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Some California milk has been found to be (exceedingly mildly) radioactive.  Glowing milkshakes, here we come!

(or maybe we'll just have cows with glowing eyes.)

(Disclaimer: Glowing eyes not actually a result of radioactivity, sorry.)

Oh right.

Jan. 24th, 2011 08:27 pm
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Not that I ever questioned my decision to leave grad school and quit with a Master's, but this video tells a story that is all too true for a number of people I've known....

hmph.  Embedding doesn't seem to work.  Follow this link to a biology lab's parody of the Lady Gaga song "Bad Romance", modified to "Bad Project."
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The Periodic Table of Videos (videos made by a group of chemists at Nottingham University who present information about the elements in fun and entertaining ways) just celebrated its first birthday!  They did so by talking about the chemistry of cake, and baking a birthday cake in the lab:

And then they attempted to destroy the cake:

It probably says something about me that I thought the neatest bit was the playing of test-tubes-cum-pan-flute, not the playing with liquid oxygen and fire, hm?

(These guys also have bloopers - failed or screwed-up demonstrations - in their "Extra Videos" section which are amusing as well; just do a text search for 'bloopers' to find them.)

Thanks, kayray!
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People have been working on stem cells for a bit of a while now, getting them to turn into this, that, and the other type of specialized cell.  Truly totipotent stem cells (cells that can turn into any kind of cell in the body) are generally harvested from fetuses/embryos or cord blood or something along those lines.  Because of moral concerns with the use of these sorts of cells, there's been a push to induce more mature (and thereby more differentiated) cells back to a multipotent state, so they can then be nudged into becoming new types of cells.  As one might imagine, this is neither an easy nor swift process.

In a newly published paper in Nature, a Stanford lab reports the thoroughly remarkable direct transformation of mouse skin cells into fully functioning neurons.  (I have yet to read the paper itself; linky link is to the Stanford Report page.)  Wow.  Just... wow.  This could be an extremely useful advance in stem cell research, folks. 

And with that, happy Friday!
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I've recently been informed that the Halloween party traditional at the annual department retreat may be replaced by "something that might resemble Oktoberfest and a short-sketch show possibly with group singing."  Being the sort of person I am, this immediately provoked a web search for science-based songs that I could sing. 

I was already familiar with a few, namely Tom Lehrer's Elements, Monty Python's Galaxy Song, and The Amphioxus Song (the latter stumbled upon when I was working at the genome center and doing amphioxus finishing).  And I knew a bunch of programmer/sci-fi filk songs (HAL's Song - it's in the comments, search for "I sent Frank to fix the antenna" and sing it to "My bonnie lies over the ocean", You Can Build a Mainframe From the Things You Find at Home), but those seemed inappropriate for the group.  Surely, surely there were more out there. 

Surprise!  There are!

The journal Nature runs a blog called The Great Beyond that has collected a whole lotta science songs, many with videos.  There's possibilities there.  They also link in one of those posts to rips of Singing Science records, a six-LP set for kids produced in the "late 1950s / early 1960s by Hy Zaret and Lou Singer. (Zaret's main claim to fame is writing the lyrics to the classic "Unchained >Melody" for the 1955 movie "Unchained", later recorded by the Righteous Brothers and more recently used in 'Ghost'.)"  I listened to much of "What is an Animal?" before I broke under the wave of saccharine cuteness-for-5-year-olds and turned it off.

Happy Friday!

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Ganked from [ profile] orichalcum , mostly for the benefit of the portion of my friendslist that doesn't overlap with hers:

Dead fish lights up when shown pictures of humans, a study that shows that neuroimaging experiments can give a lot of false positives.


In other work-related news:

• We've begun the Big Project that I've been making stuff for, like, a year for!  On a practical level, this means that I do pretty much the same physical actions day after day for probably about the next month and a half, doing a gazillion transfections.  It's tiring, believe me.

• It's nice to have a perfectly sensible explanation as to why a particular cloning didn't work.  It helps to have both enzymes functional in a double digest, just for example.

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There's a pretty interesting pair of essays over at the Wall Street Journal by Karen Armstrong (comparative theologian) and Richard Dawkins (evolutionary biologist) on the subject of "Where does evolution leave God?" 

I don't have time or energy to write a bunch in terms of my response, but briefly: if his writing is a true indication, Dawkins seems to have a rapturous experience when he considers the wealth and complexity of living things.  Some might compare  his sensation to the rapture a religious person has when in communion with the Divine, and Armstrong herself points this similarity out near the end of her essay.  Both essays are interesting reads; perhaps unsurprisingly, I come down much more on Armstrong's side of the discussion.
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A bunch of scientists at IBM.... or a handful of guys getting ready to play Rock Band/Guitar Hero with the drum kit?

You decide!

(Image ganked from this article.)

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What the heck kind of protein has a string of seven histidines followed by six asparagines???!?

No, I'm not dead. I'm just very busy looking at protein sequences, seeing if they have a sequence at the beginning to tell them to be extracellular proteins (a signal sequence) and a sequence sometime later that tells it to be stuck to the cell membrane in some way or other (which it might not have at all).

Eighteen down (over the last several days), 44 or 45 to go.

And I've even started on the next China entry! Someday, I might even be able to complete it!
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As many of you know, the Large Hadron Supercollider fires up real soon now, trying to make little black holes or the Higgs boson or something. It got asked about at the Ask a Scientist thread over on the Librivox forums, and Steampunk gave a nice description of what might happen if a tiny black hole actually got created.

He also posted a link to this explanatory cartoon. Even non-scientists are likely to be amused. :)
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I just used Google to look up 'eukaryotic codon table,' since I couldn't remember off the top of my head exactly what the three stop codons were.

The first hit? "Codon - CreationWiki, the encyclopedia of creation science."

(To be fair, it did give me the information I needed. But... wow.)

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I have just received  a protocol from another lab, which involves transferring materials from one 96-well block to another.  (For non-wetlab types, these are blocks with 96 tiny little bowls in it, in which the 'bowls' - or, more properly, wells - are arrayed in a 12x8 grid.)  There's a neat gadget called a multiwell pipettor that allows you to pick up a set volume from 8 or 12 of these wells at the same time, for dispensing into a second block. 

I kid you not, here's what the protocol says about transferring the stuff from one block to another.
Pipette first column/row.
Pipette second column/row.
Until plate is complete.
Um.  Duh.  If you don't change tips between rows, then you're going to contaminate later wells with the little bits of liquid that always get left behind from the earlier rows.  There are people who need to have this clarified???


Aug. 24th, 2008 07:47 pm
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Yow!  Three people were (as far as I know) randomly shot this morning out on El Camino, about half a mile from our house, between us and [profile] nezumiko .  Non-fatal, but nonetheless, this was literally a little too close to home.  News story is here.

Meanwhile, note to self: 50-ml conical tubes are not compatible with the fixed-angle Sorvall rotor in my new lab.  I think I might actually have known that some time ago; I guess I've been reminded now.

(Anyone know why Firefox 3.0 insists on trying to break URLs if I put them in via Rich Text?  It's really kind of annoying.  The little 'edit URL' box reappears when I add tags or try to post or do anything in the box below the entry area, and insists on putting a 'javascript void' error where the html tag ought to be.)
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According to this AP article, "The Bush administration wants federal agencies to decide for themselves whether construction projects such as highways, dams and mines might harm endangered animals and plants. The new regulations, which don't require the approval of Congress, would reduce the mandatory, independent reviews government scientists have been performing for 35 years, according to a draft obtained by The Associated Press.

...The draft rules would bar federal agencies from assessing the emissions from projects that contribute to global warming and its effect on species and habitats.

"We need to focus our efforts where they will do the most good," Kempthorne said in a news conference organized quickly after AP reported details of the proposal. "It is important to use our time and resources to protect the most vulnerable species. It is not possible to draw a link between greenhouse gas emissions and distant observations of impacts on species.


Science?  We don't need any lousy science here!

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I'm probably the only person on my friends-list, who upon seeing the slightly redesigned Safeway logo

immediately thought it looked like a C. elegans dumpy mutant

(this isn't quite the image I had in mind; there's a dumpy mutant out there that has an even more foreshortened nose and tail than this guy!).

...Yep, I thought so.
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I got handed some new library assignments earlier today.  My supervisor is kind enough to note at the top of the list what organism(s) the libraries will be made of, and I like to keep track. 

New species: Brachypodium (Brachypodium distachyon, if you're being really proper about it).  The Department of Energy has a 'Why sequence this?' page here.  Turns out it's a good model organism for stuff like barley and switchgrass.  Switchgrass is particularly interesting because it's come up recently as a good target for ethanol production (to replace the not-terribly-efficient-but-politically-strong-ethanol-crop, corn).   As usual, I won't see any of the data I generate, unless I specifically go looking for it, but it's nice to know what sort of thing will be done with the data by other people.  :)

Happy Friday, everyone!
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Yesterday evening I caught sight of this headline over at Google News, about PS3s being used in distributed computing problems.  It reminded me about a project that the huz and I had been slightly involved in some time ago, largely due to his PhD work in simulating protein folding.  Vijay Pande's lab over at Stanford University has been running the Folding@Home project for some years now.  The basic idea is that simulating a protein folding over any reasonable length of time with any reasonable amount of accuracy takes a huge amount of processing power.  The folks at Folding@Home are running a system where small bits of the processing are farmed out to many many many individual computers all over the world.  The individual computers then send back the results of their itty bitty bits of processing to the main computers back at the Pande lab, and the lab puts all the results together.  It's a pretty neat project.

Anyway, it occurred to me that my computer at work is on all day, largely sitting and running a screensaver (if it's not doing something terribly exciting such as running an Excel spreadsheet - that's most of the work-related business that this computer does!), and that I could very easily put it to work doing something that's actually useful to someone.  So I've downloaded the graphical interface module and am currently watching a model of supervillin bounce around.

If you're more into space stuff than proteins, there's also the SETI@Home project, which I believe was actually first on the block to come up with the massively-distributed-computing idea.  It distributes analysis of radiotelescope data in the search for extraterrestrial intelligence.  I probably wouldn't get into any trouble with running that at work as well, but I'd rather be running something which is a bit more closely related to what I actually work on.

If you've got some computing power to spare, do consider contributing to one of these projects.  If you start it running before you leave for the weekend, who knows what your computer might fold or find by the time you come back on Monday?  :)
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The area where we live had truly beautiful weather this weekend; temperatures were in the 60s and 70s. I was outside doing some weeding Saturday afternoon when a neighbor's little girl passed by with a paper bag in her arms. "Want some lemons?" she asked. I looked up at her and replied that sure, I'd take a couple. "Okay," she said cheerfully, continuing down the street. "I'll be right back with your lemons!"

I went back to my weeding. There had been some rain earlier in the week, and the warmth and the wet had brought up a whole new crop of oxalis, a plant that looks kind of like clover. It's a weed that's astonishingly good at spreading itself: it can grow new plants from bits of root left in the soil, it can have sex like other flowering plants, and it can reproduce asexually by means of little bulb-like appendages it grows on its roots. It's horribly pernicious stuff. Anyway,I dug and pulled a few minutes more before the little girl came skipping back, again with a paper bag in her arms. "Here's your lemons," she panted as she handed me the bag. "We're pruning our tree, and we've got this huge bag of lemons that we don't know what to do with!"

I thanked her as I received the bag. From its heft (and from the girl's comments), it clearly contained significantly more than the 'couple' that I'd said I'd take. I looked in, and sure enough there were around a dozen of the things. I stepped inside and told the huz that we needed to do something with lemons for dinner that night.

Interestingly, the lemons that we had been given were not the standard bright yellow fruits that are commonly seen in your local grocery. These fruits were lemon-shaped and smelled lemony, but their skins were quite distinctly orange. These were Meyer lemons, a cross between a true lemon and (probably) a mandarin or sweet orange (Wikipedia). The fruit is hard to find in groceries even out here, but plenty of folks have Meyer lemon trees in their yards as our neighbors do. As one might guess, Meyer lemons are sweeter and have a fruitier flavor than their true lemon cousins, but they can be used in essentially the same fashion in cooking.

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Stumbled upon this and this earlier today, surfing at random from In the Pipeline (in links collection up top).  Apparently, little kids are really really good at memorizing physical names and characteristics of Pokemon characters - not a surprise; think about the last dinosaur-crazy kid you met.  In this particular study, the children interviewed were much better at identifying Pokemon characters than they were with real-world animals.  Indicates a need for exposing them to more real-world stuff, huh.

(I haven't read the actual Science article yet; hopefully will do in the next few days.


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