Wednesday, 31 October 2012

Name the Biologist - Halloween edition

Time for some scary biologists - can you name them?

And this guy isn't a biologist but I'd definitely enjoy being able to study him - after taking all the appropriate risk assessments.

And finally, he doesn't scare me but I think he terrifies certain demographics...

Tuesday, 23 October 2012

Reference Rage!

I've been doing some mutant hunting today for some genes of potential interest and because they are fly mutants it's useful to know exactly what the mutation is as they can range from the gene being deleted, a portion being deleted or have a transposable element stuck in them - all of which effects how much of a "mutant" they are. This information is usually in a figure but sometimes, in a busy manuscript, it will be mentioned in the materials and methods. In this case the mutant was referenced as being described in another paper. Fair enough, I thought, and dutifully looked up the other paper. I scour this paper and it merely says "as has been previously described". Not in the paper, so where? In one of their previous papers? In someone else's paper?

This annoys me as I shouldn't have to waste my time chasing up dead-ends. It wouldn't be so bad if this was the first time it's happened but this is a frequent problem when you are trying to find out the exact nature of a mutant, clone construct or methodology. I don't mind them referencing the original paper if it has all the details but people who reference papers that only reference the source material again should hit over the head with a rolled up journal. It's really bad form and strikes of laziness or, worse, hints the author never actually checked the data in the original source.

If editors/reviewers can't be bothered to weed this reference riddles out, then journals should perhaps insist that the information for mutants etc be included as supplementary material - that way they'd have to cite the original if they are printing their data.

I guess the small mercy is that I at least have access to online databases. This kind of nonsense must have resulted in a lot of premature baldness back in the days when people had to go to the library to find papers.

Monday, 22 October 2012

Science Songs

A song that lends itself to many an occasion, particularly student clubs. I've noticed at science retreats this song always gets a strong response and upon reflection it makes complete sense.

"we've got to hold on to what we've got
Cause it doesn't make a difference
If we make it or not....
...We'll give it a shot"

The chorus reminds me of the PI - postdoc/ postdoc - student relationship of getting them to finish the project.

" Whooah, we're half way there
Livin on a prayer
Take my hand and we'll make it - I swear "

It ahould be an anthem to research!

Sometimes you just need an excuse to play this song :)

Tuesday, 16 October 2012

Wall of Shame

My group leader told a fun anecdote that I think deserves to be a "wall of shame" entry. He was recounting a tale of a student whose experiment kept failing despite their insistence they were following the protocol correctly. He asked they student whether they were getting the correct pH for one of the solutions and the student was insistent they were doing this correctly. Eventually he asked to see how they were pH-ing the solution and the student took him to the pH meter inserted the meter into the solution and then turned the calibration dial to the pH they desired. "Then I turn the dial to the pH I want and it's done", proclaimed the student...

A fundamental misunderstanding of how a pH meter works but an excellent idea for creating a pH-ing machine. I'd love to put a solution into a machine and turn a dial to a desired pH which would in turn convert my solution into the selected pH.

biological Interlude - What happened before the Big Bang?

It seems strange for my first post in a while (been constantly ill in some form or other of late) to be about cosmology but my mind was quite literally blown by it so I thought I'd draw peoples attention to it. For anyone with access to the BBC iplayer I'd urge you to check out one of their documentaries under the "horizon" umbrella asking "What happened before the Big Bang?".

Initially I thought it was a nonsense question as my preconception was that there couldn't be anything before the Big Bang because that's where everything started, including time. Turns out this theory is being challenged by many new ideas which think if the Big Bang even happened, it's either a cyclical event or something that occurred in a previous universe. It turns out it's quite a fertile time for alternative theories and the documentary gives each theory 5-10 minutes explaining the pros and cons. It's refreshing that the show allows the other cosmologists to comment on rivalling theories and it's fun to see how each one is convinced the others are seriously flawed.

After introducing the different theories, several of which overlap the show spends its remaining time looking at evidence that can back up, or more importantly disprove some of these theories. It's nice that the show spends some time to show this aspect of science as there's sometimes a tendency to present all these "out-there" theories as if they are accepted fact and this segment shows that these are all theories as of yet. In an attempt to draw a comparison to Biology, I think all these conflicting ideas mimic evolution in the sense that the strongest one will ultimately survive but i guess science as a whole has always been in service of natural selection in one way or other.

What was my favourite theory? I did like the idea of Big Bangs originating from a Black hole in another universe as it seemed to philosophically get round that whole "infinitely small/dense" problem. I also liked the cyclical arguments of either the universe condensing back in on itself until gravity becomes a repulsive force and the Big Bang is more a Big Bounce (Param Singh) or the similar argument that the end of the universe would actually mirror the environment before the Big Bang and therefore be fertile ground for another one (Roger Penrose). I wasn't so keen on the "Brane theory" (Neil Turok) largely because i couldn't wrap my head around it and it sounded too much like a fairy tale to a lay person like myself (although it makes excellent Sci-fi imagery). There was also a theory at the end that the shows makers and discover (Laura Mersini-Houghton) claimed worked perfectly with the mathematics in that it allowed there to be something from nothing as well as explained three observational findings in cosmology that are currently hard to explain using other models. Unfortunately I had to take their word on that as it wasn't explained why it worked. I imagine it was probably one of those things that couldn't be easily explained in a couple of minutes.

A great little documentary that ignited my imagination that took time to present multiple arguments and suggest ongoing experiments that may help prove which one (if any) is correct. The scientist's in the show all did a great job of getting across the point that even if they are wrong it's good to generate these theories to push the field forward. I was left with one remaining question though and that is whether hardcore mathematicians/physicists really do spend all day scribbling things down on a blackboard?