quote "The activity of building and validating tools makes us engineers. The activity of using these tools to create new knowledge makes us scientists. " - Duncan Hull
Nice quote... this actually makes quite a few 'scientists' 'engineers'... lot's of bioinformaticians, to start with... BTW, what defines 'new knowledge'? A new QSAR model? Hardly any new knowledge, not? QSAR-tists are thus engineers too? :) - Egon Willighagen
Well if it's a QSAR model on new data, you're using the tool to gain insight (hopefully). We need a principle of 'scientist engineer duality' :) - Rajarshi Guha
I have no problems with being an engineer. Apparently though, academic funding agencies have problems valuing people who build stuff. - Neil Saunders
Russ says: "Jeez. Who the hell reads blogs? PLOS and NATURE wanted me to write an editorial, but this was way easier and got probably as much impact already featured in a industry newsletter. I'm humbled and freaked out now." :D - Shirley Wu
Congrats! So Jan and I should have visited you in Cambridge today for the party - unfortunately Jan is drugged in a dentist's chair and getting his wisdom tooth pulled out! - Victor / Mendeley Team
Got confused here... I was in the dentist's chair just last Saturday... Oh I see: it isn't my egocentric me! - Jan Aerts
No, it's Jan, my co-founder at Mendeley. Must be Jan-at-the-dentist season! - Victor / Mendeley Team
“The Nobel Prize in Physiology or Medicine goes to Harald zur Hausen "for his discovery of human papilloma viruses causing cervical cancer" and to Françoise Barré-Sinoussi and Luc Montagnier "for their discovery of human immunodeficiency virus". Read More”
on the live webcast now there is a question about Robert Gallo as a co-discoverer of HIV, this will be an endless debate - Attila Csordas
This sounds fair to me: "Today it is generally agreed that Montagnier's group first identified HIV, although Gallo's group is credited with much of the science that made the discovery possible, and to demonstrating that it causes AIDS." http://en.wikipedia.org/wiki/R... - Attila Csordas
Attila, I cannot access the webcast, can you tell us more: who is asking the question? What is the answer? - Enro
the answer was on behalf of the official man that they think they are qualified for deciding such cases, I think the Wikipedia sentence in the comment before is fair enough - Attila Csordas
Odd they give the prize for two very different pieces of work. - Bob O'Hara
This reminds me of that comic the other day, about PhDs being pets... "Mmmm... that's a boring workshop, but my group needs to be present... Mmmm... who can I trick into going?..." - Egon Willighagen
Will that work if I want to increment the values of >= 2 keys, but don't know the keys in advance? The solution in the link worked well for me in that case. - Neil Saunders
I'm not 100% sure what you mean, but for what I understand that'd be a "yes". "demo = Hash.new(0); demo[:a] += 1; demo[:b] += 1". But best thing is to try it out, obviously. - Jan Aerts
That sounds right - thanks! In other words, the default value for any key is 0. - Neil Saunders
and indeed it does work - thanks again. - Neil Saunders
As always Deepak you're right on point and have great insight on this topic. I think part of the problem could be that scientists aren't willing to scrap their current implementation or workflow for a reported 1-5% performance increase on some dataset that isn't their own. I like the parallel you draw to Google and the search market. In order to beat Google a company can't just be a little better but you have to be MUCH better. The same goes for the researcher who is copying their trusty old charmm.inp around with few modifications from project to project or running/scoring their docking the same way because they know it's worked in the past. The barrier to adopt new methods just seems too high.
I have hope that community efforts like CAPRI or CASP can make the best methods stand out among the rest and offer that compelling reason to try something new. It's sort of depressing that we even have to talk about stagnation in such promising disciplines. - Adam Kraut
After all, if it's science, shouldn't the drive for innovation be baked-in? - Adam Kraut
That's what I was led to believe growing up. Turns out they lied to me :) - Deepak
... and it pains me a lot. That field is still the one I care about the most and in the end I believe that physical approaches are the ones that will give us the best answers, but we're essentially still stuck in 1983. Explains why I got so excited when MM-PBSA and some of those flexible docking methods came out - Deepak
All the figures were already done, but ended up being leftovers; I might as well make them available by writing a blog post around them :) - Lars Juhl Jensen
Never a bad idea :) ... now should be fun if someone actually ends up referring to that post in a more formal publication - Deepak
It sure would be nice if someone would cite this (or another) blog post in a paper (not that it is my reason for blogging). In this respect, does anyone know a way to get DOIs assigned to blog posts? - Lars Juhl Jensen
Lars: http://www.doi.org/faq.html. Far as I can tell, DOIs involve paying a registration agency, somewhat analogous to DNS domain names. Just another internet scam, in other words :) - Neil Saunders
I just checked the prices and it almost looks like a scam: with the number of DOIs you or I would need, you are looking at 4-5 EUR per DOI plus sales tax! (Unclear if this is a one-time or an annual fee). - Lars Juhl Jensen
more exciting than what the title may convey, peeps at la jolla used a rather new neat way of crystallising transmembrane proteins (in this case the adenosine2A receptor.. - laura
via Bookmarklet
Yes, good idea trying a fusion protein .. a bit like the old antibody co-crystallization trick for membrane proteins, but maybe a little less likely to distort structure and function. - Andrew Perry
Richard, I used that as a template ;) I was looking for a page on open notebook science in particular and didn't find one, so I created one. Everyone feel free to add their contribution, I am not the expert. - Andrew Lang
Wired to an unrelenting stream of data, ingesting information in frenetic and entirely new ways, our poor brains rarely get a chance to engage in more contemplative work. Yet thinking time may be an essential part of what makes us human, what gives us knowledge of ourselves and our own failings, allows us to develop a conscience and sort out right from wrong. - Neil Saunders
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More "oh noes teh internets r making us stoopid" bollocks. I wonder if idiot journalists wrote this kind of crap when the first public libraries were built? "Surrounded by books and periodicals of every kind, we flit from idea to idea, with no time for mature reflection blah blah blah"... - Bill Hooker
I remember hearing this in the form of "calculators are making people bad at math". Yes, we do become dependent on technology, and we do need to be aware of the tradeoffs. - Mr. Gunn
Yeah, they've basically picked up on Nick Carr's recent essays. That said, it's better than your average Miranda Devine article :) And there's something about the idea of occasionally stepping back from the infostream for some "quiet time" that resonates with me. - Neil Saunders
I'd like to see some studies of "non-early adopters". I'm always being told that "most people" - whoever they are - don't do this, don't do that, don't click "More", don't explore links, stick with what they know, haven't heard of (insert web2.0 service here). Like many people, I feel that it's true but without any evidence except my own experience. - Neil Saunders
Neil, Social Median wouldn't be in the position to do that, but you're right, more mainstream knowledge is needed. Strands has some interesting plans for Operation Mainstream, and we'll be watching that close. - Louis Gray
“I'm trying to compile a list of 12 (or more) microorganisms that have made (or will still make) a big impact in our lives. (Ex: P. chrysogenum -> antibiotics). Suggestions?”
Staph aureus (MRSA); Yersinia pestis (bubonic plague, may have created genetic bottlenecks); Mycob. tuberculosis, still big problem esp with drug resistance emerging; Plasmodium spp if you aren't sticking to bacteria, malaria is still a big killer; Bacillus anthracis by way of nutbag domestic terrorists; Bacillus thuringiensis by way of GM crops; E. coli for giving us EcoRI etc, I think those were the first restriction endonucleases to be discovered; Thermus aquaticus for Taq polymerase, PCR has had a huge impact on research... - Bill Hooker
However, I'm looking for microorganisms that changed our lives in a good way. Sorry, I should have made that explicit. - Ricardo Vidal
I would say P.infestans - killed million of people in Ireland in the beginning, and made the Kennedy family to move in the US. This an many similar examples nicely written in this book http://tinyurl.com/3httqh - Ntino
Rhizobium, Agrobacterium, etc -- nitrogen fixing, which no other organisms can accomplish (?); cyanobacteria and phytoplankton, fix half of the C02 in the carbon cycle -- these are groups not individual spp though - Bill Hooker
@Bill, keep them coming. Great stuff. - Ricardo Vidal
Human Immuno-deficiency Virus (HIV) , Epstein Bar , E.coli (as mentioned) , Plasmodium malariae ....... - enigma
I saw your comment later . I mentioned some hurmful ones - enigma
E coli is having a great positive impact in my life, right now! - PauloNuin
If we're including viruses, smallpox (massive death toll plus birth of vaccine science through vaccinia) and influenza (the quiet killer -- tens of thousands every year, pandemics killed millions), rhinoviruses and coronaviruses (common cold -- still no @#$%^!! cure!), HPV (e.g. HPV18 (not sure of number?), Ms Lacks and a callous disregard for informed consent gave us HeLa cells, the beginning of cell culture and an ethical black eye for our profession) - Bill Hooker
I would argue e.coli has a huge positive impact because it's used to make recombinant DNA, to produce vaccines and antibiotics, and all sorts of bioengineering applications. How about beneficial soil microbes like bacillus subtilis? - Shirley Wu
Helicobacter pylori and the link to gastric ulcers and cancer (both gastric cancer and lymphoma). Antibiotic treatment can now prevent (some) of these diseases. - Martin Fenner
Hasn't he asked for a list of microorganisms that have a positive impact in our lives? - PauloNuin
Lots of examples in the food realm including the already mentioned Saccharomyces for bread and beer. Penicillium roqueforti for blue cheese. Aspergilllus oryzae for soy sauce. Aspergillus niger is used to make Citric acid. - Jason Stajich
A prediction, then: human commensal flora have yet to make their mark, but when we start to really understand how our bodies (~10^13 cells?) interact with their microflora (~10^14 cells?) it will have dramatic consequences for medicine. - Bill Hooker
To add to Bill's comment, if viruses are included, live poliovirus vaccine. Huge impact. Only a few (like 7) nucleotide changes in its RNA genome between paralytic wild-type and vaccine strains, and those revert in the vaccinees. - Maureen
Bill beat me to it with the groups. It's hard to go past the nitrogen fixers, denitrifiers and cyanobacteria for sheer impact (on atmospheric composition). As for viruses - technically not micro (more like nano) and in my book, not organisms, but rather complex macromolecular machines. - Neil Saunders
Some great stuff here. It seems that it's way easier to name microorganisms that have done (a lot of!!) harm than those that have done, or are doing, good. How about microorganisms that are doing good but not yet on a global scale? (Ex: engineered Deinococcus radiodurans to clean up nuclear waste) - Ricardo Vidal
not really. I find the deepak/neil tech news aggregator service pretty reliable. The algorithm seems pretty robust to variation in input quality - Cameron Neylon
via fftogo
not really. I find the deepak/neil tech news aggregator service pretty reliable. The algorithm seems pretty robust to variation in input quality - Cameron Neylon
via fftogo
not really. I find the deepak/neil tech news aggregator service pretty reliable. The algorithm seems pretty robust to variation in input quality - Cameron Neylon
via fftogo
That's a generic question. Which ones are you thinking of specifically? - Louis Gray
Cameron, not from the science end. There we're doing quite well, but the tech world just gets to be a bigger echo chamber than ever. No wonder that I spend so much more time on hacker news than on techmeme. - Deepak
Louis, don't want to mention any specifically, but there were a bunch that I read regularly in my feed reader. These days I either find the topics aren't compelling or the writing isn't just as good (too much dilution perhaps). - Deepak
Deepak I think there just hasn't been any good tech news lately. A lot of it has been pretty boring. - Jesse Stay
via twhirl
Jesse, that's probably true. Explains some of the lack of interesting material. Also feel though that most of the big blogs have added so many writers they're just writing to make up the numbers, so when there is nothing interesting to write about those who are not good writers get shown up - Deepak
Its a great soundbite - I also like the fact that incremental is key - it implies the need to re-aggregate the bite sized chunks into bigger pieces - Cameron Neylon
I know that there are major hurdles to biological sample shipping into/out of Aus. As soon as you spit, it's a biological - Chris Cotsapas
Right - it may well be our tough quarantine laws. - Neil Saunders
It's possible it's quarantine, but I somehow doubt it since they are more strict about stuff coming into Australia than going out. I guess I should just email them ... (particularly now that the price has dropped, I'm seriously thinking about buying the service, just out of pure curiousity). - Andrew Perry
I emailed and got a quick response:
"Thank you for your interest in 23andMe's services. We are currently offering our service only within the United States, Canada as well as European nations. We hope to expand to more countries including Australia very soon. Please stay tuned and we look forward to having you join our global community." - Andrew Perry
That's good to know. I am quite tempted myself. - Neil Saunders
Followup: Australia now appears to be on the list ! $399 + $ 70 for shipping both ways. - Andrew Perry
Ooh. Can I justify that? Christmas is coming... - Neil Saunders
Find myself wondering if these stats should form the basis for choosing "bursty collaborations most likely to succeed" - Neil Saunders
Definitely gives you an idea about the kinds of people you might want to use if you want to discuss some thoughts and ideas - Deepak
It would be nice to be able to slice and dice by subject. I'd also like be able to pivot onto the FOAF graph and navigate between the charts for different people to find the collections of people in specific networks. - Cameron Neylon
In theory not that hard, at least that last bit. All you need is the RDF :) Unfortunately FF doesn't seem to do that any more. - Deepak
Photos of kittens dancing to old school hip hop while eating bacon/mango sandwiches & discussing noise & signal in our feeds with new Manga avatars to display how great we all look. - Mark Wilson
Talking about the day Bush is out of Office and Obama is in! - Mathew Ballard
Bonfire Night. It's Nov 5th - lots of fireworks :-) - Sally Church
ranting about work, or whatever ills you - Susan Beebe
Intelligent discussion about something other than the idiots running for prez. er I mean Vice Prez. - Gina K
"running commentary about the transition process and hilariously indignant outrage about how the public won't stand for <insert cabinet pick here>" - Mark Trapp
