Life of a Lab Rat

Funny thing, science. Most of us do experiments to show that something is so, but in reality we're excluding other possibilities. What we're doing, if we think about it, is trying to disprove hypotheses so that a theory is strengthened. Now that sounds a little odd, but it is the basis of the scientific method.

An observation leads to a hypothesis explaining that observation. We test that hypothesis by doing an experiment. We think of another hypothesis, and test that one. And we keep doing this, until we run out of testable hypotheses, to formulate a theory that is not contradicted by evidence, one that we say is 'supported' by experiment. Philosophically, it is difficult to be certain that any explanation of a phenomenon really represents reality, that is it is difficult to prove anything This is because someone with a good imagination can always come up with an explanation that fits the evidence but does not agree with your pet theory. It is much easier to disprove something.

We have Ockham, of course, but that is a philosophical concept and it although it might say something is likely or not, it does not tell us that something is. This is why good experiment design is important.

And yes, this is also why proponents of Intelligent Design do not make good scientists and and why it is bloody difficult to reason with them. They do not have any hypotheses in support of their position that are falsifiable. You can not prove them wrong, because everytime they are in a corner, puff of smoke! Dear old William can just go whistle.

But I did not want to argue about that today. I want to talk about proof, and faith.

A lot of people, and especially scientists and other rationalists, get very confused when talking about faith, and indeed proof. Is faith really a belief in the the improbable, the illogical or even the irrational? If you have evidence, does it stop being faith? If you have evidence is it necesarily proof? Surely you can only have faith in things that can not be proved, or that you know are not true? A few weeks ago someone opined that anyone who could have faith in the intangible was stupid. I wondered aloud where that left scientists, because let's face it friends, we all have faith in things we can not prove. Our experiments, our theories; we can only support from evidence, we can only prove, so much.

The company with the easily accessible information symbols is at it again.

From the (hell, let's name and shame) Fermentas' catalogue entry for Klenow fragment, the fragment of a bacterial DNA polymerase that 'fills in' ends of DNA:

flemington, n
Chocolate biscuit, with cherries. Definitely no coconut.

Darkling I listen; and, for many a time
I have been half in love with easeful Death,
Call'd him soft names in many a mused rhyme

Talking of seminars (or 'serminars', what's that Tideliar, a cross between a lecture and a sermon?), I'm sure you are familiar with that particular feeling in a warm, dark seminar room. You know what I'm talking about.

First your eyelids become unbearably heavy. Then your neck loses all strength and control, and your head slowly, oh so slowly, rolls forward and suddenly you jerk back, eyes wide open. I'm not asleep! What did I miss? The speaker drones on and on and you wish someone would open a window and why are the slides so dark and hmm I should probably increase the Tm of my PCR, and perhaps try her way of mutagenesis, I wonder if the student made up the kanamycin correctly — WHAM. Head back, sore neck. Questions? What?

And you are totally, utterly impotent against it.

It's horrible. And it is often nothing to do with the speaker, and everything to do with the soporific nature of every bloody seminar room every designed — and that most of our seminars are at lunchtime. The morning coffee has worn off and you're digesting lunch, and all you want is sleep, sweet sleep.

A while back, while our honours students were in the throes of writing up and preparing for their thesis defences, I distributed a number of links that described how to give a scientific talk. One of the points that I emphasized was that Powerpoint (spit) should be used as a tool to put your slides in front of people, not as an end in itself with pretty but distracting purple fades and those bloody annoying transitions. Leave that crap, I said, to the corporate busybodies.

It seems that I may have misjudged the corporate SS. Badly.

My spy upstairs is on his way to a Collaboration Technologies Workshop on Friday. Lucky fellow. He distributed a Powerpoint (spit) file, that claims to be

intended to support the attendees of the collaboration technologies workshop on Friday 15th December 2006.
The pack contains slides and information from various IT research services – Gartner, The Burton Group and Ovum and aims to provide a common unbiased perspective on collaboration and associated technologies.

Corporate identity-wise, I was disappointed. There's a rather tasteful rendition of the University's logo in the top left hand corner of each slide, which are framed by a thin, blue line. Nice.

Question: If you can ask if you're delirious, does that automatically mean you're not?

It's all right, I've cut the analgesic dosage (mmm codeine) so I should be reasonably coherent now.

Went to the quack's on Friday, and fortunately did not get to see the muppet who managed to miss the pneumal party when I crawled into his office last Thursday, barely able to breathe and unable to stand. Instead I saw a nice lady doctor who continued my roxithromycin prescription and also prescribed a cephalosporin. That is because I said I did not want a penicillin, as we use beta-lactamases in the lab all the time and I did not want to take the risk that anything pathological in me had managed to acquire resistance. Unlikely I know, but always a worry.

I don't actually think she knew what I was talking about, but tried her best. She had never prescribed cephalosporins before, and knew nothing about them, but spent a good few minutes looking in various books before deciding what to do. She didn't even know who Ed Abraham was, which is a shame, because I did my DPhil in The Sir William Dunn School of Pathology, where the whole antibiotic story took off.

If anyone fancies a move to Cambridge, UK, they should get in touch with me, as my old boss has got some Wellcome funding. Yippee!

lewisham™, n
industrial-strength cleaning solution.

e.g. Nothing cleans up smelly drains like lewisham!

The Myers-Briggs (personality) type indicator has a reasonable reputation in the psychological profession. It is an attempt to make C. G. Jung's theory of psychological typing accessible, that is to use psychological markers to understand real people in real situations. Essentially there are four scales - you can call them dichotomies or preferences if you prefer - on which people can be measured. I prefer 'scales' to 'dichotomies' or 'preferences' because they are each a continuum, rather than binary.

The four scales assess a person's 'favourite world' (internal or external), how they handle information, how they handle making decisions, and how they deal with other people. See http://www.myersbriggs.org/my-mbti-personality-type/mbti-basics/index.asp. You do score in a binary fashion for each of these four 'tests', but any counsellor worth their salt will bear in mind where you are along each scale. So, crudely, 2^4 = 16 basic personality 'types', although of course there is overlap (and you have to read between the fuzzy lines to find out which types are "this guy is a nasty piece of work"). The assessments should be performed by people who have been trained, and who can help interpret the results to the subject and counsel them as necessary. Knowing someone else's personality type can help you understand them - and knowing your own helps you understand yourself (#inc confucious).

Medical update.

It's not what you know, it is who you know, especially when it comes to medical matters. And if you know someone who can prescribe antibiotics and get you into A & E's X-ray unit on a Sunday morning then you must be doing pretty well. The good news is that it does not appear to be a fractured rib.

The bad news is that even if it was, you wouldn't be able to see it because of the consolidated pneumonia and pulmonary effusion ("50% of hemithorax"). My specialist's comment was "People with chest X-rays like that are usually already in hospital". Oh, and "It's getting better, but you're taking a week off".

Well, this puts the old thumb into perspective.

I appear to have a fractured rib. And it hurts. I've raided the pharmacy for anything with codeine in it and am trying not to overdose.

If I can find somewhere comfortable to sit and type I might post some of the things I've been meaning to talk about for months. But then again my brain might turn into Swiss cheese and I won't be able to think at all.

woolloomooloo, n
in anim. husb. Great noise or excitement; uproar.

e.g. I was woken at 3 by the most tremendous woolloomooloo in the croc house. Bloody possums.