Far-seeing implications of the Origin of Species

Thu
12
Feb 09
Authored by Alethea

ResearchBlogging.org

The actual post is at A Developing Passion because Darwin’s influence deserves as much positive publicity as it can get.

Also because I can get ResearchBlogging to register it, while I am waiting for the other blog to be recognized. Here are the beautifully, automatically formated references.

Amit S Verma, David R FitzPatrick (2007). Anophthalmia and microphthalmia Orphanet Journal of Rare Diseases, 2 (1) DOI: 10.1186/1750-1172-2-47

D Nilsson (2004). Eye evolution: a question of genetic promiscuity Current Opinion in Neurobiology, 14 (4), 407-414 DOI: 10.1016/j.conb.2004.07.004

E Eisenberg (2003). Human housekeeping genes are compact Trends in Genetics, 19 (7), 362-365 DOI: 10.1016/S0168-9525(03)00140-9

R. Kawaguchi, J. Yu, J. Honda, J. Hu, J. Whitelegge, P. Ping, P. Wiita, D. Bok, H. Sun (2007). A Membrane Receptor for Retinol Binding Protein Mediates Cellular Uptake of Vitamin A Science, 315 (5813), 820-825 DOI: 10.1126/science.1136244

Bouillet, P, Sapin, V, Chazaud, C, Messaddeq, N, Décimo, D, Dollé, P, Chambon, P (1997). Developmental expression pattern of Stra6, a retinoic acid-responsive gene encoding a new type of membrane protein Mechanisms of Development, 63 (2), 173-186 DOI: 10.1016/S0925-4773(97)00039-7

C GOLZIO, J MARTINOVIC-BOURIEL, S THOMAS, S MOUGOU-ZRELLI, B GRATTAGLIANO-BESSIERES, M BONNIERE, S DELAHAYE, A MUNNICH, F ENCHA-RAZAVI, S LYONNET, M VEKEMANS, T ATTIE-BITACH, H C ETCHEVERS (2007). Matthew-Wood Syndrome Is Caused by Truncating Mutations in the Retinol-Binding Protein Receptor Gene STRA6 The American Journal of Human Genetics, 80 (6), 1179-1187 DOI: 10.1086/518177

F PASUTTO, H STICHT, G HAMMERSEN, G GILLESSEN-KAESBACH, D FITZPATRICK, G NURNBERG, F BRASCH, H SCHIRMER-ZIMMERMANN, J TOLMIE, D CHITAYAT, et al. (2007). Mutations in STRA6 Cause a Broad Spectrum of Malformations Including Anophthalmia, Congenital Heart Defects, Diaphragmatic Hernia, Alveolar Capillary Dysplasia, Lung Hypoplasia, and Mental Retardation The American Journal of Human Genetics, 80 (3), 550-560 DOI: 10.1086/512203

G Halder, P Callaerts, W. Gehring (1995). Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila Science, 267 (5205), 1788-1792 DOI: 10.1126/science.7892602

Y. Onuma, S. Takahashi, M. Asashima, S. Kurata, W.J. Gehring (2002). Conservation of Pax 6 function and upstream activation by Notch signaling in eye development of frogs and flies Proceedings of the National Academy of Sciences, 99 (4), 2020-2025 DOI: 10.1073/pnas.022626999

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This post has no comments | Posted in:General

Winter storms

Mon
26
Jan 09
Authored by Alethea

I’m trying out a blog post direct from Flickr.

The tallest cedar in Toulouse (according to the other neighbor from whose garden it came) crashed down a tiny distance away from the corner of our neighbor’s house, under the influence of winds gusting to 160 km/h. No one was injured, but the road was cut off for the next day.

We were not among the some million and a half people who lost electricity, but the phone looks like it will be knocked out all week, so no Internet. It’s actually rather calm. I would much rather lose the phone (especially in the era of cell phones) than electricity! And it was up and running at work, so all is well for me, at least.

Thanks to Graham, a very clever mechanism of putting a link to your e-mail address without getting it vacuumed up by a trawling bot. At least, in theory.

This post has no comments | Posted in:General, personal

Redirection

Sat
17
Jan 09
Authored by Alethea

While I’m not giving up altogether on this blog, some may have noticed a distinct drop in posting frequency. I’ve spread myself thin. Take a look over here, if you like, to see how else I keep myself busy.

Check out the comments here, to see another locally demotivated blogger. One’s interests ebb and flow; it’s all very organic. No worries, I’m still around. I mean, how could I give up this honor?! I’ve got authority!
C-List Blogger

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Free the Palestinians from Hamas

Fri
9
Jan 09
Authored by Alethea

The following is an unauthorized translation of an editorial by the philosopher and essayist Bernard Henri-Levy, which was published on January 8th, 2009, in the widely read French newsweekly, Le Point. While I don’t want to talk about my personal taste or distaste for the writer and his particular style, he expressed my feelings about the situation in the Gaza strip quite well here. So I won’t re-invent the wheel, nor will I debate. I just wanted to inform my readers that individuals in France are no more automatically or unanimously biased than America, or Canada, or Cambodia, or any other country when judging what is happening in Israel and Gaza. But that majority opinion in Western Europe is indeed different from that of other places, and it can be uncomfortable to hold such a minority opinion as follows.

I am not a military expert, so I will abstain from judging whether the Israeli bombardments of Gaza could have been better targeted, less intense.

Since I have never over the last decades been able to distinguish between good and bad dead people, or, as Camus said, between victims and “privileged executioners“, I am obviously terribly upset by the images of Palestinian children who have been killed.

This having been said, and given the craziness that seems, once again, to reign in certain media as it always does when the subject turns to Israel, I would like to recall a few facts.

1. No government in the world, no other country aside from this Israel that has been lambasted, dragged in the mud, diabolized, would tolerate thousands of missiles falling over a period of years on its cities. The most extraordinary aspect of this situation, the truly surprising heart of it, is not the “brutality” of Israel, but rather its restraint.

2. The fact that the Qassam and, now, the Grad missiles of Hamas have caused so few deaths does not prove that they are hand-built, harmless, etc., but that the Israelis must protect themselves, that they [too] live holed up in the basements of their buildings, in shelters : a nightmare existence, on borrowed time, on a background of sirens and explosions – I’ve been to Sderot, I know.

3. The fact that the Israeli missiles, conversely, kill so many victims does not signify, as yell the demonstrators of this last weekend, that Israel is conducting a deliberate “massacre”, but rather that community leaders in Gaza have chosen the opposite attitude and voluntarily expose their civil populations: an old tactic of the “human shield” that has lead the Hamas, like Hezbollah two years ago, to install its command centers, weapons stocks, bunkers in the basements of buildings, hospitals, schools and mosques – an efficient but repugnant strategy.

4. Between the two positions there is, in any case, a capital difference and those who wish to have a fair-minded view of the tragedy and ways to end it do not have the right to ignore it: the Palestinians fire on cities, that is, on the civil population (which is, in international law, called a “war crime”); the Israelis are aiming at military objectives and cause, without aiming to do so, terrible effects among the civil population (which is, in war language, known [infamously] as “collateral damage” – which, even if hideous, reveals a true strategic and moral dissymmetry).

5. To get right down to it, one must remember once more a fact that the French press has surprisingly poorly disseminated and for which I know of no precedent, in any other war, on the part of any other army: the units of Tsahal, during the military air strikes, systematically telephoned (the English-speaking press writes of 100,000 calls [sic; I can't confirm the number]) to the residents of Gaza living near a military target in order for them to evacuate the premises; even if this gesture obviously does not change any aspect of the depair of the families, the broken lives or the carnage, it is not a completely irrelevant detail.

6. And with respect to the famous full blocus, imposed on a starving people, lacking everything and precipitated into a humanitarian crisis without precedent (sic), this is not factually exact either: the humanitarian convoys never ceased to cross, until the beginning of the land offensive, through the Kerem Shalom passage point; for the one day of January 2nd, 90 trucks of food and medication, according to the New York Times, went into the Territory; I also remind certain readers, as they seem to require reminding, the fact that Israeli hospitals continue, to this moment, to receive and provide daily care to injured Palestinians.

We all hope that combat will cease very quickly. Let us also hope that certain commentators will come to their senses very quickly as well. They will discover that day that Israel has committed many errors over the years (lost opportunities, long denial of the nation-building aspirations of the Palestinians, unilateralism) but that the worst enemies of the Palestinians are these extremist leaders who have never wanted peace, never wanted a State and have never thought of any other existence for their people than that of an instrument and a hostage (horrid image of Khaled Mechaal who, on Saturday, December 27, 2008, when the desired Israeli reprisal strikes were imminent, could only exhort his “nation” to “offer up the blood of other martyrs” – and this from his comfortable exile in a Damas hideout…)[my link may not be to the right part of the interview; Arab speakers may correct me].

Today, there are two outcomes possible. Either the Muslim Brotherhood in Gaza rebuilds the truce they broke, and while they are at it, declare null their charter based on the pure refusal of the “Zionist entity”: they will thus rejoin the vast party for compromise that has not ceased – thank God – to make progress in the region, and peace will be established. Or they will only, stubbornly, consider the suffering of Palestinian civilians in terms of how it fuels their warmed-over passions, their insane, nihilistic hate, that goes beyond words to describe. And if that is the case, it is not only the Israelis, but the Palestinians, who will need to be liberated from the dark grip of Hamas.

Shit. I see the New Republic got there, first. Back to being useful in science, instead.

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This post has 6 comments | Posted in:personal, politics

Blogiversary

Tue
9
Dec 08
Authored by Alethea

It’s been four years…

…and no comments for nearly two weeks now. Perhaps I’ve run out of titillating things to say.

There are a lot of other folks now documenting the ordinary lives of practicing scientists. If you wonderful and few but loyal readers so desire, I could point you their way, and take a blogging vacation for a while. Those who know me in person are welcome to follow me on Facebook and professionally, on LinkedIn.

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This post has 6 comments | Posted in:General

Ole!

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8
Dec 08
Authored by Alethea

A rainy, dank weekend escapade to Madrid. The only easy activity was to eat, and we indulged (Cochinillo asado, or roast suckling pig, at the Posada de la Villa, as an example in point). My husband’s hotel was very central and we walked everywhere, even when we could have taken the metro. The kids were pretty good sports, although my daughter had a meltdown in the Thyssen collection by the time we got to Mrs. Thyssen’s wing. Knowing that I will not go back anytime soon made me want to see what else I was missing – which is not the best way to proceed in a museum with children. If anyone else appreciates 20th century art, I would say do the whole museum in antichronological order. Which means go against the flow of arrows, and perhaps draw the ire of the guards or your fellow visitors. This travel piece captures the essence of the city as we tourists experienced it (and we didn’t experience anything after midnight); not much has changed in 14 years.

As impressive as Madrid was, I must say that I was not actually enchanted. The weather certainly had much to do with it; we walked in the Retiro on Sunday morning and found it to be exactly the same dreary, muddy stroll that a similar walk in the Bois de Boulogne can be. For some reason, I was particularly preoccupied with the idea that the riches accumulated by the royal power in this country had been in part distributed among its former Muslin and Jewish inhabitants, and for every show of architectural pomp, there was a little afterthought which troubled full appreciation. I have too much imagination.

The Plaza Mayor was full of stands selling figurines for creches, and the Madrilenes were out in force even in the rain, with wigs, reindeer hats, fake eyelashes and bullhorns, to mull aimlessly around the Puerta del Sol neighborhood. My two major thoughts in the Plaza Mayor were to think of all the bovine and human blood that had been spilled inside those four walls, and of the modern possibilities for terrorist action. Major crowds of people, enclosed spaces, small children nearly getting trampled as it were (especially near the display at the El Cortes Ingles), reminded me incessantly that Madrid, like so many other major cities I’ve been in, was targeted not so long ago.

It’s always party time in Spain, it seems, and Saturday was no exception – it was the 30th anniversary of Spain’s constitution. We made way for the king’s escort. Sunday was open house for all national monuments – so the parliament was open, and quite a popular destination that we had to skirt once more – and the Prado was impracticable, even after 45 minutes’ wait. I was glad we had been to a fantastic museum the day before.

We took the subway to the airport and found it to be rapid, inexpensive and easy.

Not getting a lot of science done right yet. Off to rectify the situation.

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Life science?

Thu
4
Dec 08
Authored by Alethea

There is something sad about passing the lobby of the administration building for my organization devoted to the promotion of life sciences and seeing dead potted plants behind the windows.

Back from Paris and making some headway on various paperwork that matters to me and I hope to some other people as well, else why make the effort?

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Subjunctive memories

Thu
27
Nov 08
Authored by Alethea

The subjunctive is still alive and well in French. I had to write a letter last night to the fellow who intermittently mows our lawn , in which I used the case twice and quite possibly should have done a third time, often following the word “that”:

we would prefer in the future that you bill us each time you actually come by…

Reading others’ posts on Nature Network rather than drafting my own – I was waiting to upload some photos to Flickr – I was tempted to use the phrase, “whistling in the wind”. Suddenly, I was not sure that I was using it correctly. Once I had to look up how to spell “very” as it looked strange. Brain blip.

See, in French, I would have had to write “were using it”. Maybe one should in English, as well?

So I used a search engine, and while I did not quickly find a satisfactory explanation of the idiom, I did come upon Dr. Goodword’s Language Blog, in which this anecdote was recounted:

If you don’t like off-color jokes, skip down to the next paragraph. But there is an old joke that has been floating around Boston for at least a half century about a woman who grabs a cab at the airport and asks to go to downtown Boston. On the way she effusively talks about all the things she wants to do and see on her first trip to that city. Halfway into the city, the driver asks her where she would like to be dropped off. “Anywhere I can get scrod!” she exclaims with glee, thinking of the popular New England fish. “Wow,” replied the driver, obviously not a fish-eater, “That’s the first time I’ve ever heard the subjunctive pluperfect of that verb.”

I scrolled down through August 2007’s archives and when I hit the post on the demise of melodic whistling, I added the blog to my feed reader. If I were more disciplined, I might have resisted the impulse.

Thanks for continuing to read my entries and a happy Thanksgiving to all and sundry.

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Dans le vent

Wed
26
Nov 08
Authored by Alethea

It seems that acknowledging our debts to our predecessors is coming back in fashion, which means that humility and perspective may well follow suit. Hooray!

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Original thoughts

Tue
25
Nov 08
Authored by Alethea

I should preface this by mentioning that I have had a single-digit number of hours of sleep in the last couple of days, so that is probably going to color my world view today.

I’m still receiving the NaNoWriMo pep talks for aspiring novelists in my e-mail. They may serve me in stead some other time. The advice is getting familiar. Stick with it. Push yourself past the point where you hate what you are doing to the point of accomplishment. (Many parallels to extreme sports and child-bearing.) Try not to let yourself distracted.

In fact, this sounds a lot like writing an article for a scientific journal. Or for most other difficult tasks.

When writing up scientific results, I get the added benefit of being fairly original as opposed to when I attempt fiction. Not entirely, for standing on the shoulders of giants (and not even being able to see over their heads most of the time) is the rule, rather than the exception, in science. I hadn’t realized, but how appropriate! that Newton got that metaphor from someone before him.

…have you something to say, or do you merely think you have something to say?

- On the Writer’s Philosophy of Life, By Jack London (The Editor, October, 1899)

This remains a good question, Jack. Let’s ponder it.

Nancy wrote,

You might actually expire before you get there, so why not just stop now?

Simple. Because you want to be a novelist. The difference between a novelist and someone who tinkers around with writing is this: novelists finish their books.

One subject all the pep talk writers carefully avoid is the question of worth. I know I could write a novel of sorts; I’ve written equally painful and long pieces (think, thesis) and even some fiction which is not public(/-shed). I’ve published plenty of other things. So why does anyone want to write anything at all, if you know ahead of time that there are far more books than any one person can already read, and often better than you could produce? And is strong desire alone reason in itself to indulge it?

I firmly believe that if one wants something intensely enough, there is usually a way to attain it. But should anyone want to write any more novels?

I believe the answer to this question is the pride of sharing one’s own philosophy of life. To proclaim, “I’ve worked it out!” and show how applying (or not) your principles can save or sink your characters. (As opposed to “I’ve worked it out!” and showing how applying (or not) your principles can save or sink your cell lines.)

For now, I’ll just stick to what I know, which is performing and reporting the results of experiments. But I’m eyeing a later phase in my life.

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What do you read with your children?

Tue
18
Nov 08
Authored by Alethea

I’ve recently indulged in a series of Nordic crime novels known in their French translation as the Millenium trilogy, by Stieg Larrson. You can surely find it if you want. I was amused to learn that I had read all three before that well-known and widely read critic who keeps the Petrona site, because by all rights it should have been the other way around. Maxine’s book reviews are well worth reading and I agree with them for the ones I have also read (example linked), but my taste in literature (and to a greater extent, music) is so broad it likely lacks some depth.

This is not true for all canons, though, and in particular not the English language children’s literature one. I explored that at a time in my life when I had (a) a surfeit of good guidance from those around me, (b) more time and (c) fewer passions. I arrived at the article from a tip to and link from Neil Gaiman, to whom I know I make a lot of references, not because he is the best of the many good writers whose work I go out of my way to read, but because he is talented, personable and keeps a blog that maintains my interest.

Would I could do the same. But I think I don’t want it enough.

Anyhow, I did relate to this passage in particular:

Europe and America still have a hunger for the shared topic of conversation that is the main benefit of a middlebrow literary culture. The trashy bestsellerdom of the lowbrow may be shared, but it gives us nothing to talk about. The glossy unbestsellerdom of the highbrow may give us something to talk about, but it isn’t shared. Once a middlebrow book reaches a certain number of readers, however, it begins to feed on its success to gain even higher success. Add in the even greater hunger of middlebrow parents for their children to have shared literary references, and you have an appetite ravening for something like Harry Potter to feed it.

What greater pleasure than to share a book you loved with someone you love? My son and I are reading aloud The Adventures of Tom Sawyer, and my daughter and I, Strawberry Girl (after finishing some volumes of the maligned Beverly Cleary). Anyone really from southern Missouri or Florida would laugh their pants off if they heard me, but the kids are having a fahn tahm.

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Wunderpus photogenicus!

Fri
14
Nov 08
Authored by Alethea

ResearchBlogging.orgI can’t believe that is a real species name.

I’ll be up for hearing others that make you crack a smile.

(crossposted from A Developing Passion)

Copyright patcsy888

Copyright patcsy888

Apparently one can track an individual octopus of this species by simply recording its unique pattern of white spots on its back on camera, and these don’t change over time. Much like for whales and their battle scars.

Each animal bore a circular pattern of approximately six white spots in the center of the mantle. However fusions of these spots and the location of additional small markings in this region differed among individuals. Lateral markings also appeared to vary asymmetrically.

My attention was drawn to this article because I’ve been cogitating my next pigment-related post. I’m actually not intellectually that interested in pigment cell or skin biology, but I have a vested personal interest (the Naevus 2000 association general assembly is next weekend) and in vertebrates at least, pigment cells do come from my favorite developmental cell type, the neural crest cell.

However, the octopus is not a vertebrate, as cuddly and smart as it is.

Even I can’t get access to this article but the abstract is fairly informative: the octopus has organs called “chromatophores” which contain different kinds of pigment, and are under neuromuscular control. This enables them to change patterns and camouflage with their environment. They overlie “iridophores” which provide a kind of iridescent, mirror-like light-reflecting surface over which the different colors are deployed like filters.

I don’t know if the white markings of Wunderpus photogenicus are simply the lack of colored pigment in those areas, or a concentration of a special sort of iridophore, or both. I would speculate it is the same sort of thing that keeps their sex organs white – as mentioned by the latter authors, collagen arrangements in the skin can have a high refractive index (think of the tendons in a leg of chicken).

So, as a developmental biologist, looking at this animal makes me think of a few things:

  • Is the genetic mechanism for alternative white and dark patches on the legs related to that which enables the periodicity of segments?
  • How do they get personalized patterns on their backs? And why white? Can the chromatophores cover them up?
  • Isn’t it sort of dangerous to attract predator attention to external sex organs?


Later edit: Thanks to Bob, I was able to access the large article by J.B. Messenger entitled Cephalopod chromatophores: neurobiology and natural history.

The white pigment is from a dedicated cell type, the leucophore:

Most loliginid squids lack leucophores and complete retraction of the chromatophores produces instead the transparency that can be so important for camouflage in epipelagic animals. [Leucophores] are elongated, flattened cells, approximately 20 um long, covered with over 1000 tiny, stalked ‘knobs’, the leucosomes. They are colourless but refractile, the leucosomes scattering light to produce the chalky whites seen in incident white light. {…} It should be recalled, however, that the leucophores will faithfully reflect incident light across the entire visible spectrum and that the so-called ‘white’ areas will appear blue in blue light or red in red light. This may enable the skin to match the hue of the background as well as its brightness.

Gotta love that word, loliginid.

Technorati Profile

Christine L. Huffard, Roy L. Caldwell, Ned DeLoach, David Wayne Gentry, Paul Humann, Bill MacDonald, Bruce Moore, Richard Ross, Takako Uno, Stephen Wong (2008). Individually Unique Body Color Patterns in Octopus (Wunderpus photogenicus) Allow for Photoidentification PLoS ONE, 3 (11) DOI: 10.1371/journal.pone.0003732

This post has 4 comments | Posted in:General

This is progress?

Thu
13
Nov 08
Authored by Alethea

I spent an hour and a half this morning on a regular fluorescence microscope, capturing photos much like this one. The nuclei were supposed to stain blue, and I am not quite sure why they didn’t, but I caught some interesting auto-fluorescence in a compartment which sort of resembles that of the endoplasmic reticulum. Or maybe the Golgi apparatus.

Human neural crest cells in stem cell defined medium. Red is beta-2-microglobulin. Greeny blue vesicles are yours to identify.

Human neural crest cells in stem cell defined medium. Red is beta-2-microglobulin. Greeny blue vesicles are yours to identify.

Then I grabbed a colleague who has been through the training session for the confocal microscope, and had him accompany me downstairs to the confocal so as to look at staining I had performed with a fluorophore that emits light beyond the visible range, in a “far red” (not quite infrared) spectrum (lots of technical details starting here if you want).

He was not able to help me out much with the far red visualization, so when he had to leave, I grabbed the dedicated personnel to ask for her assistance for a few minutes. Not only did she give it to me, but she said she was starting a new 4-hour training session on the confocal next Monday and Tuesday, and would I like to attend? Would I!

More speculation about the nature of the stuff that fluoresces green and blue in blue and ultraviolet light, respectively. A close-up of some odd non polymerized staining for alpha-smooth muscle actin in red showed lots of little empty blobs, which themselves fluoresce blue (and less intensely, in green) although I did not stain them in these colors. Check out especially the left side of the photo. They remind me of the phase-dark speckles I had seen in light microscopy, and indeed, seem to be in much the same position.

Golgi and perhaps melanosomes or lysosomes?

Golgi and perhaps melanosomes or lysosomes?

No fluorochromes needed.

No fluorochromes needed.

Finally, there had been a set of cells in one culture condition (the “401″ medium) that seemed to veer toward early melanocytes. I am waiting for an antibody that will help me demonstrate that, but even the unpolymerized alpha smooth muscle actin had an interesting granular, perinuclear distribution. And not in the cells where the actin had polymerized.

Alpha smooth muscle unpolymerized actin in human neural crest cells in 401 medium.

Alpha smooth muscle unpolymerized actin in human neural crest cells in 401 medium.

Melanosomes in phase microscopy?

Melanosomes in phase microscopy?

It seems like today’s post is going to near enough take the place of my online lab notebook.

This post has 2 comments | Posted in:development, laboratory

Jason’s jingle

Tue
11
Nov 08
Authored by Alethea

My cousin, Jason, is a musician. Like most others, he is struggling. He has recently taken part in a jingle contest that entails winning a car, which he could most certainly use.

His jingle has reached the ten finalist videos for a furniture store advertisement.

Bernie and Phyl’s is currently garnering votes for the videos and I am requesting that you take a few minutes, put in any birthdate of your choice (grr), and vote for Jason’s jingle by clicking on the first link above. But they do ask for an e-mail address, and follow it up with a “welcome” message. I put in a fake e-mail next, and their system seems to be happy. But I don’t know if that will help Jason much in the end, and it’s probably not the point of their voting thingy.

Any store that has a print out coupon on their front webpage entitled “The Obama administration brings us hope for a revitalized economy!” is kind of cute, and I’d be grateful on Jason’s behalf. No need to live in Massachusetts, and results on November 24th.

Thanks!

Update: he didn’t win… but got himself a gift certificate for $100 worth of furniture.

This post has 2 comments | Posted in:General

Off topic

Fri
7
Nov 08
Authored by Alethea

If this is supposed to be my column about the exciting aspects of labelling cells with antibodies against various potential components inside and then again with colored fluorochromes that will single out certain kinds of those antibodies from others, making your cells glow in wonderful colors under a fluorescent microscope, you’ve come to the wrong place.

Looking at the results is the best part, but making them is actually pretty boring.

I’ve been also trying to teach myself a software that will allow me to align millions of short sequence reads with the reference human genome, and see where more of them pile up. Such peaks will allow us to believe that the precipitation of those bits of DNA by locking on the bound proteins, then dragging them out of solution, are the normal sequence-specific targets of those proteins.

The technique is called chromatin immunoprecipitation or ChIP; my Paris student Ms. DQ is getting to be an ace at it, but we’re all learning fast on the fly. Here in Toulouse, we’re trying out writing a new protocol that includes microscopic bits of iron that will allow us to separate out the protein-DNA complexes from the rest of the cell lysate with a super-powerful magnet. I had invested in products from one company that I had used before, and then chose another in the end. Brand loyalty isn’t everything.

I’m trying to tie up loose ends in the next 1/2 hour because it’s a four-day long weekend coming up, so I need to feed my live cells, rinse my dead cells and put coverslips on, and leave!

Have a great weekend, everyone. Oh yes, here’s a delightful link for Obama fans out there.

This post has 2 comments | Posted in:General

Thanksgiving came early this year

Wed
5
Nov 08
Authored by Alethea

This IS our time. Thank you, Mr. President, and thank you to the countless people who brought you to office.

As you will see anywhere you look today, yes, we did. I’m truly proud to be American, and I finally feel like my voice is also heard, even from afar. That for the millions of voices who had not been heard, today they were as well.

Thank you.

This post has 2 comments | Posted in:politics

Blogging blackout

Tue
4
Nov 08
Authored by Alethea

I do not think I have anything particularly insightful to add to the election coverage. I voted, and am pleased to see that my candidate is a frontrunner for once. So I’ll be keeping quiet for the next twenty-four hours.

Figures: my spam filter has caught some 18,000 spam since it was first installed by the Science Advisory Board IT folks (to whom after all this time, I still can not put a name). I’ve made 462 posts since I started this blog, initially to win some lunch money for my research group, whom I thought would furnish more material than I actually feel comfortable in writing about.

For example, my postdoc is pregnant, and I’m thrilled for her, but she won’t be entering the concours this spring for new permanent positions. Which means that the following time, she had better make it; she’ll attempt to apply for university/teaching positions meantime. And I’ve already written about how easy that can be.

This post has 3 comments | Posted in:General, laboratory, personal, politics

NaNoWriMo will not happen for me this year

Mon
3
Nov 08
Authored by Alethea

But it’s not too late for you

And I’m feeling better about it, thanks to similar support to that you can get on the NNWM writers’ forums. (Forums? True, fora sounds a little strange, since it makes me think of forage and foramina, but it still seems wrong.)

This post has no comments | Posted in:General

It has been brought to my attention…

Thu
30
Oct 08
Authored by Alethea

Today on my way to lunch I passed a homeless guy with a sign that read “Vote Obama, I need the money”. I laughed.

Once in the restaurant _my server had on an Obama 08 tie,  again I laughed as he had given me his political preference–just imagine the coincidence.

When the bill came I decided not to tip the server and explained to him that I was exploring the Obama redistribution of wealth concept. He stood there in disbelief while I told him that I was going to redistribute his tip to someone who I deemed more in need–the homeless guy outside. The server angrily stormed from my sight.

I went outside, gave the homeless guy $5 and told him to thank the server inside as I’ve decided he could use the money more. The homeless guy was grateful.

At the end of my rather unscientific redistribution experiment I realized the homeless guy was grateful for the money he did not earn, but the waiter was pretty angry that I gave away the money he did earn even though the actual recipient needed money more.

I guess redistribution of wealth is an easier thing to swallow in concept than in practical application.

The anecdote cited above surfaced on the Internet around October 21st and has made the rounds of similarly minded political blogging sites. My uncle sent it to me by e-mail, trying to get a rise. He got an answer.

It may be from a public opinion piece in the (Massachusetts) Eagle Tribune – but they don’t keep such pieces more than a week online.

Paul C. Campos wrote an essay in the same newspaper the following Sunday, October 26th.

“…saying that you don’t believe in redistribution of wealth is like saying you don’t believe in gravity. All politics that deviate from the economic status quo redistribute wealth, and the present status quo itself always engaged in some redistribution of wealth from a previous arrangement.

For example, the last 30 years have featured a massive redistribution of wealth in America from everybody else to the top one percent, and, much more radically, the top one-tenth of one percent (that is, the richest thousandth) of Americans.”

The fallacy in the little e-mailed anecdote comes from the emphasis on I deemed. Luckily, we live in a democracy. If the majority decides to elect representatives who will ensure that people like this restaurant-goer have to pay more taxes, them’s the rules. Such an approach could ensure that both the waiter AND the “homeless guy” have equal opportunities to earn enough to go to restaurants and try to be similarly funny with the suffering once-essayist.

Looking forward to that day.

This post has 2 comments | Posted in:politics

Getting bigger as you get older – but shrunken when you’re really old

Tue
28
Oct 08
Authored by Alethea

This last weekend was my 20th anniversary high school reunion. I did not attend. This was not out of any principle but simply that I live too far away and have too many commitments locally to bother. I felt a twinge of regret at the time I declined the inclination, but then a Facebook group started up, and I feel no more regret. Especially after having examined a good number of the photographs of the occasion.

There’s been a lot of middle-age spread in our class of 500+ kids. Middle-age spread is a universal given for all high school reunions at t=n+20, at least for those survivors out there, which in the case of my middle-class upbringing means a vast majority of them. I’m rather glad I didn’t have to hide my first reactions of “wow – you’ve changed!” I am not so skilled at that sort of dissimulation, and they may have taken it badly. I’m also struck at the universality of how most American women style their hair nowadays, although the women have aged better than the men overall and that may contribute to it. Though I didn’t think grey hair bothered me. I saw a photo of the woman whose mother passed along her hand-me-downs for me for years, a situation I did not live well as a teenager. What on earth would I have said to her?

Instead, I spend a gorgeous long weekend in the Pyrenees with my family minus my son, who is visiting a friend, plus my brother from the U.S. and a local girlfriend of mine who joined us Sunday night. Saturday afternoon on arrival, we drove up to the end of our valley and walked up to the Col d’Azet. There was fresh snow on the top halves of all the mountains. Sunday. we hiked in to the national park along some of the little “laquettes” in the Néouvielle natural reserve and up to the Lacs d’Aumar and Aubert. My brother found that to be quite enough in his sandals. Yesterday, we drove through the Cols d’Aspin and Tourmalet, stopping to take the cable up to the Pic du Midi de Bigorre, from where we saw the bad weather sweeping in from the plains. Finally, we drove off to the Plateau de Saugué from where we had a fantastic view of the Cirque de Gavarnie and the tallest waterfall in Europe, and made it back down before the heavens opened.

May the erstwhile Tigers forgive me.

When I looked back in on Nature Network, I saw that some conversations never die.

It’s good to be back at work, but when I got called away to the fluorescence microscope, I was reminded what work really is.

This post has 4 comments | Posted in:General, personal
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