Why I think T4 is supercool

I can't believe I haven't posted this up yet. You'd think with such a blog title and hallmark illustration, I'd plaster this all over here first chance I got. Nevertheless, I now have the legitimate right to gush about how cool bacteriophage T4 is, seeing that I've delayed it so long and have posted a reasonable amount of non-T4-related posts...

Oh all right, I won't gush.

Instead, you have the privelage of viewing for yourself the coolness that is T4 in a very spiffy movie made by scientists at Purdue and Seyet LLC. Even cooler, this movie is an actual representation based on recent discoveries and earlier knowledge, using x-ray crystallography and cryo-electron microscopy data!

Original release from Purdue University found here.

Watch the movie here from Seyet LLC.


Animation and image credit: Purdue University and Seyet LLC. Click to watch large-version Quicktime animation from the National Science Foundation website. Takes a long time to load, but well worth it.

Please visit the very informative press release from the National Science Foundation, where this animation is linked from, and where you can also find a streaming RealMedia version of the movie.

You can also watch the animation in .wmv format here, from MSNBC.

[pathos worldview] This is Beit Hanoun

Beit Hanoun.

Sound familiar? Ring a bell?

If it doesn't, you need to ask why.

It may be because you've tuned out temporarily to what's going on in the world.


Or because your world has tuned it out for you.


Is it too much for humanity to reflect upon the suffering of others?


This is Beit Hanoun:

"There are pools of bloodstained water outside one of the houses, which has had a hole blown through the roof and there are shrapnel marks everywhere from the explosion."
-BBC News Nov 8. Gaza town stunned by shelling, Matthew Price. Image: Getty

.

"The situation is very, very bad," said Mahmoud. "The Israelis have destroyed Beit Hanoun - they have destroyed the infrastructure. They've cut the water pipes and the telephone lines.

"They put explosives at the doors of the houses - and then they enter on the women and children. Everybody is terrified in their homes."
- BBC News Nov 8. Palestinians gripped by fear in Gaza
----------

[pathopoetry] Going to the Wind

put on your best coat, love -
come, we're going to the wind.

is it when she sorrows
she wails and clasps the trees

is it when she wonders
she whispers to the seas

in fury does she tear her hair
and strip away the leaves

she crashes down the ocean and
she screams, she screams, she screams...


no, the wind is but a word
the weight within her name

between the kaaf and nuun contained


our fingers sweep the rivulets
our palms cushion the rain

put on your best coat, love -
come, we're going to the wind.






---------------------------------------------------------------------------------
*kaaf and nuun: two letters of the Arabic alphabet, phonetically equivalent to "K" and "N". Put together, they form the word kun - "Be". The Originator is He of the heavens and the earth: and when He wills a thing to be, He but says unto it, "Be" -and it is[al-Baqarah:117]

[pathopics] Stitching a way

[µstory] - How cahn you seeh?

This is quite remarkable. I was thinking of posting to my blog today, but didn't really have any idea what to say. But, fortunately, I have been blessed with an amusing, albeit off-putting, incident! How things turn out : )

I just came back from buying groceries with my sister on this very blustery (though pleasant) day, and we were trying to negotiate a heavy-laden trolley down a flight of stairs. I catch sight of this old lady at the bottom of the steps, and so now my task has been rendered triply difficult as I try to
a) keep my headscarf from blowing off my head
b) keep the trolley from careening down and crashing with miscellaneous fruit flying from all corners and
c) attempt to restrict myself to one side of the stairs so that the old lady can pass without incident

Ah, but successful as I was in manoeuvring the trolley to one side (my sister grasping the handle at the top and me lifting it at the bottom and trying hard not to trip on my own feet as we make our way gingerly down), the aforementioned lady climbed the steps, alas, with a wee incident. First chance I get to look up from my fluttering laces, I see this mouth-agape look of disgust. Here is the quaint exchange between us:

Her: HOW CAHN YOU SEEH?
Me: (taken aback – my sister more so)
Her: I hope you drop dead.
Me: May God guide you.*
(*I also said “Bless you” before that when I was a little dazed, but I like this response better :))

The funny thing was that, my sister was much more appalled (meanwhile I giggled at the amusing statement of “how can you see” – uhm, perhaps with these inset orbs above my nose – what’re they called again – oh, eyes). Okay, so it’s not so funny when some random person curses you with death, but hey, at least she didn’t shove the trolley down the stairs. Besides, she was old and thus can be excused from her ignorance.

Interestingly, I’ve met this lady before. I was startled once when she, in her thick European accent proclaimed loudly when our paths met, "How cahn yous see?!"
I smiled and thought, "How can you not?"

:)

[pathos worldview] Apparently, teaching Arabic is akin to terrorism?

To tell you the truth, I'm actually quite amused by this. Not to say that I'm not appalled by it nor adamantly against it, but I'm amused as well. I guess I've begun to take these things in stride : ) It's partly because the previous post was Arabic is a terrorist language, oh the irony.

S.F. STATE
Professor of Arabic barred from returning to U.S. from Canada
S.F. State scholar's visa gets canceled; case under review

An assistant professor of Arabic at San Francisco State University has been stranded in Canada for three months, unable to return to campus, after the U.S. State Department canceled his visa and began reviewing his security status.

Mohammad Ramadan Hassan Salama's troubles began in June, when he arrived in Canada for what he thought was a two-day stay to change his temporary scholar visa, which was due to expire. He planned to exchange it at the U.S. Consulate in Toronto for the more coveted O-1 visa, granted only to those with extraordinary ability in sciences, arts, education, business or athletics. By law, he had to go outside the country to get the visa.

But the Egyptian-born academic got a rude awakening June 20 when a consular official, without explanation, stamped "canceled'' on his temporary visa and refused to issue another visa. Instead, Salama said, he was fingerprinted, questioned and told he could not return to the United States until he received security clearance.

"It was just a shock for me,'' he said by phone on Monday. "It is very Kafkaesque. They just say, 'We will contact you.' I am Egyptian, and Egypt is a very hot country right now that has produced terrorists. They disregarded my Ph.D., my scholarship. My marriage, my kids were blindly disregarded, and I was told I could not come back."

Read the full article here on the San Fransisco Chronicle site.

[pathopoetry] Fighting hope

hope has dealt a glancing blow -
has grazed the brick and chipped the stone
and clipped the wings of all the crows

[pathos worldview] Apparently, Arabic is a terrorist language

I was collecting my thoughts to write a passable post on the aftermath of the war. I had originally stipulated to myself that no other posts would be written before the publication of that one. Then I saw this:

NEW YORK (AP) - An Arab human rights activist was prevented from boarding a plane at Kennedy Airport while wearing a T-shirt that read "We will not be silent" in English and Arabic.


Raed Jarrar was at the gate to board a JetBlue Airways flight to Oakland, Calif., on Aug. 12, when four officials from the airline or a U.S. government agency stopped him and told him he could not board with the shirt on, he said Wednesday.
One official told him: "Going to an airport with a T-shirt in Arabic script is like going to a bank and wearing a T-shirt that says: 'I'm a robber,"' he said.

Okay. It is difficult for me to comprehend this. How people can be so racist, narrow-minded, bigoted, and still claim to be looking out for other people's rights - I'm dumbfounded. Take a look at that last statement there. It reeks of ignorance and contempt. Arabic now equates terrorism? Last time I checked, the Quran was in Arabic. So please don't beat around the Bush.

Jarrar, who directs the Iraq project for Global Exchange, a San Francisco-based human rights organization, said he refused a suggestion from the officials that he turn his shirt inside out. In the end, officials gave Jarrar another shirt to wear over his and he put it on rather than miss his flight.

Jarrar said he was forced to give up his seat near the front of the plane and was issued a new boarding pass for a seat in the rear.

How do I discriminate against thee? Let me count the ways.

----------------------------------------------------
Article copyright The Canadian Press, and can be read in its entirety here.

[ pathopoetry] Upset, and a viewed thought

Look
if you press it hard enough
it will leave a residue

don't turn your mind that way
why must it always be
something like that

as though you can't think past
your pants

there is grey matter elsewhere

Look deep at me
you see
it crumbles

I am the advocate for
disparaging souls

[pathopoetry] +/-Sad

My head hurts.
I placed it where my heart was, added some fancy tissue paper
and closed the box.

What will it do there
where moths yearn to go?
complain to a sympathetic friend
who'll say, "it's your turn now."

[pathopoetry] Paperline

I weighed my worth in ounces
forgot the conversion factor, set
the 0 mark wrong

maybe if I shift to one foot
(the burden in the heart must count)
maybe if I lean forward

I spread my arms out, trying to expand myself

how much can you lift
with an emaciated soul
what mind can balance
on adequacy

[pathopoetry] 57

My wife was one of the 57.
Had she been 4? 14? 21?
Who made a mental note when they carried her
saw her crumpled face and thought, '34'?
Or did they do it after, on the ground
was she briefly 10 after 8...9...
covered with a sheet with her knees in the air
- too stiff to lay you down, my love!
There are no spaces for names between the stones
but isn't there a number that she can call hers?
Let them distinguish her from the dust
Give me something I can scream to the world
I tell you there was a sweetness in her
I won't let her dissolve within the words
unmarked as a person, but part of a scene
not just another bag beneath the dirt
not even a number to remember her by






------------------------------------
©pathopoet, 2006

[pathos worldview] Cry out for Qana

Man carries body of girl killed in Israeli air strike in Qana (AFP)

BBC News: Israeli air raid in Qana; Quoted throughout.

My mother sobbed today.

She sobbed because she saw a dead girl, her arms stiff in front of her, carried by a man who stumbled on, dazed with shock. She cried because of the bodies, wrapped in the same blankets they had wrapped themselves in. She cried watching fathers cry while dead limbs reached out desperately from the rubble.
And I went and wrote a blog post.

There was a TV screen between her and the carnage. There is a computer screen between me and this post. We're distanced from both, hoping to touch something with either, hopeless when we realise that neither tears, nor words, nor even blood, has managed to do anything thus far.

A rescue worker moves the body of a girl killed in Israeli air strikes on Qana(AFP)

Reporters in shock manage to put forth, "There were no rockets. This was a building carrying only refugees." No, there aren't any rocket pieces. Only body parts.

Condoleeza Rice will flash her toothy smile and pretend she is "saddened". I say pretend, because saddened people cry. Saddened people say, "That's enough. Stop this senseless killing." Saddenned people don't let other people die, while they say, "Let's wait a while."

Israeli Prime Minister Ehud Olmert said earlier that Israel was not in a hurry to agree to a ceasefire until it achieved its goals in the area.

So I'm pleading, yes pleading to everyone, please look at what's happening. Maybe you're Muslim and you've been bullied into such a corner that you're afraid to utter a pipsqueak of protest. You may be loyal (or afraid) of your Arab governments, but governments don't come before humanity. Maybe you're Jewish and have been taught that Israel can do no wrong. You may hate Hezbollah, but this is the worst way to deal with the situation. Even if Hezbollah is wiped out through this, another group will rise up from the bitter young boys who watched their mothers die as bombs destroyed their houses.

Red cross workers remove bodies of children killed in the Israeli air strike in Qana (AFP)

The ones paying for this are the children. More than 400 civilians are confirmed dead; the true number will likely top 600. Today, in a refugee shelter in Qana, the unthinkable has happened.

Sunday, 30 July 2006

More than 40 people, including 20 children, have been killed in an Israeli air strike on the southern Lebanese town of Qana.
Displaced families had been sheltering in the basement of a site which was crushed after a direct hit.

Maybe you live in North America, and don't know what's happening. You've been saturated with half the story. You've probably seen interviews of the mother of the captured soldier. You haven't seen the despair of the mother of the murdered child. You've seen citizens of Haifa hunkering down in bomb shelters. You haven't seen craters where houses used to be. You've had days where the news of a dead Israeli soldier has blared on for the whole morning. Have you had days where the news of 100, 200, 300 dead civilians, has been mentioned outside that ticker-tape hastily crossing the screen? Have you heard IDF claim they do not intentionally hit civilians, although they only use precision-guided missiles and smart bombs, given to them kindly by the U.S?

Witnesses said the early-morning strike flattened several sites on top of sleeping residents.

One survivor said the "bombing was so intense that no-one could move".

Or perhaps you're ready to dismiss human lives like Haim Ramon (Israeli justice minister) has done and say:

"These places are not villages, they are military bases in which Hezbollah people are hiding and from which they are operating." (Globe and Mail, July 28th)

Please don't come to this issue with a pre-set opinion. Your heart will become cold that way. Just like you would want the world to grieve over a suicide bombing in Haifa, I want you to grieve over a pile of dead children in Qana.
And if you do, cry out.

"May God have mercy on the children. They came here to escape the fighting"

Qana survivor

[Edit: 57 dead, 37 children (CNN international, 12:15 GMT).]
[Edit: Realities, absurdities of Israel-US policies.]

Mind of a beta-Microbiologist - #3

Clues that Microbiology is sinking into your neurons:

When you see pink streaks in a tub of old yoghurt and you don't think "ewww," you don't think "whoa,"  you think,

"Oh. Serratia."









---------------
Huh? Icky-link :)
Bacteria of the genus Serratia are often pigmented pink-red. Although some non-Serratia species can be pigmented too. Meh, Serratia are the only ones I know :P

[pathos worldview] In the fire, crouching cold

I mentioned in a previous post that when I am truly upset, I can't write a sensible thing. It certainly held true this time.

I tried to compose a post on the war on Lebanon. I tried to write a poem. I made a promise to myself that I would not write another post unless I had first written one about this inane, heart-lacerating issue. I would not be like the rest of the world: cold, indifferent, draping the sheets of barbed politics over the scenes of horror and devastation. And yet I wasn't just going to post some drabble; no, I told myself, it would provide yet another excuse to disregard or belittle what was really going on. I wouldn't rant because there was no place for that - to sprawl my emotions over the screen would be to undermine the very essence of what I was writing about.

I could have, for example, posted pictures of dead children. But I did not want to disturb the more kindhearted readers. I could have posted video of devastated buildings, airports, bridges. But that would simply be showing the obvious. I could have linked to articles on the current humanitarian crisis, detailing how these attacks have only managed to damage civilian infrastructure that will take years to rebuild, blanketing parts of the region in darkness, whilst stripping part of the people of shelter. I could have rattled statistics on how many civilians had been killed, how many billions of dollars it would take to restore countless towns, how many people were displaced, how many were left homeless, how many evacuated and how many were too poor to do so, too unfortunate to not be citizens of Europe or North America, and have the military pluck them out to safety.

But at this point, frankly, there would be no point. Find out for yourself. If you can't grasp the severity, the cruelty, the magnitude of what's going on, I'm too sick of it to tell you. I've lost faith in a large chunk of humanity. What kills me most is the cold, cold indifference. It's become apparent that people don't care enough for certain lives. "Over 300 Dead Lebanese Civilians" maybe isn't as glamorous a heading. Watching a favourite team lose in the World Cup can wring tears from the most stoic of hearts, but thinking of a bomb ripping the limbs of an Arab mother isn't as moving.

Maybe, I've realised, I've done a lot in this post that I hadn't set out to do. Maybe I've seen things that have curdled my blood. Maybe it makes you uncomfortable. It should. Your silence supports it.

We live in a world where being humane is taxing. Being supportive of your government, no matter how much it errs, no matter how much suffering it inflicts on others either directly or passively by ignoring what is right and delicately masking what is wrong, is considered tantamount to civility. But don't do the dismissive thing and brand me as "political." I'm not a vigilante. I'm a daydreaming student who won't kill an ant crawling on her keyboard even though she's allergic to ants. And no, I'm not a "terrorist." Funny word, that. How some people can put on veils and be called terrorists. And some other highly equipped people, with very large bombs, can crash them into villages and be "spreading freedom." Or "defending themselves."

It appears that I've poured out a great deal of words. I suppose it's been cathartic. Perhaps it was necessary. Perhaps it's better the dam bursts in this calm and sensible way. It's odd, I set out with this post explaining how I couldn't write. And I couldn't write, I couldn't watch; so I drew. Without much thought, my hand moved across the notepad and I looked at what I had done, puzzled. It was almost as though it was telling me, "You're sad, but it's ok." And right there and then, I redrew the sketch quickly, scanned it, and told myself, "This is what I will post." I knew it was hopelessly drab and not worth sharing (it did nothing justice), but it was what I could do at the moment, it was a testament to the confusion of my current state, and it would save me from wrenching words out of my system. I ended up writing after all, but I wouldn't have typed a single letter, had it not been for this paltry sketch, the one I took one look at and thought: This is what it is. In the fire, crouching cold.

[pathopoetry] Recovery

You've fooled her, love.
This is her scar, superficial wound
bone-deep.

Inflammation
Of the heart's blood
and pain

The fever breaks
She wonders;
Had it been latent?
Self-inflicted?

Suffering;
But it's her own
Immune response.



--------------------
©pathopoet 2006

[µstory] - What to be (excerpt)

“µstory” (“mu-story” or “micro-story”) is a categorization I use to designate a very short story, a prose-poem, or an excerpt from one of my stories/works-in-progress.
--------------------------------------------------------------------------

He had his palm on his forehead, leaning his head heavily on it, wisps of hair jutting out miserably from the crevices of his fingers. "I want to do something...spectacular," he breathed, gazing at the table as though the furrows in the grain shared with him some muted understanding. "But am I someone that can do something real? Something good? A person can do a collection of nothings and be elevated into the recognition of the world. Even be infamous if you can't be famous, notorious if you can't be notable. But I - I don't want to be anything to the world. Just to be nothing, but do so much that it's worth something. So later, you'd look around and say, ‘See, something good has happened, we don't know why or how, but it’s wonderful, it's changed.’ Yes, that’s…”
- He buried his hand deeper into his hair, furrowing his brows, closing his eyes as though the table had blinded him. "Nothing seems to be enough for people to notice the world now. It's no longer important enough, no longer severe enough, compelling enough to hold our attention. No, for that we have fiction. Blink at it, oh yes it’s happened, let’s turn to a far richer experience. A whole, real life isn’t enough, isn’t even worth a sentence; awful, wretched it is! So I can’t… I can’t just put forward some simple amount of good as all the rest like me, some small offering that will sink away… insignificant. To really do something, to shake the world and say, “Look!”, to – to help, it must be more than surreal, it must be greater than turning away, so strong it’s worth being a part of, so unimaginable it fills volumes. I don't want my deeds relegated to the prelude of a novel.”

...................................................................................



- Excerpt from a 'novella-in-progress' (for the pathopoet, everything is in progress!), "London Avery"

[pathos worldview] Though this won't help you, Gaza

But when I crudely stitch an honest thought
My falt'ring voice will crack between the lines...

When I am upset, I usually rant to my dear friends, and may turn out a few choice phrases, trying to both describe and alleviate my condition at the same time. Poetry may come out then, in bursts of consolation. But when I am truly disturbed, wholly unsettled, I can't write. I shrink from writing because I can't put something sensible together. I can't wax eloquent when my mind is spinning. But my mind is spinning, and I'm writing now. So forgive me if there's more emotion in this than eloquence.

I burnt my garlic toast just now, rushing to the computer, listening to the TV, trying to found out what was going on. In Gaza. The TV is on and there's a call-in discussion program, in Arabic. They are talking about what's going on, in Gaza. I simultaneously listen to the caller whilst frantically opening blogger to spill some of this out of my head. The ancient Arabs were unique in their ability to wax poetic no matter how dire the situation, and most educated Arabs can do the same. The caller proceeds in flowing prose, a prayer, a controlled cadence, he says, "We understand the desire to free the one soldier, what about the 400 children in Israeli jails?" He says it in more eloquent terms but I can't think well enough to remember them. His voice quavers at the end, but his sentences are flawless. The next caller is not so controlled. His voice is shaky from the start. "Brother, he says, although the word is a sigh in itself, "I feel like I'm going to incinerate."

I have just watched bridges broken, missiles hitting, streaks of powder in the sky. I have watched an man's elederly mother refuse to evacuate her house, probably because she is senile and doesn't know what's going on. That's the difference here, in the middle east. People see it with their own eyes. Most households have either CNN or BBC world, a few ones have Fox. But unlike my home in North America, there're the Arabic channels. There are the live images. On both sides. But that's another story.

The story I'm watching intermittently is the one which had been unfolding surrealy in front of my eyes. Gaza bombed, thousands are left without water or electricity. The power plant has been hit; it may tke months to replace destroyed transformers. The deafening sound of missle strikes, one right in the middle of a BBC interview with a resident. The reporter ducks and turns around - the man breifly flinches, then resumes talking.

( I stop posting briefly to hang out laundry from the washing machine. It seems inane. But the intellectually unchalleging monotony of pegging pyjamas in the balcony calms me somewhat.)

I try to sort it through in my head. The desire to return a kidnapped soldier, understandable. The decision to punish an entire community, involved or uninvolved, mwomen and childeren, unfathomable. A single soldier, captured while fighting, who sparks a full assault on an already suffering people. The soldier is named, about my age. The 400 children - below the age of 18, in Israeli prisons, who won't be exchanged for his sake, are faceless and nameless. His life is toted as important but his government won't do the one thing that would almost certainly save him. Rather, they do the one thing that make very grim the prospect of his recovery.

No exchange. Then no electricity. No water. I think of the irony - I just spent the better part of the day with no running water due to scheduled plumbing. There were buckets of water though, enough for me to do the dishes and my ablution and whatever I needed. And I knew it was coming. Yet still I lingered impatiently at the faucet.
I'm upset at my own idiocy. My own incompetence.

Then I remember a female caller on the show, long ended. "Let the people know, we are in their prayers." And I realise it's the best that I can do. So I decide to stop posting, and do the only thing I can do that will help the most.

I don't bother to read what I've written since I'm certain it's drivel. I know there are mistakes but there are worse out there in the world that I can't fix. I'm tired and upset. I want to pray and I want to sleep. I need a hug. I want to hug a child.

Mind of a beta-Microbiologist - [2]

Corny things to say when you are a Microbiologist:

#1 - "We're livin' in a bacterial world, and I am a bacterial girl..."

Mind of a beta-Microbiologist - #1

Mind of a beta-Microbiologist - observation #1:

Whenever I hear the odd word "Islamist," I think of "FluMist®" : which is a flu vaccine in the form of a nasal spray, and then I think,
"FluMist®: a live attenuated influenza vaccine"

...

Why I still remember this, yet forgot the stuff I really needed for my exams is beyond me :)