The way-it-should-be-ness

The BBC have published an audio slideshow called Chair Champions on Charles and Ray Eames, designers best known for their furniture. The Eames Lounge Chair is probably their most famous work.

I like well-designed things. Not in the sense that they look a particular way, but that they fulfil a specific function extremely well. The couple designed objects that were both functional and stylish. The following from the end of the slideshow has stuck in my mind:

“Charles and Ray had this idea that good designs had ‘way-it-should-be-ness’. If something was really well-designed, then the idea of it being designed shouldn’t come up at all.”

I love this idea of ‘the way-it-should-be-ness’. In my own work, I try to find solutions to problems that are elegant. I want my solutions to have ‘way-it-should-be-ness’. Writing my MRes report led me to reflect on the last year and I’ve noticed that this desire to get the perfect solution has actually been a bit of hindrance.

I spent far too long sat at my desk searching the literature for the best solution. When I finally settled on a plan, it was a bit of a long shot. If it worked, it really would have been awesome. But it didn’t. The paper that I based my idea on was almost certainly suspect.

Around the time I was working on the dodgy reaction I read Tim Harford’s Adapt: Why Success Always Starts with Failure. It’s quite good. He’s like a better Malcolm Gladwell. Harford summarises the way Russian engineer Peter Palchinsky, who ended up being executed by the Soviet government for criticising them, solved problems as three ‘Palchinksy principles’:

  1. Seek out new ideas.

  2. When trying something new, do it on a scale where failure is survivable.

  3. Seek out feedback and learn from your mistakes as you go along.

I like them. I do the first, but my problem lies with the other two. Over the last year everything depended on this one reaction—a risky, naive strategy. There was little feedback and refinement. I ended up rushing another reaction towards the end so that my report on ended on a high note. After all, no one likes a sad thesis.

I bet Charles and Ray Eames didn’t come up with their objects overnight. There must have been hundreds of drawings and prototypes of the Eames Lounge Chair, but it’s easy to forget them as you only think of the final product. They probably worked in a similar way to Palchinksy.

Now I’m making an effort to work more iteratively. I still think of rather grand ideas, but instead of going for it in one enormous optimistic leap, I’m working towards them bit by bit, in a process of steady refinement.

I’ve already had some success last week working in this way. It gives much more positive mindset of working too. Hopefully I’ll soon have my own chemistry equivalent of the ELC and after refining it down I’ll look at it and think “yep, that’s the way it should be.”

Forget the scotch tape: how to make loads of graphene

Earlier this year I was writing a review about transparent conducting materials for organic electronic applications. As part of it, I wrote a fair bit about graphene. One of the key problems is that it’s difficult to scale the desirable properties of small pieces of graphene to large areas without resorting to quite challenging techniques.

In 2004, when Geim and Novoselov managed to isolate single-layer and few-layer graphene, they did it using Scotch tape to “mechanically exfoliate” graphite—basically using Scotch tape to peel off a layer of graphene from the graphite.[^Geim2004]

This technique gives very high quality crystals of up to 10 micrometres in size, but it’s limited to laboratory scale production—you’re not going to use this in a factory to make components for electronic devices. When I was writing the review, I wanted to write something along the lines of “…mechanical exfoliation, whilst producing very high quality graphene, is impossible to scale up…” but my supervisor told me to change it to something less definite, hinting these things have a habit of a coming back to prove you wrong.

To my surprise, someone has managed to scale it up. Chen and co-workers recently published a paper describing mechanical exfoliation of graphite using a three–roll mill.Sketch of the three roll mill set up used by Chen et al. to mechanically exfoliate graphene.

Sketch of the three roll mill set up used by Chen et al. to mechanically exfoliate graphene.

First they prepared an adhesive (polyvinylchloride (PVC) in dioctyl phthalate) which was poured between the feed and centre rolls. They then started rolls rotating then spread the graphite powder onto the adhesive. The adhesive runs in an S shape around the rolls. The graphene is continuously exfoliated to give graphene, unlike the scotch tape method where you exfoliate once with each application and removal of the scotch tape. After 12 hours of operation, you collect the material, wash it and then burn off the PVC to get the graphene. There’s a video (direct link) in the supplementary information showing the mill in operation.

I’m not entirely sure why anyone would want that much graphene in this form. For transparent conducting applications (where you want to maximise transparency and minimise electrical resistance) it’s likely you would still have high electrical resistances between flakes of graphene and poor performance. But it’s still a clever way of scaling up what, to me, looked like a completely unscalable process. I won’t be so certain when writing in the future.

[^Geim2004]: K. S. Novoselov, A. K. Geim, S. V. Morozov, D. Jiang, Y. Zhang, S. V. Dubonos, I. V. Grigorieva, A. A. Firsov, Science, 2004, 306 (5696), 666-669. DOI: 10.1126/science.1102896.

Sentences were written

Yesterday I was dicussing a draft of my MRes thesis with my supervisor and one of my questions was whether, in a few particular cases, I should write in the active or passive voice, and if I do use the active should I use the pronoun we or I?

Active or passive?

The sentence I had written was (key bit emphasised):

Despite Bloggs et al.’s description of the growth precursor as “extraordinarily stable”, I found that the growth precursor formed a fine red-brown precipitate within approximately 30 min of being loaded into a syringe, blocking the syringe outlet.

To begin with please ignore whether you think that’s a good sentence or not (I’ve read it so many times I’m beginning to think the word order is completely wrong).

It’s written in the active voice: I (the subject) found (the verb) that something was the case. I chose to use the active because I want to make it clear that I found that the precursor was unstable, in disagreement with what some other researchers found. I also tend to choose the active voice because it’s more direct; the passive can feel rather viscous and verbose. I’m often told to make it easy for the reader.

I could take out I:

Despite Bloggs et al.’s description of the growth precursor as “extraordinarily stable”, the growth precursor formed a fine red-brown precipitate within approximately 30 min of being loaded into a syringe, blocking the syringe outlet.

It’s readable, but I don’t like it because it’s slightly ambiguous.

In the passive voice (I think—this just sounds incredibly weird to me so I could be wrong):

Despite Bloggs et al.’s description of the growth precursor as “extraordinarily stable”, the growth precursor was found to form a fine red-brown precipitate within approximately 30 min of being loaded into a syringe, blocking the syringe outlet.

Both ambiguous and horrible. Hence I chose the first option: active and I.

I, we—no one?

But the problem now is the dreaded I. It does sound a bit schoolboyish. We is used in scientific writing all the time, but I—shudder—never, because science isn’t conducted by individuals, but by groups. In fact, no, not even groups, but by the whole scientific establishment. No one does science, science does itself! Hmm… But ignoring that, I does make me cringe a bit.

Putting we in place of I is significantly less cringeworthy but completely nonsensical. It always amazes me to see a single author paper start with “We [verb]…”. Is I really that repulsive? Is it meant to give an illusion of absolute truth? Perhaps it’s meant to say “this is not my opinion , it’s scientific fact”, but there’s always a personal element in science and to pretend it isn’t there is ludicrous and delusional.

So I’ve got to decide whether to stick with I or not. It’s only my MRes thesis not my PhD thesis, but I still care about the details. I’m definitely not writing we. My supervisor was told by his supervisor to do a find on “we” and replace with “I”. I’m leaning towards I because it’s concise and unambiguous about was my work (apparently it’s good to show in an MRes that you’ve done a good amount of work) and, whilst it may be a bit cringeworthy, it is definitely the easiest to read. Hopefully the mysterious anonymous marker will agree.

Negative results and dodgy papers: keep quiet or publish?

Negative results are very rarely published in the literature. After all, the literature is bursting with new positive results and we don’t have enough time to read all of these, let alone papers describing what doesn’t work. Negative results are dull—who would want to read anything in the Journal of Negative Results?

Up until recently I haven’t had a problem with the status quo. I’m afraid the following discussion is a bit vague because I’m (still) not sure about how much detail I can go into my work, but please bear with me.

I came across a paper published this year which describes the effect of doing something quite specific in a synthesis on nanoparticle shape. Do the thing, get a particular nanoparticle shape (usually quite challenging to obtain); stop doing the thing, you get another shape (easy to obtain). I was quite excited because if it worked it would get around a major barrier to my desired nanoparticles.

I repeated the reaction exactly as the paper described, but it didn’t work.

I repeated the reaction in a flow reactor as it would make it easy to intensify the “thing”. According to the paper, this should definitely give the desired nanoparticles because the morphology selectivity/yield is directly proportional to the intensity of the “thing”. But it still didn’t work.

I’ve now given up on the reaction and moved on to something else. But that my results will not be published means that someone else could also waste a lot of time and money—on equipment, reagents, electron microscopy—repeating the experiment.

What can I do? I think I have three options:

Option 1: Do nothing.

I’ve already made it clear that I don’t like this option. I’m fairly sure the paper is wrong. It bugs me that it exists without some kind of mark against it.

Option 2: Email the authors.

I’m not too keen on this either. I suspect that my email would be ignored. Plus, I would rather any discussion happened in the open, which brings me on to…

Option 3: Blog about it (and possibly email the authors telling them that I blogged about it).

I feel uneasy about this. Could it be perceived as confrontational? Would I get a reputation as a troublemaker? I feel like it is the proper, scientific and open thing to do, but in reality it is absolutely not the done thing. I suspect most researchers would go for option one and do nothing. I could be right and the paper is wrong, but I’d be very happy to be proven wrong and get the reaction working.

What you think? Keep quiet, email or blog? Any other suggestions are welcome.

Friday Night Experiments

Tonight I watched a BBC documentary about Nobel Laureate Andre Geim. Each episode of Beautiful Minds (am I alone in thinking the title is a little bit naff?) covers the story behind the success of a particular scientist. Geim is a really interesting character and I recommend watching it.

One part I found particularly inspiring. He attributes a lot of his success to “Friday Night Experiments”, during which he does some quick experiments to try out new, more adventurous ideas. It was during one of these that he discovered that you can use scotch tape to mechanically exfoliate graphene from graphite.

Obviously there were loads of unsuccessful Friday nights before the discovery of graphene. He went on to say that the most important thing to remember is to know when to cut your losses and try something else. By trying out lots of new ideas every week, seeing what doesn’t work and what is promising, he has made some great breakthroughs in a wide range of fields.

I can see how for a postgraduate it is easy to become obsessed with getting a particular experiment to work or become completely blinkered on a particular sub-sub-sub-area of a discipline. You are meant to work really hard on a particular area in a PhD after all. But rather than working solely on one approach to my research, Geim has inspired me to get in the lab and try out some of my slightly more adventurous ideas every now and then. Most probably won’t work, but one might.

First conference: any advice?

On Monday I’m going to my first conference! It’s titled Continuous Flow Technology in Industry (more detailed information here if you’re interested). I’m not presenting anything, just attending.

I came across it on a Royal Society of Chemistry mailing list and thought it’d be good as it’s quite closely related to my group’s work[^groupwork] (four of us are going). It’s relatively small in size (no parallel sessions) so I thought it’d be a reasonable choice of first conference. I hope to pick up some ideas that will help solve a few particular problems in my own work.

I’ve been wondering whether there’s anything I should do in preparation. I’ve consulted my trusty guide The Unwritten Rules of PhD Research but, aside from networking (which I’m fairly happy about), it doesn’t have that much to say on the topic unless you’re presenting.

I’ve looked up all the speakers to have a quick look at what they do, but the majority of them are from industry so they don’t have a web page summarising their work like most academics. I’ve got myself some Imperial-branded business cards.

I’m unsure whether to take my laptop. I’m leaning towards no, as I think it’s a bit rude to sit typing away (and it won’t do my hands any good either). I could always read a couple of papers if a particular speaker is really that bad.

Does anyone have any advice? Please let me know in the comments.

[^groupwork]: See this paper for my group’s most recent publication on our work on flow chemistry.

The death of my paper lab book?

Nature recently had a feature on the “paperless” lab which mostly focused on electronic laboratory notebooks (ELNs). As a computer nerd, I’ve been thinking about using one for a while.

ELNs have lots of advantages over paper notebooks. They’re searchable, easily backed up and can automatically incorporate data from instruments—no more cutting and pasting. Businesses like them as it’s easier to find out what an ex-employee did in an ELN than in loads of paper notebooks.

I’ve always used the my department’s standard synthetic chemistry lab book which has a risk assessment and reaction scheme on every left page and lines on every right. It works quite well. I number every reaction TWP001, TWP002 etc and samples are labelled TWP001-A, TWP001-B, etc. Spectra follow a similar convention, e.g. TWP001-A_em_spec.txt or TWP001-A_abs_spec.txt, and all data and code used for data analysis is kept in a folder called TWP001_brief_description.[^git]

But there are a few things that I really hate about paper lab books. Going back through my notes when writing up work is a real chore, especially with seemingly never ending notes along the lines of “same as TWP050 except…”. Reaction TWP050 says: “same as TWP049 except…”. With an ELN you can just copy and paste.

The inherent linearity of a paper lab book is a pain. Entries are in chronological order and reactions are performed sequentially, one at a time, but I usually work on two or three reactions at a time. Leaving blank pages looks sloppy, but cramming notes into small gaps is messy.

The biggest problem is that paper notebooks have become incomplete records of research in the modern laboratory. A lab book should be a complete record of your thoughts, observations, measurements and results. However with modern lab instrumentation it’s impractical or impossible to include all the data by printing, cutting and sticking it in. For example, a search on my computer (not a look in my lab book) reveals 510 UV-vis absorption, fluorescence and excitation spectra recorded since August 2010. There’s no way I could print that out (and even if I did, the data is useless in that format). Furthermore, a paper lab book can’t capture any of the data analysis on the computer. My MATLAB (and now Python) code is riddled with comments. With paper lab books, this information is highly fragmented.

Considering these problems I’ve been looking at electronic alternatives for some time, but what I’ve disliked about them boils down to two things: inflexibility and how they handle data. They seem to try to fit everything into a particular template or form. With a paper lab book, I can write and draw whatever I want, which is important to me as I’m not a “normal” synthetic chemist—I with flow reactors and I’m more interested in my residence time than yield.

I want to be able to access my plain text data files as plain text files and not have them converted into horrible proprietary binary formats subject to the whims of the ELN vendor. Think of the hassle caused when Microsoft switched from .doc to .docx—I don’t want this happening with my data. Plain text files from 30 years ago can still be read today and will be readable for longer than I’ll be alive. It also worries me that a web based ELN could disappear and leave me with a load of horribly formatted files to wade through.

Researching online I found advocates of open notebook science—the (left field) practice of making your entire lab book and data available online as it is recorded—using blogs and wikis as ELNs. Cameron Neylon’s blog-like open lab book used the University of Southampton’s free LabTrove software. Lab book entries are like blog posts, with attachements for data, and you can organise posts using tags, e.g. “NMR” or categories, perhaps to organise posts related to a single reaction. Jean-Claude Bradley’s group notebook, called the UsefulChem Project used a wiki. I really like Bradley’s wiki and there are lots of nice examples if you click about on the list of reactions. His group upload and link to spectra and photographs—a complete research record.

I did a bit more research into using a wiki for an ELN and they seem to be the perfect match. They’re flexible in terms of organising data however I want and pages are versioned so you can see what was written when. There are loads of different wiki applications available, so I narrowed the possibilities down with the following criteria:

  • active development
  • proven large scale deployment for stability and reliability
  • open source and free
  • page access control
  • supports attachments
  • self-hosted because I don’t trust anyone
  • written in a nice programming language
  • stores data nicely, i.e. not binary formats

This boiled down to MediaWiki (runs Wikipedia), FosWiki (used for loads of corporate intranets) and MoinMoin (large scale deployments are the Apache Software Foundation, Python and Ubuntu wikis).

MediaWiki doesn’t handle attachments very well for ELNs since attachments are available globally, i.e. across the whole wiki at the top level rather being linked to individual pages. The latter makes more sense to me as spectra or photos (the attachment) are related to the experiment (the page) rather than the whole notebook (the wiki). MediaWiki is designed for open content, so it doesn’t do access control without dodgy extensions. It’s also written in PHP, which I have no intension of learning. So that’s MediaWiki struck off.

FosWiki is aimed at corporations, which I think you can tell from it’s look and feature list. It’s also written in Perl, which I really don’t want to learn. So that’s FosWiki gone.

Last is Moinmoin. Unlike MediaWiki, attachments are linked to pages. MoinMoin is written in Python, a really nice language I’ve started to use instead of MATLAB, so there’s the possibility of writing my own extensions. It’s currently at version 1.9.4, so it should be very stable, and version 2.0 is under active development. It’s very clean and tidy.

I spoke to my supervisor about an ELN and he was extremely keen so I’ve decided to give MoinMoin a go. I’ve installed it on a Linode virtual server running Ubuntu linux.[^VPS] It took a about 6 hours to install the whole server from scratch—not bad having never administered a server before! Initially I was a little worried about security, with data being on a internet server, but I’ve locked down the server pretty tight and am going to make off site backups to my office machine. If anyone is interested, I’ll write up how to set it up.

It would be cool to make MoinMoin chemically-savvy—perhaps by pulling in data from ChemSpider or Wolfram Alpha, or COSHH info from Sigma-Alrich? I think this could be done with a little Python scripting. I’ll open source anything good for others to use. I’m also planning on setting up an old scanner in the lab to upload paper drawings.

This could all prove to be an embarrassing experiment or even a complete nightmare and ending with me dusting off my most recent lab book and finding a pen. On the other hand, it could be great. We’ll have to wait and see!

[^git]: I use Git to keep track of all changes to the files in each experiment folder. I don’t know anyone in my department who has heard of it, which is a shame as it’s a great tool. I’ll blog about it sometime.

[^VPS]: I could have installed it on a dedicated machine in the office, but we’re a bit short on machines and didn’t want to have to deal with hardware.

*[COSHH]: control of substances hazardous to health *[ELN]: electronic lab notebook

Questionable research practices, peer review and an open access future?

Blimey—it’s been five weeks since my last post and I’m now a five weeks into my postgraduate studies. It’s gone quickly and I’ve been very busy.

As part of the doctoral training centre’s new/modern/[positive adjective] approach to a PhD we get (well, have) to take courses that ’round us out’ as modern researchers. A few weeks ago, we had a course on research ethics taught by Marianne Talbot. I did Philosophy A-level and especially enjoyed moral philosophy, so I was looking forward to it.

The course was attended not just by PE DTC students but also the CQD and TMS DTCs. Rather unsurprisingly (but disappointingly) there was a bit of a unfriendly vibe between the different DTCs. “We get MacBook Pros!” said one, “we don’t have to do experiments!” said another, to which we all replied “we get £18,000 to spend and we like lab experiments!” The conversation never progressed any further…

Overall the course was excellent and very enjoyable. I loved how Marianne dealt efficiently and firmly with the few people who wanted to deny the existence of everything! One of the afternoon sessions was on open access publishing, a topic I already had an interest in. I’ve read about it before but have never been entirely convinced (I’m not sure why). Marianne gave a strong case for open access is good. She referenced this website as a good overview. If you don’t know what open access is, then it’s worth a quick read. There was unanimous support of the open access concept.

Marianne then introduced a distinction I had never heard of before: green and gold open access methods. In the green method, papers are deposited in a public online repository. Papers are not peer reviewed prior to being published and anyone can upload an article. The most famous example of this is probably arXiv. In the gold method, you submit a paper to journal, it’s peer reviewed, and if accepted it’s published in a journal that is either entirely open access or permits some open access articles. An example of the former type is PLoS ONE.

The question Marianne asked us to discuss was “Do you think it is acceptable for scientist to self-archive pre-prints in repositories with peer-review?” The answers from students were quite vague. But generally it seemed that peer review was held in extremely high, almost reverent, regard.

I found this odd considering we had just been discussing questionable research practices. One example of a questionable research practice that stuck out to me was:

leaving important information out of methodology section of a manuscript or refusing to give peers reasonable access to unique research materials or data that support published papers.

One would expect that if peer review functioned as well as my fellow students said then readers would rarely come across this practice in the literature. Yet in my field of research, I encounter it all the time! Authors brag that they’ve found the way to make the biggest, smallest, longest or generally ‘best’ nanoparticle but then fail to tell you crucial information such the number of moles of reagents, reaction times and temperatures that allow you to repeat the work. I spent an unbelievable amount of time last year trying to figure out the required conditions to synthesise heterostructured quantum dots. If peer review did it’s job, then things like this wouldn’t get through.

Other students were arguing that because anyone can publish a paper in a green OA repository that there is no quality control. I disagree. I think a lot of students are assuming that readers are idiots and need peer review. If you uncritically read a paper or think that because it’s in a journal it must be true then you’re at best naive or at worst incompetent. Decent researchers will spot questionable claims and results.

Is peer review even really that good a quality control method? Typically you only have two reviewers. Can you be sure they read the paper instead of give it to a PhD/postdoc?

Imagine that rather than submitting papers to traditional peer reviewed journals researchers published their work in open access green repositories. No real scientist is going to post rubbish because their reputation is on the line. Rather than having only two reviewers as with traditional journals, you could have tens or even hundreds of reviewers. They could post their comments—the peer review—publicly on the repository article page (I’m thinking more along the lines of threaded discussions rather than linear blog-style comments).

I think it would be awesome. The authors could respond to readers’ questions, for example, asking for clarification of an experimental technique or reagent used, or post new versions of the article correcting mistakes or providing further information.

At present, reviewers’ comments are made privately and anonymously. These comments would be useful to the scientific community. There’s no reason why it should stay private. Science is all about debate, questioning and (a moderate dose of) scepticism. At conferences and in department presentations, researchers handle criticism and questions. There’s no reason why journal articles should be any different.

I do wonder whether I’m being overly optimistic or if I’ve missed out something crucial. What do you think? I’d like to know…

[^mywork]: I hope to blog about my work in less vague terms at some point but I’ll probably have to wait a while for various reasons.

*[DTC]: doctoral training centre

*[PE]: plastic electronics

Teach Children to Code

I read a fair few tweets last night on subject of teaching children to program in school. A lot of the discussion appears to have been prompted by Ben Goldacre’s link to a post by programmer/author John Graham-Cumming supporting a petition entitled “Teach Our Kids to Code”. The petition argues that we should teach kids to program from Year 5 (9-10 years old). Definitely! Just as I was about to sign the petition this morning I saw a tweet by Mark Henderson, The Times Science Editor, saying that David Willets MP had just announced a pilot programme to teach programming in schools! Great stuff.

David Willetts has just announced pilot programme to teach schoolchildren coding & to develop a programming GCSE.

11:23 AM Thu Sep 15, 2011

I was about 10 years old when my parents bought our first computer. They had saved up for a long time and I was so excited about it. I remember the day we got it very clearly. It was a Compaq Presario with 2.2 GB hard drive, 64 MB RAM and 600 MHz Celeron CPU. The power! If I wasn’t out on my bike with friends you could find me endlessly fiddling, breaking and then fixing the computer (all whilst trying to hide the fact that I had broken it from Dad—I had to fix it otherwise they were going to be pretty angry/worried that I had broken their expensive new PC).

At a young age I was a logical thinker and quickly became computer literate, teaching myself HTML and then Javascript and PHP. If I, by no means a “child genius”, can work it out on my own from Internet resources then there is no reason why other children couldn’t learn to program in school with some good teaching.[^1] I think a 10 year old could easily cope with logical statements such as “if this then that” or “while this do that”—they naturally think like it in everyday life, they just need to help to translate it into the formal instructions a computer understands. Programming is fun and intellectually satisfying, much more so than the ridiculous ICT “lessons” that I used to have: open a Word document, copy some text, print, make a change, print again. Completely pointless.

It’s a useful skill too. Being able to program has been really handy for me at university. Last year I recorded probably around a hundred absorption and emission spectra (and maybe thousands using an automated system) which would have been impossible to analyse using Excel, the standard tool of choice amongst undergrads in my department. A bit of code in MATLAB and you can analyse as much data as your computer can cope with. For some reason my department didn’t teach a programming language like other departments such as Physics who taught C++. Instead we had “maths lab” where we used Excel for numerical methods. Not very useful (and very dull). Solving Project Euler-style problems with something like MATLAB or even better a proper, open source, high level language like Python (with SciPy and matplotlib) would be much more useful. I’ve been learning it myself over the summer. It’s a fun language that I’d love to teach to a class of undergraduate chemists.

I think it’s clear that school children would benefit from being able to program. Even if they never use code again, they would gain an understanding of how a computer functions and can then use this knowledge to work out how new software works. Rather than teach specific software applications, teach computing. It’d benefit industry too. Fingers crossed that the government doesn’t force schools to teach a horrible proprietary language outsourced as a “solution” on a ludicrously expensive contract and instead choose something open source and useful. A recent report about open source in Whitehall doesn’t bode well…

[^1]: Interestingly, my teacher told my parents in year 4 that I “had reached my plateau”. I’d quite like to let him know where I am now!