Snowing Science

In an article in the American Scientist, the author argues that the real bottleneck in science is not the computational power but the speed with which scientists and engineers convert their ideas into concrete code. Bret Victor talks about similar issues in his talk, Inventing on Principle.

Here are some tools that will take a while to master, but will reap tremendous benefits once the learning phase is over:

Writing

Google n-grams

Have a doubt whether it is 'a MP' or 'an MP'? No problem! Just search for it on Google n-grams.

or

use a corpus, for example: http://corpus.byu.edu/coca/

With the advent of reference management systems like Zotero: http://www.zotero.org/, Track Changes feature in word processors, coupled with advanced equation editors, the likelihood that you still stick to LaTeX is unlikely. But if you do, it is paramount to have good language correction tools such as this: http://matt.might.net/articles/shell-scripts-for-passive-voice-weasel-words-duplicates/. Three things Matt discusses: passive voice, weasel words, and duplicates. Shell scripts to detect all of them.

Version Control (a.k.a backup by many scientists)

Why use version control? To synchronize between multiple machines, to have backups of your code and basically a total history of what you have done and tried.

Tracking Conferences

If you are a Machine Learning person, simple: make this your home page: http://www.academiccountdown.com/. Otherwise, make one for your own field ;-)

Other Tools

I often use Dropbox: https://www.dropbox.com/ to synchronize many things, e.g. my Zotero storage space is Dropbox synced.

How do you spruce up your research with technology?

Miscellaneous Resources

Blog post with links to numerous resources about version control http://esstoosci.tumblr.com/post/9594163111/version-control

Software Carpentry. I really like the name! http://software-carpentry.org/

In this famous 1974 commencement address at Caltech, Richard Feynman gives us a glimpse into what he calls scientific integrity. I think he really hits the nail on the head by answering the question: How is scientific reporting different from storytelling?

It's a kind of scientific integrity, a principle of scientific thought that corresponds to a kind of utter honesty—a kind of leaning over backwards. For example, if you're doing an experiment, you should report everything that you think might make it invalid—not only what you think is right about it: other causes that could possibly explain your results; and things you thought of that you've eliminated by some other experiment, and how they worked—to make sure the other fellow can tell they have been eliminated.

And:

In summary, the idea is to try to give all the information to help others to judge the value of your contribution; not just the information that leads to the judgement in one particular direction or another.

He then goes on to make the distinction between explanatory and predictive models.

When you have put a lot of ideas together to make an elaborate theory, you want to make sure when explaining what it fits, that those things it fits are not just the things that gave you the idea for the theory; but that the finished theory makes something else come out right, in addition.

He then moves on to confirmation bias, an especially insidious problem in young scientific fields. He describes the history of experimental measurement of the charge of an electron. Since with the first experiment by Millikan, subsequent experiments reported slightly higher values each time, until the reports converted to the value we know today.

Why didn't they discover that the new number was higher right away? It's a thing that scientists are ashamed of—this history—because it's apparent that people did things like this: When they got a number that was too high above Millikan's, they thought something must be wrong—and they would look for and find a reason why something might be wrong. When they got a number closer to Millikan's value, they didn't look so hard. And so, they eliminated the numbers that were too far off, and did other things like that. We've learned those tricks nowadays, and now we don't have that kind of disease!

Maybe in experimental physics, but I wonder how many of us can afford to be as careful or self-critical in these not-so-idealistic times of publish or perish!

There are a number of other excellent anecdotes, and the best one is decidedly something I have left out of the excerpts here. If you want to know those stories, do read the entire speech. Excellent advice for a budding experimentalist!

My takeaway:

This is a series of essays, since available in book form, written back in 2004 by former advertising professional turned professional cartoonist and blogger, Hugh MacLeod. Although it doesn't directly relate to academic research, I found it contains useful lessons for research. A bit more aggressive approach to wisdom that I prefer, but nevertheless entertaining.

In brief:

So you want to be more crea­tive, in art, in busi­ness, wha­te­ver. Here are some tips that have wor­ked for me over the years:

1. Ignore every­body.

The more ori­gi­nal your idea is, the less good advice other peo­ple will be able to give you. When I first star­ted with the biz card for­mat, peo­ple thought I was nuts. Why wasn’t I trying to do something more easy for mar­kets to digest i.e. cutey-pie gree­ting cards or wha­te­ver?

2. The idea doesn’t have to be big. It just has to change the world.

The two are not the same thing.

3. Put the hours in.

Doing anything worthwhile takes fore­ver. 90% of what sepa­ra­tes suc­cess­ful peo­ple and fai­led peo­ple is time, effort and sta­mina.

4. If your biz plan depends on you sud­denly being “dis­co­ve­red” by some big shot, your plan will pro­bably fail.

Nobody sud­denly dis­co­vers anything. Things are made slowly and in pain.

5. You are res­pon­si­ble for your own expe­rience.

Nobody can tell you if what you’re doing is good, mea­ning­ful or worthwhile. The more com­pe­lling the path, the more lonely it is.

6. Ever­yone is born crea­tive; ever­yone is given a box of cra­yons in kin­der­gar­ten.

Then when you hit puberty they take the cra­yons away and replace them with books on alge­bra etc. Being sud­denly hit years later with the crea­tive bug is just a wee voice telling you, “I'd like my cra­yons back, please.“

7. Keep your day job.

I'm not just saying that for the usual rea­son i.e. because I think your idea will fail. I'm saying it because to sud­denly quit one's job in a big ol’ crea­tive drama-queen moment is always, always, always in direct con­flict with what I call "The Sex & Cash Theory".

8. Com­pa­nies that squelch crea­ti­vity can no lon­ger com­pete with com­pa­nies that cham­pion crea­ti­vity.

Nor can you bully a subor­di­nate into beco­ming a genius.

9. Every­body has their own pri­vate Mount Eve­rest they were put on this earth to climb.

You may never reach the sum­mit; for that you will be for­gi­ven. But if you don’t make at least one serious attempt to get above the snow-line, years later you will find your­self lying on your death­bed, and all you will feel is emp­ti­ness.

10. The more talen­ted some­body is, the less they need the props.

Mee­ting a per­son who wrote a mas­ter­piece on the back of a deli menu would not sur­prise me. Mee­ting a per­son who wrote a mas­ter­piece with a sil­ver Car­tier foun­tain pen on an anti­que wri­ting table in an airy SoHo loft would SERIOUSLY sur­prise me.

11. Don’t try to stand out from the crowd; avoid crowds alto­gether.

Your plan for get­ting your work out there has to be as ori­gi­nal as the actual work, perhaps even more so. The work has to create a totally new mar­ket. There’s no point trying to do the same thing as 250,000 other young hope­fuls, wai­ting for a miracle. All exis­ting busi­ness models are wrong. Find a new one.

12. If you accept the pain, it can­not hurt you.

The pain of making the neces­sary sac­ri­fi­ces always hurts more than you think it’s going to. I know. It sucks. That being said, doing something seriously crea­tive is one of the most ama­zing expe­rien­ces one can have, in this or any other life­time. If you can pull it off, it’s worth it. Even if you don’t end up pulling it off, you’ll learn many inc­re­di­ble, magi­cal, valua­ble things. It’s NOT doing it when you know you full well you HAD the oppor­tu­nity– that hurts FAR more than any fai­lure.

13. Never com­pare your inside with some­body else’s outside.

The more you prac­tice your craft, the less you con­fuse worldly rewards with spi­ri­tual rewards, and vice versa. Even if your path never makes any money or furthers your career, that’s still worth a TON.

14. Dying young is ove­rra­ted.

I’ve seen so many young peo­ple take the “Gotta do the drugs and booze thing to make me a bet­ter artist” route over the years. A choice that was neither effec­tive, healthy, smart, ori­gi­nal or ended hap­pily.

15. The most impor­tant thing a crea­tive per­son can learn pro­fes­sio­nally is where to draw the red line that sepa­ra­tes what you are willing to do, and what you are not.

Art suf­fers the moment other peo­ple start paying for it. The more you need the money, the more peo­ple will tell you what to do. The less con­trol you will have. The more bullshit you will have to swa­llow. The less joy it will bring. Know this and plan accor­dingly.

16. The world is chan­ging.

Some peo­ple are hip to it, others are not. If you want to be able to afford gro­ce­ries in 5 years, I’d recom­mend lis­te­ning clo­sely to the for­mer and avoi­ding the lat­ter. Just my two cents.

17. Merit can be bought. Pas­sion can’t.

The only peo­ple who can change the world are peo­ple who want to. And not every­body does.

18. Avoid the Water­coo­ler Gang.

They're a well-meaning bunch, but they get in the way even­tually.

19. Sing in your own voice.

Pic­casso was a terri­ble colo­rist. Tur­ner couldn’t paint human beings worth a damn. Saul Steinberg’s for­mal draf­ting skills were appa­lling. TS Eliot had a full-time day job. Henry Miller was a wildly une­ven wri­ter. Bob Dylan can’t sing or play gui­tar.

20. The choice of media is irre­le­vant.

Every media’s grea­test strength is also its grea­test weak­ness. Every form of media is a set of fun­de­ma­tal com­pro­mi­ses, one is not “higher” than the other. A pain­ting doesn’t do much, it just sits there on a wall. That’s the best and worst thing thing about it. Film com­bi­nes sound, pho­to­graphy, music, acting. That’s the best and worst thing thing about it. Prose just uses words arran­ged in linear form to get its point across. That’s the best and worst thing thing about it etc.

21. Selling out is har­der than it looks.

Dilu­ting your pro­duct to make it more “com­mer­cial” will just make peo­ple like it less.

22. Nobody cares. Do it for your­self.

Every­body is too busy with their own lives to give a damn about your book, pain­ting, screen­play etc, espe­cially if you haven’t sold it yet. And the ones that aren’t, you don’t want in your life any­way.

23. Worr­ying about “Com­mer­cial vs. Artis­tic” is a com­plete waste of time.

You can argue about “the sha­me­ful state of Ame­ri­can Let­ters” till the cows come home. They were kvetching about it in 1950, they’ll be kvetching about it in 2050.

It’s a path well-trodden, and not a place where one is going to come up with many new, earth-shattering insights.

24. Don't worry about fin­ding ins­pi­ra­tion. It comes even­tually.

Ins­pi­ra­tion pre­ce­des the desire to create, not the other way around.

25. You have to find your own sch­tick.

A Picasso always looks like Pic­casso pain­ted it. Heming­way always sounds like Heming­way. A Beetho­ven Symphony always sounds like a Beethoven’s Syynphony. Part of being a mas­ter is lear­ning how to sing in nobody else’s voice but your own.

26. Write from the heart.

There is no sil­ver bullet. There is only the love God gave you.

27. The best way to get appro­val is not to need it.

This is equally true in art and busi­ness. And love. And sex. And just about everything else worth having.

28. Power is never given. Power is taken.

Peo­ple who are “ready” give off a dif­fe­rent vibe than peo­ple who aren’t. Ani­mals can smell fear; maybe that’s it.

29. Wha­te­ver choice you make, The Devil gets his due even­tually.

Selling out to Holly­wood comes with a price. So does not selling out. Either way, you pay in full, and yes, it inva­riably hurts like hell.

30. The har­dest part of being crea­tive is get­ting used to it.

In a first-of-its-kind memoir, Philip Guo gives a detailed account of the process of doing a PhD. From the book's homepage:

The Ph.D. Grind, a 122-page e-book, is the first known detailed account of an entire Ph.D. experience. So far, over 100,000 people—professors, research scientists, current and prospective Ph.D. students, and professionals in a variety of fields—have read it and collectively sent me hundreds of heartfelt email responses.  For example, the Director of Research at Google wrote to me: “You've done a good job of explaining just what this thing called PhD actually is, and that is a service to the world, both to people contemplating entering a PhD program, and for those who have to deal with the products of a program ...”  Click on the links to the right to read the book and other related articles. My latest Ph.D.-related article is Lead From Below.

Again, the preface of the book says it better than I can:

This book chronicles my six years of working towards a Ph.D. in Computer Science at Stanford University from 2006 to 2012. A diverse variety of people can benefit from reading it, including:

undergraduates who might be interested in pursuing a Ph.D.,

current Ph.D. students who are seeking guidance or inspiration,

professors who want to better understand Ph.D. students,

employers who hire and manage people with Ph.D. degrees,

professionals working in any creative or competitive field where self-driven initiative is crucial,

and educated adults (or precocious kids) who are curious about how academic research is produced.

The Ph.D. Grinddiffers from existing Ph.D.-related writings due to its unique format, timeliness, and tone:

Format–The Ph.D. Grindis a memoir for a general educated audience, not a “how-to guide” for current Ph.D. students. Although Ph.D. students can glean lessons from my experiences, my goal is not to explicitly provide advice. There are plenty of how-to guides and advice columns for Ph.D. students, and I am not interested in contributing to the fray. These articles are filled with generalities such as “be persistent” and “make some progress every day,” but an advantage of the memoir format is that I can be concrete and detailed when telling my own story.

Timeliness– I wroteThe Ph.D. Grindimmediately after finishing my Ph.D., which is the ideal time for such a memoir. In contrast, current Ph.D. students cannot reflect on the entirety of their experiences like I can, and senior researchers who attempt to reflect back on their Ph.D. years might suffer from selective hindsight.

Tone– Although it's impossible to be unbiased, I try to maintain a balanced tone throughoutThe Ph.D. Grind. In contrast, many people who write Ph.D.-related articles, books, or comics are either:

successful professors or research scientists who pontificate stately advice, adopting the tone of “grad school is tough, but it's a delectable intellectual journey that you should enjoy and make the most of ... because I sure did!”

or bitter Ph.D. graduates/dropouts who have been traumatized by their experiences, adopting a melodramatic, disillusioned, self-loathing tone of “ahhh my world was a living hell, what did I do with my life?!?”

Stately advice can motivate some students, and bitter whining might help distressed students to commiserate, but a general audience will probably not be receptive to either extreme.

Finally, before I begin my story, I want to emphasize that there is a great deal of diversity in Ph.D. student experiences depending on one's school, department, field of study, and funding situation. I feel very fortunate that I have been granted so much freedom and autonomy throughout my Ph.D. years; I know students who have experienced far more restrictions. My story is only a single data point, so what I present might not generalize. However, I will try my best to avoid being overly specific. Happy reading!

This is a fascinating article published in The Journal of Cell Science that talks about the importance of 'absolute stupidity' in scientific research. At one point, the author gives an anecdote of how the Nobel laureate Henry Taube did not know how to solve a problem that he was working on as a third-year graduate student.

The crux of the article can be summarized in the following lines quoted from the text:

The crucial lesson was that the scope of things I didn't know wasn't merely vast; it was, for all practical purposes, infinite. That realization, instead of being discouraging, was liberating. If our ignorance is infinite, the only possible course of action is to muddle through as best we can.

A new way to explain explanation. For the past year or so, I've spent a small fraction of my time wondering about what kind of theory neuroscience must aim for. In other words, when we finally have a theory of the brian, what would that theory look like? Instead of directly attacking this question, I have been snooping around in the archives of science history, trying to understand how physical laws were derived. I had come to understand a scientific theory as a narrative about a phenomenon that offers testable hypotheses.

In this BBC series from the later part of Richard Feynman's life, we are given a window into his recreational life during a summer retreat in England. Among the many fascinating glimpses is one of note, where the interviewer asks him whether he thinks he has more in common with a scientist from another discipline than, say, an artist or a poet.

At first, Feynman replies that he would have more to talk about with any first rate scientist than another member of the general public. However, as he is thinking through an example, he suddenly remembers an interaction he has had with an artist, and that very moment, he pauses. "I take it all back".

Most people know of Hamming from the essay You and Your Research. Recently, I stumbled upon a treasure trove of videos among which was a video of Hamming giving the same talk himself! I'll however focus on another talk among the same set of videos that were recently uploaded: "How Do We Know What We Know".

Remarkably, Hamming has a questioning attitude unmatched by most people. Questioning certain knowledge, he says:

What's more sure than one plus one is two. My reply was - you remember in coding theory, Hamming says one plus one is zero.

Explaining that the search for knowledge is essentially a search for consistency, he cites:

A child makes an assumption that this (Gladly, the cross-eyed bear) is the meaning of what she's been hearing, and one day she's corrected to this (Gladly, the cross I'd bear). We try some experiments and they don't quite work out and we're corrected to another interpretation of what we've been seeing.

Ridiculing superstition like most other scientists:

Many of us are well aware that the moon does have an effect on life on earth, very much so. Because it produces tide and various other things. But we're a little dubious about whether star 25 light years away is there or there, you're going to left handed or right handed.

More quotable quotes from the video, pick your favourite:

So, he finds from experience what kinds of noises produce satisfactory results and which ones don't.

You first have a theory before you can gather the data. You can't gather random data. 

Knowledge is a very dangerous thing - it comes with lots an lots of preconceptions.

Well, day follows night, invariably. Does night cause day?

If you have a son named Charles, you know if you stopped to think - that Charles is not the child. Charles is the name of the child.

How does a body know how heavy it is?

Our knowledge is science, everything else is constantly changing.

We want to believe we have the truth, so we constantly believe we have the truth.

If you're wrong, you'll first turn all your money over to me and two, you'll commit suicide.

Gradually, the vacation you had tend to become the words you tell somebody.

Harold Kroto, the world renowned chemist is best known for his contributions in creating the C-60 molecule. In a very engrossing discussion, he lays bare his soul explaining how many of his ideas came from arts, architecture and mathematics.

In what may seem to be many a prophetic, almost bizarre coincidence, Kroto shows a portrait of the Stockholm Town Hall which he made when he was younger - the same place where he went on to win the Nobel prize.

His scientific bent of mind can be clearly seen even in the artwork:

Here is a menu I designed - so periodic table, it's Manganese and Europium. So, Mn and Eu are an anagram for MEnu.

or this one:

Here's a design for Sussex which is a Brighton. Here's a flame of a bunsen burner in the shape of the dome of Brighton and that's another menu.

and another:

I did a lot of logos and here's a I--B--D--G ok, Inorganic Biochemistry Discussion Group and we see a flower and d-orbitals for transition metals and green leaves and quite a pretty image. I used to like that sort of challenge.

At a later point in the video, he explains that the geodesic dome designed by Buckminster Fuller had been featured in the 1967 edition of Graphis (a magazine which he had started), which offered an important clue (see video for details!) to discover the C-60 molecule.

Getting into mathematics, he explains how Euler's theorem can explain why its not possible to close a graphite chain into a molecule like C-60. Touching upon sports, he explains why footballs are so strange in shape (never noticed?) as they are.

It is well known that the biggest discoveries in science often come from very elementary ideas - Einstein's theories are based on Pythogoras theorem [needs citation/link], Newton's laws are often attributed to an anecdote of falling apples etc. This video offers a peek into the secret lives of scientists and their simple ideas cross-pollinating across disciplines. Happy watching!

There isn't a better guide available than this one. You can find the pdf version here or the html version here. Quoting Matt:

Every fall, I explain to a fresh batch of Ph.D. students what a Ph.D. is.

It's hard to describe it in words.

So, I use pictures.

It is very touching to find Matt's unwavering belief in science even in the face of difficulties:

Concluding by another quote from Matt's website:

Great conversation between evolutionary biologist Richard Dawkins and astrophysicist Neil deGrasse Tyson below on an eclectic collection of questions:

It becomes clearly apparent how great scientists learn to overcome the powerful urge to rely on the sense organs. As Richard Dawkins asks Tyson:

What we can see with our sense organs is an extremely narrow band of what there is to see and this is particularly so with the visual cells and we can see a tiny narrow band of the electromagnetic spectrum, the rainbow - but the rainbow's width is tiny as compared to the vast expanse of the electromagnetic spectrum - and I see that as a kind of symbol for how limited our understanding of the universe is.

Neil Tyson goes on to reply, first speculating on why most people have a hard time coming to terms with this:

We like having nice thoughts about ourselves rather than depressing thoughts, so we are prone to walk about celebrating the power of sight, or taste or smell - when of course when you really want to smell something, you bring a dog.

Consolidating on his point, he says

We're practically blind out there, and it's humbling. But that's the whole point of the methods and tools of science. To not only extend your senses in the domain in which you understand - but you take them to places they've never been before.

As we embark on this journey - we hope that you share with us this insight. Many of the conclusions in science may be contrary to common sense - but if you follow the line of reasoning using the methods and tools of science, it is likely that the pieces in the puzzle fit in.

It is important to have an open mind and rigorously question the premises and line of thought before accepting any conclusions. We leave you with the following lines from somebody wise: