Genomic parasites

Genomic parasites – we all have them but how are they kept under control?

You may think you are parasite free. “No malaria, bilharzia or tapeworms in me”, I hear you say… If you think this you’re actually mistaken. Humans, and many organisms besides, carry parasites within their own DNA. These parasites have left behind the ‘traditional’ parasitic life cycle, with their own body or their own cell living within us and have gone purist, trimming everything away and simply copying their genome into ours, existing alongside us for as long as humans survive. Known as transposons, these genomic parasites use our own cells to survive, using our own machinery to copy themselves, replicating and surviving just as organisms endeavour to do on the land, in the air or in the sea. They could copy themselves all over our genome making even more copies of themselves but something prevents this, stopping the transposon from overwhelming our genome and killing us. Research from the University of Cambridge, the University of Nottingham, and the Fred Hutchinson Cancer Centre in Seattle reveals why: Continue reading “Genomic parasites”

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Why have a circadian clock?

Almost every animal and plant on the planet has a circadian clock, even those that live in the depths of the sea and deep underground in caves.

The presence of clocks in almost all life-forms implies that it is a helpful or advantageous characteristic, an evolutionary adaptation, serving to improve the fitness of the organism. This argument makes apparent sense but, without testable hypotheses, has little to support it.

Two main hypotheses have been formed to explain the evolutionary benefit of having a circadian clock. The first is known as the External Synchronisation hypothesis – that the benefit to the circadian clock lies in being coordinated with the external environment, for example, the predictable daily change in light and dark that we call day and night. The second is the Internal Synchronisation hypothesis – here the clock benefits an organism by allowing it organise physiological processes in time in order to avoid conflict between incompatible processes, for example separating the process of photosynthesis from that of nitrogen fixation in the case heterocystous cyanobacteria.

These two hypotheses aren’t mutually exclusive. The internal synchronisation hypothesis doesn’t necessarily require a 24 hour clock; plenty of other periods would suit. But, timing pressure placed on an animal from the external environment could force biological processes to fit within the 24 hour day, for example, the reactions for photosynthesis. These are only necessary in the day when it is light. But since nitrogen fixation and photosynthesis are incompatible, nitrogen fixation gets restricted to the night and internal organisation has been forced on an animal from external pressure. Once established, internal synchronisation could become independent of external pressures. Perhaps, in the origin of circadian timing systems, external synchronisation came first and internal synchronisation second, but now, either one serves as a selective advantage. So, though the two hypotheses propose reasons for selective advantage a circadian clock might give to an organism, and therefore why Clocks may have evolved in the first place, arguments are complicated as whether these are the original selective pressure that formed a circadian timing system.

How might we test which which hypothesis is most important today? One way is to look at animals that live in non-rhythmic environments, those that do not experience the regular and predictable cycle of day and night. These animals offer the chance to directly test the first, external synchrony, hypothesis, since in a non-rhythmic environment, there is no need to synchronise to an absent cycle. 

The deep sea and caves are two environments that fit this description. Interestingly, most studies on organisms that live there give at least some hints that circadian clocks are present and working even here. Although, there are many difficulties interpreting and comparing this research due to the various experimental conditions used, this general observation lends weight to the internal synchronisation hypothesis – in the absence of a no cycling external environment, a ticking clock must be being used for something else, and internal synchrony is the most obvious.

My PhD research looked at one organism that lives in the depths of caves and is highly adapted to life there: the Mexican blind cavefish, Astyanax mexicanus. This fish shows wonderful daily patterns of behaviour and gene expression, confirming that it has a functional circadian clock. It also shows some interesting quirks, which give some insight into why an animal that lives in the dark and has done so for tens to hundreds of thousands of years might keep a system that generates 24 hours rhythms in physiology and behaviour.

Planet Earth Institute #scienceafrica UnConference

In case you wanted to find out a bit more about the Africa’s Scientific Independence conference, the Planet Earth Institute made a Prezi of points and pictures from the day (I’m even in one of the photos!). Catch it on the prezi website.

Watch this space for further articles on science/science communication/science education in the developing world. The Planet Earth Institute invited me to write a piece on these topics which will be posted on their website later this week.

Africa’s Scientific Independence

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Conference Poster

The 11th July saw Africa’s Scientific Independence, a day-long ‘Unconference’ run by the Planet Earth Institute, at the Hub Westminster. Chaired by Lord Boateng and featuring a number of senior scientists and policy makers in the UK and all over Africa, the event tried to get to grips with a rather large question of how we get to Scientific Independence in Africa.

Continue reading “Africa’s Scientific Independence”

Science’s Silliest Stories – Science Museum Lates

Last week I ran an event at the adult-only Lates event at London’s Science Museum titled Science’s Silliest Stories. In it I told a story of some of the odder pieces of research that have been published recently to draw out some of the more curious sides of scientific research. I really enjoyed the evening. It was great to see friends who came and the audiences seemed to really get into it – perhaps the alcohol helped! Unfortunately I didn’t manage to record it (mainly to show my wife who was away with work), but here is essentially what I said:

Science’s Silliest Stories

Hello and welcome to science’s silliest stories.

In the next 20 minutes or so I will be regaling you with some of the sillier stories from science and scientific research. I’ll take you on a journey through real recent research, from animal sex, penises and vaginas, through to findings about wobbly pregnant women, levitating frogs and cheesy mosquitos. I’ll mention Sarah Palin’s now infamous quote about fruit fly research but hopefully leave you on a positive note that scientists aren’t always out to waste your tax money.
Continue reading “Science’s Silliest Stories – Science Museum Lates”