28 September 2011

The difference between Religion and Science.

RELIGION: "Jesus is risen from the dead! Hallelujah!"
SCIENCE: "So you say; let's fire some protons at him."

Here's a 3D mouse embryo

Have your cyan/red glasses at the ready! Lots of great stuff like this
from the Edinburgh Mouse Atlas: http://genex.hgu.mrc.ac.uk

27 September 2011

What planet are they on?

I like Christians. I really do. Indeed, that's why I'm a Christian Atheist. I even have a soft spot for the craziest spittle-flecked fundamentalist loonies - they're endearing, in an unhinged concrete-mentality sort of way. They have arranged their little brains in such a way that everything makes sense to them, and everything that falls outside their comfort zone is either abomination, or the Lord moving in mysterious ways - in either case, not something to be engaged with at an intellectual level. Of course, some of their views are objectionable, and they get all cross when you call them out over them. That's the fundies; many people are of course a good deal more liberal, and have actually thought a little about the world outside. Many Christians do realise that Muslims (for example) believe what they believe with the same sincerity and using much the same arguments as the Christians do. They're happier to engage with topics that make them uncomfortable, happier to challenge their own preconceptions.
Yet even among this relatively enlightened group, it's fascinating to see that most really don't like to play "what if?" with their religious beliefs. What if Jesus wasn't the son of God? What if he wasn't born of a virgin? What if he didn't rise from the dead? These "what ifs" are questions that I tackled when I was a theist. I decided to pit my beliefs against the evidence.
If Jesus really was born of a virgin, what should we expect to find? Well, one thing might be any reference to this fact during his lifetime. It's interesting that not ONCE does Jesus himself claim to have been born of a virgin, and even the Bethlehem birth is contradicted in the Gospel of John, suggesting that the nativity stories (themselves contradictory) were simply made up.
As for the "Son of God" thing - what does that even mean? In our quasi-Christian society we have this notion of the Trinity (deeply unbiblical, but hey) instilled deep in our minds, and we have forgotten that this concept was itself a late invention, arising from the Ancient Egyptian religion, not from Judaism and certainly not from the teachings of Jesus. In the early centuries of Christianity, this was debated furiously (and often fatally) - the Trinitarians were the winners, but both groups could claim the same biblical support.
And what about the Resurrection? I've covered this topic before, but it's a favourite trope of apologists that the resurrection of Jesus is the "best attested event in history". This claim is simply a lie - even a cursory examination of the gospel texts shows that the writers started with the belief, and liberally made up "facts" to fit. Different authors made up different stories, and these stories conflict - not in the manner of minor conflicts that we might expect from different witnesses' perspectives, but in critical details of sequence and timing that show quite clearly that they are spinning yarns.
But for all that, I still do like theistic Christians, and I hope they're able to take a slightly broader view, and try - even if just occasionally - to think outside the narrow box that they've allowed themselves to become trapped within.

24 September 2011

Happy 4th birthday Olivia!

My wife bakes & decorates the bestest cakes in Northern Ireland, so she does.


Lewis found this fossil belemnite on the beach at Jordanstown.

23 September 2011

QR code

Sent from QR Reader

Plato vs Darwin

Much as I like Plato, and indeed subscribe to a certain neoplatonic mathematical notion of the origin of the universe, he got some things badly wrong, and it's a mistake that many people continue to make today. Indeed, it is an error that I frequently encounter among my philosophy pals, so perhaps I'm going to get it in the neck, similar to the umbrage that I playfully engendered with my "Show me the Sausages" post.
Or perhaps not. After all, most *real* philosophers are relatively sensible people.
Anyway, what is Plato's error? You may recall that Plato had a notion that somewhere in some eponymous platonic realm, there is the definition of the perfect "thing", e.g. the definitional chicken. This is the model example of what a chicken should be, and all chickens express this inherent "chickenness", but since they do this in the real world (where things are mucky), they do so imperfectly. So variation results from variable imperfections in the manifestation of this chickenness.
However, we now know (and Darwin blew this out of the water in "Origin") that there's not a perfect notional chicken - instead, what we do is take a population of organisms (and this works for humans too, of course), notice that they share several features in common, we throw a line around them to show that they belong to a meaningful grouping, and we attach a name to that group.
What this means is that our perfect chicken comes *after* the group of real chickens; we use real chickens to notice the things that distinguish chickens from guinea fowl, for example. But there is no inherent "chickenness" that has to be expressed by our firmly-classified bird.
It's the same for humans. Real humans are not variable manifestations of the perfect Vitruvian man (or woman), but organisms that form a recognisable biological group, so we call that group "human" and use the essential characteristics to work back to certain features we all share in common. The Vitruvian man is therefore a kind of idealised average, not a blueprint.
So the next time you find yourself thinking platonically, catch yourself on and try to think like a Darwinian.

20 September 2011


I hate fax machines. It's a deep-seated visceral loathing of a technology that is decades past its use-by (not best-before) date - a technology that is still considered (in departmental policies at least) an acceptable way of transmitting confidential information from one point to another. Consider this.
Today in our office (I work in a busy Genetic Medicine Department, and we get barrow-loads of correspondence relating to our patients every day) the fax machine broke. It's a venerable old thing, but it has now entered the realm of permapaperjam and refuses all my obsequies and pleas to unfeckingjam itself. This is bad enough, but we're awaiting an important test result from an external lab, and the external lab won't email us the report; their policy is that it can only be sent by post or by fax.
Why won't they email? Well, their policy is that they will only email to addresses ending in nhs.uk, so the fact that the Northern Ireland NHS email system ends in hscni.net is a Big Deal. We, apparently, are off the grid.
So the only way to get the result is via this useless obsolete chunk of dead beige plastic that can't even do its primary job. We have a problem, and the problem is that policies don't change very well.
Now, this is 2011. We have motorised vehicles and computational devices and electrical hand dryers and soap and stuff. We even have Pot Noodle. What in the name of all that is holy are we doing, relying on ancient insecure unreliable user-unfriendly hackable useless trash like fax machines? There are better ways of doing this - encrypted file attachments is one. Secure server download is another (and these are potentially properly auditable - calm your quaking desire, O box-tickers).
But the NHS, bless its socks, still seems to operate on the principle that sending a series of beeps across a phone line in the hope that you're connecting with a non-hacked (thank you, Mr Murdoch) machine on the other end, relying on no paper-jams and proper scanning of the feed sheets and the person manning the receiving machine being of near-average intelligence is the way to go.
End this insanity. Destroy these machines. Outlaw the fax. Join the 21st Century.

19 September 2011

Read/write DNA?

Stewart Church has a vision. Not only does he want to read vast quantities of DNA using cheap testing methodologies, he wants to edit DNA in vivo and in vitro. To step into the DNA polymer and make it dance to our tune. To treat genetic disorders. To treat cancers, heart disease, inflammatory disease. To turn cells into therapeutic vehicles. Here's a link to the BBC article. This is the future. It may take a while coming, but it'll get here. The NEW New Genetics.

16 September 2011

Halloweenosaurus Rex

1/10 approx scale prototype. We are so going to win the prize this year!

15 September 2011

#Evolution Hallowe'en!

Napkin sketches of concepts for kids' Hallowe'en party. Last year's alien and dalek were pretty darned near unbeatable. This year the stakes are higher.

14 September 2011

Stupid bird flew into the window and left this mark

Obviously quite a mucky birdprint. It just shook itself off and flew away again.

12 September 2011

Facilitating Genetic Research.

The UK is a world leader when it comes to genetics, and particularly in the application of the findings of genetics to the care of patients with rare disorders. I've been at a meeting today where we have been discussing lots of research studies and how to help them meet their accrual targets, and how to cut down on the red tape associated with getting them approved in multiple centres in the UK. Northern Ireland doesn't have the same CLRN infrastructure as England and Wales, so the support models for NI have to work somewhat differently, but good ideas are good ideas, and it is fascinating to see how people go about designing studies. There are some pitfalls which seem to be rather common.
One is to assume that just because one Trust Research Office will approve a study, that another one will, without asking for substantial protocol amendments. Another is in the number of patients you're realistically going to be able to recruit. If you can recruit a larger number than your power calculations require, that's great. If not, you have to take a long hard look at the study and see what you can change to make it meaningful.
One big lesson is that there are studies out there, and they are recruiting. We owe it to our patients to let them know about studies they may be eligible for, and indeed they may actively wish to participate in. But with a plethora of studies, how do you make sure all the clinicians know of the correct studies? Tricky. There needs to be an app for that.

11 September 2011

Do quarks work like this?

I'm a geneticist, not a physicist. But some thoughts strike me from time to time. One is that nature is 4-dimensional (3 spatial dimensions plus time); another is that you never see one quark on its own - it is always accompanied by two other quarks or an anti-quark. Now, if the universe is a space-time lattice (like all good universes should be), perhaps these "particles" are better thought of as kinks in the lattice, as below.
See you in Stockholm, losers!!!

Happy little mini #TLUD.

Tricky to get this little chappie lit, but he seems content with his slow burn. Secondary air a little restricted though. The outer shell is a soup can, and there's an inner pyrolysis chamber too, with combustion chamber perched on top. Not masses of heat output; may need some tuning.

03 September 2011