Humans in Science

In this lovely house we rent in Toulouse, there is an in-ground greenhouse with numerous old rose varieties. The damasks and the bourbon roses are remarkably perfumed. I made a gorgeous bouquet this week with a number of these, a couple sprigs of white lilac and some snapdragons.

Grr. I went to the trouble of taking a photo of it, editing it on my computer and trying to upload it, to find out that I can’t for some reason. Well, I’ll take the long way around.

So I was sent some suggested reading from a colleague (”for the beach” quoth he, though I’ll be going to the misty mountains to join my husband for the second long weekend in May so far) in PNAS, and was drawn instead to “Scent evolution in Chinese roses“.

My compliments for a simple title. The article is not, but is a great example of cross-disciplinary fertilization. These are some of the folks who did the work. I see that Roger Highfield did the work of breaking down the results to make them digestible to a public audience as soon as it came off the feed.

Myself, I really appreciated the mix of genetics, bioinformatics, plant biology, crystallography, chemistry and enzyme kinetics. However, I don’t seem to have any tea roses blooming right now (not sure there are any in the garden), so I’ll have to settle for the “floral-fruity character with a plum-like shading” of beta-damascenone, which is tantalizing to the point of making me salivate. Before moving here, I would not have qualified myself as a rose enthusiast.

I’m quite pleased to have been invited to give a talk on neural crest cell development at this course for M.D. and Ph.D. students near Bologna, Italy. It will be in English.

If you are interested by the program, it is possible to sign up for live webcasting for a fairly modest fee - unless your institution pays in dollars - and to recover copies of the speakers’ talks, as well. Click here, then go to Courses, then Hybrid Courses (in the left sidebar) to read more about this option. I think it is cool that I will be taking questions live from Croatia.

The program seems to a very interesting one in medical developmental biology with speakers I’d really like to hear. How do congenital birth defects happen, and what is the role of genes in their occurrence? Unfortunately, as it goes the whole week of May 12-15th, and I have another course to give in Paris on May 15th, I’ll only stay through Tuesday. The Paris trip will also be the opportunity to prepare our poster for the ISSCR with my postdoc.

If you also happen to be in Philadelphia in June, and are interested in stem cell biology, you should sign up for the Public Symposia. These also seem to have very worthwhile speakers and are a laudable effort for public communication about stem cell research. And if you do that and leave me a comment, I’ll buy you a drink.

I actually posted this yesterday but accidentally created a “page” rather than a post. Hope all the links carry over.

Shoutout to Ben Goldacre from The Guardian, who regularly debunks bad science in the popular media.

Dr Badylak is Acell’s chief scientific adviser, and he can be seen bravely making the best of all this unwelcome media attention by showing TV cameras around his labs and giving lengthy interviews, both now and in February 2008, when this story made the US news, and also, interestingly, in February of 2007, when it made the news for the first time, in exactly the same form, with exactly the same characters, and many identical quotes, verbatim, in the Wall Street Journal, MSNBC, and more. The injury itself, meanwhile, apparently happened (and healed) way back in 2005.

Reconstructing the media frenzy, it all seems to have kicked off - this time around - with BBC New York correspondent Matthew Price doing a very credulous set of interviews that went live on the BBC site on Wednesday at 3pm.

He nods endlessly and says “that’s astonishing” when the company founder’s little brother tells him that the tip of his finger healed. In the computer animation used by the BBC [1m10s into this video, I really recommend you watch it], a finger miraculously grows back more than half its length, at least two joints worth. At 11:30pm that same day the Press Association put out a story, but the newspapers must have had it sooner for the next day’s papers, so I guess they lifted it from the BBC, too. By May Day 3:30pm the story was on Fox news (their morning), and by 11:30pm it hit ABC Australia. All used the same quotes in different permutations. And that’s how news works.

Ben makes an audio plea for specialists to vet this sort of story and point out the obviously wrong or idiotic aspects of it before it hits the newsstands. I doubt it will happen, since deadlines are so tight for “breaking” news, but I’d be glad to furnish that kind of expertise in an ad hoc manner.

I now am using Wordpress version 2.6 - bleeding. Whatever that means for you and me, aside from a slightly different graphical interface, and access to stats once more for me.

For your delectation, here is a guide to translating scientific papers into accessible English for the layperson. It follows on a long discussion of publishing and editing that can be observed here.

In our family, we sometimes play a game called “Petit Baccalaureate” or “Petit Bac”. I’m sure it exists in English, but it’s commonly played in France. My 8-year-old daughter sometimes gets a 1.5x handicap.

Here are the rules: two or more players (the more the better) with a piece of paper and writing utensil each. Choose a series of themes: first names, animals, plants, places, football payers… in the columns. One player recites the alphabet silently and the next says “stop” to choose a theme letter. Everyone must find and write a word (name) beginning with that letter in the language you’ve chosen. The first who finds one for each category, calls out “stop” and everyone compares answers. No answer = 0 points, a shared answer = 1 point and a unique answer = 2 points. Play until your youngest player gets bored and tally up.

When you’re playing in English and need some animals that start with X, have a look at this page before starting the joust.

Northern Spain was quite lovely and an adventure, but I won’t likely have time to post photos or whatnot until I get back from this upcoming weekend in the Pyrenees. My husband is really addicted to mountains. I have a course to prepare for the following Monday, for which I need to get slides in by this Wednesday, and another the following Thursday, so posts may be few and far between in the near future.

The only reason anyone enjoys April in Paris is because it beats the five-minute samples of every weather under the sun that you undergo in March.

Every time I stepped outside the last two days, I got drenched. It was disheartening.

Got a lot done, though, in the Paris lab. Since I came for once on a Monday, I met first with my student, who is wrapping up her experiments and is at a point where she picks good things to do all by herself and teaches me about her technical approach; then I reviewed the data from our lab tech for an experiment she had conducted for a long-running collaboration with a group studying pituitary development. There was a department seminar which might have been interesting had my time not been so limited, but it put a nice bracket on these discussions and allowed me to get some lunch and check my e-mails.

Just after we had launched the last experiment, that group got scooped - it was to add some functional data to a mutation they had found in a gene important for pituitary development, but also for hearing in some patients. As disappointing as it is, the scoop wasn’t all bad. When our main contact from that group came by just after lunch to talk over the results and future strategy, we decided that:

• there was less of a rush now, since the “worst” had happened (it’s easy for me to keep perspective; she had had this idea six months ago)
• the other paper gave us a good lead for one part of our experiment that hadn’t borne fruit
• she will come by mid-May and do a follow-up

I then re-read a grant application from a master’s student I seem to have acquired, who wants to study gene expression in putative stem cells resident in a certain kind of childhood cancer that he operates (he’s a surgeon). And, even though it was only 24 hours ago, I can’t remember what else. I proof-read some colleagues’ paper for English grammar and punctuation. But I left around 8PM, and got wet both getting to and emerging from the metro.

Today: in-depth discussion with my postdoc after a soggy, slow arrival for everyone. (”Incident technique sur la ligne 10.”) She will finish sequencing a series of candidate genes for CHARGE syndrome in a series of patients not mutated in the known causative gene. We talked somewhat about an unpublished ChIP-chip experiment of which we had wind via a conference and whether the researcher had made progress on it, and/or whether we should try it ourselves but with a different technical approach, in the embryonic cells we are studying. We talked about how to make progress for three other collaborations.

Then it was lab group meeting, where I presented an overview of results for a collaboration with a local cytogeneticist and another from Tunisia who is completing her Ph.D. on a very interesting patient with a complex congenital eye malformation. Around the table, there were a couple of good ideas as to what to do further (but in a short period, as she is hoping to write up now) and to which journal she can submit the paper.

During the meeting, I also met the master’s degree prospective student with one of his mentors. That way we both have an idea of what we’re getting into. He (luckily for me) seems motivated and intelligent. One of my bosses signed me up in essence to direct his master’s thesis by playing on a misunderstanding. I don’t think it was intentionally Machiavellian but I made it clear this afternoon by phone that I didn’t appreciate being backed into a corner (he is out of town on vacation.

I ran out at lunchtime (and got wet) to drop off some clothes that my daughter’s Parisian friend had left at our house in Toulouse during her visit last week. This afternoon, I helped place orders and find the budget line for them; did some travel agent stuff so that said postdoc and I can attend the ISSCR conference and not sleep on the street; searched fruitlessly for a box of DNA; searched more fruitfully for given embryo sections for the next experiment on the pituitary-ear gene; made a list of stuff I am supposed to accomplish in the next 24 hours.

One of those items which did not get written down is to go to sleep. Now I am back in Toulouse, I’ll attempt that one first. This time tomorrow, I will be with my family in Donostia and Bilbao, Spain. It’s a long weekend here, what they call a “bridge” weekend, as the first of May is a workers’ holiday. Goodness knows I have been working, lately.

Someone in the new administration at the INSERM is feeling insecure relative to the National InstituteS of Health. So now we have eight new “institutes” in my organisation and I don’t even know to which one I belong, yet. Lots of pretty colors.

If I study genetic aspects of the development of the nervous system (which is in part the case) I am, as the French say, caught with my bottom between two chairs. Luckily I’m used to it.

Thanks to Bad Science, a link to this book review whose subject will make it onto my reading list.

It’s Doubt is Their Product: How Industry’s Assault on Science Threatens Your Health by David Michaels (Oxford University Press, 359 pages, $27.95 or £14.99)

…money has bought science, and then science — or, more precisely, artificially exaggerated uncertainty about scientific findings — has greatly delayed action to protect public and worker safety. And in many cases, people have died.

…the war on science described in Doubt is Their Product is so sweeping and fundamental as to make you question why we ever had the Enlightenment. There aren’t just a few scientists for hire — there are law firms, public-relations firms, think tanks, and entire product-defense companies that specialize in rejiggering epidemiological studies to make findings of endangerment to human health disappear.

[... - oh, there's my ellipsis!] All of science is subject to such exploitation because all of science is fundamentally characterized by uncertainty. No study is perfect; each one is subject to criticism both illegitimate and legitimate — and so if you wish, you can make any scientific stance, even the most strongly established, appear weak and dubious. All you have to do is selectively highlight uncertainty, selectively attack the existing studies one by one, and ignore the weight of the evidence.

This also works relative to teaching the concept of evolution in public school.

I see that some enthusiastic souls have set up a website for people like me to evacuate their half-baked ideas. SCIEnCE (not Science) purports to offer a wiki structure for people to build on proposed technical solutions to scientific problems. I like the idea of it, the way I like the idea of Open Notebooks, but I have a couple of concerns.

First, it’s nice to have a (fairly transparent) pseudonym. It’s strange to be confronted in the lab - and this has happened to me twice - by people who read this blog or my comments on other blogs, since this blog is as much if not more about being the human who does the science as about the science itself (which an Open Notebook ought to be, IMHO).

Second, I have been wondering for a while, after trying to get a couple of said Open Notebooks up and running, whether images of gels and in situ hybridizations that I usually tape in my notebook are considered as having been published once they are made public via the lab website. If so, does that mean I can not publish this data once interpreted, in most scientific journals? (See “The journal only accepts papers that present original research that has not been published previously. “) Does one have to ask every potential journal in which one might like someday to see one’s work appear?

I don’t know whom to ask about this, but I might try to hound a few of the prominent advocates of so-called “Open Science” as well as a couple of editors who are kind enough to get in the firing line at Nature Networks.

I just received the following conference announcement:

Featuring the latest in theoretical and applied research, EVO* topics include recent genetic programming challenges, evolutionary and other meta-heuristic approaches for combinatorial optimisation, evolutionary algorithms, machine learning and data mining techniques in the biosciences, in numerical optimisation, in music and art domains, in image analysis and signal processing, in hardware optimisation and in a wide range of applications to scientific, industrial, financial and other real-world problems.

I must admit I have no idea what “evolutionary and other meta-heuristic approaches for combinatorial optimisation” means. Not only articles should be subject to guidelines of clarity. If they wanted me to attend, raté!

What’s the best advice you received from a fellow scientist or however you qualify your career choice ?

Here’s one version from a writer:

In the shower today I tried to think about the best advice I’d ever been given by another writer. There was something that someone said at my first Milford, about using style as a covering, but sooner or later you would have to walk naked down the street, that was useful…

And then I remembered. It was Harlan Ellison about a decade ago.

He said, “Hey. Gaiman. What’s with the stubble? Every time I see you, you’re stubbly. What is it? Some kind of English fashion statement?”

“Not really.”

“Well? Don’t they have razors in England for Chrissakes?”

“If you must know, I don’t like shaving because I have a really tough beard and sensitive skin. So by the time I’ve finished shaving I’ve usually scraped my face a bit. So I do it as little as possible.”

“Oh.” He paused. “I’ve got that too. What you do is, you rub your stubble with hair conditioner. Leave it a couple of minutes, then wash it off. Then shave normally. Makes it really easy to shave. No scraping.”

I tried it. It works like a charm. Best advice from a writer I’ve ever received.

I got a good recommendation for a family car from Delphine Duprez about 6-7 years ago, long enough that we’ll have to think of separating ourselves from it as it ages. And Nicole Le Douarin told me that I had a literary bent and that I might want to pursue that rather than science. (But I think she was intentionally provoking me; she’s been perfectly charming since.)

I get skewered every single year.

I buy the freshest eggs from farmers who own the happiest, best-fed free-range French chickens there are around, and what happens?

Clumps of white stuck to the inside of the shell. So I either give up or I chop it all fine, but it looks a right mess. Nice first course.

A simple web search clears that up, but you’d think I could get around to it a week-to-ten-days ahead of time. Instead, every year I find out that I should *not* use fresh eggs as per this advice.

Happy Pesach.

(Later edit:) I got around it this year by using the blender to whip the egg whites - a little strange, I’ll allow - and then I put a slice of smoked salmon, a blob of fluffy egg white, and nestled in the middle, the lovely yellow-orange yolk that popped out surprisingly easily. This wouldn’t work with the greeny-yellow kind, but haven’t seen that for years. Anyhow, I dribbled a few drops of that outrageously expensive super olive oil that my husband brought back from last trip to Madrid on the yolk, and some pretty paprika from same trip, a couple of leaves of spicy arugula from the garden, and everyone liked it.

Lest you think I’m being snobby about the arugula, it’s easy enough for it to be a weed. You or the backyard slugs couldn’t kill it if you tried. Throw some seeds in the ground if you don’t believe me.

I presume that if you bother to read this, you are unlikely to be a creationist.

If that is a correct assumption for you, you might enjoy taking part in the English-speaking WWW contest linked here.

Then again, if you are a little tired of hearing people preach to the converted, and cross swords with intractable others, don’t bother clicking on the link.

Well, I wrote it before the weekend, at least.

Where things get asymptotic is in the corrections of the typeface of the letters, of verifying figure legends and scale bars, and we should really just send the article back to Genome Research now.

But I think I’m scared to. And my postdoc is, too.

We stand a good chance of getting rejected once more; the journal’s impact factor has gone up, meanwhile, so they’re flooded in manuscripts, and it may just be too much effort for the editors to whip it into something they think appropriate for the forum.

I’ve lost faith in my ability to gauge what is appropriate for what journal. I have three papers in limbo right now, but this one is the one that means the most to me. That’s why I am waffling so much.

I’ve also lost my faith in my co-authors a little, as not once in the last four months have any of them asked about how things are coming along, or if there is anything else they can do (there wouldn’t have been much, but I wouldn’t have minded being asked). Which is not my way of going about things. Which is why I lost a fair bit of time helping out in parallel with these other papers in publishing limbo.

I’ll be going to Perpignan this weekend to try to stand upright in the wind.

I was on my first thesis jury a few months ago, and it was a great topic: the discovery of the activity of old and new serine proteases in the outer layers of the skin and implications for diseases affecting its desquamation.

Sitting here wondering all of a sudden: if I’m digesting proteins in the bit of mouse tissue to make a new preparation of genomic DNA, and I use proteinase K to eat them up, why did I just add in the denaturing detergent sodium dodécylsulfate?

So I read up about it on the Merck site (thanks to Google) and found out first that it’s not a problem and, second, a tidbit about why it’s called proteinase K.

Proteinase K is a highly active endopeptidase with a broad spectrum of action towards peptide bonds. It was isolated and purified by researchers of Merck’s Biochemistry Department in 1970 from a culture of the fungus Tritirachium album. This fungus is able to grow  on Keratin (e.g. wool, horn particles, feathers) as the sole source of carbon and nitrogen. The isolated protease was therefore given the designation “K”.

Then I’m diddling around, seeing that it’s related in some way to subtilisins, which are used in much the same way as pancreatin and trypsin, and I’m remembering some empirical trials of using these and dispase and collagenases, for various tissue dissociations for cell cultures or microdissections. Some separate basement membranes first, before separating cells; others, like trypsin, attack the tissue directly… well, lots of people study this stuff.

Thanks, folks.

Last week, I gave a talk at a restaurant about what I do to a group of educated anglophone women who get together periodically for this sort of talk. Kind of a “salon”. The disciplines represented are very diverse: there have been recent talks about yoga instruction, meteorology (the back office kind) and Chinese guanxi. They ate it up. They asked lots of good questions about stem cell science, about genetics, about bioengineering, and would have gone on until midnight had I let them (I think some were flagging though, even so). And I had to promise to give a second talk in the autumn. Have received thank you notes by e-mail from many as well. I have never had such an enthusiastic reception. Ever. Makes me want to do it again!

So their thanking me, I pass it on to the protease researchers. Thanks for doing what you like to do; it’s interesting, and it’s useful. Glad someone’s doing it.

This is my busy catch-up week without small ones underfoot. And I’m getting run over by all the things I said I would do that I thought I could do now. Luckily my husband is similarly occupied so he doesn’t look at me strangely for going to work at 8AM and returning at 10PM (hope I can do better tonight) - as he’s doing the same.

Part of the problem is that I’m having far too much fun posting idiotic comments on the Nature Network site. Bad for blogging. Bad for science. Or it will weed out the dilettantes in any case. For example, I recently stumbled upon the website of a former high school classmate who is a hardcore, successful scientist with Nature publications (natch) and a professorship at Stanford. He quite intelligently hasn’t (yet, possibly) answered my delighted “I found you!” e-mail - as who really has time for this silly networking stuff! Notwithstanding a very useful set of reviews that rwintle over here kindly sent me.

So, today a sick future Ph.D. student dragged himself in to ask me if I had re-read his abstract, as promised.

A future collaborator caught me ten minutes after turning on the fluorescent lamp for the microscope, for a meeting we planned a week ago with a third party who had schlepped in from the other side of town. Oops. So I finished up quickly, but it wasn’t ideal.

Could I make calls to help the new Japanese post-doc line up some apartment visits? Yes, but…

Just now, a charming e-mail from one of my bosses at Necker, asking if I had got around to editing my part of the grant application he will file for our big group?

Last week, and racking me with guilt, a gentle reminder from my US collaborators that I owe them a beautiful photo spread of some of our results. (I haven’t even answered that one, will do this evening before allowing myself to go home and eat, and it’s already 8:24PM).

And I am finding out why on-line lab notebooks have not yet caught on. First, the wiki business is open, point in its favor, but the syntax is bloody arcane, which is not. It reminds me of using WordPerfect back in the late 1980’s.

Second, I caught myself as I put in a photo, which I had already posted to the website of the supplier in exchange for a 75% off coupon on my next purchase, so I didn’t plan on using that one for a publication. Isn’t publishing data on the internet, even if it is ostensibly a lab notebook, still “previous publication”? Won’t that be a problem when I do want to construct a paper with this data? What about bands from gels? How does that work?

Third, when I am (rarely) doing a wet-lab experiment (and immunohistochemistry is indeed wet), it’s really inconvenient to type as I go along, as it entails taking off gloves and not just blotting them on my lab coat to pick up the ballpoint pen, and letting the excess get soaked up by my warped and blotchy notebook pages.

Then again, it will all be keyword searchable if I can hang in there.

Personality tests are fun (right, Geoff?) in the same way that fortune-tellers and horoscopes can be - one always hopes that someone else cares enough to have a deep insight into one’s psyche that one hasn’t had on one’s own. While I’m certainly fun-loving, I’d have thought I was more a responsible Kanga type. Given that I’m incommunicando for the next 5 days from my children, whom I accompanied this weekend to Perpignan to a tennis camp, this may color my perception. Maybe that’s why I am feeling all this guilty pleasure.

The BIG PAINFUL IMPORTANT manuscript (yep, the same one) is much closer to submission; just double-checking that Supplementary Figure 2 has not been changed to 3 in the text and remains 1 in the legend, all references match up, that sort of thing.

Helping two future Ph.D. students write their projects up for funding proposals. I told one of them that, as painful as this sort of experience is, it’s already part of the learning process. Yesterday, a Ph.D. student with whom I hang around a lot became a full-fledged doctor (for the second time, as she was already doctor in veterinary medicine). She did fine.

Your Score: Roo

“We can’t get down, we can’t get down!” cried Roo. “Isn’t it fun? Pooh, isn’t it fun, Tigger and I are living in a tree, like Owl, and we’re going to stay here for ever and ever. I can see Piglet’s house. Piglet, I can see your house from here. Aren’t we high? Is Owl’s house as high up as this?”

“How did you get there, Roo?” asked Piglet.

“On Tigger’s back! And Tiggers can’t climb downwards, because their tails get in the way, only upwards, and Tigger forgot about that when we started, and he’s only just
remembered. So we’ve got to stay here for ever and ever–unless we go higher. What did you say, Tigger? Oh, Tigger says if we go higher we shan’t be able to see Piglet’s house so well, so we’re going to stop here.”

ABOUT ROO: Roo lives with his mother and his friend Tigger. He is the youngest member of the Hundred Acre Wood, and loves to go along with his friends on their adventures - when Kanga will let him. No matter what happens to Roo, be it falling into the river, getting stuck in a tree, or being kidnapped by near-strangers, he enjoys every minute of it. Roo isn’t one to worry about such things. That’s Kanga’s job.

WHAT THIS SAYS ABOUT YOU; You are a positive, fun loving person. You take life as it comes, and feel sure that everything will be all right. You can usually find a silver lining in every cloud.

It’s lucky that your friends find you so endearing, because you do tend to lean on them a lot. You tend to rely on the help of your family or friends when things get tough. You don’t always take the initiative to do things for yourself. …

(Ed: I don’t really agree with this assessment. But for what it’s worth, wasn’t that once known as “interdependence“?)

Or, as titled here, “Do you want to be a loser?”

This ties in nicely with my entirely empirical data that when I am pre-menstrual, I can barely drag myself out of bed and I have a physiological craving for high-fat, high-sugar and salty foods and drinks, that fades immediately upon the onset of the period. Then, suddenly, I’m full of pep again. This feeling is an accurate guide to how thick the pads I carry around that week need to be.

There is definitely an effect on immune and digestive functions as well. Some of this makes sense. Cool!

Sorry if I grossed some of you guys out, but I do think it’s interesting.

Procrastination.

Overcommitment.

Biting off more than I can chew. This has to do with the five hours I put in this afternoon, trying to devise an aerobics routine for my daughter’s Brownies group. I gave up. We’ll get back to it in a couple of weeks. Next time, I’ll stick to cookies.

Meantime, I learned what a serpent is this afternoon - and listened to it live. I’ve had these tickets for six months. My dad didn’t know this, but sent me the following quote (probably Love in a Cold Climate) by e-mail:

Lord Merlin wandered round with his tea-cup. He picked up a book which Fabrice had given Linda the day before, of romantic, nineteenth-century poetry.
“Is this what you’re reading now?” he said. ” ‘Dieu, que le son du cor est triste au fond du bois.’ I had a friend, when I lived in Paris, who had a boa constrictor as a pet, and this boa constrictor got itself inside a French horn. My friend rang me up in a fearful state, saying: ‘Dieu, que le son du boa est triste au fond du cor.’ I’ve never forgotten it.”

That psionic field thing seems to still be in effect.

No fangirls or fanboys come and squeal over my article-signing stand (or my posters, for that matter) at conventions. I wonder why.

In case they do, here’s an interesting set of guidelines.

I can attest to their applicability because I remain embarrassed to this day as to just how gooey I became after five minutes’ time in the immediate presence of delightful Ms. Emma Thompson back in 1993, when she was shooting this otherwise highly forgettable movie. I left lab for 24 hours and was an extra; it showed me that there are worse ways to earn money than to beg for it in grant applications.