Genome sequencing

The human genome (the entire DNA code of a human) was first mapped fully in 2003. When it was started in 1990, it was envisioned that by sequencing an entire genome we would rapidly gain an understanding of the workings of genes and quickly start to develop new medicines and techniques to deal with not just genetic diseases but also various disorders and pathological conditions.

As with many discoveries in science, the immediate benefits of knowing the genome have taken a while to filter through into useful work. One interesting effect is that it is now possible to identify genomes of other organisms much more rapidly, as the technology has advanced. Published this week in the magazine Nature was a study that sequenced the genome of the bacteria responsible for the Black Death, Yersinia pestis. It turns out that the genome is not too dissimilar to modern strains of the bacterium.

Scientists extracted the DNA from skeletons removed from medieval burial grounds. It is of interest particularly to try and identify why certain strains of pathogen seem to cause so many more problems and are so infectious (the Black Death killed an estimated 30-60% of the population of Europe at the time). It is also instructive in showing evolutionary pathways for bacteria, allowing scientists to trace back from today’s descendents and compare DNA sequences. As more and more organisms are sequenced, we are able to gain a better understanding of the similarities between organisms and see further into what comprises ‘life’.

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And now for something completely green

It’s photosynthesis time folks, just what you’ve been waiting for over those long summer weeks. It’s not really that bad, a couple of biochemical pathways, chemicals you’re already familiar with and a bit of our old favourite energy.

Since we’ve been through respiration, you should now be getting familiar with the concept of energy being transferred, or passed from one thing to another (like with the electrons and coenzymes along the ETC in the cristae). You could view organisms with the underlying idea that they are all about getting usable energy, that is transferring energy from a source to a form that can be useful to the organism. Remember that energy is used by the organism to do work – muscle movement, making new molecules, thermal energy and so on. Photosynthesis fits into this idea; we will see how the underlying process involves energy transfer.

why are plants green and not black?

Can animals photosynthesise?

What is the point of wasps?

Since summer is coming to a close, and I was in my back garden this morning, I thought I’d write a little bit on this common question from the classroom. It comes in several varieties, but mostly it has stemmed from some unpleasant encounter with the little striped beasties that resulted in stings and tears, or at the least a flurry of ineffective arm waving. It’s an interesting question because we can look at it from a number of perspectives.

1) Biological – When we talk about wasps, we are usually referring to the common wasp Vespula vulgaris (notice the latin here – Vespa is Italian for wasp, vulgar refers to common or popular, not bad taste! You will find many common organisms have the species name vulgaris in the binomial naming system). There are however hundreds of different wasp species, any of which are important parasites of other insect pests. The common wasp is omnivorous, preying on insects early in the yearly cycle (late spring to autumn) as food for larvae, and feeding on sugary nectar early in spring and summer. Larvae produce a sugary secretion the adults feed on, but later in summer this is insufficient for adults that start to feed on high sugar sources (like your drinks and food). So the ‘point’ of a wasp is the that it is a part of an ecosystem and food chain. Removing the wasps would affect other organisms in the ecosystem. From this perspective, the question of what is the point of any particular organism becomes redundant. Which brings us to…

2) Philosophy of the question – Asking what is the ‘point’ of something comes with a lot of assumptions. For example, it is an assumption that there is a point, at least in the a way that would make sense to us. If we asked what was the point of bees, worms and giraffes, you might answer something along the lines of pollination, soil aeration and…well, what is the point of a giraffe? The first two answers of course look at what is the point of the animal in relation to us – we get something out of pollination and healthy soils. This is the root of the problem; the original question could be rephrased with the missing assumption ‘What do wasps do for me?‘. Not a lot, but why do you think they should? is a reasonable answer.

This approach of seeing things through your own perspective is a subtle trap for scientists, and one that you should try to avoid. In science we go to great lengths to take the personal out of the subject; we often write using the passive voice for example, and try to avoid personal bias in research and experiments. This is similar to anthropomorphism that we have mentioned in the class – giving human attributes to animals and inanimate objects (…the sugar molecules want to move through the membrane…) and although it is difficult to avoid doing it we should make efforts to be more scientific with our language. Ascribing meaning to events only in terms of cost or benefit to ourselves is sloppy thinking.

Not bad. Not bad at all.

Incredible bit of time lapse video. Now get back to do something productive. We’re back in a week…

I found this on Phil Plait’s superb Bad Astronomy blog. He’s pretty good at picking out this kind of stuff, have a poek around his site. There’s an older cached version you can find through google with soem very good answers to some basic physics questions. Yes, I know you are doing biology but this is science. Embrace your inner nerdiness.

Writing longer answers and essays

Belated congratulations to everyone who got what they wanted from the results last week. I haven’t been into school yet so I don’t know how individuals did, other than an odd few bits that Mr Murray forwarded me.

I thought I’d suggest a few guidelines for writing out longer answers (or what we might call scientific essays). It’s not something we spend a lot of time in schools overtly teaching, and you will come across different opinions and styles for this, but I’m going to stick to ways to improve your writing for scientific purposes. Since a part of the homework for the holiday was an essay about oxidative phosphorylation, you may well get some clues here as well.

Rather than give too much away, I’ll use Krebs cycle as an example. Imagine you had a 9 mark question about Krebs Cycle on a question paper. My suggestion would be to start by getting down as many things you could think of to do with krebs, forget structure for a moment and brain-storm for a minute.

Let’s say you wrote down citrate, 654444, ATP, NAD, FAD, pyruvate, maybe you also draw a rough version of the cycle. Once you have some ideas down, you can build a structure from there. For example, drawing out the cycle might have made you think of the link reaction, perhaps you then remembered about the CO2 being removed which leads you to decarboxlase, maybe some other enzymes. Many of the structured (or long answer) questions you will come across in biology are based around step by step processes, which gives you a ready-made structure. The problem people often have is they start too quickly, forget a part of the process and then find it difficult to think backwards to what has been missed out. A good tip is to give a description for every scientific term used (within reason!), e.g. ‘…two hydrogen are removed from the citrate by NAD. NAD is a coenzyme that is reduced in this reaction, and used to carry electrons’ . You described the role of NAD which is relevant to the question, but not the coenzyme part, which would be more detail than is necessary.

When it comes to writing an essay, the process is similar but you have longer to plan things out. The first paragraph of your essay should always give the overview. A good example of this is to look at this description of the Cori cycle (don’t worry about what it is yet) from wikipedia.  The information about who it is named after is not very relevant, but notice how it encapsulates what the article is about. The bulk of the article then goes on to talk about the details; notice how you are expected to understand what most words (oxygen, glucose, pyruvate) mean. Because of the nature of wiki articles, important words are linked, remember you will not have that luxury so make sure that you describe anything that is important.