL4;UAS-hid flies that were arrhythmic in both natural light/dark and continuously dark environments. The dorsal neuron groups (DN1, DN2, DN3) are mostly unaffected by hid expression meaning that because cry-GAL4;UAS-hid flies are arrhythmic in both environments, these neuron groups are incapable of maintaining circadian rhythms independently.

Crossing D.melanogaster exhibiting the Pdf-GAL80 gene, which represses GAL4-mediated transcriptional activity, with flies exhibiting green fluorescent protein in circadian neuron groups via Pdf-GAL4 and cry-GAL4 drivers yielded flies without green fluorescent protein. This means that the cry and Pdf promotors, segments of DNA that control gene expression, coupled with GAL80 genes override and prevent their corresponding GAL4 drivers from transcribing. With the crossing of cry-GAL4 driver and Pdf-GAL80 repressor, and other mixed crosses, green fluorescent protein was observed only in some circadian neuron groups.

Crossing Pdf-GAL80 with cry-GAL4;UAS-hid allowed researchers to determine the effects of extirpating PDF+, CRY+PDF-, and CRY+ neurons on D.melonogaster circadian rhythm. They found that flies extirpated of CRY+ neurons were phenotypically arrhythmic and flies extirpated of PDF+ neurons had diminished morning lights-on anticipation with normal evening lights-off anticipation. Flies extirpated of CRY+PDF- had diminished evening lights-off anticipation and normal morning lights-on anticipation. These flies maintained a circadian rhythm in continuous darkness indistinguishable from wild type flies based unimodally on the morning oscillator. The phenotypes of these three strains of D.melonogaster are not affected by whether the environment is light and dark or continuously dark meaning that the oscillators are not driven by light. Using deductive logic, the researchers concluded that PDF+ neurons correspond to lights-on behavior and oscillate independently of CRY+PDF- neurons, which correspond to lights-off behavior.

Green fluorescent protein techniques for visualizing neurons confirm that the CRY+PDF- and PDF+ oscillators are coupled through PDF- axonal processes that protrude from the LNd neuron group into the LNv region. Immunostaining visualization techniques reveal that PDF neuropeptide travels in the opposite direction that the PDF- axons extend, that is, from the LNv to LNd neuron group. PDF neuropeptides function to coordinate the lights-on anticipation behaviors in the morning with the independently oscillating lights-off anticipation behaviors in the evening.

References:
Stoleru D, Peng Y, Agosta J, Rosbash M (2004). Coupled oscillators control morning
and evening locomotor behavior of Drosophila. Nature 431:862-868

Great glowing spiders

Blogging on Peer-Reviewed Research

I’ve known that scorpions have fluorescent cuticles — if you go out into the desert with a black light and shine it on the ground, the scorpions will often glow green and blue and be easy to spot. I had no idea that many spiders exhibit the same phenomenon, but there they are, glowing away. I may have to visit my local head shop (in Morris? Hah!) and get some black light bulbs to see what the fauna in my living room is up to.

Fluorescence is actually a fairly common property: all it requires is a molecule called a fluorophore that can absorb and capture transiently photons of a particular wavelength, or energy, and release them at a lower energy. What this means is that a fluorescent substance absorbs light at one range of wavelengths, and then re-emits those photons at a longer wavelength; there is a color shift. In the case of black light posters and spiders and scorpions, they are absorbing light at wavelengths our eyes can’t detect (wavelengths below about 400nm, or ultraviolet light) and shifting it to a wavelength we can see, for instance to a nice blue at 450nm, cyan at around 500nm, or green at about 550nm. So to test this, all you need is a dark room, a spider, and a light source that glows at the wavelength that is absorbed by the fluorophore, and a detector (like, say, your eyes) that can collect light at the emission wavelength.

[Read more…]