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November 30, 2017 / jpschimel

Do Species Matter: responding to an op-ed by R.A. Pyron in the Washington Post as a piece of writing.

R. Alexander Pyron just published an op-ed in the Washington Post arguing that we don’t need to protect species from extinction.

Many, unsurprisingly, are criticizing this piece on grounds that span from ethics to practicality. I want to evaluate it differently: as communication. Writing and rhetoric. The writing is lively and engaging; Dr. Pyron uses words well. But the core of a piece of writing is its structure and argument.

Dr. Pyron’s argument is predicated in the ethical/philosophical belief that “The only creatures we should go out of our way to protect are Homo sapiens.” One can disagree with this belief and one can be appalled by it, but one can not challenge it on scientific grounds—it’s a belief.

Instead, consider the logic of the argument that Dr. Pyron develops from that predicate. When I consider issues of writing, story structure, and even the ethics of scientific communication, I see failures in all areas.

In Writing Science I place the ethics of science central to developing a “good” story. On page 9 I pose the question “Is seeing science writing as storytelling professional or not?” I develop this by noting that “To tell a good story in science, you must assess your data and evaluate the possible explanations.”

On page 139, I state this more explicitly:

“Also remember, you are a scientist — it is not your job to be right. It is your job to be thoughtful, careful, and analytical; it is your job to challenge your ideas and to try to falsify your hypotheses; it is your job to be open and honest about the uncertainties in your data and conclusions.”

So, let’s evaluate Dr. Pyron’s argument as a piece of writing and assess whether he did this—did he live up to his responsibility to be “thoughtful, careful, and analytical”? Certainly there are a number of fundamental truths in what he wrote:

Extinction happens—some species were already doomed to extinction in the near
Planet Earth will continue and will “recover” from the current mass extinction: over
millions of years, biodiversity will recover and “The Tree of Life will continue
branching, even if we prune it back.”
Not all species have a vital role in the functioning of ecosystems. Some biodiversity is
functionally redundant.

But, Dr. Pyron makes an important statement when he says:

“All those future people deserve a happy, safe life on an ecologically robust planet, regardless of the state of the natural world compared with its pre-human condition.”

I accept that ethical predicate. Yet, it creates a crack in his argument, and that crack is based in both science and rhetoric. It focuses on the question: How do we provide those future people “an ecologically robust planet”?

Our understanding of how complex natural systems work is developing. It wasn’t many years ago that we thought the human gut microbiome was purely commensal—microbes lived within us but did nothing fundamentally beneficial for us; animals could live healthily with a sterile gut. How that understanding has changed! How then do we ensure “an ecologically robust planet” when our understanding of what that entails remains imperfect? We know that Homo sapiens depends on natural ecosystems to provide us with essential functions: food, fiber, water purification, and others; Dr. Pyron acknowledges this. But, we don’t actually know what we need to maintain those functions over the long term—centuries to millenia.

How to provide an ecologically robust planet to support Homo sapiens is the essential question at the heart of Dr. Pyron’s piece. Yet, he offers neither an answer nor even a direction as to what that means!

Without a hint of an answer, the op-ed comes across as someone trying to assemble a complex device and ending up with some spare parts left over that they don’t understand, yet then stating confidently: “I’m sure these are unnecessary.”

“We should do this to create a stable, equitable future for the coming billions of people, not for the vanishing northern river shark.” Even if I accept that, it still begs the question: can we maintain an “equitable future for the coming billions” if we don’t maintain healthy ecosystems and ecosystem services? Can we offer the people of New Guinea an equitable future if we pollute the river in which the shark lives? This is an important question that lies at the interface of ecology and sustainability and requires an answer to support Dr. Pyron’s argument.

The logical and literary failures in Dr. Pyron’s piece circle back to this issue: he embraces the idea that functional ecosystems are important to serving humans. But, then he disparages and ignores existing ecological knowledge about how to achieve that and he fails to acknowledge or accept the limits of existing knowledge.

To make a scientific argument without acknowledging existing knowledge or your own ignorance (Dr. Pyron expertise is “theoretical and applied methods in statistical phylogenetics,” not ecology) is, to me, a fundamental failure in science communication. I could go further and argue that it is a failure of science communication ethics and professional norms.

While I consider this op-ed a failure as science writing, as a piece of political writing, unfortunately, it will unquestionably be a success— it was published in a high-impact outlet, Dr. Pyron has solid academic credentials at a major University, and he makes a well-phrased and passionate argument that will resonate with many.

In Writing Science, I focus on professional skills: framing story, developing flow, and using language powerfully. But professional skills should be balanced against professional responsibilities. When you write under your professional byline, and so speak as a scientist, remember:

“It is your job to be thoughtful, careful, and analytical; it is your job to challenge your ideas and to try to falsify your hypotheses; it is your job to be open and honest about the uncertainties in your data and conclusions.”

My complaint with Dr. Pyron’s piece (speaking as a writer on writing) is that he failed to live up to this basic responsibility as a scientist writer.


NOTE: There is a postscript to this story. A colleague noted that Dr. Pyron has posted a long commentary on his Facebook page that included the following:

“In the brief space of 1,900 words, I failed to make my views sufficiently clear and coherent, and succumbed to a temptation to sensationalize parts of my argument. Furthermore, I made the mistake of not showing the piece to my colleagues at GWU first; their dismay mirrored that of many in the broader community. As I’ve explained to their satisfaction, and now I wish to explain to the field at large, my views and opinions were not accurately captured by the piece, and I hope the record can now be corrected. In particular, the headlines inserted for the piece for publication said “We don’t need to save endangered species,” and that “we should only worry about preserving biodiversity when it helps us.” I did not write these words, I do not believe these things, and I do not support them.”
(Taken from Dr. Pyron’s FB page.) 

Dr. Pyron is saying things that are scientifically reasonable in his long, thoughtful, Facebook post. Unfortunately few will ever read the FB post; millions may read the op-ed. The public gets the wrong message, and his scientific peers are dismayed. Not a good outcome. Remember, always, that communication isn’t what you think you are giving, but what the reader gets. In this case, most readers get a message that was antithetical to Dr. Pyron’s true beliefs. Ouch. That is a true failure in writing. Worse, it is a failure that Dr. Pyron is going to have to live with because published is forever. You can’t unpublish something.

Equally, this is a powerful lesson in the value of peer review: Dr. Pyron did not run the piece past his peers and so never got feedback that indicated that readers were getting a different message than that he intended.

November 9, 2017 / jpschimel

What the hell am I doing here? Impostor syndrome and role models

Yesterday I spent much of the day suffering from an acute case of Impostor Syndrome. I was in Oakland for the University of California Academic Planning Council meeting. This is a small group run by the Provost of the entire UC system and populated by two Executive Vice Chancellors, a few Deans, and leaders of the UC Academic Senate. It’s effectively UC’s “Council of Elrond”: the top-level academic planning group for all UC, the world’s preeminent University system. How on Earth did they let me into that room? All the way up through College, I was the classic middle-child underachiever; the kid overshadowed by more driven siblings who teachers said “could do well if only he applied himself.” So, yes, I spent much of the day with an intense case of impostor syndrome. OK, I am Chair of the UC Council on Planning on Budget—but that just shifts the question—how the hell did I get there?

Being here was never my goal or early career vision. When I started as an Assistant Professor at the University of Alaska Fairbanks, my goals were simple: I wanted my colleagues to not think I was an idiot, and to not think I was an asshole. I’m pretty confident I’ve achieved the first, and I think I’ve mostly achieved the second. Everything after has been gravy.

This was particularly apropos of one main line of discussion—how to improve mentoring at UC? The issue of role models naturally arose. Many students look at us and are turned off academe. I noted that in some ways we are terrible role models, simply because, no matter how extreme our own personal cases of impostor syndrome might be, we have become among the most successful and accomplished academics in the country. Our lives can intimidate our students.

I remember well hitting the halfway-through-my-Ph.D. emotional crisis. I looked at my Ph.D. advisor, Mary Firestone, and thought “I’m never going to be a Mary, so is there any point in doing this?” Mary was a wonderful mentor, but if she were the reference standard for what an academic is, she was a terrible role model. Even though she was only an Assistant Professor, she was already clearly awesome in a way I could never envisage being.

Equally, I looked at all the things Mary was doing and the way senior people in the field lived their lives—if this is Tuesday I must be in Washington. I said “I want to not do that. I want to do science. I don’t want to live my life on airplanes and in meetings.”

But then some years later, when I was getting home from yet another trip, I looked at what I was doing and asked “Uh, Josh, isn’t this what you said you didn’t want to do?”

So how did that happen? And how does all this feed into UC’s mentoring challenge? I think there are two important messages that we need to do a better job of communicating.

First and most importantly, you don’t need to become us. Being a professor at a top-tier research university is only one way to pursue an academic career. I started my career as an assistant professor at the Institute of Arctic Biology at the University of Alaska Fairbanks. It was a great place to launch a career: wonderful research opportunities, terrific colleagues, and a great community in IAB and in Fairbanks. Yeah, UAF was often amateurish and dysfunctional—a place some third-tier wanna-be administrators went to try to build their careers, and where I felt that as long as I was breathing I needn’t worry about tenure. But that mostly freed me to have fun and do cool science without a lot of stress! I remain very close to, and grateful to, IAB. I didn’t leave out of ambition, frustration, or even because I’d had enough of -40° weather, but to be with the love of my life; landing a job at UCSB seemed just good luck. I’m sure that, had I stayed at UAF, my career would have taken a different path, but that would have been fine. Various of my students and postdocs have taken jobs at universities where the pressures are less intense, including a few who’ve taken jobs at teaching colleges. They’re productive and happy, which is what matters. You don’t need to become a “Mary Firestone” to be successful and content. You don’t need to join United’s Million-Mile club to succeed in academe (or even at UC!). Other paths (in and out of academe) are deeply fulfilling.

My second insight in the room yesterday was that when I was a student, I knew I’d never be a “Mary.” But, I was wrong. I’d never planned or anticipated it, but I have become a big-wig in my field, and even within UC. When I was a student, I knew I wanted to be a scientist and to do research. I thought I wanted to be a university professor. But I didn’t really know what that meant. Much of the service work I saw faculty involved in seemed like unappealing distraction, but I’ve grown into the larger role and come to value the higher-level service. It allows me to support my community and to tend the “ecosystem” that has nurtured me. Service work may not be fun the way playing with a new data set is or like doing field work with graduate students, but it is rewarding and emotionally satisfying. I don’t do it because I have to, but because I choose to.

As my understanding of what being an academic is has grown, so too, has my willingness and desire to take on those service and leadership roles. They may still be intimidating and cause impostor syndrome, but my growth from the intimidated Ph.D. student to the UC Full Professor wasn’t a magical jump, but a slow evolution, one that resulted from my own decisions. I could have said “no.”

For me, those points sum up several aspects of UC’s role-model problem: the faculty that students most want to work with may be imperfect role models for most of those students. How do we do a better job of getting across the message that they don’t have to become us to be successful and happy. Or that those students might just surprise themselves one day by looking around a meeting room and asking “What the hell am I doing here?”

October 29, 2017 / jpschimel

A different solution to Example 9.9: undermining your conclusion

I suggested in Writing Science that example 9.9 was a really egregious example of undermining the conclusion:

Ex. 9.9:  To conclude, 3-methyl-ambrosia offers a new approach for thyroid carcinoma therapy. Our data provide evidence on safety and in vivo activity of this compound in patients with this condition, although the proof for clinical benefit remains to be established in future clinical trials.

I’d argued that the solution to this was to move the constraint up front to leave the real conclusion (this chemical looks like it works) as the concluding statement.

Ex. 9.9b:  While further clinical trials will be necessary to establish the full benefits of 3-methyl-ambrosia as a therapeutic agent, our data provide evidence that it is safe and shows in vivo activity against thyroid tumors. 3-methyl-ambrosia.

But at a workshop I was just running in San Diego, a participant noted that this could equally be turned into a powerful “question-based resolution.” The problem isn’t that it ends by suggesting clinical trials—it is the language used to make that suggestion. The original language is a definite “undermine” because the language suggests “we don’t know whether it works.” But the authors could equally have written:

Ex. 9.9c:  To conclude, 3-methyl-ambrosia offers a new approach for thyroid carcinoma therapy. Our data provide evidence on safety and in vivo activity of this compound in patients with this condition. We therefore recommend that 3-methyl-ambrosia be taken forward into clinical trials to evaluate its potential as a thyroid carcinoma therapy.

That makes a clear conclusion statement—it looks like the chemical works (and uses the original language to do so). But the follow-on statement about clinical trials no longer undermines that conclusion—rather it builds off it. It suggests that a new and different line of work is needed (clinical trials) to follow up on the findings of this project and specifies, concretely, what follow-on work is needed. Hence, this would be an effective way to end this example.

This also shows that the original authors’ version (unfortunately the one that was actually published) is, in fact, the worst of all three possible ways of writing this! With two possible good structures for the final paragraph, they picked the third, crappy structure. Oh, well. I guess I should just say thank you for providing me with a great example of what not to do!

P.S. I also wish I’d written my version a little differently. I should have written the first sentence as: “While clinical trials will be necessary to evaluate any benefits of 3-methyl-ambrosia as a therapeutic agent…” No clinical trials have been done so why did I add “further”? I have no idea. And, I could have qualified it better by saying “evaluate any benefits.” That removes the implication that they exist, which we don’t know yet. When I wrote that I was aiming to hammer the original and hammered harder than necessary—a slightly softer hammer would be more accurate and still leave a strong conclusion.

September 6, 2017 / jpschimel

Should Universities be like businesses? If so, why do we have the same rank structure as the Army?

Over the last decades, as public funding for universities has declined, there has been a lot of discussion of the idea of running universities more like businesses. Can we bring the focused efficiency of private industry to the problems of running a university? Of course, there has been a lot of pushback as well, largely based on the simple truth that a business’ purpose is to make a profit. Ours is not.

For us, the meaning of “profit” is bizarre. How would we even determine whether an academic unit is “profitable”? What should we do it were not? Close a Department because it doesn’t bring in a lot of majors (and hence undergraduate tuition) or grant funding? Of course not. The value of scholarship can not be measured by simple financial accounting. The popularity of fields also comes and goes, so “unprofitable” today might look differently next year. For example, my own program (Environmental Studies) has gone through wild swings in student numbers over its history. Additionally, businesses plan short-term: sometimes as short as quarters, although others (e.g. infrastructure-heavy oil companies or railroads) may plan for decades. Universities, however, routinely operate on decades—a normal faculty career lasts 30-40 years. Some Universities are hundreds of years old; the U.S.’s oldest Universities date to the 1600’s, while Europe’s were founded before 1100.

The failure of the “business-model” of university management has been discussed by others—notably Chris Neufield (The Great Mistake; Johns Hopkins University Press), and so I need not repeat their arguments.

Our job is not to make a profit but to serve the public. We have an integrated mission of teaching, research, and service. It is no trivial mission. As I argued in a recent post, research universities are the core intellectual infrastructure of modern society—we may not produce all the undergraduate degrees, but we produce all the professors, and while we may not do all the research, we produce the researchers and scholars. Without the education, scholarship, and technological developments that depend on research universities, the nation would stall and ultimately collapse. The modern world lives on a “Red Queens Race” where if you aren’t moving forward, you are moving backward. Research universities are the ultimate engine for moving forward. Our mission is thus the ultimate health and success of the Nation.

In many ways, therefore, the entity in the U.S. that universities most resemble is not business but the military! We each provide services essential to the safety and well-being of the Nation. Academics don’t generally get misty eyed about our mottoes the way Marines do about theirs—Semper Fi—but our Full Dress “uniforms” can be just as uncomfortable and ours are even more laden with history and tradition (try wearing academic robes designed for northern Europe during the little ice age in southern California in the Anthropocene!).

Paralleling universities and the military may seem an odd thing to do, especially given that we often don’t get along very well and our values and virtues lie at opposite ends of the spectrum. Yet, we each live lives somewhat cloistered from the experience of the general public and our distinct cultures each grow organically from our vital missions. The military asks men and women to risk and sacrifice their lives for the Nation, while military operations must be planned and carried out with clear strategy and operational plans. Thus, the military is top-down and values a core of uniformity and of following orders—too many battles and wars have been lost when subordinate officers decided to do things their own way. Universities are about creating knowledge and developing scholars—activities that depend on individual creativity and initiative. Thus, we are bottom-up and value individuality and initiative above almost all else. It’s impossible to be a good academic if all you can do is follow orders; of course it’s equally impossible to be a good soldier if all you can do is follow orders—successful soldiers need to know what orders to give and when to diverge from their orders to achieve the overall objective. That’s no different than working on a research proposal. That “no plan survives contact with the enemy” is equally true on the battlefield and in the laboratory.

Interestingly, the Army and Universities even use directly parallel rank structures! We have the same number of “Grades,” steps within each, analogous functions, and even similar amounts of time people are expected to spend in each step.

Company Grade Officers
Company grade officers do the army’s fundamental hands-on work—leading troops in the field. Through this, they prepare themselves for higher-level leadership roles. This is analogous to doing research at the bench or in the archives, learning scholarship at its basic level, preparing students to become leaders and train future researchers.
M.S. Student 2nd Lieutenant Unproven, learning the basics.
Ph.D. Student 1st Lieutenant More experienced, but still at ground  level.
Postdoc Captain Experienced at doing the basic work while taking on some leadership role.
Field Grade Officers
These are the guts of the army, responsible for leading at the operational level. They plan, oversee, and integrate tactical operations into the larger strategy. They acquire increasing responsibility for the larger organization. Promotion to Field Grade is typically after ~10 years service, similar to when someone would get hired as an assistant professor.
Asst. Professor Major Majors are being prepared for the critical position of battalion command. Essentially, they are “untenured,” learning and proving themselves as senior officers. Typically 6 years, similar to the tenure clock. 
Associate Professor Lieutenant Colonel Established leaders at the heart of tactical operations: commanding battalions (the core operational unit of the army) or research groups (in the sciences). Typically 6 years. 
Full Professor Colonel Proven, senior leaders. The intellectual heart of the institution. In the Navy, Captains command the largest warships.
Flag/General Officer
Senior administrative leaders. In charge of large scale operations and strategy. This promotion would typically occur after ca. 20 years total service.
Department Chair Brigadier General May command an independent Brigade.
Dean Major General Commands a division. Analogous to a Division (e.g. Humanities or Natural Sciences) or an independent School (e.g. Engineering or Law) within a University.
Provost Lieutenant General Commands higher-level units (e.g. corps). This is analogous to a College within a large University or a Campus within a multi-campus system.
Chancellor/President General Commands a top-level unit (Army, University)

Huh! There are certainly imperfections in the comparison, but I find it notable that promotion to field grade and professorship both typically occur about 10 years into a career (which starts after a BA/BS degree), and that the first step is in each system a trial and developmental step—major vs. assistant professor. Jim Tiedje once said he thought the happiest people in academe are associate professors—post tenure but before the administrative responsibilities of full. I’ve also read that commanding a battalion (lieutenant colonel) is the most rewarding job in the army.

Both systems have an “up-or-out” system, although the military’s is stricter, with forced retirement if you are passed over for promotion, whereas once we have tenure, we can never be forced to retire. As a result, in the military the rank pyramid is sharp, while ours is often inverted—most professors are full profs. Another is that in the military, promotion to flag officer (general/admiral) is a natural flow (though one made by only a few percent of people starting out). For academics, transitioning to administration is a distinct choice—a step away from the scholar path—one few of us make and none are required to make. In the military, people are trained their entire career in leadership and command skills to prepare the few with what it takes to make flag rank. We are never trained for the senior level leadership roles required to run the university. This gives us a small pool to select from; as a result, academic leadership often suffers.

I find the parallels between these wildly divergent cultures and systems intriguing and I suspect they reflect something deep about the nature of humanity and the natural development of skills, knowledge, and wisdom. Commanding soldiers in the fog of war and fighting new insights out of recalcitrant nature are some of the most difficult activities humans carry out. Thus, we have independently evolved analogous and surprisingly parallel structures to select, train and develop the people and systems to achieve our goals? Between us, the military and academe are institutional systems the each are fundamental to the safety and health of the Nation. Unfortunately, while most people understand what the military does, they are largely clueless about what we do or why it is as fundamental to the well-being of the Nation. As a result, while our Federal Government invests massively in the military, they mostly leave University funding to the States, and rely on it being carried on the back of the undergraduate teaching mission. Support for the, ultimately critical, integrated research/graduate training mission suffers. So we fall further behind in the Red Queen’s Race. By under-supporting the University mission, we risk our ultimate national security as much as from under-supporting the military.

July 3, 2017 / jpschimel

Why I hate it when people ask “What do you teach?”

I have never been introduced as a Professor at UCSB and not gotten the inevitable follow up question: “What do you teach?” I expect it, understand where it comes from, and I hate it.

Why my passion over an innocent expression of interest in my life?

Because people seeing my job as just a teacher reflects their deep misunderstanding of the university and its role in Society. A research university is more than just an advanced school. In fact, research universities are the fundamental “Social Infrastructure” of the modern world. And probably 99% of people haven’t a clue.

Most people only ever experience professors in our role as teachers. Even if they went on to medical or law school, they went to learn things that their professors already know. In that view, people are fundamentally wrong. Classroom teaching is important, and I love it. But is it truly the most important thing I do as a University of California Professor? No.

I got my BA from Middlebury, a Liberal Arts College where I got an excellent education. You don’t need a research university to teach undergraduates! That is illustrated even more strongly by the California State University, which awards more bachelor’s degrees than any other institution in the Nation.

But colleges and Cal State don’t produce their own most critical resource: Professors! They rely on research universities to do that. Without us, they fail.

A second key function that research universities do, of course, is research. Yet, that too can be done elsewhere. Independent research institutes, private companies, etc.—they all do research, although even companies generally can’t afford to invest in the deep fundamental research that underlies their applications. So, you don’t really need a research university to do research.

But, technology companies don’t produce their own most critical resource: Researchers and Engineers! They rely on research universities to do that. Without us, they fail.

Graduate, Ph.D.-level training, therefore, is the irreplaceable function carried out by research universities, such as UC. It is the one thing we do that no other entity can do. And, without it, society fails.

All the missions of the research university are important. As teachers, we pass along existing knowledge; as scholars, we create new knowledge; as mentors, we produce the next generation of scholars. Society relies on all three elements. These functions are completely, 100%, interwoven, but graduate education is the nexus.

Students come to UC because they want to study with top scholars. They want the deepest insights from the people who developed them, and to become involved in knowledge creation themselves. Because we attract the best students, we can do more with them and take them further. The University of California doesn’t provide better education because our faculty are better teachers than you’ll find at Cal State or Middlebury. The power of a UC education comes from the integration of undergraduate teaching with active scholarship. Our students don’t just learn things we already put in their textbooks, but things that aren’t in the textbooks yet.

It’s Ph.D. training that ultimately set us apart and makes UC the world’s most effective university system—a powerhouse for social and economic development. Training Ph.D. students, of course requires research opportunities for them to work on, weaving research and graduate training together at their root. Together faculty and graduate students form a coordinated team to produce new knowledge. Graduate students also serve as teaching assistants, and in doing so, learn to become teachers and mentors. They provide a key intermediate between faculty and undergraduates—they are closer in age and less intimidating than professors and so fill a role professors can’t. Thus, graduate training and undergraduate teaching are equally interwoven.

What makes the University of California great isn’t just great teaching by great faculty, but the integration of the pieces. We produce great undergraduates, but we also produce great scholars and great research. One can’t happen without the other. UC’s mission depends on the parts working together as a coordinated whole. California, the U.S., and the world depend on us for that singular interwoven mission.

So, it bothers me when people, and our political leaders, focus almost entirely on undergraduate education as the raison d’etre of the University of California and treat graduate training and research as at best, nice adjuncts. In fact, I could argue that they have it backwards. The essential, irreplaceable, mission is graduate training, with undergraduate education the adjunct!

So, yes, I hate it when people reduce my entire role as a professor to “What do you teach?”



June 1, 2017 / jpschimel

Citation Stacking: editorial misconduct & my response

Yesterday, I received a copy of an open letter from a group of junior European scientists expressing their concerns over “citation stacking”–that is when reviewers and journal editors pressure authors to cite papers that either they wrote or that are published in “their” journal. That letter is available at:

One of the editors who was forced to step down for such activity denies that is what he was doing. Perhaps. You can see the analyses and arguments in the material cited in the letter. To me, the real idiocy of such behavior (assuming it occurred) is that it involves great risk for essentially no reward!

I do get paid as a Chief Editor of Soil Biology & Biochemistry, but the modest stipend (for processing 180 manuscripts a year) isn’t anywhere near enough to make it worth risking my reputation and career. And there’s no bonus for increasing the impact factor. When the “crime” is so petty and the rewards so minimal, why would you risk it?

Fundamentally, we all thrive in a healthy “ecosystem”–a publication system that works to provide high quality and effective review. Such a system helped me to polish my early manuscripts into something worth reading, and so helped develop my career. As an editor, I am a steward whose job it is to maintain the health of that ecosystem and to pass it along to my successors in the condition I took it over (or even better). That “ecosystem health” is not measured by the impact factor of the journal, but by the integrity of the editorial and review process.

In any event, I wrote a response and thought it would be worth putting it here as well as in an e-mail.


Dear Colleagues who drafted this letter:

I have been a Chief Editor of Soil Biology & Biochemistry for 10 years. I can say with absolute certainty that I have never and will never do any such citation stacking as discussed in your open letter. And, I can add that I am confident that none of my colleagues who serve as Chief Editors of SBB do either. I can equally assure you that I have never received any hint of pressure from the publisher to manipulate citations. We all want to see the journal do well—but as long as we maintain the best editorial system we can, and publish the best papers, the journal will remain respected and highly cited. I would resign before I would ever cave to pressure to manipulate the process. I don’t get paid anywhere near enough to take the time, and risk, to cheat!

As a Professor, it is my responsibility to produce both science and scientists; I therefore have a vested interest in furthering the careers of my junior colleagues. Students and postdocs are typically the lead authors on the most important and novel work and I want to publish those papers, read them myself, and see them recognized. I try to carry my mentoring and career development responsibility into my editorial responsibilities.

Now, it has long been common that when papers are sent to reviewers (and editors) who are senior scholars in a field, they (we) may note several older papers that they feel are relevant to the current paper and suggest that the authors consider citing them. As an author, I have regularly received such suggestions. Sometimes those reviewers and editors are even correct about the relevance of those older papers! When that is the case, it serves effectively as one of the education functions of peer review; as an author, I appreciate such comments. If the suggestion is off-base, and I have received (and probably written) such recommendations, the author should ignore them and explain in their cover letter why (or just note the ones you have included). But this is different from the citation stacking you describe. In any case, such “old-fart” recommendations don’t displace citation to the newer papers lead-authored by junior scholars.

Remember also that an introduction is not a “literature review”—its purpose is not to describe the state of knowledge in a field or to cite every paper ever written on the subject. Rather it is to define a specific gap in that knowledge. Thus, the papers you should cite are those that frame the boundaries of that gap. There may well be classic papers in the general field which are not necessary (or useful) in defining the edges of knowledge, so don’t cite them. A reviewer who wrote those papers may note them in their review—but if they don’t help frame the knowledge gap, you don’t need to cite them.

It is equally possible that some relevant recent work may not be cited because there is such a glut of publications that it is difficult to fully keep up with everything published. I have long held what I call “Schimel’s Law of the Literature” which states “You can either keep up with the literature, or you can contribute to it.” And I fully recognize inherent contradiction in that statement—in fact, that is the point. I try to ensure we have cited the most relevant recent work when we submit papers from my group, but it is inevitable that we will miss some. To slightly misquote a classic saying: “To err is human—to forgive, canine.”

I have heard anecdotal accusations of authors being pressured to cite more papers from the journal they are submitting to, which you appropriately condemn, and I have seen some of the reports documenting such behavior you cited. But I have never experienced such behavior personally, and absolutely will not carry out such practices as an editor. Papers are cited in SBB ultimately because the authors felt they deserved to be cited.

As it has come to matter less where we publish (I think I have searched for a topic, downloaded a paper, read it, and cited it without ever noting where it was published!), publishers (and some editors apparently) have gotten more sensitive to metrics and standing. “Journal quality” actually mattered more in the hardcopy era, when we went to the library to check the table of contents for a limited number of top-tier journals. This reflects the fallacy of journal “impact factor” battles—journals aren’t “good” because they have high IF’s, but because they maintain strong editorial systems, which filter out the papers that aren’t appropriate and work to perfect those that are. Real “quality” lies with the individual paper, and that remains in the hands of the authors.

Scientific publication involves discussion and mutual education among authors, reviewers and editors. That process should work (and I believe mostly does work) to polish manuscripts into strong papers. In my experience, such misbehavior as you call out remains exceedingly rare. As both reviewer and editor I may suggest many things to authors—to think about the problem differently, analyze or interpret the data differently, and even consider (and cite) some literature they may not have been aware of. Those are all things reviewers are supposed to do. But I do not and never will pressure authors to shift their citations just to increase either my own citation numbers or the citation levels of my journal.





February 5, 2017 / jpschimel

Taken-for-granted basic science: it might save your life

Today I went to the doctor and received a death sentence. Or rather, what would have been one a century ago. Today, I barely blinked. I’ve had a persistent sinus cold for three weeks. Yesterday, I started running light fever, the cough felt deeper in my chest, and the icky gunk I was coughing up was darker. Warning! Warning! Danger! Danger! Those are classic symptoms of secondary bacterial infection—bronchitis or potentially pneumonia. This morning I went to urgent care and the doctor told me she heard  rattly noises at the base of my right lung. Pneumonia. When I was a kid, my parents’ and grandparents’ memories made that a terrifying word. When they were kids, 20% of Americans died of pneumonia or related problems—and I would have been on track to joining them.

Today, I can tell my junior colleagues that there probably won’t be a new ecosystem ecologist job opening at UCSB in a hurry. OK, there is a chance (and a larger one than even a decade ago) that this could be a resistant pathogen and that my life may become hell for the next weeks until I get better—or don’t. But those odds remain slight.

Is there any other common experience in life that so highlights the enormous power of basic science—Streptomycin was discovered in the lab of Selman Waksman, a soil microbiologist. Pennicilin was discovered by Alexander Fleming in an accidental experiment in microbial ecology—observing the interaction of a soil fungus and a pathogenic bacterium. I am likely to survive this infection with little more than mild misery because of the results of fundamental scientific research.

Antibiotics, however, are a truly terrible business proposition. A new antibiotic can cost $1 Billion to bring to market. Yet, once available, doctors are encouraged to not use it, patients probably only take it for a week, and it may only be months before new pathogens start becoming resistant. No rational company would want to invest in such a miserable product. Yet, without them, the quiet rattle in my lung is increasingly likely to become a death rattle.

These kinds of fundamental life-changing and life-saving discoveries arise from basic research, freed of an immediate demand to produce economically viable products. I could tell a similar story about the cell phone I used to text my wife about what was going on. Or why I don’t get laughed at in shoe stores anymore—try asking for size 15’s!

Open, creative research is the ultimate fuel of the technology that drives our society. Yet, the failure to adequately fund basic research in the U.S. has already threatened the health of the system as funding rates have dropped below 10%. The NSF reauthorization act during the George W. Bush administration had proposed doubling the NSF budget—but it was never funded even though it would have cost the federal government a relative pittance: under $10 Billion/year. A small price to pay for a society’s health, to say nothing of the lives of us who won’t die of pneumonia.

There has been pressure to try to force basic science to more directly demonstrate an immediate economic benefit. Had those been the rules in the 1930’s and 40’s the antibiotic era wouldn’t have started. Alternative facts aren’t very useful when a doctor hears a rattle in your lungs. Then, there is just the question: which tools derived from basic science will they use to save your life?