Posted: 12 Nov 2008 06:24 PM CST
I’ve literally got students coming out the wazoo today, so I’ll keep things short and simple…
After ranting about premature Christmas decorations and my general disdain for the holiday, I’ve been tasked with coming up with a personalized message for my company’s Christmas cards. This is, by far, the most difficult three or four sentences I’ve ever had to churn out. Any suggestions?
I’m pleased to be the host for Mendel’s Garden #26. Mendel’s Garden, the genetics blog carnival, is looking for the best genetics posts in the blogosphere. I’m hosting the December edition and am actively looking for submissions. Everything from transcription to evolution to genetic counseling and social implications of genetics research are welcome. I’m particularly interested in non-specialists, so if you’ve got something that you could tag with “genetics” send it my way. If you’d be interested in having a post featured, please e-mail me your latest and greatest to chris (at) afreeman (dot) org.
Finally, when things have gotten harried this week, I’ve turned to this video for a dose of serenity. The internets are awash with cute kid videos, but I have the cutest kid (and possibly the most patient dog) around.
I’d never heard of The Bouncing Souls until this track came my way, but I can’t stop listening to it. They’ve been around for ages and I’m thinking of checking out more of the New Jersey quartet’s music. Buy the self-titled record that featured “Serenity” and other records here.
This posting includes an audio/video/photo media file: Download Now
Posted: 12 Nov 2008 03:16 PM CST
Actually, today it's tea because I need to go easy on the caffeine. Here's what's interesting in science around the web this week:
Where did hobbits come from? Not the hobbits in the Shire, but Homo floresiensis, a diminutive hominid that lived on an Indonesian island 20,000 years ago. PBS has an essay on evolution and why island creatures sometimes get very big or very small.
Posted: 12 Nov 2008 01:41 PM CST
Two days ago, I posted a great video focusing on the major problems of healthcare systems. Then Brendan left a comment for us and introduced the Stay Smart, Stay Healthy website, the creator of the video.
Two of their many unique videos are published on Youtube.
How Does Insurance Work?
Why Is Healthcare So Expensive?
Give them feedback, promote them on your blogs and join their project on Facebook or Youtube.
Posted: 12 Nov 2008 12:15 PM CST
I do not normally write too much here about non Open Access publications but this one is so good I had to. Everyone with access to Trends in Microbiology should check out Julian Parkhill's rebuttal to an article written by David Whitworth in the same issue. Whitworth's article is "Genomes and knowledge – a questionable relationship? " and it is in my opinion, filled with some unsuppoerted and over the top statements. In essence, he is arguing that we should stop genome sequencing because there are a bunch of genomes out there already and after all, all that matters is work on model organisms so if you have enough genomes related to your model organism you should move on. Alas I do not have time to detail them here. But fortunately, Parkhill does a great job of responding in his article Time to remove the model organism blinkers. The end of his article reflects how I feel too:
In the end, when faced with the astonishing diversity of microorganisms, if all we manage to do is to describe a few random organisms in painstaking detail, then we will have failed to understand microbiology. To suggest we curtail the remit of microbial genomics is bad enough; to suggest it now, when we are on the brink of finally being able to truly study genomic diversity, is absurd.So sure, sometimes we in genomics oversell the benefits of genome sequence data (and in fact, I give out a little award here for those people). But Whitworth is at the other end of the spectrum, wearing, as Parkhill states "blinkers" to the benefits of genome sequence data. As a reflection of how much I disagree with most of Whitworth's implications, I am giving him my first "Underselling Genomics Award".
Posted: 12 Nov 2008 11:18 AM CST
deCODE’s problems should not be any surprise to those following Iceland’s massive financial crisis. Morningstar’s Matthew Coffina has now listed deCODE stock as one of five that “look completely worthless.”
Posted: 12 Nov 2008 10:00 AM CST
You would think that geneticists would have a good definition of "gene". After all, genes are what we study. In introductory biology courses, you may have been introduced to the concept of the gene as the unit of heredity. That's all well and good, but when you begin to study genes at a molecular level (i.e., looking at DNA sequences), that definition ceases to be practical. The advent of DNA sequencing led to the concept of the gene as an open reading frame, and the post-genomic era has challenged the very idea of the gene.
I've previously discussed the definition of gene (What is a gene?, What is a gene? -- yes, two different posts with the same title), but I didn't get into very many details. Alas, I don't feel like spending much time laying out my opinion, suffice it to say I think "gene" is an obsolete, overly generic term that should be replaced by a more specific term whenever possible. Luckily, the New York Times has published an article by Carl Zimmer sketching out some of the possible interpretations (Now: The Rest of the Genome ). This lets me pick and chose my favorite meaning from a variety of opinions represented in Carl's piece.Read the rest of this post... | Read the comments on this post...
Posted: 12 Nov 2008 09:59 AM CST
in The Know-It-All - One Man’s Humble Quest to Become the Smartest Person in the World by A. J. Jacobs
Posted: 12 Nov 2008 09:15 AM CST
What skills does a biotechnology technician need to know?
This seems like a simple question, but people have been struggling to define biotech skill standards since the early 90's.
Complicating this question is that many areas of biotechnology require somewhat different skills. Antibody work requires one set, plant or animal tissue culture, another; fermentation, another; manufacturing, another; DNA sequencing, yet another set. Even skills that you might think are universal, like using a microscope, are not. During my years in graduate school, I never used a microscope; I cloned genes and ran gels. Plus, many skill requirements change. These days, if I were a grad student, I'd probably be operating robots or sending my samples to a core lab.
Anyway, the Department of Labor has decided that the time has come to define the needed skills and establish a:Read the rest of this post... | Read the comments on this post...
Posted: 12 Nov 2008 09:03 AM CST
My feeling about science news reports is decidedly mixed. On the one hand, I read most of the main news services in order to keep up with research outside of my own discipline. On the other hand, I would say that about once every two or three days I find a story so silly that it makes me physically uncomfortable. This is one of those.
Evolution's new wrinkle: proteins with 'cruise control' act like adaptive machines
A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.Organisms do not "respond to natural selection". Natural selection is the differential survival and reproduction of individuals within a population. It is a population level process and it is not interchangeable with "challenges to organism survival". If all organisms in a population are able to respond to a challenge such that there is no differential survival and reproductive success, then there is no natural selection.
Adaptive evolution is the result of natural selection -- the differential survival and reproduction of randomly varying individuals on the basis of heritable characteristics. This differential survival and reproduction is, by definition, non-random. Again, organisms do not evolve, populations do.
And then it says:
The work also confirms an idea first floated in an 1858 essay by Alfred Wallace, who along with Charles Darwin co-discovered the theory of evolution. Wallace had suspected that certain systems undergoing natural selection can adjust their evolutionary course in a manner "exactly like that of the centrifugal governor of the steam engine, which checks and corrects any irregularities almost before they become evident." In Wallace's time, the steam engine operating with a centrifugal governor was one of the only examples of what is now referred to as feedback control. Examples abound, however, in modern technology, including cruise control in autos and thermostats in homes and offices.
The essay is the one presented by Lyell and Hooker to the Linnean Society in 1858, along with one by Darwin. Here is the full paragraph:
Wallace (1858):Wallace was talking about the consequences of randomly determined variants that had a change in one feature without a compensatory change in some other feature, namely that they would not survive. There is nothing in this that implies that individual organisms are changing in response to challenges or that species are directing their evolution.
It goes on, but I will jump forward:
Based on this story, it is challenging to determine just how this is differs from evolution in the usual sense. Looking at the original paper, it appears that what the authors are arguing is that 1) the constituent proteins in the electron transport chain are tuned to an extreme, 2) that this extreme is not related to the function of the proteins as would be "visible" to natural selection on the grounds of electron transport capability, 3) that the proteins in the network are optimized for redox potential, which has no consequences for the organism and therefore cannot have evolved through normal selection, and 4) that something else, i.e. self organization, is involved in producing the extreme features of the proteins. The rest is mathemagic, so someone else can wade through it and see if the argument makes sense if they like.
I am not actually concerned with whether the calculations are correct. As it so often is, the issue is about press releases and the hype and sloppy descriptions of both ideas and history that they (and, too often, the people interviewed) present.
People have been having trouble finding the article. It's here.
The authors have another paper in the bastion of bad biology, arXiv, that quotes directly from Wallace (here). Don't blame the story author, these guys lifted that out of context by their own selves.
Posted: 12 Nov 2008 07:00 AM CST
My post on social media for scientists seems to have been received rather well, with a huge amount of traffic and positive responses from various big name commentators across the networks and blogosphere.
Several scientists have already commented about the post over on Nature Networks. Nature’s own Maxine Clarke describe it as “an amazingly useful post” but was worried that there seem to be so many scientific social media clones now available. It is, she says, “It is hard to see them all enduring.” But, that’s not surprising, natural selection and survival of the fittest will kick in. Indeed, it already is happening to a degree. Some of these communities are fast approaching critical mass.
For instance, Joerg Heber is also concerned that there lots of clones and that although the trend is towards increasing fragmentation of our online identities, he points out that SciLink.com now has 44000 users or thereabouts, whereas SocialMD, claims just 3100. “In the end,” he says, “there surely will be a concentration process for all those sites and only a few will survive. There likely will be a self-accumulating user base for the most successful ones, as the more users there are the more sense they make.”
But, compare those figures with the likes of LinkedIn (30 million users) and Facebook (120 million) and one has to wonder what is the purpose of creating a niche community external to such sites, when one might simply create a group within those and have access to potentially millions of like-minded individuals. Indeed, it never occurred to me to create a standalone science writers community online, I simple organised a Facebook science writers group, which now has almost 400 members. Obviously, there are fewer science writers than scientists.
Heber concedes that LinkedIn and Facebook may not be perfectly suited to scientists, but wonders whether the networking sites I listed in the original post really are specific to scientists? “Can you share lab books and wikis?” he asks.
Martin Fenner mentioned ScienceOnline’09, which I do hope to attend (looking for a sponsor, right now). This unconference, which will be for scientists and science communicators alike will, he says, have a session on social networks for scientists, moderated by my good friends Cameron Neylon of Science in the Open and Deepak Singh of bbgm.
Fenner followed up his original comment with the following, pointing out that AAAS Science Careers (Social Networking Grows Up) also had an article on this topic [which I hadn't seen when I started writing the original Sciencebase post mid-October, db]. “They talk about a few social networking sites for scientists, but somehow fail to mention Nature Network,” Fenner says, “The article also mentions social networking sites set up by universities, including ResearchConnect (University of Manchester) and Small Worlds (University of Leicester). I didn't know about this (unless you count the Facebook organisation by universities), but it looks like a good idea.”
Brian Willson of the Microsoft Chemical Team Blog gave my post a mention and noted that most of the sites are apparently aimed at academia rather than industry. He was curious to know whether web 2.0 and online communities would impact scientists in industry, a topic he has discussed previously on the MCTB.
44000 members is impressive (for SciLink), buthave any of the social media sites for scientists really achieved critical mass yet? By which I mean do they have enough active members to become self-sustaining and useful to science and the communities they serve?
Way back in the 1990s, I used to work for two of the biggest proto-social media sites for scientists - ChemWeb and BioMedNet. The former had more members than the American Chemical Society (which at the time was around 140,000 I believe) and BMN even more at, if memory serves correctly, close to half a million, far more than Facebook and LinkedIn put together!).
Both CW and BMN were incredibly innovative (having been created by Vitek Tracz, chairman of the Science Navigation Group, and founder of the open access publisher BioMedCentral as well as the those two online communities). CW and BMN were running what were essentially blogs alongside their news and features output, providing preprint servers (in the case of Chemweb), member search tools, webinars and online conferences, and access to dozens of resources. Of course, they were never labelled web 2.0. This was, after all well before the .com bubble burst and the web was reborn.
Unfortunately, both CW and BMN were bought up by a giant shareholder-driven publisher (mentioning no names) and driven into the ground once the company realised it wasn’t making enough money from them. Which was a great shame, because they really could have made huge inroads into the very world we are discussing. ChemWeb.com lives on thanks to Chemindustry.com and is thriving in its new form as my regular readers will know from The Alchemist newsletter, but at the moment it is not quite the community-led system it once was.
In some sense, all these new social media sites for scientists are simply reinventing a well-worn wheel from a decade past and whether or not any of them will achieve the significance (at their height) of a Chemweb or a BioMedNet remains to be seen. Offline scientific networks/societies continue to grow as they have done since their earliest days in the nineteenth century and before (their online efforts don’t seem to have yet built the online communities that could exist)
Given that many of the online efforts are insignificantly small in terms of membership numbers compared to the now defunct BMN and compared to the offline presence of the bigger scientific societies, I seriously doubt that more than one or two will survive and thrive. But, we’ll have to wait and see. Perhaps it will take a killer application for one to emerge as a leader and become as essential to scientists as MySpace is to a teenybopper and Facebook is to students. That killer application, however, remains to be revealed.
Posted: 12 Nov 2008 06:44 AM CST
The 58th annual meeting of the American Society of Human Genetics is currently being held in Philadelphia. Today at 10:00AM there will be a session specifically about genetic genealogy entitled “The Social, Ethical, and Biomedical Implications of Ancestry Testing: Exploring New Terrain.” From the abstract:
The moderator of this session is Sandra Soo-Jin Lee of Stanford University. The panelists include Joanna Mountain who will talk about ‘New dimensions for direct-to-consumer genetic ancestry testing’; Kimberly Tallbear who will talk about ‘The genetic construction of indigeneity’; and Esteban González Burchard who will talk about ‘The importance of ancestry testing and genetics in biomedical research’. Additionally, the moderator will discuss ‘Racing forward: The ethics of ancestry testing.’
I don’t like the mixing of the controversial phrase “direct-to-consumer” with genetic genealogy. Of course it’s direct-to-consumer, who else would the results go to? Should your doctor or genetic counselor review your genetic genealogy results? That would be a ridiculous restriction.
The panelists will also be discussing the “ethical and policy issues” in this changing landscape. As always, I believe that education, not more government regulation, is the answer to these ethical and policy issues.
Posted: 12 Nov 2008 06:35 AM CST
A few days ago, I posted a message on Friendfeed:
Now I thought I should share the best stories with you:
Posted: 12 Nov 2008 06:20 AM CST
You can also download raw data or use the Flu shot locator.
Posted: 12 Nov 2008 02:55 AM CST
As promised, here comes more coverage on the passing of Prop 8 in California. I am re-posting a video showing Keith Olbermann's reaction to the passing of the proposition -- it is worth watching till the end. Hat tip: Greg Laden.
Also, you might have heard that nation-wide protests are being organized for November 15, so Join the Impact here or here. You can follow the developments of the fight against Prop 8 on my Twitter as well.
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