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.