By conventional photolitography, Sokolov and colleagues from Argonne National Laboratory, report on PNAS the design of microscopic gears (6 ug mass) able to extract useful work from swimming Bacillus subtilis. According to their calculations, few hundred bacteria work together in order to turn the gear at a velocity of 1-2 rpm, generating femtowatt power.
- Iddo Friedberg
from Bookmarklet
Comment posted on Blog: You say, "Here the concept is that brownian motion can generate directed motion..." I'd say it's not Brownian motion that is creating the directed motion...The bacteria actually have flagellar motors that propel the bacteria. So the bacteria provide the energy (via ATP). Non-swimming bacteria (which would undergo Brownian motion) would not propel the gears, as I...
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- Steve Koch
96well's response: "Yes, thanks. Bacteria are swimming (and not floating) because of flagella, and yes: ATP and not real Brownian motion is responsible to the movements. I feel sometimes 'brownian motion' is used (non very properly) to describe bacterial motility just because the linear trajectory operated by the flagellar motor turns rapidly into new directions with a pattern which...
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- Steve Koch
The Brownian thing made me think: is there any demonstration of behavioral swarming in microbes, the kind we get in locusts, bees & college students?
- Iddo Friedberg
I'm like the author of the article, but sometimes I wonder if I would be better off being the other way.
- Ruchira S. Datta
I don't see the need to make value judgements. Some people get deeply into a narrow field, some people cross-pollinate; both "styles" have their strengths and uses.
- Bill Hooker
Some of us are into science, even if we aren't practicing it, so generalizations are difficult. But I do think our system is at a crossroads. People who are passionate about science don't always have avenues for that passion, or at least think they don't
- Deepak Singh
Error level (near 0%) for SwissProt looks interesting. People of protein-protein interaction data claim 2-9% error rate on manually curated sets, and the same level I would expect from SP. Some things are better than I thought ;).
- Pawel Szczesny
Not too bad, but I think its even worse than they do. And evidence codes won't fix this. Manual curation and standards for automatic annotation are in dire need of a revolution, and even if we get that it'll still take years to fix.
- Paul J. Davis
@Paul How would you revolutionise it if all the data is still contained in the relatively unnaccessible journal article?
- Frank
Trust Pawel to see the half full (or 60% full) part of the glass. I agree with Frank though: it is not feasible to go through NR and fix the annotations manually. We just have to accept that NR, TrEMBL and KEGG are (mostly) over-annotating, and remember that when we rely on them when delving into the protein family level.
- Iddo Friedberg
Thanks Iddo. I lost count of how many times annotation errors came up in my discussion with experimentalists who lack experience with such databases. (Not surprisingly, they usually think these errors are negligible, especially when it comes to THEIR proteins.) Now I'll just send them a link to your post...
- Mickey Kosloff
Ask TLS: I vaguely remember a case where some closed-access publisher requested that figures reproduced from a paper published in one of its journals be removed form the author's website. Might have been Science but I am not sure. Anybody has a link?
#smallworld Which reminds me that I must chase up the lead Author of a Paper, nay, Manuscript that Shelley, I and two others have yet to finish and submit to BMC. Prof AG in Milan will be hearing from me soon !
- Graham Steel
yeah ... I never thought about fake structures. I wonder how exactly was fake about them.
- Pedro Beltrao
Built a plausible homology model and shake a bit I would guess...you know of course what will happen now when we discover someone has faked genomics/proteomics data? Omics-gate! The two most overused cliches in media and science finally united together!
- Cameron Neylon
thanks Steve .. at quick glance the common name seams to be last author in many of the papers ... that is even weirder.
- Pedro Beltrao
A posting Kevin Karplus to the pdb-l (possibly) expanding the list to 1bgx 1ay1 1hef 1heg 1sbg 1hps 1hos. Also, it seems that RosettaHoles which assesses core packing did not like 1bgx (it's in the RosettaHoles paper, linked from Kevin's posting. https://lists.sdsc.edu/piperma...
- Iddo Friedberg
From the RosettaHole paper (published online 2-DEC-2008): "Eight of the outliers, (checking for anomalous core packing, IF) (PDB codes 2A01, 1BEF, 1RID, 1Y8E, 1BGX, 1G44, 2QID, 1G40) are from the Murthy group.[9]"
- Iddo Friedberg
What is strangest to me about this story is how did a supervisor get all the other authors to go with the fake results ?
- Pedro Beltrao
"I’ve gone back to using another wonderful visualization package, PyMol. I find that it hits the sweet spot between easy setup of the scene I’d like and generating nice figures. The specific feature that I’ve come to rely on quite heavily is the built-in ray tracer. There are three available ray tracing modes in addition to the default, each of which has its uses. Mode 1 will place a black outline around your structure, which can help make the secondary structure elements visually distinct. Mode 2 is really interesting, in that it only renders the outline. I find this especially helpful if I want to show something in an overlay without obscuring what is behind it. Mode 3 produces “quantized” color in addition to the outline, giving your figure a very cartoonish appearance. I find that this one has to be used with care :) "
- Mike Chelen
from Bookmarklet
Not entirely surprising, but hey, that's part of what membership is for.
- Mr. Gunn
Have there been any articles contributed by members that had open peer-review included? That would be very cool & seems like the supplementary online material could support publishing the manuscript versions along with referee reviews. Given that there's no risk the article would be "rejected," this seems like a really great mechanism for testing open-peer-review process. And I'd think that there has to be at least a handful of academy members who'd enjoy trying this out.
- Steve Koch
Unfortunate that the bill did not pass. How others could listen to this eloquent, funny, well-reasoned, and impassioned speech and not see the validity of the arguments is beyond me - unless, of course, 1) they weren't even listening, or 2) reason doesn't factor into it. Sadly, both are probably true.
- Shirley Wu
I like the BMJ numbers. There is hope for more uptake of comments on papers.
- Martin Fenner
I should note that the data for each publisher are not exactly comparable. For PLoS, I looked at articles with the all-time most comments (data courtesy of Pete Binfield). For BMC, I looked at the most highly accessed articles in the last 30 days (with a brief glance at the all-time list for a sanity check), though I also had a short list of all-time most commented articles (data...
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- Shirley Wu
What can BMJ and PLoS do to get audience for the comments? Seems like there's no shortage of opinions on papers, rather it's a questions of where those comments are left. People tend to speak to where they have an audience, so maybe there's a way to indicate what level of audience the comments have?
- Mr. Gunn
@MrGunn, that touches on a good point - that leaving comments at journal websites is rather cumbersome, requires a login, etc, and so many people don't bother (see RPG's post:http://blog.f1000.com/2009..., more commenting might be happening on FF, Twitter, on other blogs, because it's more convenient.
- Shirley Wu
from twhirl
Yep. which brings us right back to where we were earlier this year with author identifiers needed to be able to aggregate things left all over the web. My take is that we can bootstrap an audience by aggregating content through whatever imperfect means we have at our disposal now, and when we have sufficient content, and it's discoverable, the ball will start rolling on this. I try to...
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- Mr. Gunn
It's kinda like the situation with Genbank accession numbers.People didn't start providing them until journals started demanding them, which they didn't start doing until the proliferation of sequences scattered around everywhere became a problem.
- Mr. Gunn
It's not just author IDs though. If we want this taken seriously we probably ought to include dois in these conversations as well. Need to uniquely identify both author and paper.
- Cameron Neylon
I've been reading OkTrends for a while now. I love it. Of course, remember that OkCupid was founded by some pretty bright math students, so it stands to reason that they'd geek out over those kinds of statistics. I know I do!
- Christopher Granade
Yep, this blog is great. Thanks for reminding me to check back in with it!
- Meg v. Meg v. 1.0.0.1
I'm just looking through the back catalogue of posts. Wow. There's certainly all kind of sample bias there, but still, wow.
- Michael Nielsen
Oh, yeah. Not at all rigorous, but interesting nonetheless. Definitely suggests to me that someone could write quite a few good papers on detailed studies of these kinds of effects.
- Christopher Granade