Archive for the 'Conduct of Science' category

A simple primer for those new to behavioral science assays

1) Behavior is plural

2) No behavioral assay is a simple readout of the function of your favorite nucleus, neuronal subpopulation, receptor subtype, intracellular protein or gene. 

9 responses so far

Santa Cruz Biotech fined, banned from animal use

May 20 2016 Published by under Animals in Research, Conduct of Science

The big news of the day is that Santa Cruz Biotech has been punished for their malfeasance.

Buzzfeed News reports:

After years of allegations of mistreated research goats and rabbits, a settlement agreement (pdf) announced late on Friday will put Santa Cruz Biotechnology out of the scientific antibody business. The company will also pay a $3.5 million fine, the largest ever issued for this type of violation.

The settlement is only three pages so go ahead and read it. It is pretty much to the point.

Santa Cruz Biotech neither admits nor denies the allegations, blah, blah, but it is settling. They are to be penalized $3.5 million dollars, payable by the end of May, 2016. Their animal welfare act registration is revoked effective Dec 31, 2016. They will not use any inventory of the blood or serum they have on hand collected prior to Aug 21, 2015 to make, sell, transport, etc anything from May 20, 2016 to Dec 31, 2016 (after which they still cannot, I assume, since the license will be revoked). They agree to cease all activity as a research facility and will request cancellation of their registration with APHIS as such as of May 31, 2016.

I don't know how easy it will be for the overall company to get around this by starting up some other entity, possibly off shore, but it sure as heck looks like Santa Cruz Biotech is out of business.

Hoo-ray!!

There are several specific allegations of animal use violations under the Animal Welfare Act at play. But for me there was one really big deal issue, I assume this was why the hammer came down so hard and why Santa Cruz Biotech decided they had no choice but to settle in this manner.

As Nature reported in early 2013, Santa Cruz Biotech hid an animal facility from Federal inspectors.

A herd of 841 goats has kicked up a stir for one of the world’s largest antibody suppliers after US agricultural officials found the animals — including 12 in poor health — in an unreported antibody production facility owned by California-based Santa Cruz Biotechnology.

“The existence of the site was denied even when directly asked” of employees during previous inspections, according to a US Department of Agriculture (USDA) report finalised on 7 December, 2012. But evidence gathered on a 31 October inspection suggested that an additional barn roughly 14 kilometres south of the company's main animal facility had been in use for at least two and a half years, officials said.

This is mind bogglingly bad, in my view. Obviously criminal behavior. The Nature bit described this as "another setback". To me this should have been game over right here. Obviously trying to cover up misuse of animals so my thought is that even if it worked, and you can't actually observe the misuse, well, "get Capone on taxes even if you can't prove the crime" theory.

But then there was more. In the midst of all the inspecting and reporting and what not....

In July 2015, the major antibody provider Santa Cruz Biotechnology owned 2,471 rabbits and 3,202 goats. Now the animals have vanished, according to the US Department of Agriculture (USDA).
...
the company seems to have done away with its entire animal inventory. When the USDA inspected the firm's California facility on 12 January, it found no animal-welfare violations, and listed “no animals present or none inspected”. USDA spokesman Ed Curlett says that no animals were present during the inspection.

The fate of the goats and rabbits is unclear. The company did not respond to questions about the matter, and David Schaefer, director of public relations for the law firm Covington & Burling in Washington DC, which is representing Santa Cruz Biotechnology, declined to comment on the animals’ fate.

This sounds like an outrage, I know. But the bottom line is that a company in good standing with animal use regulatory authorities could in fact decide to euthanize all of its animals. It could decide to transfer or sell them to someone else under the appropriate regulations and procedures. This is really suspicious that the company won't say what it did with the animals, but still.

It's the concealment of the animal facility mentioned in the Dec 7, 2012 report that is the major violation in my view. They deserve to be put out of business for that.

16 responses so far

Thought of the Day

May 13 2016 Published by under Conduct of Science, Ponder, Tribe of Science

I think I have made incremental progress in understanding you all "complete story" muppets and in understanding the source of our disagreement.

There are broader arcs of stories in scientific investigation. On this I think we all agree.

We would like to read the entire arc. On this, I think, we all agree.

The critical difference is this.

Is your main motivation that you want to read that story and find out where it goes?

Or is your main motivation that you want to be the one to discover, create and/or tell that story, all by your lonesome, so you get as much credit for it as possible?

While certainly subject to scientific ego, I conclude that I lean much more toward wanting to know the story than you "complete story" people do.

Conversely, I conclude that you "shows mechanism", "complete story" people lean towards your own ego burnishing for participation in telling the story than you do towards wanting to know how it all turns out as quickly as possible.

35 responses so far

Complete stories, demonstrations of mechanism and other embarrassing fictions

There's a new post up at The Ideal Observer.

Many times you find people talking about how many papers a scientist has published, but does anyone seriously think that that is a useful number? One major factor is that individual researchers and communities have dramatically different ideas about what constitutes a publication unit.

Go read and comment.

No responses yet

John Oliver Explains Science to Everyone

May 10 2016 Published by under Conduct of Science

5 responses so far

On writing a review

Apr 26 2016 Published by under Conduct of Science

21 responses so far

Shorthand

Apr 22 2016 Published by under Conduct of Science, Statistical Reasoning

Storyboard

Pretty data

N-up

Prove the hypothesis

Representative image

Trend for significance

Different subcultures of science may use certain phrases that send people in other traditions into paroxysms of critique.

Mostly it is because such phrasing can sound like bad science. As if the person using it doesn't understand how dangerous and horrible their thinking is. 

We've gone a few rounds over storyboarding and representative images in the past. 

Today's topic is "n-up", which is deployed, I surmise, after examining a few results, replicates or subjects that look promising for what the lab would prefer to be so. It raises my hackles. It smells to me like a recipe for confirmation bias and false alarming. To me.

Apparently this is normal phrasing for other people and merely indicates the pilot study is complete? 

How do you use the phrase?

33 responses so far

Post-publication priority ploy

Mar 25 2016 Published by under Academics, Conduct of Science

Don't do this. Ever.

I "think" of doing experiments all the time. As do you, Dear Reader. Dreaming up an experiment is no particular feat for a scientist who has been in the business for awhile. The trick is accomplishing and publishing the study.

If you haven't done that, then it just looks silly to go around telling people you thought of doing the work they just published.

--
H/t: You know who you are dude.

47 responses so far

#icanhazpdf and related criminal behavior

I was slow to start watching "Better Call Saul" for various reasons. Partially because I still haven't finished "Breaking Bad", partially because I couldn't see *that* as being the spinoff character and partially because I just hadn't gotten around to it. Anyway, the show is about a lawyer who we know from BB becomes deeply involved with criminal law.

There's a point in Season 1 where one character has a heart to heart with another character about the second person's criminal act.

"You are a criminal."

He then goes on to explain that he has known good guy criminals and a bad guy cops and that at the end of a day, committing a crime makes you a criminal.

Anyway, dr24hours has some thoughts for those criminal scientists who think they are good guys for illegally sharing PDFs of published journal articles.

22 responses so far

Manuscript acceptance based on perceived capability of the laboratory

Dave asked:

I think about it primarily in the form of career stage representation, as always. I like to get reviewed by people who understand what it means to me to request multiple additional experiments, for example.

and I responded:

Are you implying that differential (perceived/assumed) capability of the laboratory to complete the additional experiments should affect paper review comments and/or acceptance at a particular journal?

I'm elevating this to a post because I think it deserves robust discussion.

I think that the assessment of whether a paper is 1) of good quality and 2) of sufficient impact/importance/pizzazz/interest/etc for the journal at hand should depend on what is in the manuscript. Acceptance should depend on the work presented, for the most part. Obviously this is were things get tricky because there is critical difference here:

This is the Justice Potter Stewart territory, of course. What is necessary to support and where lies the threshold for "I just wanna know this other stuff"? Some people have a hard time disentangling their desire to see a whole 'nother study* from their evaluation of the work at hand. I do recognize there can be legitimate disagreement around the margin but....c'mon. We know it when we see it**.

There is a further, more tactical problem with trying to determine what is or is not possible/easy/quick/cheap/reasonable/etc for one lab versus another lab. In short, your assumptions are inevitably going to be wrong. A lot. How do you know what financial pressures are on a given lab? How do you know, by extension, what career pressures are on various participants on that paper? Why do you, as an external peer reviewer, get to navigate those issues?

Again, what bearing does your assessment of the capability of the laboratory have on the data?

__
*As it happens, my lab just enjoyed a review of this nature in which the criticism was basically "I am not interested in your [several] assays, I want to see what [primary manipulation] does in my favorite assays" without any clear rationale for why our chosen approaches did not, in fact, support the main goal of the paper which was to assess the primary manipulation.

**One possible framework to consider. There are data on how many publications result from a typical NIH R01 or equivalent. The mean is somewhere around 6 papers. Interquartile range is something like 3-11. If we submit a manuscript and get a request to add an amount of work commensurate with an entire Specific Aim that I have proposed, this would appear to conflict with expectations for overall grant productivity.

26 responses so far

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