25 April 2011

In which I unzip a few genomes...

Here is a post I made by way of comment on "Genomes Unzipped". Enjoy!

Elmatos, while those posts are strong on passion, they are weak on
coherence. I am a clinical geneticist, and I deal with hundreds of
families every year where the genome very much *has* delivered, and
keeps delivering. We would not currently have NGS devices/services (is
the distinction even relevant any more?) were it not for the human
genome project, and by the sound of it you wouldn't even have a job!
Think of a lot of this research money as stimulating/subsidising the
development of a new industry sector. Your boss has it all wrong if he
thinks everyone will need a sequencer. What we *need* is the
*sequence*. Your genome is essentially a big chunk of data (actually
not that big - just over a CDROMful) that you could as easily carry
around on a USB stick or upload to a server. NGS is simply a way of
getting past a firewall set by biology.

But that is what this is all about - it is not about "finding cures in
the genome" (I really don't think anyone working in the field for the
last 20 years has been anticipating this, despite the breathless hype
of the journos). It *is* about understanding the *biology*, and that
is paying off in spades. We are finding out how the human organism
functions. Genes are not "magic", nor are they "building blocks", and
they certainly aren't "for" anything directly. But thanks to our
developing understanding of the genome(s), we are putting together
some very powerful explanatory frameworks for getting to the bottom of
the biology of disease.

Now, I'm a clinical geneticist, yes, and I don't have a heck of a lot
to offer my patients other than a diagnosis and the phone number of
another family facing the same situation (actually, I underplay my
hand here - there is often a lot we can do, and this is improving all
the time). But when you tell the parents of a 20 year-old girl with
severe learning disability and epilepsy that she has a de novo
mutation in TCF4 and a diagnosis of Pitt Hopkins syndrome, after a
lifetime of the mother blaming *herself* for causing this, and
panicking over the possibility of it being transmitted to her other
children's children, then you see that knowledge itself is of real
therapeutic value.

And so the feck what if the diseases are "rare"? Rare diseases are the
natural experiments by which we have unpacked a phenomenal amount of
human biology that is directly relevant to "common" diseases.
Furthermore, there are more people collectively with "rare" disorders
than there are with most "common" conditions. And as if that weren't
enough, "rare" disorders are almost invariably more common than you
realise, and "common" disorders are almost invariably rarer.

Genomics is helping us to break down that firewall and manage genetic
information in much the same way as other digital information; sure,
we need to know how to interpret it, but we are not nearly as ignorant
of its import as many people (such as Latham) imply, and, perhaps more
importantly (and fatal to the doom-mongers' lamentations) there is no
sign of this slowing down. The advances are real, and they are
delivering *now*, just perhaps not in the way that some people in
their simplistic and medically uninformed analyses wanted them to.

-@shanemuk http://answersingenes.blogspot.com

22 April 2011

Changeable weather in Donegal

One minute it's calm and sunny. Then windy and sunny. Then windy and showery. Then calm and showery. Then back to the beginning. Lewis thinks it has something to do with us being so far from the equator. But at each of the points in the cycle we are the same distance from the equator. The earth is a giant cycler -- heat, light, wetness - there is no better place in the universe for life to evolve. Than Donegal.

13 April 2011

Clouds in my Coffee: Carly Simon wins Nobel Prize for Physics

Pour a cup of hot black instant coffee. Let it sit for a while, and
carefully observe the surface. After a short while you will see a thin
film of mist form; you can move this around the surface by blowing
lightly. If you watch it for a while, you will see little local
collapses, cracks and ruptures form and propagate through the mist,
often making interesting patterns as they do so. There is some
interesting physics going on here. What seems to happen is that there
is a vapour layer at the interface of the hot liquid and the
relatively cooler air above that creates a semi-stable (and very thin)
zone. If a particle of dust (or maybe a particle from a radioactive
decay process? Need to do some testing of this!) interacts with the
layer, it seems to cause a local collapse of the condensate zone that
propagates through the rest of the zone like a crack appearing in a
sheet of ice. So what is going on? It sure looks like an interesting
phenomenon, so I have tweeted everyone's favourite physicists
@ProfBrianCox and @JimAlKhalili to see if they know, or if there is
any literature on the topic. If not, I will make a pitch for the
IgNobels, as I think coffee is too important to be ignored.

[Works with black tea too]

09 April 2011

What sort of thinker are you? Visual or Verbal?

I'm not a psychologist. And I'm pretty glad about that. But I have in my short life noticed something very odd about a lot of intelligent people - they don't seem to understand certain concepts that appear very straightforward to me, while they may find certain other concepts easy that to me are pretty hard. It has been known for a long time that "intelligence" is a multidimensional thing. There is no one measure that can tell you how "intelligent" you are, and the "IQ" is a notoriously unreliable number to attach to it (and certainly to rank people's generic ability to perform real-life tasks). What is it really measuring? Who knows?

That said, there do appear to be at least two axes that seem somewhat meaningful in assessing people's aptitude for certain fields of endeavour, and these are what I call the "visual thinking" axis and the "verbal thinking" axis. I don't know whether they are mutually exclusive; maybe some people think excellently along both axes, and others are daft no matter which way you tilt the graph.

Visual thinkers conceive of topics by, well, visualising them. In their mind's eye they construct the concept and explore it as if they were handling it and peering into its nooks and crannies. They like diagrams; they get a lot out of practical demonstrations of procedures. They think of things as systems, rather than as discrete objects. They're good at breaking things apart and putting them back together.

Verbal thinkers are quite different. To the verbal thinker, the instructions are key. Protocols and standard operating procedures. I sometimes think verbal thinkers are more prone to accepting an authority-based view of things. Concepts are related in a rigid ontology, which can be useful for some fields of endeavour, but verbal thinkers are not great at thinking outside the box. They can be quite good at logic when terms are clearly defined, but are prone to missing obvious fallacies when terminology shifts or where words have two meanings.

And for these reasons, I think scientists tend to be more visual than verbal in their thought processes. They need to see something; understand how it breaks down and rebuilds. Verbal thinkers perhaps make better lawyers or administrators. Of course I am tarring with a broad brush (a tortured metaphor that will send our verbal-thinking pals into a headspin) - these are not exclusive, and most people probably adjust their thinking style to fit the problem they're dealing with. I am a teensy bit concerned by the tendency of some philosophy fans to major on the verbal to the virtual exclusion of the visual, and I think this traps them into unproductive loops that they have a hard time escaping from, or prevents them seeing obvious fallacies in wordy arguments.

One example of a seriously fallacious argument that traps verbal thinkers, but is obviously bogus to visual thinkers, is St Anselm's "Ontological Argument" for the existence of God. I'll come back to this in another post at some point, but google it if you're interested, and see if you can spot the howler - that little test in itself will probably tell you what sort of thinker you are!

I was thinking of all this as I watched an episode of Marcus du Sautoy's excellent BBC show "The Beauty of Diagrams". It seems to underline the point - scientists and mathematicians seem to see the world in a different way to our verbal thinking friends. To the visual thinker, a rose by any other name smells as sweet, but to the verbal thinker, if you change the name of something, you change its nature. The human brain is a very strange thing.

Is there a moral to this story? I don't think so, but speaking personally I have noticed that I get on much better with visual thinkers. If I was a verbal thinker I would probably say the opposite, and be just as emphatic in my conclusion. And here I am writing words to get that point across. Irony is not the 51st State of the USA.

01 April 2011

Apologies for the hiatus

I've been trying to get used to this Twitter malarkey, and despite the fact that it's guff, it's weirdly addictive. You can follow me on @shanemuk, but I really don't know if I'll have that much to say on it.

As in this blog, my main objective is to help heal division in the world, protect kitty-cats, save the ozone greenhouse and kill the killer whales. All laudable, all followable. Now, if I have set up http://www.twitterfeed.com correctly, this should display both on Twitter and on Facebook. What are the bets that it'll work?