science policy

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

Space dinosaurs, the saga continues

Last week I , and several others , wrote about the extraordinary and unfounded conclusions published in a JACS perspective, that dinosaurs may have evolved into intelligent life elsewhere in the universe.

Well it gets worse, because as Stuart Cantrill (editor of Nature Chemistry) pointed out on twitter (@stuartcantrill), this isn’t the first time Prof Breslow has made these claims. Nor in fact is it the first time he’s published this article. It also appeared in the Israel Journal of Chemistry last year. Huge chunks of the JACS article are copied verbatium from the IJC review.

Here’s Stuart’s analysis of the JACS article, he’s highlighted the bits that appear in the IJC review. The subsequent pages are covered with just as much highlighter pen.

I wonder if JACS’s has a policy on self plagiarism?

EDIT: Here’s the self-plagiarised sections from the remainder of the paper.
It gets worse - pages 2, 3, 4 & 5 of #spacedino Perspecti... on Twitpic

It gets worse - pages 2, 3, 4 & 5 of #spacedino Perspecti... on Twitpic

UPDATE: Breslow defends himself to Nature

UPDATE 2: Here’s a copy of the email I sent to the JACS editors yesterday. If I hear anything back I’ll be sure to let you know.

Dear Editors,
I am sure you are aware of the controversy surrounding Prof. Breslow’s perspective article recently published in JACS ( http://pubs.acs.org/doi/abs/10.1021/ja3012897). The concluding comments concerning, what has become known on twitter as, the spacedino story has been the subject of discussions on numerous blogs. E.g. http://www.chemistry-blog.com/ & http://blog.chembark.com/2012/04/12/breslow-and-dinosaurs-in-jacs-oh-my/

The consensus is that the spacedino comment was just a poor joke, however there is much more concern about the issue of self plagiarism. The majority of Prof. Breslow’s JACS article is copied verbatim from a review he published in Israel Journal of Chemistry ( http://onlinelibrary.wiley.com/doi/10.1002/ijch.201100019/abstract) last May. The fact that it then appeared in JACS seems to run contrary to your ethical guidelines ( http://pubs.acs.org/userimages/ContentEditor/1218054468605/ethics.pdf) which state:

Authors should not engage in self-plagiarism (also known as duplicate publication) – unacceptably close replication of the author’s own previously published text or results without acknowledgement of the source. ACS applies a “reasonable person” standard when deciding whether a submission constitutes self-plagiarism/duplicate publication. If one or two identical sentences previously published by an author appear in a subsequent work by the same author, this is unlikely to be regarded as duplicate publication. Material quoted verbatim from the author’s previously published work must be placed in quotation marks. In contrast, it is unacceptable for an author to include significant verbatim or near-verbatim portions of his/her own work, or to depict his/her previously published results or methodology as new, without acknowledging the source.”

I write for http://www.chemistry-blog.com and I would very much like to share your comments on this issue with my readers. We are particularly keen to hear why Prof. Breslow appears to have been exempt from your ethical guidelines.

Yours Sincerely,

By April 24, 2012 16 comments science news, science policy

5 million gallons and 2 years later…

If I were to walk outside right now and ask the next person I see what the words “Deepwater Horizon” brought to mind, I wouldn’t be surprised if he/she simply stared at me with a puzzled look. Yet exactly two years ago, we all watched the news as the story of the Deepwater Horizon oil rig explosion developed. It would ultimately become the worst man-made ecological disaster in history as the uncapped well poured nearly 5 million gallons of oil into the Gulf of Mexico. Many of us chastised the oil companies, BP in particular, for being too concerned with profits and expected the government to take action to prevent future spills. Now, two years later, the storm has quieted down but how much has things really changed? Here are some facts/figures I collected:

BP has paid out just 7.8 billion dollars for economic losses/medical bills to affected people, though it claims a total of 37.2 billion spent in response to the disaster. By comparison, BP had a total revenue of 386 billion dollars in 2011 alone.

The Gulf spill is not the only oil disaster in the last two years. Lost in the media coverage and the aftermath are spills in Utah (June 2010, 33000 gallons), Michigan (July 2010, 1.1 million gallons), Montana (July 2011, 63000 gallons), and countless other spills in foreign countries but from American companies.

Though the Oil Spill Commission ultimately concluded that BP did not sacrifice safety for profits, it also noted that a number of decisions made by BP to speed up construction of the oil rig increased the risks of a disaster. A recent report from former commission members noted that Congress has done very little to improve regulations on offshore drilling. For example, the current liability cap for an offshore oil spill is still a mere 75 million dollars.

I’m sure that decisions are made every day that have significant ecological impact but are necessary for the benefit of society. However, I certainly had hoped that the environmental impacts would remain minor. If something like the Deepwater Horizon disaster can’t galvanize the public into demanding long term changes, then what will it take? What can we do to reach a so-called “tipping point” when we as a society realize that environmental problems need to be solved now?

By April 21, 2012 5 comments opinion, science policy

Helium for balloons but none for my NMR

Our reserves of helium are finite and we’re running out. This may come as a mild disappointment to children everywhere but its really bad news for science.

My (and everyone else’s) NMR machines use liquid helium (at 3 Kelvin) as the coolant for their superconducting magnets. The same goes for MRI scanners and those cathedrals of science the particle accelerators like the LHC. And right now there’s a world wide shortage of helium which means that we may have to decommission some of our NMRs. Re-commissioning them will then cost 10s of thousands of dollars, plus it would require huge amounts of liquid helium to cool them down again.

We fill these instruments with liquid helium regularly, replacing the stuff that’s boiled off. The thing is that once that helium has evaporated off and into the atmosphere its gone. There’s no getting is back. So why don’t we bother collecting the boiled off helium? All we’d need to do is stick a balloon on top of the NMR machine, then a simple compressor could be used to turn it back into a liquid.

We don’t bother with this simple bit of recycling because there’s no immediate economic imperative. But hang on, didn’t I just say the reserves are limited, so surely helium is really expensive? Well it aught to be. According to Professor Robert Richardson, who won the Nobel physic prize in 1996 for his research on helium, a helium party balloon should cost $100. Instead they cost about 50 cents. The reason helium is sold well below its ‘real’ value is because of an odd law passed by the US congress in the 1996. Robin McKie explained some background in The Observer newspaper last month.

 In the 1920s the US decided helium would be a strategic resource. It realised that air power would be crucial in future wars, and assumed that these would be fought by airships that would use helium to float.

Then to cut costs in 1996 Congress passed a law mandating the U.S. helium reserve (the largest in the world by some way) be sold off by 2015, irrespective of market price. They set in stone the amount of helium that needed to be sold and so ever since they have been dumping it on the market.

This is a long term issue, but it doesn’t explain the immediate shortage. The problem here, as far as I can gather because our suppliers (BOC) aren’t telling us much, is that several of the worlds helium refineries are out of action. That, at least, was the case 10 months ago according to gasworld.  And they don’t expect things to improve until a new plant comes on line in 2013.

In the meantime it looks like there’s going to be a long queue for the remaining NMR machine.

25th April UPDATE :

Here’s the latest on the helium situation from BOC in the UK.