Archive for the 'Ethics' category

A Simple Question About Vendors of Science

Sep 19 2014 Published by under Careerism, Ethics

Most laboratories buy stuff that they need to do their research. It varies. From latex gloves to pipette tips. From mice to bunnies. From cocaine to ABD-xld500BZN....whatever that is. Operant boxes to sequencers. Stuff.

All of these cost money which generally comes from the laboratory budgets. Startup, unattached funds if you have 'em and, for the most part research grants.

Consider this scenario.

We usually get our genotyping done outside of the lab. I mean, I could have this service performed in house by staff but there are many small vendors in my biotech/university/science community that will do it for us.

I met this guy at the bar. Or, maybe I recently ran into an old grad school friend. Some woman I postdoc'd with back in the day. A friend of my spouse. Whomever.

This person is starting up a brand new biotech support company, mom-and-pop kind of thing. This GenesRUs company is happy to take over our genotyping services.

I secure a quote. Wow. Two times the most expensive bottom line I came up with for doing it in-house that convinced me to hit the vendors in the first place. Maybe 3X the price of other locals.

But. But. This person is so nice. And we have a personal connection of some sort. Gee, they are still so small that they will come pick up from us at basically any time we want? And have results back prontissimo?

And you know. I HAVE the grant money. It isn't going to kill our budget to dump a few extra thousands on this top-cost option every year. Even if it amounts to tens of thousands, hey, it's just grant money, right?

The question, Dear Reader, is this.

Is it okay for me to use my PI's prerogative to spend my grant money this way? Just because I want to?

24 responses so far

23andMe resumes sales: Ancestry only!

Apr 30 2014 Published by under Ethics, Medicine and Law, Public Health

Well this is interesting. After being spanked by the FDA for selling their services without proper review and approval of their medical test (as the FDA interpreted it), the 23andme company is back.

I received an email spam suggesting I purchase one of their kits as a Mother's Day present.

Intrigued, I see this in an alert banner across the linked page.

23andMe provides ancestry-related genetic reports and uninterpreted raw genetic data. We no longer offer our health-related genetic reports. If you are a current customer please go to the health page for more information.

When you go to purchase a new kit you are obliged to check a box indicating you've read an additional warning.

I understand I am purchasing ancestry reports and uninterpreted raw genetic data from 23andMe for $99. I understand I will not receive any reports about my health in the immediate future, and there is no timeline as to which health reports might be available or when they might be available.

Ok. Got it.

So what about existing customers who purchased their kit in the old, pre-ban era? Guess I'd better visit that "health page".

Current 23andMe customers who received health-related results prior to November 22, 2013 will continue to have access to that information. However, no new health-related updates will be provided to your account.

Customers who purchased kits before November 22, 2013 will still receive
health-related results.

Customers who purchase or have purchased 23andMe’s Personal Genome Service (PGS) on or after November 22, 2013, (date of compliance letter issued by the FDA) will receive their ancestry information and uninterpreted raw genetic data. At this time, we do not know the timeline as to which health reports might be available in the future or when they might be available.

Customers who purchased kits on or after November 22, 2013 through December 5, 2013 are eligible for a refund. 23andMe has notified all eligible customers by email with refund instructions. If you are eligible and have not received an email, please click here.

Ok, so they are not turning off the results already provided to the older customers. If you fell into the cease-and-desist gap, you don't get your info (boo FDA) but you can get a refund.

In the mean time, 23andme is an ancestry / genealogy company.

I suppose that is it until they pass regulatory approval for their health and trait information?

20 responses so far

23andme and the Cold Case

By way of brief introduction, I last discussed the 23andme genetic screening service in the context of their belated adoption of IRB oversight and interloper paternity rates. You may also be interested in Ed Yong's (or his euro-caucasoid doppelganger's) results.

Today's topic is brought to you by a comment from my closest collaborator on a fascinating low-N developmental biology project.

This collaborator raised a point that extends from my prior comment on the paternity post.

But, and here's the rub, the information propagates. Let's assume there is a mother who knows she had an affair that produced the kid or a father who impregnated someone unknown to his current family. Along comes the 23 and me contact to their child? Grandchild? Niece or nephew? Brother or sister? And some stranger asks them, gee, do you have a relative with these approximate racial characteristics, of approximately such and such age, who was in City or State circa 19blahdeblah? And then this person blast emails their family about it? or posts it on Facebook?

It also connects with a number of issues raised by the fact that 23andme markets to adoptees in search of their genetic relatives. This service is being used by genealogy buffs of all stripes and one can not help but observe that one of the more ethically complicated results will be the identification of unknown genetic relationships. As I alluded to above, interloper paternity may be identified. Also, one may find out that a relative gave a child up for adoption...or that one fathered a child in the past and was never informed.

That's all very interesting but today's topic relates to crimes in which DNA evidence has been left behind. At present, so far as I understand, the DNA matching is to people who have already crossed the law enforcement threshold. In fact there was a recent broughha over just what sort of "crossing" of the law enforcement threshold should permit the cops to take your DNA if I am not mistaken. This does not good, however, if the criminal has never come to the attention of law enforcement.

Ahhhh, but what if the cops could match the DNA sample left behind by the perpetrator to a much larger database. And find a first or second cousin or something? This would tremendously narrow the investigation, wouldn't it?

It looks like 23andme is all set to roll over for whichever enterprising police department decides to try.

From the Terms of Service.

Further, you acknowledge and agree that 23andMe is free to preserve and disclose any and all Personal Information to law enforcement agencies or others if required to do so by law or in the good faith belief that such preservation or disclosure is reasonably necessary to: (a) comply with legal process (such as a judicial proceeding, court order, or government inquiry) or obligations that 23andMe may owe pursuant to ethical and other professional rules, laws, and regulations; (b) enforce the 23andMe TOS; (c) respond to claims that any content violates the rights of third parties; or (d) protect the rights, property, or personal safety of 23andMe, its employees, its users, its clients, and the public.

Looks to me that all the cops would need is a warrant. Easy peasy.

h/t to Ginny Hughes [Only Human blog] for cuing me to look over the 23andme ToS recently.

18 responses so far

PLoS Genetics blew it by publishing a 23andme paper

Feb 21 2013 Published by under Ethics

As you know, the Boundary Layer blog and citizen-journalist Comradde PhysioProffe have been laying out the case for why institutionally unaffiliated, crowd funded ostensibly open science projects should be careful to adhere to traditional, boring, institutionally hidebound "red tape" procedures when it comes to assuring the ethical use of human subjects in their research.

I raised the parallel case of 23andme at the get go and was mollified by a comment from bsci that 23andme has IRB oversight for their operation. Turns out, they too were brought to this by the peer review process and not by any inherent professionalism or appreciation on the part of the company participants.

A tip from @agvaughn points to a PLoS Genetics Editorial written concerning their decision to publish a manuscript from people associated with 23andme.

The first issue that attracted our attention was that the initial submission lacked a document indicating that the study had passed review by an institutional review board (IRB). The authors responded by submitting a report, obtained after the initial round of review, from the Association for the Accreditation of Human Research Protection Programs (AAHRPP)–accredited company Independent Review Consulting, Inc. (IRC: San Anselmo, CA), exempting them from review on the basis that their activity is “not human subjects research.” On the face of it, this seems preposterous, but on further review, this decision follows not uncommon practices by most scientists and institutional review boards, both academic and commercial, and is based on a guidance statement from the United States Department of Health and Human Services' Office of Human Research Protection (​idance/cdebiol.htm). Specifically (and as documented in part C2 of the IRC report), there are two criteria that must be met in order to determine that a study involves human subjects research: will the investigators obtain the data through intervention or interaction with the participants, and will the identity of the subject be readily ascertained by the investigator or associated with the information. For the 23andMe study, the answer to both tests was “no,” ostensibly because there was never any interpersonal contact between investigator and participant (that is, data and samples are provided without participants meeting any investigator), and the participant names are anonymous with respect to the data seen by the investigators. It follows from the logic of the IRC review, in accordance with the OHRP guidance documents, that this study does not involve human subjects research.

The journal should never have accepted this article for publication. I find no mention of ethics regarding the use of human or nonhuman vertebrate animals on their guidelines for authors page but it is over here on their Policies page.

Research involving human participants. All research involving human participants must have been approved by the authors' institutional review board or equivalent committee(s), and that board must be named in the manuscript. For research involving human participants, informed consent must have been obtained (or the reason for lack of consent explained — for example, that the data were analyzed anonymously) and all clinical investigation must have been conducted according to the principles expressed in the Declaration of Helsinki. Authors should be able to submit, upon request, a statement from the research ethics committee or institutional review board indicating approval of the research. PLOS editors also encourage authors to submit a sample of a patient consent form, and might require submission on particular occasions.

Obviously, the journal decided to stand on a post-hoc IRB decision that the work in question was not ever "involving human participants" in the first place. This is not acceptable to me.

The reason why is that any reasonable professional involved with anything like this would understand the potential human subjects concern. Once there is that potential than the only possible ethical way forward is to seek external review by an IRB or IRB-like body. [ It has been a while since I kicked up a stink about "silly little internet polls" back in the Sb days. For those new to the blog, I went so far as to get a ruling from my IRB (informal true, but I retain the email) on the polls that I might put up.] Obviously, the 23andme folks were able to do so......after the journal made them. So there is no reason they could not have done so at the start. They overlooked their professional responsibility. Getting permission after the fact is simply not the way things work.

Imagine if in animal subjects research we were to just go ahead and do whatever we wanted and only at the point of publishing the paper try to obtain approval for only those data that we chose to include in that manuscript. Are you kidding me?

Ethical review processes are not there only to certify each paper. They are there to keep the entire enterprise of research using human or nonhuman vertebrate animals as ethical, humane, responsible etc as is possible.

This is why hairsplitting about "controlling legal authority" when it comes to academic professionals really angers me. We work within these ethical "constraints" ("red tape" as some wag on the Twitts put it) for good reasons and we should fully accept and adopt them. Not put up with them grudgingly, as an irritation, and look for every possible avenue to get ourselves out from under them. We don't leave our professionalism behind when we leave the confines of our University. Ever. We leave it behind when we leave our profession (and some might even suggest our common-decency-humanity) behind.

Somehow I don't think these crowdfunders claim to be doing that.

A few more examples of why we need IRB oversight of human subjects research.
UC Davis Surgeons banned
Ethics of 2 cancer studies questioned [h/t: reader Spiny Norman]

37 responses so far

A little reminder of why we have IRBs. Did I mention it is still Black History Month?

Reputable citizen-journalist Comradde PhysioProffe has been investigating the doings of a citizen science project, ubiome. Melissa of The Boundary Layer blog has nicely explicated the concerns about citizen science that uses human subjects.

And this brings me to what I believe to be the potentially dubious ethics of this citizen science project. One of the first questions I ask when I see any scientific project involving collecting data from humans is, “What institutional review board (IRB) is monitoring this project?” An IRB is a group that is specifically charged with protecting the rights of human research participants. The legal framework that dictates the necessary use of an IRB for any project receiving federal funding or affiliated with an investigational new drug application stems from the major abuses perpetrated by Nazi physicians during Word War II and scientists and physicians affiliated with the Tuskegee experiments. The work that I have conducted while affiliated with universities and with pharmaceutical companies has all been overseen by an IRB. I will certainly concede to all of you that the IRB process is not perfect, but I do believe that it is a necessary and largely beneficial process.

My immediate thought was about those citizen scientist, crowd-funded projects that might happen to want to work with vertebrate animals.

I wonder how this would be received:

“We’ve given extensive thought to our use of stray cats for invasive electrophysiology experiments in our crowd funded garage startup neuroscience lab. We even thought really hard about IACUC approvals and look forward to an open dialog as we move forward with our recordings. Luckily, the cats supply consent when they enter the garage in search of the can of tuna we open every morning at 6am.”

Anyway, in citizen-journalist PhysioProffe's investigations he has linked up with an amazing citizen-IRB-enthusiast. A sample from this latter's recent guest post on the former's blog blogge.

Then in 1972, a scandal erupted over the Tuskegee syphilis experiment. This study, started in 1932 by the US Public Health Service, recruited 600 poor African-American tenant farmers in Macon County, Alabama: 201 of them were healthy and 399 had syphilis, which at the time was incurable. The purpose of the study was to try out treatments on what even the US government admitted to be a powerless, desperate demographic. Neither the men nor their partners were told that they had a terminal STD; instead, the sick men were told they had “bad blood” — a folk term with no basis in science — and that they would get free medical care for themselves and their families, plus burial insurance (i.e., a grave plot, casket and funeral), for helping to find a cure.

When penicillin was discovered, and found in 1947 to be a total cure for syphilis, the focus of the study changed from trying to find a cure to documenting the progress of the disease from its early stages through termination. The men and their partners were not given penicillin, as that would interfere with the new purpose: instead, the government watched them die a slow, horrific death as they developed tumors and the spirochete destroyed their brains and central nervous system. Those who wanted out of the study, or who had heard of this new miracle drug and wanted it, were told that dropping out meant paying back the cost of decades of medical care, a sum that was far beyond anything a sharecropper could come up with.

CDC: U.S. Public Health Service Syphilis Study at Tuskegee
NPR: Remembering Tuskegee
PubMed: Syphilitic Gumma

31 responses so far

Hey Cat Fans, LOOK! You too can be just as stupid as a dog owner!

Feb 13 2013 Published by under Day in the life of DrugMonkey, Ethics, FWDAOTI, Ponder

Apparently some epic dumbasses decided that the common housecat, bloodthirsty lethal little murder-cat killing machine that it is, wasn't quite badass enough.

What. Is. Wrong. With. People?

11 responses so far

The "absolute monarch" of Penn State University

Nov 09 2011 Published by under #FWDAOTI, Education, Ethics

If you want to understand the child molestation case that has rocked Penn State University in full, you need to read PhysioProf's take on the matter.

Joe Paterno–who has been the head coach for 46 years is the absolute monarch of that program, with absolute power. Regardless of whether he satisfied the bare minimum of legal requirements to report what he knew about the rape of children to his “superiors”–which as absolute monarch at Penn State, he really had none

emphasis added, but not really needed.

Go Read.

2 responses so far

What does a retracted paper mean?

crossposting from Scienceblogs.

I've been having a little Twitt discussion with Retraction Watch honcho @ivanoransky over a recent post in which they discuss whether a failure to replicate a result justifies a retraction.

Now, Ivan Oransky seemed to take great umbrage to my suggestion in a comment that there was dereliction in their duty to science to intentionally conflate a failure to replicate with intentional fraud. Per usual, we boiled it down to a fundamental disagreement over connotation. What it means to the average person to see that a paper is retracted.

I rely upon my usual solution, DearReader. Select all choices that apply when you see a retraction or that you think should induce a retraction.


Direct link to the poll in case you can't see it.

My position can be found after the jump.... Continue Reading »

16 responses so far

Letters of Rec

Jun 02 2011 Published by under Careerism, Day in the life of DrugMonkey, Ethics

If you write a letter of recommendation for an undergrad in your class that you barely know you are just diluting the value of such letters. Those who are deserving are having their efforts obscured by this practice.


41 responses so far

On negative and positive data fakery

Aug 22 2010 Published by under Ethics, Science Ethics, Scientific Misconduct

A comment over at the Sb blog raises an important point in the Marc Hauser misconduct debacle. Allison wrote:

Um, it would totally suck to be the poor grad student /post doc IN HIS LAB!!!!

He's RUINED them. None of what they thought was true was true; every time they had an experiment that didn't work, they probably junked it, or got terribly discouraged.

This is relevant to the accusation published in the Chronicle of Higher Education:

the experiment was a bust.

But Mr. (sic) Hauser's coding showed something else entirely: He found that the monkeys did notice the change in pattern—and, according to his numbers, the results were statistically significant. If his coding was right, the experiment was a big success.

The second research assistant was bothered by the discrepancy. How could two researchers watching the same videotapes arrive at such different conclusions? He suggested to Mr. Hauser that a third researcher should code the results. In an e-mail message to Mr. Hauser, a copy of which was provided to The Chronicle, the research assistant who analyzed the numbers explained his concern. "I don't feel comfortable analyzing results/publishing data with that kind of skew until we can verify that with a third coder," he wrote.

A graduate student agreed with the research assistant and joined him in pressing Mr. Hauser to allow the results to be checked, the document given to The Chronicle indicates. But Mr. Hauser resisted, repeatedly arguing against having a third researcher code the videotapes and writing that they should simply go with the data as he had already coded it.

So far as we've been able to tell from various reports, the misconduct charges are related to making up positive results. This is sounds quite similar to a whole lot of other scientific misconduct cases. Making up "findings" which are in fact not supported by a positive experimental result.

The point about graduate students and postdocs that Allison raised, however, push me in another direction. What about when a PI sits on, or disparages, perfectly good data because it does not agree with his or her pet hypothesis? "Are you sure?", the PI asks, "Maybe you better repeat it a few more times...and change the buffer concentrations to this while you are at it, I remember from my days at the bench 20 yrs ago that this works better". For video coding of a behavioral observations study, well, there are all kinds of objections to be raised. Starting with the design, moving on to the data collection phase (there is next to nothing that is totally consistent and repeatable in a working animal research vivarium across many days or months) and ending with the data analysis.

Pretty easy to question the results of the new trainee and claim that "Well, Dr. Joe Blow, our last post-doc didn't have any trouble with the model, perhaps you did something wrong".

Is this misconduct? The scientist usually has plenty of work that could have ended up published, but circumstances have decided otherwise. Maybe it just isn't that exciting. Maybe the project got partially scooped and the lab abandoned a half a paper's worth of work. Perhaps the results are just odd, the scientist doesn't know what to make of it and cannot sustain the effort to run eight more control studies that are needed to make sense of it.

None of this is misconduct in my view. This is the life of a scientist who has limited time and resources and is looking to publish something that is exciting and cool instead of something that appears to be pedestrian or derivative.

I think it would be pretty hard to make a misconduct case over quashing experiments. Much easier to make the case over positive fraud than it is to make the case over negative fraud.

As you know, this is something that regulatory authorities are trying to address with human clinical trials by requiring the formal recording of each one. Might it bring nonclinical research to a crashing halt if every study had to be reported/recorded in some formal way for public access? Even if this amounted to making available lab books and raw, unanalyzed data I can see where this would have a horrible effect on the conduct of research. And really, the very rarity of misconduct does not justify such procedures. But I do wonder if University committees tasked with investigation fraud even bother to consider the negative side of the equation.

I wonder if anyone would ever be convicted of fraud for not publishing a study.

14 responses so far

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