Mendeley, we hardly knew ye

In a frenzied bout of writing for The Connective‘s 48-hour crowd sourced magazine (associated with Wired), I stumbled on some news I somehow missed. Mendeley, the popular organizational tool for academic references, was bought out by Elsevier this month for about $1 million.

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Om nom nom, open access!

Mendeley is a program that’s near and dear to my heart. I’ve been using it since the start of my grad student career 4 years ago, which is just about the time Mendeley itself popped into existence. So we’ve kind of grown up together. As a reference management tool, I can’t help but sing its praises. There are tons of features that I’ve become way too enamored with to ever help giving up now: auto-searching of article meta data (authors, publication name, year, issue, etc.), tagging and foldering, exporting of ref info for citation management, and in-text searching are really high on my list of awesomeness.

But I’ve really been impressed with is Mendeley’s gradual but systematic online-focused push toward openness, sharing, and collaboration. There are options for networked group sharing, which I’ve used with lab-mates to make reference hunting a dream. And they’ve introduced recommendation and discovery options, in which social media-like connections are synthesized based on user data. “Hey, that series of German papers on metal-catalyzed coupling chemistry which you just added to your database?Well 90% of people who have in their databases also have this one, in case you missed it.”

I was excited to see where Mendeley would continue to go. Now, I’m hesitant. That’s because Elsevier just bought Mendeley. And Elsevier is the epitome of a closed access scientific publication giant. They made over $1 billion in profit last year, largely based on the subscription and access fees to their articles. So that’s worrying.

On top of that, Elsevier was the subject of a big academic boycott starting last year. If you didn’t hear, thousands of researchers (largely mathematicians, but not exclusively), decided to boycott all of Elsevier’s nearly 3000 journals. No publishing in them, no peer-reviewing for them, the works. The main argument was that Elsevier has prohibitively at best (and intellectually destructive at worst) financial practices. The money they want is waaay more than the money they need. Tim Gowers, the researcher whose blog post launched the whole boycott, but it succinctly:

In brief, if you publish in Elsevier journals you are making it easier for Elsevier to take action that harms academic institutions, so you shouldn’t.

There’s a bit of cynicism in me that thinks the acquisition, at least in small part, may be a bit of an attempt to save face. Elsevier, to no one’s surprise, is touting the acquisition as a move toward openness. They’ve got a somewhat underwhelming Q&amp;A with Mendeley to address folks like me who are spilling a lot of digital ink about the situation. And there are a few of us.

I’m skeptical at best. But the best approach is to probably wait and watch and hope Mendeley gets to keep its awesomeness coming, rather than being strong-armed to the business interests of Elsevier.

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99 problems, and crosslinking is definitely one

Hold on to your goggles, we’re about to do some polymer chemistry!

While I wait for the final edits to come back on the paper I’ve been writing, I have been buttoning up the trusty lab coat to tackle some data for another project.  Unfortunately (but par for the research course), science isn’t doing what I want it to.

It’s based on a typical coupling polymerization, like this:

To simplify things, I’ve just got a small molecule with reactive ends A and B.  Stick a bunch of them in a pot, stir it up, and you get a polymer chain.  Tada!  Coupling polymerizations are a good friend of mine, and generally we get along famously.

What I’m really interested in doing is putting some functionality on the “block” of the small molecule, so I can use the resulting polymer chain for even more chemistry later.  It actually ends up more like this, where the extra functionality is marked C (for “criminey that’s awesome!” – what, you think I’m beholden to some bourgeois alphabetical labeling?).

That C could be anything to make the final product useful.  It could be a chemical group that emits light in the presence of a deadly toxin.  It could be a binding site for a protein you want to interact with in a medical application.  It can be a miniature Tony Stark who sits around being snarky to all the other non-awesome molecules.  Anything.  There are thousands of polymers out there with everyone’s pet side group attached to it for doing awesome physics/chemistry/biology.

And that’s the nice thing about coupling reactions.  Joining A and B is usually accomplished using a catalyst that’s been finely tuned to be highly efficient.  The catalysts work well, and bear more than a passing resemblance to Justice Scalia in that they are extremely selective for joining A-to-B with non of that unnatural horrific A-to-A homocoupling.  So generally putting that extra functional group in there doesn’t hurt too much.

Until this unexpectedly happens:

Suddenly that new handy chemical group wants in on the coupling fun!  And you end up with a giant gelatinous cross-linked mess in the bottom of your test tube.

The weird thing, and what’s happening for me, is when there’s no clear chemical route for C to start linking in with A and B.  It’s definitely happening – there’s really no other way to make grade A chemical goop.  So somehow C is getting by the Scalia-like laser vision of the catalyst, and it’s back to the drawing board for me (but not before pinning the data to the wall to maybe check out as a side project for looking into on some rainy day).

Behold the joys of research!

The All-Devouring Blob

I might be a bit late to the party, but I just saw this the other day:

Holy Tokyo-devouring B-movie blob, Batman! That is awesome! You can check out the clip here: http://www.youtube.com/watch?v=LcQ3GWpy22Y

I’m a little curious how they get the magnetic cube sitting there at the start. Maybe using a magnet underneath the table to hold it in place until the devouring begins? Minor details. 

We’ve clearly got some iron-infused Silly Putty having some fun here. I’m a big fan of Silly Putty, even the non-magnetic sort. We use it in our elementary/secondary school science demos for blowing kids’ minds. If you haven’t played with Silly Putty before (you poor soul…you should stop reading and go get some right now), I’ll tell you how.

The question is whether Silly Putty is a solid or liquid.  First you rip it:

Looks pretty solid to me. It also follows the basic definition of a solid: a material that keeps its own shape. But the real common sense clincher? I’ve certainly never been able to rip water. Solid.

Then you sit the putty on the edge of desk and come back a bit later to find this:

Credit same as above.

Liquids: they fill the shape of the container they’re in. And if that container is shaped like “there’s the edge of a table, and there’s the floor and oh geez cat, don’t knock that glass over!“, well, that’s where it flows. Now tell me that doesn’t look like a liquid.

The mind blowing works best with 4th/5th graders I’ve found, who have a strong feeling for solids and liquids, are certain that one cannot be the other, and aren’t yet too-cool-for-school like high schoolers (for them we save liquid nitrogen for the mind blowing).

Silly Putty can be both a liquid and a solid because it’s a cross-linked polymer. Which really just means it’s a bunch of veeeerry long molecules (polymers) that are anchored to each other. If you anchor the molecules just right, you can get some really wild physical properties – like the ability to confuse the heck out of people who thought they knew what liquids and solids were.

On really short time scales (like bouncing or ripping), it looks like a solid since the long molecules don’t have time to untangle themselves from the knotted ball of molecular yarn. At long time scales (like sittin around on the desk), those molecules can untangle a bit and move around and do liquid-y things. We call these sorts of materials viscoelastic – “visco” because they can be like a viscous fluid, and “elastic” because you can bounce them off your brother’s head. They’re very cool materials and very useful (helmet padding, car bumpers, wrestling mats…).

So the all-devouring blob? At long time scales, like the 1.5 hours making up that gif, the putty can flow around the magnetic cube like a liquid and get all of it’s metal-attracting bits as close to the cube as possible.  And it’s next stop after that? Tokyo.

 

In Soviet Russia, you pay for the job

Speaking of publishing science, there’s an excellent breakdown in Nature by assistant editor Richard Van Noorden of the costs of publishing in scientific journals. Also: how nobody has any idea where those costs come from. 

I’m fairly certain that you can grab it without paywall nonsense, but with my always-on Ivory Tower Internet-Spigot-of-Science, I’m never 100% sure.  There’s a lot in it, but in case you can’t, the lede hits a good note:

The biggest travesty, [Michael Eisen – molecular biologist] says, is that the scientific community carries out peer review — a major part of scholarly publishing — for free, yet subscription-journal publishers charge billions of dollars per year, all told, for scientists to read the final product.

There’s also some excellent discussion of the idea that the big journals serve to add value, either through rigorous copy editing, editorial staff contributions, or just as a plain gatekeeper of what they think should be the best science (an idea I’ve got my own serious problems with).
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