April 10, 2013 § 2 Comments
My twitter feed is on fire, since the announcement of Elsevier having bought Mendeley, after a few months of rampant rumors. “Elsevier is evil ! They will shut down Mendeley ! Mendeley lost its soul ! We should in no way contribute to Elsevier’s business and benefits”. These are a few of the reactions that quickly followed the announcement. What should I do ? Should I care ?
Elsevier has an awful track record: from fake journals to insane profits on journal bundles, to name a few. Everybody agrees on that, and for sure they realized it and are trying to make up for it, somehow. Now that they own Mendeley, they are going to do all sort of crazy things. Maybe, maybe not, time will tell. Mr Gunn seems confident at this point. Others much less, to say the least.
I have a different take on the current events. I am usually a very pragmatic guy. I used to use Endnote, like everybody else a few years ago when there were no alternatives. Their habit was to update the software every year, although I never found any significant improvement in the update. I remember that sometime the update was WORSE than the previous version, breaking my library. And I had to pay 100$, give or take, to update. Every year, although I quickly gave up on the update. No PDF organization, no way to perform full text search. No sync. Quite rough.
Then Papers came out. And it was awesome. Finally a decent PDF organizer, that quickly improved. Not having the choice of my OS (Win), I had to give up on Papers when I came back from the US. Too bad. A windows version has been developed since, but I already gave up. It’s been bought by Springer since, and I’m not sure Springer is any better than Mendeley.
And then I came across Mendeley. It more or less provides everything I need: easy import (I love the DOI look up), easy organization, full text search, cross plat-form sync. I’ve paid for a data plan for a while to have all my files synced between my laptop and desktop computer (Dropbox is not allowed where I work). Works flawlessly. Excellent to insert bibliography in papers I write. Automatic bibtex file creation when I need to use LaTeX. If only they could provide the abbreviated journal name, that would be perfect. I now trow in it every interesting paper I came across, whether it’s directly related to my interest or not. It is thus becoming my personal, curated papers database. The value I get from this software has very quickly become extremely valuable.
And now it belongs to Elsevier. Well, I try not to submit papers anymore to Elsevier journals (although Acta Materiala is a solid journal in my field), I avoid to review for them. I use Scopus less and less since Google Scholar has become extensive. I get little or no value from Elsevier’s products. But Mendeley is different. As I said, I get a lot of value from it right now, and I don’t mind paying 5$ a month for my data plan, it’s worth it. My files are synced across all on my computers. If the situation turns ugly, I don’t lose anything but the time spent migrating to another platform. So for now, I’ll stick to Mendeley, and see what happens.
March 14, 2013 § Leave a Comment
Based on my twitter feed, there were two main news yesterday: the election of an old dude in Rome, and the not very classy decision of Google to kill Reader in a few months. As you can guess, I am much more concerned about that second one, for my daily work routine. I have expressed my love for RSS previously. As of today, my strategy hasn’t changed. RSS is still the best way, by far, to keep track of new articles.
Many people today are claiming that RSS is dead, and twitter will do the job instead. Not at all, as far as I am concerned. I have a very different usage for both. I use twitter to discover recommendations and keep track of the scientific buzz around. The constant flow of tweet is nevertheless a guarantee that I will miss some stuff. It’s ok. It’s in the very nature of twitter. When it comes to tracking new articles in journals, twitter just doesn’t do the job. I use (mostly) Google Scholar to search for article on a topic in which I have some interest. Something specific. But it’s definitely not a tool for systematic tracking of new papers. My current RSS feed currently comprises around 50 journals, 30 blogs, and roughly 40 RSS feed of Scopus search results or equivalent. Since October 2008, I have read over 300k items in Reader. The counter is stuck at 300k for over a year, actually. My current feed provides about 3k items per month (I used to have much more). I spend about 10-15 min per day to keep track of new articles, and usually discover 2 or 3 new papers of interest for me, not directly related to my specific niche (freezing !). If I need to visit every single journal website to get the same information… well, there’s just no way. RSS is still the best choice. No question.
My second constraint is that during my day, I use 2 different computers, a phone and an iPad to check on my RSS feed, depending on where I am and what I do. Reader was providing a flawless solution for the sync. There will be another one soon, that’s ok.
The only question left now is: how long will Google Scholar survive? Reader was much more useful to me, and I guess I’m not the only one like this in the academic world. There are now ads in Scholar. I don’t see why they should even bother keep working on it, unless they have some long terms plans for it that goes beyond the simple search engine it is today. By which I mean an iTunes store-like system for academic papers, for instance.
Will I survive ? Of course, because I don’t have the choice. I will export my RSS feed to another service and keep using it. I will miss the convenience of Google Reader until a better solution comes up. Good bye, you’ve served me well.
January 29, 2013 § Leave a Comment
I’m currently wrapping up a long review paper (>10k words) that should hopefully be published this September. As usual, as a non-native speaker, I ran into many common grammar and style mistakes. Luckily, I have next door a native speaker, and he’s patient enough to correct most of my mistake. He’s my first secret weapon. The second one is this little gem, called The Elements of Style (4th Edition), by William Strunk Jr. and E. B. White. This book is probably the best money I’ve ever spend on a book.
So without further ado, here are my top ten mistakes, that I’ve learned to correct thanks to my two secret weapons:
- You should place a comma after abbreviations like i.e., e.g., etc.
- If you enumerate several terms with a single conjunction, use a comma after each term. Example: “… bla bla bla in materials science, chemistry, and life science”. Same if you enumerate with “or”.
- Put statements in positive forms. It is much stronger.
- Omit needless words. For some reason, we french people seem to be using a lot of these. So here you go, go and mercilessly chase expressions like “the reason why is that”, “the question as to whether”, etc.
- “Due to” is synonym to “attributable to”. Avoid using it for “owing to” or “because of”.
- “Interesting”. It might be interesting to you, but not to everyone else. Remove it. Just remove it.
- “Type” is not a synonym for “kind of”. So get it straight.
- “While”. Just stick to it if you can replace it with “during the time that”.
- Don’t say “very unique”. “unique” is good enough.
- Split infinitive: when you put an adverb between “to” and the verb. I used this form a lot and thought it was cool. Apparently it’s not. Don’t say: “to thoroughly investigate”, say: “to investigate thoroughly”.
This is just the top ten. The entire book is full of stuff like this. Go and get it. And don’t lend it to anyone, you’d never get it back. Do you have another one? Share it in the comments.
January 10, 2013 § Leave a Comment
The #overlyhonestmethods hashtag is crazily popular since it started two days ago. Thousands of tweets are flying around, in a beautiful pluridisciplinary ballet. Scientists from all over the planet are cranking their witty jokes as fast as they can, in an interesting mix of behind-the-scenes insights and private jokes. If you’re a scientist yourself, you can often tell whether it’s a witty joke or a scientific confession. If you’re not, it can be a different story. Reading non-scientists tweets and a few comments on non-scientific sites, like here and there, I realized many people took this hashtag as a confession for scientists. That’s not exactly the case. First hint: scientist are humans too, and as incredible as it may sound, some have a solid sense of humor.
In every place I’ve been, people are working way too much. Scientists are passionate workaholics. Working around the clock. On weekends. At night because that’s the only time where the equipment is available. Skipping lunch. So yes, sometime we need to relieve some of the pressure. We get tired. Our caffeine intake is high, but it’s not because we don’t have anything better than hanging around that coffee table the whole day.
Some of these tweets revealed the frustration we all share, in particular regarding some weird conventions of the writing style or the trending topics.
@eperlste: We used jargon instead of plain English to prove that a decade of grad school and postdoc made us smart. #overlyhonestmethods
@biochembelle: We decided to use Technique Y because it’s new and sexy, plus hot and cool. And because we could. #overlyhonestmethods
@Bashir_Course9: method isn’t described here b/c this High Impact Report is 200 words. see Supplement Appendix L for vague description #overlyhonestmethods
@ProfLikeSubst: This paper represents just the sexiest stuff we could skim from the data. The carcass paper will be dumped somewhere #overlyhonestmethods
Science is also expensive, most of the time. And we have to adapt your dream experiment to the practical and financial reality of the lab. We often have to improvise. And no, we don’t have access to each and every article ever published. Paywalls are still a major source of grief for most of us, my tweet on open-access got >230 RT and >100 faves (and counting). I guess I struck a sensitive point, here. If it helps us get the message to the public, it’s all good news. A few major outlets mentioned it (here and here).
@KayLa_D_87: Compound Q was excluded from study, because it was expensive. #overlyhonestmethods
@talesfromlabs: Compound A was preferred to B because there was leftovers from post-doc who left three years ago. (also B costs $$$) #overlyhonestmethods
@paulcoxon: The beam shutter was held stable by an in-house built support made from BluTak & the top off an old Biro #overlyhonestmethods
I have my share of stories like this. When we are working on the beamline at the ESRF, we work around the clock. If our in-house setup is breaking at 3AM, we don’t go to bed and come back in the morning after a good night’s sleep. We fix it. With whatever we have laying around. Oh, and these in situ freezing experiments we did ? The molds were actually straws from orange juice packs. Perfect diameter, ideal thickness. Why bother ordering expensive technical ones ? The orange juice was actually really bad. And BlueTack is a scientist’s best friend.
Science is hard. Often frustrating. People are moving in and out, and it’s sometime difficult to keep track. It often start from a failed experiment or a mistake, and then it takes a long time to understand what’s going on, so that superstition can be invoked at some point, until we figure out why it’s working this way.
@JacquelynGill: The microbalance was so temperamental that an undergrad named it “Larry” in order to yell at it more effectively. #overlyhonestmethods
@AnneOsterrieder: We don’t know how this method was performed because the PhD student’s lab book is written in a foreign language. #overlyhonestmethods
@aivelo: I’m ready to surrender and write “For no apparent reasons, my method works with only half of the samples.” #overlyhonestmethods
@james_gilbert: Apparatus was placed on the 2nd shelf up, approx 1 foot left of the spider plant. Results were irreproducible elsewhere #overlyhonestmethods
@researchremix: Data are available upon request because then we can tidy the spreadsheet only if absolutely necessary #overlyhonestmethods
@AkshatRathi: It took 10 years of work to write this 6-page long paper, but you wouldn’t be able to guess that from reading it. #overlyhonestmethods
A large number of tweets also revolved around the never-ending chase for grants.
@multisensebrain: Our results have significant implications for that we are seeking grant funding for #overlyhonestmethods
@dbmoore: Our study used string theory, global warming, and big data because that’s where the grant money is #overlyhonestmethods
@peds_id_doc: We’re submitting this half-finished experiment for publication because we ran out of grant money. #overlyhonestmethods
@paulcoxon: This work was made possible by @EPSRC Grant #1234 & @eBay from where we scrounged parts to repair our ancient apparatus #overlyhonestmethods
Finally, some revealed some of the privilege we have. Working in funny locations. Whenever we want. Choosing the people we work with. And considering the many sacrifices we accept otherwise, I don’t feel spoiled doing it.
@Gomblemomble: This part of the experimental work was carried out in Western Australia, because my supervisor has a friend there. #OverlyhonestMethods
So shoud we be worried about the way science is done ? Were these last two days a massive confession of scientific misconduct ? Not really. Partially maybe, at least that’s my feeling.
@Crommunist: I’m just making up a lot of these. #OverlyHonestMethods
We, as scientists, all know it’s a messy business. And guess what, science is performed by humans. Alive. That sometime go to the restroom, enjoy their weekend at home and have babies. But somehow it works and we make progress overall.
@researchremix: The data is old because in between writing the first draft and doing the revisions I had a baby #overlyhonestmethods
January 9, 2013 § Leave a Comment
Here is the raw list, with no particular order. Overall, I didn’t read a lot this year. I didn’t keep track of everything either, so a few are missing. I started reading a lot of popular science book, and really enjoyed it. I am planning to do the same this year. Any advice is welcome !
Non science books
- Le signal, Ron Carlson
- Les corrections, Jonathan Frenzen
- La stratégie du choc : La montée d’un capitalisme du désastre, Naomi Klein
- La Vie mode d’emploi, George Perec
- Dernière nuit à Twisted River, John Irving
- La réserve, Russell Banks
- Armadillo, William Boyd
- Catch 22, Joseph Heller
- L’aveuglement. José Saramago
- La théorie des cordes, José Carlos Somoza
- Lointains hivers. Rigoni Stern
- Paradis conjugal, Alice Ferney
- La conjugation des imbeciles, John Kennedy Toole
- Le bibliothécaire, Larry Beinhart
- Un bon jour pour mourir, Jim Harrisson
- L’île des chasseurs d’oiseaux, Peter May. My favorite of the year. Absolutely terrific. Much better than his other books.
- La promesse de l’aube. Romain Gary
- Le hussard sur le toit, Jean Giono
- Critical mass, how one thing lead to another, Philip Ball. I love Philip Ball.
- Life’s Matrix: A Biography of Water, Philip Ball. My favorite science book of the year.
- The Structure of Scientific Revolutions, Thomas Kuhn. A classic.
- Branches: Nature’s Patterns: A Tapestry in Three Parts, Philip Ball. I love Philip Ball. Oh, did I already said it ?
- Théorème vivant, Cédric Vilani. The making off of a Fields medal. Awesome.
- Reinventing Discovery: The New Era of Networked Science, Michael Nielsen. An eye-opener for me.
- Sur les épaules de Darwin: Les battements du temps, Jean Claude Ameisen. in French. If you enjoy the radio show, you’ll love the book. I already offered it twice.
January 7, 2013 § Leave a Comment
Here’s a snapshot of my main side project, using my new favorite software: Gephi. Click for full size.
Hint: this is a network of people.
October 23, 2012 § Leave a Comment
August 23, 2012 § Leave a Comment
Almost back to the lab. It’s been a good summer with the boys, mostly at home. Reading books, papers and blog posts when I had free time. Which does not occur so often with children less than 5 years old, as anyone in the same situation can testify.
A lot of heated discussion are occurring online now about open access and data mining. While some benefits are straightforward in certain domains such as genetics or chemistry, this is a brand new world to explore. I came across the fascinating comments by Philip Ball on chematica, a network of the transformations that link chemical species. Chemistry is not really my cup of tea, and I don’t have any of the coding abilities, unlike prominent data miners like Peter Murray-Rust. One thing I have, though, is a Mendeley library stuffed with papers (over 1400 as of today). Since my main focus now is on this ice-templating thing, I have a bit more than 350 papers on this topic only.
In addition, I am also fascinated by issues related to presenting data, aka the visual display of quantitative informations , as described by Tufte, among many others. I’ve been playing with Wordle before , it’s all over the internet now. Wordle are beautiful clouds of keywords, where the size of the words relates to their occurrence in a list or a text. You have a good example with the display of keywords in the right column of the blog page.
Today, I did some quick and dirty analysis of my collection of papers. Exporting the Mendeley data to a bib file, I compiled lists of titles of the papers in my library. I used the freely available wordle website. The whole process was really fast, like 15 minutes or so. The first result I got is shown below (clik to enlarge).
Well, as you can expect, being interested in porous ceramic materials templated by ice crystals, these keywords are obviously dominating the wordle. In the upper right you can find “zirconia”, reminiscent of my PhD on the low temperature degradation of zirconia containing ceramics. This was in the pre-Mendeley years, I don’t have many papers left on this topic.
Things get more interesting if I restrict the analysis to the titles of the papers related to ice-templating. I got about 340 of them. I’ve followed really closely the ceramic domain, and much less the polymer field. Polymers are thus largely under-represented in the following analysis, although ice-templated polymers came first.
The first obvious observation is the absolute domination of “freeze”, “casting”, “porous” and “ceramics”. They are almost in every tile. So if you want to be original, don’t come up with a paper entitled “freeze casting of porous ceramics”. The other dominant keywords are “structure” and “properties”, which is a pretty good image of the current approach to the phenomenon. Freeze whatever you have and look at the structure and properties. Not groundbreaking, most of the time. But the underlying mechanisms are so complex that very few people are willing to tackle them. “Tissue” and “scaffolds” are pretty strong too, and tissue engineering have indeed been one of the main focus so far in terms of potential applications. “Ice” is less prominent than “freeze”, and reflects how people are currently describing the process, “freeze-casting” instead of “ice templating”. I am not a big fan of “freeze-casting”, since it was originally used to describe the processing of dense materials. Although pretty much everyone is doing porous materials, “freeze-casting” still dominates. “Ice-templating” exclude all solvents other than water, so it’s not perfect either.
I also did the same analysis compiling all the abstracts. This is much closer to mining the full text of the papers. The output is much more balanced.
“Pore”, “porous”, “structure” and “freeze” still dominates, but the relative occurrences of other keywords is much more balanced. Since people tend to report almost exclusively positive results, we got a lot of “increased”, “high”, “new”, “novel”, “potential” “significantly” and “significant”, better represented than “low” and “decreased”. “Defects” is noticeably absent, although it remains a major issue of the process. “Control” is missing from the wordle (well, not really missing, but it’s really tiny), a fair representation of the majority of the papers, where people exert no control whatsoever. Freeze and see.
“Properties” is relatively large, although people are almost exclusively looking at mechanical properties (hence the presence of “MPa”). People became interested only very recently in other properties, such as conductivity or piezoelectricity.
Regarding materials, “silica” and “alumina” are the only ones found here. A lot of room for testing other materials, and therefore other properties. “Water” and “camphene” are of similar size, as people are equally interested in both solvents.
Missing keywords are equally interesting. “Colloids” is hardly visible, although everyone is dealing with colloidal suspensions. Ceramists are usually talking about slurries instead of colloidal suspensions, which is why we get “slurry” and “slurries” instead. Maybe. I still believe we have a lot to learn if we look at the colloid science papers.
“Interface” is the other elephant in the room. The control of the process largely depends on controlling the interface, and is something that people have largely ignored so far.
Without digging too much into the details, this quick and simple analysis is very informative about the current state of the art. Having followed very closely the domain for the past 5 or 6 years, the keyword clouds obtained here are very representative of the current state of the art. I’d love to extend this analysis to the full text of the papers, although I will need different tools to do it. Maybe I should get an access to the Mendeley API. They are responding to over 100 millons calls to their database each month, they can surely afford a few more. In the meantime, I’ll try to apply the same analysis to a different domains, using Google Scholar or Scopus and Mendeley. More later if I’m successfull.
Funny coincidence, this month’s issue of Nature Materials was released today while I was playing around with this analysis. Check out the front cover…
August 11, 2012 § Leave a Comment
It’s really hot in summer, where we live. Usually the hottest place in France, actually. From mid-day to late afternoon, it’s usually better to stay inside, where it’s a lot cooler. A good period to read books. I read three good scientific ones lately.
H2O, A biography of water, by Philip Ball. He’s probably my favorite science writer, and I enjoy his frequent columns in Nature or Nature Materials, among others. He’s the one that taught me, following our Science paper, that ice has been used as a structural material… for planes ! This book is truly excellent. Philip Ball is giving us a grand tour of water, through history and the various domains of science, from chemistry to biology or geophysics. I particularly enjoyed the history of water through the centuries. Hi style makes it a joy to read, I could hardly put it down. Lots of gems like this one (maybe because I’m getting into antifreeze proteins lately):
If fish conducted scientific research, you might expect them to set up whole institutes devoted to studying supercooled liquids, since their very existence depends on this precarious state.
Design in Nature: How the Constructal Law Governs Evolution in Biology, Physics, Technology, and Social Organization, by Adrian Bejan and J Peder Zane.
I wasn’t aware of the constructal theory until I read that book, and that was quite a fascinating read. The constructal theory is about how design in nature arise from a simple law, the constructal law, which is basically how stuff (mass, materials, ideas) flow. Design of things are evolving towards an always better flow. The authors are aiming high, applying their theory to pretty much everything you can think about, from lungs, rivers and trees to universities and animals. Although I don’t agree with all of their ideas, such as their claim about the very existence of trees (which are supposidely the most effcient way of moving water from the soil to the atmosphere), it was a stimulating read nonetheless.
Visual Strategies, A Practical Guide to Graphics for Scientists and Engineers, by Felice C. Frankel and Angela H. DePace.
This one is all about how to design figures or graphics to convey scientific ideas, whether it’s for a paper, a poster or a grant application. Beautiful illustrations and some interesting stories, but I found too many examples and too little theory. If you are not familiar with graphic design, it’s difficult to translate the examples provided into usefull lessons you can applied. A good book, still.