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Category → The Working Scientist

Behind the Wood Shed with the ACS

You’ve been very bad boys. Credit: Stephen Horncastle/Wikimedia Commons

Forgive me for sporting my crankypants today but I had originally intended to be in Islamorada right now, snorkeling and kayaking. Between the PharmKid hurting her wrist in nature camp (4 weeks in a cast) and my 4 weeks in an ankle brace, the PharmFamily took advantage of the wise purchase of trip insurance and stayed home to nurse our wounds.

So, I’m not in much of a happy mood with two of this week’s developments with the American Chemical Society, one of which revisits a longstanding argument over the organization’s pricing of its scholarly journals.

If you haven’t heard, yesterday’s clusterfluster was with regard to the library of the State University of New York at Potsdam (SUNY Potsdam) choosing to forego the purchase of ACS journals this year.

Here’s the post from the Attempting Elegance blog of SUNY Potsdam Director of Libraries, Jenica P. Rogers, MLIS, and an accompanying article by Jennifer Howard at The Chronicle of Higher Education.

From Jenica’s self-described tl;dr summary:

SUNY Potsdam will not be subscribing to an American Chemical Society online journal package for 2013. We will instead be using a combination of the Royal Society of Chemistry content, ACS single title subscriptions, the ACS backfile, and ScienceDirect from Elsevier** to meet our chemical information needs. We’re doing this because the ACS pricing model is unsustainable for our institution and we were unable to find common ground with the sales team from the ACS. Instead, we explored other options and exercised them. You could do the same if you find yourself in a position similar to ours as ACS standardizes their pricing, and maybe together we can make enough choices to make our voices heard in meaningful ways.

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On the loss of a mentor: Al Malkinson, lung cancer researcher, scholar, gentleman

Note to Readers: After reading through my writing here and at my Take As Directed blog between October, 2011, and October, 2012, I’ve decided to submit this post as my entry for The Best Science Writing Online 2013, formerly The Open Laboratory. The 2012 version was published by the Farrar, Straus and Giroux imprint of Scientific American.

While the post details my emotions and recollections over a personal loss, I believe that it best reflects one of my strengths as a science writer: use of a personal story to touch on our own universal experiences as human beings who chose science as our vocation. All of you must have someone like Al Malkinson in your life. And he supported women in science long before special discussions groups on the topic even existed.

Finally, I also feel that my closing discussion — the lost art of the Festschrift — is an issue we must revitalize in modern scientific research. We rarely recognize our mentors and leaders while they are alive. I hope that my writing here motivates me (and you) to take action to formally celebrate the contributions of those who are still with us.


 

Alvin M. Malkinson, PhD. Credit: University of Colorado Denver, Skaggs School of Pharmacy

Those who make the deepest impression on you become the fabric of your being. Think about those who’ve passed through your life and have influenced your approach to science, society, family. . .

Even if years have passed since seeing one another, the lessons and attributes of these very special people continue to stay with you. But rarely do we truly get to express to these treasured souls just how much they have meant to us.

My first faculty mentor, lung cancer researcher Alvin M. Malkinson, PhD, passed away last Friday in Boulder, CO, at age 71.

Professionally, Al was Professor of Biochemical Pharmacology in the Department of Pharmaceutical Sciences at the University of Colorado School of Pharmacy, now on the Anschutz Medical Campus in Aurora. But if you were fortunate enough to know him, you learned that he was a scholar of the world, lover of the arts, and true gentleman.

I last visited the pharmacy school two years ago and had learned from colleagues that Al had been ill. He apparently deteriorated rapidly during this July and passed from pneumonia secondary to other complications.

I hadn’t been able to get back to Denver last summer or this year but I now realize that wasn’t an excuse not to at least call Al. I always remember Al as a vibrant, worldly soul whose intellectual energy, I thought, was likely to power him for a couple more decades. Alas, he has left us early – far too early – and without some of us being able to say goodbye.

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The Colorado shooting suspect: how “smart?”

Apologies in advance to any readers who might be put off by my writing about the science aspects of the Colorado movie theater tragedy. I was a faculty member at the University of Colorado in Denver from 1992 to 2001 and was in the area during the Columbine High School shooting rampage. I also still have some friends out there and feel a personal connection to the place and people who helped launch my independent research career. Nevertheless, I claim no special knowledge of the current inner workings of the University – all of my sources for this and other posts come from publicly-available information sources.

I write this disclaimer because Marisol Bello (@Marisol_Bello) and Dan Vergano (@dvergano) have an intriguing article today at USA Today on the relative level of specialized intelligence of the Colorado shooting suspect. The suspect was one of six students on a NIH neuroscience training grant – called a T32 Ruth L. Kirschstein Institutional National Research Service Award, or just T32 or NRSA. The specific grant that supported the suspect for his first year of graduate school at University of Colorado Denver is described here at the publicly-accessible NIH RePORTER database.

An “institutional” training grant?
These are training grants awarded to institutions, not specific students, that are noteworthy for having an excellent and comprehensive training environment for predoctoral students. The institutions awarded these grants then have the discretion to appoint the candidates for grant support.

This NIH notice (NOT-OD-12-033) describes the support given to each student appointed to the training grant: a stipend of $22,032 per year (to which Colorado adds to bump it up to $26,000), “training related expenses” of $4,200/year to cover things like health insurance, another $4,200/year to host laboratories to offset the costs of laboratory supplies, and 60% of the trainee’s tuition and fees up to $16,000/year (to which most schools add to completely cover tuition.)

Being appointed to one of these institutional training grants is generally considered to be less prestigious than winning an individual NRSA. These individual grants are awards given to the student’s mentoring professor based on the individual research project and training environment of the individual host laboratory, in addition to institutional considerations.

Still, institutions are judged on the quality of the students they appoint to institutional NRSAs. So, the Colorado shooting suspect had to meet some minimum undergraduate GPA and standardized GRE test scores.

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Did theater shooter use lab address to procure regulated hazardous substances?

This post probably belongs on The Safety Zone blog but I was struck by a comment just made during a news conference in Aurora, Colorado, this afternoon. Aurora Police Chief Dan Oates noted that over the last four months “the suspect had a high volume of packages to both his work and home address.” Oates indicated that these shipments may account for the large amount of ammunition and booby-trap incendiary devices currently being disarmed in the suspect’s apartment.

Work, of course, was the neurosciences PhD program at the University of Colorado School of Medicine on the Anschutz Medical Campus. According to The Scientist, the suspect had done at least two laboratory rotations with faculty in the Department of Pharmacology. (Note: The websites for both the interdisciplinary neuroscience program and the pharmacology department are closed to public access to protect personal contact information for faculty.

While we don’t yet know the precise identity of the explosives in the suspect’s Paris Street apartment building in Aurora, I hypothesize that he took shipments at work of the more eyebrow-raising chemicals. As CU laboratory staff are likely questioned about the suspect’s year in the PhD program, I wonder if anyone might have accidentally opened one of his packages and asked who ordered the [flammable and/or explosive compound].

On a personal note, my heart goes out to the victims of the shootings, their families and other loved ones. I also have immense respect for all of the first-responders and medical staff who have been tending to the victims. I spent ten years of my career at the CU Health Sciences Center in its old location in Denver and have several friends and colleagues in basic science and clinical departments at the Aurora campus. My heart aches for all.
 


 

Update 5:12 pm EDT: I just saw a tweet from Matthew Keys, Reuters Deputy Social Media Manager, quoting Chief Oates as saying there was, “[n]o evidence that shooting suspect had access to “dangerous materials” at Colorado medical school.”

Update 12:21 pm EDT, 22 Jul – Gillian Flaccus and Nicholas Riccardi at AP have confirmed my suspicions:

The University of Colorado said Sunday it was investigating whether mass shooting suspect James Holmes used his position as a graduate student to order materials for the potentially deadly booby traps that police said they found in his apartment.

Holmes, 24, got deliveries over four months to his home and school, authorities have said.

The university is looking into what was received at the school to assist police, said spokeswoman Jacque Montgomery.

 

Update 9:00 pm EDT, 23 Jul – Officials from the University of Colorado Denver | Anschutz Medical Campus held a press conference earlier today to discuss issues of campus security and some questions about the former student. This is the official summary from the University press office. I’m surprised that no one from the national media asked why the campus is called “Denver” when it is fully in Aurora and in another county.

WaPo: Not enough jobs for science PhDs

Tomorrow’s frontpage of The Washington Post will run an article by Brian Vastag (Twitter, WaPo bio) on the employment challenges facing science PhDs. The difficulties are no secret to our readers – whether you are a freshly-minted PhD or a 50-something subjected to downsizing – but I believe that this is the highest profile treatment of the subject in the US print media.

The article even cites the closure of the Roche campus in Nutley that we discussed two weeks ago and, below, employment numbers from the annual ACS survey.

“Scads and scads and scads of people” have been cut free, [former Sanofi-Aventis scientist Kim] Haas said. “Very good chemists with PhDs from Stanford can’t find jobs.”

Largely because of drug industry cuts, the unemployment rate among chemists now stands at its highest mark in 40 years, at 4.6 percent, according to the American Chemical Society, which has 164,000 members. For young chemists, the picture is much worse. Just 38 percent of new PhD chemists were employed in 2011, according to a recent ACS survey.

Although the overall unemployment rate of chemists and other scientists is much lower than the national average, those figures mask an open secret: Many scientists work outside their chosen field.

What amazes me are the number of comments already. I already followed Vastag on Twitter and when he tweeted about the article at 4:44 this afternoon, it had 22 comments. Right now, at 9:50 on Saturday night, the article has accumulated 504 comments. Some of these are nonsensical or non-sequiturs but the bulk are robust and on-topic. I can imagine that the sober assessment of PhD training vs. job market demands will be discussed far and wide on Sunday and in the coming week.

One thing missing from the article was a discussion of the so-called alternative career paths where one uses PhD training but not in an academic or industrial setting. Even a typical non-lab career of science writing is becoming extremely competitive, both for salaried positions and freelancers.

I hesitate to say this without complete data but we may indeed be reaching a point where more PhDs are being produced than can be absorbed by both academia/industry and non-laboratory positions.

Source:
Vastag, Brian. U.S. pushes for more scientists but the jobs aren’t there. The Washington Post. 8 July 2012.

Nutley nostalgia on Roche campus closing

The most-viewed article at C&EN online over the last seven days was news from Lisa M. Jarvis on the announced closing of the venerable Nutley, NJ, campus of Hoffmann-La Roche – better known today as simply Roche. A mere 13 miles from Manhattan’s Times Square, the US headquarters of Swiss company moved to Nutley in 1929.

A total of 1,000 jobs will be lost when the campus closes late in 2013 – Susan Todd at The Star-Ledger has a pair of articles with the details (1, 2). Todd also used the term, “venerable.” The Nutley campus is legendary for the discovery and development of major drugs – isoniazid for tuberculosis, for example – and the manufacture of vitamins. At one time, it was the example of how a pharmaceutical company could run an independent research institute with its Roche Institute of Molecular Biology.

But this week, we lament the sadly unsurprising loss of employment for many of our friends in chemistry and pharmacology, as well as a host of good folks in administration and support services. Despite its contraction from a high of 10,000 employees in its heyday, Roche continued to provide 9-10% of the tax base for the city.

Roche, Building 76, Nutley, NJ following 2010 renovation. Credit: green@worktoday

My nostalgia for Roche extends back to my childhood, growing up on a hill five miles across the Passaic River in the predominantly Polish town of Wallington. From a clearing in the woods on the hill, the major landmark across into Essex County was the Roche tower, built the year before I was born and known by the unglamorous name of Building 76. The route my family took while driving back from the official state pastime of mall shopping invariably took us past the Roche campus on the Route 3 side. This drive past Roche from the west was preceded immediately by a glorious view of the New York City skyline, almost straight on with the Empire State Building. Whenever I see these two landmarks, I know that I’m almost home.

My Uncle Tommy was a facilities maintenance worker at Roche for about 30 years. Readers here are certainly concerned about the loss of scientist jobs – but Roche provided upward mobility for high school and GED graduates like my uncle. He used to buy us our vitamins from the employee purchase plan. My daughter – and much of the internet – absolutely hate the smell of multivitamins. When I stick my nose deep into a bottle, I smell nurturing, love and care. Roche brought the first synthetic vitamin C to market using the combined microbial and organic synthesis method of Nobel laureate Tadeus Reichstein.

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Bad news for Bionovo and herbal drug development

A pharmacognosy colleague contacted me on Friday morning with word that the botanical drug development company Bionovo was closing its chemistry group.

Well, the news is actually worse as judging from this 8 pm Friday press release:

Bionovo, Inc. (OTC Link Platform: BNVI.PK) today announced that it will need to obtain substantial additional funding to achieve its objectives of internally developing drugs. The Company reduced its workforce by over 90%. The remaining management of the Company will receive reduced cash compensation until either adequate financing can be obtained or the Company is sold.  The Company can not make any assurances about either of these events.  As previously announced, management and the board of directors are continuing to explore strategic options for the Company.  Management is currently reviewing the status of the ongoing clinical trial for Menerba.

The Company does not currently have adequate internal liquidity to meet its cash needs.  If sufficient additional funds are not received in the near term, the Company may not be able to execute its business plan and may need to further curtail or cease operations.

Bionovo has been the rare superb example of a company that’s been trying to develop FDA-approvable drugs based on Chinese traditional medicine. Led by Isaac Cohen, a UCSF guest scientist and Doctoral of Oriental Medicine, and chief medical officer, Mary Tagliaferri, Bionovo took a hard, science-based approach to identifying herbal extracts for cancer and women’s health issues. Cohen and colleagues at UCSF and elsewhere examined Chinese herbal medicines for their biochemical and cellular effects based upon their traditional use.

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#icanhazpdf: Civil disobedience?

Some lively Twitter banter has arisen this evening regarding the practice of sharing PDFs of scientific articles when one does not have personal or institutional access.

Specifically, some among my stead have taken to tweeting requests for articles using the #icanhazpdf hashtag.

For non-open-access articles, does this practice violate a publisher’s copyright?

Discuss.

(And I welcome input from my ACS overlords.)

 

Update 24 December: I have changed the title of this post to reflect a comment below by Michael Eisen that sharing PDFs of journal articles is an act civil disobedience toward the scientific publishing enterprise. I had previously compared the practice to the Underground Railroad or Napster music file sharing. I deeply regret the use of the analogy of PDF file sharing to the Underground Railroad, a network of abolitionists who facilitated the safe escape of enslaved African-Americans in the southern US to freedom in the North and northward to Canada. I, in particular, should be especially sensitive to making such an ill-considered analogy of one of the most degrading episodes in US history to an intellectual discussion of sharing scientific papers. It was wrong, period. I apologize deeply to those offended by my thoughtless mistake.

Call For Social Media Success Stories in Academia

"Do you know the way to San Jose?" (with apologies to Dionne Warwick, Burt Bacharach, and Hal Davis, 1968)

We’re packing up the world headquarters of Terra Sigillata this afternoon and high-tailing it out to San Jose, California, for the annual meeting of SACNAS – the Society Dedicated to Advancing Hispanics, Chicanos, and Native Americans in Science. It’s a tremendous organization comprised of several of my former students and faculty colleagues from over the years and I’m ecstatic about reconnecting with them.

With the initiative of my colleagues – Alberto Roca of MinorityPostdoc.org and Danielle Lee of The Urban Scientist at Scientific American blogs (plus a whole host of online activities) – we pitched and were accepted to present a session on Blogging, Tweeting, & Writing: How an Online Presence Can Impact Science and Your Career.

I’ll be discussing how a responsible, online presence on blogs, Twitter, and Facebook can enhance networking opportunities for graduate students, postdocs, and faculty. Specifically, I’ll introduce how I’ve increased the exposure of my students who are RISE Scholars at North Carolina Central University. In this NIGMS-funded grant, I’ve been helping my students capture their research experiences in their own words (with previous review by their P.I.’s of course, to prevent accidental disclosure of unpublished data). The students have been surprised by the level of engagement and support they’ve received in the comments from scientists all around the world.

But I know of many other students who use blogs and Twitter to engage with the scientific community in ways that brings them positive recognition outside of their academic and laboratory work.

To better prepare for this session, I’d like to gather some advice from you, Dear Reader:

Who are some of students, trainees, and junior faculty, who best exemplify the use of social media for career advancement?

Are you a student who has had Good Things happen to you because of your social media activities? How did that transpire?

If you have any responses, please drop a link in the comments with a brief explanation – or longer if you’d like! And also feel free to recommend the sites and stories of others. I’ll be sure to promote your responses in tomorrow’s talk and direct attendees to this post for future reference.

The three of us thank you so much in advance for your suggestions!

On journalists copy-checking with scientist sources

Should science journalists solicit scientist sources to fact-check article content prior to publication?

Or do scientists have no more right to do so than, say, politicians previewing the latest criticism of their policies.

"Just try fact-checking with me, pal." The legendary Helen Thomas. Credit: helenthomas.org

I have to admit that I had not quite anticipated the magnitude of interest in these questions when I first wrote about the topic in late September at my Take As Directed blog on the PLoS Blogs network.

The backstory: I had been watching an episode of Vincent Racaniello’s excellent netcast, This Week in Virology (TWiV), from the the International Conference on Antimicrobial Agents and Chemotherapy (ICAAC) in mid-September. The first 35 minutes saw Vincent and Rich Condit turn the tables to interview Chicago Tribune science and medical reporter, Trine Tsouderos. Trine is perhaps best-known of late for her coverage of the faulty link between XMRV and chronic fatigue syndrome as well as the suspension of Dr. Mark Geier, a physician using a chemical castration drug to treat people with autism.

Trine mentioned in the interview that she often runs passages of complex science from her articles past the scientists she had interviewed for the piece. She doesn’t do so for approval or in any way to affect the tone of her writing but rather to be sure that she has interpreted the scientific findings accurate (my words, not hers).

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