Everyday Scientist

am i finished using Papers?

I’ve been using Papers for years. When Papers2 came out, I was quick (too quick) to jump in and start using it. It’s worst bugs got ironed out within a couple months, and I used it happily for a while. Papers2 would let you sync PDFs to your iPad for offline reading, but it was slow and a little clunky. Papers3 library syncing is not for offline reading and it is VERY slow and VERY clunky. And it relies on Dropbox for storage. The plus of this is that storage is free (as long as you have space in Dropbox); the downside is that they syncing isn’t clean and often fails.

Mendeley has proven itself the best at syncing your library and actual PDFs to the cloud (you have to pre-download individual files for offline reading you can sync all PDFs in iOS in settings). Papers PDF viewer is still better, but it’s not worth the hassle: Mendeley syncs cleanly and the reader is fine. Not only that, but Mendeley has sharing options that make managing citations possible when writing a manuscript with co-authors (as long as they’ll use Mendeley).

Mendeley is also better than Papers at automatically finding the metadata for the paper (authors, title, abstract, etc.). The program simply works (most of the time), so I’ve given up and finally started using it. Almost exclusively.

PubChase syncs with Mendeley and recommends related papers weekly. (Update: the recommendations update daily, and they send out a weekly email with updates from that week.) They also have some pretty nice features, like a beautiful viewer for some journals and alerts when papers in your library are retracted.

Readcube still has the best recommendations. And they update daily, unlike PubChase’s weekly. And you can tell which recommendations you’ve marked as read, so it’s very quick to scan the list. But that’s really where Readcube’s benefits end. The enhanced PDF viewing feature is nice (it shows all the reference in the sidebar), but not really worth the slow-down in scrolling performance. The program is just clunky still. (I thought Adobe was slow!) And there’s no iOS/Android app yet. It’s on its way, allegedly, but I need it now! Readcube is really taking off, so maybe in a year it will be perfect. But not yet.

Edit: Readcube has a new version of their desktop application. Maybe it’s faster? Wait, did the references sidebar disappear? No, wait, it’s there. Just not on by default.

2013 Nobel predictions

The Curious Wavefunction, Thompson-Reuters, ChemBark, and In the Pipeline have all started making Nobel Prize predictions for 2013. Last year, I correctly predicted Kobilka for GPCRs. In 2010, I got Heck and Suzuki. (You can find my previous predictions here: 2012, 2011, 2010, all Nobel posts.) Here’s this year’s stab at it…

Chemistry

Moerner [awarded in 2014] and Orrit for single-molecule spectroscopy. Zare could easily be #3. Now that single-molecule imaging is effectively a routine tool in biophysics and single-molecule superresolution techniques like PALM/STORM are all the rage, it’s high time for a prize for this science. [FULL DISCLOSURE: I did my PhD with Moerner.]

Kris Matyjaszewski and Jean Frechet for polymer synthesis. Frechet invented chemically-amplified photoresists and developed dendrimer synthesis. Matyjaszewski was awarded the 2011 Wolf Prize. (Of course, others were involved in both discoveries.)

Al Bard and Harry Gray for bioinorganic chemistry and electron transfer. Both won Wolf prizes in the last decade.

Medicine

Gero Hütter for curing AIDS. Once.

Art Horwich & Franz-Ulrich Hartl for chaperonins. Unlikely a chemistry Prize, because GPCR won last year, and they probably won’t do another biomolecule this year. They won the 2011 Lasker Prize.

Ron Vale, Jim Spudich, and Mike Sheetz for biomolecular motors. Remember, they won the 2012 Lasker Prize! Maybe a chemistry prize, but same issue as with Horwich and Hartl above.

Carl Djerassi for the Pill. Unlikely, because they gave a prize for test-tube babies a couple years ago, and that would have been a perfect time to include Carl.

Jim Allison [awarded in 2018], Ellis Reinherz, John Kappler, and Philippa Marrack for the discovery of the T-cell receptor. Oops, that’s too many people. Might not happen for that reason.

Physics

John Pendry and Steve Harris for cloaking and nonlinear optics.

Peter Higgs for that boson.

Peace

Bill and Malinda Gates Foundation for malaria and vaccine work.

George W. Bush for PEPFAR funding in Africa, now that AIDS rates in children are lower.

readcube and deepdyve update

I just wanted to reiterate how great the ReadCube recommendations are. I imported all my PDFs and now check the recommendations every day. I often find great papers (and then later find them popping up in my RSS feeds).

Also, I wanted to let folks know that DeepDyve, the article rental site, is now allowing free 5-min rental of journal articles. Try it out!

block?

Sidewalk infographic fail.

You think Stanford would know how to spell Felix Bloch’s name.

PubReader review

I’ve reviewed several PDF reader/organizers, like ReadCube, Papers, and Mendeley. Currently, I use Papers for organizing my PDF library on my computer. I also like Papers a lot for reading PDFs, because it displays in full screen so well. But I’ve started using Mendeley for adding citations to Word documents, because it makes it really easy to collaborate with other people who have Mendeley.

Now check out PubReader! It’s really cool. Pubmed has the advantage that it requires all research publications resulting from NIH funding to be uploaded to their depository. And they don’t just grab a PDF; they get the raw text and figures and they format it their own way. I used to think that was silly and overkill, but now I see that that approach was genius: it now allows Pubmed to reformat the papers into more readable shapes and sizes … and they can reformat in the future when the old format becomes antiquated. You can’t really do that with a PDF.

It’s always been nearly impossible to read PDFs on a phone or an e-ink tablet like the basic Kindle. Now, with PubReader and the beta option to download the article in an ePub format (for reading in iBooks or Kindle or something), that option is here. Or on its way, at least.

PubReader on a computer:

PubReader on iPad:

ePub in iBooks:

Now PubReader just needs to display the references in an elegant way like ReadCube, and it will be the best!

It makes me think the future of reading and storing scientific papers is not the hard drive, but simply reading on online depositories. Pubmed allows you to create collection and star favorites, so you can just use Pubmed to store your collection of papers and never have to download a PDF again in your life!

readcube review

I recently tried Readcube, which is a PDF reader and organizer. I did so because Nature has been using it built into their site, and I like how it displaying PDFs. The article data downloads seamlessly for most papers, and  interface is quite beautiful:

The really cool feature is that Readcube automatically downloads the references and the supporting information documents and can display them at a click of a button. More importantly, it displays the references in the sidebar. It makes an excellent reading experience!

The final interesting feature is that Readcube offers recommendations based on your library. From my quick scan, the recommendations seem pretty good.

Other than that, Readcube is quite feature poor. It doesn’t have a way to insert citations into a Word document, like Papers and Mendeley does, although you can export to Endnote. I don’t see a way to read in full screen nor does it let you view two pages simultaneously, like Papers does.

The screenshot above is from Papers fullscreen view, which is how I really like to read PDFs.

But Readcube is still in beta, and they’re starting from a really nice starting point. I’m not ready to give up on Papers for reading (and I’ve been using Mendeley for Word citations, because it has really nice collaborative features). But I might try Readcube some more, mainly because of the awesome ability to see all the references and the paper simultaneously. I really wish I could mash Papers, Mendeley, and Readcube all together into one feature-rich program…

ActiveView PDF

Does anyone else love ACS’s ActiveView PDF viewer for reading PDFs and seeing reference? And Nature’s ReadCube, too. Great stuff.

Of course, after I scan the ActiveView, I still download the old-fashioned PDF and use Papers (or Mendeley) to read and manage my library.

google reader alternatives

Now that Google Reader is going the way of the dodo Google Gears, how am I going to keep up with the literature?!? I read RSS feeds of many journal table of contents, because it’s one of the best ways to keep up with all the articles out there (and see the awesome TOC art). So what am I to do?

There are many RSS readers out there (one of my favorites was Feeddler for iOS), but the real problem is syncing! Google servers took care of all the syncing when I read RSS feeds on my phone and then want to continue reading at home on my computer. The RSS readers out there are simply pretty faces on top of Google Reader’s guts.

But now those RSS programs are scrambling to build their own syncing databases. Feedly, one of the frontrunners to come out of the Google Reader retirement, claims that their project Normandy will take care of everything seamlessly. Reeder, another very popular reader, also claims that syncing will continue, probably using Feedbin. Feeddler also says they’re not going away, but with no details. After July 1, we’ll see how many of these programs actually work!

So what am I doing? I’ve tried Feedly and really like how pretty it is and easy it is to use. The real problem with Feedly is that its designed for beauty, not necessarily utility. For instance look how pretty it displays on my iPad:

But note that its hard to distinguish the journal from the authors and the abstract. And it doesn’t show the full TOC image. Feedly might be faster (you can swipe to move to the next articles), but you may not get as much full information in your brain and might miss articles that might actually interest you.

Here’s Reeder, which displays the title, journal, authors, and TOC art all differently, making it easy to quickly scan each  article:

And Feeddler:

I love that Feeddler lets me put the navigation arrow on the bottom right or left, and that it displays a lot of information in nice formatting for each entry. That way, I can quickly flip through many articles and get the full information. The major problem is that it doesn’t have a Mac or PC version, so you’ll be stuck on your phone.

I think I’ll drop Feeddler and keep demoing Reedler and Feedly until July 1 rolls around.

are fuel economy gauges doing math wrong?

A few years ago, there was a piece in Science magazine about how we should all be using GPM instead of MPG. Here’s a link to my post about it back then. The main point is that the relevant unit for fuel use should be fuel divided by distance, and than MPG is inverse, which is harder wrap our puny brains around.

Back then, I looked into how fleet fuel economy averages were calculated, because I was worried that one single crazy-high MPG model could artificially skew the average high without actually making the fleet more fuel efficient. It turns out that the US requires automakers to calculate their fleet average fuel economy the correct way: convert each model’s economy to GPM, find the mean, then take the inverse again. Phew.

(not my car)

But now I wonder if the computer programmers at the automakers know how to calculate an average. My computer fuel gauge is always inflated compared to what I calculate from the fuel pump amount and odometer reading. Every time. And I’m not alone. So, either the gas stations are messing with their pump readings, or the average MPG on my dash is miscalculated. I wonder if the computer just takes a continuous average of the measured MPG values, which would definitely result in an inflated number at the end of a gas tank. (That’s because 10 miles of driving at 35 MPG after 10 miles at 25 MPG does not average to 20 miles at 30 MPG. It’s actually 29 MPG.*) If the computer just averages the MPG numbers, it will be 2% inflated from the actual value. That inflation would get worse if you drive down a hill for a mile and go 50 MPG, then back up that hill and drop down to 10 MPG: instead of an average of 30 MPG, the true average is only 17 MPG!

Of course, if the computer just takes the total miles driven and divides by the total gallons of fuel used (since the reset), than the average would be calculated correctly. But is that what’s happening?

Does anyone know anyone who works at an automaker who can check how they do the math?

* Here’s my math. Driving 10 miles at 25 MPG uses 0.4 gal of fuel. Driving 10 miles at 35 MPG uses around 0.29 gal of fuel. That’s 20 miles driven and 0.69 gal fuel used, or 29 MPG. Not 30 MPG. For the hill example, down the hill uses 0.02 gal for the mile, and up uses 0.1 gal. That’s 2 miles and 0.12 gal, or 16.7 MPG.

great chemophobia article in Slate

I’ve argued in the past that the Precautionary Principle is logically flawed, even dangerous. A recent article on Slate gives a great job giving an example of when the Precautionary Principle goes bad. In response to a NYT article on alternative medicine, the Slate article compares the FDA-approved drugs to the alternative medicine that a mother is more comfortable giving her son. (Surprise! the alternative medicine also contains chemicals.)

The reality is this. [The NYT author] has been tricked by the language, maliciously or not, into considering switching her child from a carefully measured weekly dose of this molecule:

To four doses a day of an unknown amount of this chemical:

Really?

I want to be absolutely clear. Neither of these chemicals is benign or nontoxic. The LD-50 (the “lethal dose” amount that kills 50 percent of mice fed the chemical) is about the same for quercetin as it is for methotrexate, roughly 150 milligrams per kilogram of body weight.

…

Berberine, one of the drugs found in four-marvels powder, has been documented to cause brain damage in infants. Hello? Exactly how much of this have you been giving your son?

…

[The NYT author’s] “better the molecule I don’t know, than the molecule I do” stance may help her sleep better, but it is ignorance nonetheless. The chemicals are still there, even when you squint your eyes closed so you can’t see them.

This is really scary to me, that parents are giving their children unknown doses of potentially dangerous drugs. This is exactly the danger of the Precautionary Principle: people seem more comfortable with unknown dangers than known and carefully quantified risks. That’s a silly approach to risk, but I think it might just be how our brains work. And knowing that, we should be careful to guard against it.

Another concern not mentioned in either the Slate or NYT article is the drug interactions when taking a prescribed medicine with unknown alternative drugs: because they aren’t tested, alternative medicines have the potential for devastating interactions. The FDA should require at least safety testing (if not efficacy) of all medicines, both modern-medicine and alternative. NIH has an alternative medicines institute, but I wonder how quickly they can test all the options out there.

I want to also add that I completely understand the NYT mother’s concern about giving her son drugs every day. And I completely agree with the mom’s effort to find diet changes that help: the body is a complicated network, and diet can have a huge effect on health. And the immune system is in some senses a black box that we’re only beginning to understand. A variety of alternative treatments and diet changes should be tried, but eating a bunch of unknown chemicals because they have prettier names is really concerning.

I really feel for the boy and his mom, and I wish there was a magic wand to take away his pain. But even if there were, we should probably ask about the side effects of the wand.

no ensemble averaging

I’ve been making these nerdy CafePress products for many years. The most “popular” idea I came up with was a pin that denounced ensemble averaging in favor of single-molecule spectroscopy. (At some point in 2006, I saw random science folks wearing my buttons and they claimed that someone their lab made them, so I added the copyright. But I’m more than happy to have other people “borrow” the design.)

For the 2010 Single-Molecule Approaches to Biology Gordon Conference, we made a slightly different design and W.E. handed them out to attendees.

I used to own a car with several of these bumper stickers on it, and I thought I was a super-nerd. Well, I’ve been way out-nerded: a friend (Jan Lipfert via Adam Cohen) emailed me these photos from BPS in Philly.

That really cracked me up! Does anyone know who this super-nerd is?

So, to keep up with the times, I’m creating a new product. It celebrates the state-of-the-art efforts to break the diffraction limit of light microscopy.

I’m inspired to detail my car, but I don’t think my wife would appreciate it.

Update: It’s Yale E. Goldman. Apparently, he needed to cover a big scratch! Best. Reason. Ever. A tractor trailer veered into his lane and the wheel scrapped away his paint. He sent me this before-and-after:

laser pointer and a fluorescent lanyard

This is one of the coolest things I’ve seen all year! I have a habit of shining my 405 nm laser pointer at fun things. But I was really surprised when I donned my safety goggles and the beam hit this Chroma lanyard:

Wow! I think what’s happening is that the fibers are acting as light guides—like fiber optics. So you see the fluorescence travel along the fibers, which are weaved diagonally up along the strap, over the edge, then diagonally back down. Super cool. Chroma should use this for marketing.

urine biophysics

The Shape of the Urine Stream — From Biophysics to Diagnostics.

Definitely an Ig Nobel contender.

lion hunter?

What are the chances that the only person cc’d on this email would be “LHunter”?

Also, anyone wanna go get coffee? I know a shortcut through the woods. Here, put this antler hat on.

2012 nobel in chemistry: Kobilka and Lefkowitz

Well, I predicted G-protein coupled receptors (GPCRs) and Brian Kobilka, but not Robert Lefkowitz. Congrats to both!

GPCRs are cell-surface receptors that translate signal from an extracellular ligand to a G-protein, a molecular “switch” turned on and off by GTP. (The discovery of the G-protein was awarded the 1994 Nobel in Medicine). GPCRs are very important in a variety of signaling in the human body, and most modern drugs target GPCRs.

Kobilka and Lefkowitz first had inklings of the structure of GPCRs in the 80s, when they began isolating and purifying the β₂-adrenergic receptor (βAR). They eventually realized that the protein had seven transmembrane helices; to their surprise, that hinted at a very similar structure to rhodopsin—the component in the eye responsible for detecting light—another GPCR. This discovery implied that all the receptors that couple to G-proteins might have a conserved structure! Over the last few decades, Kobilka, Lefkowitz, and others have produced a bunch of structures for GPCRs, which should aid in future drug design.

I think it’s fascinating is that Kobilka was a postdoc with Lefkowitz many years ago. I wonder how often it happens that both the professor and a student/postdoc share a Nobel? Of course, Kobilka has performed enough work during his independent career to earn a Nobel, but I still think it’s cool that he won the award with his former professor. I’m not sure why Stevens or Palczewski were not also included in the prize, but it seems that the committee (given only three available slots, of course) stuck to the early discoveries that lead to the GPCR structures.

And I must discuss the concern from many corners that this is not “chemistry.” Why did it not win the medicine prize, instead? Well, I don’t know. It certainly could have won the prize in the medicine category, because of GPCR’s huge role in medicine! But the Nobel Committee seems to often place protein structures into the chemistry category [Update: see this great history]. I think that is reasonable: the task of isolating, purifying, crystallizing, and determining the structure of a protein is basically biochemistry, not medicine. And many of the individuals in the lab performing the tasks are probably chemists and biochemists. Maybe the lab isn’t located in a chemistry building, but neither is the lab that I work in, and I am certainly a chemist performing chemistry. (Well, right now I’m blogging.) I continue to think that these type of discoveries being labeled “chemistry” is great for the field of chemistry. Maybe I feel this way because I don’t perform “traditional” chemistry synthesizing small organic molecules. My research has spanned polymer physics, spectroscopy, optics, and cell biology. But I have applied my skills and knowledge of a physical chemist to all those sciences. As I said in my interview with Slate.com (where I did not predict GPCRs):

The line between chemistry and other fields (especially biology) is often blurred, and that’s a wonderful thing; but this fact sometimes results in a chemistry Nobel Prize being awarded for a decidedly biological discovery (like the 2009 prize for the structure of the ribosome). This may be exacerbated by the fact that the physiology or medicine prize tends to go to things directly related to health, and the chemistry prize often is used to cover the more basic biological science feats. Personally, I think it is a testament to the central position the field of chemistry holds in the Venn diagram of science.

Biology is the next frontier for the physical sciences! There is so much to learn about how biomolecule, cells, and organisms work. Let’s embrace biology’s commingling with chemistry with all our hearts!

You can read more about GPCRs here:

http://www.nature.com/news/2011/110824/full/476387a.html

http://cen.acs.org/articles/89/i11/Picture-Pill.html

http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2012/advanced-chemistryprize2012.pdf

http://cen.acs.org/articles/90/web/2012/10/Robert-Lefkowitz-Brian-Kobilka-Share.html

http://blogs.scientificamerican.com/the-curious-wavefunction/2012/10/10/
g-protein-coupled-receptors-gpcrs-win-2012-nobel-prize-in-chemistry/

Other bloggy commentary here:

http://blog.chembark.com/2012/10/09/liveblogging-the-2012-nobel-prize-in-chemistry/

http://www.coronene.com/blog/?p=1569

http://wavefunction.fieldofscience.com/2012/10/gpcrs-win-2012-nobel-prize-in-chemistry.html

http://wavefunction.fieldofscience.com/2012/10/crystallography-chemistry-and-nobel.html

http://pipeline.corante.com/archives/2012/10/10/
the_2012_nobel_in_chemistry_yes_chemistry.php

http://cenblog.org/terra-sigillata/2012/10/10/lefkowitz-and-kobilka-win-2012-chemistry-nobel-for-gpcrs/