Answers in Genes

In which I have a fight with an Australian lady on the radio

2012-01-29T19:11:00.001Z

Well, today was certainly an interesting one. Hot on the heels of the recent report in the Lancet about how cells derived from embryonic stem cells have safely integrated into the maculae of patients with macular degeneration, I was on BBC Radio Ulster defending the ethics. Quick summary - these cells were injected into the eyes of patients with degenerative disorders of the retina; the cells have integrated, and are apparently functioning well. This is exciting and promising research, for people with visual disorders, and many other degenerative conditions.

I think Embryonic Stem Cell Research (ESCR) is a highly ethical avenue of research, but my opponent thinks otherwise. She is Josephine Quintavalle from a lobby group called "Comment on Reproductive Ethics" (CoRE); they take a fairly hard-line embryo-is-a-full-human-person tack, pretty much in accordance with the official position of the Roman Catholic Church (which I find wholly ridiculous, but I may post on that some other time).We had a very polite discussion, expertly chaired by the indomitable William Crawley, but I'll leave the listener to decide whether I did a good job or not.

In retrospect, I wonder if I should have been a little more aggressive. The arguments against ESCR are pretty weak, and are based around a fundamental misunderstanding (or downgrading) of what it means to be a human person.

Anyway, have a listen - our bit starts at about 33 minutes: http://t.co/V0Rr94dP

Please leave any comments below - I would love to hear 'em.

Human Genomics Strategy Group releases report

2012-01-25T11:43:00.001Z

Here's the skinny:
http://mediacentre.dh.gov.uk/2012/01/25/genomic-innovation-will-better-target-treatment/
This is a topic dear to my heart, so expect more blogging about it
soon. I've had a quick look at the document, but this sort of thing
requires Deep and Ponderous Consideration. From the press release (25
Jan 2012), the main recommendations are:

• [Government] to develop a cross-cutting strategic document, to set
out the direction on genomic technology adoption in the NHS;
• [Government] to develop a national central genomic data storage facility;
• NHS Commissioning Board should lead on developing genomic technology adoption;
• to work to develop a service delivery model for genomic technologies;
• NHS should continue to develop genomics education and training;
• to raise public awareness of genomic technology and its benefits.

These are OK as far as they go, and I think the UK is already in a
great position to bring these objectives and their attendant benefits
to realisation. Whether we would be able to do that with Mr Lansley's
proposals to "reform" the NHS in England is another question (I
respectfully differ with the government on this issue - I think the
proposals in the forthcoming NHS Bill are utterly wrongheaded, and
will actually harm the harnessing of genomic advances, but that's
another story).

The first point is important; the second is a very welcome proposal -
we need to set up such a unit as a "Trusted Third Party" repository of
genetic and genomic information. Third point - yes; fourth - yes -
Clinical Genetics Units can form the nucleus of this model. Points 5 &
6: of course - these are no-brainers. Perhaps the most important thing
we need to add to these is a strategy for rigorously gathering
evidence to see how much our greater genomic capabilities actually
influence the health of real patients. Everything about Medicine must
keep an eye to the evidence.

We have 23 established centres of genetic (and increasingly genomic)
excellence in the UK, namely the Regional Clinical Genetics Units.
These units already work closely with other medical and surgical
specialties to bring the fruits of the genetic/genomic revolution to
patients and families with both rare diseases and common diseases, so
a fantastic infrastructure already exists. We are already
"Mainstreaming". If we develop and resource that infrastructure
appropriately, great things are possible, and the UK can continue to
lead the world in both the research and translational aspects of
Genomics.

[The link to the full report on the DH website doesn't appear to be
working yet, but I'm sure that'll be fixed soon].

I would love to hear folks' thoughts on this - this is a major plank
in the future of Medicine.

Some thoughts on prescribing

2012-01-19T23:18:00.000Z

Those of you who know me will know that I am no shill for Big Pharma. I conservatively reckon that you could strip our pharmacopoeia down to maybe 30 drugs, and still be able to successfully manage the large majority of medical conditions that come our way. OK, 30 may be a bit tight, but even so, it seems that we as doctors are bombarded with ever more snippets of trial data that supposedly demonstrate the superior efficacy of Fuckitol over Bollexin and such like.

Every now and then I like to remind our medical students of a few salient points when deciding whether a patient needs a certain drug, or whether their medication needs changed at all. These are in no particular order; they are not meant to be comprehensive, nor are they meant to replace the Ten Commandments of Prescribing that I've mused on previously. However, they may help in that decision-making process when you're weighing up the findings of studies.

Statistical significance is not the same as biological significance.
Just because you see a really impressive p value, this does not mean that prescribing drug A will be much more effective than drug B (or even nothing at all). You need to ask yourself: what is the size of the actual effect that is being measured? Is this a clinically relevant distinction - i.e. will your patient be much better off on drug A than they would be otherwise?
Relative risk is clinically meaningless - you need absolute risks.So what if drug A has twice the risk of complication X than drug B? If the complication only arises in 1% of patients on A, that means that only 2% of patients get the complication on B. That's still not a lot. Furthermore, for rare complications, the numbers are typically very low indeed, so calculating this relative risk is difficult, and the confidence intervals tend to be large.
Trial results are very different from real world results.
Drugs are trialled on relatively standardised patients being monitored in standardised ways, and the subjects and researchers are typically super-motivated to make sure they're taking the drug properly and doing everything by the book. So even if the superiority of drug A over drug B is truly demonstrated in a trial in a certain group, it is very rare that the same degree of superiority persists in the Real World, which is where your patients live.
Trials rarely include elderly patients on polypharmacy with multiple co-morbidities.
This is important, because very often these are precisely the people in whom you will be prescribing drug A or B. It's related to the point above - patients are complex. If you are going to start a patient on a drug, be aware that it is very likely that they would not have made the entry criteria for the study that assessed its efficacy in the first place, so exercise appropriate scepticism that you're doing any damn good at all.
A percentage improvement in a surrogate marker is not the same as effect on underlying disease.
Perhaps one of the most important points. All young doctors have it drummed into them: treat the patient, not the blood result. Lowering someone's cholesterol from (say) 6.0 to 4.5mmol/l is of no value whatsoever unless you can show that you have reduced their risk of heart attack (and not increased their risk of other problems). It does not matter what the rates of heart attack are in the population for patients with cholesterols of 6.0 vs 4.5 - the relevant measure is: what is the rate of heart attacks in patients whose cholesterol has been lowered from 6.0 to 4.5. These are not the same thing.
Differences between treatment and control groups in trials do not equate to the probability of improvement if you treat your individual patient.
This is a slightly more complex one. Say you have a drug A which has been shown in a trial to be effective against The Purple Heebie-Jeebies (PHJ). In a big trial the group of patients on A showed improvement in 50% whereas the control group had a 25% rate of improvement. In walks wee Mrs Miggins, and you confidently diagnose PHJ. Now you might think that if you start her on drug A she will have a 50% chance of getting better, whereas if you didn't, her chances are only 25%. Sounds good. However, let's assume that the trial data are correct, and she fits the bill. You have 4 Mrs Migginses, and you start them all on drug A; 2 of them get better, whereas only one would have got better otherwise. But you have treated FOUR patients in order to get a clinical improvement in one. Suddenly this doesn't look so impressive, even if the data are correct. This concept is the "Number Needed to Treat" (NNT), and it is perhaps the hardest yet most important concepts in all of therapeutics.
Numerical difference between groups is not the same as individual improvement score.
If 50% of patients on drug A show an improvement, whereas 25% of controls show improvement, that is very much not the same as saying that the patients on the drug do twice as well as the patients in the control group. This sounds obvious, but all it means is that a greater number of patients show improvement, not that all the patients show a greater improvement. Subtle, but important.

So there you go - just a few little items among many to get us thinking about whether we are doing the right thing with Mrs Miggins when her Purple Heebie-Jeebies start flaring up. Please add your thoughts to the comments below. Am I being unfair? Go to it.

Is it time to reclaim the word "Spirituality"?

2012-01-09T23:04:00.001Z

The shorties: probably not.

Here's why I think in such a churlish way. "Spirituality" is one of those nicey sounding words that carries a huge amount of baggage. It seems so benign, so uplifting, so positive. How can anyone not love it?

Well, groups like the Templeton Foundation (more on those punters later) love to point at the "Spirituality" of scientists, and in the simple sense, many (if not most) scientists experience a sense of awe and wonder at the vastness of the universe or the complexity of molecular pathways or the differentiation of cells. And many people feel perfectly happy to call this experience a "sense of spirituality". So far, so labelly.

However, then we run into the problem of disingenuous religious apologists identifying this sense with some sort of recognition of the divine - an appreciation of some sort of transcendence that necessarily (in their wee heads, bless 'em) means that there has to be a god to make this all hang together. The ever-entertaining Christian apologist - sorry - analytic philosopher - Alvin Plantinga likes to link this to a "sensus divinitatis" - an innate "sense of the divine". This is a weird concept dreamt up by the lunatic theocrat of Geneva, Mr John Calvin - a nasty piece of work if ever there was one, but more on that Johnny anon. Alvin thinks that with Atheists, their "sensus divinitatis" is defective, and this is a "spiritual" flaw. Maybe he's right, but I would regard it as a sublime virtue. He might want to sort out his moralisations.

Anyway, using this and other methods, some people take the word "spirituality" from a context where it is meant to denote that entirely human feeling of awe and wonder, and subtly shift the meaning, so that we get the gods in by the back door. That is pretty greasy, and indeed dishonest.

So my suggestion is that we just let this word go. Lose "spirituality" altogether from our science-life-lexicon. Just stick with awe and wonder, and don't let it become a Trojan Horse for those whose agendas are far from noble.

Good news! (P)Residents of South America, relax.

2012-01-08T22:04:00.002Z

Venezuelans send good wishes to Uncle Hugo.
(Image linked from BBC News website)

Anyone who has followed the marvellous career of Venezuelan president Hugo Chavez knows that he's a bit of a loose cannon. I can't go too hard on the chap because he has been treated for some unspecified cancer, but the apparent rate of cancers among South American leaders has led him to suggest (perhaps jokingly) that there was a US plot to encancerate left-wing presidents in the continent.

Well, happily it turns out that at least one of those cancers can be removed from the list - President Cristina Fernandez de Kirchner of Argentina turns out to have benign thyroid disease, rather than papillary cancer of the thyroid as had first been suspected.

It rather looks like Hugo has been overselling his conspiracy theories, but sure I told you that before - even when President Fernandez was still thought to have a cancerous tumour. I'm delighted that President Fernandez is OK, but the egg on Hugo's face will not last very long - we can be sure of that.

Integrated Care: some clarity?

2012-01-07T16:18:00.000Z

Over at the Nuffield Trust, Dr Judith Smith tries to get us enthused about Integrated Care. It would seem that Integrated Care is a good thing, particularly for vulnerable and frail patients in the NHS. In principle I am happy enough with that, and for certain definitions/specifications of "Integrated Care", I would be delighted to see a greater emphasis on this.

However, I see a problem. "Integrated Care" is far too easy to say. It trips off the tongue and sounds like it carries significant import. It sounds like something everyone should want, and, moreover, if you say that the NHS needs to implement Integrated Care, it implies that a/ this is a radically new idea, and b/ that it's not already being done.

Now, I accept that the care of many patients could do with being a LOT more joined up than it currently is, but we need to be clear about some things. Most doctors and other health professionals in the NHS are already aware of the need for a patient's overall care to be considered in the round. We already have very dedicated GPs and others who try to take an overview of the patient and the decisions that need to be made at certain points to help them navigate towards the best outcomes possible.

So Integrated Care is not a new idea - at best it is just a new label for what we (largely) try to do already, and indeed is arguably a core principle of the National Health Service. It can be improved, and possibly it can be improved a lot. What is needed to achieve improvements in the integration and linkages of healthcare needs for individual patients (not as snappy a title, I'll grant you that, so from here on, if I use the term Integrated Care, that's what I mean) is not diktat that this radical new policy be implemented, but better targeting of resources to build on what is currently going on.

If one were cynical, one might think that this is a softener - a pre-emptive strike by the government to address one of the key objections to their ill-conceived Health Bill in England - that demoting health care services to "Any Qualified Provider" will inevitably lead to fragmentation and a loss of the Integrated Care that already exists structurally (if imperfectly) within the NHS. How better to grease the pill than to pretend that the NHS is not doing Integrated Care, then put it (only as words, mind you) at the forefront of the proposals to destroy the NHS?

Making sure patients receive joined-up care is a well-duh. Let's not allow politicians to pretend that they've only just come up with the concept, and let's make the case for support for health professionals to continue to deliver an excellent service for the benefit of their patients.

The New Therapeutics: Ten Commandments

2012-01-06T12:03:00.001Z

Read, learn, implement. This is the best medical advice you will receive all year.

Thou shalt treat according to level of risk rather than level of risk factor.
Thou shalt exercise caution when adding drugs to existing polypharmacy.
Thou shalt consider benefits of drugs as proven only by hard endpoint studies.
Thou shalt not bow down to surrogate endpoints, for these are but graven images.
Thou shalt not worship Treatment Targets, for these are but the creations of Committees.
Thou shalt apply a pinch of salt to Relative Risk Reductions, regardless of P values, for the population of their provenance may bear little relationship to thy daily clientele.
Thou shalt honour the Numbers Needed to Treat, for therein rest the clues to patient-relevant information and to treatment costs.
Thou shalt not see detailmen, nor covet an Educational Symposium in a luxury setting.
Thou shalt share decisions on treatment options with the patient in the light of estimates of the individual's likely risks and benefits.
Honour the elderly patient, for although this is where the greatest levels of risk reside, so do the greatest hazards of many treatments.

Originally formulated by Prof J Yudkin, From:
http://blogs.bmj.com/bmj/2012/01/03/richard-lehmans-journal-review-3-january-2012/
- it's well worth reading the full article.

Tweet people love playing "Divide and Rule"

2012-01-06T09:29:00.001Z

Dianne Abbot MP may not be stupid in general, but her famous tweet*
was a stupid thing to say, and, yes, it was a racist thing to say. But
seriously, is this a major problem? Kick her arse and move on; let her
move on too.

One of the most tedious things about Twitter is the number of people
prepared to get enormously outraged at every silly wee thing; if you
had listened to Twitter, you'd have thought the Alternative Vote was
in the bag. You'd have thought that the NHS Bill would have foundered
in the early stages. You'd have thought that no-one would be stupid
enough to re-tweet "I'm doing an experiment to prove to my wife how
great Twitter is" crap.

Twitter, I am sorry to say, is a *shite* barometer of the wider
Zeitgeist, and people (including @shanemuk - pls RT my wife thinks I
waste too much time LOL FTW w00t etc etc #inaneCrap) need to get over
themselves a bit. A lot.

[*: "White people love playing Divide and Rule"]

Luna & Jove

2012-01-02T18:45:00.001Z

Tonight!

More Christmas atheism

2011-12-30T11:30:00.001Z

This time from Alom Shaha (reared as a Muslim, but now an Atheist):
http://www.guardian.co.uk/commentisfree/belief/2010/dec/24/christmas-atheist-celebration?INTCMP=ILCNETTXT3487

Atheists at Christmas - a view

2011-12-30T11:23:00.001Z

http://www.guardian.co.uk/lifeandstyle/2011/dec/24/christmas-atheists
I think Alain de Botton is on to something here - something that
chimes with Atheistic Christianity in a big way. I'd be interested in
your comments, either here or over at the Church of Jesus Christ
Atheist:
http://churchofjesuschristatheist.blogspot.com

If you're on Twitter (I'm @shanemuk of course), you should also
consider following @thechurchmouse for somewhat intelligent religion
tweets, as well as @revrichardcoles for a breath of fresh air.
De Botton line (see what I did there?) is that you don't have to
believe in gods to enjoy many aspects of religion, and I rather think
that Richard Dawkins would probably agree, although he might draw the
line at a different point.

Indeed, Dawkins has been quite specific on this issue - he loves
Christmas carols, and likes the benign machinations of traditional
Anglicanism. He's quite happy to be a "Cultural Christian" (yes, I
need to find you the link, don't I?). However I feel we might be able
to go one step further, and remove "belief" altogether, and be quite
open about Atheistic Christianity - a worldview that we know we humans
have constructed, one which affirms tradition and the place of the
biblical texts in where we are now at, but isn't afraid to revise
aspects that turn out to be wrong, objectionable, or even just plain
crazy.

And indeed to borrow from other traditions - to be syncretistic, but
grounded, and not to be afraid to clear out the trash from time to
time. To be freethinking, but never dogmatic. To be willing and able
to engage with others who don't share our views - to celebrate and
mourn alike with them.

Is it possible to hijack this jumbo jet called Religion, and set it on
a path to where it actually builds community and makes life better for
people, or is it better to find a nice safe place to land, evacuate
passengers and crew, and blow the mofo to smithereens? I think that
would be a loss.

I merely ask.

Charlatanry

2011-12-29T15:51:00.001Z

Check it out: http://scepticalletterwriter.blogspot.com/2010/10/dr-andres-miracle-cancer-treatment.html
- a blog on quack cancer treatment in Brighton. Vision of Hope, my
backside.

The Law of Probability in South America

2011-12-29T10:12:00.001Z

Sparky Venezuelan President Hugo Chavez thinks the US is giving cancer
to South American leaders. This seems to be on the basis of his
diagnosis of cancer, and a smattering of cancers that have been
detected in the presidents of Brazil, Argentina and Paraguay. BBC
LINK: http://www.bbc.co.uk/news/world-latin-america-16349845
Mr Chavez is reported to have said that this is "difficult to explain
using the law of probabilities". The lifetime cancer incidence is
almost one in three. There are 12 countries in South America. The
leaders of four, who range in age from their 50s to 60s (when cancers
start to get common) have had various types of cancer. This does not
look like a violation of "the law of probabilities" to me - more like
a chance outlier, and not even a very big outlier at that. He's only
remarking upon it because it has happened - if it hadn't happened,
no-one would be saying anything.

As for the evil Americans, Chavez goes on to say: "Would it be strange
if they had developed the technology to induce cancer and nobody knew
about it?" Er, yes, it probably would, and it would also be strange if
everyone knew about it. And it would be strange if they had developed
the technology and chose to use it this way. What is really strange is
that someone who is supposed to be the head of an important country in
South America should make such silly and uninformed statements without
the slightest embarrassment of his ignorance of science and indeed
those mysterious "laws of probability". What he really wants to do is
employ Bayes' Theorem, and phrase the question like this: "GIVEN the
rate of cancers among South American leaders, what is the probability
that the US have been deploying a secret oncogenic technology against
said leaders?" That probability is not going to be terribly high. What
Hugo needs is more evidence. A LOT more evidence.

I wish Mr Chavez and his fellow leaders speedy and complete recoveries
(enough of this silly talk of "battling" and "beating" cancer - cancer
is a disease, not a divine/demonic test of your moral mettle), but
before coming out with silly paranoid nonsense, I do wish they would
learn a little bit more about cancers and probability.

It's not just about the Higgs

2011-12-22T14:51:00.001Z

New results from the ATLAS experiment at the #LHC!
http://www.bbc.co.uk/news/science-environment-16301908

Gawd, these days I'm never sure whether to write in the first person
or adopt Slicer's technique (see previous episodes) of referring to my
good self in the third person. I think I'l try to keep things up-close
and personal, subject to the rider above, that I don't necessarily
believe everything I post, and I strongly suggest that my esteemed
readership similarly approach my scribblings with the circumspection
that they merit.

Anyway, the clever Johnnies at CERN (and these Johnnies are among the
cleverest) have uncovered evidence for the fleeting existence of the
Chi_b (3P) state, which is a quark combo of a beauty and anti-beauty.
Regular readers will be aware of my little fantasy that the universe
will one day be shown to be a (big) meshwork of interconnected nodes,
so I'm going to have to have a look and see if these new results give
any further credence to such a concept, or if they make my Nobel
dreams recede even further (as seems fairly likely, I have to admit).

Perhaps anyone better acquainted with the physics can enlighten me?

Do numbers "exist"?

2011-12-21T13:36:00.001Z

I've previously suggested that mathematics might be the underlying
foundation of reality, and this has (perhaps not unreasonably) been
viewed by some as a rather provocative thing to say. I'll edit this
post later to provide some links, but in the meantime it might be
helpful to think about poor old Pi. As every schoolchild knows, the
value of Pi is 3.14159etc and cannot be accurately represented as a
ratio between two integers; there will always be a remainder, however
small. Some people argue that Pi is merely a consequence of the
Euclidean geometry we use to describe space, and therefore merely a
consequence of rules we set up in advance.

I'm not so sure - I think there is something fundamentally spooky
about numbers like Pi, which crops up all over the place in areas
where geometry is neither here nor there. It occurs in probability
theory, complex number calculations (which I suppose can be considered
as Euclidean, but hey), quantum mechanics, thermodynamics - pretty
much any area of mathematics and physics, regardless of any axiomatic
specification of the nature of the space into which we draw circles.
Where I think part of the problem lies is that people commonly think
that Pi is *defined* by the relationship between a circumference of a
circle and its diameter, whereas I would simply say that we can
calculate the value to be equivalent to Pi, but Pi itself (and 2*Pi,
or "Tau", which some argue is a more relevant quantity) has a sort of
independent "existiness" that does not depend on Euclid's axioms, for
example. Pi is a property of integer mathematics, and it is hard to
get much more basic than that.

Philosophically (aarrgghh!) this is a tricky one. Some people, such as
the renowned "Slicer" at the blog http://t-rinder.typepad.com, suggest
that mathematics and logic need an underpinning deity of sorts (who of
course pitches out as the JudeoChristian construct commonly known as
"God", but that's a WTF for another day). Maybe I am blind or too
dismissive or hard-hearted, and I cannot appreciate the very clever
subtlety of this suggestion, but it seems like crap to me. Even
Stephen Hawking approvingly quotes the old canard "God created the
integers" in his classically wry fashion, so I'm not sure whether
Hawking is agreeing or disagreeing with my feeling (let's put it no
more strongly than that) that numbers have a kind of existiness that
is different from the existiness of chairs, tables, donkeys and
bloggers.

Anyway, this is to throw things open to the crowd out there
(especially @bagguley - comments most welcome!) to see if anyone can
help clarify my simple brain, because Slicer (no, that's not his real
name - it may be taken from something he got a head injury from in
childhood) thinks that I am epistemiologically rudderless and only
capable of insulting his wee heroes. Have at it, people (if indeed
there is anyone there...)!

Higgs Diggs

2011-12-19T09:24:00.001Z

I'm having a fun chat with Slicer about the Higgs boson, the failure
of Plantinga and the analytic philosophers and such like. Feel free to
join us over at his blog (or continue here - whichever)!
http://t-rinder.typepad.com/blog/2011/12/through-a-particle-accelerator-darkly.html

In the belly of the beast

2011-12-16T22:32:00.001Z

Lovely flame layer in the "ShortArse" model Happy Little TLUD.

Happy Little #TLUD "ShortArse"

2011-12-16T22:28:00.001Z

A little design modification & fan-assist. 500ml paint can shell, 400ml soup can pyrolysis chamber, further 400ml can support & fan duct for primary air. This design works *really* well! Good 15-20min reliable burn, lots of heat out.

Christopher Hitchens, we'll miss you!

2011-12-16T09:27:00.002Z

[Image from BBC Website - URL in meta]

I was saddened to hear on the BBC that Christopher Hitchens has died. He has rolled up the curtain, but not joined the Choir Invisible. Not for Hitch, that going gently into that good night. He went out, all guns blazing against the sanctimonious vultures of religion, those cackling gargoyles who cajoled and harangued him to renounce his "outspoken atheism" and embrace the clying comforts supposedly offered by a belief in Santa or the Afterlife or the Baby Jesus or fairies or some such. In such a prolific career there is probably much to disagree with, but we can be thankful to Hitchens that he has left the world a much wiser and better place, and he has encouraged many people to stand up against the affront that organised religion/superstition presents to basic human dignity. Well done, sir!

In case anyone thinks I am the only one who thinks Plantinga is an idiot

2011-12-16T09:17:00.001Z

Here's Rosenhouse in 2007:
http://scienceblogs.com/evolutionblog/2007/03/plantinga_on_dawkins_part_one.php

Look what I made!

2011-12-10T19:12:00.001Z

Had some old bits of cedar left over, so I made this angel.

The only book on the #Philosophy of #Science you will ever need.

2011-12-09T16:17:00.001Z

"Worms in liquid form" FFS!

2011-11-30T11:16:00.001Z

BBC, you can do *so* much better than this.
http://www.bbc.co.uk/news/science-environment-15897803

Let's just clarify. The worms are IN a liquid, they are not in "liquid
form". They were launched up into space in a broth, and they survived.
Great! Quite how much this aids human spacefaring is difficult to
assess, but at least we may be able to sup worm soup up there. That's
a result in itself, I suppose.

Common sense prevails.

2011-11-29T21:47:00.001Z

It's nice to see things restored to normal once again. Thanks everyone for your support. Now, where were we?

Vision for Vision for President of RCGP

2011-11-26T16:06:00.001Z

No stranger to controversy, me.

Over at Dr Una Coales's (@drunacoales) blog she sets out a vision for her bash at presidency of the Royal College of General Practitioners. I need to declare that I am not a GP, so I'm not in a position to vote on this. However, being a kindly soul, I am happy to offer Una some advice on how to present a vision that people can actually get behind. I'm posting this here because for some reason Una doesn't have comments enabled on her blog. I'm sure this is simply a technical oversight, and I hope it gets fixed soon.

Well, the post is a bit of a mess. It's far too long, and doesn't help the reader make an assessment of what Una can bring to the important position of President of a major medical Royal College. It meanders all over the shop and contains numerous platitudes and pointless anecdotes that add nothing to the overall thrust (if there is one). There are also some alarming aspects that certainly raise my eyebrows, for example:

I reiterate the U.S. policy that the GMC should ONLY deal with proven cases of medical negligence, i.e. when a patient dies unnecessarily, when a death could have been prevented but occurred due to negligence.

I am something of a cynic when it comes to the General Medical Council. I agree with Una that many of its systems and processes are long and harrowing, and that the GMC can be abused as a weapon against doctors by people with a grudge. However, to restrict the GMC to dealing with "proven cases of medical negligence" is a very very strange thing to say. The "i.e." implies that a patient has to die before anyone gets pulled up on their practice; I charitably presume that Una meant "e.g." here (I hate it when people misuse these important little abbrevs), but if this is meant to be a bar indicating the severity of malpractice meriting a referral to the GMC, then medicine really will be in trouble. What about inappropriate sexual advances to a patient? What about financial pressure, or coercing patients to write the doctor into their will? What about grossly incompetent surgery where the patient doesn't die, but ends up disfigured or in pain? Surely no competent doctor would wish to see the GMC restricted to dealing only with patient deaths, but wants to have a regulator that upholds standards of excellence in patient care, right the way down to ingrowing toenails or accurately assessing and communicating risk (important in my own specialty of Genetic Medicine).

And then we need to ask what constitutes a proven case of medical negligence? Who does the proving? In the UK, that is generally the GMC, so Una seems to have hit a bit of a Catch-22 here; if the GMC only deals with proven cases of negligence, and for a case of negligence to be proven, that requires a GMC adjudication... You can see the problem. Certainly Una is right if she's saying the GMC should not pry into people's personal lives, religious beliefs, sexuality etc. if the doctor nonetheless practices excellent medicine without fear or favour. But in matters of medical practice, it has to be the GMC that decides what constitutes negligence or incompetence (these are not the same thing). Una is of course also correct in implying that the processes need to be sped up to weed out vexatious referrals or complaints where there is no case to answer. The GMC is not and must not be a grievance body.

What do doctors (and patients) really need in a president of the RCGP? Vision is one thing; clarity of vision is another. I suggest they need grit and determination (Una certainly has these in spades), but also a commitment to practical everyday excellence, constructive engagement, and the development of a truly responsive and equitable health service. In order to avoid over-lengthiness and meandering I'm going to leave it there for now; do have a read of Una's post, and perhaps we can discuss further in the comments below (which I allow on my blog).

[UPDATE: Image changed because of threat of legal action to the tune of $150,000! Current image at the head of this article is copyright BBC and the BBC are welcome to contact me to get this changed if they have any problem with it; I will of course comply immediately, as I regard copyright infringement as a very serious issue.]

Israel's tech startups: @basilmccrea take note!

2011-11-25T09:26:00.001Z

It's happening again - every time our local representatives are
required to set foot off the soil of Ulster to get some work done, the
worthies get up in arms about "junkets", as if a trip to San Diego is
just a holiday. http://www.bbc.co.uk/news/uk-northern-ireland-15882358
for info, if you want it. Don't get me wrong - San Diego is a lovely
city, and it's warmer than Augnasheugh, but it is also a place where
you can Get Stuff Done, and where there is some spectacular R&D
getting translated into economic benefit.

Another economy, whatever one's views of the general situation there,
that is making serious waves is Israel, and it is here that I think
Northern Ireland needs to get some big lessons in how to grow an
economy. This BBC report http://www.bbc.co.uk/news/business-15797257
demonstrates how Israel has become a global technology and business
start-up giant, even given its meagre population of 8 million. No
other country has produced so many science Nobel prizes per head of
the population.

So what is Israel's secret, and how can Northern Ireland learn from
it? Well, for one thing Israel has a pioneer spirit. Sometimes that is
a very bad thing, as we have seen in the aggressive behaviour of
illegal settlers in the West Bank and formerly Gaza. However, it is
often a very good thing - people are prepared to take risks and to
roll up their sleeves to try to make life better and make their
country better. Another thing, perhaps one of the most remarkable and
admirable legacies left by Judaism over the centuries, is a profound
respect for science. Science is rewarded in Israel. It is a mark of
major prestige to be a scientist, or for your child to go into
science. The fact that this translates into technology and business
success is not an accident.

Now there is no doubt that I am generalising hugely here, and my
Israeli friends will no doubt inform me that Israel puts nowhere near
the right emphasis on science that it should. There are deep
inequalities in Israeli society, with a cadre of plutocrats jealously
clutching the dosh, and failing to allow this to trickle down to the
ordinary population. This was the seed of the massive street protests
earlier this year, and the problems are far from fixed.

However, we in Northern Ireland have a broken society too. But we
concentrate far too much on our legacy of the past. The pioneer spirit
that built Kentucky and Tennessee seems to have emigrated from our
shores. The attitude that made such a success of our engineering
industries in the previous century has been replaced by a maudlin
backwardness that prefers to write morose poetry, rather than to
explore and understand the universe.

So, Basil, please do take the committee to San Diego, but also take
them to Tel Aviv. Invest in our educational infrastructure; destroy
the sink-holes that are sapping our young people into a life of
perpetual stupid; boost the sciences, boost engineering, boost
technology - not just in investment (because this will come), but in
terms of social prestige. Let's get this country off its knees.

And perhaps people will even enjoy doing it.

Thanksgiving #TLUD

2011-11-24T23:03:00.000Z

Happy little stove - new design (minor tweaks). Still needs better airflow...

Contact established with Phobos-Grunt!

2011-11-23T09:51:00.001Z

Here's the info: http://www.bbc.co.uk/news/science-environment-15850516
The Russian Phobos-Grunt mission was to send a probe to the Martian
moon Phobos, land, pick up samples, and return them to Earth. If
successful, this would be a fantastic scientific and technological
achievement. Sadly the mission didn't get past Low Earth Orbit, where
it remains, effectively stuck, and up to now incommunicado. If they
can re-establish communications with the spacecraft, it may still be
possible to diagnose the fault and get the little ship on its way,
although this remains (in my considerable space science experience,
which is not considerable at all) something of a long shot. So, in the
best tradition of the rationalist scientific endeavour, I suggest we
all pray. In the meantime, the engineers and programmers on the
mission will be trying to do stuff that actually has a hope of
working.

Religions of the World

2011-11-15T19:14:00.000Z

Courtesy of my little brother... There is Wisdom here.

I seem to have incurred some wrath...

2011-11-13T11:09:00.001Z

If there is one thing that gets right up my nasal passages, it's the encroachment of fluffy ideologies into the realms of science in general and medicine in particular. It has been my view for quite some time (and as I get older, this is concretifying rapidly, if that's even a word) that there's a group of no-doubt well-meaning but scientifically illiterate punters who are trying to develop a framework of talking about human behaviour, at all levels from the individual to the societal, based on whims and arcane concepts that have no useful mapping to anything scientific.

This is the world of pseudophilosophy (or maybe "Philosophy as She is Writ), where concepts are "isms" and everything belongs to a rigid ontological hierarchy. It's the world of CP Snow's Two Cultures, except that the scientists are the baddies, and to get anywhere you need to be able to drone at length on "post-structuralism" and "dialectics" and the like.

Anyway, within the constraints of the 140-character limit of Twitter, I became embroiled in a discussion of the value of concepts like "structure" and "agency" in addressing inequalities in health. Now I have nothing against terminlogical shortcuts per se, but the reason for my being brought into this discussion was not because I care how "social scientists" (more on that term later) view health inequalities, but because of a previous discussion with someone over what exactly "agency" was. The skinny on this is that my correspondent was trying to make the claim that "agency" implied "free will" (whatever that is). So what's this "agency" malarkey?

Some "social scientists" (commenters on public affairs, I suppose) suggest that there are two big factors in How Stuff Works in society. One is Structure, which is effectively the environment - the bricks and mortar, effectively. The other is Agency, which is what people do. Now you don't have to be a genius to figure out that these are not rigidly separate categories, because much of what is Structure is set up by the Agency of our punters (members of the ape species homo sapiens), and that Agency is influenced by the Structure, not just at the macro level, but at the very specific micro level that applies to discrete individuals. And since the Structure also has to contain the genetic background of your population, the baseline disease patterns, neural connections, personality traits, biochemical disturbances, outside influences and so on, it becomes difficult to make a good case for distinguishing Structure from Agency anyway.

Well, my ennui at this sort of cobblers spilt over to something of a diatwibe (that's a diatribe on Twitter) against "social science". Because this is where the problem really lies. "Social Science" is a spectacularly ill-defined entity; basically it acts as a rag-bag of several different disciplines, including history, archaeology, geography, that don't fit easily into what's commonly thought of as "Science". This is a shame, because the very name "Social Science" seems to lend an air of respectability to the rags within the bag, some of which deserve that respectability, and some of which manifestly do not.

It also results in the sad situation where people can call themselves "Social Scientists", and attain some sort of protection of the herd, while being able to twaddle on with nonsensical and jargon-laden pablum that has no prospect of informing policy, furthering research or leading to understanding.

I suggested (testily) that the entire literature base of social science could be destroyed, and we would be no worse off. I guess I hoped that some of the social scientists soi disant would leap to the defence of particular disciplines within the rag-bag, and indeed my original correspondent (our tussles aside) was the only one in the little Twitter group to even make a stab at disentangling the mess.

So we're stuck with what is actually the key problem. People whose understanding of science is purely based on a sociological paradigm proposing sociological models and sociological approaches to issues that deserve much more precise and evidence-based approaches. And when we are looking for evidence, rather than the opinions of "thinkers", we are into the realm of science. Proper science - not "qualitative research", not Google-bombs. We need approaches that can be tested so that conclusions - proper conclusions - can be drawn and built upon. That is something that many "social scientists" are spectacularly ill-equipped to do. Our world is complex; there are multiple feedbacks and dependencies. If we insist on adopting the top-down philosophies that percolate out of "social science" thinking, we are going to make expensive mistakes that we have no way of knowing that we're making.

Am I hammering the humanities here? No. I had the real pleasure of getting one meagre "social science" qualification, namely a Certificate in Egyptology from the University of Manchester, a couple of years back. Yes, I am told now that Egyptology is one of the social sciences. Yet within that, I found researchers and lecturers who were well versed in science and hugely sceptical of the fluffy mindset that comes from "sociology". Here were people planning proper experiments, adopting a highly scientific and rigorous approach, appropriately reticent to being too dogmatic about their conclusions, ready to be flexible and to think outside the box. Lumping Egyptology into "social science" seems such a shame.

Am I being too derogatory? Does "Social Science" proper actually exist, and does it have a role to play? Is there a real peer and post-peer review process ongoing? Is anyone leaving out the trash? No doubt your comments will help correct any of my misapprehensions...

The Adoration of the Magi

2011-11-09T22:08:00.001Z

Another lovely old tile panel from The Royal Belfast Hospital for Sick Children. I think there are about 15-20 such works dotted around the hospital. There's something very beautiful about them. Look how the lines follow the tiles...

The Finding of Moses

2011-11-09T22:04:00.001Z

One of the beautiful 1930s tile panels from the Royal Belfast Hospital for Sick Children. There are a number if these, and they're amazing!

Alternative #TLUD feedstock drying apparatus

2011-11-05T12:35:00.000Z

Using the small TLUD, an old ceramic plant container (open bottom) and an inverted metal bin lid. Joy!

#TLUD on TLUD

2011-11-05T12:14:00.001Z

Using my little TLUD to dry more fuel - it's amazing how much water is present even in supposedly "dry" fuel. Dampness decreases efficiency enormously - always use nice dry feedstock!

Alternative Medicine that WORKS - Taking WCTB Therapy into the mainstream

2011-10-23T21:03:00.003Z

We know that Homeopathy works no better than placebo. We know that for many people a placebo effect can be helpful. Crazily, and completely counter-intuitively, we also know that placebo effects can persist, even when the patient KNOWS that what they are receiving is a placebo (Ben Goldacre has a great line in this stuff). Each year the NHS in the UK spends over TEN MILLION POUNDS on homeopathy - that very specific, very deceitful, entirely pointless placebo, when we know that a/ we don't need to lie to our patients to get a placebo effect (and homeopaths are either deluded or they do lie - we know there is no active principle involved in homeopathy), and b/ there are other forms of therapy that are *at least* as likely to engender a response as homeopathy, and indeed are likely to have a much greater and more beneficial long term response. The general population, gulled into shelling out their hard-earned cash, spend far far more - homeopathy is big business, and it's all wasted. Something needs to be done. Something CAN be done.

Ladies and gentlemen, after a very useful Twitter discussion with some learned colleagues (and helpfully storified and blogged by my inestimable colleague @anarchicteapot), I introduce WCTB Therapy.

WCTB is intended to replace all forms of "alternative medicine" - it is indeed an invaluable alternative to the alternatives. WCTB has all the advantages claimed for alternative medicine, with none of the side effects. You don't have to interact with a bunch of New-Age crystal-hugging Earth drongoes; you don't have to sing silly chants or sell your soul to Zuul or believe stuff that your brain is screaming at you for even contemplating. You don't have to sacrifice your intelligence, you don't have to shell out loads of money for fake remedies. Yet this radical new programme of treatment holds enormous promise at a number of levels:

Individual wellbeing
Improved mental health
Interaction with others
Social cohesion
Economic regeneration
World Peace

What is this new miracle treatment? What portal to the fundamental life-force of the Universe has been opened to be accessible to mere mortals? How can these grandiose claims be made for a complementary medical therapy? And what IS WCTB? Let me explain.

Wee Cup of Tea and a Biscuit (WCTB):

It is our contention that many disease symptoms and psychological issues can be resolved by sitting the fuck down with someone prepared to listen and to care, and to share a wee cup of tea and a biscuit. Our initial research suggests that the precise brand of tea and type of biscuit may not be terribly important (further research is needed). But after a programme of WCTB therapy, we feel (see the Twitter link above for my co-authors in this) that many patients will experience significant benefit in a wide range of acute and chronic disorders.

We do not propose WCTB as a cure for all ills, but there are very few conditions where WCTB is not likely to be a helpful adjunct, whether administered to the patient, or a worried relative. WCTB is cheap, requires minimal training to deliver, and, in fact, wonderful health practitioners and caring individuals in society have been delivering it for years with great effect.

Indeed, it is an indictment on our society that WCTB is not more widely available. If the government were to sink *half* the amount of money into WCTB that they flush down the drain in wasteful nonsense such as homeopathy, we predict that it would save the NHS vast sums of money - fewer complaints, more rapid recovery, greater community cohesion, improved mental health and general fitness - there is no downside.

So throw away those stupid homeopathy pills. Close down the various homeopathy hospitals and convert them into fully funded WCTB units where people can come in free for a regular dose of WCTB. Create WCTB Units in areas of social deprivation and unemployment, as well as major transport interchanges. Teach WCTB principles in schools and universities. Encourage people to offer their services as WCTB Therapists - all they need is a listening ear and a caring and compassionate nature. Stop wasting money on insane crap like homeopathy and Reiki and crystals etc.

And, you know what? We might just change the world.

Philosophy of Science

2011-10-20T17:42:00.001Z

@John_S_Wilkins (whom I respect a great deal) suggested I may have been shooting my mouth off a bit in abject ignorance in some of my recent Twitter attacks on the discipline of the Philosophy of Science. OK, he was a lot more subtle and polite than I've framed it. I confess - my knowledge of, and irritation at, the field does not stem from an in-depth analysis of what people have actually been writing (apart from reading a load of Popper in my tender years), but from various articles (pro and con) in the popular press, or opinion pieces in journals, or in media interviews etc. I may have been a little hasty.
Don't get me wrong - the way some philosophers like to classify everything into "isms" is really fecking irritating to a scientist or even a visual thinker, and leads to fallacies and boundary errors galore. Also, some people like Stevie Fuller or John McGrath, who pretend to be PhilsOfSci as a front to misrepresent and subtly attack science in the name of theism, give the field a bad name. In my line as a geneticist, it's creationists that I run across most frequently, so I'm perhaps guilty of tarring some very capable and wise thinkers with the same brush I use for outright loons.

Many great philosophers of science ARE or WERE great scientists, and many amazing scientists (Albert Einstein and Richard Feynman for example) have contributed a great deal to how we think about science and the scientific process.
So I have a contrite question: what should I be reading that will mend my view of the Philosophy of Science as the discipline currently stands? Am I focusing on bad apples? Is there such a thing as a good Philosopher of Science who has never been in the lab? Are there good apples? Give me some pointers, folks!

Oh look. It's #Unison and #NIPSA.

2011-10-16T17:20:00.000Z

Lab spam

2011-10-04T09:31:00.001Z

I get shedloads of guff wanting me to buy pipettes and lab reagents
and the like, but this is the best:

"SterilEnz® fittings are the only pre-gasketed and hermitically sealed
sanitary fittings designed specifically for single-use systems."

So now I have this mental image of hordes of little cave-dwelling
recluses pre-gasketing and sealing sanitary fittings, and it gives me
a warm glow in my heart and a potential consumer confidence that money
can't buy. I have no idea what the feck they're selling - I just know
that I *want some*...

Dammit, my #TLUD is going great today!

2011-10-02T10:25:00.001Z

@bugsymckee, watch and learn! Fuel: woodchips (thanks, Bug!), some dried unstructured biomass beneath, top-lit for freshness.

Tyrannosaur Halloween costume - current status

2011-10-01T15:09:00.000Z

I've had to take some liberties with the anatomy for construction purposes, but with teeth and lower jaw, this will be scary!

The difference between Religion and Science.

2011-09-28T22:01:00.003Z

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

2011-09-28T14:44:00.001Z

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

What planet are they on?

2011-09-27T21:30:00.000Z

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.

Happy 4th birthday Olivia!

2011-09-24T13:21:00.001Z

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

Belemnite.

2011-09-24T11:00:00.001Z

Lewis found this fossil belemnite on the beach at Jordanstown.

QR code

2011-09-23T22:15:00.001Z

Sent from QR Reader

Plato vs Darwin

2011-09-23T13:33:00.002Z

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.

How I look to my 3-and-a-half year-old.

2011-09-21T22:18:00.001Z

I'm flattered.

GOD HATES FAX.

2011-09-20T21:47:00.002Z

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.

Read/write DNA?

2011-09-19T21:58:00.002Z

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.

Halloweenosaurus Rex

2011-09-16T21:16:00.001Z

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

#Evolution Hallowe'en!

2011-09-15T18:53:00.000Z

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.

Stupid bird flew into the window and left this mark

2011-09-14T17:40:00.001Z

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

Corporate branding #fail.

2011-09-13T12:02:00.000Z

My pants are fine, thanks.

Daddy, everything looks 3D...

2011-09-13T07:00:00.001Z

Facilitating Genetic Research.

2011-09-12T18:04:00.000Z

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.

Do quarks work like this?

2011-09-11T20:54:00.000Z

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.

2011-09-11T13:11:00.000Z

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.

#TLUD experiment: Hot Rocks!

2011-09-03T18:31:00.001Z

Let's see if we can build a TLUD storage heater...

Combo #TLUD joy!

2011-08-28T19:33:00.000Z

So I took my abortive previous design and stuck it on top of my trusty Thomas TLUD - it now acts as a combination concentrator and wind-guard! Even though it's blowing pretty hard today, the trusty little stove was quite happy. As aficionados know, it's all about air flow. Next step will be to integrate these lessons into a unified ab initio design.

#TLUD needs some work...

2011-08-28T07:15:00.000Z

Hmmm. My new "Hero" TLUD doesn't seem to work very well. I think I need to throttle the pyrolysis/combustion interface a bit more. May be a problem with the feedstock though. More later...

Awesome new #TLUD!

2011-08-23T19:58:00.000Z

Meet Thomas the TLUD - top-lit up-draught stove. This one is made from a 5L paint tin pyrolysis chamber inside, an old wastebin on the outside, and a 3L paint tin chimney/combustion chamber. And it goes like the clappers! 4L of wood chips gives a beautiful 20min burn that provides stacks of heat and generates about a litre of charcoal. I'll run some more tests and get some proper figures on this.

Suffice it to say that the TLUD is the way of the future. Forget braziers and patio heaters - this is hot hot heat from fully renewable sources.

More #TLUD love

2011-08-17T21:37:00.001Z

There is something almost mystical and *alive* about a little TLUD happily burning wood gas and generating charcoal. Look how happy the little chap is! See his jolly flame leap into the air! This is the world of the top-lit up-draught stove, or TLUD.

I made this wee beauty from an old paint tin, a tin of dried baby milk and a tin of pineapple chunks. Additional equipment: a hammer, nail, old scissors, tin-opener and pliers.

The principle of the TLUD is simple - burn the gas, not the wood. As wood is heated it gives off various gases in a process known as pyrolysis. Usually these rapidly combine with oxygen resulting in a relatively inefficient local burn, but if you heat the wood in the relative absence of oxygen, the gases can be channelled for secondary combustion. The result is a very clean, efficient burn that delivers most of the wood's energy to the gas flame. If used for cooking, it is many times more efficient than an open fire. You need a lot less fuel, and you generate a lot less smoke. The applications for the developing world are obvious. Since it generates charcoal, you can bury this as biochar, making the process carbon negative - ie you are effectively removing carbon from the atmosphere.

So spread the TLUD gospel! Get out and make your own! Experiment with different designs and tweaks.

#LondonRiots, @BbcCode, @MarcusDuSautoy and the Stoopid of Crowds

2011-08-12T08:27:00.001Z

There has been a huge amount of drivel written and spoken about the
recent riots in England (funny - they are calling them "UK Riots" now,
but Scotland, Wales and Northern Ireland seem miraculously spared).
It's all supposed to be down to this government or that government or
social inequality or absent fathers or police brutality or base
criminality or some such horseshit. Don't get me wrong - some of those
may be enabling factors that need addressed, but focusing on these
issues alone is missing the elephant in the room. That elephant is the
behaviour of people when they are in groups.

In the BBC documentary series "The Code", presented by Marcus du
Sautoy (sorry for the earlier twitterification of everything, but you
may want to follow Marcus!), there is a really fascinating sequence
involving starling flocks in Denmark. This enormous flock of birds
behaves almost as a single vast organism, and you'd think it needs a
vast controlling intelligence to make it move. However, the rules
governing the behaviour of a flock are surprisingly simple - indeed
spectacularly so. All each individual starling needs to do is keep an
eye on it seven nearest neighbours, and match what they do - speed,
direction, etc, and avoid predators. The behaviour of the huge group
emerges from those simple rules - complexity emerging from deep
simplicity. It turns out that humans are really no different - our
incredibly complex behaviour is the result of very simple rules.

So how do we apply this to the utter arsebiscuits that went on in
London? Is it a disaffected generation venting its social isolation,
or is it something a lot more simple than that? Is the looting and
rioting any different *really* to the banking crisis or MPs' expenses?
I would suggest that they are all *precisely* the same phenomenon.
Here's why. A store gets broken into. Some people (Bad People) start
taking things from the store. Other people see this and think: hey,
it's unfair that they should be able to get stuff that I can't. I'll
go and take something too. Someone else sees this, and breaks into
another store for the same reason, and so on and so forth. It is the
perception that members of your peer group are getting things that
you're not. You feel disadvantaged, not because of social ills, but
merely due to the fact that by holding back, you're missing an
opportunity. So you join in the group behaviour. No complex
co-ordination - just group behaviour. Morality, after all, is a social
contract, and if you feel that the rules have shifted (rightly or
wrongly), you are more likely to join in the "new" rules, rather than
stand back and take a good look.

And in the midst of all this, this is the realisation that society
needs to deal with. In crowds, people can do astonishingly stupid and
immoral things. If we want to prevent rioting and looting, we need to
acknowledge this, and develop strategies for applying it, instead of
wringing our hands and indulging in the sort of self-righteous
angstgasms that have coruscaded over the media and Twitter the last
few days.

Things #TLUD related

2011-08-02T15:26:00.000Z

I have a few more photos of my Top-Lit Up-Draught stove on Twitter - just follow @shanemuk if you don't already. I'll get them up on the blog when I get some time.

Several people have commented that much cooking in the Developing World is done on open fires or in environments that are not exactly efficient or healthy; fires produce lots of smoke, require lots of energy, resulting in respiratory diseases, fires themselves, and environmental damage. If families could be shown how to construct spectacularly cheap TLUDs and use these instead, the environmental impact could be enormous. AND since a TLUD produces charcoal as a by-product, this could also be used either as biochar to enhance crop yields and sequester carbon, or even as a fuel in charcoal-fed appliances (of which there are also numerous).

So all of you outdoorsy types - become a TLUDdite - develop your own TLUDs and share the designs. I'll post mine soon when I've finished drawing up my retrospective blueprints...

Carbon Negative Coffee

2011-08-02T10:27:00.001Z

Thanks to my wonderful #TLUD. The black stuff is biochar - carbon that can be buried and is now out of the atmosphere. The fuel was wood chippings from pruning round the garden. Dried, of course.

Resurrecting the #Resurrection

2011-08-01T21:02:00.000Z

Yes yes yes, I know I have been indulging my #Maker side (check out the hast tags - this gets fed to Twitter!) and neglecting really important things such as the complete gobbledegook that gets spouted by apologists over the alleged resurrection of Jesus. Now I have to admit that I am something of a fan of Jesus - I think he was on to something before it all went pear-shaped for the poor bloke. Not that we can trust the gospels especially - not a single gospel was written by a witness to any of the events, and the three earliest are actually largely based on the same documentary sources, so there are really only three gospels. Confused yet? Well, a useful trick (if you're interested in real history like I am; if you're just here for "belief" then you can scroll to the bottom) is to take a pair of scissors and six bibles, and chop up Matthew, Mark and Luke, and align the texts together. Six because you have the forward and reverse of each page (recto and verso as we papyrologists like to say). Alternatively, copy and paste the text in a three-column WP page.

Anyway, what you will find is that the authors of Matthew and Luke did pretty much the same thing - they borrowed very very extensively from Mark. And this is one reason why we can be very sure that they based their documents on documents, not on eyewitness accounts. And it also makes the discrepancies very very interesting. Not because they are discrepancies per se, but because of the spin the different authors put on the stories to advance their own personal agendas. Not the agenda of Jesus, but the agenda of "Matthew" and the agenda of Luke.

Try it - have a really good look at the different stories around the resurrection in particular. If you are interested in actual history, it's well worth it. And don't bother going near the apologetic rubbish that seeks to harmonise the stories. That's just lame.

Great gas almighty!

2011-08-01T15:18:00.001Z

Meet my home-made gasifying wood stove, made from a couple of old paint cans! Burns wood chips like a beauty, creating charcoal in the process. Enough heat output from one fill of wood chips to boil a litre of water, and very efficient. I'll be experimenting with other designs in preparation for the coming collapse of civilisation...

Pot luck

2011-07-30T19:01:00.000Z

So number 2 son pesters dad to go into the amusements at Largs. Goes to the claw-grab-soft-toy machine. Sticks in his pound. Bam Bam- machine grabs him a big teddy first go. AND refunds his pound! What are the odds?

This does not work as an iPhone signal booster

2011-07-29T21:09:00.000Z

But as it is made with a can-holder, a jumbo paperclip and some blue plastic sheathing, that should not be a surprise. So it is now in the bin. And my office is still something of a not-spot :-(

Best. Nature. Cover. Ever.

2011-07-21T12:29:00.000Z

Nom nom nom nom!!

On the Historicity of Goldilocks and the Three Bears

2011-07-18T22:08:00.000Z

Since the advent of trendy theology in the 19th century, it has become fashionable to regard the Goldilocks narrative as just a story - that it didn't really happen. Nowadays many Christians even dismiss it as a myth, yet they still call themselves Christians. This is an appalling state of affairs, and it is even more tragic that few of the major Christian apologists have tackled this issue head-on. It is time to set the record straight, and affirm the historical Truth of the Goldilocks narrative. I intend to show that it is overwhelmingly more likely that the Goldilocks story is literally true than not, and not only does it constitute Warranted True Belief, it is *necessarily* true in a deep ontological and cosmological sense, i.e. if the G3B model was any different, our universe would be deeply inimical to human life, and we would not even be here.

Firstly, we must look to the person of Goldilocks herself. In the sacred texts she is described as a young human female with long golden locks of hair. Females make up half of the population (approximately). We can estimate that her age was between 8 and 12 years. Only about one in eighteen people fall into that category. She is human - the vast majority of creatures on this planet are non-human (including the three bears who are central to this incident), so even giving this a 1/1000 probability is probably being generous. Only about a quarter of Northern Europeans are sufficiently fair-haired to be called "goldie", and even some of these are bald, but Northern Europeans only represent about 10% of the Earth's population.

So we can see that in putting these parameters together, we have an overall probability of less than ONE IN A MILLION that Goldilocks would meet the criteria that we already KNOW she fulfilled!
Those who would deny the story therefore start off in the very difficult position of explaining away this highly accurate Swinburnian analysis of the data. Some commentators have called this "The Rare Goldilocks Hypothesis" (RGH).

We then come to the issue of the Three Bears. Note that the parameters are incredibly fine tuned. If there had been only 2.99999999999999999999999 bears, the story would not work at all. To dismiss the fact that there were THREE bears as "just a coincidence" or "due to chance" is frankly ridiculous. Clearly this has been intelligently designed, and the correspondence is massive evidence in favour of this story representing a real historical incident. Further evidence for fine tuning comes from the fact that there were THREE bowls of porridge, THREE chairs, THREE beds - all these parameters had to match PRECISELY.

The three bears went for a walk IN THE WOODS - again, this is EXACTLY what we know bears do (they do other things in the woods too). Yet this story was written down by simple Galilean fishermen who knew plenty about fish, but not so much about bears. But they could write with the authority of a PhD in Ursology from the University of British Colombia. Powerful evidence that the G3B assertions are FACT.
Let us now look at the porridge. Nutritional scientists with PhDs that they haven't made up or bought off the back of a Special K packet have confirmed in numerous sciency studies that porridge contains the PRECISE balance of whole grain and yummy oaty goodness to set a bear up for the day, at least until he or she catches a big salmon or a deer or something more appropriate to its carnivorous physiology. Chance? I don't think so, and therefore neither should you.

We also note some charming aspects of the story which help to confirm its authenticity. Despite the size ranking of the bears - large, middle-sized and small, it is the *small* bear's parameter set which most closely match the pre-existing preferences of the blonde female humanoid juvenile. But they don't just closely match - they are JUST RIGHT - again, phenomenal fine-tuning, demanding both the presence of an intelligent designer, and supporting the essential historicity of the G3B framework.

There are many more pieces of supporting evidence that could be brought to bear (yes, I know), but perhaps the most incontrovertible, the most poignant, the most devastating is the eyewitness testimony of Goldilocks herself, as she ran screaming from the bears' house, fully conscious of her sinful state. Yes, dear friends, the realisation of her Fallen status was brought home to her by *bears*. For all have eaten porridge, broken chairs, slept in beds, and fall short of the glory of God.

If you do the statistics on all this, as has been done by such creative mathematicians as Alvin Swinburne and Richard Plantinga, you will find that the probability that all this could be due to chance is just one part in a zillion bagillion, and even Professor Brian Cox (noted atheist, physicist and keyboardist with indie pop quartet sensation "Papa Higgs and his Crayzee Boson") remarked: "It's really vast!"

So let us not forget what we learn from Goldilocks in this True and Valid account. After all, what would she gain by lying? Would she go to a horrible death for a *lie*? It is such an incredible story, it HAS to be True.

And if you don't believe it, you'll go to hell for all eternity.

[I should also point out that the Holy Trinity of the Daddy Bear, Baby Bear and Mummy Bear bears (again) an uncanny similarity to the Father, Son and Holy Spirit - yet more evidence.]

Our future in space?

2011-07-17T20:45:00.001Z

When the touchdown of the Space Shuttle Atlantis, STS135, brings an era of human spaceflight to a close, it'll be a somewhat sad day. In many ways the Shuttle has been a marvel of technology and has opened up new vistas on the entire Universe, not just the low earth orbital realm inhabited by the International Space Station. Shuttle has launched some of our most important orbital science platforms, including the Hubble Space Telescope, arguably one of the most productive science machines ever implemented.
But now it is coming to an end - hopefully in a whimper. Where do we go from here? I was only a fetus when Armstrong and Aldrin landed on the Moon, and as a kid I thought we would at least be at Mars by now. I was reading Asimov & Clarke before Janet & John.
Does the decommissioning of the Shuttle fleet mean a step backwards in our exploitation of space, as the cancelling of Apollo meant a very real retreat from the Moon? Or does clearing the deck of a programme whose expiry date has come mean that the field is now clearer for development of smarter and cheaper ways of getting humans into orbit and beyond?
Part of me would have liked to have seen Atlantis stay docked long-term at the ISS, and the crew come down on a Soyuz. Prep the old girl in orbit for attachment to some boosters for a mission to Mars. Sure, that's nonsensical - it is not the vehicle for such a mission, but it would be a nice thought to have a jalopy parked in the yard for some spins around the block and further afield.
As it is, I firmly believe that we need to get back into space in a major way, both to protect our place on our own planet, and establish ourselves on others. We need to develop the technologies for living and working away from Earth, as well as reversing the cynicism that has set in since kids started reading Harry Potter instead of 2001 - A Space Odyssey.

Is this elevator going anywhere?

2011-07-06T22:12:00.000Z

#Elevatorgate is all the rage in the #atheist twittersphere at the moment. In what has to be seen as a rather crass and uncharacteristically hurtful post, Richard Dawkins (a man whom I hold in rather high regard, actually) wrote a very disparaging and frankly sexist and dismissive set of comments in response to Rebecca Watson's perfectly sensible and reasonable post dealing with the fact that she dislikes being propositioned in an elevator (that's a "lift" for those of us in the UK).
Now it seems things have got a bit out of hand, and I think everyone should just step back a bit and calm the heck down. Richard, please read over the comments you have received, and apologise. It's not that you are wrong in that the injustices and abuse that many women have to suffer are far worse than being propositioned in an elevator - they are. It is that your post was dismissive of a problem that is real and distressing - and *dangerous* - in our current cozy Western society. And that is the objectification of women. The notion that treating them as sex objects is OK, and they don't have a right to be upset about it. The bottom line is that religious thoughtlessness cannot reasonably be condemned for the same sorts of lapses that we perpetrate ourselves. If we are criticising others for their unacceptable behaviour, we need to recognise it in ourselves. Sometimes it needs to be pointed out to us, but when it is, we have to be gracious enough to accept it when it's correct, suck it up, apologise and move on.

I think this is my floor.

Talk by libel hero Peter Wilmshurst!

2011-06-18T07:15:00.000Z

Peter Wilmshurst, previously the subject of a malicious libel suit by the now-defunct medical devices company NMT Medical (there IS a god, LOL!), will be giving a talk in Cardiff on "Dishonesty in Medicine" on 26 June. Should be an excellent talk, and your BMA rep should attend, as it is far more important than the official faithy alternative. Here are the details (courtesy of Ant Lempert of the Secular Medical Forum):

Peter has kindly agreed to come and speak at a Secular Medical Forum (SMF)-hosted event in Cardiff on Sunday 26th June. He will speak about 'Dishonesty in Medicine', a topic he's had more than his fair share of involvement with and for which he won the 2003 Healthwatch award.

The SMF welcome reception coincides with the BMA's own Reflection and Thanksgiving Service/Meeting (RATS) which traditionally takes place before the official start of the Annual Representatives Meeting (ARM). In previous years, the BMA has publicised the SMF welcome reception but this year they have refused to do so. Their refusal may relate to some awkward questions we have put to them about the religious format and funding of the RATS and the reason why special status is given to this one 'fringe' meeting when no other fringe meeting is funded by the BMA. These questions remain unanswered.

Whatever your views of the BMA, Peter Wilmshurst is an excellent speaker, the meeting is being held in a private venue paid for by the SMF and is not restricted to BMA members so please come along.

The BMA ARM organisers would prefer that representatives came to their faith-based meeting than to hear Peter Wilmshurst talk about dishonesty in medicine. Please tell your local BMA reps about this meeting.

Sunday 26th June 17:45-18:45
Civic Suite 4, Park Plaza Hotel
Greyfriars Road, Cardiff, CF10 3AL

Goodies over at Genomes Unzipped

2011-06-07T22:18:00.000Z

The fine chaps and chapesses at Genomes Unzipped have a few guest bloggers writing excellent posts about the implications of cheap and quick genome sequencing. I don't think I have opined much on this topic on my own blog, but I'm turning into a bit of a genome bore on other people's blogs. Do your civic duty, and dilute my inane comments with some of your own! I particularly liked Clive Jones's recent post, but Adam Rutherford's is also good.

Genetics is entering a new era; Clive calls it "disruptive" - in the same way as mobile phones were a disruptive technology that totally changed the communications sector. I agree. This is where medicine is at, and we need to think smart to maximise the benefits.

My new philosophy pals: any comment?

2011-06-04T20:17:00.000Z

I'm delighted to welcome some philosophers to my humble blog, and thank them for their astute (for the most part!) comments on my little post about Sausages. It seems a chord of sorts has been struck, which is a good thing (don't sweat what I mean by "good", folks. I wear my heart on my sleeve).

I would now like to divert some of the learned attention towards a previous post on my blog: "THINGS do not possess ATTRIBUTES; SYSTEMS exhibit BEHAVIOURS". I respectfully propose that much of what is thought of as "analytic philosophy" is playing with words that may or may not be good labels for their proposed referents, and may change meaning over the course of the argument, rendering an apparently valid argument pants (in a new terminological structure). The solution is to remember that things in our world are in fact systems; attributes are not sensible things to attach to them. Like "redness", "softness" etc - these are not attributes that things possess, but descriptors of behaviours when these systems interact with other systems. That changes the game somewhat.

Discuss :-)

Show me the Sausages!

2011-06-02T12:01:00.003Z

A philosopher designs a marvellous sausage machine. A scientist comes to marvel at this wonderful creation, and raises an eyebrow.
The philosopher says, "Ah, behold the wonderful cogs and sprockets and temperature-controlled mixing chambers in my wonderful machine - surely you can see how it must produce the most fantastic sausages!"
The scientist says "Yes, that is all very interesting. Show me the sausages."
The philosopher says "How dare you, a mere scientist, question my wonderful philosophical reasoning?"
Scientist: "I'm not questioning your reasoning - I want to know if your machine really produces sausages."
Philosopher: "Can you point to any flaw in my argument that it produces sausages?"
Sci: "I don't know - I just want to know if it produces sausages. Here is some meat. Why don't you feed it through and see if you get any sausages?"
Phil: "And sully my wonderful machine with mere offal?"
Sci: "You said it was a sausage machine. I want to see the sausages."
Phil: "Are you questioning my ingredients?"
Sci: "I'm just questioning whether it produces sausages or not. Show me the sausages."
Phil: "Ah, so you cannot attack my premises and you cannot attack my argument. Therefore I'm right and you lose."
Sci: "Don't be such a melodramatic prancing arse. Show me the sausages."
Phil: "The sausages inevitably flow from the argument. You see my fine machine. You can even inspect the meat & onions. The sausages necessarily flow."
Sci: "Show me the sausages or I'm off to Tesco."
Phil: "You are a mere scientist with no understanding of philosophical matters."
Sci: "Bye."

Boat for sale: Jaguar 21, great condition!

2011-05-28T12:48:00.000Z

"Sonata", Jaguar 21 sailing boat. Excellent condition, great fun to sail. 21ft, lifting keel.
[Photos to come, but it's nice!]

Location: Greenisland, near Carrickfergus, Northern Ireland.
Complete with trailer, sails, 6HP Mariner outboard motor, cushions for interior, Garmin Fishfinder sonar.
£6000 o.n.o.

Leave a comment below or tweet @shanemuk if interested.

BBC News Article on Evolution Gets It Wrong

2011-05-19T09:30:00.001Z

I'll post more on this later. Have a read of this article, and if by the point where it tells you that this process is somehow unrelated to natural selection you're not tearing your hair out, you either have considerably more tolerance for silliness than I do, or you haven't a notion about what the concept of natural selection actually implies. Here's the link: http://www.bbc.co.uk/news/science-environment-13445951
I think I'll have a lie down now.

In which I unzip a few genomes...

2011-04-25T17:55:00.001Z

Here is a post I made by way of comment on "Genomes Unzipped". Enjoy!
http://www.genomesunzipped.org/2011/04/the-genome-hasnt-failed.php

----------------
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.

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

Changeable weather in Donegal

2011-04-22T14:30:00.000Z

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.

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

2011-04-13T09:39:00.002Z

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]

What sort of thinker are you? Visual or Verbal?

2011-04-09T21:24:00.000Z

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. What is it really measuring? Who knows?
That said, there does 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.
Verbal thinkers are quite different. To the verbal thinker, the instructions are key. Protocols & standard operating procedures. I sometimes think visual 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.
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. I don't know.
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.

Apologies for the hiatus

2011-04-01T20:13:00.000Z

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?

Follow @shanemuk on Twitter!

2011-03-15T22:21:00.000Z

Yeah, I know I've been neglecting this place. Stuff to do and all that. But I have started using Twitter a bit in order to see what all the fuss is about. So far I haven't figured that out. But I shall persist for a while. So if you want my inane cobblers about life, the universe and the contents of my sock drawer, head over to http://www.twitter.com and follow @shanemuk

It's free, and you won't be put in jail for it.

No Religion, One Community

2011-03-03T22:37:00.000Z

Or at least religion should be irrelevant. Since the time of the Good Friday Agreement in Northern Ireland - indeed, since well before that, legislation in the name of "Equality" has required employers and other groups to monitor people in terms of their religious affiliation, and in other axes in accordance with Section 75 of the Equality Act.

So people in NI are regularly made to fill out forms, basically to say whether they are Protestant or Catholic. Indeed, that's not even enough - the question is often worded to ask whether you might be *perceived* as a member of the "Catholic Community" or the "Protestant Community", as if these were distinct entities.

Now, I know we have a history, and I know what the reasoning behind this all was in the first instance, but surely this shite is past its sell-by date? There is a new generation in Northern Ireland - a new set of people who do not identify themselves as "Protestant" or "Catholic" - just "human". We do not want to be "perceived" as "belonging" to categories of Prod or Taig, just to suit some number crunchers somewhere. I'm fecking fed up to the back teeth with this sort of bollocks, so I am respectfully suggesting to anyone in NI who might share my view that we should make a concerted effort to answer these questions in a way that indicates that we are a member of NEITHER the "Protestant" or "Catholic" communities, and then maybe this stupid exercise in legacy sectarian arsery will wither and die. And good riddance to it if that happens.

More theological insights

2011-02-25T23:47:00.001Z

Can beauty exist without its opposite? Can good exist without evil? Can derpants exist without underpants? Questions like these have puzzled philosophers for millennia, but thanks to some groundbreaking philosophical research by Prof K Perry from the Super Hot Institute of Theology, it can be conclusively demonstrated that apparently opposite attributes can be present in the one individual contemporaneously.

The implications for theology are obvious.

Freudian Slip: Then She Smiles

2011-02-24T21:45:00.000Z

Blast from the 1990s - that Dungannon rock band that dare not speak its name...
Enjoy!

Renaissance in Egypt...

2011-02-18T11:15:00.001Z

OK, just floating this as an idea - now that Egypt is taking steps towards a new society, is it time to re-open, re-consecrate, or simply *build* some new, fully-operational temples for the worship of Amun-Re, Hathor, etc? We could use the very best Egyptological knowledge to reconstruct our best-guesses as to Egyptian religious practice. Some people might find that it suits them - as long as they don't take the *belief* aspect too seriously...

Let's face it - religion is a tourist draw. The upper echelons of the theologians of every religion know perfectly well that they are dealing with a purely human cultural creation - the "gods" are human constructs, and their "presence" is a group phenomenon when you get a bunch of people together - an emergent thing.

Imagine the beauty of a revived Opet festival, the procession heading between Karnak and Luxor, with flags snapping and obelisks gleaming. Of course there would need to be some changes made to make things more accessible, but that could be done, and it would potentially be a fantastic vehicle for teaching Egyptology itself.

So perhaps a true test of the tolerance and respect agenda that should be emerging in the world should be a concentrated effort to re-establish Ancient Egyptian religious practice in the Land of the Nile, and in the spirit of the New Egypt, I invite comments.

The most profound theological insight of the 21st Century

2011-02-16T09:35:00.000Z

God is Snoop Dogg, the Universe is a giant candy casino, and we're all California Gurls.

Any questions?

My new neighbour

2011-01-31T16:57:00.000Z

Barack takes care of the groundwork before getting down to business.

Meet the latest blow-in to the Shore Road - Mr Barack Ollama. After a particularly disturbing series of sheep-worrying attacks by canines unknown, my neighbour has decided to employ some Peruvian tactics to protect Flossie and her pals. Let's hope it works, but in the meantime he seems like a very civil chap, and takes his responsibilities very seriously.

Some thoughts on the convulsions in Egypt

2011-01-30T08:02:00.000Z

These are difficult and turbulent times for Egypt, and it is difficult for outsiders like me to get a clear view of what is going on, or what the likely consequences will be. There is no doubt that there are serious dangers, and it is vital that the international community plays its part to support the Egyptian people. I think there are several points that need to be made in relation to Egypt's place in history.

1. PAST
Egypt has a stunning past, stretching back in historical continuity for over 5000 years. During that period, this Gift of the Nile has seen some remarkable developments, as well as times of major turmoil. The people of Egypt have inherited the legacy of the Pharaohs, the Romans, the Christians and the Muslims. They are guardians, to put it one way, of a major slice of Western history and civilisation.

2. PRESENT
More recently they have suffered as their democratic rights have been suppressed, and their opportunities to shape the destiny of their country have been severely curtailed. There is widespread dissatisfaction with the current regime, and that has led to the situation we have right now. The people need liberation. But there is a catch.

3. FUTURE
It is too easy to see "liberation" as an event, but liberation is not true liberation unless it is an actual dawn of an age of freedom, rather than simply a regime change. If Mubarak is toppled (as seems inevitable), one of the worst possible outcomes would be the rise to power of a fundamentalist religious regime. If liberation is not followed by real meaningful freedom, then liberation it is not. This is a time where Egypt's allies need to realise that our obligation and allegiance is not to the regime of Mubarak, but to the people of Egypt, and our debt is to its history, which is our history too. If Mubarak is not replaced by a truly representative and inclusive democratic system, with clear separation of religion and state, and a major programme of regeneration and social equality, then "liberation" will simply be a one-off event, a gateway from one dictatorship into another - a brief glimpse of the sky while being moved from one prison block to another.

So we have to stand with the people of Egypt and give our full support during this period. Any solution must be an Egyptian solution, but these remarkable, resourceful, admirable people deserve a country that leads on the world stage.

Join the Facebook group (if you're on Facebook) "Egyptologists for Egypt".

Ethics: The [Off His] Trolley Problem

2011-01-29T10:55:00.000Z

One of the contributors to my esteemed blog's comments section sent me the following ethics problem. I will allow him to de-cloak if he feels willing to do so, but I absolutely refuse to let such a practical everyday ethical issue go unaddressed on this blog. Because these issues are important. If we are in the proposed scenario (and, let's face it, who is likely to avoid this?), we need to think carefully about how we will act. Take it away, Mystery Man! (oops - I revealed the sex there... that narrows it down...)

A brain in a vat is at the wheel of a runaway trolley. There are only two options that the brain can take: the right side of the fork in the track or the left side of the fork. There is no way in sight of derailing or stopping the trolley and the brain is aware of this, for the brain knows trolleys. The only living beings saved on railway tracks are saved in one, and only one, of two ways. (i)They can save themselves. (ii)They are saved by a brain-in-a-vat changing the direction of a runaway trolley.

On the right side of the track there is a single railroad worker, Jones, who will definitely be killed if the brain steers the trolley to the right. If the railman on the right lives, he will go on to kill five men for the sake of killing them, but in doing so will inadvertently save the lives of thirty orphans (one of the five men he will kill is planning to destroy a bridge that the orphan's bus will be crossing later that night). One of the orphans that will be killed would have grown up to become a tyrant who would make good utilitarian men do bad things. Another of the orphans would grow up to become a used car salesman, while a third would invent Pringles. The rest will consume carbon fuels and fatty foods at unreasonable rates.

If the brain in the vat chooses the left side of the track, the trolley will definitely hit and kill a railman on the left side of the track, "Leftie", and will hit and destroy ten rabbits on the track that could (and would) have been used to feed starving children. If the railman on the left side of the track lives, he too will kill five men, in fact the same five that the railman on the right would kill. However, "Leftie" will kill the five as an unintended consequence of saving ten men: he will inadvertently kill the five men rushing the ten rabbits to the local poor shelter. A further result of "Leftie's" act would be that the busload of orphans will be spared. Among the group of men killed by "Leftie" is both the man who wrote the theme tune to “Friends” and Michael Barrymore. If the ten rabbits and "Leftie" are killed by the trolley, the ten starving children will die and their kidneys will be used to save the lives of twenty kidney-transplant patients, one of whom will grow up to cure cancer by illegal experiments on death row inmates in Iraq, and one of whom will grow up to be the next Dr Who. The kidney patients will be operated on without their informed consent.

Assume that the brain's choice, whatever it turns out to be, will serve as an example to other brains-in-vats and so the effects of his decision will be amplified. Also assume that if the brain chooses the right side of the fork, an unjust war free of war crimes will ensue, while if the brain chooses the left fork, a just war fraught with war crimes will result. Finally, the brain in the vat knows that there is a bomb on the trolley, and unless it pulls the lever on the trolley the bomb will explode and kill it.

Question: The brain has no arms and can’t control the direction of the trolley. But what should it want to do?

Well?

Genome-wide association studies and the "missing heritability".

2011-01-29T08:31:00.000Z

From The Golden Helix blog:
" If complex diseases are driven by susceptibility alleles that are ancient common polymorphisms, as the common diseases-common variant hypothesis proposes, we should be seeing a larger portion of the heritability of these traits being accounted for by these associated polymorphisms. The alternative hypothesis that must now be considered is that complex diseases are actually driven by heterogeneous collections of rare and more recent mutations, as with most Mendelian diseases!"

Quite a lot of us have been considering that hypothesis for a rather long time. GWASs have been able to detect quite a number of genes involved in complex and common disease, but common variations in the population can only explain a relatively small amount of the "heritability". A rough way of thinking about this is to consider all the genetic variation that we know about in a population - every new generation injects a vast amount of completely new variation - you contain about 100 mutations that your parents did not have. Your kids will each have another 100, and this is happening for everyone within the population. Many of these mutations are going to occur in genes that participate in pathways that will affect disease susceptibility - it is unavoidable.
For the purposes of this discussion (the reality, as ever, is a bit more complex), "Mendelian diseases" are those rare (but actually not that rare!) disorders that are caused by mutations of large effect on one critical gene; different disorders are caused by mutations in different genes, and exert their effect by disruption of different biological pathways. Having a rare disorder is a common problem - something like 10% of families are impacted by a serious genetic disease. They crop up all the time; that being the case, why should it come as a surprise that genes influencing heart disease or autism crop up all the time at a low enough frequency to be missed by GWAS, but frequent enough to make the diseases themselves very common?
Clinical geneticists have been saying this for a while now - but are they correct? The exciting thing is that the possibility to test these ideas is arising from the technology that allows us to sequence large numbers of human genomes relatively cheaply, and to analyse biological pathways in unprecedented depth. With large datasets like these, we will be able to avoid the inherent bias of GWAS for common genetic variants, and get a better picture of the fine scale genetic structure - many many rare variants in gene pathways that can cause disease susceptibility. That is when the fun will really start.
But it'll be nice to be able to say "We told you so!"...

Transformations of the Transfiguration

2011-01-18T21:40:00.000Z

OK, we're having some fun with crayzee interpretations of the Transfiguration yarn that appears in the Synoptic gospels (Mark, Luke and Matthew). But what do they really say? It seems appropriate to post the actual texts, here rendered from the King James Version, seeing as how this is the 400th anniversary and all, and shed a little light on how this tale evolved.

First up is the first gospel (chronologically and the source for the other two tales), Mark 9:2-8:

²And after six days Jesus taketh with him Peter, and James, and John, and leadeth them up into an high mountain apart by themselves: and he was transfigured before them.
³And his raiment became shining, exceeding white as snow; so as no fuller on earth can white them.
⁴And there appeared unto them Elias with Moses: and they were talking with Jesus.
⁵And Peter answered and said to Jesus, Master, it is good for us to be here: and let us make three tabernacles; one for thee, and one for Moses, and one for Elias.
⁶For he wist not what to say; for they were sore afraid.
⁷And there was a cloud that overshadowed them: and a voice came out of the cloud, saying, This is my beloved Son: hear him.
⁸And suddenly, when they had looked round about, they saw no man any more, save Jesus only with themselves.
⁹And as they came down from the mountain, he charged them that they should tell no man what things they had seen, till the Son of man were risen from the dead.

Here's Matthew 1-9, which is clearly textually derived from the document of Mark (or a close precursor):
¹And after six days Jesus taketh Peter, James, and John his brother, and bringeth them up into an high mountain apart,
²And was transfigured before them: and his face did shine as the sun, and his raiment was white as the light.
³And, behold, there appeared unto them Moses and Elias talking with him.
⁴Then answered Peter, and said unto Jesus, Lord, it is good for us to be here: if thou wilt, let us make here three tabernacles; one for thee, and one for Moses, and one for Elias.
⁵While he yet spake, behold, a bright cloud overshadowed them: and behold a voice out of the cloud, which said, This is my beloved Son, in whom I am well pleased; hear ye him.
⁶And when the disciples heard it, they fell on their face, and were sore afraid.
⁷And Jesus came and touched them, and said, Arise, and be not afraid.
⁸And when they had lifted up their eyes, they saw no man, save Jesus only.
⁹And as they came down from the mountain, Jesus charged them, saying, Tell the vision to no man, until the Son of man be risen again from the dead.

And now for Luke, who was also working off the document we now know as Mark:

²⁸And it came to pass about an eight days after these sayings, he took Peter and John and James, and went up into a mountain to pray.
²⁹And as he prayed, the fashion of his countenance was altered, and his raiment was white and glistering.
³⁰And, behold, there talked with him two men, which were Moses and Elias:
³¹Who appeared in glory, and spake of his decease which he should accomplish at Jerusalem.
³²But Peter and they that were with him were heavy with sleep: and when they were awake, they saw his glory, and the two men that stood with him.
³³And it came to pass, as they departed from him, Peter said unto Jesus, Master, it is good for us to be here: and let us make three tabernacles; one for thee, and one for Moses, and one for Elias: not knowing what he said.
³⁴While he thus spake, there came a cloud, and overshadowed them: and they feared as they entered into the cloud.
³⁵And there came a voice out of the cloud, saying, This is my beloved Son: hear him.
³⁶And when the voice was past, Jesus was found alone. And they kept it close, and told no man in those days any of those things which they had seen.

No serious scholar disputes the fact that these texts are intimately related from a documentary point of view. They are not (as a few evangelicals like to assert, in the teeth of the evidence) the work of "independent eyewitnesses" or the "guidance of the Holy Spirit", but Matthew and Luke working off Mark. That's OK, but it is the little embellishments and wrinkles that are fascinating.

For instance, have a look at v31 in the Luke rendering - the stressing of Jerusalem. Why Jerusalem? Luke has a serious thing about Jerusalem. In the other gospels, Jesus appears after the crucifiction to his disciples back in Galilee, but that is in direct contradiction to Luke's account - for Luke's developing story, he has to keep everything in Jerusalem, because he's going to bring Saul Paulus in later, and that requires a Jerusalem focus. Still, it sits very oddly in the text. You'll also notice that Luke makes it very clear that the disciples were in some sort of sleep-induced stupor.

I'm sure that Ian over at Irreducible Complexity (one of my favourite blogs) could do a funky textual analysis on it and draw some nice graphs based on the original Greek, but it's one of those wee things that gives us an insight into the spin and tweaking that the different gospel writers used to try to brand "their" Jesus. What was going through the minds of "Matthew" (not the real Matthew, obviously) or Luke as they copied "Mark"? Why did they feel the original text needed correcting?

Luke's version of the Resurrection

2011-01-11T23:11:00.000Z

Muehlhauser, that is. Here is the link: http://commonsenseatheism.com/?p=11338 - the point is established that the notion that Jesus *actually* rose from the dead is unbelievable, and the "evidence" in favour of a resurrection is only remotely persuasive if you already believe it. Instead, the evidence actually shows that the stories were sexed up to spin a fiction.

The Great Transfiguration Debate

2011-01-09T23:17:00.000Z

Ike wanted me to say what I think happened at the supposed Transfiguration of Christ event. As those of you with bibles will know, in the synoptic gospels (but not in John, oddly, because John was supposed to have been there), Jesus allegedly was transfigured on a mountain, and visited by Moses and Elijah.

As far as I am concerned there is nothing to say about this. There is no evidence that such an event ever happened, nor is there any evidence to suggest that the two chappies alongside Jesus were indeed Moses and Elijah anyway. The tale, idle as it may be, is a fiction to impress a specific point - Jesus is the Messiah, and he is greater than Moses or Elijah.

But was it a real event? Could Jesus's followers have been mistaken? Instead, could Jesus have actually been visited by aliens, and lit up by the headlights of their flying saucer? Maybe they were arranging a meeting in Gethsemane later, but like totally forgot to show up, much to the chagrin of Jesus himself. And all that even after organising donkeys and upper rooms and stuff. Pesky aliens! Unreliable, the lot of them.

So in the absence of anything remotely resembling evidence, the Transfiguration goes down as just another wee story; we can derive metaphorical "truth" from it if we will, but it's not historically useful.

The Great Resurrection Debate

2011-01-03T11:39:00.000Z

Over on my Facebook page, GV, IOA and I are having an interesting spat about the historicity of the resurrection of Jesus the Nazarene. Needless to say (I suppose), I regard the supposed historicity of this event as almost laughably inadequate, and I think that many historians have been scared off the topic by the somewhat crazy reaction. The bottom line, I feel, is that there are plenty of perfectly adequate explanations for the resurrection stories (plural) in the gospels that do not need to invoke an actual resurrection. Furthermore, the actual stories as we have them contain evidence for the development of the tale as a set of myths and rumours that subsequently became fixed into a dogmatic belief shibboleth for entry into Christianity.

Naturally, I contest that - you don't need to believe in God or Jesus's resurrection to be a Christian, as the Church of Jesus Christ Atheist tries to show. Anyway, here is some of our discussion thus far. Feel free to continue the debate in the comments thread. Enjoy!

SMcK: And as for the resurrection of Jesus, that is for theists to prove as a historical event. The actual evidence is very very strongly against Jesus having risen, and very very strongly in favour of this being simply a story that accreted over time. But we've been there before!

IOA: GV and Shane, this all comes down to what we mean by 'science.' Science is a way of studying the events, processes and phenomena of nature through the analysis of data. As the US National Academy of Sciences puts it, anything for which ...it is not possible to obtain empirical data is outside the realm of science. This puts most of the 'origins' outside of science, as it is not possible to obtain any data about these things. It also puts most of history outside the field of science.

I do not wish to argue that there were just two members of Homo sapiens when the species emerged, but how does anyone know that that that was not the case?

There is no real conflict whatsoever between science and religion, as these two relate to different aspects of the life of our universe. Science is about things regarding which we can obtain empirical data. Religion is about things - the existence and activity of supernatural beings - regarding which we cannot obtain any empirical data. The mistake that many people make is to say that because we cannot obtain empirical data about supernatural beings that means that such beings do not exist.

There is so much upon which we rely in our everyday lives regarding which we cannot obtain any data at all. And even in our clinical practice, we face the same situation: for example, no one doubts the existence of general anaesthesia, but we have no data whatsoever about how it is produced.See more

IOA: Shane, what is the evidence that Jesus did not resurrect?

GV: Well, I agree that I need to lie down! Sunday afternoon nap, and all that. You're probably right about the asylum as well. There's only so much "puppet ministry" that a grown man can take.

As for Adam and Eve, if you rule out the possibilit...y of revelation, then you've no reason to believe in them. I can't see how science could say anything about the possibility of revelation, one way or the other. But it does seem to challenge one doctrine about original sin. Christian apologists use Fine Tuning and Big bang Cosmology. So there is some interaction between Science and Christianity, sometimes, and Christians have to take the rough with the smooth.

But Science has *nothing* to say about the value of metaphors! That's crazy talk. If Paul, as Dunn thinks, just thought that this was a story that gave us insight into the human predicament, and if Paul thought (again as Dunn asserts) that there never was an Adam and there never was an Eve, then Science has nothing at all to say about Romans 5, 7 & 8.

GV: BTW my concerns about "Science says.." really stem from the way that Al Gore uses it in "An Inconvenient Truth". It's a powerful rhetorical tool. There's a difference between "Science says the Earth goes round the Sun" and "Science says the Polar Bears are drowning".

IOA: GV, I think we can agree that science - by which we mean the natural, empirical and formal sciences - is not equipped to make assertions about everything: its range is limited to matters that can be studied using data.

Shane: When you ...are ready, please let us have the scientific evidence that Jesus did not resurrect. [You may be tempted to say that it is up to those who say that He did to prove their statement; but try not to go there.]

SMcK: GV, there is what science says and what people say science says. As it is, we can formulate the Adam and Eve hypothesis; this is scientifically testable using genetics - and it fails miserably. Adam and Eve never existed as the human progenitors. The fact that Original Sin is an incoherent brainfart is a secondary issue.

IOA: Shane, whilst waiting for your evidence that Jesus did not resurrect, I add another question: What is the evidence that Adam and Eve did not exist as progenitors of humankind?

SMcK: IOA, scientifically we can look at the resurrection stories, and they show unmistakable evidence of embellishment, post hoc rationalisation and narrative contradiction. Scientifically we know that people resolve cognitive dissonance with confabulation. So the evidence we *do* have suggests that belief in the resurrection was not based on real appearances of the risen Jesus. You can do history scientifically, you know.

IOA: No, Shane, the only evidence for the non-resurrection of Jesus would be either His preserved body or bones clearly identified as His.

The apparent contradictions in the stories do infact provide confirmation of resurrection because of what ...we know about eyewitness accounts - they are rarely identical.

SMcK: IOA, that's cobblers. The differences are systematic and damning. They strongly indicate that the resurrection was an invention, not an event.
As for the science disproving the A&E hypothesis, that's genetic coalescence. Irrefutable, I fear.... Sorry!

IOA: Shane, show me ONE difference in the resurrection accounts that you find 'damning.'

Sweeping statements are not the stuff of science.

You have not answered either question, Shane, and the reason is obvious: the answers are not in science.

The basic position, I think, Shane, is that you do not believe that resurrection is possible. As it is not part of your worldview you reject its possibility.

SMcK: IAO, don't be silly - it's not that it's not possible; it's that it didn't *happen*. it's just a story. Jeez! The damning evidence is in Mark's non-mention of the resurrected Jesus, Matthew's clear hyperbole and Luke's manipulation of the source text to support his Jerusalem stanza. It's not too difficult.

Btw, not one of the resurrection stories was written by an eyewitness - IOA, you're showing ignorance and disrespect for the texts.

GV: People in glass houses should stay clear of howitzers Shane. For a start, let's take Matthew's hyperbole. Compare it to Dio Cassius' account of Claudius' death, or his account of Egypt's enslavement by Caesar. Or you could compare it to Jos...pehus' account of the Temple's Fall. Wondrous signs often accompanied historically significant events in ancient writing. Evidence from Lucian suggests that this was widely recognised as symbolic language; whatever the case, Matthew reads as positively restrained in comparison.
                  Let's also take the silly idea that Mark does not include the Resurrection. Mark 8v31, 9v31 and 10v33-34 put that notion to rest. Mark 16 v7 shows knowledge of appearance narratives - and predictions - not mentioned in the Gospels. And there is practically unanimous agreement that appearance *traditions*, as in 1 Cor 15, were part of the kerygma.
                  The hypothesis of legendary development encounters significant difficulties. The idea that a bodily resurrection developed over time suggests that the Churches traditions became more Palestinian-Jewish exactly when the Church was becoming more Hellenistic. (The idea that Paul did not preach a physical resurrection seems to have been thoroughly debunked BTW).

                  It also faces the problem of the texts themselves. There is no apologetic force in Mark 16, as this theory requires. Instead there is a note of fear, which Mark normally uses to exhort his readers. Both Mark and Matthew are forced to include embarrassing details, such as the primary witness of women, and the accusation of grave robbery (equivalent to an accusation of witchcraft!).
                  The legendary-development hypothesis depends on the argument that the narratives of empty tomb and resurrection appearances that we have in the Gospels developed out of the kergyma: first the summary, then the narratives formed to illustrate the kerygma in preaching. But there is at least one more massive problem here: Paul's list of appearances in 1 Corinthians and the resurrection narratives in the Gospels are remarkably illmatched. The wrong "legends" appear in the Gospels. We have no narrative for the appearance to Peter, or for the appearance to James. This extraordinary lack of correspondence between the kerygmatic summary that Paul quotes in 1 Corinthians, and the resurrection narratives in the Gospels strongly suggests that we are dealing with two fundamentally independent forms in which the Easter events were transmitted in the first Churches.
                  As for eyewitnesses, we have statements written down by eyewitnesses for the main events of the extraordinary career of Augustus. The Gospels are literary units. But they are composed of oral traditions that circulated in the Early Church. The evidence clearly indicates that many began to circulate during Jesus' ministry.
                  The Gospels theology depends on their historicity. So they must make every effort to be faithful to the traditions. And it is impossible to explain why these traditions mention Mary of Magdala if she did not exist, and was not an eyewitness. She is associated with demon possession, so she is not the ideal witness. Clearly identifying a witness when anonymous witnesses could have been used by preachers, or when reliable male witnesses could have been invented, points to Mary's existence and role as an early eye witness. If you've a better explanation - that deals with the nature of the texts - I'm all ears!

SMcK: Er, GV, none of that remotely deals with the problem that you have here. Legendary development is clearly demonstrated in the gospels - YES, it is the development of the legend AFTER it is "established" that Jesus has risen, but we see ...both Matthew and Luke embellish a *written* source, not an oral one. What you have here is an early *belief* that Jesus rose from the dead, based on a missing corpse (from the viewpoint of the followers), and a bunch of ill-formed ghostie stories that eventually got untidily gathered up and strung together by the gospellers (and Saul Paulus, who has to get his own oar in, of course). Your appeal to Mary Magdalene is pointless - we already know that John and the Synoptics make completely different hay with her, and this notion of her not being the "ideal witness" in the minds of the followers is not tenable - after all, she is the ONLY linchpin they can hang their story on. No-one else saw Jesus, apart from visions and spookie ghostie incidents.

So we have the issue where an early resurrection belief has become distorted and embellished (your references to other early sources of historical events is pointless - no-one really believes the list of portents in Dio, for example, even if the event itself is accepted) specifically in order to fulfil an apologetic role (Matthew and John admit as much). Since these accounts (including Saul) only establish the parameters for what *had* to be believed by people to join the Christian sect, they provide no good evidence at all for the veracity of the core premise. You can be pretty damn maximal in what you let the gospels away with, and you still only end up with an empty tomb, a family who disagreed with Jesus's tack, and some punter at the temporary tomb/storage spot telling the women that they had taken Jesus's body back to Capernaum for definitive burial.

That's where the evidence points - it most certainly does not point to an actual resurrection, and silly speculation about what the followers "would" have done is not mirrored by the way humans actually behave, and especially not by the mindset we *know* was common in C1CE palestine, where every fart's turn of a preacher was some prophet or other risen from the dead. There is a crazy fallacy at work in apologetic circles that the disciples were detectives trying to figure out what happened. Not so. They were ordinary people in cognitive dissonance who got caught up in the development of a myth. The gospels are far more readily explained by this model than by an actual resurrection.

GV:                  ‎1) Name *one* other preacher who claimed to be Resurrected in 1st Century Palestine!
                  2) The point about Josephus/Dio Cassius is that symbolic embellishment need not count against the historicity of the core event.
                  3) If the Gospels were in t...he business of legendary development, Joseph of Arimethea, or the young man who followed at a distance, or another character like "the beloved disciple" would have been invented from the aether. Mary of Magdala would not have been used.
                  4) This is not a matter of "apologetics"! In mainstream research all of the relevant issues - the empty tomb, the appearances etc. are up for grabs.
                  5) The use of Mark should draw your attention to the point that the Gospel writers were careful with their sources. You can clearly see that the tendency of the Synoptic tradition is not one of legendary development! You may expect to find legendary development, but that is not what the evidence shows!
                  6) We also know from Mark and Paul that there were appearance traditions that they did not write down. So it is no surprise to find some occurring in Matthew and Luke that do not appear in Mark. Everyone agrees that they had access to oral traditions.
                  7) So then we have the conspiracy theory - which is at a polar opposite to the legendary-development theory. Conspiracy theories agree with the Gospels that the core events occurred, but argue that the disciples misinterpreted the core events.
                  In the 17th and 18th Century rationalist explanations for Jesus' miracles abounded. So Bahrdt could explain the Feeding of the 5000 as an Essene plot, with Essenes secretly located in caves to hand out loaves to Jesus' disciples. Jesus' walked on water by placing planks just below the surface (near the shore presumably!) When Jesus said "be calm" he was addressing the disciples. By chance, the storm calmed down soon after this command. And so forth.
                  Now Strauss rejected these explanations, and used the category of myth to explain the miracle stories. No one, to my knowledge, has resurrected them in mainstream scholarship. The unspoken principle seems to be that explanation by a conspiracy theory is no more plausible than an explanation by a miracle.
                  However, rationalist explanations are allowed for the Resurrection. Ehrman advances one in his debate with Craig. He is more cautious than the rationalistsm and merely insists that it is more plausible than the Resurrection, not that it is historicaly probable. Any non-miraculous explanation must be more probable than a miraculous explanation in Ehmran's view. But that seems to fly in the face of the consensus of historians from Strauss onwards. In any case, is it revealing that mainstream scholars will fly back to H.E.G Paulus to explain the Resurrection traditions, but not the feeding of the 5000 or the calming of the Storm?
                  After all, if we can allow that some conspiracy or coincidence lies behind the Resurrection traditions, then why not Jesus walking on water, or the exorcism of Legion? If we can use psychological explanations for the post-mortem appearances of Jesus, why can't we use them for the nature miracles?
                  And the conspiracy theory that you have put forward relies on so many improbable events coinciding that a miracle seems much likelier.See more

SMcK:
‎1. JTB was Elijah; Jesus was alternately JTB or one of the prophets of old. No preacher seems to have made this claim on his own behalf (that we know of), but plenty of people appear to have been willing to attribute it to them. I think my... point is made.

2. Josephus & Dio etc: yes, it doesn't count against the core event, unless the core event itself is spectacularly incredible, and we can sketch a real temporal layering of the embellishment. Which we can, so it means a/ the gospels contain embellishments (so why is the resurrection not itself an embellishment?), and b/ they are clearly not "inerrant" in any meaningful way. See?

3. Who said anyone was invented from the aether? Use of existing personages as props is standard fare for legendary development. No-one is saying that is necessarily *conscious*! This is how stories grow and evolve.

4. Mainstream research? Yer arse! The empty tomb is part of the *same story*! But even if we concede an empty tomb, the post-resurrection stories are just that - stories. NOT "appearances". Furthermore, they are inconsistent - you might as well believe Jesus's ma really appeared at Lourdes.Some historical rigour please!

5. This is flatly contradicted by the gospels, where you do see embellishment and attempts to "fix" Mark. Matt and Luke used a documentary source(s), not an oral tradition.

6. For "oral tradition" substitute "rumours". Saul's stories do not match the gospels because these were freeform legends, not established episodes. If you actually read them, you will see very clearly that there is simply nothing there.

7. Be careful. Not all conspiracies are equal, but I would have to say that human gullibility and brainfartedness in the face of cognitive dissonance is perfectly adequate to explain what we see - no conspiracies (before Saul anyway) or miracles are required. The feeding of the 5K or the calming of the storm do not need "explained" by miracle or conspiracy. They were not witnessed by the author, and stories of famous punters doing miracles are two a penny. We expect them.

I have not advanced a conspiracy theory. There is no need for one. The evidence that we do have firmly establishes the gospels as embellished narratives that really require nothing more than a lost body as the spark that set the whole silly fiction into motion. You're hiding behind poor historical scholarship, GV. The reality is not that complicated.

Think yourself into their situation in C1CE. Pretend you're Mary of Magdala. You find the temporary tomb has been opened and the body's not there, and in your confusion you don't listen properly to the young chap who tells you that they've taken the body to Capernaum for proper burial. You already believe in resurrections and crazy shit. Suddenly the solution presents itself.

Go figure! Not only is a resurrection *improbable* given these circumstances, even if one *actually happened*, the evidence we have does not allow us to upgrade it from "astonishingly unlikely" to "just maybe".

IOA: The resurrection stories that were later written down were originally told by eyewitnesses. St Paul went through a long list of people to whom the Risen Christ had appeared - before he had his own experience of Christ on his way to Damasc...us to persecute Christians.

I am pleased to read that you accept the possibility of resurrection. That is a mighty step forward, Shane. I recommend this review, as it is very well researched:
http://en.wikipedia.org/wiki/Resurrection_appearances_of_Jesus

SMcK: IOA, with the single exception of the R2D episode, which is inconsistent, but itself no more than a vision, there is *not one single* eyewitness account of the risen Christ. Not one. The accounts that we do have are hearsay, and of no more value than the feeble prattlings of some teenage delusionist from Lourdes or Knock.

GV: On your evidence for other "Resurrection"s -
Of course, the problem with using these texts is four fold.(a) These texts are all associated with Jesus’ ministry. So the only “Resurrected prophet” remains Jesus. There is no evidence of any ot...her “prophet” (like Theudas or the Egyptian) being associated with Resurrection (b) Matt 17 v1 – 12 makes it clear that John the Baptist takes on Elijah’s role. So he is figuratively, but not literally, Elijah (c) Elijah never died. So even if John the Baptist was meant to be literally identified with Elijah, this would not be a resurrection (d) it only makes sense to identify John as Elijah if he ushers in the age to come. The only group who claimed that John did this was the Early Church. So resurrection would be associated with Jesus ministry, but you would not have any evidence for a wide spread belief in Resurrected prophets.

Your focus on the literary history of the Jesus traditions is poorly informed. If you want evidence of oral traditions, compare Matthew 8 v 5-13 and Luke 7 v 1-10. The story does not “fit” Q’s content, and there is so little agreement in the wording that another literary source is unlikely. Evidence of a shorter oral tradition surfaces in Luke 24 v 34, which does not fit with Lukan syntax, or with the flow of the passage.

That's just two off the top of my head.

It’s simply a fact that oral traditions were used by the Gospel writers, and that these traditions should not be modelled on modern Western assumptions. In 1 Cor 9 v 14, 1 Cor 7 v 10, 1 Cor 11 v 23–25, 1 Thessalonians 5 v 2f, 1 Cor 13 v2, Rom. 13 v 8-10and Romans 12 v 14-15 we have clear evidence that Paul was aware of Jesus’ teaching on ethics and the apocalypse. And Paul is explicit in 1 Cor 15 – he is handing on oral traditions.

Jacob's Legacy

2011-01-02T21:54:00.001Z

I'm currently reading "Jacob's Legacy: A Genetic View of Jewish History" by David Goldstein on my Kindle (it makes it far too easy to buy books - I need to find some way to control myself!). I've always been fascinated by genetics (obviously) and by the Old Testament and the history of the Jewish people. In this accessible and fascinating book David Goldstein (something of a legend among population geneticists) uses the techniques of his field to see what the genetic makeup of today's Jewish people tell us about the events that shaped this amazing group. Particularly impressive is the work on the Y chromosome that demonstrates that the line of the Cohanim (the paternal priestly line going back to the legendary Aaron) really does seem to be different from that in "ordinary" Jews (where the maternal lineage is the main determinant).
I'm only part of the way through at present, but it's a gripping read, and acts as something of a taster to the wonders that may await us as genetic technology progresses, and we can start mapping the origins of many many more genetic variants. When we look at a family tree, we often only focus on one line, yet if you go back just ten generations, there are potentially over a thousand people contributing to your genetic heritage! Go back twenty generations, and it's a million. Thirty generations (that's getting to about 750 years), a billon.
Now of course that's more people than would have been on the planet back then; what is going on of course is that there is not full outbreeding - the lines of descent cross frequently, so although a couple might not know they are related, it may be that only a few generations back they share a common ancestor. I did get a bit of a shock when I found that happening in my own family (OK, back to the 1700s, but that was only 8 generations! And even then, that's only along one line that I know about).
Genetics allows us to unpick these relationships - especially when you think that if 1000 years is only about 40 generations, and the entire sweep of Jewish history is only 120 generations at the very most, we really should have the resolution to address some very specific questions. That is what David Goldstein has done with several Jewish populations over the world, and although I haven't finished the book yet, I would strongly recommend it.
Dan Bradley did something a bit similar in Ireland a few years ago - turns out the McKees are closely related to Niall of the Nine Hostages, the brigand king who abducted an unlucky Anglo-Roman lad called Patricius from somewhere on the west coast of Britain, and brought him over to Ireland, thereby setting in train all of our problems...

[UPDATE 4/1/2011]
I've now finished the book - it's quite short and very readable. This is a Good Thing in my estimation - too many books (and blog posts?) pad themselves out with unnecessary verbosity. After dealing with the Y chromosome inheritance of the Cohanim and the Levites (again showing a signal suggestive of a restricted pool of progenitors, including the Cohanim Modal Haplotype - CMH - the variant of the Y chromosome seen at a much higher level in Cohanim), David looks at the ladies - what about mitochondrial DNA? In Jewish societies, "Jewishness" is often considered to be *matrilineal* in inheritance, i.e. like mitochondria, you inherit it from your mother. In various scattered Jewish communities he again finds evidence of a mitochondrial "bottleneck", and speculates that this might be due to males founding the communities in their travels, with local lassies for brides, but once the community became established, matrilineality kicked in. There are interpretative difficulties with all this, and I would have liked more in-depth discussion as to how these are resolved, but that perhaps puts things into a more esoteric level that might put off the casual non-geneticist reader.

Then there is the burden of genetic disease supposedly afflicting the Ashkenazim in particular. I have to say I am never that impressed by the incidence levels of genetic disease in the Ashkenazi - they are not *that* spectacularly more likely to have genetic diseases than many other populations, and although certain disorders are carried at a slightly higher frequency than we see elsewhere (e.g. Tay Sachs disease), it's far from clear (to me anyway) that this represents anything other than founder effect and ascertainment bias. This is an ongoing debate - I think I prefer the sidelines!

What of the future? Well, mitochondria and Y chromosomes really only give a partial picture, and they are susceptible to all sorts of confounding effects. The autosomal DNA (the main part that is inherited the same whether you are male or female) is trickier to follow and interpret, but as DNA sequencing gets cheaper (it's falling by a factor of TEN every two years or so, which is incredible, although that's levelling off a bit now), more sequence data becomes available, and the resolution with which we can look at genetic factors in populations improves. Techniques may well become available for pinpointing the origin of genes much more precisely, and we may be able to integrate this information with other sources, such as the Y and mitochondrial work, as well as archaeological and historical data. A further tantalising prospect is the ability to perform whole genome analysis on ancient samples, such as has been recently reported for the Denisovans by Svante Paabo and colleagues at the Max Planck.

Things are set to become very interesting - not just for the Children of Israel, but everyone interested in our origins. Each of those genetic sequences has come down through a series of real people - it would be wonderful to be able to tell their personal stories as well as the stories of their genes.