Today I learned about acetoin, a chemical found in many foods and fragrances. It tastes buttery.

Acetoin can be produced by some strains of bacteria, especially if they've been engineered to do so. (That's true about many, but certainly not all chemicals.) It's especially convenient to do so if you're trying to control the flavor of a fermented product like wine or soymilk.

Just don't do it.

If you're going to lie to someone about your work, don't do it in science.
If you're going to lie to someone about your scientific work, don't do it in biomedical research and especially not when researching potential gene therapies.
If you're going to lie about your gene therapy findings, don't do it repeatedly and egregiously for almost a decade and never do it to the source of your funding.

Dr. Li Chen did all that. The NIH (and by extension, the US Dept. of Health and Human Services) is not pleased with him. It's bad enough that his former lab had six retractions all around the same time in 2010. Dr. Chen was intimately involved in the whole mess.

His punishment is essentially a 3-year ban from federal funding and involvement. I'm inclined to think that the investigations and retractions are damning enough. This guy now has a smoldering crater in his CV. Even once he's eligible for federal funding again, I suspect he'll have some trouble getting his grant applications approved. That's a life-threatening condition in any field of science.

Let's see what happens when we add an extra letter to some popular web addresses.

You'd think they'd all be trying to ride on the fiber optic coattails of their more popular brethren. You may be correct in many cases.* Here are a few exceptions.**

• dreddit.com

It's an archive of the FAQ from the Usenet group alt.magic, a group for magicians to discuss their craft. The most recent updates to the FAQ are from 1998 and they're mostly listings of brick-and-mortar magic equipment suppliers. I wonder how many of them are still in business.

A choice quote from one of the supplier descriptions: "He uses a tremendous amount of hyperbola in his advertising..." Are these people magicians or mathematicians?

• twikipedia.org

An Amsterdam-based web design studio. They seem like they made a good choice.

• etwitter.com

Redirects to a site for some manner of art-printing business. The images are largely uncredited, leading me to suspect they were hijacked from Flickr. They also offer a sizable collection of Licensed Artwork From Star Wars, so if you're still looking for that finishing addition to your Boba Fett-themed living room, try Amazon because there isn't a retail frontend on this site.

*Most single-letter modifications to google.com appear to lead straight to Redirect City by way of the Download This Surreptitious Software Bypass.

**atwitter.com is for sale!

Today, I learned about the existence of RoMEO, a database used to answer a very specific but often problematic question about peer-reviewed journals. The question is "Can I store and share the work I've published in this journal with people who want to read it?" and the answer is often "No, nope, never, probably not, you don't have that right, this is ours now, bwahaha, etc. etc." RoMEO lists which publishers feel that way and which publishers have more open attitudes toward self-archiving.

StackExchange is so nice, I don't even mind spelling its name with CamelCaps. It has specialized niches like Reddit, an expert community like Quora has in its better moments, and a genuinely effective user-moderated reply system. The best part is finding new subforums: I just found one for German language questions and one for sound design. Whenever I find forums like these on Reddit, they're usually ghost towns or full of users with far more questions than answers.

I found some new tools for protein interaction alignment today. My PI forwarded me this paper:


Clark, C. & Kalita, J. A Comparison of Algorithms for the Pairwise Alignment of Biological Networks. Bioinformatics btu307- (2014). doi:10.1093/bioinformatics/btu307

Clark and Kalita seem to really like NATALIE, a tool which ignores parts of the network which don't appear to align well (Lagrangian relaxation!). It's part of the LiSA software collection and looks like it was last updated in 2012. I'll have to see how easy it is to implement - some of these kinds of tools may work really well but are just painful to get working, especially if their documentation is sparse.

Here's a quick Excel trick for averaging duplicate values. It's the kind of simple command that I probably should have learned years ago, but it's only been available since Excel 2007 so at least there's that excuse.

Anyway, it's the AVERAGEIF function, used as follows:

=AVERAGEIF(the column with the duplicate values, a single value to get the corresponding average for, the column with the values to be averaged)

formatted so the first and last columns are static, like this:

=AVERAGEIF($A$1:$A:$1234,A1,$B$1:$B$1234)

I'm certain that something very similar can be done in a shell script based around uniq.

I’ve been taking a personal development class for the past few months (GRAD611 at Virginia Commonwealth University, part of the nascent BEST program). The class had some broad objectives: to “develop leadership and professional development opportunities for professional, graduate and post-doctoral students that will enable them to thrive in today's professional environment and empower them to make meaningful contributions to society as they realize their potential as future leaders” and to “build a network of internal and external partnerships and identify resources to support and guide leadership and professional development initiatives for professional, graduate and post-doctoral students”. Those are the course goals as they’re written on the syllabus. They’re very ambitious. When the course started a few months ago, I was very skeptical as to whether I’d gain anything from it. I tend to take most personal development strategies with a sizable grain of salt. Too often, these concepts are rife with one-size-fits-all solutions and silver-bullet problem solving strategies.

In the end, I was pleasantly surprised! I suspect that it will be difficult to tell if any new opportunities are now available to me until I can apply what I’ve learned. The second goal listed above is even trickier to address. Have I been able to access a new network of “internal and external partnerships”? Will I know when I see such opportunities in the future?

More importantly, what have I learned about myself? Let’s list a few changes:

•          I’ve noticed lately that I’m much more tolerant of how people portray themselves. I used to find it irritating that any individual would be so myopic as to define themselves in terms of an occupation or an interest. Everyone has a multifaceted personality – no exceptions. The trouble arises from trying to communicate that diverse set of personality traits to others. I can’t just introduce myself to someone and expect them to understand who I am, nor can I try to describe every aspect of my identity to them in a brief meeting. These things require time and solid relationships. It also isn’t fair for me to find others short-sighted when they try to put their identity on display. They’re human, they’re complex, and they have their own sets of strengths. These traits may be immediately obvious or they may require communication.

•          I’m not sure if I’ve identified my authentic purpose. I’m not sure if “authentic purpose” is an authentic concept. It was frequently addressed on the periphery of the class materials but rarely discussed directly. It sounds questionable to me because I don’t believe in a discrete, guiding force. Everything happens for numerous reasons but these reasons may not conspire to guide me toward a purpose. They are natural forces as much as gravity is. That force doesn’t press me to the ground because it wants me to study geology. It has that effect because I’m conveniently made out of matter. That being said, perhaps “authentic purpose” is less of a force in itself and more of a general description of how I react to forces. I have many options in life but some options do feel more “authentic” than others.

•         I’ve become more accepting of the strengths of others. It’s easy to dismiss ideas when they don’t fit into your perspective and it’s easy to dismiss others when they don’t approach problems the same way you do. I tend to approach the world in a broad but systematic way. There’s so much interesting material out there for me to absorb, but I also need to make logical sense of it all. That’s less of a priority for some people. They may be more focused on winning people over or placing information in historic context. I like to do those things as well but they’re certainly not my first impulses.

•          I’ve also become more accepting of my own strengths. It’s quite easy to lose sight of personal strengths when there’s so much to lose from having weaknesses. Spending so much time in science and academia may contribute to that phenomenon: I tend to spend a lot of time each day worrying about what could go wrong with my plans (or, even worse, if anything has already gone wrong but I haven’t noticed). It’s a habit that extends to my own self-conception. Over the last few months, I’ve been increasingly able to see my own shortcomings as lesser strengths and my more obvious strengths as foundations to build upon.

•          I’ve been attempting to use more filters when it comes to gathering sources of input. It’s quite difficult for me to separate signal from noise when I’m searching for interesting information, whether it’s research or just the daily news. The problem really comes down to how I tend to find everything interesting: even when the metaphorical signal-to-noise ratio isn’t so great, I can still get lost in the noise. Reducing the amount of input I attempt to tackle at any one point has helped with that issue.

There are changes that I’ll continue to work on:

•          I'll try to meditate more regularly, though I don't think I'll set any numerical goal on the number of times to do so. I just know that I get more done when I'm aware of my own happiness. Being productive adds to the contentedness and completes the cycle. It’s not even a matter of sitting in once place for a while and focusing on one thing. I’m glad just to notice a momentary, beautiful detail in the world around me.

•          I’ll think more critically about what I consider failure. In a world without failure, I would become very confused and suspicious as to why I wasn’t failing at anything. Failure is a natural part of life and an educational one. Much of what people refer to as failure may just be evidence of authentic challenge.

The GRAD611 course was genuinely one of the more unusual yet useful courses I’ve taken during my graduate career. It’s provided me with a wealth of material to think about. I've listed some fairly abstract observations, but the lessons about time management and conflict resolution have already proved valuable as well. I’ll have to see what kind of lasting effect all this material may have in six months or a year from now.

"...every one of them is slowly going mad."

I found this blog entry about how much programming sucks though Lifehacker today. If you were to ask me what the top problem with programming is, I'd say something to the effect of "programs are written for computers rather than for people" or "code is like a hammer you have to read" and so on. (You didn't ask me about programming but I'm going to tell you anyway.) I'd suspect that most of what makes code "bad" comes down to the inherent differences between computers and human beings. Humans tend to freak out without context while computers don't need reasons to get things done. Humans see value in hard work, so they'll hammer away at the same problem for weeks or years; a computer will do the same but we don't see any value in its long-term labor unless there really isn't a faster way to do it.

So, I think I interpreted the blog post differently than Lifehacker did. Their idea was "The good news, if you're learning to code, is you don't have to worry (too much) if your code is bad." The impression I get is that you just can't write good code unless you're also doing good writing. That means you're simultaneously writing for an audience with perfect comprehension and no consciousness (computers, that is) and for human beings with plenty of consciousness but far from perfect comprehension. That doesn't sound fun at all. The solution most programmers use is to not even bother.

A few choice quotes from the post echo these sentiments:

Not a single living person knows how everything in your five-year-old MacBook actually works. Why do we tell you to turn it off and on again? Because we don't have the slightest clue what's wrong with it, and it's really easy to induce coma in computers and have their built-in team of automatic doctors try to figure it out for us. The only reason coders' computers work better than non-coders' computers is coders know computers are schizophrenic little children with auto-immune diseases and we don't beat them when they're bad.

The human brain isn't particularly good at basic logic and now there's a whole career in doing nothing but really, really complex logic. Vast chains of abstract conditions and requirements have to be picked through to discover things like missing commas. Doing this all day leaves you in a state of mild aphasia as you look at people's faces while they're speaking and you don't know they've finished because there's no semicolon. You immerse yourself in a world of total meaninglessness where all that matters is a little series of numbers went into a giant labyrinth of symbols and a different series of numbers or a picture of a kitten came out the other end.

It's a good post. It's very cathartic.

Today's paper is: 

Legrain, P. & Rain, J.-C. Twenty years of protein interaction studies for biological function deciphering. Journal of proteomics (2014). doi:10.1016/j.jprot.2014.03.038.

I keep changing the reference format. This really shouldn't bother anyone but me.

The take-home message: There's a lot of protein interaction data out there! Contrary to popular belief, most of it isn't just false positives. Rather, most of this data reveals actual biological complexity. Proteins may just interact with more binding partners than we originally thought.

A few awkward points:

• Both of the authors are experts in the field but are also employed by Hybrigenetics, a company providing protein interaction screen services. They don't advertise the company's services specifically so I suppose it isn't really a conflict of interest. I still grow concerned about such things.
• The title sounds odd. Couldn't it have been "Twenty years of biological function deciphering by protein interaction studies"? I think it's the word "deciphering", mostly.
• The entire review sounds a bit strange, actually. I assume it's a result of English as a second language. It does make some conclusions hard to understand, i.e. "Almost 2000 different proteins were analyzed over six time points, covering four orders of magnitude in terms of protein abundance. In those papers, the aim of the purification process is no more the isolation of a protein complex but just a way to zoom in a specific part of the proteome", which sounds dismissive.
• More specific references to recent interactome-dependent functional studies would have been nice. As they mention, there have been thousands, but it continues to be an active research venue. It looks like the authors just forgot to add some references in other sections: i.e., "..in different cellular contexts (for review on affinity-purification coupled to mass spectrometry, see)".

These guys made an early protein interactome of Helicobacter pylori so I can't complain too much.

I never seem to remember the name of the film Mafioso. It's the one with the Italian guy who gets shipped to NYC by the mob. It comes up in conversation every so often but its title is just so generic that it's hard to recall.

Here's a neat little story about frozen frogs. The basic idea is this: wood frogs freeze solid over the winter, though that's not a problem since they can keep ice out of their cells (otherwise, all those ice crystals can really mess up those frog tissues). They do it by using glucose as a cryoprotectant and a specialized glycolipid as an antifreeze.

The paper in the Journal of Experimental Biology is here.

Beats!

Music for today - like many on Youtube, this guy does very high-quality song covers. The difference here is that he covers electronic-heavy songs that would be impossible for anyone to cover without a finely-trained ear, perfect timing, and just the right batch of equipment. I usually prefer covers to move in entirely new directions (the lady and I have been musing about what a female-fronted cover of December, 1963 would sound like*) but these are impressive on a more technical level.  Here are a couple.

A cover of Lovely Bloodflow by Baths. That whole album is wonderful.

A cover of Windowlicker by Aphex Twin. He doesn't quite capture as much of the original's classically weird atmosphere but that may be impossible.

A cover of Lost and Found by Amon Tobin. This is the live version, for reference.

Courtesy of this Metafilter post.

*A good cover. There are some on Youtube but this is the best one I could find, if that tells you anything.

Hello there! You may have noticed this blog transitioning to more of an electronic portfolio. This means that it will be less of a collection of musings and more of a collection of musings with a good bit of Context included. The rambling journal entries are still a primary focus. Now, however, you can learn about me in the "About" tab up there. I've included my personal mission and Curriculum Vitae. There's also a tab for Research: this page describes my current area of study. More material is on the way.

On networks of the social variety

It's a strange time when I'm feeling better about Facebook and more uncertain about more specific social networks. In theory, the Book of Faces really is the internet's Walmart: it's a place to get all your social interaction needs as long as your needs aren't too specific. It's great for small talk but actually quite inefficient for any kind of extensive dialogue (to see what I mean, try picturing your next Facebook comment thread as a real-life conversation. It gets pretty difficult in those 10+ comment rigmaroles). The same goes for Twitter.* Even so, there's something to be said for small talk. It's better than no talk at all.

The constant level of background chatter is also preferable to noise with a perceived sense of urgency. In real-life terms, I'm talking about ringing phones, ambulance sirens, or other warning klaxons. These are notifications designed to get your intention; they signal immediacy and the need for rapid action. That phone isn't going to ring all day and that ambulance may need the road you're on. A bit of that urgency shows up in email and social networking messages. In each case, we see a tally indicating how many new requests for our attention there are today. Most of those cases aren't even as urgent as a ringing phone. We can ignore most of what happens on Facebook without any cost.

I've been trying out Researchgate over the past few weeks. It's one of the smaller, more specific social networks I alluded to above. It came strongly recommended by folks in my personal development class. Researchgate is essentially a social network specifically for scientists. Each user has a profile as with other sites, but the focus is less on their biographic details and more on their scientific accomplishments (read: publications). The site is well-designed and leverages a more natural approach to networking than sites like Linkedin do. Connection suggestions are frequent but appear to be weighted in favor of real-world contexts (i.e., colleagues in your department, people in your field, or authors you've cited) rather than a largely generic network structure.

The mildly irritating part about Researchgate is the question-and-answer portion. Much like Stackoverflow, it's a forum for technical questions sorted by method or scientific topic. Unlike Stackoverflow (or even Reddit, for that matter), the moderation is minimal. Many questions are hardly questions at all. I can excuse the lack of English proficiency in many cases but it renders many questions impossible to interpret. In other cases, the phrasing is nearly perfect but the question asker fails to provide anything but the most basic details. The worst part may be the sense of urgency: these questions give the impression that entire careers are on the line. A wrong answer, employed in earnest, may waste weeks or even months of valuable research time. I know it isn't my fault if people don't know how to ask helpful questions or how to take advice from internet strangers.** Social networks are just enough of a potential waste of time as it is.


*I'd suggest that Twitter is the Starbucks of social interaction. It's ubiquitous, frequently noisy, and redolent with fashionable credibility, yet even the people who use it often don't seem to devote much mindspace to it. It's usually pleasant yet generally forgettable.

**This is the way.


Additional note to self: don't forget that Biostars exists. It's Stackoverflow for bioinformatics.

Today I found out about the grid.arrange function for R (it's in the gridExtra package). It's one of those things which would have been useful to know about years ago. I just found it on a Stackoverflow answer today. The function just takes plots and squishes them together into a single canvas. It's easy, too: just enter

grid.arrange(p1, p2, nrow=2)

and you have everything in one place. The results look great with ggplot's faceting, too!
The extensive package library is absolutely one of the nicest things about R.

Despite the absolutely ideal weather this past weekend*, I spent a small chunk of time beginning to learn Ruby. The programming language itself seems fun and friendly; it's billed as a conceptual hybrid of Perl and Python with the object-oriented nature of something like Java. There are a few reasons why I'd like to learn the language:

1. Learning new programming languages enhances understanding of the others. My Perl and Python can always be improved.
2. I've seen a few bioinformatics-related job postings lately which specifically mention the desirability of Ruby experience. They're usually talking about Ruby on Rails and its use in web development. 
3. It's either that or go back to learning Haskell. As far as learning a new language goes, most programmers seem to take Ruby seriously, at least.

I do have a few concerns.

1. Is Ruby (or Rails) becoming obsolete? There's clearly room for a great diversity of frameworks in the scope of web application development. I'm also not qualified to answer such a question. Programming is just one of those areas where a newly-learned language or skill can quickly become a dusty relic. Every framework might as well be Esperanto in the long run: they all have their strengths, even if the only strength is facilitating communication between the right people.
2. Will I ever really need to know Ruby (or Rails)? This question is even more difficult to answer, but I'll give it a try: "probably not." There will always be someone with better code than mine and it may even be in a different language or even an entirely different framework (for all I know, even scientific applications will be most frequently run in a mobile OS in a decade from now). 

Learning for fun seems like the best plan of attack. I can do it at my own pace without worrying about how applicable it is to Doing Bioinformatics. I'll just have the background to know it when I see it. 

*Here's a shot of the grounds at the University of Virginia.

Brooks Hall.

I've been enjoying the short "Futures" science fiction stories in Nature since they started. They tend to be concise, punchy, taut, and perfectly suited for the science-savvy audience. The most recent entry, "How Kameron Layas rode out the crash", is an ideal example. It breezes through some post-cyberpunk hallmarks without getting bogged down in anything but the most critical details, yet hints at a fully-fleshed periphery. It might even make a nice novella.

The author is Rahul Kanakia. The guy studied economics at Stanford but now writes SF. It's a natural progression but not a common one. He's also just a tad older than I am, a sure fire trigger for the "what are you doing with your life when this guy has already written a bunch of novels" effect.  This is alleviated somewhat by his great blog.  It's very analytical and unpretentious. If I ever decide to give up science for science fiction, I'll have to follow some of his examples. He's not big on advice, though.

This is the Donnelly Centre for Cellular and Biomolecular Research at the University of Toronto.

That's a nice-looking building. It was built in 2006 and really captures a particularly minimalist glass-and-color-burst aesthetic (the building reminds me of a larger, more technical Pompidou Center at least, and that building has been around since 1977). I'm curious about how energy-efficient all that glass is.

I think I just like labs with plenty of window space. It may be that the natural light cycles provide a constant reminder of the power of omnipresent natural processes. Or, it may be symbolic of the open exchange and transparent review characteristic of an ideal scientific process. The colors are nice, too. They're always a great way to find your way around a building and orient yourself.* Little details like that can really make the process of science much more enjoyable and efficient.


*In the absence of colorblindness, of course. Perhaps each area of a building could have a corresponding color and pattern.

I felt very caffeinated today. For me, the line between "fairly awake" and "very caffeine-stimulated" mostly appears to be a function of when I'm drinking it rather than a function of coffee volume consumed. Late afternoon seems like the time when caffeine is most effective (or maybe a little too effective, depending upon the level of focus the day requires). A few recent papers and at least one science blogger explain this effect in terms of cortisol levels and the circadian rhythm. See also: the concept of the zeitgeber.

I'm also reducing the level of anonymity for this blog, as you may have already noticed. This trend will continue. The person writing this is the same person who does everything else that person does every day.