Post Tagged with: "Nature"

The Source Code Debate

Few researchers were using computers 30 years ago.  This quickly changed with the release of several commercially viable personal computers in the 1980s. Since then, processing power has increased and the cost of computers decreased at an exponential rate (see Moore’s Law).

It’s no surprise that computers are now pivotal in chemistry research. We use them in a wide range of calculations – from determining the 40th decimal place of the absolute energy of He to modeling the release and distribution of toxic chemicals in river basins. The software used to address these complex problems is becoming increasingly accessible and easy to use too. There are already a variety of cell phone apps for chemistry related problem solving.

Yet, while the prevalence of software and computer-based research continues to grow, the rules for publishing results and sharing software lags behind. The magical/miracle nature of black-box calculations is disconcerting to individuals that want to know how the answers were obtained (see Sidney Harris cartoon).  A palpable concern is growing in the scientific community around the sharing of software – and the foundational source code -necessary to reproduce published results. Two recent opinion pieces, one in Science titled, “Shining Light into Black Boxes” and the other in Nature titled, “The case for open computer programs” are trying to bring attention to this issue. The articles discuss the advantages and apprehensions of sharing, as well as suggest possible changes. Below is a summary of the points raised by the authors of the two articles – as well as the thoughts others (including myself).

Advantages to sharing software and source code:

  • Reproducibility: As stated by Ince et. al., “The vagaries of hardware, software and natural-language will always ensure that exact reproducibility remains uncertain…” without the release of source code in its entirety.
  • Catching errors: A simple mistake in converting units, assigning missing values as zero, rounding errors, or a misplaced decimal point, can wildly skew outcomes (see Office Space). We can only see and correct errors if we can see the source code.
  • Facilitating progress: All publications require that data, equations, materials, methods, and instrumentation are disclosed so that the results can be tested and furthered by others. We are all better served when source code is disseminated in a similar manner so that programs can be studied and repurposed in future research.
  • Teaching tools: Real, applied examples – that are relevant to research – are useful for new students and researchers learning to program and develop code.
  • Openness: Despite the competition to acquire funding and to publish first, we are all joined in the endeavor of understanding the rules that govern the universe. The open sharing of information has been and will continue to be the foundation of scientific progress.
  • Relying on faith: No matter how prolific or respected you are as a researcher, the implicit assertion, “Trust me, the program works the way I say it does” is not an acceptable means of justifying your results. On a fundamental philosophical level, black box justifications like that should be socially unacceptable in the sciences.

Apprehensions against sharing software and source code:

By May 4, 2012 7 comments science policy

Nature Has a Graphical Abstracts Problem

Or I should say, it had a problem. The most annoying thing about Nature journals, not including Nature Chemistry, is they do not have a graphical abstract associated with their rss feed or even in their Table of Contents. However, I made a hack to view Nature with an associated graphical abstract over at ChemFeeds.

link: Nature via ChemFeeds

I also went ahead and made it for all the other Nature journals.

If you happen to be a Nature lover you can see them all with this link: All Nature.

If some of the feeds don’t have many abstracts within them it is because they are very new and more abstracts will be added automatically as Nature updates their AOP feeds.

Update: PNAS ADDED!

Update 2: Science Added.

Mitch

By May 25, 2010 6 comments chem 2.0

How Can Science Embrace Web 2.0: A Response to Rudy Baum

(This post is in response to the May 10 editorial in C&E News.  For the response to the April 19 editorial, click here)

First, I want to thank Rudy Baum, editor-in-chief of C&E News, for taking the time to respond to my commentary.  I know he probably has other issues he’d rather talk about on his editorial page, and I appreciate the engagement in this dialogue.

I’d like to continue the dialogue here and I hope to keep this conversation going – at least informally – for a long time.

Mr. Baum and I seem to agree that Web 2.0 is a part of science now; however, we may disagree on the merits of SciW2.0.  If you don’t believe SciW2.0 has arrived, consider that the fact that you are even privy to this conversation.  Not only do I have a W2.0 platform upon which I can comment on C&E News editorials, but within days the comments were populated with a who’s who of SciW2.0 leaders offering their opinions and helping shape the conversation.  And the conversation became so loud that it prompted an editor-in-chief to write an entire editorial in response to, essentially, a nobody in the chemistry world (let’s face it.  I certainly don’t count myself in the elite of chemistry, blind or not).  That all of these things can happen within a month – and without any face-to-face meetings between any of the players – proves the establishment of SciW2.0 as a communication tool.

Now, before we continue, I want to re-link to this blog post on Nature‘s Nascent blog.  In my opinion, this post is a must read for anyone who wants to engage this discussion.  It is a nice overview of SciW2.0, its strengths and especially its weaknesses.  Why there’s resistance to SciW2.0, why academic and industry leaders aren’t all buying in, and why he’s committed to making SciW2.0 successful.  It really is mandatory, and I’ll wait for you to click over and read it now.

(lounge music break) 🙂

While severely cautioning people about SciW2.0 (but not denouncing), Baum seems to want to walk a fine line.  It’s dangerous, it’s not a panacea, he reads blogs, he’s not an opponent of all W2.0, he agrees with author Jaron Lanier when he warns scientists not to adopt W2.0 ideals, and he finds proponents of W2.0 overenthusiastic.  Perhaps he is just cautioning scientists against ‘irrational exuberance’ when it comes to buying in to SciW2.0.  And those warnings would be well heeded (although I doubt we’re anywhere near the irrationally exuberant days of SciW2.0).  My question for Baum is: if he doesn’t think SciW2.0 is a panacea, does he think the current model for scientific communication (peer-reviewed journals) is a utopia?  And if not, what would he suggest happen differently?

As to his comment about the panacea of W2.0 and how it ‘changes everything’ as he says W2.0 proponents adamantly claim, I suspect he’s referring to Don Tapscott’s and Anthony Williams’ book Wikinomic: How Mass Collaboration Changes Everything.  I haven’t read it, so I can’t comment on it.  But I would imagine, as is true in other areas of life, when people mention ‘everything,’ they rarely mean things like cutting edge academic and scientific research.  Rather, I imagine people mean ‘everyday things,’ usually for everyday people.  I’ll link here to notes by Will Richardson on W2.0 and how it’s changing politics, government, journalism, and business, and how it is starting to change education.  So while it seems to be changing certain industries, I’ll admit that it’s not changing everything.  In fact, I don’t think any of the commenters on the other post thought so, either.  Pop science is not the same as pop culture and does not think the same way.  Comments made in one arena are not necessarily transferable to the other arena.

But rather than getting into a hair-splitting contest over who used what words and who meant what, I propose to move the conversation forward in a different direction.  My open question: What should SciW2.0 look like, and how will we know it’s successful?

W2.0 is ultimately a communication tool.  It harnesses the power and dexterity of the internet and allows people to communicate with each other in ways never before possible and on timescales never before possible.  In certain circles (politics, pop culture), if you’re not actively following the W2.0 scene, you’re way behind and have nothing to bring to the table.  Not so in SciW2.0.  If you’re following SciW2.0, you’re reading about and reacting to people’s analysis of things that happened in the past.  Missing a week or two won’t put you behind, because by and large you’ve already read the same papers and seen the same announcements.

I doubt that SciW2.0 will become an instant data/paper communicating tool for hard science anytime soon the way it has in other aspects of life.  I agree with the reasoning by Timo Hannay in the Nascent link:

[E]ven if the direct financial cost of sharing this information is low, the cost in terms of scooped findings, rejected papers and grant applications, and perhaps even diminished reputation could be very high. … It’s sad, but most scientists don’t publish in order to share results with their peers, they do so in order to secure grant funding and promotions. We know this because when we provide ways of sharing information that do not affect their likelihood of getting funding or promotions – such as preprint servers for biologists – most don’t use them.

There will always be a place for reactionary SciW2.0.  Communities of people talking about science and sharing ideas and information cannot hurt anyone.  But because there’s rarely breaking news coverage on SciW2.0 (see Totally Synthetic’s sodium hydride oxidation post for an example of breaking news coverage), the majority of chemists don’t seem to find the need to tune in regularly.

Before we’ll get large numbers of people on board, in my opinion, might we need to make SciW2.0 less reactionary and more innovative?   I think we’ve started seeing bits and pieces of that scattered throughout, and that might be how we make it more appealing to the science community at large.  I mentioned in the comments previously that ACS had their NanoTube contest, which asked users to upload original videos explaining ‘What is Nano’ in an clear and entertaining way.  Perhaps this is the way science utilizes W2.0 in a productive manner.  Demystifying aspects of science to make it accessible to anyone curious about science, but perhaps without the training.

But, as the Nascent link alludes to, other types of crowd sourcing have not been as successful.  Nature‘s open peer-review system posted a small number of ‘opt in’ papers online and asked the crowd to review and comment on them before being accepted to the journal.  The open peer-review process happened concurrently with the ‘typical’ closed, anonymous peer-review process.  As noted if you listen to the audio version of the talk, it added no apparent value, but a lot more work for the Nature folks, so they abandoned the experiment.  I suspect it was just ahead of its time.

We may look to the results of a current crowd sourcing experiment to see if the time is right yet.  The Haystack, one of CENtral Science’s child blogs, reports on the expansion of the Pool for Open Innovation against Neglected Tropical Diseases.  In this experiment, scientists dump patented information into an open pool, and different users around the world are able to access the data to try to make progress on treatments for neglected diseases.  It will be interesting to watch that story unfold over the next few years.

I guess I don’t really know what SciW2.0 needs to look like to be successful. … But I bet I know a way to get some of the brightest minds in the field together to think about it communally! 🙂  I’d love to hear from people what their ideas are for the future of SciW2.0 and how to make it more commonplace in the field.

Finally, I’d like to say to Baum (and everyone else reading), if you haven’t read Who Moved My Cheese?, then pick it up from the library on the way home tonight and read it.  It will take maybe an hour, and it can be read in the easy chair after dinner while watching 24 if you’d like.  The cheese is moving, Rudy, I just don’t know where to, yet.

By May 10, 2010 8 comments chem 2.0, opinion

Is Chemistry Incompatible with Web 2.0?

(This post is in response to the April 19 editorial in C&E News.  For the response to the May 10 editorial, click here)

A recent ChemJobber post notes that C&E News Editor-in-Chief Rudy Baum‘s editorials sometimes have a tendency to approach the controversial – and sometimes the purely political.  I wanted to discuss this weeks editorial which threatens to call into question much of my online existence (sorry, Mitch.  If Rudy’s right, I think you’re about to spontaneously e-implode).

In this week’s editorial, “The Limits of Web 2.0,” Baum decries the cliché “information wants to be free” for both its out-of-context usage (the full quote says information wants to be expensive because it is valuable and free because the cost of information dissemination is shrinking almost hourly – thus a struggle) and for its lunacy (information can’t wish for anything – it’s inanimate).  Rather, Baum says that it’s people who wish that information would be free.  I’d amend Baum’s correction slightly.  People really want information to be free and readily accessible.  I’d argue public libraries have long made most information “free,” if you were willing to do the legwork to get it.

But the bulk of Baum’s editorial promotes Jaron Lanier’s book You are Not a Gadget: A Manefesto, and summarizes Lanier’s main points, namely that the wisdom of crowds can be dangerous and science should be loath to adopt web 2.0 ideals.  Lanier points out that around the turn of century, a “torrent (a word hijacked by the web 2.0 crowd -ed.) of petty designs sometimes called web 2.0″ flooded the web.  And through the use of web 2.0, we apparently are losing sight of the trees for the forest, er, the taggers for the cloud.

Baum writes in his editorial (cross-posted for free on the web 2.0 CENtral Science blog, natch), “The essence of what Lanier is saying is that individuals are important and that we’re losing sight of that at our own peril in elevating the wisdom of the crowd to a higher plane than the creativity of a single person.”  That is, we are valuing the cloud more than the individuals, when the cloud can’t exist – and has no meaning – without the existence of the individuals.  Lanier notes that collective intelligence can be used well, but only when guided by individuals who can direct the course of the hive mind and help steer clear of common groupthink pitfalls.

But the most interesting quote comes near then end, when Baum quotes Lanier as saying that scientific communities “achieve quality through a cooperative process that includes checks and balances, and ultimately rests on a foundation of goodwill and ‘blind’ elitism.”  I’m not really sure what that means…

But to Lanier’s thesis that science ought to be wary of embracing web 2.0 and its ideals, I find it interesting that Baum writes his editorial at C&E News, the magazine of the ACS, whose flagship publication, the Journal of the American Chemical Society, has featured a JACSβ page for some time now.  The same C&E News whose blog has become so popular that it had to split off into several child blogs.  Where each post for each ACS article has links to share the article on one of several social networking sites.  Where scientists can now browse their favorite article on their iphones with ACSMobile.  While perhaps late to the party in some areas, the American Chemical Society has certainly ‘logged on’ to web 2.0 as a way to export content to the web-savvy scientist.

Plus, we have our own Mitch, a one man walking encapsulation of web 2.0.  His most successful application is, in my opinion, the chemical forums, which typically sees between 8,000 and 11,000 visitors per day.  This blog seems to be a big hit, and his ChemFeeds is a one-stop source for your aggregated list of your favorite journals’ graphical abstracts.  All this innovation on Mitch’s part earned him an interview with David Bradley (of ScienceBase) in his chemistry WebMagazine, Reactive Reports.

There’s also the Chemistry Reddit as another outlet of chemistry news and notes.

In the inaugural issue of Nature Chemistry, the Nature Publishing Group recounted how they have completely bought into web 2.0 as a means of science communication – each issue of Nature Chemistry even features a roundup of their favorite posts from the chemical blogosphere (which reminds me, to the left, Mitch has also created an aggregated rss feed of several popular chemistry blogs).

And, of course, web 2.0 in the sciences has been discussed in the blogs several times over the years.  We have over 3 pages of posts categorized Web 2.0, mostly Mitch’s posts on new web 2.0 platforms he’s developed.  Jean-Claude Bradley writes about web 2.0 in response to a very interesting post at Nascent, a blog from the folks at Nature.

So, all of these prove that web 2.0 has been talked about many times in the context of science.  Has it worked?  With the exception of blogs, sadly I’m inclined to say no.  At least not yet.  And even with blogs (with the possible exception of All Things Metathesis, and In the Pipeline, though Derek isn’t allowed to talk about his work b/c of intellectual property issues), not a lot of academic or industry leaders are prone to blogging.  It’s not like we’re reading Phil Baran’s blog and getting inside his head on a daily basis.

Sure, there is a subculture of people who are active on the web 2.0 scene, but it surely hasn’t taken off as a medium for all chemists to enjoy.  It theoretically should.  Chemists are always benefited from communal sharing of results and information.  But there are still (and probably always will be) people who seem reluctant to join the new technological paradigm.  I like the way Timo Hannay words it in his post on Nascent,

“But it’s not up to the doubters to ‘get it’, it is up to those of us who support these developments to demonstrate their value. And if we can’t then they don’t deserve to be adopted and we don’t deserve to be heard.”

Especially if there are people at the position of Editor-in-Chief for arguably the top chemistry magazine denouncing the web 2.0 movement, clearly it has a ways to go before it will be appreciated by all to the point where web 2.0 is ‘taken for granted,’ where we don’t even realize what we’re doing when we post results and opinions via web 2.0 technologies.

Let’s get moving!