You talk with an accent, where are you from?

GMP (aka "Academic Jungle") started a great discussion about people with accents, and about how everybody asks them "Where are you from?", and about how it can be extremely annoying.

I totally agree that it may be very annoying. As a Russian, I rather dislike talking about vodka, Putin and differences between Moscow and the rest of the country. At the same time, I realize that people on average don't know that much about Russia and Russian culture, and they are trying their best to relate. And I appreciate that.

And that's why, after reading all replies to that GMP's post, I have to disagree with most commenters, and explicitly state that it's OK, and moreover necessary to ask people where they are from. Even if it is annoying =)

Why? Because it's better to try to find some common ground with people, rather than stay cold, indifferent, sterile and perfectly un-annoying. It's better to be boringly curious than boringly uncaring and apathetic. It's better to fail in communication than not to communicate at all. It's better to be mistaken about people's background (as long as you try to fix your mistakes and learn more about them) rather than ignore this background, and assume that everybody are essentially same and identical, and do not even deserve to be asked about where they are from.

When people ask me if I like vodka I cringe. But at the same time I am grateful to them for this small pathetic effort to find something common between their life and mine. It's important for me to know that they did not treat me as "just another compatriot of whatever origin I don't care about", but tried to see me as somebody with a potentially unique attitude towards life. And if they are mistaken for the actual content of this attitude... Well, there are complex socioeconomic reasons for that, and it is fine. It is not the worst starting point for a discussion, after all.

My compliments go to those who ask "where are you from". My sympathies to those who are tired of providing stereotypical answers. But saying that it is bad to be interested in people's origins is just plain wrong =)

Google as a bibliography software

It looks like Google have introduced some bibliography software functionality to their Google Scholar. Now you can add Google Scholar results to your personal "library" of papers. And you can also assign labels (essentially - tags) to articles.

http://www.google.com/intl/en/scholar/help.html#library

The interface for adding labels is slightly awkward (a bit too Gmail-style for my taste), but usable: to add a label to a paper you should first create a label (it will be empty just after you created it), then click on the paper title, get to the "paper page" (where the abstract is whoen), and there use a drop-down menu. A bit too many clicks to enjoy the process, but it's usable.

Linkedin endoresments

I like how on Linkedin I have 7 endorsements for "confocal microscopy" (which I in fact only tried for about a week), but just 1 endorsement for "patch clamp" (which I did for 3 years). Naturally, all from people who knew me ~7 years ago (before I tried either). Is not it nice?

Also one endorsement for "Communication audits" (I don't even know what this thing is. How did it even get there?)

Conclusion: endorsements totally don't work if most of your connections are from your previous career. People just choose words that sound nice, and then via positive feedback (most endorsed skills being shown at the top) these flukes perpetuate, and get written in stone.

I am now tempted to delete "confocal microscopy" from my list of skills altogether =)

Number of PhDs

Back from SfN. People still don't understand that the trendy motto "Limit the numbers of PhDs" inevitably comes together with "Make it harder to get to a graduate school".

Which, in turn, means "Make GPA mean more than it does now" (aka "No way back", or "You have only one chance"). Which would totally screw "non-traditional candidates" of all kinds, as well as "hesitant candidates", such as women, minorities, first-generation scientists, converts from other educational paths, people who had a baby, people who took some years off away from academia, etc.

The numbers are not the problem; it is the training program that should be improved (and there's more than one way to do it).

English language

ze = terrible
hirself = terrible
s/he = rather terrible
she or he = OK, but longish
they = great, correct, traditional, and sounds good!

On Researchgate

As people around me are designing their posters and "science cards" (aka "business cards") for the SfN meeting, I see several of them using QR codes that link to their Research Gate profiles.

Now, I do find ResearchGate useful. It gives you space to host your papers, so that people could download them for free, bypassing the paywall. It also comes up pretty high in Google results, so if you want to look professional in Google search, you'd better start an account there. As well as at Linkedin, Google Citations, and Mendeley.

But at the same time, it is just such a half-baked, half-functional site! If a person, a casual visitor, is not registered there (and also logged in by default!) it doesn't even allow them to see your profile! Instead it produces a pop-up, and then flanks the profile with some ridiculous invitations to register that together take up almost half of the screen. Compare it to Linkedin that at least shows your CV all right, even if the visitor is not logged in to the system.

And also ResearchGate just isn't flexible enough to store your CV. It can represent your publications rather decently, and you can put your awards there, and maybe your positions and education history are also OK, but they totally don't have a proper section for teaching experience. They have some weird "Skills" section, that is common in Resumes, but aren't traditionally included into CVs. But they don't have a good way to reflect your teaching. It's just not an optimal way to store a CV online, and certainly not the best way to represent it.

Or maybe I am just too harsh on them?.. I don't know.

Surely it's still better than nothing. But every time I visit ResearchGate, can't help but feel the pain from seeing all these opportunities wasted.

Alternative SfN browser

In case you haven't seen it before, here's an alternative (and really pleasant) browser for SfN abstracts:
http://sfn13.hubbian.com/

Also you can vote your favorite abstracts up =) Not many people seem to be doing it, but I think it's fun.

On psychological integrity

It must be hard to participate in diversity programs these days. I mean, I know people who spend considerable amount of time encouraging, say, women, or people of color, to join graduate programs in science. But these same people spend at least a hour a week ranting about an oversupply of PhDs, and the scarcity of job offers. Mathematically both claims are 100% correct and valid: we DO need more women in science, and we definitely need more people of color in science, even with current job market situation, but psychologically it must be hard to switch between these two mindsets.

At least I totally don't know how to switch between these mindsets effectively. I seriously considered going to an outreach session like that, because it's fun, and a right thing to do,  but then I realized that I'm rather likely to have a slip of the tongue, and say something inappropriate, or even embarrassing. Because how do you even phrase it? Hey people, this whole graduate school thing is an extremely risky, and in fact somewhat silly and delusional affair, and only about 5% of 1st year graduate students will make it to a TT position. But please come, because your chances (as, say, diversity candidates) are actually somewhat higher, and at least 10% of you will get TT jobs! Which is like a lot higher, if you think of it, twice higher than the average, but still - really - it is so unbelievably risky! How do you encourage people en masse to follow a path that is that uncertain?.. Or rather, how can you do it responsibly, without compromising your conscience?

I don't know. That's a freakishly hard, complicated, and loaded topic. For now I decided to just quietly withdraw and hide from this particular type of outreach. Encouraging people to go into college, or to a medical school, is easy and pleasant. Straightforward psychological "You can do it" type of encouragement totally works here, I think. But with the graduate school - maybe not so much. I guess I'll take a pause and wait for a while, at least until my mind clears.

Eating food for science: on the importance of it

The biggest problem with our local Neuroscience department is the absence of a canteen, or a cafeteria of any kind. And the issue here is not that we are undernourished, but that the science suffers.

Think of your favorite conference. The talks may be nice, and the posters - quite awesome, but arguably the most important information you can get, be it some nitty-gritty aspects of experimental techniques, anecdotal findings, wise career advice, or even  scientific gossip - all this stuff gets discussed at the lunch tables! It's similar to how most important ideas come to people when they are taking a shower, or are walking back home: the same exactly thing is true about the scientific interaction. It works best when it is fluid and casual.

And don't even get me started on the necessity of sharing tables with people you don't know! People working in different labs, fields, even disciplines! So what is that you study? Reticulopenducular network of the freshwater sea urchin esophagus? And how is it going?

Lunch talk is the column, the pillar, and the basement on which the building of Science stands!

And still we don't have any canteen here. Not even a set of dirty red coaches around an expensive coffee machine. Even this would have worked! But we have nothing. I guess whomever planned this building was pretty ignorant about science. So we just sit in our lab spaces, barely knowing names of people working on the same floor. What's about one floor up or down, you say? Don't be ridiculous. I would not be able to even recognize them on the street.

Something should be done about it =)

PeerJ is moving forward

I really like the PeerJ initiative for some reason, and while I have not yet published anything there myself, they seem to become more and more attractive as a venue. Recently they got indexed by PubMed (as well as other scientific indexing services), and also they now let undergraduates publish for free (assuming that they have a "normal" senior co-author publishing with them).

Now look at this beautiful little paper:
https://peerj.com/articles/64/

...and realize that practically there's no excuse in having orphan data anymore. Anything that was done properly should be published, even if it's negative data, or the project was abandoned, or it does not tell a story, or whatever.

And a bonus: some nice infographics, also from PeerJ =) Evolution of de-facto grammar standards for the names of some famous diseases:

(source: https://peerj.com/articles/67/)

This whole "alternative careers" thing isn't worth the fuzz

I don't get it when people say that "alternative careers" in academia are not supported enough. How so? Virtually all academic training is about the alternative career!

That is the main career path, the one followed by ~90% of grad students and postdocs, the one that involves leaving academia at some point, that is not paid enough attention to. Even though most people who are working in academia this very moment will eventually leave academia, they don't receive enough training to prepare them for this step. This is bad.

Conversely, the "alternative path", taken by only 5-10% of people, which eventually leads to a tenure track position in a research university, is surprisingly well covered. All these postdocs, publications, conferences... All for one small alternative path. Isn't it strange?

So stop complaining about "alternative careers", and better concentrate on the "mainstream career": the one that leads out. At least pay some attention to it. Think of it. It's much more realistic.

Google decided to close the Google Reader service

Wow, bad news. Just half a year passed since I started reading Neuroscience-related blogs on a regular basis, and now Google takes from me the way to read them. I almost can not believe it. Google Reader seemed to be such a great, sane alternative to all these attention-snatching noisy services like Facebook and Twitter... Slow, careful, thoughtful environment. And now it is there no more. What a shame!

Here's a nice discussion about the whole affair. And, well, I don't yet know what to do. Maybe I'll find another RSS aggregator (maybe this one, or this. Or maybe this.). But just in case, let me list here some key blogs I read. Just as a reserve copy (even though this blog platform is also owned by Google... oh screw it!)

(cups his hands around the mouth and shouts) - Google, if you hear me, don't be evil!

Anyway. Here's the list.

http://isisthescientist.com/
http://scientopia.org/blogs/proflikesubstance/
http://scientopia.org/blogs/drugmonkey/
http://scientopia.org/blogs/bridgeblog/
http://scientopia.org/blogs/drbecca/
http://scientopia.org/blogs/neuropolarbear/
http://drtheron.com/
http://neurodojo.blogspot.com/
http://sciencebysummer.com/
http://babyattachmode.blogspot.com/
http://academic-jungle.blogspot.com/
http://persistentastonishment.blogspot.com/
http://mindfulhack.blogspot.com/
http://rxnm.wordpress.com/
http://scientopia.org/blogs/trainingprofessor/
http://thetightropeblog.wordpress.com/
http://scientopia.org/blogs/science-professor/
http://phenomena.nationalgeographic.com/blog/the-loom/
http://phenomena.nationalgeographic.com/blog/not-exactly-rocket-science/
http://phenomena.nationalgeographic.com/blog/only-human/
http://phenomena.nationalgeographic.com/blog/laelaps/
http://mikethemadbiologist.com/
http://calnewport.com/blog/
http://blogs.discovermagazine.com/discoblog/
http://blogs.discovermagazine.com/d-brief/
http://blogs.discovermagazine.com/gnxp/
http://blogs.nature.com/actionpotential
http://neurologicalcorrelates.com/wordpress/
http://www.guardian.co.uk/science/neurophilosophy
http://neurocritic.blogspot.com/
http://dynamicecology.wordpress.com/
http://getalifephd.blogspot.com/
http://theprofessorisin.com/
http://bjoern.brembs.net/

The Wheel of Time book series: the dynamics of sequel ratings

I am reading The Wheel of Time series. I've just finished volume 3, and by now I am somewhat tired, but not quite tired yet to quit. Still I am kind of unsure and undecided about whether I should go further or not. Or maybe take a break. Or maybe skip a volume or two.

To answer this question I downloaded book ratings from GoodReads, and visualized them. So for those of you who care, let me share the results =)

Most books are rated by quite a few people (about 30 thousands at least), so in terms of the spread these values should be quite tolerable. The biggest methodological problem with these numbers is that the further into the series, the more faithful and fantasy-oriented the readers in the pool would become, and it should certainly introduce a bias. I prefer to ignore this bias however, as I have no idea about its direction! More faithful readers may score the books slightly higher (because they are faithful, and so like them!), but at the same time they are also humans, and so they should gradually get tired, and thus score the books lower compared to the first volume. Also faithful readers may have higher standards for the books of this kind, as presumably they read dozens of them; unlike those who only "tried" the series... So, I don't know how to correct for this bias. Let it be.

Another thing we could look at in the GoodReads data is the "Readers retention score": share of people who managed to read book #i+1 after finishing the book #i. There's a pretty stable decline in reader numbers through the series, with the first book scored by 96 thousand people, and the twelve-st scored "only" by 38 thousands. At the same time, surprisingly, if you calculate the retaining index, it doesn't change that much across the series, except for a huge outlier at the book #11: the last one R. Jordan managed to write before he succumbed to cancer. I don't yet know whether the book is really that good, or whether it is just extremely intriguing, or maybe fresh, or maybe people paid attention to this whole real-life story around the fantasy world, with one author dying, but leaving extensive notes to his colleagues to finish the series... It may be. But it means that at least this book should probably be read, even if I decide to skip a few in the middle.

I can not use this index to measure books #13 and 14, unfortunately, as book #14 is the last one (i+1 doesn't exist), while book #13 was published too recently, and so has a relatively low number of readers. I guess, it also means that this plot has an even stronger positive bias just because of unequal exposure of books to time, so to say. It does probably also have a positive bias due to the "self-selection of faithful readers" described previously... Still it is funny that the "retention values" don't correlate with the rating at all (r = -0.2; p = 0.5). It's kind of weird.

Anyway, for me personally this data probably means that I'll try the fourth book. But if it doesn't quite work, I'll skip straight to book #11.

A postdoc song?

I have stumbled upon a song that neatly summarizes my experiences as a postdoc. It may not be 100% true, but it covers most of the phenomena! It is actually surprising that the title of the song doesn't even mention postdochood. At the same time, it may be a conscious omission. Just to make the hints more obvious =)

In support of Gmail (and against Microsoft)

I hate Microsoft's "Scroogled" campaign so much that I will even post about it.

So, they claim that Google reads your mail (mainly to provide you with contextual ads, they admit), and it is a breach of your privacy, and so (surprise!) you should switch to Outlook. All heavily stylized, on a red background, with almost-blinking exclamation marks, and so on.

So, let me elaborate why Microsoft is wrong, and Gmail is actually good:

1. Spam filters. The best way to stop the spam (and the only effective way available at the moment) is to use the collective intelligence, the web2.0 approach, so to say. That is, to provide individual users with a "report spam" button, and to filter messages that have overcome a certain threshold of reports. But you know what? The implementation of this algorithm actually requires the software to scan through your letters. And you do want it, because you don't want spam.
2. Non-context-driven advertisement is bad; which means that context-driven ads are at least not as bad, or maybe even good. Now, this is a strong belief of mine; one with which many people would not probably agree immediately, but consider the following. Ads (general ads, like those on TV) create information noise around you. In a sense they aren't much different from spam: they just load you with unnecessary information you didn't request; they take your time, your thoughts, your life. They try to trick you into doing things you don't need, or want. Also from purely financial point of view, if a product is heavily advertised , it means that marketing expenses constitute a substantial part of its price. So by buying products that are advertised you are essentially paying somebody to have your TV-shows interrupted. You are paying somebody to have your internet-magazines and web-sites cluttered with useless ads you don't read anyway (or at least try not to read). You provide positive reinforcement to them! The only rational response to advertisement actually is not to buy the brands that are advertised, as you want to pay for the product, not for the noise about it directed at you. There's only one thing that is good about ads: that they can potentially expose you to something you do actually need, but are simply not aware of. Now, if you think of it, contextual ads is the only realistic way to minimize the bad components, while increasing the good. That's the only way to make ads informative and useful, and maybe even interesting, while reducing the total amount of noise in the system. For you personally, mind it.

That's two good points in favor of Google. Now two bad points against Microsoft:

1. Microsoft's "Scroogle" campaign is inspired (visually and in spirit) by hysterical conspiracy movements, such as, say, anti-vaccination movement, or tea-party style propaganda. And as such, it actually promotes this style of thinking. Making the world a slightly worse place to live.
2. It pushes the privacy-related discourse into wrong direction. Now, this is again somewhat controversial, but I think it is fair to say that privacy as we knew it for decades, is dead. We leave so many traces in the world (mainly digital, but not only), we are so interconnected, and the computational power and information access available to each of us are so great that given enough time and will anybody can learn anything they need about any other person. I think the "Vanish" project is one of the best illustration of it, but not the only one of course. Anyway, the sooner we start re-thinking the concept of privacy; the sooner we realize that we just can not hope to hide from the world around us anymore, the better the outcome will be. Privacy is at decline, and just hiding information about us can not solve our problems anymore. It may give us a false sense of protection, but it would only increase the risks, as it would make the stakes higher. We need to think of other mechanisms to protect our lives from bad will and bad luck. But the first step towards the solution is to accept the problem. Not to pretend you can deny it by switching from one IT leviathan to another.

Building a personal Knowledge Base: a follow-up post

So, some time ago I wrote about building your personal knowledge base, and how personal wikis can be nicely employed for this purpose. Here's a follow-up post.

TLDR: I tried several, and settled on the... Microsoft Word =)

Details:

I started from the Wikipedia list of personal wikis, and then checked those that looked promising. Namely:

OneNote
http://en.wikipedia.org/wiki/Microsoft_OneNote

• Pros: while not exactly a Wiki, you can make wiki-style references there. Also it's extremely pleasant to work with, especially if you are a visual thinker, as I am.
• Cons: easy to delete your work accidentally (as it's a note-taking tool, not a personal Wiki). Hard to make back-ups. While export to html is available (as a third-party plugin), it doesn't export wiki-style cross-references correctly, and is thus mostly useless.

I ended up using OneNote for note-taking, but not for knowledge building. It's actually a really great tool, a serendipitous discovery that made my life much easier! Yet everything you do there is just a bit too ephemeral to use it for knowledge-base building purposes.

WikidPad

http://en.wikipedia.org/wiki/WikidPad

• Pros: it's a personal wiki that works.
• Cons: It isn't WYSIWYG, which renders it almost unusable (I'll spend most of time editing the Knowledge Base, not reading it, thus the edit mode should look neat and uncluttered)

Zim

http://en.wikipedia.org/wiki/Zim_(software)

• Pros: Works. Has a nice, simple interface. Allows export to html (which I'd really love to have, both for back-up and compatibility reasons), creating a set of linked html files. Also stores the data in a set of plain txt files, which is good, as theoretically even in the worst case, if the tool crashes permanently, one would still be able to read these txt files one by one.
• Cons: I managed to crash it twice in my test wiki with 20 entries, which is not good. To tell the truth, it happened while I was renaming entries violently, which is a rather esoteric activity, but anyway. Thus decided not to use.

Tomboy

http://en.wikipedia.org/wiki/Tomboy_(software)

• Pros: Works. The interface is even neater, almost conceptual. Does really good on-the-fly linking between entries. Exports to html (in a giant cross-linked file, which I actually like even more than a set of separate html files). Renames links nicely.
• Cons: Strange way of storing data (machine-readable, but not human-readable). Can do synchronization on its own, but it is also not quite transparent. And as my whole life) will, in a way, depend on this knowledge base I'm building, I'm just afraid to entrust it to a system I don't quite understand. When exporting to html, into this giant html file, it cannot order the entries alphabetically, but puts them in the "tree-crawling order". It is a logical thing to do, but it looks strange. Also you cannot have a word "dogs" link to the entry "dog"; it would be two different entries for Tomboy, as the title of the entry is the link to the entry. There seems to be a plugin to fix it, but I have not tried it.

TreePad

http://www.treepad.com/

It's not quite a wiki, but rather a structured tree-like note taking system. Yet it has one major flaw that rendered it perfectly unusable: it doesn't work properly with unicode.

Microsoft Word

(On which I have finally settled, at least for my main Knowledge Base)

• Pros: In Word you can do cross-referencing within a document, from every word to every title. Thus you can create a one-document Wiki. Also you can use the Draft mode with Outline on the left to work with a tree of entires, thinking about your knowledge in a structured manner. And most importantly: you can save or print your document at any moment, as if it were a plain text.
• Cons: It takes some time to format a link. Also I'm not sure how fast the processing will be when my document grows a hundred pages long or more (right now it is at ~30 pages, and doesn't seem to have problems, so there's a hope).

A non-profit in Florida firing all postdocs with 1 mo notice?

I've just heard that allegedly a Torrey Pines Insistitute in Florida is firing all their postdocs with 1 month notice. Well, all postdocs that don't have a funding on their own (but apparently not many of them have it).

And it's really weird actually, as a friend of mine was just hired there as a postdoc about half a year ago! Didn't they anticipate the funding going dry? Why did they hire them to begin with?

The drama gets even more intense because my friend is on the H visa, and thus doesn't have a grace period: the hour they lose their job they become illegal immigrants in the US, violating all possible laws. In practice that means that they can gamble, and desperately look for a job, but if they don't find one, they spoil their relationships with the US visa machinery for a long time. Alternatively they can buy tickets for their entire family to their respective country, but with 1 mo leadtime these tickets would be quite expensive. So essentially that's a trap.

Not that other people suffer less. As a person from Europe, I was really puzzled by the fact that here in the US, from the majority of jobs, you can fire a person immediately, without a warning, without any explanations at all. In my country it would be unthinkable. But anyway, a one month warning probably doesn't sound that bad in the Unites States. Still, when foreigners are concerned, a one month warning is a disaster, because you can easily screw somebody's career this way, even from purely financial point of view! For a family of 4 it would mean spending ~4 $M on the tickets back home, getting rid of all their belongings, selling a car at a loss, loosing the rental deposit... Probably about $10 000 of instantaneous loss. Even with careful budgeting, not every household living on a ~45 $k/y income would have a cushion to easily survive unforeseen expenses like that.

Scientific Spam

Each time I get spam about pipetters and RNA in my e-mailbox I  feel guilty.

Because what's the natural reaction to a spam letter? Hitting the "Report spam" button almost automatically! Die, die, you useless spam letter, and burn in the spam filter, so that other good and honest people would be spared of your loathsomeness.

But when I get a spam letter about axon tracing, it's not that easy anymore. What if I actually use this company? Or may use it in the future? If I now put their e-mail in a black list, would I be sorry about it later? What if they were at SfN, and scanned my badge? Does it mean that now I'm obliged to delete their letter calmly and carefully, without cursing it forever? And also, aren't we in the same boat? Like, if I meet them in a bus, I would treat them as a friend, as a colleague, and we'd find something to talk about. They are doing something similar to what I am doing. Aren't we brothers? Aren't we fighting for the same common goal? Like for light of knowledge, and the betterment of the world?

...But still it's obviously a spam letter, shameless and unsolicited...

I am actually surprised how uselessly emotional I get about it, and how I actually start thinking before finally pressing the "report spam" button. It's just crazy. Why would I care? Spam is spam, regardless of the topic! Yet for some bizarre psychological reasons I now hesitate.

The "official best practice" however is still to press the button. Because spam is noise, and noise is evil. If you  send unsolicited communications, you deserve your sales to go down. Period =)

Update for toad videos

By the way, as I finally managed to watch those wonderful toad neuroscience videos I posted here earlier (those based on work of Jork-Peter Ewert), I realized that they show 3 scientists in this short movie, and all three of them are women. Isn't it nice? It's early 90s, by the way.

Even more reasons to like the guy =)

Giant tadpoles in Providence, RI

About a month ago I have drawn this historical painting. Not many people remember these days that in the middle of 19th century giant tadpoles were widely employed as a means of transportation, for both goods and people, here in New England, and generally along the East Coast. Alas, they went extinct since then. Probably a fungal infection, or predatory steam engines: nobody knows for sure.

Neuroethology of toads

It turns out that Youtube hosts a great mini-documentary about those old famous experiments in the toad, in which, depending on what kind of a black shape you show to the animal, it either tries to catch it, or avoids it.

That's the foundation of neuroethology, and a great educational video to show! (I usually give videos as a homework. I guess watching videos is easier than reading papers, and thus makes a more humane homework)

The video is split in 3 parts, and is about 30 minutes in total.

Keywords: worm, antiworm, nucleus isthmus, visually guided avoidance behavior, prey capture, frog, toad.