My scientific writing workflow

I am not fond of MS-Word. Correction: I cannot really tolerate MS-Word, and the only times I really use it are for work, where documents must be shared, modified, commented upon, and tracked for changes between multiple authors, contributors and edit cycles. For those particular circumstances there really isn’t another viable alternative to MS-Word, is there.

But of course, the criteria for my own scientific writing are very different. The only sharing and discussion is with my dissertation adviser, and I can easily handle one other contributor without needing MS-Word. So, of course, I’ve moved as far away from that bloated, cranky piece of software as I can—which is to say, completely away.

Instead, here’s what I use.

My word processor of choice on the Mac is Mellel. It’s beautiful, runs smoothly, and is a joy to use. Its listed feature set is vastly inferior to that of Word, but the features it does carry are executed extremely well. After all, what use are a plethora of features that really make the program bloated and difficult to use? (Please, go read that article; it’s cathartic for frustrated Word-users.) Plus, these features are more than sufficient to meet my needs (and, I think, that of most other scientic writers). I have not felt the need—yet—to incorporate the math rendering excellence of LaTeX, and for all other purposes, Mellel works great.

Mellel in Full-screen mode

Mellel in Full-screen mode.

But here’s the thing. I don’t like writing in word processors. Even in great ones such as Mellel, you’re distracted every once in a while by the formatting, and how the headings are looking, and whether a paragraph should flow on to the next page, and so on. Plus, I’ve developed a universal distaste for proprietary document formats, and this extends as much to Mellel’s proprietary format as to Word’s. I’d like to read and make sense of my documents irrespective of which software I happen to have available for use.

For another thing, I’ve really taken to John Gruber’s simple text document markup format, Markdown, and since discovering it have started using it for almost everything I write—including blog posts like this one. Well, it turns out, there are a number of extensions to Markdown, among which Fletcher Penney’s Multimarkdown must take pride of place. And what do you know—Multimarkdown even has provisions for including references, cross-references and footnotes! How much more perfect can it get!

A related app that has quickly become indispensable for me is Marked. This nifty tool shows a ‘preview’ of what your markdown (or multimarkdown) document looks like, and directly provides output documents in various formats, including PDF, RTF and HTML. This is excellent for quickly creating an RTF document to send to my adviser for review.

Marked preview of this blog post

Marked preview of this blog post.

If you’ve been keeping count, the only piece of software necessary for scientific writing that I haven’t mentioned is a citation/bibliography tool. Endnote is a popular choice for many, and I’m sure it’s pretty good, but there’s a couple other excellent Mac apps for this–Bookends and Sente. Based on online reviews and forums, I ended up selecting Bookends a few years ago, and I haven’t regretted the decision. As a bonus, Bookends integrates perfectly with Mellel, making life very easy indeed. (I noticed while writing this post that Sente’s pricing terms seem to have changed quite a bit since I was researching it, and for all I’d heard, Sente is excellent too.)

There’s another Mac writing tool that’s great for writing long documents, especially where the document is divided into chapters and sections. This is Scrivener. Plus, the basic document format for Scrivener is plain text, which straightaway satisfies my wariness for proprietary formats. Scrivener is also excellent, and would have suited my type of scientific writing perfectly, except for one solitary reason. It doesn’t play well with Bookends. To use Bookends, you have to export your document to an RTF file, and then use Bookends. This means you’re once again left with an extra step of having to include formatting. Not good for me, and Mellel wins. (Scrivener, on the other hand, is the only app in my list that is also available for Windows. If you’re a Windows user, this is an excellent app that you should certainly explore.)

So now that we’ve identified the pieces of software that I use, here’s my workflow.

  • Choose any text-editor (Sublime Text, BBEdit, Text Wrangler, or even the ever worthy, simple TextEdit), and write the actual text in Multimarkdown format. Include citations as required; for the ‘citation’ portion, use any label of your choice, and for the ‘link’ portion, include the identifier string from Bookends that you must use to finally automatically create the bibliography. This way, when I use Marked to export to RTF, my citations are already automatically shown as citations, even though I haven’t done anything with Bookends yet. The bibliography section at the end looks funky, but that’s not a problem with documents in progress.
  • When ready, export the document as RTF, and copy-paste the entire contents into a new Mellel document.
  • For each citation, replace the custom label I had chosen with the Bookends identifier. This is a simple matter of doing a ‘Find-Replace-All’ for each citation.
  • Use Bookends to add the bibliography!

Here are the advantages to this scheme:

  • No use of MS-Word, but you’re able to export to RTF or .doc format, if needed, from Mellel.
  • You’re always able to deal with plain text for all your documents, up until the very last stage where page-setting must come into the picture.
  • Even for a document in progress, it takes only a moment to create a perfectly readable document, via Multimarkdown, that includes inline citations instead of the ugly Bookends identifier.

If you don’t care about using plain text formats, or are simply not comfortable or don’t want to get used to Markdown, just replace MS-Word with Mellel. You can still do all your document writing in a word processor, just like in Word, and you’ll quickly find that it’s way more efficient to use Mellel. You’ll love it—guaranteed.

Chicago Sun-times fired its photographers. How’s that turning out?

A few weeks ago, the Sun-Times fired its entire photography staff, and decided to train their reporters to shoot with their iPhones.

Here’s the result.

(Go visit the link above, and come back to read the rest. I’ll wait.)

Here’s a tip: photography is quite a bit more than knowing how to operate a camera. Anyone can operate a camera; not everyone can be a photographer.

Worse, it’s really, really hard to be on photography assignment and do anything else at the same time. This sometimes gets to the extent of not being able to fully experience the surroundings you’re in, because your mind is constantly thinking of what the best vantage points might be to capture the moments unfolding.

I’m sure it’s the same for journalists and reporters, who are similarly too busy focusing on the news to do the photography job well, even if they are otherwise excellent photographers.

I think we’ll soon find the Chicago Sun-Times reversing their decision and making alternative arrangements. One thing is for certain: the top brass that made the call have no idea about what photography is, and that’s a pity, coming from a group that’s running a newspaper.

On using (or abusing) bio-technology

I wrote a small piece on fair use of our biotechnology on my Tumblr, but since I’m planning to write longer pieces on this blog, I wanted to cross-post it here as well.

Joe Hanson, of It’s Okay To Be Smart, wrote:

Can Biotechnology and Genetic Engineering Save an American Icon?

What I find so interesting is that the techniques being used to save this tree, and one day reintroduce it to the wild, are not that different from those that are used to create genetically modified crops. How does saving a dying species by inserting a gene differ from creating an herbicide-resistant soybean, or rice that produces extra vitamins? I have my opinions, but I want to know: What do you think?

My thoughts are below.

The two are different in only the following way—in one case, we’re using our technology to help another being survive better; in another case we’re using technology to extract more from a being we intend to use as a ‘resource’, in this case food.

I think they’re both fine uses of our technology.

As humans, we have always wanted to modify our surroundings to suit us better. That’s who we are; that’s what defines us as a species and helps us move unflinchingly deeper into the unknown.

It was the same when we invented agriculture; it was the same when we domesticated animals; it was the same when we forced natural selection to go in a certain direction to create “man’s best friend”.

The only difference today is that instead of indirect approaches, we’re learning to make pin-point, particular modifications exactly as we require.

Yes, this is a sensitive topic, and rightfully so. With great power does come great responsibility, and we’re only now learning to harness the power of genetic engineering. I feel we should find it easy to stay on the straight and narrow as long as we remember one rule—no interference for the fun of it. I’ll explain more.

Only organisms capable of photosynthesis are able to produce their own energy. Every other living being must depend on other living beings for energy and sustenance, and we are no different. As long as our genetic engineering endeavours are focussed towards areas that we must harvest for our nutrition, we should be okay. Genetically modified crops are okay—as long as we understand the effects of what we are doing. Edit*: There is a lot of ambivalence towards genetically modified food crops, but the problem isn’t the technology itself, but that we don’t yet understand* the technology well enough to implement it perfectly. Let’s keep at it; we’ll get there.

In addition, being the sole species on this planet with advanced technology, we owe it to our planet-mates to share. Just as in this example of chestnut trees dying from a fungus, when we see an organism dying from infection, and we realize we can help—by all means, we should! We already try to help species that we are afraid will become extinct (often, unfortunately, to our own greedy exploits)–why should that help not include our latest and greatest knowledge?

Let’s just not play with our planet-mates simply because we can. That would be abuse of power, no?

The problem facing scientist writers

I was lamenting on the scarcity of engineering blogs, even though there are a plethora of excellent science and other technical blogs on the internet.

That got me thinking about why relatively so few scientists in general, and engineers in particular, write and publish on the web. Here’s the problem, I think–

  • We never receive any proper writing training throughout our careers.

    We learn the other stuff, all the theories and how they work and so on, and even how to publish our work in peer-reviewed journals, but rarely how to competently and forcefully express ourselves and communicate with the world at large. That’s a problem, isn’t it? After all, a scientist is as much a writer as anyone else—what use is my earth shattering research if I can’t explain it to everyone else?

    And no, ‘math does the talking’ is no excuse. Math isn’t for everyone, and it’s very useful to be able to communicate ideas outside of mathematical jargon. Even a brief “Here’s an idea. Now if you really want to know, go learn the math!” is extremely valuable.

    Here’s an example, via an article at Project Wordsworth: the Japanese mathematician Shinichi Mochizuki posted four papers on the internet, purporting to prove the ever-enigmatic ABC conjecture. The only problem? No one understands his work:

    The question which quickly bubbled to the top of the forum, encouraged by the community’s “upvotes,” was simple: “Can someone briefly explain the philosophy behind his work and comment on why it might be expected to shed light on questions like the ABC conjecture?” asked Andy Putman, assistant professor at Rice University. Or, in plainer words: I don’t get it. Does anyone?

    Oops! (And remember, we’re talking about the mathematics community here, not the lay public.) Dr. Mochizuki was invited to give lectures on his work, to explain and educate. He refused.

    Of course, his peers are irked:

    “You don’t get to say you’ve proved something if you haven’t explained it,” [former math professor Cathy O’Neil] says. “A proof is a social construct. If the community doesn’t understand it, you haven’t done your job.”

    If you can’t communicate, are you really a great researcher?

    Mochizuki has reported all this progress for years, but where is he going? This “inter-universal geometer,” this possible genius, may have found the key that would redefine number theory as we know it. He has, perhaps, charted a new path into the dark unknown of mathematics. But for now, his footsteps are untraceable. Wherever he is going, he seems to be travelling alone.

    This is, of course, an extreme case, but I think the larger point holds too—that engineers/scientists should be able to competently express themselves and communicate with the larger community, and not only in journal articles.

  • We are not trained to be truly internet-savvy.

    I don’t mean this in terms of knowing how to navigate the internet and check email and visit websites and perform Google searches. I mean this in a larger sense—in knowing (and being comfortable with) how to create and maintain blogs, in managing our internet personas and profiles, in creating and designing websites.

    There are ample tools and resources out there, and we don’t all need to be trained in computer science to thrive—but we often rarely know how and where to begin. Some take the time to teach themselves, but what of those of us whose knack is not in internet technologies? We really do need to do more to expose ourselves more to internet publishing.

    We personally and professionally know of many scientists and researchers who are truly great teachers and communicators—but how many of these brilliant people are writing and publishing on the internet for the community at large?

If you’re an engineer or a scientist, and are a good communicator, please do consider writing and publishing on the internet! The rest of us will be the richer in experience for it. :)

Where are the engineers’ blogs?

I wish there were more people writing about engineering mechanics research. It’s certainly a fascinating area, and while perhaps they wouldn’t be as popular as the tech-media blogs, or the awesome science blogs that everyone can identify with, they’d still be pretty good, right?

I really like and follow Dr. Drang, who seems to occupy the perfect niche—mechanical engineering and computer programming. And through Dr. Drang I’ve recently discovered the blog of J. Ben Deaton, but haven’t had the chancce to explore in detail yet. (BTW, Deaton’s site is also powered by Octopress, with the default Octopress theme that I mentioned.) Then there’s Engineering is Awesome, which is also excellent.

But other than that, I don’t know of any engineering or mechanics blogs. There may be some great ones that don’t show up in Google searches—if you know of one, would you let me know? :)

There are quite a few science blogs though (example, example), and they are excellent and fascinating. But where are the engineers? Are engineers really that boring compared to other scientists? :)