Throwing Down the Gauntlet for my Fellow Geeks
by Jeremy on Feb 03 2009 (3352 Views)I love Wikipedia. I think deep down we all do. There’s something truly amazing about accessing hordes of (useless) information simply by entering a few keystrokes in a giant search engine. At times, Wikipedia’s better than “Googling” simply by virtue of the fact that each topic is referenced (most of the time) and peer-reviewed. By analogy, can you imagine the quality of published work if the ACS didn’t require references in a submitted manuscript or operate a peer-reviews-type system?
Wikipedia is great for getting an objective “big picture,” rapidly in a fairly organized format, but it has its limitations. Do you need to know the origins of Evacuation day in Boston? Use Wikipedia. Do you need to know the economic impact of the 11-month British seizure of Boston? You’re better off consulting a textbook or bugging you local history scholar.
By contrast, my “ranking” professors largely despise search engines such as Wikipedia. I think they frown at the ease of accessing a tool that anyone can alter for finding physical constants (i.e. the density of aniline) or understanding conceptual material (i.e. Zimmerman-Traxler transition state models). I once heard a professor claim, “If it’s published on the internet, there’s really no way to verify if the information is true.” In a sense, he was correct. The internet is a terrific source for (mis)information, and Wikipedia is really no exception to this phenomenon. Hell, my wife (trained as a chemical engineer) has witnessed physical constants change on Wikipedia on several occasions.
Science is a largely unspoken art. Sure, there are lectures and textbooks that “guide the way.” However, every research scientist mines information from the stockpiles of primary literature in an effort to piece together relevant aspects of his or her project. I imagine that if I were to search for a procedure for using SOCl2 today (Lord knows I wouldn’t consult my PI), there are probably 49 other people in the world this week looking for a similar procedure. This means that 50 of us will spend valuable time crawling through the literature looking for a similar ballpark procedure. To make matters worse, on my campus, the SciFinder subscription is only available at a library where waiting for a computer is akin waiting for the Kansas City Royals to win a World Series. A lot of these problems could be fixed with the development of a free scientific database.
I think charging several hundreds of dollars for crappy textbooks is criminal. I also think that a scientist’s time is too valuable to be wasted crawling through primary literature looking for the proverbial needle in a haystack. Knowledge should be available to the general public, hence libraries. But, we live in a digital age where copious and sufficient information can be accessed with the click of a mouse. Don’t get me wrong. I believe in peer-reviewed publishing. However, the organization of that information (specifically scientific) is what kills me.
I propose the creation of a knowledge database. In the spirit of Dan Carlin’s last podcast, I say let it be produced by the militia—by the people for the people. You sign on. You contribute. You enter the associated references. Do you need to know the side reactions of a Pictet Spengler reaction? Maybe someone in Patrick Bailey’s group just added a reference from a recent paper last week. Need a technique for depositing silver nanoparticles? That would be easy to find if someone in Louis Brus’ team contributed a procedure. Earlier this morning, a friend of mine just came by my office looking for a quick, easy way to make trityl tetrafluoroborate. Imagine how easy it would’ve been for him to access a free database that references 50 different procedures (BTW, his group has complete access to SciFinder outside of the library). Don’t feel left out you biologists out in Internet-land. You could have access to PCR techniques, free sequencing software, and even references to protein crystal structures.
My argument is this: there is so much useful information that needs to be organized in a format that is free, navigational and easy to access. One person cannot do it alone; we all need to contribute for the betterment of science, in general. I envision a hybrid of Doug Taber’s Organic Chemistry Portal, Wikipedia and a condensed version of SciFinder. I’ll gladly contribute! How do we get the ball rolling?
What? Why didn't you use this link for the Royals WS title drought?
And can we talk for a second how upsetting it is that ChemFinder completely revamped its interface and all the good stuff is now behind a subscription? Not that the subscription is hard to get (anyone with ChemDraw has the subscription), but it's still annoying to have to go through that one extra step to get to my physical constants.
The resources I use most frequently (besides SciFinder) are ChemFinder, the Aldrich Website (if I need to), SDBS, Taber's OChem Portal (but more for mechanisms... not so much for references), and Evans' pKa table. I'll sometimes head over to Not Voodoo or Al's Notebook, but not very often.
I think the main problem is the Wikipedia Effect. Anything user generated must be taken with a larger-than-normal grain of salt.
Maybe a couple more boards could be added to the ChemKnowHow site for references/tips.
I thought it was funny to see Royals "fans" making a push for the playoffs in '09. My hat's off to them. I'll stick with my BoSox.
I've never seen the ChemKnowHow site. Spent a couple minutes learning how to grow good crystals for XRD. It seems to be a good resource. Even still, why can't all of these sites be condensed into one useful, encompassing, practical database?
I completely understand the concept of the Wikipedia Effect. But, you can circumvent a lot of these problems by requiring a reference. In theory, the site could be self-policing. And, if in a case where the data's wrong it can be immediately corrected.
I'm not disagreeing with you. I think it would be an immensely useful resource. Especially if there was a section for 'failed experiments,' so I have an idea if something will work or not.
So's Wikipedia. Although I still use Wikipedia regularly.
Failed experiments would be most excellent!
It would be a monumental task just to organize tried and true procedures for organic or inorganic reactions, let alone all the spectra and ancillary details! Still, I'm sure it's possible, but I'm also sure it would be one hell of a project.
I'm surprised not to have yet found a blog or rant on how ridiculous expensive a seat for sciFinder scholar is. It's something like $15,000 per seat and in reality, all it does is index journals' and papers' abstracts, one still needs to pay for the papers!! Beilstein/Gmelin's Crossfire can't be much (if any) cheaper. Seriously, why is access to these reference sources so expensive?
While it may lack some of Wikipedia's amazing breadth, Scholarpedia does have a lot going for it. It's open access, peer-reviewed, and written by experts.
Unfortunately, it doesn't look like they've got a ton of Chemistry articles yet. The Physics section seems pretty impressive, though.
I also use Org Synth if I want to quickly find a procedure for organic synthesis.
Evil but fun game: change a Wikipedia entry to something outrageously false and see how long it takes to get corrected. My friends and I have also joked about vandalizing an entry related to a class we're taking, and seeing if any of our classmates include our made-up facts in their papers.
Org Synth rocks. It's great for old-school reactions. Though, it does have the occasional hiccup (a procedure I once followed called for the addition of "glass saddles" to a glass column).
Or, say, a ridiculous procedure like this for the production of hydrogen cyanide. Make sure you check out Note 1.
Holy S. That can't be real. I'm printing that out and putting it on my hood.
Oh, it's real... and it's spectacular.
What's wrong? Never worked with neat Prussic acid? Every now and then there's a procedure that calls for it as a solvent
It's easier to deal with than LNH3 in a Birch, 'bout the same color too!
I'd rather work with neat HCN than neat HF, having worked with both.
The problem is your goals are too big. The best way to tackle this, is to pick a niche where you see something seriously lacking and go after it.
Example: If you want a resource to mine failed experiments, then we could make the Chemistry Journal of Failed Experiments. We can solicit manuscripts, have a quick peer-review and throw it on the server and make a nice dedicated website to it. Or we can slim down the ambitiousness, and have a database where people can type there reactants, catalyst, products, yield, etc...
If you come up with something you want to pursue let me know; I can code most any idea. I've also had similar thoughts in the past, but it is impossible to implement with only one person taking the lead.
I'm curious to know if there's one common problem plaguing organic chemists. My biggest problem is reagents. Whenever I set up a reaction in my notebook, I look up physical constants for the reagents I'm about to use, then try to get a feel for what they can/might do in the reaction, if they're associated with any side reactions, how to work the reaction up, etc.
Though, a database of failed reactions (I'm laughing at this idea) would be most excellent. I'm laughing because I can see someone writing something like this: "Table sugar and DBU in water does not, in fact, give ecstacy on workup."
Maybe this database could be a topic of discussion in SLC.
I'd actually be more nervous about submitting my manuscript.
"We regret to inform you that your manuscript has been rejected because two of the reviewers noted that changing the solvent to THF resulted in a 77% yield. Moron."
But, then you would know how to get your product!
A lot could be achieved here with Wikipedia, and decent scientists who understand referencing. You know if Wikipedia does one thing in its life, it would be to teach the public about the value of references.
You hit the nail on the head, though, when you say "I’ll gladly contribute! How do we get the ball rolling?" It's amazing how many people complain about Wikipedia, as if it's some kind of service. Motto to whiners: Stop bitching about it and CONTRIBUTE.
Y'all young academic types are NOTORIOUS for trying to start stuff like this and then bailing once it gets inconvenient (which is usually sooner than later). Finish your dang ol' Ph.D first, procrastinators!
However, an idea: This should be obvious, but there is already a great deal of free information available on the internet on several topics. Even if restricted to one specific topic such as organic synthesis, the material available is far more than the average human would read and fully assimilate. Perhaps a good first step would be an indexing of this information, for searchability?
Not a bad idea Gus. Indexing would certainly help.
I think a first step would be to gather data from fellow scientists. See what tools they need (insofar as information is concerned).
However, after thinking this project through a bit, I think I've come up with a reasonable first iteration. Though, I'd have to run it by my fellow bloggers first to see what they think.
You definitely piqued my interest...
As Mat noted I think your willingness to contribute is the key. Technology is not the bottleneck. If you record as much as you can about what you do and know on social software, Google does a pretty good job of connecting you up with people looking for that information.
As far as communicating your "failed" experiments, a convenient solution that we've used in my lab for some time is simply to make our laboratory notebooks public:
http://usefulchem.wikispaces.com/All+Reactions
We've also been collecting non-aqueous solubility data for common chemicals:
http://onschallenge.wikispaces.com/list+of+experiments
By storing these on a public Google Spreadsheet, Andy Lang and Rajarshi Guha have written services to make these available via intuitive interfaces like drop down menus, substructure searching and concentration ranges:
http://rguha.ath.cx/~rguha/cicc/jcsol/sol.html
If you are interested in using some of these tools for your own fields of interest let me know.
I happen to think that a database of "failed reactions" is not quite as good of an idea as many may think.
Most importantly, sometimes you really do just have to try things out for yourself.
Furthermore, for me to be convinced that a reaction is a "failure," I would need quite a bit more detail than your run-of-the-mill grad student is typically willing to put into something that serves as little more than a cautionary tale to others. (Spectra, ID of side-products, TLC at a bare minimum) A good example of this kind of fallacy exists like a disease among amateur software authors. They are excited to build and hack together their programs and get them working, but the machine grinds to a halt when it's time to write up the documentation. Sound familiar?
Documentation doesn't work because there are no carrots. We have a nice 1,000 pound carrot we're talking about behind the scenes, so I doubt we'll run into your analog's problems.
1k # carrot, you say? If you folks are looking at starting some online project for this sort of thing, I'd possibly be interested helping.
I think I would be interested in helping out. A good model is that of openwetware.org, which is mostly for biological procedures, but gets the idea correct. It would need a good hosting point, and a good structure searching engine, but I think it could be done. I don't know if the openwetware people would be interested in expanding to org chem, but we can certainly glean format and layout ideas from them. Who's got the server space to host this thing? I can do some of the back-end setup, but I don't have the ability to host the traffic.
Patrick...take a look at ChemSpider. It's a good hosting point already, has a structure search capability and already hosts synthesis protocols etc. Also, take a look at the ChemSpider Journal of Chemistry as an alternative venue. http://www.chemspider.com/journal