30 December 2011

More Christmas atheism

This time from Alom Shaha (reared as a Muslim, but now an Atheist):

Atheists at Christmas - a view

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

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

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.

29 December 2011


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

The Law of Probability in South America

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.

22 December 2011

It's not just about the Higgs

New results from the ATLAS experiment at the #LHC!

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?

21 December 2011

Do numbers "exist"?

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

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...)!

19 December 2011

Higgs Diggs

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)!

16 December 2011

In the belly of the beast

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

Happy Little #TLUD "ShortArse"

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!

[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

Here's Rosenhouse in 2007:

10 December 2011

Look what I made!

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

30 November 2011

"Worms in liquid form" FFS!

BBC, you can do *so* much better than this.

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.

29 November 2011

Common sense prevails.

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

26 November 2011

Vision for Vision for President of RCGP

Do we really want to go back in time
to the bad old days?
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 - Dec 2011: Image changed because of threat of legal action to the tune of $150,000!]

[UPDATE2: 1/3/2012: Previous still image from Mentorn Media's production for the BBC "The Big Questions" (broadcast 12/2/2012) has been removed after a request from the company. I wish it to be clear that this was completely voluntary and amicable, without coercion of any kind.]

[UPDATE3: 1/3/2012: Keep an eye on the blog for the latest!]

25 November 2011

Israel's tech startups: @basilmccrea take note!

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.

24 November 2011

Thanksgiving #TLUD

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

23 November 2011

Contact established with Phobos-Grunt!

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

<IMG SRC="http://news.bbcimg.co.uk/media/images/56590000/jpg/_56590200_013258733.jpg">

15 November 2011

Religions of the World

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


13 November 2011

I seem to have incurred some wrath...

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...

09 November 2011

The Adoration of the Magi

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

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!

05 November 2011

Alternative #TLUD feedstock drying apparatus

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


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!

23 October 2011

Alternative Medicine that WORKS - Taking WCTB Therapy into the mainstream

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 feck 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.

20 October 2011

Philosophy of Science

@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!

04 October 2011

Lab spam

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*...

02 October 2011

Dammit, my #TLUD is going great today!

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

01 October 2011

Tyrannosaur Halloween costume - current status

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

28 September 2011

The difference between Religion and Science.

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

Here's a 3D mouse embryo

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

27 September 2011

What planet are they on?

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

24 September 2011

Happy 4th birthday Olivia!

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


Lewis found this fossil belemnite on the beach at Jordanstown.

23 September 2011

QR code

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Plato vs Darwin

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

20 September 2011


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

19 September 2011

Read/write DNA?

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

16 September 2011

Halloweenosaurus Rex

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

15 September 2011

#Evolution Hallowe'en!

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

14 September 2011

Stupid bird flew into the window and left this mark

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

12 September 2011

Facilitating Genetic Research.

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

11 September 2011

Do quarks work like this?

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

Happy little mini #TLUD.

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

03 September 2011

28 August 2011

Combo #TLUD joy!

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...

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...

23 August 2011

Awesome new #TLUD!

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.

17 August 2011

More #TLUD love

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.

12 August 2011

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

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.

02 August 2011

Things #TLUD related

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

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.

01 August 2011

Resurrecting the #Resurrection

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!

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...

30 July 2011

Pot luck

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?

29 July 2011

This does not work as an iPhone signal booster

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 :-(

18 July 2011

On the Historicity of Goldilocks and the Three Bears

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.]

17 July 2011

Our future in space?

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.

06 July 2011

Is this elevator going anywhere?

#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.

18 June 2011

Talk by libel hero Peter Wilmshurst!

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

07 June 2011

Goodies over at Genomes Unzipped

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.

04 June 2011

My new philosophy pals: any comment?

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 :-)

02 June 2011

Show me the Sausages!

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."

28 May 2011

Boat for sale: Jaguar 21, great condition!

"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.

19 May 2011

BBC News Article on Evolution Gets It Wrong

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.

25 April 2011

In which I unzip a few genomes...

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

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

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

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

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

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

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

22 April 2011

Changeable weather in Donegal

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

13 April 2011

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

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

[Works with black tea too]

09 April 2011

What sort of thinker are you? Visual or Verbal?

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

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

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

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

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

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

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

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