Do you want to study complex systems? M.Sc. admissions open until 3.1.2020!

Complex systems

Are you looking for a master’s programme? Admission is now open for our Life Science Technologies master’s programme at Aalto University, Finland, Europe; there is a Complex Systems major within the program and I am the responsible professor. And I am looking for talented and motivated students from all parts of the world!

What’s in the major? A lot of interesting and cool things: network science, data science, machine learning, nonlinear dynamics, to mention a few! Here’s why networks are the thing. And if you want to know more about what complex systems are, just have a look at previous posts in this blog, e.g. on mobile-telephone calls, ants, and the immune system.

Here is a complete list of courses in the complex systems major for this winter (only minor changes coming in 2020).

There is a lot of freedom in designing your own curriculum: there are many courses to choose from, including courses by other Life Science Technologies majors. This makes it possible to mix and match: want a combination of machine learning and complex networks? Check. Want to be a network neuroscientist? Check. Want to get a broad training in data science? Check.

Note: even though the programme is called Life Science Technologies, you can almost completely avoid anything that begins with “bio” if you so wish. As an example, I have students who focus on social networks, computational social science, or public transport networks, and who I believe haven’t taken any biomedical courses. But, if bio is your thing instead, there are plenty of opportunities here too!

One more thing: the doctoral track. If you are talented and your grades are excellent, you can apply to the doctoral track where your final target is not the master’s degree but a PhD; your studies are tailored towards that goal and you’ll get to spend time as intern in our research groups, with the aim of publishing the first journal article(s) of your thesis already before you get the master’s degree.

So, what are you waiting for? Apply here! The deadline is on Jan 3rd, 2020.

What is scientific creativity—and how do you feed it? (Part I)

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Last winter, on a speaking trip to Norrköping, someone asked me to write about skills (and meta-skills) that scientists and PhD students need, beyond writing papers. Turns out that this is a lot more difficult than writing about writing, where the end product—a scientific paper—is something tangible and amenable to analysis: how do great introductions look like? How do the greatest writers finish their papers? It is much more difficult to write, say, about learning to be creative, which is what I shall try to do here. But what would be more important for aspiring scientists than creativity?

Science is all about creativity: coming up with the right questions, developing clever methods to answer those questions, and connecting the answers in imaginative ways to learn something greater. But we rarely talk about creativity as a skill—often, people view it as something that you either have or don’t have, just like an ear for music or an eye for design. And just like with music and design, this view is wrong: everything can be learned. So how do you learn to be creative?

Before attempting to answer this question, let’s take the bull by the horns and ask what creativity is. If by creativity we mean the ability to bring forth ideas that are entirely new, we are immediately hit by a very difficult, philosophical question: where do new ideas come from? At least to us (recovering ex-) physicists, the emergence of something that wasn’t there before is kind of strange: aren’t there conservation laws that forbid this kind of travesty from happening? What is it that gives birth to new information (because that is what happens when a new idea emerges, whether it is a question or an answer)?

If physics doesn’t provide us with answers, let’s drop it for a while and put on the hat of a biologist: in the realm of living things, don’t new things gradually emerge, driven by the slow Darwinian evolution? Notice the word “gradually”—biological evolution is slow tinkering, a process where existing forms and shapes and organs are gradually transformed into something new, of dinosaurs developing feathers that eventually help some of them to learn to fly, of finches’ beak shapes adapting to their habitats. So in biological evolution, everything that is “new” is built on top of a lot of something old, and this happens slowly: a slow expansion into the adjacent possible, if you’ve read your Kauffman.

Are there some other natural processes where new forms emerge more rapidly? The human immune system provides a great example. Somewhat surprisingly, not all our cells carry the same sets of genes: the T and B cells of our immune system, our ultimate smart weapons against viruses and other invaders, display an enormous diversity of different receptors that recognise those invaders. This diversity results from those cells carrying some randomised (but not too randomised) parts of our genome. The precursor cells that eventually become T and B cells have strings of different modules in their genetic code, and in the process of randomisation, some of those modules are randomly picked and joined together (the rest are discarded). Then, a bit of extra randomness (extra letters, deleted letters, and so on) is added to their junction. So to arrive at new kinds of receptors, our bodies randomly merge things that are known to work (those receptor modules) and then add some noise on top. Again, “new” equals “old, but with added something.”

Let’s now return back to creativity, in the context of science or otherwise. The above examples point out that the old rhyme—“something old, something new, something borrowed, something blue”—is scientifically highly accurate, except for the blue bit perhaps. In other words, the things that we think are new are in fact modifications and clever combinations of old things, with perhaps some small amount of additional randomness. Ideas do not live in a vacuum, they emerge because of other ideas.

Therefore, creativity is the ability to merge existing ideas in new ways (while possibly adding a magic ingredient on top).

This brings us to a fairly simple recipe for feeding one’s creativity: collect lots of things that can be combined/transmogrified into something new, and then just combine them! In other words, first, feed your head with lots of information—and not just any information, but preferably pieces of information that haven’t yet been combined.

To maximise the chance of something entirely new emerging out of this process, your input information—the stuff that you feed your head with—should be diverse enough. There are, however, different possibilities: on the one hand, if you know everything that there is to know about your field, you can probably see where the holes are and combine bits of your knowledge in order to fill them. On the other hand, if you know enough about a lot of fields, you might be able to spot connections between them (think of, say, network neuroscience, applying network theory to problems of neuroscience). There are different styles here, but even if you choose to go deep instead of wide, do keep the diversity of input information in mind: just for fun, learn some mathematical techniques that people do not (yet) use in your field! You never know, those might turn out to be useful later.

To be continued…

How to Choose the Title for Your Paper

“Any word you have to hunt for in a thesaurus is the wrong word. There are no exceptions to this rule.” ― Stephen King

How to Write a Scientific Paper book cover

This post is a chapter from the book “How to Write a Scientific Paper.”

After you have written your abstract, the next task is to consider the title of your paper. If the abstract is a compressed version of your storyline, the title of your paper is even more so. Titles are hard—it is often surprisingly difficult to come up with a short, informative, and catchy title. For me, this has at times felt like the hardest part of writing a paper.

The title of the paper serves a dual purpose: it delivers information by telling readers what your paper is about, and it serves as a marketing tool that makes others want to read your paper. Unfortunately, unlike the abstract, there is no general-purpose formula to follow when thinking of a title. There are, however, some points that you should consider.

The title has to be in perfect sync with the abstract—they have to tell the same story. Make sure that your title and abstract use the same words and concepts. Also, make sure that everything that is mentioned in the title is discussed in the abstract.

Use words that everyone in your target audience can understand. Avoid subfield-specific jargon. Simply does it! The paper’s title should only contain concepts that can be understood on their own, without any explanation. While there is some room in the abstract for explaining one or two important concepts in brief, there is no such luxury in the title: the reader should already be familiar with every word used in it.

The title should be focused and clear. If it is possible to give away the main result in the title, do so. Avoid vague titles, such as “Investigating Problem X with Method Y”. Instead, go for something more concrete: “Investigating Problem X with Method Y Reveals Z.”

A small request: please never, ever use a title of the “Towards Understanding Problem X” variety. Just don’t do it. Pretty please. If your research is worth publishing, you have arrived somewhere. Just be confident and tell the reader where this is, instead of telling them where you would rather have gone! It is OK to say something about the bigger picture in the title, as long as your key point plays a leading role. But to keep your title concise, it may be better to describe long-term goals elsewhere in the paper.

It helps if the title is catchy as well as informative. But do not exaggerate—consider how your title will look 10 years from now. Will it stand the test of time? If the title is too gimmicky or contains a joke that becomes stale after you’ve heard it a few times, it won’t. You should also avoid jargon and buzzwords that may go out of fashion before the paper gets published.

Consider search engines and online search. Your paper needs to be found if it is to be read, so the title should contain the right keywords or search terms. As a network scientist, I almost always include the word “network” in my paper titles, even if this makes the title longer or if other network scientists would understand the title perfectly well without networks being explicitly mentioned. Without the word “network”, they would not necessarily find my paper when they hunt online for new reading material.

Keep your title short. Research has shown that shorter titles attract more citations—see Letchford et al., R. Soc. Open Sci. 2(8):150266 (2015). This should not come as a big surprise: long and cluttered titles are not as contagious as simple, focused ones. If the title is convoluted and hard to grasp, then the paper probably is too.

Sometimes there are field-specific conventions that you should be familiar with. In some biomedical fields, for example, the paper’s title often expresses just the key result—“Transcription Factor X is Involved in Process Y”—and the titles can be fairly long. In some areas of physics and computer science, shorter and less informative titles are the norm. Have a look at other papers in your field, and try to imitate their best titles.

If you get stuck at this point and find it hard to decide on the title, it might be easier to initially lower your bar a bit. Just come up with some candidate titles that do not have to be perfect. Then ask your colleagues—your fellow PhD students, your supervisor, anyone—to have a look at the list and to pick the most promising candidates for refinement and final polishing.

Get the ebook from your favourite digital store! Paperbacks are available too (Amazon only!)

Cheatsheet: How to Revise Your 1st Draft (2/2)

Here is the second cheatsheet on how to revise the first draft of your scientific paper, focusing on sentences and words. (Here is the first one if you missed it). Enjoy!

For a hi-res PDF, please click here!

Want more? In my book How to Write a Scientific Paper you’ll learn a systematic approach that makes it easier and faster to turn your hard-won results into great papers. Or check out the series of posts that starts here.

Cheatsheet: How to Revise your 1st Draft

Cheatsheet: How to Revise Your 1st Draft (1/2)

Hi all,

as I hinted at earlier, I’ll be releasing a couple of cheatsheets on scientific writing based on the writing series/book, mostly because I love to play with Adobe Illustra^H^H^H because I’m sure you’ll find them useful 🙂

Here’s the first one; click here for a high-res PDF version.

Want more? Get my little writing guide where you’ll learn a systematic approach to writing papers that makes the whole thing easier, faster, and less painful: How to Write a Scientific Paper!

Cheatsheet: How to Revise Your 1st Draft

How to deal with reviews (2/2) (paper writing for PhD students, last part)

This post continues directly from part 1/2.

One way of making the referees happy is to always acknowledge that they have been heard, whatever it is that they say. Never treat a referee with disrespect, even when what they propose is wrong, or when they have misunderstood things because they obviously didn’t bother to read your manuscript carefully enough. Always give them something.

If the referee misunderstood something that is obvious, write another sentence on whatever the obvious issue is and add it somewhere. Thank the referee for pointing out that your paper was not clear enough on the issue, and tell her that you have now added a clarifying sentence. If the referee’s comment or question is so confused that you cannot even figure out what it is that the referee wants from you, do something about it nevertheless. Pick some sentence or paragraph that might be related to whatever is confusing the referee. Then rewrite it: try to make it more clear, or at least rearrange the words… Finally, write a polite answer to the referee: tell that to the best of your understanding, her problem was probably related to the issue discussed in this sentence or paragraph, and that you have now tried to make it more clear. At times, the referee is confused enough not to know herself what the original issue was, and gladly accepts this act of repentance from you.

The above does not mean, however, that you should always do what the referee tells you to do. If the referee asks you to do something that you feel is wrong or doesn’t make sense, don’t do it. You should, however, explain in detail in your rebuttal letter why you chose not to do it. But, if possible at all, change something in the text, however small. Then, the referee will feel that she has been heard.

It is common for the referees to get speculative and to come up with so-called bright ideas. While this may be genuinely helpful, it can also be a nuisance if those ideas are tangential to whatever it is that you are doing. If the referee asks you to do something that sounds sensible but is clearly outside the scope of your paper, insert a sentence into your discussion section where you mention that it would be useful to do in the future whatever it was that was suggested by the referee.

It may also be that the referee is both hostile and wrong: you know that your results hold, but the referee does not believe you and does not want to believe you. In this case, you must make your stand and defend your results. Be polite, constructive, and firm. Why does the referee act this way? If it is because you have not provided enough evidence to support your conclusion, apologise for lack of evidence and provide more (even if there was enough already). If it is because the referee feels left out (often indicated by requests to cite some of her own work), you can give her credit for some earlier work in the introduction or discussion, but you should not cite papers only because you are forced to do so.

There may even be more nefarious reasons for referee hostility – the referee trying to block competition for instance – that may be hard to detect or disentangle from general grumpiness: perhaps the referee simply had too low blood glucose levels, you never know. Even if you suspect something like an attempt at blocking, be polite but firm while writing your responses in a way that they are also meant for the editor’s eyes. If someone has decided to block your work, you cannot turn that person’s head, but the editor might be able to spot what is happening. And if a referee is clearly being unethical, you should confidentially let the editor know this.

But most of the time your referees have good intentions: being critical is not the same as being mean. If you treat your referees with respect, if you make sure that they feel that they have been heard, and if you always give them something, they will be happy or at least happier, and because of this, they will accept your paper more willingly.

This concludes the series (for now). I may post summaries, cheat sheets etc later. Thanks for reading!

Breaking news: the ebook based on this series is out! Go get it!