Fancy electron microscope…
…uses a game controller to manipulate the internal robots. Ha!
For instance, I’ve enjoyed shooting the beam through tonic water and seeing the fluorescence from quinine. Here’s some total internal reflection:
Any other ideas for cool “experiments”?
(Note, please be careful with this or any laser pointer. Although the purple light emanating from this pointer doesn’t look bright, it can damage your eye or skin. Even if your eyes aren’t sensitive to 405 nm, that doesn’t mean they can’t be damaged by 405 nm. This pointer is dangerous to be viewed even in diffuse reflections.)
(P.S. The sorta shitty photo credited to E.Y.L.)
UPDATE: It turns out that urine is also fluorescent:
Especially after taking a multivitamin.
UPDATE: My friend on Facebook pointed out that Figure S5c in the supporting info is even more fishy (click on the image below to see a zoomed-in version). Clearly, some portions of the image were pasted on top of other parts. On the right, it is obvious that the top part of the image is from a different frame as the bottom part. On the left, it looks like there’s another image hidden behind (see the strip showing through on the left top part of the image). I’ve added red arrows to aid the eye.
This could possibly be mistakes by someone who doesn’t know how to use Photoshop layers, but I’m thinking there might have been some intentional manipulation of the data. Either way, this type of slicing and stitching and Photoshopping of scientific data is totally unacceptable. I think Nature editors and referees should be more than ashamed to have let this slide.
Nature editors announced that they are investigating.
(Original post below.)
This paper in Nature contains some serious errors: some of the images that are purportedly from different samples (different mice, even) appear to be identical! Note the triangle of spots in the two images below:
Many commenters have noticed the weirdnesses in the figures. This is my favorite comment so far:
2011-04-22 09:31 AM aston panda said:
This is an excellent article shows extraordinary .. skills and amazingly repeatable data. for example
Fig.1a, 2 middle vs 3 bottom left
Fig.1c, 2 right side vs 3 left side
Fig.S4, 1 left side vs 2 right side
Fig.S5, c4 middle right vs e4 middle left
I suspect that some sloppy organizing by the authors led to them mixing up some files on their computer. That’s my optimistic view. If they were trying to fabricate data, they wouldn’t use the same region of the same image of the same sample! It must have been sloppy bookkeeping. I hope their results stand up after they correct these errors.
It just goes to show that real science can’t get accepted into Nature and Science. ;)
UPDATE 2: RetractionWatch is surprised that this paper eventually was published with only a correction!
Any cyclist knows that the left bike pedal is left-hand (i.e. reverse) threaded. This is so the pedal doesn’t unscrew itself while you’re pedaling. But go grab a bike and spin the pedal and crank around and you might be a little confused. Last time I did this, I thought, Wait why isn’t the right pedal reverse threaded? When you spin the pedal and crank forward, as if you’re actually powering the bike, the effective spinning of the pedal around its axle (AKA the spindle) should actually unscrew both pedals: lefty-loosey on the right pedal and righty-loosey on the left. Did every bike manufacturer get this wrong?!?
Of course not, and the real answer blew my mind. (Probably because I’m not a mechanical engineer.)
It is not, not mind you, because of the effective unscrewing force from the non-zero friction of the ball bearings. Instead, it is an effect that works in the opposite direction (in this case): mechanical precession:
“Precession is the process of a round part in a round hole rotating with respect to that hole because of clearance between them and a radial force on the part that changes direction. The direction of rotation of the inner part is opposite to the direction of rotation of the radial force.”
The source of the screwing/unscrewing force is thus radial on the spindle—the downward force you put on the pedal—instead of the twisting force from the ball bearing friction. This radial force translates into a screwing/unscrewing force because there is a small amount of clearance between the spindle and the threaded hole in the crank. I picture it like a pencil in a toilet-paper tube: crank the end of the pencil around, and there is a force that wants it to rotate on its long axis (from friction with the wall of the tube).
The screwing force from precession (on a reverse-thread on the right pedal) is much stronger than the unscrewing force from friction of ball bearings, so bike manufacturers ignore the latter.
I wish I could find an animated gif of mechanical precession, but I haven’t found one. Anyone have a book on “advanced thread theory” and want to make an animation?
UPDATE: Here’s a nice animated figure from Wikipedia:
Before the Spring meeting has even started? This is not cool.
It’s almost impossible to actually find out, but the deadline for submitting an abstract to the ACS Fall meeting in Denver has already passed. This is how I tried to find out:
First, I went to the ACS website, and clicked on the “Meetings” tab. The Fall 2011 meeting isn’t even listed there (see screenshot on the left). OK, that’s silly.
Next, I searched “deadline” from the ACS homepage and clicked on the top link, “Events & Deadlines.” That brings me to the Events & Deadlines page. Where the Denver meeting doesn’t even have a link. The Anaheim meeting’s link is live, but you can’t click on the Denver meeting. OK, maybe that means the deadline is so far away that you don’t need to worry about it. Wrong. Apparently, the Events & Deadlines page is only for past deadlines. Why have a deadlines page only for past deadlines?!? Wouldn’t future deadlines be a bit more helpful? I guess, the “Events & Deadlines” page is more a shrine to the deadlines you’ve already missed, not intended to help you meet future deadlines.
OK, let’s try going directly to the Denver meeting homepage. Not a lot of info there. But it turns out that, if you click on the symposia link, you’ll find that many of the deadlines have already passed!!! And the Spring meeting hasn’t even started yet! (There’s also this strange PDF I found somewhere on the ACS website; it list different deadlines.)
That really, really sucks. I feel like, with all the stupid emails I get from ACS every day, I’d have seen this deadline coming. I suppose it’s all my own fault: I should have been paying attention. But I figured that the deadline for the next meeting wouldn’t be before the current meeting starts. And I do blame the ACS website: I’ve been looking at the “meetings” tab for info on Denver, but it isn’t even there yet.
My suggestion: Why doesn’t ACS have one deadline for all the divisions, have it after the current meeting is finished, and actually announce that deadline on their webpage?
I am annoyed.
Harvey, A.; Zukoff, S. Wind-Powered Wheel Locomotion, Initiated by Leaping Somersaults, in Larvae of the Southeastern Beach Tiger Beetle (Cicindela dorsalis media). PLoS ONE 2011, 6(3), e17746. http://dx.doi.org/10.1371/journal.pone.0017746
Escape mechanisms in the animal kingdom can be pretty cool. Or just downright entertaining. This little guy does a somersault, grabs his tail, and rolls away in the wind (see Video 1). Check out Video 4 for a slo-mo version.
DOI is magical. Why is it taking so long for the same thing to happen with authors? Arguably, having unique author IDs is more important and helpful than document identifiers. Yet it’s 2011 and there’s no standard way to ID an author.
Thompson has it’s ResearcherID, but it hasn’t really seem to have caught on. And it’s certainly not a open or universal standard, given it’s based off of ISI. ORCID seems to be (slowly) working on a solution to that. NIH claims that it’s working on a Pubmed Author ID project, but what’s the holdup? Hasn’t the problem of multiple authors with the same or similar name been recognized for years?
There must be some technical and economic hurdles that I don’t quite understand. DOI seemed to arrive on the scene pretty early after the internet started becoming mainstream. That was a few years ago.
Here’s why I disagree:
- OOL research is not (directly) practical. Studying OOL won’t directly result in new technologies, products, or cures that the public can use. I prefer the Deutch and Whitesides approach. There are more pressing challenges that chemists can contribute to solving (cancer, disease, chemistry of biology, global warming, alternative energy sources, etc.). OOL comes across as an intellectual pursuit for armchair chemists.
- OOL is politically, emotionally, and religiously charged. The last thing we need is idiots trying to cut chemistry funding because their faith says something different than the science. Studying OOL is the perfect way to offend a bunch of folks and make the field of chemistry a target of religious nuts. I don’t think we should guide our research on what religious nuts want, but why kick the beehive?
- OOL is basically unanswerable. We might be able to test theories of the OOL, but we won’t be able to observe the true origins of life on this planet. Until we invent a time machine. That makes OOL research speculative and uninteresting to me. And even if we could find out, who really cares? Will that change our day-to-day life? OOL seems like more of a religious question than one of science.
Of course, some chemists should work on OOL. Just like some physicists should work on counting the number of alternate universes. But I don’t think chemistry as a whole should devote a major portion of its efforts to the “big questions” like OOL and what the universe was before the Big Bang. Chemistry is a practical science that answers questions about our everyday life. Let’s harness that power instead of trying to be as “cool” and big-question oriented as physics.
There. I hope I offended everyone who works on OOL. :)
P.S. Harry Gray and Jay Labringer have a recent editorial in Science stating that the Big Questions in chemistry are harder to see. They suggest understanding photosynthesis as one of those Questions.
My favorite is still Papers. It’s clean and simple and beautiful. It works awesome on my iPad: reading PDFs is more enjoyable on the Papers iPad app than on my laptop. Syncing to the iPad over wifi is simple and practically bug-free. Syncing libraries between my home and work computers is also possible by putting the Papers folder in Dropbox. (Although Dropbox syncing isn’t technically supported by Papers, many folks use it to sync across computers. I’ve been doing that for half a year without a problem.)
The major downside with Papers is that it works only on Mac OS. Papers2 is now on Windows, too. On my PC, I use Mendeley. Mendeley is nice because it is free and has native syncing to the web and between computers. The reason I’m not completely sold on Mendeley is that it’s just not as clean as Papers yet. Mendeley is not as buggy as it was a year ago, but it still doesn’t seem to find metadata as well as Papers. But, if you’re starting from scratch, Mendeley is a great option. (Edit: And I like the syncing to iPad/iPhone that Papers offers.)
And now Papers2 was just released! Honestly, Papers2 is a little disappointing, so far. But I suppose I was expecting a lot. But I still have high hopes for it. The support staff is working very hard to fix bugs and add functionality that users are screaming about on the discussion boards.
Some of the cool features of Papers2 include:
- A quick way to add citations to Word (or any other application on your Mac) directly from Papers
- Easier keyword tagging
- Automatic metadata importing (although I haven’t seen this work, yet)
- Linking supplemental info to the paper it corresponds to
- Searching multiple databases (e.g. Pubmed and arXiv) simultaneously
The automatic metadata grabbing might be nice, if it ever works. Mendeley tries to do that, too, but I’ve never been impressed. I really liked that Papers1 made manual matching easy (by highlighting the DOI, for instance). The new interface and searching mechanism seems much clunkier in Papers2, and the support staff has already acknowledged as much.
There are several other issues, that make Papers2 feel very beta. Given that it’s brand-new, that’s not exactly surprising. But Papers1 was so refined, that Papers2 seems very clunky in comparison. But I think Papers2 does have a lot of potential.
For those worried about trying Papers2, have no fear: the new version doesn’t overwrite your Papers1 data and PDFs, so you can use both versions side-by-side until you’ve made up your mind. During the 30-day free trial, for instance.
For the Mac, Papers1 has been the cleanest, coolest, and bestest PDF organizer. Hopefully Papers2 cleans up nicely and becomes my new favorite. But right now, Papers2 is not clean enough for me to recommend anyone using Papers1 switch over to the new version.
UPDATE: In the last two weeks, Mekentosj has provided two updates to Papers2 that have made it significantly better. Papers2.0.2 has fixed a lot of the bugs and annoyances in the version I reviewed above. For instance matching is much much better. Like I expected, the folks behind the program are working really hard to make it the best program, evar!
UPDATE2: I use Papers2 daily and I love it. It still has some things on the wishlist that I look forward to, but I think it’s a great program. I guess it just had some bumps at the beginning.
UPDATE3: Papers2.1 is now out at better than ever. Definitely better than Papers1. I can recommend without hesitation that you get this software!
UPDATE4: A bookmarklet for JSTOR.
Red: You either don’t really care if anyone can see what you’re pointing at or you’re cheap and you use the free pointer you got from a vendor at the expo. Of course, you could be one of those considerate folks who buy very bright red pointers, because you stubbornly like what red looks like even though human eyes are not sensitive to 633 nm. That’s fine.
Green: You want your audience to see what you’re pointing at. Unless you bought a 5+ mW laser (either because you’re showing off or because you didn’t realize how sensitive the human eye is to 532 and bought the brightest laser you could find). In that case, you’re blinding your audience. If you’re going to get a 5 mW laser, get it in red. That’s classy and visible!
Blue: You’re a bad-ass. You don’t care that blue lasers are more expensive and slightly harder to see, you want the audience to know that you’re a real laser jock. (Or maybe you’re worried about leaking 1064 nm from green laser pointers.)
Purple: You’re so bad-ass you’re crazy. You don’t care that the human eye can hardly detect and can’t focus on 405 nm. You want to show that you support Blu-ray.
Yellow: You think blue lasers are soooooo 2009.
Invisible: You have a UV or IR laser pointer? Maybe a tripled or undoubled Nd:YAG? You’re nuts.
Maser pointer: I want one.
I’ll be in Baltimore Saturday-Wednesday for the Biophysical Society meeting. If you’re going to be there, leave a comment with your poster or talk number and I’ll try to swing by!
A (grad?) student walked into a seminar lecture, went up the the speaker in mid-sentence, and said, “Sorry to interrupt, but can I borrow some chalk?”
Everyone in the seminar room started chuckling at the kid. It was strange and awkward.
What a dumdum.
UPDATE2: OK, it turns out that the daily(ish) email isn’t too terrible. I now use it and I’m no longer upset that they don’t have an RSS feed. I correct myself and now fully endorse F1000!
Faculty of 1000 is extremely powerful with a lot of potential, but simultaneously completely worthless.
F1000 is like mini-peer-review post-publishing: it uses its “Faculty,” experts in various fields, to rate publications that those experts think are worth reading. It’s like … nay, it is … getting suggestions on what to read in the recent literature from a large group of experts. That is very cool. Of course, there are various databases like Cite-U-Like and Mendeley that are trying to mine their data to find interesting papers, but there’s something great about getting little mini-reviews from actual people.
OK, so why am I annoyed? F1000 doesn’t have an RSS feed! So I have to remember to go and check the website every week. Even if I happen to remember, there’s no way to mark which reviews I’ve already seen and the new ones. What is this, 2002?
UPDATE: rpg comments below with some good news: F1000 is actively trying to get RSS on the site. The comments also explain why it’s a challenge. I eagerly await RSS.
Before I say anything, I have to clarify that I am not a tax expert. Don’t listen to anything I say.
OK, taxes for grad students and postdocs can be complicated, especially dealing with fellowship stipends and tuition reimbursements.
Tuition and the 1098-T
The way Stanford sends 1098-T forms is via some really sketchy website 1098t.com, run by Affiliated Computer Services. They send the most spammy looking emails I’ve ever seen:
But it’s not spam. The 1098-T is basically worthless for grad students whose tuition is paid for by their PI or their department. In those cases, the students can’t claim the tuition on their taxes, because they didn’t actually pay it. In general, the “Amounts billed for qualified tuition and related expenses” box should have a very similar number as “Scholarships or grants”, but they may be significantly different if the department ends up paying your tuition in a different year than it’s billed. If you just input those incorrect boxes into your favorite tax software, it will calculate that you have a tax burden or deduction. That’s not correct. (Of course, those should cancel out over your entire grad career, because the department’s payments made on the prior year’s bill will eventually catch up. But it’s simpler to just report what actually happens, not what the 1098-T thinks is happening.)
I think the best thing to do is ignore the 1098-T. Instead, add up all the bills you get from the university that year, and add up all the payments to the university from your department, and report the difference that you actually paid. The difference should be what you actually paid: the fees billed directly to you and not reimbursed by the department. This will be a small number, and probably won’t affect your taxes. Keep those documents in case the IRS comes calling!
The most risky thing to do is claim that you paid tuition that you actually didn’t. I suspect that annoys the IRS. (Of course, this will be different for grad students who actually pay tuition. The Hope or Lifetime Learning credits are designed for those folks.)
Is a Fellowship Self-Employment?
Generally, the answer is no. And that’s a good thing, because you have to pay a 13.3% self-employment tax if you are self employed. Postdocs and grad students on fellowships may not be “employed” by their university, but they are not exactly self-employed, either. The way it’s been worked out, students and postdocs on fellowship generally pay their own income taxes (the university doesn’t take out taxes from their paycheck) in estimated taxes, but don’t pay the extra self-employment tax.
Do Postdocs Pay Social Security Taxes?
This question is more complicated. Students don’t have Social Security taxes (officially called FICA) withheld from their paychecks. But are postdocs “students” in the eyes of the IRS? Currently, they are. Universities usually don’t withhold FICA from postdocs’ paychecks. (Sometime, grad students have FICA withheld during summers, usually if they aren’t charged tuition and are paid as employees for the summer.)
There is some disagreement around this, and the IRS may start asking for Social Security payments from universities and postdocs. For instance, medical residents just lost a case against the IRS; now they have to pay Social Security taxes. It makes me wonder if postdocs will be next.
Check it out: azmanam has a new version of the chemistry dictionary for Word:
Now you can eliminate all those red squiggly lines under half the words in your document.
Prof. Royce Murray’s recent editorial in AC is fun. I actually do find these type of sarcastic instructions for writing a paper helpful. To an extent. These devices are great reminders of the essentials to making a paper readable. I might find even more helpful a template of a paper that tells you what each paragraph and caption should say. Maybe I’ll make that someday for teaching purposes…
My fav line is: “Diagrams are worth a thousand words, so in the interest of writing a concise paper, omit all words that explain the diagram, including labels. Let the reader use his/her fertile imagination.”
Another anti-suggestion from Royce is: “It should be anathema to use any original phrasing or humor in your language, so as to adhere to the principle that scientific writing must be stiff and formal and without personality.” Which reminds me of this line from an old Chem. Rev. paper: “Evans boldly put 50 atm of ethylene (C2H4, trans-C2H2D2, or C2D4) in a cell with 25 atm of O2. The apparatus subsequently blew up, but luckily not before he had obtained the spectra shown in Figure 8.”
P.S. I see that CBC scooped me on Royce’s editorial!
I found this awesome old lab notebook in my lab.
The owner of this notebook had amazing taste! Apparently, he loved dinosaurs and liked to “work it.”
That made me smile today.
That’s very pure EDTA:
Nature Jobs has encouraged folks to spread the word of their failures, as well as their successes. So I made a CV of my failures. I’m probably forgetting a lot of failures, but I’m not really motivated to spend a lot of time trying to remember. Anyone else want to air their dirty laundry?
So why is gold valuable? NPR’s Planet Money has a fun podcast exploring the chemical reasons that humans value gold as a currency. Prof. Sanat Kumar goes through all the elements on the periodic table, and explains the reasons that each element couldn’t be a currency. For instance, lithium can be explosive when exposed to air, noble gases are really hard to keep in your pocket, silicon is too abundant, etc.
The podcast concludes that it was inevitable that humans would choose gold as currency. Cute.
Some profs at UCSF have concerns about the radiation dose of backscatter scanners, specifically that all the energy is deposited in the skin instead of being spread throughout the entire body. So the dose is concentrated in time and volume. Basically, it sounds like TSA hasn’t done enough safety testing on these machines.
I would like to see a risk analysis of the probability of the screening causing cancer vs. the reduced threat of airline passengers dying from terrorism. The problem is that all these are very low probability events.
Anyway, this is my response to the entire fiasco: http://www.youtube.com/watch?v=wRpWnK6Rg3E
The best one I found was on Steve Boxer, mostly because of the photo and caption:
And several articles on Zare, like this one.
History is fun.
UPDATE: A quaint story about a growing department at Stanford.
Also, a cool pic of my old building, from 1961! That building still has those same windows.
Today my labmate suggested someone start the Journal of One Try. It could have two sections per issue: “worked” and “didn’t work.”
JOOT would be dedicated to publishing scientific experiments tried only once. It would be an excellent resource for young graduate students to see if they should try an experiment (i.e. if it’s been published in the “worked” section) or try a different route (if it’s been published in “didn’t work”).
This is different than the Journal of Irreproducible Results: The results in JOOT would be reproducible … probably … just no one tried. Because it worked (or didn’t) the first time. Also, it wouldn’t be silly or funny science, simply experiments no one had the patience to try again. And this is different from the Journal of Negative Results, because many of the results would be positive. Well, once.
Maybe I’ll start that journal someday…
The strange thing is that, despite our suggestions otherwise, the Nature folks chose a not-the-most-interesting figure from the paper. Of course, I’m more than happy that they showed any of our awesome figures! But, instead of showing one of the super-resolution images that Hsiao-lu made, the highlight shows a proof-of-labeling image, which is diffraction-limited. That said, they did select one of the live-cell images. I suppose it could be worse: they could have picked one of the controls. Or not displayed a figure at all.
Thanks Nature. I don’t mean to look a gift horse in the mouth.
Well, I’ll highlight our paper here. And choose my favorite figure (it’s protein localization in a little-bity bacteria):
Postdocs at Berkeley (in fact the whole UC system) formed a union a few years back. Recently, the union negotiated a better contract with UC, which brings the postdoc pay up to … wait for it … the NIH minimum! That’s actually a big step. (Read more about it in Nature.)
- I can listen to Woody Guthrie without feeling guilty
- it supports a good cause: I do think that postdocs need someone looking out for their interests
- it is a relatively small amount of money to ensure that postdocs have representation
- it costs 0.28% of my paycheck to join (although that’s only around $100)
- my money might go towards those terrible political ads on TV
- the general possibility of making my relationship with my PI more adversarial
I’m conflicted. Thoughts?
For your Tuesday.
No that’s an oversimplification of his editorial. Actually, his worry is that science blogs are more fun and easier to read than real science journalism (which, by the way, is hard to find); meanwhile, bloggers have no required credentials, no accountability, and might just be lying to everyone.
UPDATE: In case it isn’t clear, Royce Murray is one of my favorite chemists and teachers. UNC is my Alma Mater, and I really appreciated his class. While most bloggers are pretty unhappy with Royce’s editorial, I wasn’t offended. I basically agree that neither the public nor scientists should be getting information from blogs without a grain of salt. Especially this blog. I’m sarcastic 83% of the time.
Hmmm. IVF but no The Pill. (Actually, I think that would have been a good split prize for Medicine. Would have been a big FU to the Vatican, though.)
Scotch tape graphene won the physics prize. Weird. Graphene is very new and basically unapplied as yet. But the Nobels are supposed to go to discoveries, and pulling graphene off of graphite with Scotch tape is a discovery.
And it was cross-coupling for chemistry (our #16 prediction): Heck, Negishi, and Suzuki. Oops, we mispredicted Sonogashira. I don’t know enough about organic reactions to know if this was the right move, but most folks are saying Negishi deserved it.
Congrats to all these well-deserving laureates! Hearts out to all those who were hoping for the prize this year, and didn’t get the call. (Especially Sonogashira, who must be pretty bummed right now…)
Read Paul’s liveblogging of the announcement.
Now just waiting for Twitter to win the Peace prize!
UPDATE: A guide to reporters by Chemjobber.
Or crazy swirling patterns:
For these awesome results, I’m awarding the authors an EDSEL for “Coolest paper (if it isn’t faked) of little filaments spinning around in circles of 2010.”
Not that I have any reason to think that these results are faked. They just seem so crazy and beautiful. Animated, even.
Some revealing letters of Francis Crick have been found—mostly to Maurice Wilkins—and they discuss Rosalind Franklin. Here are some of the excerpts that I found interesting. For instance, this letter from Wilkins to Watson and Crick after they proposed the double-helix model:
My dear Francis,
I gather you have got the coordinates of your model or some worked out. Do you think we could have a copy of what you have?
The crystalline data is clearing up nicely. To think that Rosie had all the 3D data for 9 months & wouldn’t fit a helix to it and there was I taking her word for it that the data was anti-helical. Christ.
We have redone a lot of the 3D more accurately on mouse & will need all the extra accuracy for dealing with some of the finer points.
Regards & to Odile too.
P.S. I think I have a flat.
But “Rosie” had been focusing on the A structure of DNA, which generated clearer crystal diffraction pattern images. Unfortunately for her, crystalline DNA-A wasn’t helical. Crick agreed when he eventually saw her data:
This is the first time I have had an opportunity for a detailed study of the picture of Structure A, and I must say I am glad I didn’t see it earlier, as it would have worried me considerably.
All in all, it sounds like Franklin was generally unfriendly to her colleagues (and competitors). Wilkins wrote to Crick of Franlkin’s leaving King’s College:
I hope the smoke of witchcraft will soon be getting out of our eyes.
It sounds like her colleagues didn’t like her too much. But there was friction from the beginning: Wilkins thought that Franklin was going to work for him … or at least they would work together on DNA … and Franklin had been told that she would work independently. What a mess.
I feel bad for Franklin having to deal with these sexist jerks. Watson and Crick were probably the most annoying, because they didn’t do any experiments; instead, they’d listen to Franklin (and others) present their data, then run off and make a model. Annoying. Intellectual thievery almost. (And Watson and Crick admit as much, referring to it as “burglary” in one of their letters.)
But on the other hand, it seems Franklin made some serious mistakes interpreting her data and was quite abrasive. No angels here. No devils (or witches?) either.
I suspect that if everyone had worked together and been friendly, Watson and Crick would have proposed the correct structure much earlier. Not only that, but I think Franklin would have been given more credit by the boys. But that’s just my speculation. I just know that I’d prefer to collaborate with folks than fight with them.
Phew. That was a long wait. Since 1995.
But the wait wasn’t really worth it. NRC released basically a gimungous table of data, and didn’t actually give departments rankings. I don’t have time to wade through all this data. Someone needs to tell me that my department(s) are better than Harvard.
To make things worse, their spreadsheet doesn’t work on MS Excel 2008 on Mac (only on 2004). Maybe I’ll update sometime if I can wade through the data. In the meantime, see if your school has posted its own analysis. (Berkeley has. It looks like Stanford is still in the process of manipulating the data to make themselves look awesome.)
Here are the top chemistry programs (ranked on research activity):
And programs containing the word “biophysic”:
So there. You can go make your own tables. I find this very confusing.
UPDATE: Not surprisingly, there are some serious errors being found in the piles and piles of numbers being released by the NRC ranking. And come to think of it, since when does Stanford chemistry have 50 faculty members??? Something is very wrong…
NRC should just list schools according to the US News and World Report rankings and keep their data hidden. jk.
This was on The Simpsons last night:
(the screenshot is from 1 min 22 sec on Hulu)
I may update my predictions to reflect the venerated opinions of cartoon writers.
By the way, seeing my PhD advisor and a member of my dissertation committee listed on The Simpsons feels really strange.
(My/our real predictions are here.)
I really think this is a joke: old-man baiting, if you will.
In response to the discussion on whether the word “seminal” is sexist as well as sexual, there are two points to be made, and I would also like to offer a potential solution. First, seminal carries forward the homocentric view of scientific research from a time when males were predominant and considered more important researchers in science. Consequently, it is a sexist term unless one is talking about physiological or related dynamics.
As for seminal being seen as a sexual term, I am not sure that we should necessarily eliminate all such terminology from the dialog in science just because it refers to “sexuality.” One need only look at the extensive literature that conflates birth sex with gender. The question “What is your gender?” is incorrect unless you are doing research on gender identity. The correct question is “What is your sex?”
Many individuals incorrectly conflate the word “sex” with sexuality. Consequently, numerous scientific papers, research surveys and discussions misuse gender as an equivalent to birth sex or natal sex in response to the aforementioned difficulty.
I propose the following solution, that I have used for years. When suggesting that a particular piece of research is “seminal” simply replace the word “seminal” with the word “seminovarian.” Everyone gets equal play. Of course, we could take up the question of which should go first, but that’s another letter to the editor altogether.
Tarynn M. Witten
I mean, this is getting hilarious.
But maybe this isn’t a joke. First of all, it turns out that the first letter was serious (see “Only Males Respond“). Also, this second letter makes be think that it’s from some liberal-arts student, mostly because it is terribly written. The rambling tangent on “sex” vs. “gender” is very academic, and I can tell that the author likes using the thesaurus: what “dynamics” are related to sperm physiology? Flagellum switching?
Maybe I should be more sensitive. I don’t like the fact that females have been second-class citizens (if citizens at all) throughout our history. But when it comes down to it, sexual references are funny. And I will giggle like a middle-school boy every time.
UPDATE: Oh shit. Dr. Witten is a bio prof at VCU. Which means she probably knows a lot more about dynamics than I ever will. Oops.
(In reference to How to tell if your rabbit is dead.)
Apparently, you can’t tell.
By the way, one of those organisms is my friend.
(source: “Evolution: What Is an Organism?“)
I was forced to update all my ACS feeds in my RSS reader (Google Reader). None of the ACS feeds I follow had updated for a couple days. I think ACS switched over to Feedburner and their old feeds stopped updating. Anyone else have this problem?
And TOC images seem brokenish with the new feeds…
UPDATE: Alex updated us on the issues. I’m happy that ACS is migrating to a better system. They really tried to redirect, but there are some problems. I think the new feeds seem to be working well now!
In previous years, I’ve awarded Edsel-Nobels, which no one really cared about. Maybe this is the year I’ll make predictions for the actual Nobel. Paul at Chembark already started his predictions, and everyone else will be buzzing about it soon enough.
In no particular order (and without much forethought):
- Solar: Grätzel
- Super-resolution optical microscopy: Betzig, Hell, Zhuang, Hess
- Cloaking: Pendry
- Birth control: Djerassi
- Laser-induced fluorescence: Zare
- Inorganic: Gray, Lippard
- Single-molecule spectroscopy: Moerner, Orrit, Rigler, Xie
- Chaperonins and protein folding: Horwich, Hartl, Lindquist, Ellis
- DNA fingerprinting: Jefferys
- Electrochemistry: Bard, Nocera
- Polymer synthesis: Matyjaszewski, Wang
- NMR and membranes: McConnell
- Discovery of kinesin: Sheetz, Vale, Brady
- Nano: Whitesides
- Peace: Twitter
- Cross-coupling: Suzuki, Heck, Sonogashira
- Electron Transfer in DNA/Electrochemical DNA Damage Sensors: Barton, Giese, Schuster
- Pd-catalyzed Alkyne/Alkene Coupling and Atom-Economy: Trost
- Nuclear hormone receptors: Chambon, Evans, Jensen, O’Malley
- Two-photon microscopy: Webb, Denk, Strickler
- DNA microarrays: Brown
- NLO: Harris (as predicted by The Simpsons)
So there. The only one I’m confident about it Twitter.
Please feel free to add more in the comments. I will probably continue to update this…
UPDATE: Paul now has updated odds. Very impressive. He’s put a lot more thought into this than I. I’ve added cross-coupling to the list. Additions are in italics.
UPDATE: Can you name all the Chemistry Nobel winners?
UPDATE: Thompson has released their predictions.
I don’t mean that if someone makes one mistake they’re gone, but if they consistently put themselves and others in danger, they should be fired. Or do theory.
Dangerous chemists are the ones who don’t know how to perform labwork safely, but think they do or refuse to ask for guidance. They are the ones that everyone else in lab knows is unsafe. They make the same mistakes over and over. They regularly work in lab alone. They don’t update their labmates about the dangerous compounds or reactions they are using.
Dangerous chemists are inconsiderate, put others at risk, and should be fired.
I started writing this a while back because I’d heard stories from friends about a chemist. His labmates are scared of his experiments because he was reckless, ignorant, and didn’t talk to people about what he is doing. He performed dangerous reactions on the work bench instead of the hood.
For instance, his labmates noticed that he was holding his breath while in lab, making adjustments to some reaction. When asked why he was holding his breath, he answered that the reaction produced dangerous fumes. So, instead of properly venting the reaction, discussing the reaction with his lab/PI, or warning his labmates, he just held his breath.
And yet this chemist was allowed to continue working in lab, even after many complaints to his PI and others in authority. He should have just been fired; I’m sure there’d be someone capable eager to take his spot!
I wasn’t going to post this, because it there were some funnier things to blog. But now the story of Preston Brown blowing off his fingers after grinding up 10 g of very explosive hydrazine. (The returned ChemBark also blogged this!) Now, I feel sad for Brown: he did not deserve to be injured, even if he was being reckless. But I also think that he should have been fired long before this accident occurred. It sounds like his labmates knew he was dangerous.
If there’s someone in your lab who you think is dangerous (who, if he or she blew up the lab, your first reaction would be, I saw that coming), do the following:
- First talk to him/her. Voice your concerns and offer to help train him/her in proper technique.
- Talk to your PI. State clearly that you are concerned for your personal safety in lab because of your labmate’s dangerous behavior. Make sure the lab has an SOP for every dangerous procedure in lab. And make sure the SOP is enforced.
- Talk to the authorities. If your PI refuses to make the situation safe, go to the department safety coordinator or the EH&S.
- Refuse to work around dangerous chemists. It’s not worth putting your life at risk. You’d have ground for a lawsuit if they fire you for refusing to work in an unsafe environment. (Hell, you may not even be covered by worker’s comp if the idiot hurts you!) Stand up for your rights: grad school is not a sweatshop.
- Document. Save emails and sent paper letters, just in case you need to sue. ;)
That said, I suspect that most things never have to go past step 1. I think most dangerous things done is lab are mistakes or lack of understanding of the correct protocols. Rarely, someone repeatedly ignores protocols and their PI’s instructions to intentionally perform dangerous experiments. But those rare instances is what I’m talking about. Those fools need to be fired.
I do want to note, Brown’s story is not final. Maybe it’ll come out that he was not as reckless as it seems from the C&E News article. In fact, it’s entirely possible, that he just wasn’t trained well enough. My point is that it is his PI’s responsibility to train him in safety, and fire him when he refused to be safe!
And I want to say again that he did not deserve to be injured. I feel really bad for him. A quote from the investigation transcript: “OK. Thanks again for coming to the house. I know. It’s a little more hassle. … I was left handed. I’ll have to be right handed now.”
UPDATE: Chemjobber has a nice post about why the faculty members bear some responsibility in the Texas Tech case.
UPDATE 2: AGAM has a post reminding us not to be too cocky in our safety knowledge. A good point: we all should regularly be boning up on our safety train, and communicating with our colleagues about best practices. Here are links to Prudent Practices and working with azides.
My (very nerdy) friends started a internetted-web-blog to celebrate/mock hilarious/terrible table-of-contents images: TOC ROFL. (In reference to NCBI ROFL.) I might even submit my own once in a while; you can too!
Senators McCain and Coburn (who is a physician!) released a political report complaining about stupid stimulus projects. Now, it’s not surprising that Republicans are calling for cutting science funding and mocking silly-sounding science, so of course there are several science programs funded by stimulus money that this report calls out. Here are a couple:
“A Better Way to Freeze Rat DNA”
[S]cientists at the University of Missouri received stimulus funds “to develop freezing protocols for epididymal rat sperm which would allow reconstitution of genetics by using standard artificial insemination and in-vitro fertilization methods.” The scientists note that “[o]ver the last few years, our laboratory has generated ample amount of data related with optimal sperm handling.
“Reducing Menopausal Hot Flashes Through Yoga”
“Weather Predictions for Other Planets”
“In a time when jobs are hard to come by, several high school and college students have gotten federal funding to inspire their scientific curiosity.”
OK OK, I understand that some of these seem silly, but when Senators start mocking scientific programs without acknowledging the broader context, those Senators come across as ignorant and foolish. The rat DNA one is especially annoying: Hehe, it says sperm! What, do they get middle-schoolers to write this stuff?
We could make any scientific project sounds silly if we wanted: Scientists try to send light down a tiny glass tube; federal government spending billions to develop satellites that will see where your phone is; some nut is trying to make a horseless carriage.
The point of gov’t stimulus is to get money flowing and jumpstart the economy. Most economists acknowledge that Federal spending has a significant multiplier effect, so spending money on construction projects, scientific research, and infrastructure isn’t really that silly. I can understand how some would question how studying rat DNA could make any money flow back into the economy, but those people would be forgetting about scientific-supply companies like Nalgene (originally of Rochester NY), ThermoFisher (of Waltham MA), Invitrogen (of Carlsbad CA), Sigma-Aldrich (St. Louis MO), etc. I’m sure those and many other companies that employ Americans are very happy about stimulus money going to scientific research!
Still, I do agree that these spending projects should not be beyond reproach. I’m not convinced that science funding is always the most efficient approach to stimulating a national economy in the short run. We should check up on our stimulus funding and try to measure how well each project is benefitting American taxpayers. But what McCain and Coburn have done is lazy—and ignorant. Instead of mocking science because it involves sperm or yoga (or even both), step up and take a mature approach to critiquing our spending policies!
OK, this really cracked me up:
“I’m currently being held prisoner by the Russian mafia penis enlargement penis enlargement and being forced to post spam comments on blogs and forum! If you don’t approve this they will kill me. penis enlargement penis enlargementThey’re coming back now. vimax vimax Please send help! nitip penis enlargement penis enlargement.”
NIST is warning us that some cheapo green laser pointers might be unfiltered and dangerous. Some manufacturers skip installing the IR filter, thus making a laser pointer that has a high-power invisible beam along with the green light.
The “green” of green laser pointers is 532 nm, doubled frequency of the 1064 nm emission from a neodymium (e.g. Nd:YAG, Nd:YLF, or Nd:YVO4) laser. A diode (e.g. 800 nm) pumps the neodymium laser, which emits 1064 nm light; a doubling crystal produces the green 532 nm light. But the doubling crystal is not 100% efficient, so an IR filter is necessary to block the remaining 1064 nm light that isn’t doubled (as well as block the 800 nm pumping light). The plot above shows how much 1064 nm light escapes if the filter is removed: it’s much more than the green light—if the 532 nm is 20 mW, the IR might be as high as 100 mW, certainly potentially damaging to the eye!
IR is especially dangerous laser light. First, it is invisible, so it is more difficult to identify and avoid stray beams. In this case, that’s less of a worry, because the green beam coaligned is visible. However, the second reason IR is dangerous is that, because it is invisible, you can’t tell how bright it is (see below). The final reason IR is dangerous is the biology of the eye, which is transparent to IR light, and focuses it to the retina (the nerves). IR can easily burn the retina permanently (causing blindness), or burn other parts of the eye or skin.
The simple method NIST suggests we can use to test our laser pointers is described in the announcement. Basically, they use a CD as a diffraction grating and a cheap webcam. The sensor of a digital camera is sensitive to IR light, but usually has a filter to see only visible; it is simple to remove the IR filter of a cheap webcam to make an IR sensitive detector. (Unfortunately, the sensitivity cuts out before 1064 nm, so the camera can only see the 800 nm pump light). The picture above shows the diffraction of the visible light with a normal digital camera; the bottom image is using the IR webcam. You can see the extra diffraction spots from the 800 nm light. Note also how much brighter the IR light is from the laser: even though you can’t see it with your eyes, it is very bright and dangerous.
By the way, my favorite line in the NIST report is the following: “The infrared light spreads out beyond the green, which could be injurious, for example, to a cat closely chasing a spot of green light.” Actually, that’s kinda sad: I hope the NIST folks didn’t discover this problem after they blinded their pet.
Fluctuations in a “cold” room I walked past.
That’s not good.
I was walking up Hearst near campus. I said to a friend, “Well, I never got into Harvard.”
A nearby hobo overheard me and said, “You didn’t miss much! Anyway, I chose to go to Princeton in the end.”
I now have a longer commute, with at least 30 minutes of quality reading time. I don’t really want to carry my laptop everyday, so I’m seeking a better way to read journal articles. I’m not going to print them out, so don’t suggest reading them on paper. :)
Of course, cost is a factor, but I don’t want to go for the cheapest option if I end up never using it! My guess is that the Kindle DX is the best for reading PDFs, but loses on other fronts (e.g. large, expensive, limited, only grayscale). The iPad is a versatile color reader and I can sync with programs such as Papers or Mendeley (soon for the latter), but it is very expensive. Also, the screen isn’t as nice for reading print. The iPhone is way too small to read PDFs.
Man, I need to test-drive these devices for a month!
I thought this TOC looked pretty awesome.
Jeremy over at Chemistryblog posted a few sites with info on academic lineage of many chemists. That inspired me to finish researching my academic genealogy. Kallie’s page at UT’s site was a nice confirmation of the lineage I had independently found. But I actually found links further back (through Rowland to Helmholtz, and eventually back to Leibniz’s dad); I’m not exactly sure why the UT page stops at Mendenhall.
I also explored my lineages from my undergrad and postdoc advisors. Interestingly, those two lines meet up in the mid-1800s (Liebig).
Anyway, below is the entire tree.
(I know this is a little self-indulgent. But whatever.)
Sam’s Academic Genealogy (via PhD advisor)
Samuel Joseph Lord
Postdoctoral research 2010- (under Jay T. Groves)
PhD Stanford 2010 (under W.E. Moerner)
BS University of North Carolina at Chapel Hill 2004 (under Sergei S. Sheiko)
William Esco Moerner (Stanford)
PhD Cornell 1982 (under A.J. Sievers)
BS Washington University 1975
Albert John Sievers III (Cornell)
PhD Berkeley 1962 (under Michael Tinkham)
BA Berkeley 1958
Michael Tinkham (Berkeley, later Harvard)
PhD MIT 1954 (under M. W. P. Strandberg)
BA Ripon College
Malcom Woodrow Pershing Strandberg (MIT)
PhD MIT 1948 (under A.G. Hill)
BS Harvard 1941
Albert Gordon Hill (MIT)
PhD Rochester 1937 (under Lee Alvin DuBridge)
Lee Alvin DuBridge (Rochester)
PhD University of Wisconsin–Madison 1926 (under Charles Elwood Mendenhall)
Charles Elwood Mendenhall (Wisconsin)
PhD Johns Hopkins 1898 (under Henry Rowland)
Henry Augustus Rowland (Johns Hopkins)
Civil Engineering degree Rensselaer Polytechnic Institute 1870
later studied under Helmholtz in Berlin
Hermann von Helmholtz (Berlin)
PhD Royal Friedrich-Wilhelm Institute (under Johannes Peter Müller)
Johannes Peter Müller
Bonn University (under Philipp Franz von Walther & Karl Rudolphi)
Karl Rudolphi … Friedrich Leibniz (1597-1652) [Gottfried Wilhelm Leibniz’s father]
Philipp Franz von Walther … Gerard van Swieten (1700-1772)
Sam’s Academic Genealogy (via postdoc advisor)
Samuel Joseph Lord
Postdoctoral research Berkeley 2010- (under Jay T. Groves)
PhD Stanford 2010 (under W.E. Moerner)
BS University of North Carolina at Chapel Hill 2004 (under Sergei S. Sheiko)
Jay T. Groves (Berkeley)
PhD Stanford 1998 (under Steve Boxer)
BS Tufts 1992
Steven G. Boxer (Stanford)
PhD Chicago 1976 (under Gerhard L. Closs)
BS Tufts 1969
Gerhard L. Closs
PhD Tübingen 1955 (under Georg Friedrich Karl Wittig)
Georg Friedrich Karl Wittig
PhD Marburg 1923 (under Karl Friedrich von Auwers)
Karl Friedrich von Auwers
August W. von Hofmann
Justus von Liebig
. . .
Niccolò Leoniceno (1428-1524)
Sam’s Academic Genealogy (via undergraduate advisor)
Samuel Joseph Lord
Postdoctoral research Berkeley 2010- (under Jay T. Groves)
PhD Stanford 2010 (under W.E. Moerner)
BS University of North Carolina at Chapel Hill 2004 (under Sergei S. Sheiko)
Sergei S. Sheiko (UNC)
Habilitation University of Ulm 2000 (under Martin Möller)
PhD Institute of Chemical Physics of the Russian Academy of Sciences 1990
MS Moscow Physico-Technical Institute 1986
Martin Möller (Ulm)
Postdoctoral research University of Massachusetts (under Robert W. Lenz)
PhD University of Freiburg 1981 (under Hans-Joachim Cantow)
Hans-Joachim Cantow (Freiburg)
PhD University of Mainz 1950 (under G.V. Schulz)
Gunter Victor Schulz (Mainz)
PhD Kaiser Wilhelm Institute of Physical Chemistry and Electrochemistry 1932 (under Herbert Freundlich)
Herbert Freundlich (Kaiser Wilhelm Institute)
PhD University Leipzig 1903 (under Wilhelm Ostwald)
Wilhelm Ostwald (Leipzig)
PhD 1878 Dorpat University (under Carl Schmidt)
Carl Schmidt (Dorpat)
PhD University of Giessen 1844 (under Justus von Liebig)
Justus von Liebig
. . .
Niccolò Leoniceno (1428-1524)
OK, what the heck is the “permanent press” cycle on my washer? On the dryer, I think it just adds a cool tumble to the end to avoid wrinkles. But what about for the washer?
Wiki says that some machines might spray a little water during the spin, but I’m fairly sure that my cheap washer does not have that feature. From what I can tell, the perm press wash cycle is 2 min shorter than the “normal” setting, and the second rinse is a “cool down” rinse. However, my washer make the second rinse cold anyway, so I don’t think this makes perm press special. I wonder if the agitation is weaker (or stronger) for perm press compared to normal, but I sorta doubt it.
So, in conclusion, I have no idea what the “permanent press” settings on my washer are for. Maybe they just had extra space on the settings knob, so they added some fictional settings?
UPDATE: I called GE to ask them this question about their washer. The woman at the technical service said, “I have no idea.” And sorta laughed. No help there.
What the what?!?
JACS will now consider Communications of any length up to 4 journal pages and will include the Abstract in the PDF and print versions, starting with Volume 132, issue 27 (July 14, 2010). Authors should refer to the online Information for Authors and use the Communications template when submitting Communications.
Four pages is not a letter. That’s an article, dammit. And abstracts for letters. WTF? No no no. This is all wrong.
What’s the best part of JACS Comms? That they’re short and sweet. You can actually read the damn things, instead of just reading the abstract and looking at the pretty pictures (like we all do with full articles). No longer. Now JACS Comms will be long and complex. Boo.
Instead of destroying the sanctity of the blessed JACS Comm, ACS should have added an intermediate category between Comms and Full Papers.
(Unlike FSP, I really am a curmudgeon.)
Sorry I haven’t posted anything for such a long time. I’ve been on vacation before my postdoc starts. I’ve been out of the loop, mainly because I don’t have access to journal articles until July. The break has been nice, but I am sorta looking forward to doing some science soon!