Category Archives: science

More JSmol2wp testing

As of version 0.7, I wonder whether having two posts with viewers causes applet name clashes. The prediction is that this would work while viewing one post, but not on the home page. This prediction turned out to be true.

This first item loaded the first one from the next post, while the first item in the next post didn’t load. Should work now in 0.8

Load 1PRC


Load file from Henry Rzepa's blog



Testing JSmol2wp

lambda repressor headpiece


Last week we had a meeting to discuss enhancements for the department website. One thing that came up was the idea of better eye candy to highlight the research we are doing.  As a biochemistry department where many people are doing structures and structure-function studies, an obvious capability to add is a molecular graphics viewer. Fortunately, I had some experience through EcoliWiki with Robert Hanson’s Jmol project, which uses a Java Applet to embed viewers in websites.

Of course, the Jmol developers recognized several years ago that alternatives to Java were needed, especially for viewing molecules on phones and tablets that lack Java. As a Mac user, I also find Java to be problematic. So Jmol spawned a sister project: JSmol, based on javascript. Since I have some experience with writing WordPress plugins, I adapted JSmol for a plugin, which I call JSmol2wp.  Here’s what it looks like:

Dragging should rotate the model, which is embedded via a shortcode that passes a bunch of parameters, including the PDB accession, the caption, and code to create custom buttons and other interface elements. The buttons run Jmol scripts to select, zoom, recolor etc. The plugin detects multiple instances of the shortcode that creates the applets as long as they use different pdb accessions.

This is the structure of the CynR DNA binding domain from a local file


What do Americans and Finns know about Ammonia?

Via Jon Eisen on twitter, Hal Levin at MicroBEnet has gotten himself into trouble with this post (now deleted as not reflecting the views of MicroBEnet). The part that annoyed readers (including me, after seeing the tweet calling it out).

On May 8th, CNN reported on “Top 20 most polluted cities in the world.” An esteemed colleague sent an email today to a small, informal discussion group of building scientists (the majority are former EPA scientists), that read as follows:

“Only in America would people be dumb enough to talk about the “diameter” of a non-spherical particle. I bet even in Finland they know that ammonia is a gas and not a particle, and I’m not aware that these others mentioned are carcinogens. .
From the web today:
CNN reports, “PM2.5 refers to the diameter measured in microns of particulates such as ammonia, carbon, nitrates and sulfate — which are small enough to pass into the bloodstream and cause diseases such as emphysema and cancer.”

I hesitate to provide the link to the CNN post, but if you still want to, you can find the CNN story at

If you follow the link to the tweet, you can see that I weighed in with some replies. As an alternative way to procrastinate the work I should actually be doing on a Sunday afternoon, I decided to dissect this. The first irony about “only in America” is that CNN reporter Madison Park is currently working out of the Hong Kong Bureau of CNN. I suspect she could be an ABK, and she went to UC-Berkeley so I guess we can blame America for her reporting. But she was a journalism and history major, so despite covering health for CNN, I suspect she defers to her sources in writing things like the passage that offends Levin’s email correspondent. The information she’s reporting on is from the World Health Organization and searching their website for “ammonia air pollution” gives this page from the WHO media centre as one of the hits. What does it say about ammonia and particles?

Particulate matter

Definition and principal sources

PM affects more people than any other pollutant. The major components of PM are sulfate, nitrates, ammonia, sodium chloride, black carbon, mineral dust and water. It consists of a complex mixture of solid and liquid particles of organic and inorganic substances suspended in the air. The most health-damaging particles are those with a diameter of 10 microns or less, (≤ PM10), which can penetrate and lodge deep inside the lungs. Chronic exposure to particles contributes to the risk of developing cardiovascular and respiratory diseases, as well as of lung cancer.

There must be some way to blame George Bush or the Koch brothers for this info on the WHO website, right?

It’s somewhat interesting that an email list full of former  EPA scientists might have let this pass, as I would imagine that some of them might have worked with their counterparts at WHO. But not being privy to this email list, I can’t assume that nobody pushed back.

I was also struck by a couple of other things:

Only in America would people be dumb enough to talk about the “diameter” of a non-spherical particle.

There are plenty of things that have diameters that are not spherical. Circles, cylinders, and cones, for example. We speak of the diameter of the earth although it is not perfectly spherical. Moreover, even highly irregular solids, such as proteins, can be discussed in terms of their effective radii and diameters: the Radius of gyration. From the point of view of passing through filters or blood vessel walls, this seems perfectly appropriate to me.

I bet even in Finland they know that ammonia is a gas and not a particle

In the twitter discussion I wondered what the emailer has against Finland. But here I wanted to discuss a few other things:

  • As long as we’re being nitpicky: Ammonia is a gas at ambient temperature and pressure in the cities being reported on, but it’s not always a gas.
  • The average American thinks of ammonia as a liquid because they can go to the supermarket and buy cleaning products labeled as ammonia. The one shown is actually from Australia, so even if they don’t have this kind of stuff in Finland, it’s unlikely that usage that fails to distinguish ammonia from ammonium hydroxide solutions is limited to the US.
  • Unless I missed a revolution in chemistry, gas molecules are particles.

The decision to take it down at MicroBEnet makes sense, insofar as the goal of that site is to educate the public about the microbiology of the built environment, not to divide readers into those who agree and those who are offended. Insofar as is funding a collaboration between Eisen and Levin, this kerfuffle may have some unfortunate hangover effects for an interesting project. Let’s hope this doesn’t poison the built environment.

What I find both sad and interesting in the now-deleted post is: What drives someone to take a set of minor issues in a news story that are arguably not even errors and not only decide that this reflects a kind of egregious ignorance that is unique to one country, but also share that opinion with a bunch of strangers? It seems likely that both the emailer and Levin thought that this view of Americans (and Finns?) is not only accurate but also obvious.

Who gets NIH grants and is it a problem?



Drugmonkey posts a graph from showing distribution of grants by institution. A series of follow-up posts at Grantome includes one that looks beyond the top 50 institutions and concludes:

The NIH website reports that more than 80% of its budget goes to over 2,500 universities and research institutions. Yet for the R01 – which is arguably the most sought-after, prestigious grant that is the financial staple of many medically oriented research laboratories in the U.S. – the bulk of the grants are distributed to 4% of these 2,500 institutions. It therefore appears that the division of R01 grants among institutions parallels that of wealth among individuals in the U.S. population. It is highly unequal, with the bulk of the pool held by a lucky few.

Drugmonkey asks both in the comments and on twitter:

50 institutions get 60% of the #NIHGrants. Good, bad, or meh?

The distribution of grants is interesting, but it leads to the obvious question: what should it look like? I don’t think that is knowable from the data provided, and it may not be knowable, period. The description of the top group as “a lucky few” suggests a perspective from a particular point of view. As with the reactions to the Alberts PNAS paper (which is now taking comments btw) scientists/PIs tend to view the question from the perspective of what is good or “fair” to scientists. But  it is important to remember that just as pro-market is not the same as pro-business, what is good for Science is not always the same as what is best for scientists. Or, as I tell graduate students about the importance of working hard: the NIH is not supposed to be a welfare program for smart people. I usually add what Bob Sauer used to say to every new person in the lab: you don’t have to be that smart to do Biology. If you were really smart you’d be doing math or philosophy or shit like that.

The correct but painful question then is not whether PIs are being treated fairly, but rather whether federally funded science agencies are doing a good job of optimizing the taxpayer/citizen return on investment in research. In the case of NIH, the investment is in biomedical research (preferably a big tent definition of biomedical, IMO). In general, while I still tend to think that the peer review systems at NIH and NSF are like democracy (terrible but better than most the plausible alternatives), I do worry that the system is getting worse at approximating an ideal system for maximizing the taxpayer investment in research. But I am not sure whether a system with the nonexistent perfect program officers , SRAs, and reviewers would increase inequality or decrease it.

Lots of interesting reading at the links, in any case.

Do architects get what we do in the lab?

This post is what I wrote in February of 2009 on the old blog. I was prompted to dig this post up by Virginia Postrel tweeting about this article in Slate. I pulled the text from a database dump of the old blog. The images are old too, but were not in the original post (found them in my iPhoto library).


Derek Lowe discusses the new biochemistry building at Oxford (see Nature and their VR tour). Derek:

… I kept wondering, where have I heard descriptions like this before? Oh yeah, the last time I moved into a new building. Actually, every single time I’ve moved into one, come to think of it. I was part of a gigantic corporate move in 1992 into what was billed as a “high-interaction facility”, which was nothing of the sort. And then at the Wonder Drug Factory, one of the new lab buildings had the whole research area behind a large glass wall; it was the first thing you saw when you came into the place. Unfortunately, since it was full of snazzy equipment, it became part of the standard tour for visitors (the combichem labs were largely abandoned by then), and the people working there sometimes felt like zoo animals. And my current building has the labs all around the outside walls, and a huge atrium in the middle of the building (to what purpose, no one is sure; it’s completely empty).

Microbial Sciences Building at Wisconsin. The “high-interaction” propaganda reminds me of the junket I was on a few years ago where we visited Stanford, UCSF, and Chiron. The Clark Center at Stanford was an extreme case of the open floor plan concept to promote interaction, and as far as I could tell, that was a failure. As Derek’s commenter Kako notes about (perhaps) a different building, a big problem with open floor plans for labs is that they are really noisy. What we saw was lots of people with iPod headsets, small equipment rooms being taken over to be used as offices, and the portable furniture being rearranged so people could get a small amount of privacy. We heard that the original plan was to have the PI offices in the midst of the open plan… until someone pointed out that this was not going to work when the tearful undergrads needed to see the profs about their grades. Also, Kako points out:


Atrium of the Microbial Sciences building at Wisconsin

Security – every door is open. Bye laptop! Bye purse! Gradually getting better, if only cos people learn *never* to leave things unattended.

The Clark Center did have something that was a successful high-interaction space: a Peets Coffee shop on the top floor. I spent many afternoon breaks there when I was on sabbatical.

The Genentech building at UCSF suffers from overblown scale, but the arrangement of the labs and offices struck me as smart. The faculty officesThe comment about the atrium reminds me of what some of my friends said about the clustered around common spaces, so the PIs and members of different labs would interact in each “pod” of groups. People interact in those spaces, but can retreat to a more private space to focus in smaller groups, or alone.


A lab in the Clark Center. Note the equipment room taken over as an office to get some privacy

Looking at the virtual tour views of the Oxford labs, it looks nice, but I’m wondering about the way the desks open onto the shared space. I suspect there will be a lot of iPod headsets used there too.

When I first got to TAMU, I had more interactions with people because my office was close to the rest rooms on my floor. Debby has argued that interactions can be promoted by putting restrooms and the mail room on opposite ends of the building. Not sure if that still works anymore since so much correspondence is by email. In BioBio, having lots of common use equipment promotes interaction. Having more whiteboards in the halls would promote interaction – I’m not seeing those in the Oxford pics.

Human subjects and education research

At Retraction Watch, there’s a story of a paper about ethics training retracted due to IRB human subjects protocol problems. We tend to think of human subjects research as involving things like drug trials, but a lot of it is things like this:

This was an IRB-approved paper-pencil study investigating how certain features of ethics case studies influence knowledge and application of case study principles to new ethical scenarios.

In other words, if I’m understanding the post and the excerpts, the investigators were studying what works and what doesn’t work for how to teach higher levels in Bloom’s taxonomy in the field of teaching about ethics. So what went wrong?

Several administrative issues influenced our Institutional Review Board’s decision to not allow the data from this study to be used for research purposes. One of these had to do with the fact that some of the course instructors were not listed as key study personnel and they handed out and collected the study materials and informed consent forms. Even though they did not have any other involvement in the study, we recognized this oversight. Additionally, we implemented two minor changes to study materials, including dropping two items and renumbering 8 items, and did not obtain re-approval for these changes. Lastly, through this review process, we became aware that roughly half of the informed consent forms (ICFs) were not on file. Although we kept a clear record of who consented and who did not through the use of a training checklist, we recognized this was a data storage lapse. We worked with our IRB to fix these problems and have better processes in place to prevent similar issues from occurring in the future. Although the senior editor for the journal did not think that these issues warranted retraction of our paper, our university’s decision that we could not share the data publicly influenced our decision to voluntarily retract the article.

I understand the basis for the IRB/Human subjects rules, but this case illustrates a problem for all of us as educators. Every time I teach any course, I am doing an experiment in what works. It’s usually an uncontrolled experiment with unconscionably bad record-keeping, but it’s still an experiment and my students are subjects. As there is an increased emphasis on doing more rigorous assessment of student learning outcomes, we will try to be more rigorous about gathering and analyzing data from assessment instruments, which can be done without IRB approval as long as it’s not for publication. Consider how different that is from a drug trial!

As I understand it, doing a proper human subjects protocol for assessment of teaching requires outlining ahead of time all the interactions the assessor will have with the students/subjects. Deviation from that protocol (analogous to changing an FDA approved drug manufacturing protocol) is a no-no – as in the case above. This makes it almost impossible for the actual instructors to also do the assessment… and creates a barrier to dissemination of interesting STEM teaching methods being tried by scientists who don’t have the right collaborators for assessment.

Genomes and phenomes

Via Jonathan Eisen, NSF is using a wiki to get input on genomes and phenomes

BIO seeks community input on Genomes-Phenomes research frontiersJohn Wingfield, Assistant Director of the National Science Foundation Directorate for Biological Sciences (BIO), is pleased to announce the posting of a Wiki to seek community input on the grand challenge of understanding the complex relationship between genomes and phenomes.  The Wiki is intended to facilitate discussion among researchers in diverse disciplines that intersect with biology, such as computation, mathematics, engineering, physics, and chemistry.The Wiki format encourages open communication, captures new viewpoints, and promotes free exchange of ideas about the bottlenecks that impede progress on the genomes-phenomes grand challenge and approaches or strategies to overcome these challenges. Information provided through the Wiki will help inform BIO’s future research investments and activities relevant to understanding genomes-phenomes relationships.To provide comments, ask questions and view input from and interact with other community members, first-time users should sign up for an account via this link:Sign-up.  Once registered, users will be directed to the main page of the NSF Wiki to accept the terms and conditions before proceeding.  Additional guidance and subsequent visits can be accessed via this link: Genomes-Phenomes Wiki.Community members should feel free to forward notice of this to anyone they think might be interested in contributing to the discussion. Questions regarding the Wiki should be sent to

I agree withthat phenome is a #badomics term but not with this:

How exactly is this different from “phenotype”?

Phenotype is singular.  Phenomes, for lack of a better term, are collections of all phenotypes. Part of what makes it a #badomics term, IMO, is that the good omics terms like genome, transcriptome and proteome describe sets where completeness makes sense. Phenotypes, as observable manifestations of genotypes in environments, depend on the capabilities of the observer. New technology can create new phenotypes. While new technology can improve our ability to detect genes or transcripts or proteins, they did not come into existence by virtue of our being able to see them.

Incidentally, I’m wondering why I didn’t get the email. Perhaps it’s because I don’t currently have an NSF grant. However, I’ve reviewed for NSF a lot, I participated in the NSF-funded Phenotype Research Coordination Network workshop in Arizona earlier this year. And I work on the NIH-funded Ontology for Microbial Phenotypes. We have to get OMP into better shape and publish for our renewal application this summer, but we’ve talked about it at Biocurator meetings.

Open source communities are different

Via Althouse, Farhad Manjoo argues in the NYT that Brendan Eich had to resign because:

Mozilla is not a normal company. It is an activist organization. Mozilla’s primary mission isn’t to make money but to spread open-source code across the globe in the eventual hope of promoting “the development of the Internet as a public resource.”

As such, Mozilla operates according to a different calculus from most of the rest of corporate America.

Like all software companies, Mozilla competes in two markets. First, obviously, it wants people to use its products instead of its rivals’ stuff. But its second market is arguably more challenging — the tight labor pool of engineers, designers, and other tech workers who make software.

When you consider the importance of that market, Mr. Eich’s position on gay marriage wasn’t some outré personal stance unrelated to his job; it was a potentially hazardous bit of negative branding in the labor pool, one that was making life difficult for current employees and plausibly reducing Mozilla’s draw to prospective workers.

A commenter or Manjoo’s piece adds:

I wonder why this man was given this position in the first place if his views are so counter cultural at Mozilla. Or, if the views were unknown, what does that say about management of the company?

A reply points out that Brendan Eich, as a cofounder of Mozilla, might be in a better position to be familiar with the culture of Mozilla than Eleanor from Augusta Maine. There’s a basic problem with this argument: it presumes that the labor pool is contains more talented people who object to Mr. Eich’s private political activity than talented people who now will avoid working for Mozilla due to concerns about working for a project where outside activities are a litmus test. The idea that programmers and engineers are homogeneously enlightened progressives is… let’s just say counterintuitive. Eich is himself the counterexample to political homogeneity of talent. He’s not a John Scully from Pepsi going to Apple. The man invented Javascript, which runs a large fraction of the current web.

In my view Manjoo and Mozilla’s management have it exactly backwards. Depending on a community makes it even more important to defend the right of people you disagree with on extracurricular matters to participate. Importantly to this question, as far as I can tell, there have been no reports that Eich’s political beliefs manifested as creating a hostile work environment beyond those who are sensitive to the existence of those beliefs per se. It’s not like I’m seeing reports that Eich did anything like the infamous Larry Summers talk about women in science (I find this story interesting in part because of parallel issues in academia and science).

peptidoglycan transpeptidase diversity and nomenclature

A couple of weeks ago the Biochemistry Graduate Association Gyanu Lamichhane to give a seminar on his work on peptidoglycan transpeptidases.  In his very nice talk Lamichane told the story of how a search for transposon mutants with virulence phenotypes led him to work on an unexpected peptidoglycan transpeptidase. Lamichhane’s talk prompted me to look at what is needed to represent peptidoglycan transpeptidases in the Gene Ontology. This post is my notes so far on figuring out what is needed.

Some background is in order to explain why this enzyme was unexpected. Peptidoglycan makes up the bacterial cell wall. Because it’s not found in eukaryotes (e.g. humans), and it’s needed to keep bacterial cells from exploding, peptidoglycan synthesis has long been the target of clinically important antibiotics.  In the textbook version of peptidoglycan, an intermediate precursor is constructed where a pentapeptide is built up on a UDP-MurNac. This MurNac-pentapeptide is linked to a UDP-GlcNac to make a disaccharide with an attached pentapeptide.  This is transferred to a carrier, flipped to the outer surface of the inner membrane, and polymerized into the growing peptidoglycan. Crosslinks catalyzed by peptidoglycan transpeptidases create a polypeptide orthogonal to the polysaccharides.

In many organisms, including E. coli and M. tuberculosis, the unit can be written as:


in others, including Enterococci, it’s


20131026-224803.jpgm-DAP is meso-Diaminopimelic acid, also known as D, L-Diaminopimelic acid is made in a few different ways, but is an intermediate in both peptidoglycan and lysine biosynthesis. Lysine is made by decarboxylating the D end of mDAP. The L end is what gets incorporated into peptidoglycan.

The textbook version of peptidoglycan has crosslinks made by a transpeptidation reaction where the D end of mDAP (the acceptor) replaces the terminal D-ala on another pentapeptide.  This could be called a 4-3 D,D transpeptidation reaction with the D-Ala from the 5 position being the leaving group.

Lamichhane’s transpeptidase links two m-DAPs at the 3 positions directly together, with the side chain of one attacking the backbone of the other, with the release of D-Ala-D-Ala.  The donor is the L end of the mDAP, so I think this is why I’d call it a 3-3 L,D transpeptidation.  The nomenclature here is related to, but not identical to, what I’m seeing in the papers, where they talk about 4-3 and 3-3 crosslinks and D,D and L,D transpeptidases.

The reason we need names that are more specific than L,D and D, D is that it gets more complicated. In E. coli, in addition to the D,D 4-3 transpeptidases there are five L,D transpeptidases. Two make direct 3,3 links like Lamichane’s enzyme from TB. Three others use the ε NH2 of the C-terminal Lysine of Lpp (aka Braun’s lipoprotein) as the acceptor, resulting in attachment of Lpp to the peptidoglycan.

Meanwhile, in Enterococcus, what I wrote is oversimplified L-Lys replaces m-DAP at the 3 position, but sometimes the Lysine is modified to form things like (N ε-D-Asx)-L-Lys in E. faecium.  And this just scratches the surface of chemical diversity in bacterial peptidoglycan.

  1. Gupta, R, Lavollay, M, Mainardi, JL, Arthur, M, Bishai, WR, Lamichhane, G et al.. The Mycobacterium tuberculosis protein LdtMt2 is a nonclassical transpeptidase required for virulence and resistance to amoxicillin. Nat. Med. 2010;16 (4):466-9. doi: 10.1038/nm.2120. PubMed PMID:20305661 PubMed Central PMC2851841.
  2. Magnet, S, Dubost, L, Marie, A, Arthur, M, Gutmann, L. Identification of the L,D-transpeptidases for peptidoglycan cross-linking in Escherichia coli. J. Bacteriol. 2008;190 (13):4782-5. doi: 10.1128/JB.00025-08. PubMed PMID:18456808 PubMed Central PMC2446776.
  3. Magnet, S, Bellais, S, Dubost, L, Fourgeaud, M, Mainardi, JL, Petit-Frère, S et al.. Identification of the L,D-transpeptidases responsible for attachment of the Braun lipoprotein to Escherichia coli peptidoglycan. J. Bacteriol. 2007;189 (10):3927-31. doi: 10.1128/JB.00084-07. PubMed PMID:17369299 PubMed Central PMC1913343.
  4. Mainardi, JL, Morel, V, Fourgeaud, M, Cremniter, J, Blanot, D, Legrand, R et al.. Balance between two transpeptidation mechanisms determines the expression of beta-lactam resistance in Enterococcus faecium. J. Biol. Chem. 2002;277 (39):35801-7. doi: 10.1074/jbc.M204319200. PubMed PMID:12077139 .
  5. Wehrmann, A, Phillipp, B, Sahm, H, Eggeling, L. Different modes of diaminopimelate synthesis and their role in cell wall integrity: a study with Corynebacterium glutamicum. J. Bacteriol. 1998;180 (12):3159-65. . PubMed PMID:9620966 PubMed Central PMC107817.
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