You'd Prefer An Argonaute

Harry Noller got shafted by the 2009 Nobel Prize in Chemistry

Posted in Gallimaufry, Media by YPAA on October 7, 2009

“For studies of the structure and function of the ribosome,” the prize was awarded. Why not Harry Noller then, whose entire illustrious career has focused on the structure and function of the ribosome? That’s bullshit.

Unfortunately this egregious omission by the Nobel Assembly pollutes recognition of momentous work that has taught us so much about what RNA can do.

(Santa Cruz Sentinel article with Harry’s reaction here.)

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Da Prize

Posted in Gallimaufry, Media by YPAA on October 5, 2009

You’ve probably heard the news by now: the 2009 Nobel Prize in Physiology or Medicine was awarded to Elizabeth Blackburn, Carol Greider and Jack Szostak for the discovery of “how chromosomes are protected by telomeres and the enzyme telomerase,” in the words of the Nobel Assembly. Awesome. Congrats to these superb researchers for their smashing work.

The Sounds of Science

Posted in Gallimaufry by YPAA on July 26, 2009

While sifting through my iTunes library recently, I came across more than a handful of songs on the subject of science. Sometimes the lyrics directly address science, sometimes the reference is more tangential, and sometimes only the song title is relevant. I’ve included links to audio/video (of mixed quality).

Biology

Do The Evolution – Pearl Jam

Do it. Dooooooo it.

This land is mine, this land is free
I’ll do what I want but irresponsibly
It’s evolution, baby

General

The Sounds of Science – The Beastie Boys

I’ve got science for any occasion
Postulating theorems formulating equations
Cheech wizard in a snow blizzard
Eating chicken gizzards with a girl named Lizzy
Dropping science like Galileo dropped the orange

The Scientists – Hum

She said I made some new connections to astound them all
in ways we’ve never dreamed about

This is what we all dream about in lab. One of my favorite bands couldn’t have stated it better.

My Mathematical Mind – Spoon

Yeah, damn this thing. Why must it insist on half-a-tick-mark accuracy on my P1000?!

Physics

Why Does The Sun Shine? (The Sun Is A Mass Of Incandescent Gas) – They Might Be Giants

Ok, this song definitely takes the cake for the scienceiest song from a legitimate rock band I’ve ever heard.
You must listen to it–it’s a real hoot.

The sun is a mass of incandescent gas
A gigantic nuclear furnace
Where hydrogen is built into helium
At a temperature of millions of degrees

What Is The Light? – The Flaming Lips

What is the light
That you have
Shining all around you?
Is it chemically derived?

Colours – Hot Chip

Colors are a fascinating physical phenomenon. This song has a real nice melody, and sounds really sciencey too.

Chemistry

Polyethylene (Parts 1&2) – Radiohead

So sell your suit and tie and come and live with me
Leukemia schizophrenia polyethylene
There is no significant risk to your health
She used to be beautiful once as well

Plastic bag, middle class, polyethylene
Decaffeinate, unleaded, keep all surfaces clean

The Chemistry Of Common Life – Fucked Up

Here but for the spinning of a sphere,
Electric skies and vibrations rise the breach,
the birth, the seed inside,
The chemistry of common life

Chemical Elements

Lithium – Nirvana

Cobain was speaking about atomic number 3; or maybe he was talking about mood stabilizing drugs.
Who cares the song rocks.

Aluminum – The White Stripes

The great Detroit troubadour Jack White went simple for the lyrics to this song.
Oh yeah, and this track is off their album White Blood Cells.

AAaahhhhhhhhhhhhh!
AAaahhhhhhhhhhhhh!
AAaahhhhhhhhhhhhh!

BioMedicine

Better Living Through Chemistry – Queens Of The Stone Age

The blue pill opens your eyes
Is there a better way?
A new religion prescribed
To those without the faith

Sister Morphine – The Rolling Stones

Here I lie in my hospital bed
Tell me, Sister Morphine, when are you coming round again?
Oh, I don’t think I can wait that long
Oh, you see that I’m not that strong

Cocaine Blues – Bob Dylan

Hey baby you better come here quick
This ol’ cocaine is making me sick
Cocaine all around my brain

Yeah, it’ll do that.

Space

Man On The Moon – R.E.M.

If you believed they put a man on the moon, man on the moon
. . . Newton got beaned by the apple good. Yeah, yeah, yeah, yeah
. . . Mister Charles Darwin had the gall to ask. Yeah, yeah, yeah, yeah

The Apollo Programme Was A Hoax – Refused

No it wasn’t. It happened. Listen to the R.E.M. song.

Polemic and Beyond

Science – System Of A Down

Science fails to recognize the single most
potent element of human existence
letting the reigns go to the unfolding
is faith, faith, faith, faith

What Would Wolves Do? – Les Savy Fav

The world may seem cruel
The world may hate us
In time we will show the world why the world made us

God Makes No Mistakes – Loretta Lynn

You might be wondering why a song with this title is on this list. I find the lyrics really fascinating actually; while a scientist’s explanation for these “mistakes” may be far simpler, they are probably unlikely to resonate as profoundly as Lynn’s with most people.

Why I’ve heard people say
Why is my child blind
Why is that old drunk still livin’
When a daddy like mine is dyin’
our blessed father gives us life
has the power to take it away
There’s no reason for what he does
God makes no mistakes

Hawt RNA Blogs

Posted in Gallimaufry by YPAA on July 6, 2009

Yikes.

As YPAA seeks to spread its scientific cred throughout the blogosphere, I am keen on knowing what other RNA blogs I will step over. So what’s the other hot RNA blog right now? Probably this one: The Romantic Novelists’ Association Blog.

Their name is much more descriptive than YPAA; the topic is far more sensorial. My blog has recently spotlighted literature with titles like, Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps. The other RNA blog, No Longer Forbidden and  Surrender to the Playboy Sheikh,  among others. A recent update of theirs has a recipe for ice cream, which apparently goes really well with romance novels.

So I ask, what goes really well with RNA primary literature?

Pizza. Pizza is the answer.

mediabistro.com

mediabistro.com

spicemagazineonline.com

spicemagazineonline.com

Wikipedia

The History of the Argonaute, Part 1

Posted in Gallimaufry by YPAA on June 27, 2009

Why was the the Argonaute (Ago) protein named “Argonaute?” Why wasn’t it named “The Slicenator”, or “Chopinator” or some other cool sounding name reflecting the activity many Ago proteins possess? Or, following Eric Lander‘s description of Ago’s activity as “enzymatic kung-fu” (beginning at 7:20 in Part 1) in the wonderfully done NOVA program introducing RNAi below, how about “sensei”?

Part 1 of the NOVA RNAi program:

Part 2 of the NOVA RNAi program:

 

The answer to the above question is that the cleavage activity of plant AGO1 of nearly perfect matched targets was not completely worked out at the time it was named. What follows below is a simple graphic depicting the most well characterized domains of Argonaute, a very brief history of how the protein was named, and where the name comes from.

 

Argonaute

The above graphic is from a class presentation I gave in 2007. Not shown/labeled are the N-terminal or Mid domains also common to eukaryotic Argonaute proteins.

 

 

arabAgo

Arabodopsis AGO1 mutant, 1998 (1)

Drawing of Male and Female Argonaute, (not to scale), 18th century

Drawing of Argonauta Argo, male and female, 18th century (2)

The name Argonaute comes from phenotypes observed for AGO1 mutants in Arabidopsis thaliana by Bohmert and collaborators in 1998 (1). To the researchers eyes, the plants resembled the tentacles of the pelagic octopus, Argonauta argo. In the paper, the authors state:

Because of their unusual appearance, which reminded us of a small squid, we named these mutants argonaute.

So then how were the marine Argonauts named? It is thought that early taxonomists were enamored with tales of sitings of Argonauts “sailing” along the surface of the sea; females using their paper-thin eggcase shell as a boat, and their webbed dorsal arms (in the drawing above the webbed portions are resting against side of shell) raised above the surface acting as sails (6). (This method of propulsion is today considered a myth, as it has never been observed by marine scientists.) To these taxonomists perhaps this image bore semblance to great ancient wooden sail ships, like “Argo”, (built by Argus, who may have come from the city of Argos), sailed by Jason and the Argonauts in Greek mythology. The Argonauts –named for the ship they sailed– were a group of brawny, fearless men selected by Jason to join him on his perilous journey to recover the “Golden Fleece”, an undertaking that would finally allow him to rightfully claim the throne as king of Iolcus.

In 1963, a movie was released depicting this mythical tale. The movie is pretty good, and apparently was a special effects pioneer in its day. An unofficial trailer:

The word Argonaute has been used in a variety of other contexts as well. For example, in the 1950’s the French navy named their flagship submarine “Argonaute.” The “Argonaut Conference” was the codename for the Yalta Conference held in Crimea in 1945 that brought together Winston Churchill, FDR, and Joseph Stalin.

Wikipedia

In attendance at the Argonaut Conference, 1945: Winston Churchill, FDR, and Joseph Stalin (3)

Argonaute tree, present day (5)

Argonaute phylogenetic tree, present day (5). Argonaute-like group in black, PIWI-like group in green, C. elegans group 3 in red

A sharp increase in genome sequencing and small RNA research in the last decade has lead to the discovery of many more Argonaute genes (including Ago, PIWI-like, and Group 3 in worms (4)), a trend that will surely continue.

Presently in C. elegans, there are >25 known Argonaute genes; 10 in plants; 8 in humans (4 Agos and 4 PIWIs) (5).

Feeling a bit depleted of Argonautes myself, I reckon I’d prefer a few more.

References:

  1. Bohmert et al., The EMBO Journal Vol.17 No.1 pp.170–180, 1998.
  2. Internet (reference forthcoming)
  3. http://en.wikipedia.org/wiki/Yalta_Conference
  4. Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi.; Cell. 2006
  5. Hutvagner and Simard, Nature Reviews Molecular Cell Biology 9, 22-32, January 2008.
  6. http://researchdata.museum.vic.gov.au/argosearch/index.html

Hummers sell paranoia

Posted in Gallimaufry by YPAA on June 15, 2009

While walking through the MIT campus this evening I passed by a parked red Hummer truck emblazoned with the word “BioDefense.” The ostentatious and environmentally ruinous Hummer as a vehicle to protect life from harm? Ironic yes, but actually probably a travel vehicle, and advertisement, owned by a company named BioDefense corporation. They sell a device called the “MailDefender”, a chamber that converts your anthrax, smallpox, plague, E. coli, influenza, HIV, botulism, ricin, and bird flu laced mail into safe reading.

OK, I don’t mean to be facetious – I’m aware people have died from such bioterrorist mail – but I’m amused by any product advertised on the side of a Hummer.

view

Surely the long-range lights (see roof) stop anthrax in its tracks. And botulism is no match for that grill bar.

I drove a Hummer once and couldn’t stop laughing. It was a big, bright orange disaster, with enourmous tires so tall that they reached my belly. You know a street vehicle is ridiculous when you need to grab a handle to pull yourself in.

So I was sad when I read Chinese investors decided to buy the Hummer brand. Hummer is the one GM species I wanted to see go extinct.