Now on ScienceBlogs: Science Poem Manifesto
Human evolution, genetics, genomics and their interstices
April 4, 2010
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If you link to this weblog from your weblog, please update links:
http://blogs.discovermagazine.com/gnxp/
If you have not updated your feeds, please do
so now:
http://feeds.feedburner.com/GeneExpressionBlog
The old feed address will point for another week or so to the new feed, but eventually it will cease working.
Posted by Razib Khan at 2:06 AM •
March 26, 2010
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Update your bookmarks: http://blogs.discovermagazine.com/gnxp
And RSS: http://feeds.feedburner.com/GeneExpressionBlog
If you have a weblog that links to ScienceBlogs GNXP, I would appreciate you update the link for the same of PageRank.
There isn't much to say about the move. There wasn't one big precipitating reason, a variety of reasons coalesced to make this the right thing to do for me. I would like to give a shout out to Erin Johnson, who from what I recall has been the longest serving ScienceBlogs community manager in the history of the website. One bittersweet aspect of leaving the network now is the arrival of awesome blogs such as Observations of a Nerd, along with old friends such as Dr. Daniel MacArthur of Genetic Future.
I was approached by Chris Mims of Seed Media Group over 4 years ago to contribute to ScienceBlogs. I'm an "original," along with Adventures in Ethics & Science, Aetiology, Deltoid, Dispatches from the Culture Wars, GrrlScientist, Pharyngula and Uncertain Principles (some others have left the network, or blogging, such as John Lynch and Evolgen). I really didn't know what to expect, but it's been fun overall, and I've met many interesting people. By the time I'd arrived at ScienceBlogs I've been blogging for almost 4 years, since April of 2002. To a great extent it had become a solitary endeavour. ScienceBlogs made me a bit more social in my online interactions. In particular during the first few years RPM of Evolgen and Chris of Mixing Memory were good friends. The ScienceBlogs summer meetups were pretty fun too, and allowed me to convince Mark Hoofnagle that I was The Scientific Indian. I've also made some friends offline, such as Jake Young, with whom I've partied in New York.
A domain is just a string of letters, and I don't expect much to really change. I hope to reach a new audience, and keep the current one, and still continue to have fun.
Posted by Razib Khan at 3:16 PM •
March 24, 2010
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That's all I have to say to Eric Michael Johnson's post, Ann Coulter, Hate Speech, and Free Societies. OK, seriously, from what I recall Eric is an American, though resident in the forgotten north. American absolutist stances on free speech are not shared by most Western societies, so demanding total free speech is quixotic and culturally tone deaf. Granted, Europe or Canada are not barbaric like China or Muslim societies when it comes to speech, so that communication about this issue is possible. But here are the exceptions to free speech enumerated in the European Convention on Human Rights:
The exercise of these freedoms, since it carries with it duties and responsibilities, may be subject to such formalities, conditions, restrictions or penalties as are prescribed by law and are necessary in a democratic society, in the interests of national security, territorial integrity or public safety, for the prevention of disorder or crime, for the protection of health or morals, for the protection of the reputation or the rights of others, for preventing the disclosure of information received in confidence, or for maintaining the authority and impartiality of the judiciary.
I bolded aspects which I think Americans would assume are going to be open to abuse. The new Irish blasphemy law is rumored to be motivated by a fear of Muslim violence aimed at those who defame their primitive superstitions (the cowardly Irish atheists know that Western Christians tend to be lax about agitating violently on behalf of their superstitions, so they blasphemed Catholicism, this was an error, see below). Though it isn't just Muslims who are barbaric, a few years ago Sikhs in Britain rioted over a blasphemous theater production, and the arguments that it isn't speech if it "hurts feelings" were voiced by them as well. This is a normal human viewpoint, protection of patently offensive speech is probably a cultural aberration. What to Americans seems a universal human right is actually a perverse extremism from the viewpoint of outsiders (though do note that the abolitionists seemed to be perverse extremists in their time, so numbers don't always predict where history will flow)
One of Eric's stupid commenters linked to this op-ed, Ann Coulter, Hate Speech, and Free Societies:
This is why Coulter's speech is not just "free" (i.e. bias-free, objectively sent out into the atmosphere). The effects of her speech when launched into public space are not simply situational. They are another series of burps in the historical and currently existing framework that has normalized a particular way of thinking about Muslims, gays and lesbians, and other marginalized groups.
Pretty funny that Muslims are marginalized along with homosexuals, since when Muslims are a majority they have a tendency to persecute or kill homosexuals with more efficacy than other cultures (though not homosexual behavior). Naturally Muslims in the West are exempt from the injunction toward not engaging in homophobia, as it's naturally part of their barbaric set of beliefs. The op-ed continues:
From this framework, we can see how free speech is a slippery problem. Ironically, it seems to surface when there is a need to stifle speech that challenges social power (which is what the U of Ottawa students were doing - challenging the inequitable social power relations that Coulter's "speech" upheld).
Really someone should ban the usage of quotations, because morons like this will get drunk on them. Though seriously, I'm expressing a very cultural biased viewpoint here, an American one, and I'm of conscious of this. I really don't see a point in castigating Canadians for being Canadians, they're not China or Syria, but neither are they the United States. Even the British have insane libel laws which stifle speech operationally, though there's a chance that the law might be tightened up. We alone should be the City upon a Hill where the blasphemers and peddlers of bigotry can take refuge, because we're already the last best and only hope.
* I use the term "barbaric" to refer to societies which I feel express values which are fundamentally different from those of my own so that there is a lack of commensurability of discourse. From the perspective of many Muslim societies American culture is barbaric and kuffar, while the Chinese have their own set of values as evident with the recent conflict with Google over censorship. I use the term "savage" to delineate those societies which dehumanize other cultures. So the Aztecs were savage because they waged wars against other polities for the sake of harvesting sacrificial victims, who were later cannibalized.
Posted by Razib Khan at 5:47 PM • 50 Comments
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The complete mitochondrial DNA genome of an unknown hominin from southern Siberia:
With the exception of Neanderthals, from which DNA sequences of numerous individuals have now been determined...the number and genetic relationships of other hominin lineages are largely unknown. Here we report a complete mitochondrial (mt) DNA sequence retrieved from a bone excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago. This indicates that it derives from a hominin migration out of Africa distinct from that of the ancestors of Neanderthals and of modern humans. The stratigraphy of the cave where the bone was found suggests that the Denisova hominin lived close in time and space with Neanderthals as well as with modern humans....
The tree gets bushier? Just see John Hawks and Carl Zimmer.
Posted by Razib Khan at 3:04 PM •
March 23, 2010
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In this diavlog with Glenn Loury the behavioral economist Sendhil Mullainathan recounts the results of an experiment.
- If given the option of paying $100 for an item vs. $80 for an item, but in the second case having to go across town for the item, respondents choose $80 and going across town
- If given the option of paying $1000 for an item vs. $980 for an item, but in the second case having to go across town for the item, respondents choose $1000 and not going across town
Posted by Razib Khan at 8:26 PM • 21 Comments
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You've probably heard about the research in the press, but please see Derek Lowe for perspective. The difference between high fructose corn syrup and sugar as an additive may, or may not, be problematic. But the uncertainty in this area is why I try and avoid excessively processed foods*, there's just so much we don't know. If you're poor and short on cash perhaps the high ratio of calories per cent of processed foods are simply necessary, but for people of even modest means I don't think it is that difficult to cut most consumables which come out of boxes from your diet.
Again, I want to reiterate that I don't necessarily have an atavistic fear of food science and industry. Or think that "nature always knows right." The human state of nature is Malthusian and characterized by high mortality. But I think some trends in the modern food industry driven by demand side pressures result in medium-to-long term gains in morbidity in return for short-term spikes in pleasure.
* If something has fewer than six ingredients, and you know what the ingredients are (i.e., they're not obscure chemicals), I don't know if I would avoid that. After all, cooking is in many ways a form of processing too. As are cheeses and pickling.
Posted by Razib Khan at 7:45 PM • 10 Comments
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Not Exactly Rocket Science, authored by a certain Edmund Yong. Congratulations Mr. Yong, but I will admit being less than surprised.
Update: And also, congratulations to all the other winners, several of whom are in my "regular reads."
Posted by Razib Khan at 7:36 PM • 1 Comments
March 21, 2010
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I have a short piece up at Comment is Free at The Guardian, The origins of morality do not matter. Its flavor is a bit different from my typical blog posts because the format enforces more brevity, so I decided to try and leverage some analogies. I conclude:
... Our moral consensus is a river whose course shifts across the plain, constrained by the hills thrust upward by biology. Only history knows where the river will flow next, though evolution can hint at the range of possibilities.
On a note related to this piece, I will be posting a review of The Price of Altruism: George Price and the Search for the Origins of Kindness in a few months.
Posted by Razib Khan at 11:09 PM • 16 Comments
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The Andrew Pollack piece which I hinted at came out a few days ago: Consumers Slow to Embrace the Age of Genomics. For what it's worth, I think this chart from Dr. Daniel MacArthur is right on:
This too will pass. I believe that like the internet the knowledge and analysis of our genetic information is going to be ubiquitous after a rough period when most of the dreams of grandeur from the first generation entrepreneurs fade.
Posted by Razib Khan at 8:21 PM •
March 19, 2010
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Posted by Razib Khan at 11:19 AM • 1 Comments
March 18, 2010
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Henry Louis Gates Jr. is looking for his male Irish forebear using genetics:
Well, it turns out that the men sharing that Ui Neill haplotype tended to have certain surnames. If we use those surnames, we narrow the number of possibilities in Allegany and Hampshire counties to 178 men born between 1800 and 1830 bearing 22 surnames.What's so exciting about this? Well, it turns out that the men in the Gates family line have a particular mutation, a slight variation, in our Ui Neill haplotype. And we inherited that slight mutation, a spelling variant in that DNA signature, through one of those 178 guys. If the father of Jane's children, my Irish great-great grandfather, has any other male descendants walking around on the planet, he will have exactly the same y-DNA signature, with this particular variant, as my father, brother and I do.
And so, we are advertising for any male descendant of one of these 178 men to contact us and take the DNA test. With a (wee) bit of luck, one of the millions of unsolved genealogical mysteries facing African Americans today can be solved.
Descendants of slaves naturally have less of a paper trail than most people (Chinese clans often trace descent on the order of one thousand years, though some of this may be fictive). This is where even simple uniparental lineages can offer some psychic utility.
Posted by Razib Khan at 2:12 PM • 10 Comments
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The Evolution Of Symbolic Language by Terrence Deacon and Ursula Goodenough. Deacon's The Symbolic Species: The Co-Evolution of Language and the Brain is a book I liked a great deal, though in hindsight I don't think I had the background to appreciate it in any depth (nor do I now).
Posted by Razib Khan at 4:25 AM • 6 Comments
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At least in this case, Troglomorphism, trichobothriotaxy and typhlochactid phylogeny (Scorpiones, Chactoidea): more evidence that troglobitism is not an evolutionary dead-end:
The scorpion family Typhlochactidae Mitchell, 1971 is endemic to eastern Mexico and exclusively troglomorphic. Six of the nine species in the family are hypogean (troglobitic), morphologically specialized for life in the cave environment, whereas three are endogean (humicolous) and comparably less specialized. The family therefore provides a model for testing the hypotheses that ecological specialists (stenotopes) evolve from generalist ancestors (eurytopes) and that specialization (in this case to the cavernicolous habitat) is an irreversible, evolutionary dead-end that ultimately leads to extinction. Due to their cryptic ecology, inaccessible habitat, and apparently low population density, Typhlochactidae are very poorly known. The monophyly of these troglomorphic scorpions has never been rigorously tested, nor has their phylogeny been investigated in a quantitative analysis. We test and confirm their monophyly with a cladistic analysis of 195 morphological characters (142 phylogenetically informative), the first for a group of scorpions in which primary homology of pedipalp trichobothria was determined strictly according to topographical identity (the "placeholder approach"). The phylogeny of Typhlochactidae challenges the conventional wisdom that ecological specialization (stenotopy) is unidirectional and irreversible, falsifying Cope's Law of the unspecialized and Dollo's Law of evolutionary irreversibility. Troglobitism is not an evolutionary dead-end: endogean scorpions evolved from hypogean ancestors on more than one occasion.
More at ScienceDaily. Those with broader knowledge of different species can weigh in, but for some reason I always felt skeptical of the idea that specialization was a dead end...though I suppose it could be analogized to an asexual clonal lineage which is at some adaptive peak. A naive idea I had in mind is that specializations are at least as likely to be gain of function mutations as loss of function mutations, and it is easier to go from functional variants to non-functional ones. But in any case, biological generalizations almost always have a lot of exceptions, the question is the extent of the exceptions, and whether that makes the generalization useful or not.
Citation: Cladistics, 26:2, doi:10.1111/j.1096-0031.2009.00277.x
Posted by Razib Khan at 1:13 AM •
March 17, 2010
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A few weeks ago I commented on the paper about the origin of the small dog phenotype in the Middle East. Now The New York Times has an article on a newer paper, New Finding Puts Origins Of Dogs in Middle East. Here's the conclusion:
Dog domestication and human settlement occurred at the same time, some 15,000 years ago, raising the possibility that dogs may have had a complex impact on the structure of human society. Dogs could have been the sentries that let hunter gatherers settle without fear of surprise attack. They may also have been the first major item of inherited wealth, preceding cattle, and so could have laid the foundations for the gradations of wealth and social hierarchy that differentiated settled groups from the egalitarianism of their hunter-gatherer predecessors. Notions of inheritance and ownership, Dr. Driscoll said, may have been prompted by the first dogs to permeate human society, laying an unexpected track from wolf to wealth.
Humans are often conceived of as the selection pressure on our domesticates, but clearly this is a two-way street. Cows have strongly shaped the human genome in the form of lactase persistence. And of course there have been many pathogens which have jumped from domesticates to humans, including ones which might change human behavior. The evolutionary process in this conception is a complex series of interactive feedback loops, and the task of reconstruction is going to be a laborious, but fascinating one. And luckily, we have "control" populations who have been little impacted by domesticated animals.
Here's the letter in Nature.
Posted by Razib Khan at 7:45 PM • 13 Comments
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A week ago I observed that commenting was being transformed with the spread of Disqus and Echo. The Big Money has now introduced Echo:
The comments themselves are also more interactive. Any of your postings can be shared with your friends on Facebook, followers on Twitter, or any of your connections on the other supported services. You can also reply to fellow commenters, tell them you like their posts, or flag any inappropriate or spam messages that you see. All commenters have their own profiles, which you can find by clicking on their profile names and viewing their details. There you'll be able to find all the comments they've recently left, allowing you to develop commenter-crushes on the smartest TBM readers.
Since no biomedical firm has developed a drug which allows you to become "sleepless" as in Nancy Kress' Beggars series comments and comment structure has to be value-added. As I made clear earlier, I don't generally see much value-added in comments on many websites, but that's just me. I depends on what you want to get out of comments, and how much marginal time you have in your life I guess. Flagging/comment rating systems are probably good though. I like Less Wrong's system for what it's worth, even though I've gotten voted down for kind of being a dick over there. It's better than nothing.
The readership of my weblogs are rather select, so I have to delete very few transparently stupid comments (that is, stupid because of the endogenous stupidity of the commenter, not because someone is being a jackass for fun or spite). Consider the highest educational attainment of the readership of this weblog for American readers:
84% have at least a bachelor's degree
19% have a master's degree
13.5% have a professional graduate degree (JD, MD, etc.)
20.5% have a non-professional doctorate*
I assume that a substantial number who haver only a bachelor's degree are likely graduate school drop-pouts, or currently pursuing graduate degrees (going by the age distribution, which is skewed toward those in their twenties and thirties). Additionally, 83% of readers have taken calculus. These variables should argue against stupid comments (I have a friend who is a quantitative social scientist who can't blog about quantitative social science because his readers on his popular weblog are simply too stupid to really understand distributions, so the comment threads devolve from the get-go).
On the other hand, 86% of readers are male, and 12% are virgins. These are two demographics more likely to engage in what I might term "Usenet" behavior.
Note: ~25% of Americans aged 25 or older have bachelor's degrees, for point of comparison.
* Of those with non-professional doctorates, 60% are in math, science and engineering. 23% are in social science, such as psychology and economics. The balance are in other fields, with a little over half of those in the humanities.
Posted by Razib Khan at 6:51 PM • 8 Comments
PZ Myers 07.29.2010
PZ Myers 07.28.2010
Ed Brayton 07.29.2010
Orac 07.29.2010
Ed Brayton 07.29.2010
