You know you’re in an emerging field when you see things like this:
…Asia’s oldest bioinformatics organisation set up in 1998. (Bioinformatics research in the Asia Pacific: a 2007 update)
I simply find it worthy of note that I work and study in a field whose ‘old and venerable’ organizations are between 10-20 years old.
Makes you realize how far we’ve come in such a short time.
Posted: February 14th, 2008 under bioinformatics, hmmmmm.
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There are some interesting science images over at National Geographic.
Click on the image to go directly there.
Posted: September 28th, 2007 under interesting stuff, science.
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One of my recent projects has been to map short sequences of DNA (tags) to specific positions in transcripts (ie. exons, introns, UTRs). Everything was going along nicely, until I was looking through my output data and saw something weird.
I had one sequence map itself to an exon and a 5′UTR - on the same transcript. This caused me some concern (and an afternoon of frustration), because it seemed that according to the Ensembl database, this one position is both an exon and a 5′UTR. I thought I had done something wrong in my code, such as calculating the start and end position of the UTRs wrong or pulling out the wrong starting position for the start of translation.
Seems that wasn’t the problem. What it turned out to be was partially my fault, but also partially the fault of the Ensembl gene annotation.
Posted: July 15th, 2007 under bioinformatics, hmmmmm.
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I recently stumbled upon this paper:
Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns
Rie Takahashi & Jeffrey H Miller
Genome Biology 2007, *8*:405
_”The primary goal of this work is to convert genome-encoded protein sequences into musical notes in order to hear auditory protein patterns.”_
This is an interesting - and unique - approach to analyzing protein sequences. They’ve taken many things into consideration, including codon distribution and amino acid frequency. They’ve developped rules for rhythm, range, dynamics and note lengths. Unlike previous efforts which have tried to directly translate an amino acid to a musical note, this approach uses chords and musical rules to generate these compositions.
Posted: July 8th, 2007 under bioinformatics, unique.
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Blogs are a great way to get involved in the bioinformatics/computational biology/systems biology world. At the most basic level, it allows you to learn what others are doing, how they’re doing it and what problems they’ve encountered. It can also point you in new directions, by referencing papers, people or sites that are good/bad/instructional and why. Additionally, there’s also the networking aspect of it, where if you’re persistent enough (but not stalker-persistent), you can gain valuable colleagues and resources. Because if you haven’t figured it out yet, in any scientific field, collaborations are gold. (Our lab in particular is involved is at least 6-8 different collaborations at any given time. This means more published papers, which leads to more funding and bigger projects.)
But blogging isn’t just about you getting involved in the field. It’s also about distribution of knowledge, transparency in science and global communications, which all lead to a better you. Having a conversation over a blog post can be a great way to develop your reasoning and researching skills. A lot of people starting out - especially those who haven’t gone through a thesis defence - have a hard time holding a reasonable ‘on topic’ conversation with their colleagues/peers. In most cases, it’s not because of lack of knowledge, but because of an ability to express your ideas in a concise and reasoning manner. A good ‘on topic’ conversation between two people in the same/similar field will be intelligent, well articulated and will make each participant consider new ideas or perspectives. (This type of conversation or debate is not solely isolated to the science field, but that’s what I’ll concentrate on.)
Posted: June 25th, 2007 under bioinformatics.
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So I was looking around Information Aesthetics and found an interesting piece on DNA visualization. It seems some guys took the entire human genome, assigned a colour to each of the four bases (plus grey for ‘undetermined’), and rendered pictures based on our genetic code.
Looking at them, I’m reminded of those annoying 3D pictures that only ever worked when I was too tired to concentrate on anything other than keeping my eyes open. And while they do make for interesting pictures, I’m not sure you can really consider this ‘art’. I certainly don’t.
It a unique idea - of sorts - but in the end it’s all just static. And the entire issue about ‘patterns emerging from our DNA’, I think, is kind of misleading. The ‘patterns’ or ‘bands’ seen are merely a biproduct of how the pictures were rendered in the first place. ie. where the ‘newline’ is placed.
And DNA is in actuality one long string, so how can you show it in a 2D image format, and expect it to be representational of the human chromosomes? (There’s an interesting discussion over at Slashdot about this entire project.)
But this all led me to the discovery of DNA11 - From Life Comes Art
Again, really cool pictures (better than the 3D-DNA-rainbow-thing ), but when you get right down to it, these are blown up gels. Way to bastardize the technologies that revolutionized molecular biology and genetics!
They also do fingerprints.
While these are interesting ideas and all, it’s like sending your social insurance number out to be blown up and framed so you can hang it over your mantel. DNA and fingerprints are that personal.
But if you don’t mind having your genetic markers or unique identifiers up on the wall for all the world to see, that’s your call.
Just don’t commit any crimes, cause then you’re screwed. (ie. freely displayed = no warrant needed)
Posted: June 17th, 2007 under genetics, hmmmmm, interesting stuff, science.
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I’m ashamed to even be remotely associated with this.
Posted: June 11th, 2007 under *facepalm*, science.
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So, to follow up on the Cheerios thing from HERE….
An actual paper was found! ::shocked gasps from the audience::
Apparently, the data is from Wesnes KA, Pincock C, Richardson D, Helm G, Hails S. Breakfast reduces declines in attention and memory over the morning in school children. Appetite. 2003 Dec;41(3):329-31. Colour me shocked, though I suppose I should have expected it. No company - these days - is going to put something like this on their product, without the evidence to back it up.
A very nice review of the paper and how Nestle interpreted the results can be found HERE.
“… If we leave out the amazingly bad graphics, there is still the data. First, there is apparently no attribution of where it came from, except that it was done by CDR and Reading Scientific Services. No paper citation, no link. Is that too much to ask for? While a scientific paper may still scare away people, these days nobody will run screaming away from the breakfast table when encountering an URL. To my mind any unreferenced claims like this should be regarded as “we made it up”. …”
There is a bias in the data though, which is fairly obvious. They tested Shreddies, Cheerios, a ‘glucose drink’ and ‘no breakfast’, leaving out other, healthier choices. (Though they do claim that it’s all measured against a baseline of a complete breakfast, they never define what that was.)
And despite the fact that there is scientific evidence to back this up, I’m still sticking this with the ‘bad science’ tag.
Posted: June 10th, 2007 under bad, science.
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There are projects in the works along the coasts of Canada, to track the migratory pattern of fish. And other ocean life.
I’ll give them points for thinking big, but that’s about it. First came POST (Pacific Ocean Shelf Tracking), which is ostensibly off the West coast of Canada, from Alaska to Oregon. They’re using surgically implanted acoustic tags to track the movements of young, wild salmon. The entire project is actually very well thought out and planned, though I think they’re putting too much faith in their technology. Read more »
Posted: June 7th, 2007 under science.
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Today’s lesson…
Cheerios - better for you than starvation
And I have to re-iterate the question raised by some people…..
How does the ‘Power of Concentration’ relate to ‘Delay in Reaction Time (msec)’?
Honestly, msec? Does 1/10th of a second really make you want to run out and buy the honey-nut goodness? And who has 0 delay in reaction time? Ever?! Who ran this so-called ’study’?
I want to see their experimental model and research data.
Posted: June 2nd, 2007 under bad, science.
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