Research Is A Dangerous Business

When people talk about risk at work, they normally mean the risk of getting laid off, terminated, losing a business deal, and probably encountering some minor accidents like electrocution while charging their electronics. 

Unlike these risks, the risks you encounter during research are far more unpredictable because you work with unpredictable subjects; the weather (climate scientists), wild animals (zoologists), chemicals (chemists), toxic jellies (marine biologists), unpredictable monkeys (lab scientists) and sometimes, the product of your own research - worm holes and such (physicists). Even in social sciences, the research is often far more dangerous than your average nine-to-five job.

Research isn't your typical 9-5 job.

Image: www.the-scientist.com

One particular technique in psychology, called participant observation, involves taking part in the activities of those you want to study. For example, if you wish to study the drug cartel, you would need to actually get your hands dirty. Sociologist Mick Bloor, a professor at the Cardiff School of Social Sciences once ended up in a bar fight while studying male prostitution in Glasgow. Lorraine Dowler from the Pennsylvania State University was forced to flee when her interviewee became the target of a street-level assassination attempt. Social scientist Frank Burton woke up one morning to find a submachine gun pointed at him. The body of Ken Pryce was found washed up on a Caribbean beach after investigating criminology in Jamaica.

These are just of the few workplace hazards that face researchers at work. We have yet to include stories of marine biologists who have face sharks and other dangerous marine predators, zoologists battling malaria, herpetologists getting bitten by snakes, and conservationists and medical scientists battling fanatic animal-rights activists. All very real possibilities in the modern world.

In April 2013, an animal-rights group that calls itself Fermare Green Hill (or Stop Green Hill) occupied an animal facility at the University of Milan, Italy, at the weekend, releasing mice and rabbits and mixing up cage labels to confuse experimental protocols. Certainly makes a strong case for microchip IDS and tattoos. Researchers at the university said that it will take years to recover their work. Michela Matteoli, a neurobiologist who works on autism and other disorders and lost most of her own research in the attack, says that she found some research students crying in the disrupted facility on Monday morning. Many of the animals at the facility were genetic models for psychiatric disorders such as autism and schizophrenia.

A study conducted in 1994 by Brian D Crandall and Peter W Stahl intended to investigate whether humans could digest bones. They trapped some shrews and after skinning and brief evisceration, they boiled one of the carcasses for approximately 2 minutes before swallowing it whole; head, limbs, body and tail. Without chewing. Talk about taking one for the team.

So it's very disrespectful for anyone to brush aside any researcher's project and label them as useless.

Research is not just for geeks. It's also for James Bond. 

Tuatara Thursday

Tuatara holds clues to human evolution

 A recent paper in Journal of Heredity by Craig Lowe, David Haussler and colleagues at the University of California provides an excellent example of this in action, using sequences from the tuatara genome to identify the evolutionary origin of parts of the human genome.

Lowe and colleagues were looking for functional elements (like parts of genes and their regulatory regions) in the human genome that originated from retrotransposon insertions.  Retrotransposons are mobile bits of DNA that have a tendency to make copies of themselves and insert themselves in various different places in the genome.  They contain everything needed for this copying, plus often include functional modules like exons of genes, or transcription factor binding sites.  These functional modules may be co-opted for a new function in the new site, a process known asexaptation.  Once a retrotransposon is inserted in a new location it is often inactivated, and then begins to accumulate mutations which render it unrecognisable as a retrotransposon. This makes it difficult to identify exaptation events in any given genome and hence trace the origin of many of the functional elements of that genome.  However, by comparing the genomes of many different species in different lineages it may be possible to identify ancestral versions of these elements, and so trace their evolutionary history.
Lowe and colleagues found a previously unknown retrotransposon in the small part of the tuatara genome that has been sequenced.

This retrotransposon is of a type known as a LINE – Long Interpersed Nucleotide Element - and was named EDGR-LINE  (endangered-LINE).  A search of human genome against this sequence found 18 elements that are likely to be the result of insertion of this retrotransposon into the genome at some point in evolutionary time.  Seventeen of these elements are gene regulatory regions and one is an exon of a gene calledASXL3.  ASXL3 is important for regulation of other genes during development and the additional exon co-opted from EDGR-LINE appears to help control its expression.

These 18 exaptation events likely occurred early in mammalian evolution, but the retrotransposon itself has long since been inactivated in humans so all traces of it have been lost.  The functional elements it contained are able to be identified because they are under strong purifying selection (i.e. have not accumulated many mutations), so can still be aligned with the tuatara sequence.  Its only through this comparison that it is possible to know that these 18 elements originated from the same retrotransposon.
EDGR-LINE was also found in the lizard, frog, and coelecanth, but no traces of it remain in mammals, crocodylia and birds.  EDGR-LINE appears to be more slowly evolving in tuatara than in lizards, so is closest to the mammalian ancestral version of EDGR-LINE and hence more informative for identifying elements in the human genome. In fact, 10 of the 18 elements could only be identified by comparison with tuatara and not with these other species.

Evolution of the EDGR-LINE in vertebrates. The EDGR-LINE appears to have been introduced in the common ancestor of tetrapods and lobe-finned fish, and lineages where the LINE was active are shown with green. The LINE is not noticeable in mammals, crocodylia, aves, or testudines, so it has already been inactivated at least twice in evolution.

This is not the only example of genomic information from a rare species shedding light on the evolutionary history of human genome.  The genome of the threatened desert tortoise Gopherus agassizii also harbours an ancient LINE that has enabled functional elements of the human genome to be identified.  Lowe and colleagues speculate that this may be due to the very nature of endangered species, and ran simulations to show that theoretically, mobile elements like LINEs are active for longer and evolve more slowly in small populations.   This effect comes about because of the relationship between population size and selection – selection is more efficient in large populations so is more likely to remove genetic variants which are mildly harmful (or deleterious) to the organism, and to fix mutations which are beneficial.  The smaller the population, the more likely it is that deleterious genetic variants will become fixed in that population and beneficial mutations will be removed.  Insertion of mobile elements into new places in the genome is almost always deleterious, as it messes with existing genes and their regulatory regions.  Thus small populations will be more likely to accumulate additional copies of the mobile elements, and less likely to accumulate mutations which would remove or inactivate them.  I should point out here that tuatara are not actually classified as endangered (as the paper claims), but they have had a historically low population size, with probably a severe population bottleneck during the oligocene inundationof the New Zealand land mass.  In addition, we now know that even large tuatara populations can have a small effective population size, as few individuals actually contribute to mating at any one time.
Lowe and colleagues point out that without the tuatara, we would not have been able to identify these particular functional elements in the human genome, and that we never know what additional information about human evolution we might glean from threatened species in the future.  This underscores the importance of projects like the Genome10Kinitiative to sequence 10,000 vertebrate genomes.  Of course I would add that we should preserve these species for their intrinsic worth not just because of what they can tell us about human evolution, but this paper does highlight the unexpected ways that genomic data from diverse species can help us understand evolution.

Lowe, C., Bejerano, G., Salama, S., & Haussler, D. (2010). Endangered Species Hold Clues to Human Evolution Journal of Heredity DOI:10.1093/jhered/esq016

Hair- what good is it?

Why Are We Not Hairy Like Other Apes?

We humans are dubbed the "naked apes" because, well, obviously not many of us have hairs all over our body. If evolution is true, we should be hairy like bonobos, no?

Image: fanpop.com 

Darwin said our ancestors discarded coarser hairs since it's warm like sauna out there on the savannah. And he suggested that we looked sexier without the hair covering our sexual features. Seriously though I can't imagine getting turned on by primates.

Contrary to popular belief, we aren't entirely naked. We do have hairs covering our body, and they are called the vellus hair. And we do have the same density of body hair as other apes of our size.

Image: http://www.squidoo.com 

In a study published in Biology Letters last year, Isabelle Dean and Michael T. Siva-Jothy from the University of Sheffield, UK wrote that fine body hair improves our detection of parasites.
They recruited 29 university students through Facebook, aged between 19 and 27 years for the experiment. Each participant had one of their arms shaved. The researchers then drew a rectangle of Vaseline on both their forearms, and while the volunteers looked away, the duo placed a bed bug within the rectangles.

Image: knifesharpeningtips.com 

Dean and Siva-Jothy found out that the participants took longer time to detect the presence of bed bugs on their shaved arm. Also, vellus hair made it harder for the bugs to find an ideal spot to suck on. On unshaved arms, the parasites took between 22 and 26 seconds to find a good place, compared to just 18-19 seconds on shaved arms.

The results showed that fine hair helped us to avoid falling prey to parasites. The researchers further highlighted that other blood-sucking parasites prefer to bite hairless sites on bats and the featherless areas of birds.

So now you know why mosquitoes always bite you at the relatively hairless underside of wrists and ankles.