Tag Archives: evolution

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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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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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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Recombination in the X and Y Chromosomes

ResearchBlogging.org

Rosser, Z., Balaresque, P., & Jobling, M. (2009). Gene Conversion between the X Chromosome and the Male-Specific Region of the Y Chromosome at a Translocation Hotspot The American Journal of Human Genetics, 85 (1), 130-134 DOI: 10.1016/j.ajhg.2009.06.009


There is new paper is out in American Journal of Human Genetics about how the X and Y chromosome might not be as separate as we think, and in fact might undergo regular recombination in certain regions (you can read a press release for the paper here).

Specifically, the paper is a resequencing study of the X and Y chromosome homologues PRKX and PRKY in around 60 individuals, looking for signatures of recombination. In summary; it is an interesting and well supported paper in as far as it goes, but it raises more questions about Y chromosome evolution than it answers
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On Lamarck and Trees

Over at Genetic Future, Daniel MacArthur quotes Joel Parker berating as ‘embarrassing’ biologists who claim that it was Darwin, and not Lamarck, who came up with the idea of an evolutionary tree:

I have noticed many evolutionary biologists making an embarrassing mistake of falsely attributing the first use of the tree analogy to Darwin. This has occurred in numerous documentaries and on websites which I will pass on naming here. Ironically, the earliest use of the tree analogy diagram to depict evolution was published in the year of Darwin’s birth (1809) by Lamarck in his book Philosophie Zoologique (see pg 463, http://tinyurl.com/knt7vr). Lamarck even uses botanical terms (branches and rameaux) to describe the origin of animals with respect to this figure. The figure that is usually cited from Darwin’s notebook is from 1837 (http://tinyurl.com/6hs5uv), a full 8 years after Lamarck’s death. Even with our high admiration for Darwin, we should at least give credit where credit is due, and not forget that much of evolution was becoming understood before Darwin. Explaining the mechanism of natural selection was Darwin’s great contribution.

This is actually largely correct; Lamarck did have a view of evolution that involved what we would now call evolutionary branching, though it was very different from what we now know to be the case. Lamarck deserves to be read and understood as one of the first people to put together a coherent view of evolution.

However, the statement is very wrong in a number of ways. It is far from a mistake to refer to Darwin as the originator of the evolutionary tree, and those of us who do so do so not out of ignorance.
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Research Interests Translated

I recently updated the information on my website, and in doing so I decided to produce two versions of my research interests. The first is for other scientists, and the second is a translation for lay people. I would be interested to know how people think this is pitched; is the lay-information too confusing, or is it too simple and patronising?

I think every scientist should try and do this at some point. It is an interesting exercise to see how well you can communicate and summarise the entirety of your research in a way that doesn’t use the shared lingo and knowledge base that you have access to when taking to other scientists. Plus, of course, communicating your work to the world outside of academia is generally A Good Thing.
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An Ammonite Tree

I was clearing out my photos this weekend, and I found a number of pictures that I had taken on my trip to Amsterdam Zoo a few months ago. One exhibit consisted of a long tree/time-line of Ammonite evolution, stretching from the Devonian up to the KT Boundary, showing which groups were descended from which. I found it wonderfully presented, with different colouring representing the different suborders, and fossils attached at various times, so you could see how the different forms changed over time. I really am a sucker for phylogenetic trees, especially those that manage to integrate other visual information.

The exhibit was slightly sad, however. It was up a relatively hidden away staircase in an already pretty out-of-the-way building. I stood there looking at it and taking pictures for a good half an hour, and nobody even came into the room, let alone spent any time looking at the exhibition. I found it a little tragic that someone had put so much effort into presenting so much information in a way that could be easily understood, and now it sits where not many people will see it. Added to this, I expect (though don’t know) that not many people will be interested in following ammonite evolution, especially when there are dinosaur bones around.

My hope is that the University of Amsterdam makes use of these sorts of resources in their classes: I remember loving the undergrad classes which involved wondering around the Cambridge museums, especially those that went through different groups, describing how they fit together in a classification system, and what that can tell us about how they evolved.

Anyway, I stuck the pictures I took together to reconstruct part of the exhibit. Click the (rather large) thumbnail below to see low quality .gif of it; when I get back I’ll upload a higher quality one.

UPDATE 17/04/09: Uploaded higher quality version, click thumbnail to view.

amniotes.gif

On Darwin Day and the Cosmic Web

Good Morning, reader (if it is not morning, due to laziness or the inevitable passing of time, then Good Day). More importantly, Happy Darwin Day. Today is the 200th Anniversary of Darwin’s birth, and various events are taking place today and throughout this year, notably the Natural History Museum’s special exhibition. Nature has put on a special issue to mark the occasion, as well as a free podcast. I am also looking forward to the Endless Forms exhibition at the Fitzwilliam Museum here in Cambridge, about the connections between Darwin and visual art. And, as I know you love words as much as I, Ben Zimmer (brother to Carl Zimmer, one of my favourite science writers) has a blog post about Darwin’s influence of language.

On an unrelated note, my astrophysicist friend Olaf Davis, co-author of our game Biology or Physics (as featured on German TV!), has started up a blog. It is called Cosmic Web, and he intends to talk about astronomy and more general science communication. Olaf is a pretty awesome writer, and good at explaining complex ideas in simple ways, so the blog should we well worth checking out.

On Michele Hanson and Game Theory

I read the Guardian newspaper on a semi-regular basis, and I find their coverage to range from Pretty Good to Good Lord No, with a peak around Not Bad (the quality is somewhat moot, since the ever-delightful Ben Goldacre, among other loved columnists, guarantee that I will always return).

However, there is the occasional distressing piece from an individual notably unaware of the complexity, and often the substance, of what they are talking about. One source that provides such tidbits with unfortunate frequency is in the G2 columnist Michele Hanson. Now, her column usually just offers Humorous Anecdotes and Gripes, which is fine for a supplement, but she also spends plenty of time commenting on science subjects from a platform of ignorance and, more worrying, derisive scorn. From yesterday’s column:

A bumper crop of bad science plopped out of our universities and hospitals this week. Three lots at once, and all about relationships. The first gang, from UCL, LSE and Warwick Medical School, have “developed a mathematical model of the mating game to help explain why courtship is often protracted”. Or as every girl’s mother has probably told her, “Don’t do it on the first date. If he can’t wait, he’s not worth it.” [...]

I would like to tear my hair out. I ought to be used to professors churning out this sort of old-hat, inapplicable drek, time after time, but for me the shock never fades. How do they get away with it? Has Professor Robert Seymour, of UCL, been shut away in the groves of academe since birth, and does he really think that we don’t know that “longer courtship is a way for the female to acquire information about the male”. Has he ever met a female person? Or a male from the outside world? Did he not know already that we know that you can’t get to know someone all that well in the course of a quick bang?

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