The eminent young Anthony Fejes has written an excellent post recently entitled 4 Freedoms of Research.

He starts off by saying that we have no rights – meaning, we have no particular swearing-in ceremony by which we say we will adhere to certain universal ideals. I thought he meant we have no right to determine our research subjects and no particular right to funding, which is not completely off the mark.

As an aside I am struck by how the hot topics of the day in biology have evolved over my fairly short professional lifetime from topics in cancer to topics in longevity. Aside from anything having to do with contagious viruses. Will the hegemony of baby boomers and their preoccupations never cease? Will my generation (in my case, born precisely one generation later) forever be paying to support them, not to mention keep them alive ever longer? < /rant >

Anthony points to Science Buddies and their flowchart – or now I’m learning to call such procedures workflows – on the scientific method. There is a more recursive – and therefore, realistic – version cited right here.

He goes on to distill the rights of scientists down to:

1. Freedom to explore new areas
2. Freedom to share your results
3. Freedom to access findings from other scientists
4. Freedom to verify findings from other scientists

and then demonstrate that all of these freedoms are slowly being eroded. Or maybe we did not really ever enjoy them all to their full extent.

As a palliative, Anthony suggests that we can, among other things, but he is still taking suggestions:

1. Publish in open access journals to help disseminate knowledge and bring down the barriers to access
2. Maintain blogs to help disseminate knowledge that is not publishable

I would say that to the best of our individual abilities, informing the public (who can be your father-in-law) about the importance of your work is key in ensuring that funding exists which can underwrite all of those freedoms. Freedom can be an expensive venture. But information need not be.

No, not those! (Though it probably doesn’t hurt, in the list below.)

Just to remind myself and others that when you are feeling stressed or misanthropic, nothing beats ensuring the following bodily needs are met:

1. Sufficient sleep (at least two nights in a row of seven-eight hours)

2. Sufficient non-junk food (stuff your grandmother would recognize as edible) and water

3. Sufficient physical exercise. In my case that was upper-body work this weekend – painting the interior of cabinets – mowing the lawn, and trimming down the ivy. Biking to work today.

That’s it for today’s pearls of wisdom. Make yourself a necklace and show me how much better it looks on you.

P.S. Fourth grant rejection in a row today, and since #5 was a Challenge grant response…

I don’t work on cancer – and my ideas are too novel, more’s the pity… hmmm, new blog post coming on. Maybe.

First.

My plane from Paris to Toulouse tonight was delayed by 1.5 hours because of an air traffic controller strike in Greece.

Second.

I had parked my car in the parking lot of my husband’s workplace near the airport, but because of the delay, the security had barricaded me in, and hubby had not left me the remote control in the car to open the barricade because I have never needed it before. 30 minutes more.

Third.

I received a gently worded message that can only be read to mean that one of my two group directors in Paris thinks I might not be providing optimal quality guidance to a master’s student, for whom the other director forced me into accepting a co-tutorship on a project I didn’t want to work on from the outset. The student is a nice guy, and should not have to pay a price because I caved in – part of why I did, is that he would have paid much more had I not. The co-tutor is well-intentioned, but it was obviously not going to work with her alone.

I can be such a sucker. I said I would be the point person in the laboratory for this student for a project that I made sure to obtain in writing, and would arrange for him to get what he needs. The student hasn’t complained to me, nor to my knowledge to anyone else, but he would like to have his project evolve in all sorts of ways that I don’t want to oversee.

There is a great proverb in French, “les absents ont tort”. Meaning literally, those who are absent are wrong. Think about it. It applies well to meetings, to voting, and certainly, to trying to run research activities on two sites.

One of the nice things about being a woman of child-bearing age is that I can fantasize briefly about getting pregnant accidentally-on-purpose and telling all my colleagues to go to hell and make do without me for three years of parental leave (which right to unpaid leave was established after I had my children).

Then I remember that I actually do respect and like all of these people, and that I’m probably just tired, and need to go find my soft bed to get over the earlier, minor frustrations of the day (not all of which mentioned) that have likely conditioned my reaction.

…I could, in addition to other unnamed duties and pleasures:

• blog on a daily basis

• twitter cleverly and multiple times a day

• check out and properly use all those social media for scientists – all my PDFs are still not imported into Mendeley, much less tagged

• teach my lab members wiki markup and make them use the online notebook

• play my clarinet more than twice a year

• think of and carry out those experiments on the cells in the culture room

• cut my own histology sections and do more experiments

• find new contractors for remodeling the apartment

• learn Python (like I once hoped to learn perl)

• oh yes, take up knitting again. Purl, that is.

• do my tax forms (I don’t owe any money. Yet.)

• think about investments (with the money I’m not paying to the US government)

• keep my home immaculate

• water and weed my garden enough

• et cetera, ad nauseum

Off to Paris again tomorrow for another hurried round with my PhD student, visiting student from the Netherlands, masters’ students preparing final reports, and visiting my postdoc and her new baby. Among other interactions.

But at my back I always hear
Time’s wingèd chariot hurrying near…

Spending time learning the most basic commands from information gleaned on FAQs and other help pages is not gratifying. Even the vocabulary is abstruse – one “compiles” rather than “installs” and where the heck was that zlib.h, in the end? I’ve apt-got lots of stuff.

But then again, decalcifying tissues for future embedding, tracking down lent-out antibodies in the building and a number of other wet-science-related tasks today were not much more exciting.

After my third install of Ubuntu 9.04 on my home computer, I think I have it. I might finally be able to run Maq, and possibly Bowtie, should I so wish. Thanks in part to Richard for getting me over the hump by believing I might have the ability to deal with such things.

These programs will allow me not to rely only on the goodwill and free time of collaborators, but actually map many millions of short sequences to a reference genome sequence. The human one. While it is not the largest genome out there, it’s plenty enough to overwhelm the ability of my laptop’s Windows to deal with the 2.9 Gb of text in the human reference genome available here. So I had to learn how to use a Linux-based operating system that somehow does something nifty with 64 bits. It has been explained to me but it just will not stay in my head.

I had been meaning to take the plunge for a long while, but who has multiple full days to learn a new way of doing what one managed to do earlier? It entailed a situation in which it was not possible to manage, to push me over the edge. I had to find out how to stick lots of text (from each chromosome) together – that would be by a series of commands along the lines of:

$ cat chr*.fa >> ref.fasta

Lots of people in my acquaintance could have told me how to do that. But I found out myself, which is much more fun when it finally works. Here it is, already midnight, and I have also found out how to cut and paste in a terminal window, and a few other goodies. Meanwhile, Stephen is barbecuing on a Friday night, and I am a wee bit jealous.

Finally, I also found out that I downloaded the wrong version of the human genome, and there is a new reference that has been available the last few months. So, instead of seeing whether or not my Maq program is really capable of running, I’ll have to go to sleep and leave my computer to acquire a new human genome.

I wonder if the two versions might undergo some sort of homologous recombination during bedtime?

The Astronomy Picture of the Day went up on the internet. Its fantastic archive is here.

For its birthday, check out this one over İzmit Bay by Tahir Sisman:

Mine is resolutely geeky. I am happy to be learning new command line vocabulary. I also like cutting up and identifying bits of vertebrate embryos for future use – at heart, I am a true conservative: one who conserves. Waste not, want not. Apparently, Protestant-type thrift (sorry for the ad-laden intro at that link) is back in fashion among a certain socioeconomic set.

We had a party for around 70 people in our rented home and garden yesterday. There are those for whom that would have been torture. We’re old enough to not care quite as much, and I actually had a great time. There is still a bit to pick up, but absolutely no regrets, and some super memories.

After the party, I went out to water the plants at dusk, which at this time of year is around 10:30 PM. (I also have pretty functional rods.) I heard a panicked scream streak by me, followed by the distinctive lope of our neighbor’s black-and-white cat. It wasn’t even making an effort, but the little rabbit it was chasing was panicked to death. Can you imagine, having a monster three times your size and clearly stronger and faster, toying with you before it would rip out your guts from your conscious body? Unfortunately, I can, and I’ve heard it before.

I chased after the cat and hissed it back to its own yard, but did not dare to leave the little leveret shuddering under our doorstep, for fear that its nightmare would catch up to it. My husband came out, and of course wanted to caress the creature. By the time I warned him off, it loped slowly away using what was left of its adenosine triphosphate into the other neighbor’s yard. We were both relieved we did not have to care for it. If it was subsequently disemboweled, at least I didn’t know. It may have joined the hedgehog that we fished, alive, out of the swimming pool that morning.

If anyone comes eating my petunias, though, I might well be placing a contract with our neighborly hunters.

I’m also quite glad to have such domestic preoccupations. My Iranian friends are irate; given how I felt after Bush was more-or-less elected, I can sympathize to some extent, but I’m conscious that I can not really imagine how it feels to hope so much for a country that has been so torn with strife in recent history, and then be disappointed. All I can offer is that usually, the pendulum swings back, and I can only hope that the period is as short as it is in my native country.

I don’t want to move.

In about eight weeks, though, that is exactly what I will be doing. Again. And then possibly again, nine months or so later. (No, I am not pregnant, but that’s about the length of an academic year, and Mr. Etchevers has received the first of what we hope will be a couple of job offers, and it’s not quite where I wish to be.)

Not only will I be thinking about what is necessary for getting the household up and running smoothly, but all the usual September stresses will be in place to welcome us back to Paris: figuring out the most efficient way to not be late to new schools, piano and sports lessons, catching up on “what did you do over the summer” and “what did you do over the last three years?” Undertaking some redecoration (paint and quarter-century carpeting to replace) before moving in.

Deciding whether I try to repack my cherished centrifuge and other such kit and slip them into my personal moving stuff or tag along with another colleague who is also moving his lab up to Paris in the fall. Choosing what to leave, and which cell vials in the liquid nitrogen, and which paraffin blocks, so the students here can continue working comfortably.

Lots of things for which I would just as well put my head in the sand.

My job will be the same at least in the Paris lab, and I have been keeping my foot in the door by showing up like clockwork for two days every fortnight, or three days every three weeks, for the last three years. But even so, I’m rather out of a number of loops, now, and there will be some adjustment necessary.

My one Ph.D. student is defending her thesis in early October, and I will not take another student on right away. Too many medium-level responsabilities. It has been a long time since I said no to a collaboration. Yes is more of a habit, and a way of avoiding hearing any expression of disappointment from across the table or the Internet. But the first opportunity has presented itself today, because I just said yes to two others in the last two days.

Meanwhile, two gigabytes of sequencing data await my inadequacy, and I have to learn Ubuntu-based programs so as to run them on a 64-bit operating system. That should not be impossible, but in what time can I acquire that knowledge?

Who was that deluded optimist who invited some sixty-odd people over for a potluck this weekend, anyhow?

Have you ever put off going to lunch until 2:30 PM because that way, the morning would not yet be over? Every day is like that, now.

Certainly not all in academia.

I had the following exchange with a well-placed person in the administration of a new “senior postdoc” program run by the INSERM. (In French, so I am paraphrasing.)

Me:

I have a great postdoc in my group. Because INSERM did not give me the money promised to recruit a postdoc, I have been paying her with U.S. NIH money since 2006.

She came to my group right out of her Ph.D. at the University of Paris. She went for a month to our U.S. collaborator’s laboratory to learn a complex technique which she brought back and that led to an article on which she is first author.

For various reasons, it’s unlikely she will want to undertake a second postdoc abroad. But the senior postdoc program mentions that an “international mobility” is a criterion for selection. Is she still eligible?

Response:

She would have to be really good to get around that criterion. Could you send me her name so I could look at her publication record, especially those articles in first/last position?

My reply:

Here is her list of [nine] publications, since she has a pretty common name and you would not have found them on your own. I’m a foreigner originally. What’s so great about being abroad, if one has already gone to do a postdoc with the “triple mobility” criteria of changes in subject, institution and laboratory?

The unequivocal answer:

Mobility for a foreigner is not judged the same way, and of course moving between labs is important. The real problem in my opinion for your postdoc is the quality of her publications in all [two of] the laboratories in which she has worked.

Her two first-author publications in good journals, Hum Mol Genet and PNAS, were only in 2008-2009.

If the two publications in 2003 were during her Ph.D., they’re fairly weak, as only one is a first author publication in a specialist journal. From 2004-2007, while she was in theory publishing with you [hey, I did say she arrived in 2006!] she has no first authorships. That will be interpreted as her willingness to collaborate but incapacity to appropriate a subject for herself.

Also, if this researcher has been with you for more than two years, she hasn’t got a snowball’s chance in hell, since the jury will favor postdocs who are moving to a new group to start a new research theme. The others can try to get a “charge de recherche” position [yes, the ones that are in such short supply that programs such as this have been added to try to relieve the pressure].

Hope that helps you in encouraging her to apply or not.

It certainly helped me but hardly the person who could have really used the help in the first place. I also think it’s quite unfair that she is being penalized for sticking with a subject with a Ph.D. advisor who did not ensure that she could get on later with her career, rather than being rewarded for choosing a postdoc lab that lets her show the stuff of which she is made.

That postdoc lab wasn’t even so good for her, really, because the project which she brought to fruition was a really tough nut to crack and it took two full years before she could publish it. And she said yes to a bunch of other collaborations. But don’t tenacity and intelligence count for anything?

We’ve got a little less than a year’s funding left for her. Is there no place in academia for scientists who slowly publish good quality science?

This phrase, from Lincoln’s marvelous Gettysburg address, seems to have long been taken in American politics to support a populist stance. May the simple man, the Mr. Smiths in Washington, bring truth, honesty and other values worth fighting for to those whom they represent.

We saw how far that ideal was applied in the last couple of administrations. As discussed by Dr. Simon Langstoff: “Is it too unreasonable; is it impossibly naive to hope that they might look to our interests (and not just our wants) and offer a realistic programme for good government?”

Lately, the U.S. State Department has taken a leaf from the TED notebook by sponsoring the TED@State series. It’s a relief that it appears to be acceptable to be an intelligent person in the U.S. once again. Our State Department is our public face to the world; that face is finally no longer that of a buffoon.

Yesterday, Europeans had the opportunity to vote for their national delegates to the European Parliament. Approximately 43% of eligible voters actually cast their vote across the 27 nations. While that is not a large proportion of voters, and the sad fact is that in the most stable societies, we undervalue this privilege we have the right to exercise, that is still a large absolute number of citizens who bothered.

The number of seats allotted to a country is more or less proportional to the number of citizens; there are eighty-odd for France, which is one reason why the country is so particularly hostile to Turkey’s entry in the E.U. But France was by no means the country with the most far-right representatives elected, and other countries will a much larger proportion of either islamophobic or nationalist or even anti-European Union delegates.

I am amused by the prospect of getting oneself elected to a quite cushy position as Member of the European Parlement on an anti-European Union platform. It’s not straightforward finding out how cushy that is – Wikipedia cites something around 7K euros a month, which is quite comfortable from a French scientist’s point of view – but the statute referenced says that “The amount of the salary shall be 38.5% of the basic salary of a judge at the Court of Justice of the European Communities.” Which is really helpful. Here it intimates that (in 2004) half the salary = 8500 euros/month. So, you scientists can figure it out.

There are a couple of pirates who got elected, as well. The presumably well-meaning, Robin Hood kind. I suppose that’s worth a chunk of my taxes, just for the spectacle.