{"id":568,"date":"2011-02-09T00:10:31","date_gmt":"2011-02-09T00:10:31","guid":{"rendered":"http:\/\/occamstypewriter.org\/scurry\/?p=568"},"modified":"2011-02-18T22:22:04","modified_gmt":"2011-02-18T22:22:04","slug":"small-and-very-far-away","status":"publish","type":"post","link":"https:\/\/occamstypewriter.org\/scurry\/2011\/02\/09\/small-and-very-far-away\/","title":{"rendered":"Small and Very Far Away"},"content":{"rendered":"

As Father Ted<\/a> might have explained<\/a> it to Dougal, this one is very small:<\/p>\n

\"Atom\"<\/a><\/p>\n

Atom<\/em><\/p>\n


\n<\/em><\/p>\n

but that one is far away<\/em>.<\/p>\n

\"Mars\"<\/a><\/p>\n

Mars (NASA<\/a>)<\/em><\/p>\n

And yet it is the distant planet and not the nearby atom that seems to excite the greatest interest in the public mind. I blame Carl Sagan<\/a>. And bloody Brian Cox<\/a>. And a dozen other popularisers of science (that git Simon Singh<\/a> springs to mind) who have done such a fantastic job of bringing the solar system and the rest of the glimmering cosmos into our homes and into our heads. How come the same attention isn’t lavished on atoms and the wondrous things that can be made from them \u2014 molecules<\/em>. I spend my life on molecules but I’m not sure other people are interested.<\/p>\n

I was struck by the criminal inattention paid to molecules as I tried out Cmol<\/a>, a nifty program that allows interactive display of their structures on the iPad (and the iPhone). As a professional structural biologist I make my living by figuring out what protein molecules look like and spend a lot of time looking at them. It seemed to me a no-brainer that someone clever would come up with a decent app to let me view my precious molecules on a glossy Apple tablet.<\/p>\n

Well Helen Ginn is someone clever and her Cmol<\/a> app is pretty damn good. It might need a couple of developmental tweaks (which she’s told me are in the works) but the program is already relatively powerful. I’d say it’s on the verge of being a serious professional tool. It certainly beats the only other contender, Molecules<\/a>, into a cocked and poorly rendered hat.<\/p>\n

In Cmol I can view structures that I’m currently working on or download any molecule that is available from the Protein DataBank (PDB<\/a>), the free public depository of biomolecular structures (proteins, DNA and RNA). There are then a variety of ways that I can select and represent different portions of the structure. In the example below \u2014 a picture of the albumin protein found in your blood serum \u2014 I am showing the bonds between protein atoms as sticks coloured by atom-type: oxygens are red, nitrogens blue, carbons grey and sulphurs yellow; the atoms of the fatty acid molecules that albumin carts around your body are represented as coloured spheres using the same colour code. It’s a complex image but I hope you can get some sense of how it might be deciphered.<\/p>\n

\"Human<\/a><\/p>\n

The real success of Cmol is the way the program levers the interactive capabilities of the iPad. With one finger you can rotate the molecule, with two you can move it across the screen or zoom in. The view may be two-dimensional but the interaction \u2014 the hand-eye coordination \u2014 makes the encounter truly immersive<\/em>. It is almost<\/em> as good as using 3D goggles, which we wear in the lab for heavy-duty structural work.<\/p>\n

Now that’s all very well for me and for other structural biologists but few outside our monkish, molecular discipline can access this lovely experience. For many biologists and biochemists, never mind the public at large, the idea of downloading and displaying a PDB file \u2014 the structure of a protein molecule, say \u2014 is about as conceivable as parsnips on Pluto. Despite some laudable efforts, such as the PDBwiki<\/a>, the complexity of these structures and the abstruse coding of PDB files hides them from view.<\/p>\n

For the general public, apart from the iconic image of the DNA double-helix, I suspect there is little grasp of the molecular intricacy that sustains life, and therefore no feel<\/em> for the subject. The molecular question simply doesn’t arise and that is a disappointment to me. The starry universe out there is familiar to many people, but there is a whole universe inside every living thing on Earth that, sadly unknown to most, seethes with as much variety and wonder<\/a> as the contents of the night sky.<\/p>\n

Paradoxically, the big stuff that is so far away is much more familiar than the small stuff \u2014 the molecules \u2014 of which we are made.<\/p>\n

But there’s no paradox. Sagan, Cox, Singh and their ilk have helped us to befriend the universe by revealing our connection to it. That supernova might be light years away but it was just such an explosion that created the elements that made us and our home planet. The fascination with the possibility of life on other worlds is fuelled by the dreadful excitement of how that would change our conception of ourselves.<\/p>\n

And so it should be with molecules. Is it intrinsically more difficult to tell the story of the multitudinous building blocks of the living cells of our bodies? I don’t believe it; or don’t want to. After all, the connection<\/em> is obvious, even if it is too often blindingly so. But I know from experience that making the connection to the reader is not easy<\/a>. To tell a gripping molecular tale, you probably have to work at least as hard as Father Ted.<\/p>\n","protected":false},"excerpt":{"rendered":"

As Father Ted might have explained it to Dougal, this one is very small: Atom but that one is far away. Mars (NASA) And yet it is the distant planet and not the nearby atom that seems to excite the … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":7,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[20,21,6],"tags":[31,32,29,30],"class_list":["post-568","post","type-post","status-publish","format-standard","hentry","category-astronomy","category-protein-crystallography","category-science","tag-cosmos","tag-father-ted","tag-molecules","tag-proteins"],"_links":{"self":[{"href":"https:\/\/occamstypewriter.org\/scurry\/wp-json\/wp\/v2\/posts\/568","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/occamstypewriter.org\/scurry\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/occamstypewriter.org\/scurry\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/scurry\/wp-json\/wp\/v2\/users\/7"}],"replies":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/scurry\/wp-json\/wp\/v2\/comments?post=568"}],"version-history":[{"count":0,"href":"https:\/\/occamstypewriter.org\/scurry\/wp-json\/wp\/v2\/posts\/568\/revisions"}],"wp:attachment":[{"href":"https:\/\/occamstypewriter.org\/scurry\/wp-json\/wp\/v2\/media?parent=568"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/occamstypewriter.org\/scurry\/wp-json\/wp\/v2\/categories?post=568"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/occamstypewriter.org\/scurry\/wp-json\/wp\/v2\/tags?post=568"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}