Yearly Archives: 2009

Christmas Thoughts

A late Merry Christmas, and a marginally early new year to all. A few Christmas-based observations, from various lines of thought that have been knocking around my head over the festive period.

Cooking and the Internet

The internet can sometimes birth amazingly useful things in unexpected fields. The one I am thinking of at the moment is in cooking; I have been cooking a lot of food this Christmas, and I have built up a reputation in my family for being someone who can make traditionally ‘complicated’ things (pie crust, Yorkshire pudding, etc). To clarify, I am not a good cook, or at least the food I invent myself is not liked by others (I like my mustard and chili pasta sauce, or my three-mushroom fried rice, but no-one else seems to). However, I have been shown by some more food-literature friends of how the internet can turn someone like me into a competent chef.

The hidden secret is the BBC Good Food website (which is distinct from the BBC Food website, presumably dedicated to bad food). The website consists of a crazily large number of recipes written by professionals; however, the real secret is that there is a very dedicated readership of amateur cooks who report their experiences, and rate the recipes on a scale of 1-5. It is this later part that really makes the website great; while a random recipe from a chef will often be relatively good, those that have been rated as 5 stars by the community are, virtually without fail, excellent.

The interesting thing is that many of the recipes look very weird at first, but turn out to work amazingly well. Cut the skin off gammon, and cut slits before roasting? Add flour to the filling of an apple pie? Pastry that should ‘look like scrambled egg’? These are the sort of thing that make you look to your family like an expert cook; you end up doing things that to them (and indeed you) look like madness, despite actually working.

Keynesian Christmas

I read a fun and insightful essay, reprinted at OpenDemocracy, about the Keynesian economic bases of a Christmas Carol. The idea is that the early 1840s were a time of deflation; the value of money was shrinking, and the value of goods were shrinking faster still. The economy was sinking into recession; deflation meant that investment wasn’t worth while, but because goods were worth less each year, people avoided buying things as well. Added to this was a Malthusian attitude that the world was too full to support population growth, and that saving and parsimony was the order of the day.

These fears combine to make a villain that is both indicative of, and the cause of, the recession. The miserly rich man, fearful of financial uncertainty, who hoards money without spending it either on themselves or others. And when Scrooge learns the spirit of Christmas, he also learns to be the sort of person that the economy needs for recovery; someone who gives and spends without thought for the cost, who buys things for the sheer joy of doing so, not because they are good value or even needed.

There is a similar feel to the carol Good King Wenceslas, which was also written in the 1840s; the Saint, upon seeing a poor man in the cold, on a kind-hearted whim calls out for flesh, wine and firewood to make a feast for the peasant. It is the spontaneity, the lack of economic calculation, that makes him a Saint; he spends on others for the sheer joy of doing so.

Oddly, these values are close to what we now call consumerism; buying things for the sake of it, not because they make your life better. This ties nicely into a post by Ed Yong; consuming goods, spending on yourself, does not give you happiness (most of us have more than we need anyway). However, spending on others, like Scrooge or Saint Wenceslas, can bring you happiness.

Saint Nicholas

As a final Christmas thought, before I put away childish things for the year, is this: Has anyone ever considering going to the Basilica di San Nicola at Christmas Day, in order to visit Santa Claus’ grave? One for the kids, perhaps.

The Economist Mangles Disease Genetics

The Economist has a rather distressingly bad article by the evolutionary psychologist Geoffrey Miller, about the supposed general failure in human disease genetics over the last 5 years. The thesis is that Genomes Wide Association Studies (GWAS) for common diseases have been a failure that geneticists are trying to keep hidden, and that the new techniques required to solve the problem of disease genetics will raise ‘politically awkward and morally perplexing facts’ about the different traits and evolutionary histories of races. The former claim is pretty much the same as Steve Jones Telegraph article earlier this year, and is just as specious. I will look at both claims separately.

A quick point of terminology: Miller uses ‘GWAS’ to refer to studies that look for disease association in common variants using a genotyping chip, and acts as if sequencing studies are not, in fact, GWAS. In fact, a sequencing association study is just another type of GWAS, just looking at a larger set of variants.
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How Many Ancestors Share Our DNA?

This post was written four years ago, using a quick-and-dirty model of recombination to answer the question in the title. Since then a more detailed and rigorously tested model has been developed by Graham Coop and colleagues to answer this same question. You can read more about the results of this model on the Coop Lab blog here and here. Graham’s model is based on more accurate data, more careful tracking of multiple ancestors and a more realistic model of per-chromosome recombination, and thus his results should be considered to have superseded mine.

Over at the Genetic Genealogist, Blaine Bettinger has a Q&A post up about the difference between a genetic tree and a genealogical tree. The destinction is that your genealogical tree is the family tree of all your ancestors, but your genetic tree only contains those ancestors that actually left DNA to you. Just by chance, an individual may not leave any DNA to a distance descendant (like a great-great-great-grandchild), and as a result they would not appear on their descendant’s genetic tree, even though they are definitely their genealogical ancestor.

At the end of his post, Blaine asks a couple of questions that he would like to be able to answer in the future;

  • At 10 generations, I have approximately 1024 ancestors (although I know there is some overlap). How many of these ancestors are part of my Genetic Tree? Is it a very small number? A surprisingly large number?
  • What percentage, on average, of an individual’s genealogical tree at X generations is part of their genetic tree?

I think that I can answer those questions, or at least predict what the answers will be, using what we already know about sexual reproduction.
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ASHG: Quantifying Relatedness and Active Subjects in Genome Research

Well, the American Society of Human Genetics Annual Meeting is coming to a close for another year. My talk is done and dusted, so I no longer have to lie awake at night worrying that I will forget everything other then the words to “Stand By Your Man” when confronted by the crowd. My white suit is now more of an off-white suit, with regions of very-off-white and pretty-much-entirely-out-of-sight-of-white. I’m looking forward to getting back home to catch up on my sleep.

For the last time, I’m going to give a little summary of talks today that I thought were interesting, or gave some indication of where genetics may be heading in the future. I will write up some more general thoughts about the meeting in the next few days, as soon as the traveling is out of the way and my mind has recharged.

If you would like some second opinions on the conference, GenomeWeb has a number of articles, including a couple of short summaries, as well as a nice mid-length article about the 1000 Genomes session; there are also a number of articles over at In The Field, the Nature network conference blog.
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ASHG: Finding Mendelian Mutations and Inclusive Population Genetics

Third day down, one to go. I am starting to suffer from conference fatigue somewhat. I’m not going to any other talks this evening, so I am going to try and get some relaxation time in from this point on. But first; the summary of Day 3.

Today I saw a lot of talks over three sessions, and many of them were very interesting. However, I won’t talk about everything, or even my favourite talks. I’ll go for the talks that seem to tie together into nice stories about a few directions genetics seems to be heading in.
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ASHG: Statistical Genomics and Beyond GWAS in Complex Disease

The second day of the American Society of Human Genetics Annual Meeting is drawing to a close; here’s a lowdown of what talks I’ve enjoyed today.

Remember, follow @lukejostins on Twitter if you want more up-to-the-minute details on the ASHG talks.
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ASHG: Chatting with the Sequencing People

While I am here, I though I’d take the chance to chat to the people at the booths for the three major Second Gen sequencing platforms (Illumina, SOLiD and 454). It was surprisingly fun, the guys I talked to all seemed enthusiastic, and it was nice to find out where the scientists in the companies think the technology is going.

In the interests of openness: the 454 booth gave me a cool T-shirt and poster, so this may well have biased my opinion of them
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ASHG: Rare Variants, and the 1000 Genomes Project

Hello all (it is taking every bone in my body not to say ‘Aloha’ here).

So, today was the first real day of the ASHG Annual Meeting; after accidentally falling asleep for basically all of yesterday, it was good to finally see some familiar faces and dig my teeth into some real science.

I’m going to write a little about the first couple of sessions I’ve seen, and say what sort of themes are being shouted loud enough to get into my jetlagged mind. I have also been tweeting the conference at quite a high frequency (about 30 tweets so far), and in more detail than I have given here; follow me on @lukejostins if you are interested. To see all the ASHG twittering, check out #ASHG2009.

The blogs posts over the next few days will be aimed mostly at those who are, at least vaguely, In The Know about genomics. However, if there are people who would like a less jargonistic lowdown of the conference, please leave a comment and I’ll see what I can do.
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Scientia Pro Publica #14

Welcome to the 14th Edition of Scientia Pro Publica (Science For The People). This blog carnival collects together the best non-technical science writing that has appeared around the blogosphere in the last few months, to promote and celebrate science, nature or medicine blogs written for the public.

In this edition, we have a glut of posts related to climate change, and an equally large group of posts about the interaction of science and society. Along the way, we will also cover some basic science posts from physics and biology.
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Scientia Pro Publica, and Off To Hawaii

Next week, two things will be happening. Firstly, on Monday I will be hosting Scientia Pro Publica, a blog carnival for communicating science to the public. If you have an entry that you feel explains a scientific subject in an easy-to-understand way, please submit it here.

Secondly, I will be traveling off to Hawaii, for the American Society of Human Genetics Annual Meeting, a very large genetics conference. I will be giving a talk on Imputation (abstract 240 in the Speakers book) at 7.45am on Saturday, if any imputation-loving insomniacs want to attend.

Perhaps more relevantly, I have bought myself a little Eee PC Seashell, on the condition that I make a serious effort to blog and tweet the conference. My plan is to do a short daily low-down of what is going on, with things that I see that seem significant or new, as well as live tweeting at least a few talks a day over on my Twitter feed. I’ll be tweeting with the hashtag #ASHG2009.

Daniel MacArthur, who has a somewhat better reputation for blogging conferences than I do, will also be there, and it will be well worth your time to follow his blog and his Twitter feed.