Have you ever had been frustrated because you have a great idea but so-called “time commitments” or “lack of qualifications” prevent you from executing it?

Look no further than the internet. It has literally been staring you right in the face this entire time! (Unless you’re like me and you get your RSS feed dictated to you by robot servant while you close your eyes in bed each morning).

The internet is an undrank milkshake worth of people who have a lot of time on their hands. You don’t have to look very far to be convinced of that [link to Digg comment flame-war here]. For that reason alone I implore all idea hoarders to go out on a limb and release their conceptual burdens in blog form for the joy of others.

• Best case: someone does a great job with your idea and gives you credit.
• Worst case: someone gets rich off your idea and doesn’t give you credit. Good thing it’s time-stamped on your blog! You may not get any credit, but you get to be bitter that they stole your idea and you get to learn the lesson that money isn’t everything in life, money can’t buy happiness, happiness is a warm gun, or something along those lines.

So make the internet a better place and blog your ideas! If you need some encouragement check out the great work being done at the Free Idea Factory. But what’s with all this art stuff? What can art retarded scientists do?

Don’t look at me. I have no time to make a “Free Science Idea Factory” (time-stamped on July 31st, 2008), but here’s a nice idea I had recently.

In the same vein as the Molecule of the Day blog, an Equation of the Week blog written by a savvy mathematician would be fantastic! I’ve noticed that Built on Facts has a Sunday Function, but I was thinking something a little more elaborate…

Every week an equation could be chosen and profiled with any of the following:

• Using it in a worked through example
• Linking to current popular science articles which rely on it
• Discussing what makes it unique
• Explaining its applications in different fields
• Discussing social significance (Perhaps an equation that made the moon landing possible)
• Mentioning it’s history, first time it was published, or story of discovery
• Fancy graphical depictions and plots
• Discussing it’s limitations (Where it’s relevant and where it’s not)

What’s the best way to bypass expensive conference fees as an undergrad? Volunteering of course!

This year I’m volunteering at the ISMB 2008 conference in Toronto, which, for a minor time commitment, entitles me to hear fascinating presentations on all aspects of computational biology and bioinformatics. One of these was a tutorial on ncRNA (noncoding RNA) gene finding, given by Jan Gorodkin and Ivo Hofacker.

First, a quick intro.  Most of what we know about the genome deals with coding sequence:

• DNA that’s transcribed into messenger RNA (mRNA) 
• mRNA that’s translated into proteins

But only 1.3-1.6% of the (human) genome codes for protein!  The rest, despite the popular misconception, is not “junk DNA“.  DNA and the transcribed non protein coding RNA have many functions, a few of which we know about [PDF].  The recent ENCODE pilot project estimated that as much as 97% of the human genome is transcribed into mRNA at some point. But what does it do?

There are many different classes of ncRNAs.  First, you’ve got transfer RNA (tRNA) and ribosomes, which have functions in translation of mRNA to peptides.

Another type of ncRNA are MicroRNA, or miRNA.  These are short sequences of RNA that are complementary to (protein coding) mRNA.  They act as downregulators (suppressors) of genes, by attaching to the mRNA and getting in the way of the translational machinery.

Discovering ncRNA genes can be tricky! This is mostly due to the fact that ncRNA function is in many cases tied inextricably to the structure of the transcribed RNA.  RNA, being single stranded, can double up on itself and form loops and helixes (as pictured below).  These crazy loops are called the secondary structure. The secondary structure of RNA is what results from the first pass of folding, and serves as a simplified (but useful) model for the 3D structure of the RNA.

Because the secondary structure results from the pairing of bases, any of the so-called canonical base pairs (C-G, A-U, U-G, and the reverse of all three) can occur.  Mutations can occur that change the sequence, but keep the bases paired in the same way, leading to structures that are the same, but with sequences that are very different.  

However, a single nucleotide that no longer base pairs the same way can produce a completely different secondary structure.  In the world of bioinformatics this can make it difficult for computer algorithms relying only on nucleotide data to align sequences that are too dissimilar.  There are algorithms that can align sequences based on conserved structure, but they are computationally expensive both in terms of memory and CPU time.

That said, sometimes alignment based only on sequence are good enough.  Sequence alignment tools are fairly common, and alignment data across many species is available for downloading.  Algorithms can use these alignments to discover the genomic locations of new ncRNA genes.  Because the sequence (well, structure) of an ncRNA gene will stand firm while the sequence around it mutates, functional genes will stand out as regions with high conservation across an evolutionary tree.

The alignment of multiple sequences is used in a few different ways to discover ncRNA genes.  Some of them use the known evolutionary tree in a probabilistic way (how likely is it that this nucleotide mutated from A to U?  What if it’s part of a base pair?) to try and find a consensus structure.  Others calculate the stability of the stuctures formed.  Sequences with the most stable structures tend to be functional.  There are algorithms that combine the two approaches.

The sets ncRNA genes predicted by these different matches have little overlap.  This may be due to lots of false positives being predicted, or it may be because certain approaches are more likely to find ncRNA genes of certain types or with certain properties.  Improvement of these methods, as well as secondary-structure based sequence alignment and prediction of RNA structure and function, remain areas of ongoing research.  It’s clear that we’ve already begun to crack the genetic code.

The secondary structure of ribosomal RNA from E. coli.

The FADER called it. LA Times called it. Random blogs have called it. Just like gold and fluorescent are the new black, hypercolor clothes are about to replace acid wash jeans as the nerdiest textile. It’s about time! What’s more stylish than wearing micro encapsulated PH indicators?

I guess I’m kinda fashionable but I was never on top of the hypercolor fad of the 90′s. If only I had realized the chemistry involved in these garments I’d probably be dressed in a hypercolor unitard through public school.

How does it work though? Gordon Nelson gives you the summary in his paper “Application of microencapsulation in textiles“: 

There are two major types of colour-changing systems: thermochromatic which alter colour in response to temperature, and photochromatic which alter colour in response to UV light. Both forms of colour-change material are produced in an encapsulated form as microencapsulation helps to protect these sensitive chemicals from the external environment. Today manufacturers are able to make dyes that change colour at specific temperatures for a given application, e.g. colour changes can be initiated from the heat generated in response to human contact.

Wikipedia breaks down the science, albeit unsourced, in greater detail:

The liquid [inside the micro capsules] is a leuco form of a dye (in this case crystal violet lactone), a weak acid (1,2,3-benzotriazole), and a quaternary ammonium salt of a fatty acid (myristylammonium oleate) dissolved in a solvent (1-dodecanol). At low temperatures, the weak acid forms a colored complex with the leuco dye, interrupting the lactone ring. At high temperatures, above 24-27 °C, the solvent melts and the salt dissociates, reversibly reacts with the weak acid and increases the pH. The pH change leads to closing of the lactone ring of the dye, which then regains its colorless (leuco) form.

At least it should tie me over until the wearable computer fad comes back into style…

Now that I’m finally The Dread Zoologist Roberts, I feel a need to help the people. The confused people. People confused about wives tales, folk taxonomy and poorly researched news stories. People confused about whether the appropriate short form of Charles Darwin’s name is Chas D, Char Dar, or Chuck D (in fact, all three are acceptable, along with “Charwin“).

But as my first order of business, I’d like to demolish some zoological misconceptions I commonly come across. I hate zoological misconceptions! Let’s begin:

1. Assuming you live in the New World, honey bees are not your friends. Nor are they friends with your true bee friends, the native bumblebees. Honey bees were introduced to the Americas by European apiculturalists, making them an ALIEN/INVASIVE species. So, it shouldn’t be any wonder that they are “declining“, given that they didn’t belong here in the first place (OH SNAP).

2. Daddy Long-Legs are not spiders, nor are they poisonous. They are harvestmen. Also, check out the weird pro-harvestmen science bias in the Wikipedia article:

Because they are an ubiquitous order, but species are often restricted to small regions due to their low dispersal rate^{[citation needed]}, they are good models for biogeographic studies^{[dubious – discuss]}.

Indeed! Dubious!

3. Polar bears are not a distinct biologically species, separate from grizzly bears and brown bears (which themselves are not biologically distinct). In other words, polar bears, grizzly bears and brown bears are in fact all the same (biological) species, and hybridization is possible!

4. Monkeys and Apes are different things! Chimpanzees, Bonobos, Gorillas, Orangutans, Gibbons and Humans are apes. Apes, I say! Monkeys are things like Tarmarins, Capuchins, Owl Monkeys (above), etc. So, next time your esteemed associates say “Humans are descended from monkeys!” you can say “That statement is incorrect, associates! They are descended from, and still are, apes!”.

5. Killer whales are oceanic dolphins, not whales. Similarly, Koala bears are not bears.

Do you feel informed? I have many more such facts, stay tuned!