Monday, December 17, 2012

Misconduct accounts for the majority of retracted scientific publications.

Proc Natl Acad Sci U S A. 2012
Misconduct accounts for the majority of retracted scientific publications. Fang FC, Steen RG, Casadevall A.

Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.


A detailed review of all 2,047 biomedical and life-science research articles indexed by PubMed as retracted on May 3, 2012 revealed that only 21.3% of retractions were attributable to error. In contrast, 67.4% of retractions were attributable to misconduct, including fraud or suspected fraud (43.4%), duplicate publication (14.2%), and plagiarism (9.8%). Incomplete, uninformative or misleading retraction announcements have led to a previous underestimation of the role of fraud in the ongoing retraction epidemic. The percentage of scientific articles retracted because of fraud has increased ∼10-fold since 1975. Retractions exhibit distinctive temporal and geographic patterns that may reveal underlying causes.

Sunday, December 16, 2012

Primate center leader shouldn't be allowed to talk to children

A friend recently sent me a quote from Jon Levine, the relatively new Wisconsin National Primate Center director. Levine was interviewed by the university’s On Wisconsin Magazine; you can read it here. When he was asked what he thought the primate center’s biggest challenge was, Levine answered that it was money, the implication being that Levine doesn’t seem to think that finding cures or making some progress in the treatment of human diseases is as large a challenge as keeping the dollars flowing in. Maybe Levine knows in his heart that the likelihood of human benefit from the center’s work is pretty much nil anyway, so he probably just wants to work toward something attainable – like a fancier building.

I’d read the interview before (and left a comment), but did again, and something he said caught my eye. Here’s the question and answer:
Q: What do you tell someone — a child, for example — who asks you about the use of monkeys for biomedical research?

A: That we are the good guys. We play by the strictest of rules, intended to ensure the humane and careful utilization of a precious resource. And we have the best of reasons for the work we do. I do not hesitate to give children an explanation in terms they can appreciate. For example, many kids know someone who has been diagnosed with some form of leukemia. We are developing methods to take blood cells from cancer patients and reprogram them into “induced pluripotent stem cells” — make them younger versions of themselves, before they became cancerous. Those induced cells can lead us to an understanding of how blood cells become cancer cells and how we might better treat leukemia.
He’d have been more succinct if he’d simply said, “I side-step the question and lie to them.”

The primate center's staff has a long history of lying and breaking the rules. They lied matter-of-factly and in writing to Dane County officials multiple times over an eight year period as they secretly and in direct violation of their written promises that they wouldn’t, took monkeys from the Henry Vilas Zoo, experimented on them in their own labs, and sold them to other labs around the country.

They lied again and covered up the horrible details of their experiments when they shredded 628 videotapes documenting nearly two decades of experiments on monkeys. They destroyed them when it looked very likely that a public records request was going to force them to give a copy of one of the tapes to anticruelty activists who they must have imagined were likely to make it available to the public.

Play by the rules? Not hardly; that’s something the real good guys do.

Levine says he gives children explanations for the things they do to monkeys in terms children can appreciate. Utter nonsense. He says: “many kids know someone who has been diagnosed with some form of leukemia.” In fact, relatively few children are likely to know someone who has been diagnosed with leukemia.

Here’s what the National Cancer Institute says:
On January 1, 2009, in the United States there were approximately 271,880 men and women alive who had a history of leukemia -- 152,698 men and 119,182 women. This includes any person alive on January 1, 2009 who had been diagnosed with leukemia at any point prior to January 1, 2009 and includes persons with active disease and those who are cured of their disease.
According the US Census Bureau’s Quick Facts, in 2010, there were approximately 73,172,693 children (someone under 18 years of age) in the U.S. According a mathematically inclined friend, this means that if Levine was talking to a class of 20 students, it’s likely that two of them would know someone with a history of leukemia.

But what about his claim that scientists at the primate center are “developing methods to take blood cells from cancer patients and reprogram them into ‘induced pluripotent stem cells’”?

There are two main ways I go about fact checking a statement like this. I look for publications that demonstrate such research being conducted at the primate center, and I look for active projects underway at the primate center that mention some iteration of “induced pluripotent stem cells” or leukemia or cancer.

Searching PubMed, the National Library of Medicine’s extensive on-line database, I was able to locate 137 scientific papers from scientists working in labs in Wisconsin that have the word pluripotent in the title. Of these, I found only one that involved the use of monkeys: Pluripotent cell lines derived from common marmoset (Callithrix jacchus) blastocysts. Thomson JA, Kalishman J, Golos TG, Durning M, Harris CP, Hearn JP. Biol Reprod. 1996.

The large majority of published papers that focus on induced pluripotent stem cells from scientists in Wisconsin use human cells. Some older ones involve the use of mice, a few use other animals, but none other than the one above seems to report on the use of monkeys.

Turning to on-going projects at the primate center, the NIH on-line search tool RePORTER returns 32 currently funded projects at the University of Wisconsin, Madison when using the search term pluripotent.

Of these, only one involves the use of monkeys (Project Number: 1R01NS076352-01A1 Contact PI / Project Leader: ZHANG, SU-CHUN Title: INDIVIDUALIZED CELL THERAPY FOR PARKINSON'S DISEASE).

As far as I can tell, the closest thing to a match for Levine’s claim is the work of Igor Slukvin, who has an office at the primate center. He says that his research focus is: “hematopoietic development from pluripotent stem cells; de novo generation of hematopoietic stem cells.”

Hematopoiesis is the scientific term for the formation of blood.

He conveniently lists ten of his publications. Of those (again using PubMed), none involve the use of monkeys. Slukvin seems not to have published a paper involving the use of monkeys since 2007, and only the very last one of those, a report on possible ways to mitigate the inadequacy of monkey as models of hematopoietic stem cell therapies in humans is even vaguely in line with Levine’s claim. (Differential requirements for hematopoietic commitment between human and rhesus embryonic stem cells. Rajesh D, Chinnasamy N, Mitalipov SM, Wolf DP, Slukvin I, Thomson JA, Shaaban AF. Stem Cells. 2007.)

So, getting back to what Levine says he tells children:

1. “we are the good guys.” Wrong.
2. “We play by the strictest of rules... ” Wrong.
3. “... intended to ensure the humane and careful utilization of a precious resource.” Wrong.
4. “And we have the best of reasons for the work we do.” Wrong. It’s all about money.
5. “I do not hesitate to give children an explanation in terms they can appreciate.” Wrong.
6. “For example, many kids know someone who has been diagnosed with some form of leukemia.” Wrong.
7. “We are developing methods to take blood cells from cancer patients and reprogram them into “induced pluripotent stem cells” — make them younger versions of themselves, before they became cancerous.” Wrong. Or maybe, but if so, it has nothing to do with monkeys. At best he's misleading children with a bait and switch tactic.
8. “Those induced cells can lead us to an understanding of how blood cells become cancer cells and how we might better treat leukemia.”

His last point is interesting. Coincidentally, I recently finished Siddhartha Mukherjee’s Pulizer Prize winning history of cancer and oncology, The Emperor of All Maladies. Mukherjee is an oncologist. I’ll wager that he knows a bit more about the history of cancer and the present state of cancer research than Levine. Nowhere in his book does he mention the use of “induced pluripotent stem cells” to model cancer cells.

Mukherjee points out that hematopoietic stem cells seem to possess the characteristic that sets cancer cells apart from other cells: immortality, or at least the ability to divide many many times before becoming quiescent. But the characteristic of endless dividing is the common feature of all cancer cells. Understanding the cause of this unique characteristic is likely to be discovered by comparing the cells that have it rather than the cells that seem to have something akin to it occasionally. Furthermore, even if the examination of induced pluripotent stem cells might be useful to understanding cancer, there would be no reason not to use induced human pluripotent stem cells. So, to the degree that Levine was trying to defend or justify the use of monkeys by imagining some way they might be used, he is wrong again.

Real good guys generally tell kids the truth.

Wednesday, December 12, 2012

12-12-2012: Only Eleven Days Left to the End of the World as We Know It.

So I’m an optimist. More likely, things will just keep rolling along, like a big ball of crap picking up more shit as it continues going down hill.

Terrance McKenna, the late ethnobotanist and fearless explorer of plant-induced alternate realities, sometimes referred to as a psychonaut, visionized from his drugged perspective that the Mayan calendar’s so-called end date, December 21, 2012, is actually an asymptote, the point in time when, according to him, complexity becomes infinite and the world as we know it ends.

Things have become more complex over time and in some areas of some people’s daily life complexity does seem to be accelerating. Many of us now carry small hand-held devices that allow us almost instant access to a large and fast growing body of digitalized stuff; the devices take photos, videos, play music, keep the time and let you play Scrabble with people across the globe between phone calls. As one ad tells us, “when there's no limit to what Droid gets, there's no limit to what Droid does.” No limit... that’s an arithmetic increase as opposed to the exponential advancement envisioned by McKenna.

But many things seem to be stuck in time. Very little changes in some areas of everyday life.

Take public relations and the cruelty that occurs in the nation’s many animal labs. Not much acceleration in that arena. Suffering, lies, suffering, cover-ups,
suffering,.... it just seems to keep rolling steadily along. Absurdity, stupidity, and greed seem a pretty constant part of that area of life as well. Maybe rubber stamps have a magical power to stop time; they definitely have the power to create Hell on Earth.

One of the stuck-in-time, routinely dull and witless things I’ve seen from the lab crowd recently involves the willingness to swallow whole a completely ridiculous claim and then rely on that massive and matter-of-fact glob of nonsense to justify immense suffering. As always in this arena, money and station trump normal human emotions like mercy and compassion.

Here’s the big glob of nonsense: Ned Kalin, a vivisector at the University of Wisconsin, Madison says that his newest experiment on baby monkeys will lead to a new drug that will prevent or cure “anxiety, depression, and other forms of psychopathology” caused by “parental stress, physical, sexual, emotional abuse, neglect and inadequate parenting.” And two oversight committees swallowed it whole, belched a bit, and then gave it their stamp of approval. You can read his protocol here. The quotations above are from a letter he wrote to a reporter about his project.

If Kalin had a string of wildly unlikely successes from his past research maybe the committee members would have had a reason to swallow this wild claim and endorse this new round of cruelty, but he doesn’t. It’s hard to find anything beneficial that has resulted from his decades of hurting and killing animals.

Why would anyone believe such a wild claim from someone who has nothing to show for decades of similar claims? Why would they say OK, go ahead and hurt and kill some more monkeys?

Unlike the world of increasing complexity McKenna thought he saw, this situation isn’t even complicated. It’s not new or any different from what has been happening in the labs since about the mid to late 1940s when the U.S. government began pouring money into basic biomedical research. (That stream of money has grown rapidly, so maybe there’s hope yet for McKenna’s prophesy.)

There are three basic reasons the members of the committee swallowed that bolus of garbage and gave him the go-ahead. In decreasing order of significance, these are: the power of the System, money, and the PI’s prestige, standing, tenure, position, power, etc.

The System here is the phenomena discussed widely and supported by much experimental social and psychological research demonstrating that people operating within such systems are controlled by it. In this case, the System is designed and expected to approve research project. So it does. The cogs all do their jobs and the output is as it was intended it would be.

The System controlling the behavior of the committee members is designed to approve projects because they come with large dollar sums attached to them. This money, approximately $200 million in the case of the UW’s funded experiments using animals, is lifeblood to the institution. Turning down even a bit of it down would be like putting a tourniquet around your thigh and letting your leg die. Kalin has a proven track record of contributing to this stream of money for the institution; the System encourages him.

Prestige and the power it brings with it in the System probably came into play in this particular case. Kalin is the chair of the Department of Psychiatry. His colleague Paul Kaufman, also a primate vivisector, is the chair of the Department of Ophthalmology. University staff has refused to give their opinions of his glaucoma research because they feared his power. Kaufman’s lab has had problems with its animal care, but his experiments are always approved. I only speculate, but it’s likely that if some junior newly hired vivisector had asked for permission to resurrect Harry Harlow’s infamous methods of inducing depression and anxiety in baby monkeys, even if they had been promising a cure for cancer, they might not have had their project approved out of some concern about possible bad press. But then, if it came with enough money, maybe they would have; money trumps prestige, even the lack of it.

Only eleven days left.

Sunday, December 9, 2012

Laboratory Dreams

Animals dream. Imagine, if you can, that you are a monkey born in a lab somewhere. In all likelihood, your universe -- the breadth of your knowledge and experience -- is limited to the stainless steel box you live in and the occasional visits from masked things that sometimes put food within your reach, and sometimes manhandle you, and occasionally take you somewhere where frightening and sometimes painful things are done to you.

What would your dreams be like? If all you knew was the bleak laboratory world, that's all you would have to dream about. You would not be able to escape even when sleeping.

Such a life would be much worse than that of any human held in any prison. Human prisoners at least have memories of experiences outside prison.

For the monkeys born in a lab, there is no escape. I doubt that the bleak hopelessness of these animals' lives is a topic that ever appears in a lab's oversight committee meeting minutes.

Saturday, December 8, 2012

be here now

It’s pretty common to read that the main thing separating humans and other animals is language. Many people acknowledge that many animals communicate, but argue that the communicative ability of normal humans is so much greater that it amounts to something wholly different than the basic communication we have been able to identify in other animals.

I tend to agree with this argument, but expect that there is more going on when other animals communicate with each other than we have yet discovered. I also don’t see how a greater communicative ability translates into higher moral standing, which is one of the implications that some make when pointing to other animals’ communication abilities.

But all our hyper-communication abilities aside, I’m struck by the irony in the claims about our communication ability and our society-wide effort to experience life in the absence of language.

This effort is a common and often central goal of religious/spiritual traditions around the world. It’s particularly ironic that Buddhists frequently refer to our inner chatter as monkey mind. Even though many people argue that monkeys can’t experience this inner stream of “verbalized” thought because they don’t possess language.

The interesting thing to me is the fact that the mental state achieve by stilling one’s inner chatter is perceived by many of those who have attained it as the highest mental state; some say it allows one to experience or even merge with the Cosmic Consciousness or God directly. Names for this state vary, but they include being "filled with the Spirit of the Lord", samadhi, satori, nirvana, enlightenment, kemal, etc. Yet animals, who apparently are in this state naturally are claimed not to have the same moral standing as the yogis, priests, nuns, sadhus, sages, saints, lamas, mystics, and everyone else striving to silence their monkey mind and experience things the way most other animals apparently do all the time.

"A watershed moment for animals and animal issues."

Margo DeMello has recently published a new book. I just ordered a copy after reading a review in VegNews:
The recent publication of Animals and Society by Margo DeMello is a watershed moment for animals and animal issues. The book is the equivalent of the Beatles appearing on The Ed Sullivan Show in 1964: there is no going back. DeMello has produced a volume that should be required reading for all freshmen college students and will become the textbook of the nascent field of human-animal studies. Yes, Animals is a 400-plus page behemoth that leaves no issue untouched, one that elevates animals to a level of respect and relevance never before seen in academia. Yet Animals is also accessible, comprehensive, and easily referenced. In four sections and 20 chapters, plus ample references and an extensive bibliography, this is a book almost begging to be plagiarized. It's the textbook we all wish existed when we were in college. DeMello has earned her PhD.

Monday, December 3, 2012

Public opinion on medical testing on animals changing quickly.

Gallup released the latest results of its annual polling series asking American’s about their opinions on a set of moral issues in May, but I hadn't looked at the results very carefully until Suzanne M. Rivera, Ph.D. made a silly claim about people's opinions and called attention to it.

The issues they ask about include abortion, gay or lesbian relations, embryonic stem cell research, the death penalty, sex between an unmarried man and woman, doctor-assisted suicide, gambling, divorce, and cloning animals, and medical research using animals. They have been asking the same questions since 2001. The changes in the public's answers to Gallup's questions over time suggest that opinions about the use of animals are changing faster than are the opinions on any other issue except gay and lesbian relationships. I've tabulated their results below which come from their explanation of their methods. [Click on the image for a larger version in a new window.]