March 14, 2010
Category: Science Communication
This week a couple of my Sciblings have been abuzz about an article published in some journal I'd never heard of... a minor impact journal...the Journal of Who Gives a Fuck Science Communication. Bora has a great break down of some of the major criticisms. Drugmonkey, one of the subjects of the "analysis" in this article, is also displeased and critical of the author's conclusions.
I've
since read
the offending article and can only tell you this - I have no
idea what the balls the author is talking about. Seriously, this
article is about as informative as this:
Video 1: A current favorite at the Isis house. When emailed this video, PhysioProf
replied, " Couldn't they afford to animate some fucking legs on those
fuckers?" I have always wondered why Mr. Lunt has no eyes.But, for those of you who are still interested, here's the run down...
Inna Kouper,
a graduate student in Library and Information Science at Indiana
University, somehow magically chose 11 blogs to study, one of which was
Pharyngula. Now, I'm not hating on Pharyngula. PZ plays an important role in the blogosphere and, while I think that sometimes
his commenters get out of control,
he's got a unique voice and an uncanny ability to rally the troops. No
one can deny that the climate at Pharyngula is not necessarily
reflective of the entire blogosphere. Still, the fact is that Inna
Krouper sampled 11 blogs. There are 80 blogs currently at
ScienceBlogs, 8 more at Discover Blogs, and a bazillion independent and
network blogs indexed by the Nature Network. Yet, somehow Inna chose
these 11 blogs as representative of the genre and one of them was
motherfucking Pharyngula. Then, she did this:
A
combination of quantitative and qualitative techniques of content
analysis has been used in this study. The qualitative analysis
involved iterative close reading of posts and comments with the purpose
of identifying common types of statements and activities
conceptualized as modes of participation. This conceptualization was
informed by the speech act theory and the pragmatics perspective yet it
was purposefully left rather loose and open to allow for the categories
to emerge from the data. Each time a mode of participation was
identified, it was entered into a catalog, and then a post or a comment
was assigned a corresponding code. Along with the modes of
participation, the posts were coded for topics and sources of the post;
the comments were coded for the reader's identification elements (e.g.,
a nickname, first name, full name, link to blog, or blog author).
Subsequently all codes were counted and the analysis proceeded with the
examination of the most frequent and rare patterns and their groupings.
Translation?
Figure 1: Inna sat down one night, read some blogs, and then wrote some shit. She must really be itching to finish the ole thesis.I
mean, I truly am baffled by these methods, especially when the author
brags that "it is necessary to analyze current practices of science
blogging. To date no attempts have been made to do that. The present
study is the first step in this direction." This article is a step
alright...
Figure 2: Problem is, none of realize where that step is taking us until it is too late to unlearn the stupid.I'm
just plain ole disappointed by the "methodology." This author could
have taken the opportunity to perform a carefully controlled study with
randomly-selected non-scientists. She could have shown them blinded
content and administered questionnaires. Instead she wrote 10 pages of
opinion and passed it off as science.
After pages upon pages of presenting cherry-picked content, Inna concludes this:
Science
blogs examined in this study are very heterogeneous. They provide
information and explain complicated matters, but their evaluations are
often trivial and they rarely provide extensive critique or articulate
positions on controversial issues... It appears that science blogging
can also be characterized as relying on reductive analysis and
dependent reporting and drawing caustic and petty commentary. These
characteristics may as well be applied to the newspaper and magazine
science communication, but with the newer science communication outlet
such as blogging they indicate that the potential of blogging to do
something differently, e.g., to provide informed expert and citizen
commentary, is not realized. In their current multiplicity of forms and
contents science blogs present a challenge rather than an opportunity
for public engagement with science. Lack of genre conventions, which
for the audience translates into broken expectations and uncertainty,
impedes the development of stable readership and participation from the
larger public, which may also be very heterogeneous. The "neighborhood
bar" or "water cooler" commentary creates a sense of community with
shared context and culture, but at the same time it creates a barrier
that prevents strangers and outsiders from joining the conversation. As
a community of scientists or individuals close to science, the
existing readers may enjoy the entertaining nature of science blogs and
not need science blogs to serve as a place for discussion and rational
debate. Relying on such community of readers, bloggers may reduce their
interpretive activities and resort to copying, re-distributing, and
re-packaging of the existing information, which is still quite
rewarding given the background of the majority of current readers and
yet requires much less time and effort. This study provides further
evidence that blogging as a web tool has no magic properties on its
own. Without a concerted effort of different social actors involved it
will not solve any problems...
Reading this, I
realize that I did my PhD in the wrong damned field. I would be a much
more prolific publisher if I had entered a field where I could have
written whatever bullshit moved me on any given day and called it
"research."
I also wonder how many of you feel like you
simply add "caustic and petty commentary"? I question how Inna can
conclude that blogs pose a barrier to the conversation. That's a
difficult statement to take seriously, knowing that Inna had no access
to traffic data for any of the blogs she read. For me, I know that a
single blog will be read by 1000s more non-scientists than any original
scientific article I publish in a peer-reviewed journal. And, she
certainly wouldn't have found the analysis trivial if she had read some
of
Ed Yong or
Carl Zimmer's work, not that I find any of the blogs she included trivial. Then again, I think it is the diversity of voice is what makes the blogosphere so beautiful.
My
sample size = 1 is probably no better than Inna's sample size = 11, but
I can at least offer my experience to the data set. I get many letters
a week from young people interested in science careers and soliciting
advice on graduate school, fields of study, and professional
development. The number of people who have come to my office in person
to have these conversations is trivial in comparison. Thus, these data
would lead me to conclude that my blog presence has lowered the barrier
to engagement with this audience.
I'll also never forget one of the occasions,
quite a while ago, that I wrote about some novel research. It was a
topic semi-related to my expertise. One of you then went to PubMed (or
some other search engine) and called bullshit on me by citing some of
my lab's own work. It was glorious and I was proud of my scrappy
little muffins for months.
Inna does not take in to account the
benefit of blogging for the blogger. First and most importantly,
blogging is hilarious. I have met some tremendous people in the
blogosphere who have become valuable resources. I use a lot of the
folks here to bounce career ideas off of and I have met scientists that
are using techniques that I might not have considered. I suspect that
it is because of blogging that I am now totally bff with my academic
society. I might never have been noticed if I hadn't taught Marty
Frank the word "cocknozzle." Finally, blogging has allowed me to forge
some professional relationships that might not otherwise have been
available to me. I feel fortunate that MRU will eventually be a stop
on
Rebecca Skloot's
book tour.
Many of the people in the administration here were both thrilled and
surprised that anyone had contact with her. I only know her because
we're both kick ass, totally hot bloggers.
I'm not going to
take this article too seriously. I am, however, going to challenge
academic researchers to think more critically when they assess the
blogosphere. As scientists, we have access to an extensive toolbox and
a multitude of metrics that could be used to evaluate the impact of the
blogophere, without having to rely on Inna Kouper's poorly-organized,
half-assed ramblings as the first "scientific analysis."
Surely, we can do better than that. I mean, even this is a more honest analysis..
Figure 3: Joseph Hewitt's comic interpretation of the ScienceBloggers. That's Dr. Isis in the top panel putting the choke hold on some dude and calling him a "muppethugger." For the full-sized image, hilarious commentary, and clues to who's who in the 3rd panel, click over to Joseph's website. Man, Ed Brayton is one ripped, muscley dude!
Additional Reading
Inna Kouper (2010). Science blogs and public engagement with science: practices, challenges, and opportunities Journal of Science Communication, 9 (1)
Posted by Isis the Scientist at 11:19 PM • 3 Comments • 0 TrackBacks
March 12, 2010
Category: Ask Dr. Isis • Science Careers
If you've been following the Twitter, you've seen that viruses and bacteria continue to colonize the Isis house. We're basically fighting mutations of a plague we picked up in January. I'm going to shake it. I really, really am. If I don't fully recover in the next few days, I am going to consider autoclaving my house and just starting over.
Figure 1: An artist's rendition of Casa de Isis on this upcoming Sunday.
It's been strange to be away from blogging for several days. I think this is the longest amount of time I have gone sans post. So, I'm going to ease my way back in slowly with an email from one of you lovely little muffins. I have been so terribly neglectful of you all.
Reader Bella PhD writes...
Dear Dr. Isis,
I have pretty much read every single word you have ever written as I am addicted to you and your blog and everything you write. I love love LOVE your blog, your writing style, your raw honesty and your pure desire to help eradicate sexism and misogyny, one step at a time. [This letter is starting strong...]
Plus you have hot shoes and I have to tell you, I have slowly been evolving from tom-boy to semi-girl over the past few years and you are the reason I bought my first pair of heels (a pair of Naughty Monkeys, in case you were wondering) :)
I have a question for you - I know you came to academia from industry and I was hoping you may be able to help me.
I originally went into my PhD thinking I wanted to be a faculty member and nothing else. Last few years of my PhD showed me enough horrors that I started to have doubts about wanting a faculty position - at least not for now, and maybe not ever.
I started a postdoc because my advisor refused to write me recomm. letters for a non-academic job because he thinks it would be such a huge loss to science if I left academia (he's usually a good guy, but he has his "I know best moments"!). Anyway, I am about 5 months into my first postdoc and absolutely miserable. My PI not involved, I work directly with a Res Prof (RP) who works with my PI, so I am only in contact with the RP. And RP is the most obnoxious, sexist, manipulative, patronizing person I have ever met (he treats everyone like this, not just me), and I am even more miserable now than I was in grad school (and I never even thought that was possible, so that's saying something!!). And the icing on the cake, he belittles my ideas and tells me how stupid they are, only to go around and modify a tiny angle and re-suggest my ideas as "his". Plus, I constantly get to hear that all papers produced from the lab result only from his brilliance idea, but because of the flawed system, he is robbed of being first author and it goes to us lowly postdocs.
And yes, I did ask the right questions in the interview - I was interviewed by PI, asked all the right questions and did the research about PI, about whom everyone could only rave.. and was surprised to learn when I started that I was not working directly with the PI. And no, talking to the PI about RP will not work - others before me have tried extensively, and I have tried briefly, but in PI's eyes, RP can do wrong and it is all our fault!
This is the only major research uni in the vicinity, and I can't go looking for a postdoc elsewhere in the univ as they all collaborate with each other and if I leave, I'd still have to work with him, only then he would hate me and I have seen what he does to people he hates - I don't even want to attempt that.
And I can't leave the area I am currently in as because of my husbands work - we are stuck here for at least 2.5 years while he wraps things up.
Anyway, the bottom line is, I want out of my current postdoc. I figure I can spend the "postdoc years" in industry, and if/when the horrors of the past few years ever fade, I may return and apply for a faculty position, but that's definitely not the path I want to be on right. So the point of all this rambling is... how does one goes about searching for a job in industry? I have no idea how to go about it and could use ANY advice you could provide, either from your experience or from others you know
Thanks so much!
Bella
First, a bit of a disclosure. I have confess that the entire time I was reading Bella's letter, I kept thinking about this:
Read on »
Posted by Isis the Scientist at 2:39 PM • 17 Comments • 0 TrackBacks
March 8, 2010
Category:
I have a bazillion things to do tonight, including a real blog post to write...
...but then Hathor texts me "EMERGENCY!! Bring your makeup kit."
Really, what is s girl to do? Clearly, I must rescue Hathor.
Posted by Isis the Scientist at 8:11 PM • 7 Comments • 0 TrackBacks
March 6, 2010
Category: Blogrolling
...or something like that.
Last night as on the way home, as a bit of "something for Mommy" after several night of middle of the night albuterol for Little Isis, I went and bought myself an iPhone.
Now, you have to understand what a big step this is for me. I have been carrying a 4 year old, pirated Go Phone that did pretty much nothing but make calls. I had pretty much convinced myself that I didn't need no stinkin' interwebz on my phone.
Now,
get offa my lawn!
But something in the last two days has come over me and I have become convinced, for no apparent reason, that I needed an iPhone. I didn't have iPhone envy. I did have a little bit of "can't find my little tiny phone" frustration. What was the first thing I did with my iPhone? I took a picture of some
Cadbury Creme Eggs I had bought earlier in the day. Those little things are my favorite.
I then called my friend and lamented to her that I secretly wished our Lord and Savior had been crucified several times throughout the year so that I could get Creme Eggs all year long. She accused me of
blasphemy. She's probably right.
Then I read one of my new favorite blogs,
The Problem With Young People Today Is... Seriously, this dude is hilarious. In a recent post, he described the things things that old better are better at than young people. Here's my favorites from the list:
Serve in the U.S. Senate
When was the last time you saw a damned teenager serving in the U.S. Senate?
I'll tell you when - never! And that's because everyone with a lick of sense
knows that if you want to run a decent society you need to populate your
governing bodies with nothing but really old white men.
Bake
My old mom could take two wormy apples, some turned lard, a handful of spice,
a ball of knotted twine and an old newspaper and turn it into the most delicious
homemade pie you've ever tasted. Young people? If it involves anything more
complicated then combining cake mix with cannabis and then stuffing it in an
Easy Bake oven, they'd burn the house down.
Write a letter of
Complaint
Young people today lack the vocabulary, backbone and brains to write anything
more than an inarticulate, half-assed flaming outburst in a moronic chat room. A
decent letter of complaint is a powerful tool and one that requires mental
agility, discipline and liberal use of phrases like "road apples" "balderdash"
"hooey" and "gumption."
Select Appropriate Pets
Iguanas, ferrets, snakes and rats aren't pets - they're vermin. In my day
people didn't invite them into our homes and make them a part of the god damned
family - we clubbed them with sticks, pelted them with rocks and used them as
ingredients in our delicious homemade pies.
I trust I've made my point, damn it.
This guy is one seriously funny, cranky old dude. And, I can tell that this iPhone is going to get a lot of use for things like taking picture of random shit that you all don't really want to see, and reading hilarious blogs. Huzzah for technology!
Posted by Isis the Scientist at 1:26 PM • 28 Comments • 0 TrackBacks
March 5, 2010
Category: Lovely Sciblings
Did any of you see Ed Braytonon Rachel Maddow? He was glorious!! Here's the clip that just includes being famous and amazing:
The full video of the segment, including the context of Ed's comments, can be found here. Also, here's Ed's hilarious post about the experience.
Posted by Isis the Scientist at 9:53 AM • 7 Comments • 0 TrackBacks
March 4, 2010
Category:
So this afternoon the little dude coughed himself blue. We took him to our friendly neighborhood physician and it turns out the little guy has pneumonia.
Balls.
Not pneumonia of the balls. Just, well, balls.
Posted by Isis the Scientist at 9:52 PM • 24 Comments • 0 TrackBacks
Category:
Having a sick child really sucks hard. I don't know how I am going to function tomorrow and be alert for students.
He's asleep next to me, but talking like Swiper the Fox.
I don't have any hilarious pictures for this.
Posted by Isis the Scientist at 3:00 AM • 10 Comments • 0 TrackBacks
March 3, 2010
Category: Motherhood • Science Careers
The other day I was having a lovely email conversation with Arlenna from ChemicalBilology. Arlenna recently had a beautiful new baby and is at the point where she is thinking about returning to work. Part of returning to work post-spawning is finding suitable childcare for your favorite little diaper dirtier. Go read Arlenna's post about looking for daycare and her experience with the university-based daycare system. I assure you that you will not be disappointed. Arlenna has "photo chopped" an image a la Isis, because I told her I thought university-based daycare "may be a fantasy, like unicorns and fairies ". Arlenna is hilarious.
Below the jump, I'll tell you about my own experiences. But, before we go any further, I'd like to invite anyone who wants to try their Photoshop skills to submit their Photoshop interpretations of university-based daycare to me for posting via isisthescientist at gmail dot com. This could be good for more than a few giggles...
Read on »
Posted by Isis the Scientist at 4:43 PM • 39 Comments • 0 TrackBacks
March 1, 2010
Category: Peer Review • Physiology
Last week I attended the International Stroke Conference in San Antonio. Scientifically, it was a very interesting conference. It was extremely clinically oriented, with heavy emphasis on the outcomes of clinical trials.
The session that I found the most interesting was a debate on the surgical closure of a cardiac structure called the foramen ovale in patients who have had a cryptogenic, or unexplained, stroke. You folks know how much Mama loves the heart and I was happy to see a bunch of brain-loving folks show a little love for my favorite organ. What was so fascinating about this discussion was that it was completely apparent that this is an area in which medicine is operating unguided by science. In fact, most of the real "evidence" for surgically closing the foramen ovale comes from a bunch of little pearls of data, strung precariously together by a lot of dudes with opinions, and renamed as "evidence."
Figure 1: Science-based medicine be damned! Also, never Google the phrase "pearl necklace" in an attempt to be hilarious without your safe search on while sitting in a crowded airport. The look you'll get from the woman sitting next to you will not be hilarious.
So, given that recommendations are currently being made about this procedure without clear, randomized and controlled trials, I thought I'd review what we know about this surgical procedure and its effectiveness in preventing the recurrence of stroke.
What is a patent foramen ovale?The foramen ovale is a normal flap-like opening between the right and left atria found in the developing fetus that allows blood to bypass the lungs in utero. Here's how blood flows through the heart in most of us:
Figure 2: This is a figure I gave to PalMD last year when he was writing about Great Vessel Transposition.
- Oxygen poor blood returns from the body and enters the right atrium
- Oxygen poor blood passes from the right atrium to the right ventricle. The
right ventricle then pumps the oxygen poor blood into the pulmonary
artery. Sometimes people are confused by the pulmonary artery because most
people think of arteries as having oxygen rich blood. The true definition of
"artery" is any vessel that takes blood away from the heart.
- Oxygen poor blood from the pulmonary artery travels to the lungs where
the oxygen is replenished.
- Oxygen rich blood returns from the lungs and enters the left atrium
- Oxygen rich blood passes from the left atrium into the left ventricle. The
left ventricle then pumps oxygen rich blood into the aorta.
- Oxygen rich blood from the aorta is then circulated through out the body.
The oxygen is utilized and the blood becomes oxygen poor. Return to step 1 and
begin the cycle again.
In the developing fetus, there is no need to send blood to the lungs to be oxygenated. Blood is oxygenated by the placenta and returns to the heart with generally as much oxygen as the fetus needs. So, much of the blood that enters the right atrium passes through the foramen ovale to the left atrium. It is then pumped out to the rest of the body.
Figure 3: My favorite PFO picture. See the flaps on either side of the opening? At birth those overlap and close the foramen ovale.At birth, when the baby takes its first breath, the foramen ovale closes. When the foramen ovale fails to close, we call it "patent," or "open." Hence the phrase, "patent foramen ovale." In many people, the foramen ovale seals completely and disappears within the first year of life. Except, that it doesn't completely close in all of us. Data from autopsy studies performed in 965 postmortem patients indicate that 34% of people under ge 30 and 25% of people between 30 and 80 still have their foramen ovales. The incidence may actually be higher. In my laboratory, five of us have had our hearts examined by
echocardiogram and four of us have patent foramen ovales. My personal patent foramen ovale is really hot.
Figure 4: A foramen ovale in an adult heart at autopsy.Why Could My Patent Foramen Ovale Put Me At Risk For Stroke?
Many of us know that the lung is important because it delivers oxygen to and removes carbon dioxide from our blood, but it is also a very important filter. All of our deoxygenated, or venous, blood passes through the lung. Blood clots that form in veins get trapped in blood vessels in the lung and are prevented from lodging in other important organs, like your brain. Indeed, the lung is like a huge fishing net for blood clots. Immune cells in the lung can clear small clots. A larger clot can cause a
pulmonary embolism (but that's fodder for another post, really).
Theoretically, having a patent foramen ovale provides a route by which blood clots can bypass the lung filter, directly enter the left side of the heart, and travel to the brain.
Several small studies have shown slightly
increased incidence of
patent foramen ovale in patients with unexplained stroke. However, and this is important, not everyone with a patent foramen ovale has a stroke. Also, current data suggest that patients who have a patent foramen ovale and have had a stroke are at
no higher risk for
a second stroke than than
patients who do not have a patent foramen ovale.
What Are Some Doctors Currently Doing?There are currently devices on the market that are approved for repair of congenital defects (ie, holes) of the atrial septum. These repairs are frequently performed in young children and the devices are being
used off-label to close patent foramen ovales. In children having heart defects repaired, these devices are surgically implanted in the holes and the heart tissue grows over them to repair the defect. Here's a great video of one of these devices being placed in a defect between the ventricles:
Video 1: This is a device called the Amplatzer. I like how smoothly the placement goes in the video.Why Shouldn't We All Have Our Foramen Ovales Closed?Simply, because we don't have data from randomized, controlled, clinical trials to assess the safety or efficacy of the closure in adults. What we do know is that the potential risks are important. For example:
Figure 5: The bottom panel of this figure (from here) shows a device that has separated from the repair site. And...
Figure 6: This image (from here) shows blood clots in the left atrium after the placement of one of these devices.We have no idea how often these complications happen or what the long-term outcome for patients with these devices really is. All we know is that there are physicians who are currently recommending closure of the foramen ovale to patients deemed to be at "high risk for a stroke". In fact, at the conference I attended where I saw the discussion on PFO closure,
Dr. Aimee Armstrong presented a (dare I say) inappropriately, emotionally-charged presentation entitled:
No Need to Wait for Data, PFO Closure Is Here to Stay. No need to wait for data? The apparently thesis of her talk? "We're already doing it, so go big or go home."
Figure 7: Foramen ovale closure at Dr. Armstrong's institution comes with this complementary tattoo. At intervals during the surgery, the nurses stop to cheer, "We don't need no stinkin' data." All of this in the face of this statement from Dr. Norman Kato, an expert on the
FDA's Circulatory System Devices Panel who recommended the FDA require randomized controlled trials for devices:
There is insufficient evidence for effectiveness of either surgical or
endovascular closure of PFO in the face of cryptogenic stroke. The day that we can say that this is no longer a 'cryptogenic'
stroke but a 'PFO-related' stroke will be the day that I can say, yes, let's go
ahead and close that PFO. Otherwise . . . this is a device trying to make the
anatomical defect a part of the disease process and in fact in should be just
the reverse. The science should be there that conclusively establishes the
causation link between the anatomic defect and the clinical outcome: then and
only then can you go ahead and create devices or medical therapy or some other
type of therapy to test whether that is safe and effective.
So, What the Hell Are We Doing?Balls if I know, folks. Balls if I know. The FDA and
scientific experts are demanding randomized, controlled trials. There is currently a randomized, controlled clinical trial (the
RESPECT trial) being conducted on the outcome of folks with surgical foramen ovale closure, but in some cases it seems to be being sabotaged by our own. There is money to be made by device manufacturers, many physicians see a plausible connection between foramen ovale and stroke, and helplessness is a scary thing. Because people are already having their foramen ovales closed off-label by cardiac surgeons (and probably cardiologists and interventional radiologists), and insurance companies are paying for it, patients are opting for closure rather than participation in the trial. I wondered to myself during the meeting how that might bias the trial data. It's clear, however, that there is a large subset of physicians who are going to keep doing something rather than do nothing - even though we don't know whether that something is beneficial for the patient.
Stroke is a frightening condition that is frequently associated with the loss of speech, motor function, and a serious decline in the quality of life. That motivates many to act. However, continuing to close the foramen ovale without sufficient data on outcome, especially in the face of week supporting evidence, is unequivocally the wrong action to be taking.
Additional Reading
Mas, J. (2001). Recurrent Cerebrovascular Events Associated with Patent Foramen Ovale, Atrial Septal Aneurysm, or Both New England Journal of Medicine, 345 (24), 1740-1746 DOI: 10.1056/NEJMoa011503Homma, S. (2002). Effect of Medical Treatment in Stroke Patients With Patent Foramen Ovale: Patent Foramen Ovale in Cryptogenic Stroke Study Circulation, 105 (22), 2625-2631 DOI: 10.1161/01.CIR.0000017498.88393.44Tong, D. (2004). Patent Foramen Ovale and Recurrent Stroke: Closure Is the Best Option: No Stroke, 35 (3), 804-805 DOI: 10.1161/01.STR.0000117964.10781.BA
O'Gara, P., Messe, S., Tuzcu, E., Catha, G., & Ring, J. (2009). Percutaneous Device Closure of Patent Foramen Ovale for Secondary Stroke Prevention: A Call for Completion of Randomized Clinical Trials: A Science Advisory From the American Heart Association/American Stroke Association and the American College of Cardio Circulation, 119 (20), 2743-2747 DOI: 10.1161/CIRCULATIONAHA.109.192272
WEBSTER, M. (1988). PATENT FORAMEN OVALE IN YOUNG STROKE PATIENTS The Lancet, 332 (8601), 11-12 DOI: 10.1016/S0140-6736(88)92944-3
Posted by Isis the Scientist at 10:58 PM • 33 Comments • 0 TrackBacks
