31 December 2013

More Genetic Ancestry Fun

I reanalysed my 23andMe data using the Dodecad algorithm, this time with the latest Globe13 parameters, and here's what came up:

                            (n=17)    (n=12)
  0.09%  Siberian            0        0
  0.56%  Amerindian          0.4      0.1
  0.00%  West_African        0        0
  0.00%  Palaeo_African      0        0
  2.32%  Southwest_Asian     0        0.5
  0.00%  East_Asian          0        0
 33.12%  Mediterranean       33.7     34.8
  1.00%  Australasian        0        0.3
  0.37%  Arctic              0        0.2
  8.77%  West_Asian          6.2      5.7
 52.50%  North_European      59.1     57.8
  1.27%  South_Asian         0.6      0.7
  0.00%  East_African        0        0

So the column on the far left is my personal output against the notional "population of origin" of bits of my genome (if that makes sense - please attach a pinch of salt to all this; especially the Amerindian bit - can't see that happening, but you never know!). The other columns represent an average of 17 Irish individuals and 12 British (by "ethnicity").

It's difficult to know how much significance to attach to the variations between mine and the average - you can see that if you pool my "Asian" component, you get 12.36, which is a good bit higher than the Irish average (6.8) and the British (6.9), and most of that is at the expense of my "Northern European" component. What are the error bars around this? Is this telling us anything interesting?

In fairness, it probably isn't. Genes are remarkably fluid, and this sort of analysis can really only give us a rough guide. Still, it's fun, and every now and again it may reveal something important... you never know.

30 December 2013

My Genotype Results: Mostly Harmless

So I put my DNA in to 23andMe before the FDA curtain came down. Here is my ancestry, computed through Dodecad software:

  9.27%  East_European      
 53.29%  West_European      
 25.92%  Mediterranean      
  0.00%  Neo_African        
  7.80%  West_Asian         
  1.91%  South_Asian        
  0.24%  Northeast_Asian    
  0.44%  Southeast_Asian    
  0.00%  East_African       
  1.00%  Southwest_Asian    
  0.01%  Northwest_African  
  0.10%  Palaeo_African     

I guess that makes sense for an Irish boy. It turns out that I'm also Y chromosome haplotype R1b1b2a1a2f2, which lodges me firmly in the common Northern Irish gene pool. My mitochondrial haplotype is H, which links me (apparently) to Napoleon Bonaparte, Susan Sarandon, Luke the Evangelist, and about 50% of Europe. So I'm not terribly special. Which is not necessarily a bad thing!

26 November 2013

Genomic adventures with The Science Squad!

Back in September, Kevin Mitchell @wiringthebrain and I hauled fine Southern TV & Radio Science Broadcaster Jonathan McCrea over some genomic coals. It's here: http://www.thesciencesquad.ie/videos/tss2-ep-3-human-genome/


29 October 2013

Why Anselm's Ontological Argument is a Big Fat Fail

St Anselm of Canterbury
This is a quickie. There is an argument for the existence of God, formulated by the medieval scholar St Anselm, known as the Ontological Argument (OA). It's pretty well known to apologists and counter-apologists alike, and is widely regarded as being invalid. However, it does pop up from time to time in those head-desking discussions that people occasionally have with those trying to build a case for their particular version of a god being the architect of the universe, and their particular restrictive theology being the formula that the rest of us must live by or risk hell-fire.

Briefly, the argument goes something like this:

  1. God is defined as "that, none greater than which can be conceived"
  2. An entity that exists in reality is necessarily greater than one which exists in the mind
  3. Therefore, God must exist in reality.
It should be clear that this argument is ridiculous, yet it pops up from time to time, and is deployed by apologists with scant regard to its inherent fatal flaws. In premise 1, we're *defining* God. That seems, if nothing else, a little rude. But we'll run with it for now. It's premise 2 that is a great festering fail-monkey. If we "conceive" of something in our mind, it doesn't *exist* in the mind - we merely put a mental signifier on it. If I "conceive" of an Apple Macbook, it is ludicrous to think that I have the position of every atom, the state of every electron, referencable within my brain. If I conceive of America, the America that exists in reality is "greater" than the images in my brain, but then so is pretty much anything.

So if we fully understand Anselm's argument, even the fully-specified physical state of a bacterium that exists in reality is greater than *anything* that we can fully conceive in our minds, yet I don't think any apologists would claim a bacterium is God. Or which one.

Anyway, have fun. Apologists are always coming out with silly arguments like this. My favourite is the Kalam Cosmological Argument from the uber-apologist William Lane Craig. I'll get tore into that at some point too - if only because it's utterly flawed in some very interesting and enlightening ways (which means that Craig may have done Atheism some very big favours).

28 September 2013

The Great DDD Bike Ride

Common things are common and rare things (collectively) are even more common. Thus runs my mantra for the medical students. If you hear clippety-clop outside your window, you are often told, you should think of a horse before you think of a zebra. WRONG, I say. You should think of a horse and non-horse, attach appropriate probabilities to each, and make sure you know what you're doing before taking any decisions based on your assessment.

The Irish DDD riders assemble in Kilkeel

Rare diseases are a lot more common than you (and most doctors) think, and they need to be tackled. The DDD Project, based at the Wellcome Trust Sanger Institute in Hinxton, near Cambridge, is a groundbreaking study using sequencing of the entire coding region of the human genome to try to uncover the basis for many rare and severe birth defects and malformation syndromes. It involves collaboration with all 24 Genetics Centres in the UK and Ireland, in order to recruit 12,000 patients for analysis. It is supported by the rare disease community, and in an attempt to raise awareness and give something back, the geneticists and genetic counsellors involved in the study are cycling all over these islands this weekend (28-29 September 2013).

CLICK HERE to support the effort (we're trying to raise £12,000 for the charities Unique, GRDO and SWAN).

Riders from the Belfast and Dublin genetics centres met half-way (sort of) in the beautiful County Down town of Kilkeel at the foot of the stunning Mourne Mountains to do their bit. As you can see from the photo, we were a fairly motley crew, and although our ride route turned into a bit of an exploratory expedition rather than a point-to-point, the glorious weather and the cheery encouragement of the locals spurred us on, as we visited such amazing spots as Silent Valley dam, Attical, and the astonishingly-named Aughnaloopy Road (yes, it's real).

We respect the atmosphere at Silent Valley Reservoir
Now I'm not saying that other regions of the UK and Ireland are not exceptionally lovely, but you would be hard pressed to find scenery more amazing than the Mourne Mountains. Our route skirted the foothills, but we managed to avoid any injuries (large agricultural machinery being a particular fun challenge on some sections) and arrived back in Kilkeel just in time for afternoon tea. A superb effort by all concerned.

And of course all of this is about rare disorders. One person in 17 in the Western World has a rare disorder, the majority of which are genetic. One in ten families are affected directly by such a rare disorder, and that number may itself be an underestimate. The impact on these families can be enormous, and they can be very expensive to manage and to live with. So they are common, they need research, and they need awareness. The bike ride is just a small step, or a turn of the pedals, on this path. Please support this effort, and encourage your political representatives to do likewise.
Two primitive MAMILs in their natural habitat.

21 September 2013

FutureProof at the Science Gallery

If you'd been in Dublin on 19 June, you might have toddled along to the Science Gallery and seen Tara O'Neill, Kevin Mitchell, me and others discussing Jonathan McCrea's DNA. But if you missed it, you can see it again here!


Enjoy! I'm on from about 40 mins in, but make sure you don't miss our fantastic Genetic Counsellor Tara O'Neill and the razor-sharp analysis of the excellent Kevin Mitchell prior to that. Watch all the way through for maximum education and entertainment...

22 July 2013

Hyperloop to Space

So I'm blogging this from the phone in the idyllic Northern Ireland sunshine. It's not quite equatorial, but as my thoughts strayed south, I felt I should share with you, dear geek reader, my idea for cheap, reliable, energy-efficient and safe access to space.

I came up with this a few years ago - I'm sure I'm not the first. Basically you have a hollow evacuated tube that encircles the Earth at the equator. One part of the tube touches the ground, the other is up in space. To get to space, you basically drive up up up and away!

But how does it stay up? you ask. Well, inside our tube are a load of pigs running round the earth very fast. Not real pigs of course - orbital velocity counterweights, accelerated by electricity and magnetically held off the inner walls of the tube. Thousands of them (actually a million or so). As they hurtle round the tube, effectively in "orbit", they provide the lift to hoist the "space end" of the tube off the surface of the planet. Adjusting the velocities of the pigs allows us to control the stability of the ring and keep one end down and the other up. The pigs will travel at tens of kilometres per second inside the tube; the whole thing remains stable.

This system, effectively a bridge to space, has several advantages over the classical space elevator concept. For one, the additional technologies required are far lower; everything sits within the realm of the currently-available. We don't need masses of material already in orbit, or super-strength carbon nanotube cable.

Construction will present challenges - how do we build and protect a ring around Earth while we fill it with pigs and fire them up? How do we negotiate the Pacific and Atlantic, and the numerous national territories, shipping lanes and airspaces during both construction and operation? Where do we site the "ground" station? Is it vulnerable to weather, natural disasters or attack? What safety systems will be necessary?

Perhaps we lack the determination and vision to build this. But, if created, it would open up space like nothing on Earth.

First stage assembly complete. Now load up the pigs!

27 June 2013

Podcast: FutureProof


In which Kevin Mitchell, Tara O'Neill and I take Jonathan McCrea through the thorny process of genetic testing. This podcast was part of the FutureProof radio show on NewsTalk FM, recorded at the Science Gallery in Dublin on 19 June 2013. 

We cover issues relating to genetic risk estimation, ancestry, genetic counselling and what our genes can really tell us about our health. Enjoy!

13 June 2013

Thoughts on Myriad Issues

The genetics world is abuzz with the news that the Supreme Court of the United States has struck down Myriad Genetics's patent on the genes BRCA1 and BRCA2, mutations in which can confer a greatly increased risk of breast and ovarian cancer. This is Good News, because in aggressively defending these immoral and undeserved patents, Myriad were playing a game that was disingenuous at best, and frankly profiteering at worst.

The arguments used by Myriad in the long course of this battle, which has been back and forward in various levels of the quaint US legal system for years now, were seen to be without merit, although their sophistry is dazzling. One argument was that Myriad had put a lot of effort and money into finding the genes, and therefore this should be rewarded. The Court rightly decided that that was a silly argument, and the rights to intellectual property of any kind can't simply be granted because someone feels they should be rewarded for work - the product has to be patentable in the first place.

A related argument for gene patenting in general is that if patents are not granted, companies will have no incentive to fund research and development that might lead to better tests and treatments. It is not even remotely clear that this is the case; in fact, if anything, closing off access to genes is a sure-fire way to prevent the development of tests and treatments by stifling competition. Furthermore, it encourages a "land grab" for genes that means that researchers have to spend most of their time in courts rather than getting on with the important job of using this scientific knowledge, which is the shared heritage of humanity, to make life better for people. There are few if any examples of gene patents actually leading to patient benefit. Get your intellectual property by legitimate means, people.

The Court did, however, reveal in its ruling that the judges really didn't have the first clue about molecular biology. Even after careful, and one would hope open-minded, consideration of the background and the evidence in the case, the ruling contains a number of howlers and bizarre misuses of terminology. For one thing, it suggests that while the raw DNA sequence is not patentable, cDNA (complementary - not "composite", you wallies - DNA made from the edited RNA transcript - hey, look it up - I don't want to make this blog too long) could be patentable. This is illogical, as firstly cDNA was not invented by Myriad, and the sequence is the issue, not the physical carrier, and they've already said the sequence can't be patented. Silly silly silly. Besides, you don't need cDNA to test a gene these days. It's 2013, not 1993. It gives you some indication of how thick the previous lower judges who made the initial rulings must have been.

Anyway, in case you were wondering whether US investors were sensible, you can dismiss that thought - after the ruling, shares in Myriad actually rose, presumably because a company that had survived on spin and misrepresentation were able to spin and misrepresent their defeat and make it look like a victory. Some investors are likely to lose quite a bit of money, and slap it up them.

Justice has been done. It would have been nice if it had been done with a little more finesse.

[Link to WSJ rendering of judgement]

10 June 2013

TLUD meets BBQ

So here it is! I have hitched a Top-Lit Up-Draught (TLUD) stove design to an old barbecue, allowing cooking on gas on one side and char barbecue on the other. It works extraordinarily well - boils water in minutes. 

17 May 2013

Turn the big yellow giant green!

It's big. It's yellow (or orange, depending on your political persuasion). It's not beautiful, but it's there. And the south side catches a LOT of sun. It's Belfast City Hospital, and I have a proposal.

I work here, and it's a lot of fun. It takes a lot of energy to keep the Belfast Trust running. but look at the sides of this building. Those yellow stripes up the sides are purely protective facing units of painted yellow aluminium. They are a waste of architectural space in this day and age.
I propose replacing them, lock, stock & barrel on the sun-facing aspects of the building with an array of solar panels. They would be cheap to install, modular, better looking than the current stripes, and provide a large part of the energy needed by the Belfast Trust.
Most would probably be photovoltaic, but we could try water heating pipes as well as thermal risers (the building is pretty tall!) with turbines at the top - admittedly a bit more of an engineering challenge. But this could all be done without making the building look any more hideous, and as one of the most iconic elements of Belfast's gorgeous skyline, it would send out a strong renewable energy message.

So, Belfast Health & Social Care Trust, please give it some thought.

08 May 2013

What's this? A scientist supporting the ARTS?

 Yes, yes, I know I'm supposed to be a hard-nosed left-brain analytical type, but I have my arty side too. Indeed, if anyone has been following my little blog, you'll know that I write the occasional song, and sometimes it's not about genetics or science. Part of the business of healing (and that's what being a doctor is all about) is catering for that side of the human psyche that might be called the "soul" (whether you're religious or not - run with me on this).

To that effect, Dr Robert Cuthbert and some colleagues have put together a fantastic selection of goodies in an arts festival at Belfast City Hospital, with a concert on 16 May at May Street Church "Urban Soul Cafe" at 19:30. This is dedicated to our patients.

All proceeds will go towards arts activities at Belfast City Hospital, where I also work. Click on the poster (left) for more info, as well as how to get tickets (email Robert - see the poster for the address). Come on - it'll be a great night, and it's for a very good cause.

I'll be performing "Canyons of Mars" and a wee surprise number. This is a WORLD PREMIERE! Plus, if you're in the City Hospital around lunch time, you might even get the opportunity to come up for a wee jam.

View Larger Map
See? We scientists and doctors have a creative artsy side too. And it's "Arts Care" not "Art Scare", although you may be forgiven for thinking the latter if you watch my video...

17 April 2013

Terra Perma - Permaculture to terraform Mars

Image: permaculture.org.uk
Mars is the Red Planet. Earth is significantly greener, and there is one factor above all that makes the difference - LIFE. If we are to send explorers and ultimately colonists (or maybe even just colonists) to Mars, we need to build systems to allow them to survive in that hostile environment.

The traditional approach to this is to build machines to scrub carbon dioxide from the enclosed atmosphere within the habitats, to recycle and purify the water, to provide heat etc. Of course provision is made for plants and even small animals to provide food, but the effort is designed to set up and maintain a system that will require continual substantial energetic and maintenance effort to keep it running. The problem with this of course is that it maintains a shackle to Earth - the colonists would find it extremely difficult to run and maintain basic life support, never mind expansion and extension, without constant resupply from the home planet. And that is astonishingly expensive, never mind very fragile and dependent on Earth being willing or able to foot the continual bill for the sake of a few colonists.

What we really need to do is to build systems on Mars that are able to be maintained locally, that can be extended substantially without need for import from Earth, and that are robust and fault tolerant. On Mars that is a very tall order indeed. What Mars (or at least habitats on Mars) needs is not a mere life support system - it needs an ecology.

Now perhaps ecologies of some form already exist on Mars. Deep below the surface there may be indigenous microbial communities happily prokaryoting away and munching each other. Personally I doubt it, but in the case of Mars we simply don't know. In any case, it'll not support human life, so as a life support system for our colonists it's no good. What we need to do is build ecologies on Earth - interacting systems of biological organisms and geophysical processes that are effectively self-sustaining and propagating - and packaging and exporting these to Mars for reassembly, boot-up and growth. And we need these ecologies to provide for the needs of the first human Martians.

The concept of Permaculture is working with nature to create systems that are self-sustaining, or at least require a minimum of effort & expense to maintain, which can provide for our needs to a greater or lesser extent. Attempt to reduce intervention, enhance robustness, use as few complex chemicals and "artefacts" as possible, allow the system to "grow" or be extended with minimal external intervention. These principles are ideal for colonisation of planetary surfaces, but can they actually work on Mars?

There are a number of remarkable permaculture initiatives on Earth, and indeed "light touch" gardening (which is itself a form of permaculture) is one of the most popular hobbies here on Earth. Yes, we do have air and rain and warmth, as well as soils that have been worked over by organisms for millions of years, so on Earth it's relatively easy. Can we boot up such an enclosed, but expandable, ecological system on Mars?

Well, we know that the soil is favourable, at least if the results from the Mars Science Laboratory on the Curiosity Rover are anything to go by . We know there is at least the prospect of getting water ice that (again if MSL results can be applied more widely) may be pure enough, with enough trace minerals, to support plant growth in enclosed pressurised greenhouses. There is light from the sun. There is carbon dioxide in the very sparse atmosphere, that can be concentrated as required. As plants grow, they generate oxygen and organic matter for food and composting to further improve the soil. They can generate materials that can be used to extend the greenhouses further, and so the cycle can be maintained and extended.

There are significant complexities that this simple scenario does not address, but if we are going to colonise Mars and other off-Earth locations, we need to find ways of generating and supporting ecosystems that are stable, robust, and largely sustain themselves, as well as a space-faring human population that will be busy doing what we have sent them to Mars to do.

And eventually, if we can make these systems grow enough, we may be able to turn Mars green, as well as protect ecosystems here on Earth.

Tw: @shanemuk

22 March 2013

Atheism on the defensive

I admit it - I actually quite enjoy a good debate in the classical formal style. Opening arguments, rebuttals, counter-rebuttals and closing arguments - it's all good fun, and the Christianity (for Christianity it usually is) vs Atheism debates do, when well done, make for a laugh. It is true that Cosmological and Moral arguments for the existence of God are almost as ridiculous as the ball-bouncingly daft Ontological arguments, but we do love 'em anyway.

However, framed like this, I do sometimes worry a bit. Atheists who get involved in these debates are often forced into a position of being almost cruel towards religion, and religion being what it is, it starts looking like they are cruel to the adherents of religion, as well as kittens and All That Is Good. I think this is a sad state of affairs, and it is certainly milked for all it is worth by theists who care more about winning "the argument" than about Truth or Fairness.

As novelist and philosopher (I prefer the former designation, really) Alain de Botton puts it, of course God doesn't exist. There's no point in arguing the toss over it. It's a silly idea, end of. We therefore need to move on to how we ought to behave (and no, pedantic theologians, "ought" does not assume a god) towards each other, and leave the arguing behind.

It's tricky though. For many years I tried arguing with atheists (and even myself) that God existed, and that (implausibly) he should be connected with the God of Traditional Christianity, which is a sort of pastiche gleaned from carefully selected biblical proof texts and Ancient Greek notions, retro-fitted clumsily to the remainder of the bible. It was only when I looked more into the bible itself that I was able to recognise it as a purely human creation with no input from any divine source.

And the funny thing is that many people who describe themselves as "Christian", regardless of whether or not they actually go to church or what they profess in their meetings, don't actually believe it is True. They don't believe Jesus is the Son of God or that he was raised from the dead (unsurprisingly to anyone who actually reads the gospels), don't want atheistic arguments, because they don't want to give up what they find nourishing and useful.

So why argue this relatively boring point? Instead I think atheists should concentrate on showing how gods are unnecessary to science, to morality, to civilisation - to anything.  To do so in a caring and open way is the best way to get the message across, because in many many cases we are dealing with people who are expressing a humanistic worldview through a Christian (or Muslim or Jewish etc) theistic framework. Let's help, rather than hinder.

10 February 2013

My Scientific Valentine

On the amorous emotional state projected towards a beloved by an ardent admirer.
U. R. Mydestiny (1)

(1) Department of Lurve, University of Ichliebedich.

Background: Several authors have commented on the observation that blossoms of the common rose (Rosea berberifolia) are frequently perceived in hues towards the red end of the visual spectrum, whereas those of the violet (Viola spp.) tend towards the blue end. Although this in and of itself does not at first sight appear to have consequences for romantic interactions between members of the species Homo sapiens, an association has often been assumed.
Objective: To explore the relationship between the perceived colours of these blossoms and the depth of desire of a mystery lover for the recipient of a small decorated folded piece of card.
Methods: All available geographical obstacles and challenges were met - mountains were climbed, seas were swum, valleys were walked. Furthermore, fires were crossed, wild beasts faced, and songs and poems were listened to as well as composed.
Conclusion: The honourable and fervent erotic desire of the author for the intended recipient of the cellulose-based missive is asserted, and preliminary data appear to confirm this view. However, further research, focusing on physical proximity and close interactional analysis is urgently required.