Monthly Archive: April 2013

Apr 25

Lacklustre butterworts

Pinguicula agnata [CC-BY-SA-3.0 Steve Cook]

I’d like to be more excited about this than I am, but Pinguicula agnata is not the most crowd-pleasing of my butterworts, even whilst in flower (as it currently is). Ho hum. Strange specific epithet though. No idea why Casper (whoever s/he might have been) thought it appropriate. Could be worse though, I guess.

Apr 23

Metabolic pathways don’t really have end products

Metabolic pathways [CC-BY-SA-3.0 Zephyris from w]

The end product of glycolysis is pyruvate This, and equivalent statements about other metabolic pathways: The products of Krebs cycle are ATP/GTP, NADH and carbon dioxide are not exactly wrong, but they are easily over-interpreted in a way that leads to misunderstanding. They are also  easily swallowed as explanations without considering quite what ‘end product’ …

Continue reading »

Apr 17

Organism of the week #12 – Preying mantis

This is mostly just to see if I can get embedded video to work. Mantis religiosa… Om nomnomnom. Explain again why I need to install a plug-in to get WordPress to embed video from its own local media library?

Apr 14

Down amongst the butterworts

I lived within 30 minutes’ drive of Charles Darwin’s house for the whole of my childhood. It’s been open to the public since it was acquired by English Heritage in 1998. I’ve been a biologist of sorts for about 18 years. It’s taken me until today to actually visit Down House, and to wander down …

Continue reading »

Apr 12

Moose objects and roles

Mr Moose’s Newfangled Object Framework Creating objects from scratch by hand-rolling them is somewhat fragile, and you end up drowning in the writing of endless boilerplate accessor methods. I would strongly suggest that rather than doing objects the hard way, you use the Moose object framework unless there’s some particular constraint (speed, memory footprint) on …

Continue reading »

Apr 10

The kraken wakes

Pinguicula cv. Tina (awakening) [CC-BY-SA-3.0 Steve Cook]

My butterworts have been waiting with unbated breath for the long, slow arrival of the spring. In winter, they cut their losses and produce small non-carnivorous leaves as there’s not enough prey around to justify investment in glue. In spring, they awaken and start making larger, insecticidal leaves again. Tina has already captured a fungus …

Continue reading »

Apr 09

Enzymes don’t necessarily increase the rate at which products are formed

An enzyme increases the rate of product formation What happens if you add the enzyme malate dehydrogenase to a mixture of of its substrates NAD and malate (both at 1 mM for the sake of argument)? A brief look on BRENDA indicates that the reaction malate dehydrogenase catalyses is: malate + NAD → oxaloacetate + …

Continue reading »

Apr 09

The product of succinate dehydrogenase is ubiquinol not reduced flavin

Succinate dehydrogenase [CC-BY-SA-3.0 Steve Cook, based on PDB 1NEK: Yankovskaya, V., Horsefield, R., Tornroth, S., Luna-Chavez, C., Miyoshi, H., Leger, C., Byrne, B., Cecchini, G., Iwata, S. (2003) Architecture of succinate dehydrogenase and reactive oxygen species generation. Science 299:700-704 doi: 10.1126/science.1079605]

Succinate dehydrogenase (SDH) produces reduced flavin (FADH2) as a product This misconception is so widespread, even the exam boards get it wrong. Page 41 of the Edexcel GCE specification for A-level biology (2008 onwards) states that students should be able to… Describe the role of the Krebs cycle in the complete oxidation of glucose and formation …

Continue reading »

Apr 09

Misconceptions in life sciences

Last month, I was involved in teaching on a life science communication course, some of the results of which you can see on Wikipedia. One of our guest speakers was Alom Shaha, who demonstrated the misconceptions students have about e.g. the forces acting on a ball in flight: A typical response demonstrates some common misconceptions, …

Continue reading »

Apr 08

Organism of the week #11 – Not even primitive

Psilotum nudum (Oxford Botanic Gardens) [CC-BY-SA-3.0 Steve Cook]

It’s not much to look at, but Psilotum nudum‘s naked fronds hold a cautionary tale for biologists: Psilotum looks a great deal like some of the earliest fossils of land plants. One of the earliest such fossils is Rhynia, the first specimens of which which were unearthed in Aberdeenshire around 1910, a mere 410 million years after they were …

Continue reading »