Via AiE&S, I found an article in the esteemed Chronicle of Higher Education discussing the prevalence of digital manipulation of figures in scientific articles. This is an issue of interest to be, because I’m something of an amateur digital manipulator myself.  For years I’ve taken part in online Photoshop contests, and even won small monetary prizes here and there for my efforts.  One of the reasons I do this (in addition to how much fun I have with it) is the potential for applying the skills I learn to my work.  Mostly by this I mean my web design hobby, but knowing your way around Photoshop really helps when making presentations or other science-related graphics.  The problem is that there is a very fine line between making something look nice and altering the scientific meaning.

Papers are starting to employ tools to look for digital tampering:

New tools, such as software developed by Mr. Farid, are helping journal editors detect manipulated images. But some researchers are concerned about this level of scrutiny, arguing that it could lead to false accusations and unnecessarily delay research.

I have to say I fall on the side of the “concerned researchers” here. In my experience, you tend to have two groups of people. There are those who understand image manipulation, its strengths and weaknesses, and when it can be appropriately implemented. Then there are others who don’t understand what’s going on and tend to think that if you even open your TIFF file in the program you’ve just sabotaged it’s scientific validity. I worry that we will end up with a situation of photoshop = bad, and that’s simply not true at all. As a matter of fact, the very description of the software being employed indicates that this is already the path we’re heading down:

The software looks for patterns in the digital code underlying an image. When files are opened and altered in Photoshop, for instance, codes are added that Mr. Farid’s software can detect.

I can hardly think of a single image I haven’t opened in such a program (I usually use The Gimp though).  Almost every figure needs at least to be cropped, have a label or two added, and saved out as different formats.  Does that mean every figure in my papers will be throwing up flags?

To be fair, it seems like the journals themselves are still taking a level hand for the most part:

So far the journal’s editors have identified 250 papers with questionable figures. Out of those, 25 were rejected because the editors determined the alterations affected the data’s interpretation.

10% rejection because of altered meaning seems to indicate that the vast majority of digital editing is not scientifically harmful.

And, as we so often see, Open Access may lend a hand in solving the problem:

One new check on science images, though, is the blogosphere. As more papers are published in open-access journals, an informal group of watchdogs has emerged online.

“There’s a lot of folks who in their idle moments just take a good look at some figures randomly,” says John E. Dahlberg, director of the division of investigative oversight at the Office of Research Integrity. “We get allegations almost weekly involving people picking up problems with figures in grant applications or papers.”

I’m not sure that I approve of the online witch-hunt oversight scenario this seems to set up, and this type of method won’t detect image tampering prior to publication (or at least online availability).

It’s a sticky problem, to be sure.  It’s clear that image manipulation programs allow for data falsification that is almost indetectable to the human eye, especially when done by an expert in the use of the software.  These same programs (and largely identical usage of the programs) can pull new scientific information out of otherwise useless images.  In my opinion, specific alterations should be mentioned in the figure captions.  I do this when I present figures at group meeting, for instance noting that I’ve adjusted contrast for easier viewing.  I wouldn’t mind in these cases a requirement to submit both images to the journal, so that they can judge for themselves the validity of the manipulation.  I just don’t want scientist to be discredited simply because they are trying to, with the best of intentions, improve communication of their findings.

I’m not a psychologist, sociologist, or anthropologist (as a matter of fact, I’m not any kind of -ologist), so today’s post might meander even farther from the realm of accuracy than is typical even on a normal day.

I’ve been thinking a lot lately about the issues of internet anonymity, rational discourse, and the psychology of the village (or small group if you like).  In my mind, there was a time in the not too distant past in which most people lived in relatively small communities.  Those inside the community were neighbors, friends, and family while those outside the community were strangers.  To this day we’re tought as children to mistrust strangers; they might try to hurt us.  As time has gone on, advances in communication technology have enlarged our “community” - that is to say the group of people with whom we can rapidly share news and information - more and more.  The largest community of all is the internet of course.

We are all familiar with the social buffoonery that takes place daily across the web.  We have new words for these actions - spamming, trolling, griefing, etc.  It’s the 21st century version of the stranger who comes into town and steals a sheep.  The problem is that on the web, we are all strangers to one another - there is no real community.  Sure, certain groups may congregate to certain web sites and forums (I think it’s clear that a certain self-selected personality type is in residence at Digg, for instance), but the members of that community don’t really know one another.  The flux of incoming and outgoing members, the ease of creating a new identity, and other similar factors mean that the community never settles down and becomes a wholly familiar environment.  I think that this factors heavily into the reason that negativity gets much more play online than positivity.  The posts in which I am more harshly critical tend to get more views and more commentary than those that are supportive.  Since (as for all bloggers, most likely) I enjoy knowing that someone is paying attention, this is a pressure to write more negatively, which I can’t say that I like.

Now I’ve said all of this while tangentially considering how this applies to the Open/Semantic/Social science movement.  Those who have spent any time around scientists can attest that there are already feuds and animosity amongst competing investigators.  My concern is that if a higher percentage of this interaction moves online, we’re likely to see a deepening of these divides.  The reason is simple: if two people argue during the question and answer session at a conference, they can still go out for a beer afterwards.  If two people argue on the internet, all they do is steam up and get more angry.

You can see this already from time to time around the more popular science blogs on the internet.  There is a certain acidity to the discourse that often seems to be amplified by a misunderstanding, overpersonalization, or overly vehement attack - all hallmarks of web discourse as a whole.  When discussing philosophical ideas or opinions this is fine, but I don’t know that it would better the advancement of science if we debated research findings in a similar way.

Don’t get me wrong, I don’t want to come off as a luddite who thinks that all scientific communiques should be sent via telegram (and I would hope if you’ve read any of my other posts you are aware that it’s quite the opposite).  My point is just that, as we push the practice of science more and more into the impersonal online arena, we should take pains to ensure that the discourse remains civil.

But this week’s show (Mistakes Were Made, episode #354) did include an attribution of their use of NIN’s music from Ghosts, an issue I wrote about some time back.

In reading my old post, I realize I probably came off as sort of a jerk.  It’s always weird to go back later, and see how you can write something while of one frame of mind and it ends up sounding like something quite different.  At the time I wasn’t really trying to call out the show for being music thieves, but truly didn’t know the answer to the question I was asking - the proper way to use the CC license that the work was released under.

Regardless of whether they were influenced by PlausibleAccuracy (yeah right), I’m glad that they added the attribution at the end of the show this week.  Also, it was a pretty interesting show this time… go listen to it.  And then (if you like) donate a dime or something to cover your bandwidth (freeloader).

Last night I was having a discussion with Mrs. PA.  She was worried that a paper she was writing (yes, it’s a two scientist household) was a bit long for publication.  I told her “Hey, I bet you can find an OA journal, such as PLoS One, that will not bind you to arbitrary page limits”.  I then launched into my (new and unpolished) sales pitch on why publishing in an Open Access journal would be better overall for the paper, and showed her some other papers in her field that have been published in PLoS One.  Then I came to the hard part - the increased page charges that she would have to sell her advisor on.  I mentioned that for PLoS One these come to $1250, which probably isn’t that much more than they would end up paying anyway to the closed-access journal they were thinking of publishing in.  Then I noticed a line on the PLoS site which stated that Institutional Members got a discount on top of this.  Not hoping for much, I went to the list of members, and lo and behold, our school was on it!  I’m really excited about this, because I think it will make convincing faculty to publish (in at least this particular OA journal) much easier.

I also learned that the University has put in place a support system for graduate students who lose their adviser.  If you read my 3-part post on misconduct, you’ll realize that this is very important to me.  I’m checking into it for more details, which I’ll probably write about later.  Unfortunately, the current policy on research misconduct investigations (dated 9/07) fails to mention students once, and is still chock full of the secrecy and careful political maneuvering that caused problems in the situation I was involved in.

The drug companies and health insurance companies provide a criticial service to the people.  They can act either in benevolent ways, ensuring that the most people get the best health care possible, or they can act like mafia extortion men, holding health and happiness hostage for ever-increasing amounts of money.  I think it’s clear which way they have leaned, especially in the recent past.

Case in point, this article from the New York Times.  It describes a practice that insurance providers have put into place, in which for specific drugs which are expensive, the insurance pays a percentage of the cost rather than everything above a limited co-pay.

From the article (emphasis mine):

No one knows how many patients are affected, but hundreds of drugs are priced this new way. They are used to treat diseases that may be fairly common, including multiple sclerosis, rheumatoid arthritis, hemophilia, hepatitis C and some cancers. There are no cheaper equivalents for these drugs, so patients are forced to pay the price or do without.

These are not “optional” drugs, nor is this a case of people choosing name-brand over generic because of some sense that they are better. These patients need these specific drugs to be healthy.  This policy has a terrible impact on people already struggling with serious diseases:

There must be a mistake, Ms. Steinwand said. So the pharmacist checked with her supervisor. The new price was correct. Kaiser’s policy had changed. Now Kaiser was charging 25 percent of the cost of the drug up to a maximum of $325 per prescription. Her annual cost would be $3,900 and unless her insurance changed or the drug dropped in price, it would go on for the rest of her life.

Of course the insurance companies sell this using a populist message: make the sick minority pay for their drugs, and your premiums will be lower.  Never mind that this goes against the very purpose of insurance.

I’m not quite sure who to blame here.  The drug companies are almost definitely overcharging for these drugs, based on a business model that relies on double-digit profit margins and advertising budgets that outstrip research budgets.  Insurance companies are literally parasitic, profiting by making America sicker.  The only real option is a comprehensive overhaul of health care, which I hope the next Administration can push through.

I mention in some of the background information on this site that I’m currently in the process of writing my thesis.  However, you won’t find this work-in-progress on any publicly accessible site.  Does that make me a big hypocrite?

Before jumping in, I’ll point out that some people do (rarely) write their thesis and academic publications online and in a raw sort of “as you go” style, although to be fair these are often researchers who are at the bleeding edge of open access.  See Pimm or UsefulChemistry for examples.  I’ve thought about doing this myself, and as someone who cares so deeply about advancing Open Access, why not?

(more…)

I’m an admitted NPR junkie.  I will listen to just about anything on the local station, although the quasi-religiosity of A Prairie Home Companion is starting to wear on me quite a bit.  My favorite show, however, is This American Life.  It’s pretty much a straight human interest show, with several stories each week based around some common theme.

This week’s episode, #352, was a bit different in that the entire episode concerned a single story; that of a kidnapping from 1912.  I don’t consider it one of their stronger episodes (the story itself didn’t interest me that much), but what did interest me was their choice for some of the music.

You see, I recognized it, because I had just bought the album - it was off of the NIN Ghosts set that I blogged about last week.  Now, I’m not 100% familiar with how these things work, but I do know that the album is governed by a Creative Commons BY NC SA license, which in plain English means that the work must be attributed, used non-commercially, and any derivatives must also use the same license.  This American Life, to the best of my knowledge, did not comply with these restrictions.

They don’t attribute the music (relying on their standard tagline: “Musical help this week provided by [staffers]“).  It’s a “commercial” work (debatably, considering it’s NPR), and although I’m not sure of what copyright the show employs, I doubts that it’s the CC-BY-NC-SA variety.

There are rules governing the usage of music in radio and advertising (a Google search turned up this book result).  The crux of the matter as it relates to the album is whether or not the radio show is a derivative work of the music.  What is interesting to me are the implications of the Creative Commons license/freedom of the original music and the interplay with the rules governing its use as music on a radio show.  Because the license permits remixes into an audio track, presumably this also includes something like a radio show.  This would seem to indicate (to me) that the show should then also be bound by the CC-BY-NC-SA license.  If, on the other hand, the producers of This American Life licensed the recording in the standard way for radio show music, then the issue isn’t relavant and I’m writing this all for nothing.

To me, the non-commercial section of the license is also critical.  If indeed the show producers licensed the music through the typical channels and then incorporated it into a commercial work, does that place their use of the album under a completely different copyright scheme?  Once NIN has released it under a CC license, are they allowed to selectively permit people to use their product in ways which do not adhere to the license?

All of these things will become more important as more and more artists release their work in a similar manner.  It may seem like pedantic nitpicking now, but that doesn’t mean that it won’t matter down the line.

You would think that potential employers would value honesty in their incoming candidates.  From my experience in the past several months of job hunting, however, this wouldn’t seem to be the case.  There is almost no faster way to be culled from the pool of applicants than to simply be forthright and straightforward about your own strengths and weaknesses.

Take a look at any interview advice column.  Every single one that I’ve read focuses on that odious concept of “spin”.  You should minimize talking about your weaknesses.  Always follow them up with how you overcome them or a strength that balances them.  Gloss over any rough patches.  It’s mild dishonesty in my opinion, and I don’t like it.

(more…)

This is the story of a scientific ethics incident. The names have been obscured, but the events are true. I know because I was part of the lab group it involves.

I’ll be telling this story in 3 parts, which I’ll link here when they are written.

Part One | Part Two | Part Three

Part Three: “What do we do now?”

The bombshell had dropped.  Dr. C’s students now knew that, within several months, their lab would no longer exist.  They still didn’t know why, and no one who knew was talking.   In addition to trying to make sense of what had caused this sequence of events, the lab members were now also thrown headfirst into a very practical concern: salvaging their careers as best they could.  In the end, the justification for the firing of Dr. C would be an ancillary issue.

For about a week or so, no one did much of anything in Dr. C’s lab.  They sent overtures to Dr. C in the form of letters and emails, which were met with little to no response.  The word was that Dr. C was distraught and angry, and couldn’t face the students.   Quickly they realized that they couldn’t wait for an explanation; it was time to go into damage control mode and recover as best as they could.

(more…)

This is the story of a scientific ethics incident. The names have been obscured, but the events are true. I know because I was part of the lab group it involves.

I’ll be telling this story in 3 parts, which I’ll link here when they are written.

Part One | Part Two | Part Three

Part Two: “There will be a meeting”

Months had passed since the computer incident of Part One.  Things in Dr. C’s lab had returned more or less to normal, with the day-to-day drudgery typical of research pushing aside any misgivings about what was going on outside of the lab.  There hadn’t been any further incidents to raise suspicion, so it was a case of “out of sight, out of mind” for those working in the lab.
(more…)