Chris Miller
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Monday at 8:55 am - ascii.textfiles.com - Link
We’re talking about terabytes, terabytes of data, of hundreds of thousands of man-hours of work, crafted by people, an anthropological bonanza and a critical part of online history, wiped out because someone had to show that they were cutting costs this quarter. - Chris Miller
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FreeMat is a free environment for rapid engineering and scientific prototyping and data processing.
FreeMat is a free environment for rapid engineering and scientific prototyping and data processing.
Sunday at 5:34 am - freemat.sourceforge.net - Link
This is similar to commercial systems such as MATLAB from Mathworks, and IDL from Research Systems, but is Open Source. FreeMat is available under the GPL license. - sofarsoshawn via Bookmarklet
I've never seen Matlab/Freemat working. Can it be described just as a GUI over 'R' ? - Pierre
What is the difference to Octave? - joergkurtwegner
@Joerg: It's in the FAQ: http://freemat.sourceforge.net... "Who said choice was a bad thing?" :-) - Pierre
I don't do a lot of Matlab, but I'm glad to see projects like this going strong. The world needs high-quality, open source Matlabs and Mathematicas. Here's hoping it's as successful as R is some day. - Chris Miller
This is in the standard Ubuntu repository. Just do a sudo apt-get install freemat. - imabonehead
This is pretty neat, has anyone tried this? I'm curious about its performance and numerical accuracy. I know MATLAB is supposed to have some super-special matlab-fu to enhance its performance as well as proprietary algorithms for their PDE solvers -- does this match up? - Benjamin Tseng
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Sunday at 10:18 am - liveleak.com - Link
Which campaign promises has he kept? - Chris Miller
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Saturday at 8:15 am - scienceblogs.com - Link
Blistering rebuttal of some high-profile alternative medicine advocates - Chris Miller
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Saturday at 8:08 am - today.msnbc.msn.com - Link
Possibly even creepier than 'real dolls' - Chris Miller
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January 1 at 8:38 pm - getsatisfaction.com - Link
imports the meta info, including ratings, from an iTunes library into Songbird. - Chris Miller
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December 31 at 10:34 am - theskyinmotion.com - Link
time-lapse film of southern stars - Chris Miller
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December 25 at 10:28 pm - nytimes.com - Link
I'm third author on the piece. The pretty picture was generated with Circos, a GPLed software package. - Chris Miller
Congrats Chris! nice work :) - Susan Beebe
Congrats! - imabonehead via fftogo
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“Question to science bloggers: what other passion you blog or have blogged about?”
December 23 at 11:04 am - Link
I was blogging about night photography. - Pawel Szczesny
Food, and New Orleans. - Mr. Gunn
drawing, comics, astronomy - Pierre
I currently have dormant food and book blogs. The book blog I periodically restart then run out of steam. - John Dupuis
politics, religion, Balkans, North Carolina, horses, food, The Web, journalism/media, the changing face of "work". - Bora Zivkovic
Music - Deepak
Reading - maxine. - Maxine
politics/civil liberties, religion (or lack thereof), - Chris Miller
Philosophy, Personal Fulfillment, I write some stories which aren't posted yet, Entrepreneurship, Identity - Danielle Fong
tech, innovation, iPhone, Arduino, RFID, DIY, a little bit of philosophy (related to life extension), journalism, movies - Attila Csordas
sci-fi/fantasy books - Nir London
My karate studio, family blog & local news, restaurants - Jim Hardy
Video game development, Nintendo Wii and Linux. On blogs separate from my science-related blog. - Andrew Perry via NoiseRiver
Once I joined a group blog focusing on snooker... :) - Berci Mesko
Tech, politics, very many geeky things... - Benjamin Tseng
Food and wine - Sally Church
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December 21 at 2:04 pm - media3.washingtonpost.com - Link
Frightening. - Chris Miller
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December 21 at 1:09 pm - cscs.umich.edu - Link
You should treat "Thou shalt comment thy code" as a commandment which Moses brought down from Mt. Sinai, written on stone by a fiery Hand. I will treat it so when I grade you. - Chris Miller
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December 20 at 6:23 pm - news.bbc.co.uk - Link
"In Lebanon, geneticists led by Dr Pierre Zalloua have managed to identify the Phoenician gene." - Neil Saunders via Bookmarklet
*bangs head against wall* - Bob O'Hara
groan - Maxine
The BBC's science reporting team do need a smack around the back of the head sometimes - Daniel Swan
J=0,3x0.5x0,8x0,7=0,08. J value of less than 0,1 isn't good, but it's my subjective one, will you have worse or better ?: http://tinyurl.com/7xlje3 - Nils Reinton
@Daniel - I'll say. Just yesterday, I smacked them over a breast cancer article. http://is.gd/cNZd - Chris Miller
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December 19 at 8:07 pm - xkcd.com - Link
So true - Chris Miller
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After Credentials
December 19 at 5:44 am - paulgraham.com - via Reshare - Link
Paul Graham postulates that credentials are becoming increasingly obsolete as small companies are paying people by performance, not by seniority. How does this relate to academic scientists? - Michael Kuhn
Paul Graham believes the solution to all of society's ills is the creation of more small startups. He is a man with a hammer in search of nails. - Chris Miller
Having been in both large (IBM) and small (startup) companies, it is hard not to agree a bit with Paul Graham. - Anders Norgaard
It's a bit tenuous, but it somewhat relates via the gradual disappearance of tenure and continued focus on performance beyond year 7. =) - Donnie Berkholz
I am with Donnie. Tenure MUST go - Deepak
Graham's argument is unrelated to academic culture. The argument he makes is (1) the trend in organizations is to smaller companies; (2) smaller companies will tend to select more based on performance, rather than credentials. The reason he gives for (2) is essentially an argument "in the limit", to use the mathematicians' phrase: if all companies had just one person, then it would obviously be true. Therefore, you'd expect this to be more true in smaller companies. (cont) - Michael Nielsen
(cont) regardless of whether you believe any of this, none of the reasoning applies to academia, where the trend is to larger teams and larger organizations. - Michael Nielsen
Getting rid of tenure will lead, in my opinion, to a far more fashion-driven approach, with ever more people concentrating on this year's fad, to make sure their contract is renewed. The current grant system surely leads to enough fashion-driven research. (A few years ago the Australian Research Council announced "priority areas". Applications in those areas doubled in the first year, leading to a great concentration of Australian scientists working in a few highly fashionable areas. Not good, IMO.) - Michael Nielsen
Small companies put more value on street credentials (which expire fast) than on academic credentials. Big surprise. But is this really a new (or even growing) trend? Moreover there don't seem to be a lot more small companies relative to large companies (at least in the U.S.) than there were 10 or even 20 years ago: http://manyeyes.alphaworks.ibm... - Eric Jain
Eric, I've posted a link to that page at a forum Paul Graham runs (http://news.ycombinator.com/it... ). With some upvotes, it'll get on the front page, and get some discussion. - Michael Nielsen
Michael Nielsen, I don't think tenure makes hiring any more or less fashion-driven than it already is... (1) b/c everyone already is fad-oriented, (2) there's no reason to assume that tenure is what drives quality of scientific output, and there's no reason to assume that once tenure disappears professor positions suddenly become impossible to hold on to (e.g. the private sector -- lack of tenure doesn't mean mass firings, and even if it did, who's to say those firings aren't good?) - Benjamin Tseng
Regardless of if you agree or disagree with the institution of tenure, Freakonomics author (and John Bates Clark medalist) Steven Levitt's comments are interesting to consider: http://freakonomics.blogs.nyti... - Benjamin Tseng
There does need to be a route by which people can pursue what interests them, whether or not anyone else cares about it. Tenure at an academic institution seems to be that route, and it works OK AFAIK. - Mr. Gunn
We all probably agree that it is important to let a scientist be able to pursue what they want and tenure is a mechanism to do that. My problem has always been the criteria which get people tenure? It seems to put an emphasis on volume rather than quality doesn't it? Maybe things have changed, but life as an assistant prof who wants to do something interesting can be pretty hard, especially as you try and build up a group - Deepak
Well you could look at the life of an asst prof as proving he can do the required/sensible/tradtional stuff - if it's good enough, he gets tenure and then pretty much do any random thing, whether it works, is useful etc or not - Rajarshi Guha
Also,m if tenure were done away with and profs were on fixed term contracts, would it be expected that their salaries increase? - Rajarshi Guha
I see the tenure system as a way for the society to get two things out of each scientist: 1) some good, safe, incremental science (in order to get tenure) and 2) some novel, daring, risky, potentially revolutionary science (after gaining the protection of tenure). Both types of science are needed and the system tries to make sure both types are done (but no system is perfect, of course). - Bora Zivkovic
Tenure provides two things, financial security and ability to publish in well-read journals. The bigger issue is with the latter - you are _allowed_ to have brilliant ideas published only if you're tenured, or have a strong support from tenured professor. If you want to hear that you're an idiot (literally) from an editor send a brilliant paper to our favourite prestigous journal as a grad student (real, first hand story - or stories, as I know two such cases). - Pawel Szczesny
This reminds me of something a while back on FF: The PhD used to be a necessary and sufficient credential needed to get tenure, and once upon a time most people with PhD's actually were more or less guaranteed faculty positions: http://friendfeed.com/e/fb006e... - Michael Kuhn
In the economic world, all you need to do is open up a new market and you have a successful start-up. Basic research doesn't have this immediate economic return, so there needs to be another measure to reward performance. As Pawel pointed out, you largely need backing by big-shots to get something into CNS. There is no real unbiased "marketplace of ideas" that would give rewards to people without the right credential... - Michael Kuhn
@Bora: So in effect you're not in a position to do "daring" and "risky" work until you're old enough to no longer feel inclined to do so... - Eric Jain
No, as someone above noted - you can do that if you have a support of your PI: http://scienceblogs.com/drugmo... or if you are in a particular field it gets easier. I noted it's not perfect, meaning both that you can continue the bandwagon after tenure and that it is possible to make breakthroughs before - but both of those are against the system which favors the other way round. - Bora Zivkovic
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December 18 at 9:40 pm - miscellanea.wellingtongrey.net - Link
U-S-A!! U-S... oh. - Chris Miller
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December 17 at 1:51 pm - thedenverchannel.com - Link
Probably a case of a partially-developed twin getting absorbed into the surviving fetus. Don't miss the picture. - Chris Miller
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December 16 at 11:15 pm - nytimes.com - Link
"Physicians have financial incentives to perform procedures that further drive up overall health care spending" - Chris Miller
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December 16 at 3:28 pm - insanecoding.blogspot.com - Link
Amazing that Ubuntu has hacked together something that works well out of this mess. - Chris Miller
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December 15 at 9:31 pm - politigenomics.com - Link
Great overview of the current technologies. - Chris Miller
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December 15 at 9:30 pm - homesicktexan.blogspot.com - Link
Made this last weekend. Actually worked better with canned jalapeños, because the juice spread the flavor through the bread - Chris Miller
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December 15 at 9:29 pm - instructables.com - Link
Why haven't I seen these before? I'm now thinking about making one. - Chris Miller
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December 15 at 9:28 pm - poignantguide.net - Link
Fantastically amusing and helpful. I've picked up 3 or 4 new tricks in the first few chapters - Chris Miller
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December 14 at 9:58 am - sciencemag.org - Link
(sorry, behind a paywall) The gist: Journals are de-emphasizing methods and thus hurting the scientific process. - Chris Miller
I mean, have you ever tried to recreate computational analysis from another group? No parameters, only the faintest idea of what preprocessing was done - it's damn near impossible. (More: http://www.chrisamiller.com/bl...) - Chris Miller
Have not read the article at your link, but at Nature we encourage extended methods in the online part of the paper, and also encourage full protocols to be uploaded to the free service Nature Protocols (other users can then comment on/refine protocols). - Maxine
@Maxine FTA: "Other journals have almost completely moved the Materials and Methods section from the main text to online supplements. These journals are conveying the message, however inadvertent, that the sine qua non of the scientific method, the Materials and Methods, is the least important part of a scientific publication." - Chris Lasher
Thanks, Chris. At Nature, we offer authors more space for their methods, and although this is online-only (HTML/full-text and PDF), the extra methods are fully integrated into the online PDF when it is downloaded. The details of the methods are of interest and are very important to others in the field, but not so compelling to those in other disciplines. - Maxine
@Maxine Good response. FWIW, I do all my journal reading online, and the original author's comments don't represent my own. I really can't recall the last time I browsed a journal in dead-tree format. Perhaps this point grows more moot as we move to the online-centric model. - Chris Lasher
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December 9 at 7:58 pm - in-sequence.com - Link
"The commercial system will be able to sequence genomic DNA, cDNA, or PCR products and accept linear or circular template DNA, said Martin. The polymerase will incorporate at least three nucleotides per second. Since the reactions are measured in real time, the speed of the system will be high: at short or medium read lengths, an experiment can be completed within approximately five minutes, according to Martin." - Deepak via Bookmarklet
Five minutes ... sanger size reads .. holy crap - Deepak
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December 5 at 8:57 am - rseek.org - via Reshare - Link
I guess most of the people in this room knows about it, hope this helps the others - Yann Abraham
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“Any of you had any experiences with caBIG?”
November 19 at 7:57 am - Link
nope, what is caBIG? - Paulo Nuin
An over architected biomedical grid/service discovery framework https://cabig.nci.nih.gov/ - Deepak
Is there any other kind? - Euan
I hope there are. - Deepak
What causes projects like these to become "over-built"? In this case, I suspect that the effort to bridge multiple institutions with complicated research, information, and regulation structures might be to blame. - Jere
caBIG provides a scalable infrastructure for discovering and obtaining grant money - Eric Jain
@Jere: If the solution isn't complicated, you won't get a whole lot of money to implement it... - Eric Jain
@Eric, nice :) - Rajarshi Guha
@Eric: So true! - Jere
@Eric ... lol ... - Deepak
@Eric ... rotfl... cabig is BIG and can't be ignored, difficult to integrate with because they are very strict about what is in and out of cabig in my experience - Duncan Hull
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November 12 at 9:51 pm - google.org - Link
Amazing little piece of technology - Chris Miller
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“Why don't scientists do more (X)?”
November 10 at 6:16 pm - Link
Where (X) is blogging, social networking etc. Topic seems to come up regularly, but I think there are 3 simple answers: (1) They don't know about it; (2) they're not interested in it; (3) they don't make time for it. - Neil Saunders
I think 2 and 3 are relevant to many things we all don't do in life, and 1 is sometimes true, when 2 and 3 are. For example, I don't have much interest in TV (2). I don't know what's on because I don't look (1). I don't make time for it anyway (3), as I'm always doing something else. - Ian May
Yes, these are generic answers to "why doesn't (insert person/people) do more (insert activity)". - Neil Saunders
I would say usually it's (1) plus (4) they don't see value in it. - Richard Akerman
I would add that these are not activities that naturally fit into the things that scientists already do as part of their work. e.g. most scientists (that I know) can't be properly bothered with dealing commercialisation processes because they move away from what people are familiar with, take up time, and don't seem to feed back in to the kind of things that they're already doing - Cameron Neylon
I am with Richard. There is also a lack of understanding (not just among scientists) of sacrificing long term efficiency for short term expediency - Deepak
I agree with these comments too. Most scientists still don't really do "work" on the web, beyond cutting and pasting. It's hard to transpose their current practices. - Matt Wood
Deepak, I really like this sentence - Pierre
4 is probably the most important reason, as well as a perceived threat to "quality" because it's "the internet". - AJCann
as well as a threat to quality, the internet is not seen as a place of work to most scientists, it is something to waste time on, not a tool to be made to work for you. - Jo Badge
Because outreach is not a component of funding decisions. If it were, they'd prioritize it. Also, if we weren't all chasing a slice of a shrinking pie, it would be easier to persuade people to give up some of their valuable time. - Chris Miller
That's actually the kind of thinking (Google vs. Microsoft) that Spolsky was talking about in the Stack Overflow podcast episode referred to in my recent blog post. The fact that for microsoft, a spellchecker (for example) was written with the narrow mindset of the desktop and thus the individual, while for google the spellchecker was written with the mindset of the web, and thus for collective intelligence - Deepak
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