Jack July

This is the structure of the protein Cip1, which calls itself...

Fri, 04 Dec 2009 19:38:06 -0500

This is the structure of the protein Cip1, which calls itself CDKN1A when it’s hanging with cyclin-dependent kinases, and p21 when it’s stressed out and reminiscing over its time as an anonymous 21-kilodalton migrating protein band.

p21 works with p53, who acts as a gatekeeper for cells that are deciding whether to divide. When p21 and p53 aren’t around, all hell breaks loose, though they’re still much too small for the diatom party (?).

Special thanks to my 1986 mac for crashing 8 times while posting this and for refusing to insert links.

Dear Yuban: Fuck your coffee.

Tue, 24 Nov 2009 19:37:57 -0500

Yu(ban) bastards, it has been months since I’ve been this angry at a *thing*. Yur coffee is not simply weak or unimpressive, the route to mediocrity taken by coffee served in sports bars, realty offices, hospital waiting rooms, and movie theaters. No. Yu push the envelope, yu develop a coffee that is AGGRESIVELY BAD. Each time I drink it, I literally have to brush my teeth before speaking with anyone (note: this is true). A deep, thorough brushing like arriving in prison or waking up in a storm drain.

Yu have raped my mouth, yuban coffee; yu have given me a new compulsion, yuban coffee, so fuck yu.

Jack Burden, the protagonist in R.P. Warren’s All the...

Mon, 23 Nov 2009 22:02:09 -0500

Jack Burden, the protagonist in R.P. Warren’s All the King’s Men, calls himself a ‘student of history’, believing that the present and the future are not simply products or consequences of the past, but are in fact the past transformed. All of the past for Jack Burden therefore lives, its continuity never hidden but still unseen.

Stalin, himself a student of history, maintained an obsessive grip on the present through the manipulation of the past. Here, Stalin appears in a photo with and then without Nikolai Yezhov (also known as ‘Blackberry’), the one time head of the NKVD and a cult of personality during the Great Purge. During Yezhov’s rule of the NKVD, he ruthlessly prosecuted its former head, Yagoda, fabricating evidence against him and others which led to the execution of thousands of party officials. Yezhov then himself fell by the same means, his power usurped, his own motives scrutinized and twisted until he crumbled, eventually confessing to crimes which warranted death. Following his fall and execution, Yezhov was removed from Soviet history, not simply renounced but disappeared, leaving not a blemish but a vacuum.

Ån Anecdote: The Terrific Storm of the 12th of July Last:

Wed, 04 Nov 2009 17:00:59 -0500

During the terrific storm of the 12^th of July last, a labourer’s cottage was struck by lightning at Leagrave, near here. The lightning descended, according to an eye-witness’s report, like a “spout of fire,” and struck and descended the chimney, which it destroyed. In the room below there was an old shepherd, an invalid woman, a child and a shepherd’s dog. The shepherd was sitting in a chair leaning on a stick, a kettle was boiling on the fire, and the door was open. The lightning entered the room simultaneously by the chimney and an adjoining window. The window was utterly destroyed, and the kettle was thrown from the fire across the room, the stick on which the shepherd was leaning was torn from his hand and also thrown across the room, the lightning entered a cupboard containing glass and crockery and destroyed every article, and plaster was torn from the walls. The man and woman remained unhurt, but the child was thrown down and its knees stiffened. The dog was struck perfectly stiff, “like a log of wood,” and was considered dead. The room seemed full of fire, water, and sulphur, and the occupants said the smell of sulphur was so strong that they would certainly have been suffocated had it not been for the open door. After the storm had abated, the dog, with all its limbs stiff, was laid in a barn, where it very slowly and partially recovered. It long remained both deaf and blind, and was entirely dependent upon smell for its recognition of persons and things.

-An 1889 account in Nature-

Diatoms and algae, from this pictorial. Also my first glimpse...

Sat, 17 Oct 2009 15:01:56 -0400

Diatoms and algae, from this pictorial. Also my first glimpse of the diatom party.

3.5 billion-year-old stromatolites composed of fossilized...

Mon, 05 Oct 2009 18:08:38 -0400

3.5 billion-year-old stromatolites composed of fossilized cyanobacteria in Glacier National Park.

From the wikipedia page on abiogenesis, the arisal of life on earth from inanimate matter. At 4.5 billion years old, the Earth plenty of time to think things over before the animalcule party arrived.

It has been shown that simulating the conditions of the early earth allows for the spontaneous synthesis of certain molecules necessary for life, though such spontaneous generation has not been demonstrated for other molecules (or for other planets). To prove the feasibility of biological self-assembly from non-biological precursors, several groups aim to synthesize entire proto-cells, hypothetical precursors to self-replicating bacteria, for example. Some of the problems encountered involve the generation of lipids for membranes, the self-nucleation of enclosed vesicles to delineate a distinct internal chemical environment, and the passage of nucleic acids through membranes and into the protocellular space, where they can act as information storage molecules, or, as in the case of ribozymes, can catalyze chemical reactions. Harvard’s Jack Szostak, who won the Nobel Prize today for unrelated work, leads this field and has some excellent simulations of nucleic acid passage and lipid growth here.

noosphere: Susanna Hertrich: Reality Checking Device (via ...

Tue, 22 Sep 2009 20:59:47 -0400

noosphere:

Susanna Hertrich: Reality Checking Device

(via Information Is Beautiful)

Note that the biggest hazard (and the biggest outrage) of all, the shark attack, is absent. Coincidence? Another example of the people with the data making sure that YOU, the swimmer, don’t have it. Fact: One third of all recreational swims end in disaster.

As a tumor grows and develops, new blood vessels form within it,...

Mon, 21 Sep 2009 19:36:05 -0400

As a tumor grows and develops, new blood vessels form within it, robbing its host of nutrients and feeding back into itself an enhanced ability to continue pillaging. Destroying the network of blood vessels supplying tumors is a theoretically plausible way to fight cancer, although it hasn’t had much success yet. Visualizing this destruction—and the efficacy of the drugs which execute it, has until now been nearly impossible.

Using a complicated network of software, microscopy, and a brilliant harnessing of the Doppler Effect created by the movement of blood cells within vessels, Harvard researchers have now pushed the depth of visualization of tumor angiogenesis to 2 millimeters, a practical light year in this type of work. Above, the vascularization of the mouse brain, from last week’s Nature Medicine.

Dalton, a squirrel monkey, enjoys fruit following gene therapy...

Wed, 16 Sep 2009 13:27:41 -0400

Dalton, a squirrel monkey, enjoys fruit following gene therapy which corrected his color blindness. Dalton, who was treated at the University of Pennsylvania, Philadelphia, plans to become a test pilot for the Royal Air Force.

Brainscapes, Vivian Budnick From PLoS biology, an illustration...

Wed, 02 Sep 2009 20:09:33 -0400

Brainscapes, Vivian Budnick

From PLoS biology, an illustration of membrane shedding during the growth of the synapse.

GPOY Shoulder By ‘Melvin’, x-ray technician

Fri, 21 Aug 2009 19:01:37 -0400

GPOY Shoulder

By ‘Melvin’, x-ray technician

New installment of good-looking science. Recent good-looking...

Wed, 19 Aug 2009 13:42:21 -0400

New installment of good-looking science. Recent good-looking science: A B C D

(Bipolar cells of the mouse retina. From today’s Nature.)

Microtubules (green) traverse cells, establishing lines for...

Mon, 17 Aug 2009 20:06:59 -0400

Microtubules (green) traverse cells, establishing lines for shipping of cellular cargo, aiding cells in structural integrity, and helping to drive cell division. Loss of their integrity in neurons can result in failure of normal development; malfunction in muscle cells can lead to defects in the ability of muscle fibers to contract normally. In the above image, the top muscle fiber comes from a mouse with muscular dystrophy, and clearly lacks the organization of the normal muscle fiber below. From JCB.

A section from the CA1 pyramidal neurons of the mouse...

Wed, 12 Aug 2009 20:33:19 -0400

A section from the CA1 pyramidal neurons of the mouse hippocampus. This cell is from a mouse model for Alzheimer’s Disease, in which a protein called Presenelin is over-abundant, leading to the buildup of detrimental plaques within neurons. In the early stages of this model, the mice surprisingly showed an increased ability to learn, possibly due to the increased intercellular connections which arose from the overabundance of this presenelin protein. The areas at which the neurons connect with one another are the little blobs on the branches in the picture.

From today’s Journal of Neuroscience

"One can be, indeed, one must strive to become, tough and philosophical concerning destruction and..."

Tue, 11 Aug 2009 19:43:56 -0400

“One can be, indeed, one must strive to become, tough and philosophical concerning destruction and death, for this is what most of mankind has been best at since we have heard of man.”

- James Baldwin, from a letter to his nephew, on the hundredth anniversary of The Emancipation.

Heaven and Hell by M.C. Escher, on display at the PDX Art...

Mon, 27 Jul 2009 23:21:25 -0400

Heaven and Hell by M.C. Escher, on display at the PDX Art Museum

Fractals, shapes which can be split into smaller but very similar copies, commonly appear in nature—in branched plants, in snowflakes, and in corals. Perhaps this the root of the paradox in the piece above—it feels natural, despite its impossibility.

Galileo’s moons of Jupiter. (from top) Ganymede,...

Tue, 21 Jul 2009 16:07:00 -0400

Galileo’s moons of Jupiter. (from top) Ganymede, Callisto, Europa, Io. Photos from the Galileo spacecraft.

—-THE AMAZING BONOBO—- The bonobo (above) is...

Fri, 17 Jul 2009 23:00:12 -0400

—-THE AMAZING BONOBO—-

The bonobo (above) is absolutely the most amazing non-human animal alive today, and I am obsessed with disseminating my new bonobo fandom. If you take the time to watch this awesome video on the bonobo, you are guaranteed AN EMOTIONAL ROLLERCOASTER RIDE AND AN EXPLOSION OF INTELLECTUAL PROVOCATION. Some quick stats:

$$ Not featured in most zoos due to a human-like sexuality which ‘permeates their entired lives. A google search yields mostly pictures of them in the missionary position.

$$ Can passively learn a vocabulary of 500 words

$ Often walk upright

$$$ Make stone tools

$$$$$ Can learn primitive written language systems

This photograph of Macau is among the earliest existing...

Sat, 11 Jul 2009 20:00:53 -0400

This photograph of Macau is among the earliest existing photographs of China, taken some time in the 1840s. Everyone in it is dead; their children’s children are dead and their memories are dead. The photograph is not dead, but it is not a memory. We experience through sensory information—colored by other experiences, and encoded in an un-understandable cascade of electrochemical signaling. Each time we view a memory, we do so from farther away, and some fidelity is lost. Memories are infinitely reducible and labile. Finding an unremembered memory can evoke a painful emotional response, perhaps by virtue of its still native perfection against the experience it represents. Photographs have the quality of being unchanging, though our experience of them may change. They provide us with the starting materials for a new memory as much as they modify the memories we already own. Memories alone are destroyed and rebuilt, but photographs become stakes to which our memory is forever tethered, a position to which the rebuilding of memory is constantly drawn. In this way photographs not only eclipse and obscure elements of experience; they give to us the starting materials from which to build memories not experienced.

The vast majority of Henrietta Lacks was dead by the Fall of...

Tue, 07 Jul 2009 13:30:37 -0400

The vast majority of Henrietta Lacks was dead by the Fall of 1951, buried without a tombstone in Halifax County. Only 9 months earlier, she had been diagnosed with cervical cancer.

Cells from her cervical tumor were isolated, grown, and distributed. Due to the ability of some cancer cells to grow and divide without regard for their environment, these immortal cells quickly became a bottomless source of research material (without her consent), and were sent all over the world, and even into space (to determine whether human cells can survive zero gravity). The cells continue to divide today (above, via electron microscopy), in tens of thousands of laboratory incubators, and in such number that I wonder whether their mass now exceeds that of Lacks.