google reader alternatives

April 3, 2013 at 8:12 am | | everyday science, literature, science community, software

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:

feedly

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:

reeder

 

And Feeddler:

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?

March 26, 2013 at 3:27 pm | | stupid technology

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

February 11, 2013 at 10:02 am | | pseudoscience, science and the public

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:

Chemical structure of four marvels.

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

Chemical structure of a drug.

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

February 7, 2013 at 12:24 pm | | nerd

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.)

newnoEA_copyright sms-bio

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.

no ea car1no ea car2

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.

no lambda over 2na

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:

no ea car3 no ea car4

laser pointer and a fluorescent lanyard

January 8, 2013 at 8:24 pm | | nerd

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

October 17, 2012 at 1:50 pm | | literature

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

Definitely an Ig Nobel contender.

lion hunter?

October 11, 2012 at 1:16 pm | | nerd

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

October 10, 2012 at 9:52 am | | news, nobel

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/

slate

October 3, 2012 at 2:39 pm | | news, nobel, science and the public, science community

Paul and I were interviewed for a Slate.com article about Nobel Prize predictions. More details back at my original post on the 2012 Prize.

the precautionary principle is flawed

October 1, 2012 at 10:28 am | | news, science and the public

I’ve always warned against the Precautionary Principle, mainly because it has a fatal flaw: no one applies the same principle to the alternatives. The Precautionary Principle assumes a product (or medicine or technology) is harmful until it is proven to be safe, instead of the other way around. This sounds nice, but the problem is that it doesn’t take into account the dangers of the alternative products (or medicines or technologies). That is, at least how most consumers apply the principle.

I warned against this when the BPA kerfuffle emerged. Many people started to get concerned about bisphenol A, which is a monomer for polycarbonate used in many plastic bottles. Some BPA can leach from the plastic into food or liquids, and there has been some evidence that it may mimic hormones in the human body and may have negative health effects especially in children. So everyone started banning BPA bottles and switching to other materials. The main alternative is “BPA-free” plastics. When this happened, I asked, “But what are those plastics made of??”

Basically, everyone switched over from a known product (polycarbonate) that might have some deleterious effects, to a proprietary polymer (Eastman’s Tritan) that we knew nothing about. And everyone felt safe.

But what if Tritan is a thousand times more dangerous? What if the glass bottles that some people switched to leaches lead (although I doubt many parents are giving their kids crystal to drink out of)? What if those steel water bottles put chromium into your water? (The aluminum ones like Sigg are coated with a plastic, anyway.) It doesn’t really make tons of sense to throw away your old water bottles to buy brand new ones that have a new, proprietary plastic that can leach new, unknown chemicals into your water.

C&E News has a story about Eastman’s Tritan and it’s possible health dangers. We should all throw away our new water bottles and start drinking out of another unknown material so another company can make billions off of our fears. Or just start drinking directly from the faucet.

The only correct application of the Precautionary Principle is to have someone measure the safety of all the materials used to make water bottles and baby sippy cups and weigh the dangers against each other. Maybe Eastman should pay for that. ;)

(That said, I must admit that I drink out of glass, a coffee mug made in China, and a steel water bottle. Who knows what I have in my body.)

Thanks for the tip, Chemjobber.

2012 nobel prize predictions

September 10, 2012 at 1:35 pm | | nobel, science community

It’s time again for my annual blog post Nobel Prize predictions. This year I’m limiting to the chemistry prizes. Of course there are many more individuals and discoveries that should be listed below and even more who deserve a Nobel Prize!

 

Single-Molecule Spectroscopy

Moerner, Orrit

Single-molecule imaging has matured to an important technique in biophysics. Just go to a Biophysical Society meeting and see all the talks and posters with “single molecule” in the title! Single-molecule techniques have begun to answer biological questions that would be obscured in traditional imaging. Moreover, super-resolution techniques such as PALM and STORM rely directly on detecting single molecules and the spectroscopic techniques developed in the late 80s and 90s. W.E. Moerner won the 2008 Wolf Prize in Chemistry.

 

Electrochemistry/Bioinorganic Electron Transfer

Bard, Gray

Al Bard won the 2008 Wolf Prize in Chemistry; Harry Gray won it in 2004.

 

Polymer Synthesis

Matyjaszewski, Frechet

Jean Frechet invented chemically-amplified photoresists and developed dendrimer synthesis. Kris Matyjaszewski won the 2011 Wolf Prize in Chemistry for ATRP polymerization. Of course, others were involved in both discoveries.

 

GPCR Structure

Kobilka, Stevens, and Palczewski

Biomolecule structures have won chemistry Nobels in the past, so I’m including G-protein coupled receptors here. A lot of buzz in the last couple years about GPCRs and Nobel. Good article here.

Update 10/10/12: Kobilka wins.

 

Chaperonins

Horwich, Hartl

Although these are biological molecules, they are still molecules. And many Chemistry Nobels have gone to bio-related discoveries in the last couple decades. Both won the Lasker Award in 2011.

 

Biomolecular Motors

Vale, Spudich, Sheetz

Another bio subject, but you really never know with the Chemistry prize. All three just won the Lasker Award this year.

 

(BTW, check out other predictions at ChemBark and The Curious Wavefunction and Thompson. And my prior predictions.)

(P.S. W.E. Moerner was my PhD advisor. Also, I worked in a collaboration with Kris Matyjaszewski when I was an undergrad.)

Update 9/11/12: I added chaperonins and biomolecular motors because I figure this year’s Chemistry Nobel might be more biological.

Update 10/3/12: Paul and I were interviewed for a Slate.com piece on Nobel Prize predictions. I like Paul’s section, especially about Djerassi. Anyway, here is what I said:

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.

My top prediction is for single-molecule spectroscopy. In 1989, W.E. Moerner at IBM (now at Stanford) was the first to use light (lasers) to perform measurements on single molecules. Before this, millions or trillions of molecules or more were measured together to detect an average signal. His amazingly difficult feat required ultrasensitive detection techniques, perfect samples, and temperatures just above absolute zero! A year later, Michel Orrit in France observed the fluorescent photons from a single molecule. With those early experiments, Moerner and others laid the experimental groundwork for imaging single molecules.

Single-molecule spectroscopy and imaging has become a subfield unto itself. I performed my Ph.D. research in the Moerner lab, and I know firsthand that the technique reveals events that would otherwise be hidden in averages of “bulk” measurements. Biophysics, the field of understanding how cells and biomolecules operate on a physical level, is particularly aided because rare events can have major effects in biology. (Think of a single cell mutating and then dividing into a tumor.) For example, Sunney Xie at the Pacific Northwest National Laboratory (now at Harvard) performed the early work on how individual enzymes experience multiple states, which otherwise would be averaged away in a bulk experiment. More recently, imaging single molecules has been instrumental in novel “super-resolution” techniques that reveal structures in cells at tenfold higher resolution than ever available before. Several companies (Pacific Biosciences, Helicos, Illumina, Life Technologies) have either released or are developing products that use single-molecule imaging to sequence individual strands of DNA. My prediction is bolstered by others along the same vein. In 2008, Moerner won the Wolf Prize in Chemistry, which is often considered a harbinger for the Nobel. More importantly, The Simpsons were betting on Moerner in 2010. Of course, that was Milhouse’s prediction, and maybe it’s more reasonable to go with Lisa.

My other prediction is for biomolecular motors (aka molecular motors). These are proteins in cells that move important cargo around, and on a more practical level, make muscles contract. Ron Vale (now at University of California, San Francisco) and Michael Sheetz (now at Columbia) discovered kinesin, a protein that walks along tiny tubes and pulls cargo to different parts of the cell. This is supremely important because it would take far too long (months in some cases) for diffusion alone to bring nutrients and signaling molecules to all parts of the cell. (Interestingly, kinesin was discovered from the neurons of squids because they are extraordinarily long cells!) Jim Spudich (at Stanford), Sheetz, Vale, and others have developed many important techniques for studying the actions of these tiny machines. Spudich shared this year’s Lasker Award, which many see portending a Nobel, with Vale and Sheetz.

It’s hard not to allow hope to creep into almost anything we humans do, and I have clearly failed to prevent my own desires from influencing my predictions: I would be thrilled to see either of the above discoveries—or any that I list on my blog—win a prize. But there are many, many deserving scientists who have discovered amazing things and helped millions of people. Unfortunately, only a handful of these amazing individuals will be awarded the ultimate recognition in science. So it goes.

DIY spectrometer

August 30, 2012 at 1:44 pm | | hardware, science@home, wild web

A Kickstarter project is aiming to make a kit for simple DIY spectroscopy. For spectra-nerds, this is pretty cool.

(Hat tip Austin.)

Atoms and Molecules – A Child’s Guide to Chemistry

June 27, 2012 at 2:22 pm | | literature, science and the public, teaching

My labmate wrote a chemistry book for children … and his daughter did the illustrations. It succinctly describes atoms, orbitals, bonding, molecules, and biomolecules.

I highly recommend it.

the matrix begins

June 27, 2012 at 10:56 am | | literature

Implanted Biofuel Cell Operating in a Living Snail.”

Implantable biofuel cells have been suggested [BY MACHINES] as sustainable micropower sources operating in living organisms, but such bioelectronic systems are still exotic and very challenging to design.

One thing I never understood about the Matrix was how the machines were getting more power in electricity out of the human farms than they had to put in as food. Don’t the machines know the three laws of thermodynamics? Or just the three laws of robotics?

PeerJ

June 8, 2012 at 9:39 am | | literature, science and the public, science community

This is an interesting idea. PeerJ sounds like it’s going to be an open access journal, with a cheap publication fee ($99 for a lifetime membership). I wonder if it will be selective?

I’m more excited about HHMI’s new journal eLife.

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