For JollyRgr

I'm posting this here because stoopid LiveJournal isn't letting me post comments on DocStymie's blog...

The good Doc had blogged about a recent paper that appeared in the (new) scientific journal PloS Biology. This concerned modeling all the proteins in the yeast proteome.

The recently-shaved JollyRgr had asked:
"yeast proteome something like human genome in general concept????

Am I on the right path???"

So here's the answer...

Kinda sorta. The genome is the set of blueprints (genes) for making the various components of a living organism. Think DNA = genome. Each gene encodes a component. Proteins make up many, probably most, of those components. The proteome is the set of all proteins in an organism. So the genome encodes the proteome, plus more. Yeast, like humans and all other living organisms, has a genome and associated proteome. We use yeast as a model organism because it's genome, and proteome, has many of the same components as the human versions.

So there you go.

I'm back...

Actually have been for almost a week. Too much life happening here.

Anyway, the trip was good. The Kaddo Borawni was superb, as was the Lamb Lawand... Hmmmm, goooood!

Not much to say other than point out Vista has turned out to be, well, a typical Microsoft product as demonstrated here and here. Is anyone surprised?

In all fairness, Apple is not without it's issues. DocStymie, you may want to be aware of this one.

Finally, it's World Cup time! Cricket that is. Ireland tied Zimbabwe. How cool is that?

Instead of a word of the post, here's little quote from the online commentary of the England-New Zealand match from the BBC:

"Whoosh - almost a disastrous run-out as KP calls for an insane single. Vettori hurls the ball at McCullum with Vaughan half a pitch short, only for the 'keeper to fail to gather the ball. Massive let-off.

In reply to those of you asking for more info on the gaggle (this in reference to an earlier comment about a group of young women)- specifically, how many are international class - I say two things: firstly, that that sort of sexist badinage has no place on the BBC, and secondly, about half of them."

I love the English commentators...

It's that time of year again

Time for me to go hang out with 5000 other geeks. Yes, it's scientific meeting time. Time for bad talks, overwhelming numbers of people, too much coffee, beer and good science. This year it's in Baltimore. I'll also get to go to one of my all time favorite restaurants - the Helmand. Maybe more than once.

Sorry you won't be there DocStymie. You'll be missed. I'll have some Kaddo Borawni for you.

After Baltimore I have to spend a couple of days at a workshop at the National Science Foundation in Washington, DC. It'll be a long trip (for me) - Friday to Friday. I hate being away from the family that long. The meeting will be good, but not being with the lovely L and the kids will suck.

No word of the post tonight. I'm too knackered.

Irony

I believe I used this as a word of the post before, but this is too good an example to pass up...

Word of the post:

i·ro·ny
n. pl. i·ro·nies

The use of words to express something different from and often opposite to their literal meaning.
An expression or utterance marked by a deliberate contrast between apparent and intended meaning.
A literary style employing such contrasts for humorous or rhetorical effect.
Incongruity between what might be expected and what actually occurs: "Hyde noted the irony of Ireland's copying the nation she most hated" (Richard Kain).
An occurrence, result, or circumstance notable for such incongruity.
Dramatic irony.
Socratic irony.

Example: See here.

Detective iTunes?

Who would have thought a music player/library program could detect fraud?




Word of the post:

bloviate \BLOH-vee-ayt\
-intransitive verb

To speak or write at length in a pompous or boastful manner.

Example: I have never bloviated in my blog. Never. Honest.

Thinking quotes

Our University publishes a research magazine about every quarter. Generally it's not very interesting, at least to me. However, on the last page they tend to have a series of quotes. These quotes are related to one another in some way. The current issue has a series of quotes regarding thinking. I thought some were worth sharing:

"The important thing in science is not so much to obtain new facts as to discover new ways of thinking about them."
- Sir William Bragg

This is more true than many non-scientists might think. My postdoctoral advisor was very fond of saying "If you want to find a really good research project, just open a textbook and find a passage that starts with 'It is well known that...' There's your research project." My own work involves expanding upon observations first made over forty-five years ago!

"A great many people think they are thinking when they are really rearranging their prejudices."
- William James

"A conclusion is the place where you got tired of thinking."
- Harold Fricklestein

"Today, if you are not confused, you are not thinking clearly."
- Irene Peter

Talk about a great excuse for my constant state of confusion...



Finally, here's one for the current occupant of the White House and his cronies:

"All war is a symptom of man's failure as a thinking animal."
- John Steinbeck


Word of the post:

ob·strep·er·ous [uhb-strep-er-uhs]
–adjective

1. resisting control or restraint in a difficult manner; unruly.
2. noisy, clamorous, or boisterous: obstreperous children.

No example. I just like the way obstreperous sounds.

Yesterday was a good day

We heard from the National Science Foundation that a proposal I had submitted last August is funded. This is to run a summer undergraduate research program. We're going to host eight undergrads in our labs and give them research projects to do. Pretty cool. My chairman is very happy about it. He told me so. Twice. Of course now the real work begins...

Being a typical government agency, the NSF has given us funding right at about the time we should be finishing our recruiting for the summer. So we have to recruit very quickly. Oh yeah, we're also supposed to have a detailed website for our program by yesterday, or even earlier. So I'm busier than a one-legged man in a bum kicking contest.

And the NSF is requiring me to attend a workshop in DC in March... Fortunately this starts the day after a meeting I'm attending in Baltimore ends. So I've extended my trip. I'm not terribly happy about being out of town so long, but that's the way it is.

Word of the post:

kvetch \KVECH\

adjective:
1. To complain habitually.

noun:
1. A complaint.
2. A habitual complainer.

Example: One of our less successful faculty has become a kvetch. It's very irritating. Not that I'm kvetching.

For DocStymie and P

This shouldn't happen.
I'm sorry Doc.
Odyssey


Mi Shebeirach

Lyrics by Debbie Friedman and D'rora Setel

Mi shebeirach avoteinu
M'kor habracha l'imoteinu

May the source of strength who blessed the ones before us,
Help us find the courage to make our lives a blessing
And let us say: Amen.

Mi shebeirach imoteinu
M'kor habracha l'avoteinu

Bless those in need of healing with refuah sh'leimah
The renewal of body, the renewal of spirit
And let us say: Amen.

Happy Australia Day!!!!

May the snaggers be hot,
the stubbies ice cold,
the fireworks bonza,
and all yobbos stuck at home crook.




Word of the post:

egg-nishner
Strine

A device for cooling.

Example: Geez it's bloody hot mate! Pass a bloody stubbie and turn up the egg-nishner.

A Happy New Year to One and All!

And what better way to start the New Year than pondering the fates of those who saw fit to remove themselves from the gene pool.




Word of the post:

ev·o·lu·tion [ev-uh-loo-shuhn or, especially Brit., ee-vuh-]

-noun

1. any process of formation or growth; development: the evolution of a language; the evolution of the airplane.
2. a product of such development; something evolved: The exploration of space is the evolution of decades of research.
3. Biology. change in the gene pool of a population from generation to generation by such processes as mutation, natural selection, and genetic drift.
4. a process of gradual, peaceful, progressive change or development, as in social or economic structure or institutions.
5. a motion incomplete in itself, but combining with coordinated motions to produce a single action, as in a machine.
6. a pattern formed by or as if by a series of movements: the evolutions of a figure skater.
7. an evolving or giving off of gas, heat, etc.
8. Mathematics. the extraction of a root from a quantity. Compare involution (def. 8).
9. a movement or one of a series of movements of troops, ships, etc., as for disposition in order of battle or in line on parade.
10. any similar movement, esp. in close order drill.

'Tis the season

'Tis the season when the local newspaper receives multiple letters complaining about the "War on Christmas".
There isn't one.
'Tis the season when saying "Happy Holidays!" is construed to be a slight against Christianity.
It isn't.
'Tis the season when politicians preach good will towards all men.
They don't mean it.
'Tis the season when rampant consumerism goes way beyond "rampant".
Not what it should be about.
'Tis the season when homeless people freeze to death unnoticed.
Remember them?
'Tis the season when genocide goes unchecked while the first world turns the other way.
Darfur.
'Tis the season when many of us eat more in a day than many others have for a week.
Do you really need a third helping? Do I?

But despite all this,
'Tis the season where I wish one and all

PEACE


And that is the word of the day. No definition required.

Thoughts on thinking

Ever think about the form in which you think? I have been lately. As I type this I'm thinking in words, more or less. But I also sometimes think in pictures, both static and moving. Or mixtures of words and pictures. Although I haven't talked to people about this, I suspect this is true for many people. But those aren't the only forms in which I think...

When I think about my science, my research, I think in molecules. Spinning, writhing, twisting, tumbling molecules. Amino acids, peptides and proteins. Water and ions. Atoms bonded to one another, interacting with bangs, thumps and bright colorful sparks. Molecules dancing around one another, twisting in knots. Crashing into one another. Sticking to each other like tiny fragments of velcro, or being flung apart by rainbow sheets of repulsive energy.

I see a weird and wonderful world in my head that cannot be seen using existing technology. This of course can be a bit of a problem for me. I can "see" in my head how some of the systems I work on behave, but I don't have the tools in the laboratory required to measure what I see. This can be frustrating. Of course what I see in my head could be wrong. But I don't think it can be completely wrong. My molecule thoughts have their basis in what I've found during my research, what I've read, and from talking to fellow scientists. I think my molecule thoughts are more right than wrong. But I can't prove it.

There are many scientists who would respond to my admission by deriding it as pure fantasy, nonsense, or the product of a disturbed mind (which it may well be). Not, I'd wager, those whom I admire, whose work has, and continues to have, profound influence upon mine. They might think in molecules. Or they might not. It doesn't matter. They would understand.



So there you have it. I'm weirder than you thought, if that's possible. Accept it, move on, and tell me, in what forms do you think?



Word of the post:

pre·sen·ti·ment
-noun

A sense that something is about to occur; a premonition.

Unsolicited advice

Don't eat beans before a plane ride.




Word of the post:

im·prov·i·dent [im-prov-i-duhnt]
–adjective

1. not provident; lacking foresight; incautious; unwary.
2. neglecting to provide for future needs.


Example: See story linked above.

Yes, yes, I know...

...it's been a long time between posts. It's not that I have nothing to say. There's just so much to choose from; Darfur, Microsoft's Zune, Iraq, the Ashes series in Australia, the perennial blather topic of Bush, Docstymie's discovery that he is one degree of separation from J. Robert Oppenheimer, Father of the Atomic Bomb (which means I'm also one degree of separation from him, and we're both two degrees of separation from Edward Teller, and probably no more than three from Albert Einstein)... No, it's not a lack of subjects. It's a lack of time. So, dear readers, I present you with this gem from Norway, land of smoked salmon and tax-free strippers.


Word of the post:

ineluctable \in-ih-LUCK-tuh-buhl-adjective

Impossible to avoid or evade; inevitable.

Example: “Those war plans rested on a belief in the ineluctable superiority of the offense over the defense” (Jack Beatty).

The evils of the iPod

Bill O'Reilly (extreme right-wing demagogue) has decided iPods are evil.

Says O'Reilly: "I don’t own an iPod. I would never wear an iPod...If this is your primary focus in life - the machines...it’s going to have a staggeringly negative effect, all of this, for America...did you ever talk to these computer geeks? I mean, can you carry on a conversation with them?" (Quote taken from the DailyTech article linked above.)

FYI, you can hear all this in O'Reilly's Talking Points podcast...


Bonus word of the post:

i·ro·ny
n. pl. i·ro·nies

1. The use of words to express something different from and often opposite to their literal meaning.
2. An expression or utterance marked by a deliberate contrast between apparent and intended meaning.
3. A literary style employing such contrasts for humorous or rhetorical effect.
4. Incongruity between what might be expected and what actually occurs: “Hyde noted the irony of Ireland's copying the nation she most hated” (Richard Kain).
5. An occurrence, result, or circumstance notable for such incongruity.

Example: See above.

As a parent...

There are few things as beautiful
as a sleeping child.




Word of the post:

Avagudweegend
-slang

It's means exactly what it says. Popularized in Australia by a series of television ads for Mortein, an insecticide.

You don't need an example, you need to go and have one.

More celebration

It looks like the Democrats have taken control of both the House and Senate. Even the Republicans have begun to concede that. The Republicans are also turning on their leadership. Could be quite a bloodbath.

It's about now that various quirks and oddities from the elections become known. this one comes courtesy of my younger brother.


Word of the post:

brob‧ding‧nag‧i‧an  [brob-ding-nag-ee-uhn]
–adjective
1. of huge size; gigantic; tremendous.
–noun
2. an inhabitant of Brobdingnag.
3. a being of tremendous size; giant.

Example: The Republicans have taken a beating of brobdingnagian proportions.

Yes!

My faith in the American public has been restored now that they've sent a clear message to King George and his toadies that "staying the course" is unacceptable. And you know the most amazing thing about the whole election? The Democrats have no plans. No plan for dealing wth Iraq. No plan for dealing with the deficit. No plans. Apparently the American public believe that's better than the Republican's plans.

Amazing!



I'll post a word of the post tomorrow. It might be colonoscopy. That's what Bush will need to find his "mandate".

River Runs Red

Recently I've been struck by some quite old CD's seem more apropos now than even when they were first released. Have a listen to U2's War or Midnight Oil's Blue Sky Mining.

As an example, here are the lyrics to "River Runs Red" from Blue Sky Mining:

"So you cut all the tall trees down, you poisoned the sky and the sea
You've taken what's good from the ground
But you've left precious little for me
You remember the flood and the fall, we remember the light on the hill
There should be enough for us all, but the dollar is driving us still

River runs red, black rain falls, dust in my hand
River runs red, black rain falls, on my bleeding land

So we came and we conquered and found
Riches of commons and kings
Who strangled and wrestled the ground
But they never put back anything
Now I'm trapped like a dog in a cage
Wherever the truth is pursued
It must be the curse of the age
What's taken is never renewed."



So tomorrow, if you're a US citizen, vote.
Just vote.
It's not a right, it's a duty.
Your failure to vote is your failure to your country.
Vote.


Word of the post:

de‧moc‧ra‧cy  [di-mok-ruh-see]
–noun, plural -cies.

1. government by the people; a form of government in which the supreme power is vested in the people and exercised directly by them or by their elected agents under a free electoral system.
2. a state having such a form of government: The United States and Canada are democracies.
3. a state of society characterized by formal equality of rights and privileges.
4. political or social equality; democratic spirit.
5. the common people of a community as distinguished from any privileged class; the common people with respect to their political power.

Why do they have to make it so difficult?

Bush's popularity is low, low, low and dropping. People have had it with the Republicans and "staying the course". The Democrats look like they have the best chance in years of obtaining a majority in the House, and maybe even the Senate. Things are looking hopeful.

And then, John Kerry opens his mouth....

This is so typical of today's Democrats. Everything is handed to them on a plate and they just have to try to spoil it. I'm as liberal as they come, but frankly there's no way Kerry should be forgiven for his "botched joke" until he apologises. Sincerely. Idiot.



Word of the post:

Incogitancy

n. [L. incogitantia.]

Want of thought, or of the power of thinking; thoughtlessness; unreasonableness.

Example: 'Tis folly and incogitancy to argue anything, one way or the other, from the designs of a sort of beings with whom we so little communicate. --Glanvill.