31 July 2010

Living without a stomach

Most of us take our stomachs for granted, but for some families the risk of cancer of the stomach is exceptionally high, often occurring at a young age. This story from BBC News relates how two sisters with a mutation in the E-Cadherin (CDH1) gene have been coping after having prophylactic gastrectomy - the only treatment known to reduce the risk of developing gastric cancer.

CDH1 is a fascinating gene; I've been interested in the cadherins since my time in Birmingham when we published the first reports of CDH1 mutations in UK gastric cancer patients back in 1999, and also linked it to colorectal cancer (although the risks of this appear a good deal lower). If you carry a disruptive mutation in CDH1, you have a high risk of developing diffuse intestinal-type stomach cancer, and females are at increased risk of lobular breast cancer. Cadherins are proteins involved in cell to cell adhesion in many tissues, and there are quite a few of them. Their stickiness is based around their molecular structure and their ability to bind calcium ions.

More recently I was involved in some work which connected a very rare and intriguing form of epilepsy, EFMR, to a protocadhern gene PCDH19. EFMR - (Epilepsy affecting Females, with Mental Retardation) shows a very odd inheritance pattern; it is X-linked, but while it affects female carriers (who have one faulty PCDH19 gene and one normal gene), males (who only carry one copy of PCDH19) are left completely spared, although they can pass the disorder to their daughters. The phenomenon seems to be due to "scrambling" of the connections between cells, due to a process in females where one X chromosome is switched off in each cell, resulting in some cells running off one of the Xs, while the rest run off the other.

These are fascinating molecules, involved in a wide variety of disease processes, and make exciting targets for therapy. It shows that the common claim that the Genome Project has had minimal impact of human disease is a load of bunk. Our ability to get down and dirty with the genes is already yielding major benefits, and these are being rolled out to patients every day. Is it easy? No. Does it offer a panacea? No. But we are making a heck of a lot of progress, and genetics remains the most exciting and active field in medicine today.

[Click the image for more info from Breast Cancer Research]

What would Dawkins Do?

It's argued by some that even if religion (specifically Christianity) is false, it still might be useful on occasion to some people. Certainly on the face of it, this might have some merit. Here's a story about a would-be Christian robber being turned from his evil act (still running away though) by the words of the Christian shop assistant [BBC News].

Once certainly has to admire the presence of mind and the calm resolve of Ms Nayara Goncalves, the shop assistant, and good for her, I say. She defused a very dangerous situation - OK, the gun was only a replica, but she wasn't to know that, and one gun attracts others, and these situations frequently end up messy in the USA.

So suppose an *atheist* robber comes face to face with an *atheist* shop assistant? What then? How could that situation be handled? I can't see how a lecture about The Blind Watchmaker or memes or the ahistoricity of the resurrection myth or speculation about the origins of life is going to cut the mustard - you need a soft yellow underbelly. In the case of the theist, that SYU is the meek and mild Jesus thingy, washed down with a bit of fire and brimstone, no doubt. The atheist's weak point is *where*, precisely?

It's good to be green

Now this is seriously cool. A salamander with intracellular photosynthetic algae! No, really. Check it out in Nature News. Maybe photosynthetic humans are not too far away.

30 July 2010

The Smoking Donkey

Back on the Donkey post (seriously, guys, are you REALLY trying to claim that the anonymous author of the Gospel of "Matthew" was trying to make a deep point, or is it actually Facepalm Sunday??), Peter took exception to my characterisation of "Matthew" sexing up his dossier. Am I looking for Donkeys of Mass Destruction? Or the Mother of All Donkeys?

It's all very simple. Yea verily, Matthew was trying to link the story of Palm Sunday to the prophecy in Zechariah 9. As was Jesus. Except that Zechariah only has ONE donkey, and he emphasises this by the parallelism of "a colt, the foal of a she-ass". A bit like "the son of man", I suppose.

But there it is. The simplest, easiest, most clear-cut example you could wish for that the bible is 1. prone to error, and 2. not the word of god. And, as is perfectly obvious to millions of people, the historical basis for the supposed resurrection is revealed to be very shaky.

So why do some apologists continue to claim there is any historical basis to the resurrection at all?

Special treat for Graham...

29 July 2010

Tim Minchin was wrong!

Yep, just when you thought that someone had come up with the perfect peace anthem for the Israel/Palestine issue...

...someone goes and spoils it all.

Back to the drawing board, folks - we need to come up with another solution to this vexing issue.

Church upholds sanctity of marriage shocka!

A vicar has been found guilty of conducting sham marriages to attempt to bypass immigration laws.

Giving evidence, [Father Alex] Brown insisted he only ever married couples he was sure were together for the right reasons and said he only made exceptions if the bride-to-be was about to give birth.

Archdeacon of Hastings and Lewes, the Venerable Philip Jones, said it was a very unusual case

He admitted he occasionally forgot to check passports of foreign nationals and said he became suspicious of one or two couples, but only because of the vast differences in age between bride and groom.

360 of them to be precise. In FOUR YEARS. Busy little beaver.

I admit to having something of a soft spot for the Anglican church. They are not as nutty (usually) as the Calvinist brigade. But it is appalling that people within such an organisation can maliciously warp and abuse the law of the land for their personal gain, defrauding and manipulating people in the process. But maybe that's par for the course...

Good old Willo!

That's my dad :-)

28 July 2010


Polymeron, one of the nice commenters over at CommonSense Atheism thought this was a pithy statement, which makes me happy. It actually exemplifies the reason why I get rather frustrated when listening to people who are supposed to be high-end philosophers, making the same old essentialist fallacy time and time again.

Don't get the wrong idea - I try not to make a habit of hanging out with such types, but we had a chap called Brian Leftow over in Belfast last year, and he gave a talk on the existence of God, which was chocka full of the essentialist fallacy - there is a dude called Alvin Plantinga who tried to reformulate St Anselm's tired old Ontological Argument (check Wikipedia if I'm losing you here), and basically comes up with one that again milks this fallacy like a prize cow. As if "God the Thing" can have "Omnipresence the property". Silly silly silly.

Maybe it's because in medicine we are used to breaking things down and reassembling them, and seeing whether what holds at the micro holds at the macro. Maybe we can see big pictures emerging from the little pictures more acutely than some (not all!) of our Philosophy pals. Indeed, Richard Swinburne was over also, and he made similar mistakes to Plantinga and Leftow in assuming that "mind" and "soul" were *things* that you could say stuff about, rather than viewing the human organism as a system, with internal states, inputs and outputs. Maybe we are just aware that we can mislead ourselves very subtly in our reasoning, and we are careful not to make claims that we can't back up with evidence from another source, or use to generate testable predictions.

I rather think the job of philosophy would be a good deal easier, and half the punters would be able to be more gainfully employed, if this simple principle was emphasised a little more - not just in academic philosophy, but in life in general. Systems display behaviours, folks. Got it?

Now THAT was high-brow for this time of the evening, wasn't it?

27 July 2010

Segmentation in Arthropods

Face it - you've always wanted to know whether segmentation was present in the common ancestor of the bilaterians, and whether the modes of segmentation in (say) different arthropod groups reflect divergence from an ancestral mechanism, or whether they are independently derived in the different lineages. Your genes say one thing, your fossils and embryos say another. What to do? What to DO??

Fret no more - my good friend Dr Ariel Chipman from the Hebrew University of Jerusalem will set you straight. I like this video because we humans use the delta-notch signalling pathway (as do other chordates) to set up our somites and hence our body segments, and it's interesting to see how other critters accomplish this remarkable feat that is segmentation.

More Mathematical Universes...

I'm really grateful to Yair (we ran into each other in a discussion elsewhere) for coming over here and giving the Mathematical Universe Hypothesis a bit of a blasting. Instead of just adding to the comments, I thought I would be lazy, and cheat a bit by replying to Yair's comments in a brand new post. Scurrilous, I know, but I had to do a bit of thinking and typing, and that tipped me over the character limit. For the context, please see the comments on the original thread. So here goes... enjoy!

Hi Yair,
Excellent points; I don't know if I have sufficient philosophical or mathematical background to tackle them, but I'll give it a go... I'm cutting and pasting a bit here; hope this makes sense.

I suspect Godel puts an end to a true TOE.

I have a sneaky suspicion that may be correct - for beings *within* the system. If the MUH (for want of a better term) is correct, then THIS universe has its own rules, but is essentially of the same status as a universe based on the rules of Conway's Game of Life. If you can imagine sentient critters within the GoL, I wonder whether it is possible for them, no matter what experimentation they do, to perceive that they are in fact running in an instance of GoL? For sure, they might hit upon the solution, but could they *prove* it? I don't know. Yet in that case, we can say that a ToE *exists*, and in principle they could know those rules - just (perhaps) not whether they apply to *their* universe.

The MUH says that the right description of reality is not some particular description/TOE, but specifically the most general description we can think of.

Not quite - there is a TOE for THIS universe, and that is quite specific; however, *every* TOE has its set of universes (e.g. the GoL rules will have a set of universes - to all intents and purposes *infinite*). For each universe, its TOE defines *it*. A TOEE (Theory of EVERY Everything) is, as you say, essentially Mathematics itself. At least that's how I understand it...

Third - How did our mathematical faculties evolve? I believe they evolved as they did due to the Boolean nature of classical physics.

Actually, I don't think that's correct. I think we (somehow) hit an evolutionary trajectory wherein it was advantageous for our brains to evolve the capacity for doing mathematics, but we do still find it rather hard, and I think that suggests that our abilities have evolved to solve some of these general problems because the mathematical nature of the universe makes it behave that way, rather than these being an *arbitrary* feature of the universe.

Hmmm, maybe badly phrased again... However, it is really *very* striking that when we move away from classical physics to the quantum world, mathematics is really rather insanely good at describing what we should expect to see - even when it is hugely counter-intuitive. Again, to me that suggests that our brains have hit on an ability to do maths in the abstract, quite apart from how we perceive reality. I admit this is a tricky one, and I do feel (as a medical doc) a little out of my depth.

they capture a feature of physical reality, an order and regularity that can be expressed mathematically - but not the mathematical object itself.

Actually I think you are right here, but I don't think that affects my point. We make models, but the models are at best representations of *subsystems*. The deeper mathematical reality could (I think) be represented mathematically, and if you were able to do this for the universe, you would have a complete description (just like the Game of Life) that would be isomorphic with the "real" thing, so a subsystem within the real universe would have no way of knowing whether its universe was "real" or mathematical, because in either instance it would *feel* real.

Mathematical truths don't hold in the world.

But the *right* ones do, which is the interesting thing.

there is no further requirement that this massive combinatorial construct will match the structure of reality itself.

I'm not sure how this corresponds with Turing's notions of computability; it would seem that with a few very *very* basic axioms (and I admit to assuming these, but they "seem" OK for this purpose), we can pretty much get anywhere we want to, and moreover the universe appears to be the sort of structure that is describable in these terms (although not *easily*, I'll grant you).

I'm working my way (very slowly) through Penrose's "Road to Reality", which is rather good, if hard going for a biologically-minded person. He seems to argue for the "existence" of mathematical truths in quite a hard way.

can you imagine that only a small world exists, where a single intelligent being is busy thinking? He can imagine alternate reality, but by assumption these do not exist in our hypothetical. Why can he imagine worlds that don't exist? Why can't we?

Because I think(!) that when we use mathematics, we gain *access* to alternate realities (read-only). I have already mentioned our worlds that "don't exist", such as GoL instances. Yet if the MUH is correct, they DO "exist", but are only seen as such from the viewpoint of those *inside* them. Like us inside ours.

Thanks again for your input, Yair - much appreciated. As I mentioned, I think I'm running out of philosophical road here; might be good to have Max Tegmark himself (or Roger Penrose) take this on :-)

[Is that you that I found in Google at the HUJ? If you ever find yourself hanging out with any of the evo-devo crowd, I have a very good friend who heads one of the labs there.]


26 July 2010

Fakery and propaganda in the bible

Back when I was in Sunday School, Mrs Hansen told us that the bible was true - every word. And we had to read it diligently, and believe it, because it was the Word of God. The problem, of course, is that every word in the bible is certainly *not* true; there are numerous contradictions, mistakes, ahistorical fabrications, spin efforts and blatant porkies, and any serious scholar of the biblical texts will tell you as much (although if they are in a post paid for by one of the churches, you may have to ply them with a few drinks first). But this is not really in debate - it is certainly the majority opinion amongst biblical scholars; your minister will not tell you this. Even though he *knows*.

But that is by the by; this post is just to highlight one that I rather like, because it is SO blatant, SO clearly fabricated, and is an excellent example of the sort of process that went into creating a gospel back in the late first century, when Jesus had already been dead for decades. The story is that of a donkey. Or maybe two donkeys. Well, really ONE donkey.

It's Palm Sunday; Jesus is about to make the triumphal entry into Jerusalem. The author of Mark (not really Mark, of course - we do not know who wrote any of the gospels, not even Luke) takes up the story: [ASV, BibleGateway.com]

1 And when they draw nigh unto Jerusalem, unto Bethphage and Bethany, at the mount of Olives, he sendeth two of his disciples,

2 and saith unto them, Go your way into the village that is over against you: and straightway as ye enter into it, ye shall find a colt tied, whereon no man ever yet sat; loose him, and bring him.

3 And if any one say unto you, Why do ye this? say ye, The Lord hath need of him; and straightway he will send him back hither.

4 And they went away, and found a colt tied at the door without in the open street; and they loose him.

5 And certain of them that stood there said unto them, What do ye, loosing the colt?

6 And they said unto them even as Jesus had said: and they let them go.

7 And they bring the colt unto Jesus, and cast on him their garments; and he sat upon him.

8 And many spread their garments upon the way; and others branches, which they had cut from the fields.

9 And they that went before, and they that followed, cried, Hosanna; Blessed is he that cometh in the name of the Lord:

10 Blessed is the kingdom that cometh, the kingdom of our father David: Hosanna in the highest.

OK, that's fairly straightforward. I wonder what the (again anonymous) author of Matthew has to say on the topic?

1 And when they drew nigh unto Jerusalem, and came unto Bethphage, unto the mount of Olives, then Jesus sent two disciples,

2 saying unto them, Go into the village that is over against you, and straightway ye shall find an ass tied, and a colt with her: loose them, and bring them unto me.

3 And if any one say aught unto you, ye shall say, The Lord hath need of them; and straightway he will send them.

4 Now this is come to pass, that it might be fulfilled which was spoken through the prophet, saying,

5 Tell ye the daughter of Zion, Behold, thy King cometh unto thee, Meek, and riding upon an ass, And upon a colt the foal of an ass.

6 And the disciples went, and did even as Jesus appointed them,

7 and brought the ass, and the colt, and put on them their garments; and he sat thereon.

8 And the most part of the multitude spread their garments in the way; and others cut branches from the trees, and spread them in the way.

9 And the multitudes that went before him, and that followed, cried, saying, Hosanna to the son of David: Blessed is he that cometh in the name of the Lord; Hosanna in the highest.

Interesting. Mark has a colt; Matthew has a colt and its mother. Contradiction? Well, if that's all there was to it, it would not be that impressive. Maybe Mark just didn't bother mentioning its mother. Maybe there were really two donkeys, but only the colt was important. However, that is not the interesting thing here. What IS interesting is that this is not Matthew's separate perspective - Matthew is working off the same TEXT as Mark - indeed, it is spectacularly obvious that when Matthew is writing his document, he has the book of Mark in front of him. He is COPYING it, and FIXING it where he thinks it is wrong.

However, if you flick back to Zechariah, you will see that it is *Matthew* who has not properly understood the prophecy; Zechariah only mentions ONE donkey, but repeats and emphasises the donkeyness of our donkey by a poetic technique known as parallelism - the Old Testament is full of it, and we do it in English too. It is similar to repetition for dramatic effect. But poor old silly Matthew thinks there are two donkeys, so he fixes Mark to make it look like the prophecy was fulfilled. Just like he fixed the "virgin birth" because he did not have a Hebrew bible to work from; just the Greek (which mistranslates "young woman" as "virgin").

Now, again, scholars have known this for donkeys' ages (sorry). But they didn't tell YOU that, for very obvious reasons. The thing is that the Gospel of Matthew is absolutely *riddled* with fixes like this, where the "real" story of Jesus (or at least the story that he had received - remember, the author had never met Jesus, and was writing at least 40 years after Jesus had died) didn't match some prophecy, or it lacked dramatic effect, so Matthew "sexed up" the document.

He faked a prophecy: "He shall be called a Nazarene" (Matthew did not realise that "NazarENE" had NOTHING to do with the small new town of NazarETH, but was a completely different term); he faked the angels at the tomb; he faked the *guard* of the tomb, he faked the earthquake and the dead rising and going into Jerusalem. He faked the post-resurrection appearances (the original, Mark, *never* mentioned any appearances of Jesus after his death - just an empty tomb).

But it is fascinating to see that part of the "Word of God" is a clumsy attempt to sex up another gospel that the author thought was deficient in a number of areas. Not only are the gospels NOT the "Word of God", it is clear that the authors *knew* this; they were perfectly aware that they were not writing "scripture", but marketing blurb. They were advertisers, and dishonest ones at that. And of course, there is no reason to suppose that what goes for Matthew does not also go for Luke and John (and Mark too, for that matter).

The whole basis for Theistic Christianity - crushed under the hooves of The Donkey That Broke The Gospel's Back.

18 July 2010

Sexy scientists?

Hmmmm. The devilishly clever (and I'm told somewhat sexy if you like that sort of thing) Luke Muelhausen from Common Sense Atheism has got himself into a spot of hot water after posting a list of "sexy scientists". The accusation is that he is being sexist (they're all girls, except for the triceratops at the end, draping itself voluptuously under the great PZ Myers), but *worse*, it would appear that not all the subjects could really be described as *scientists*. Whether one finds them sexy or not, I suppose, is a matter of taste. If we're trying to get the young generation to admire scientists who triumph over the odds to become leaders in their fields - and, let's face it, there would seem to be a glass ceiling in science - should we not be vaunting other attributes than their "sexiness"?

I'm torn. Sexy is great, but particularly for women in science, I think we should be celebrating excellent brain work, drive, determination etc.

But then in highlighting the sexy aspect, perhaps this throws an ironic light on the whole thing, thereby enhancing the profile of women who really have made a significant difference in science. And anyway, what's wrong with a bit of fun?

Irony is good too.

[Also check out Tiny Flame's view on the subject...]

02 July 2010

Science! It must be - Bob Jones says so!

Thanks to the inestimable PZ Myers, my attention has been drawn to a "science" text book for children published by Bob Jones University in the US. Have a browse through the sample chapter and the "Look inside" pages. It does make you despair for the lost generation of American kids who are undergoing the systematic decerebration of Christian Homeschooling. But it makes you despair even more to think that an *adult* put this crap together in the belief (unsupported by evidence) that they were creating a book that was worthy to have the word "Science" in its title.

And it also says something about the integrity of the whole crazy institution that saw fit to grant Mr Ian RK Paisley an honorary "PhD", as if enough had not been said.

THIS is why it is important to tackle creationism. Richard Dawkins is absolutely right - this is the intellectual abuse of children.