Aaaarrrrggghhh!!!!!

Here's one from the little bro...

My pirate name is:

Dirty Tom Rackham

You're the pirate everyone else wants to throw in the ocean -- not to get rid of you, you understand; just to get rid of the smell. You have the good fortune of having a good name, since Rackham (pronounced RACKem, not rack-ham) is one of the coolest sounding surnames for a pirate. Arr!

Get your own pirate name from piratequiz.com.
part of the fidius.org network

Eight things

I read this over at the Doc's place and have tagged myself.

Here are the rules:
Each player lists 8 facts/habits about themselves. The rules of the game are posted at the beginning before those facts/habits are listed. At the end of the post, the player then tags 8 people and posts their names, then goes to their blogs and leaves them a comment, letting them know that they have been tagged and asking them to read your blog.

1. I walk the two miles to work each day. And back. I'd like to be able to claim I do it for the exercise, or to help save the environment, but I don't. I do it because I enjoy it.

2. I went to high school with a guy who was an Olympic gold medal-winning swimmer. He was a jerk. JollyRgr can confirm that.

3. I saw Inxs play in a pub long before they recorded their first album.

4. I have colleagues I don't respect. Sure they're good scientists, or at least they do all the things that supposedly make you a good scientist. But they treat the people in their labs, and the administrative people in the department, like dirt. For that I can't respect them.

5. I spent five years learning to play the cello. I haven't as much as touched one since high school.

6. My first paper as a postdoc, the one that really launched my career, almost didn't get published. After collecting all the data, writing the paper, sending it out to the journal, and receiving positive reviews that guaranteed it would be published (in a fairly high profile journal no less), I found a bug in the computer program I had written to generate the data. A big bug. A really bad big bug. I got lucky. We were going to withdraw the paper, but the editor handling it put it on hold instead until we could figure out if and how things changed. Luckily for me, the data changed just a little, and the conclusions not at all. I got published and here I am.

7. I find it almost impossible to resist a fresh (still warm!) cinnamon donut. Or a frosty cold beer. Unless it's mass-produced swill masquerading as beer.

8. Despite the facts that I'm a faculty member in a biochemistry department, I teach biochemistry, and I do biochemical research, I have never taken a biochemistry course. Or even one in biology. Not even in high school. The academic system can be very strange sometimes.

So there you go. I must say it's quite difficult to come up with eight things. Or at least it was for me. Of course now I'll post this and immediately think of eight different, more interesting things... C'est la vie.

Well duh!

They needed "experts" to figure this out?????

Tee hee

One day, three boys were walking over a bridge when they heard a guy yelling for help. It was President Bush. He was drowning, and the three boys rescued him. He thanked them dearly and promised them whatever they wanted as a reward.
The first boy wanted $10,000, so Bush gave him the money. The second boy wanted a Ferrari, so Bush gave the boy a Ferrari.

The third boy wanted a wheelchair, Bush said, “Why do you want one of those, son, you're not handicapped.” The boy replied, “I will be when my dad finds out whose life I saved.”

The BBC and sports on the web

The BBC sports web site does a masterful job of providing an over-by-over description of international cricket matches. They even manage to capture the uniquely dry wit of the British sports commentators. The web site also has live coverage of European football (soccer) matches. But I think they've gone a little too far with their live coverage... Now they're providing live coverage of World Snooker 2007! Snooker is a very clever and difficult game, far more so than pool. I even used to watch it every now and then televised on "Pot Black" back in Australia. But it makes for the most incredibly boring web coverage...

Truer words never spoken...

...than the conclusion of this little gem.

Mac's vs. PC's

Making a forest

I'm putting together this book. You may recall I've blogged about this enterprise in the past. It's nearing completion (and none too soon!). There are now four outstanding chapters. One of the authors hasn't answered a single email from me this year, so I've written him off. Two others promise their chapters are on the way. One of them told me today that I would have his by Wednesday (tomorrow). We'll see.

The fourth chapter? That would be mine. Hey, I'm the editor of the book, I can set my own rules, right? Just because everyone else was supposed to get their chapters done by mid-February doesn't mean I had to. As it was, almost none of them got their's to me on time.

So I've been busy writing my chapter. It's supposed to be a review of my research on unfolded protein states. Basically a summary of my current body of work, linking it all together and placing it into perspective with respect to everyone else's work. I'll be damned if it doesn't all make a lot of sense and hang together. My work that is. It's almost as if I had carefully plotted out the direction of my work over the past decade. I didn't. Research doesn't work that way. Research evolves. It goes where it goes, not where you try to make it go. I've been so busy planting trees (working on various research problems) that I hadn't noticed that I've managed to make a forest. It's pretty cool. At least I think so.

Once I've finished this chapter I think I'll add a stream to my forest. And maybe a lake.

Word of the post:

foofaraw \FOO-fuh-raw\
-noun

1. Excessive or flashy ornamentation or decoration.
2. A fuss over a matter of little importance.


Today's trivia question:

In our initial trivia frenzy we established the Beatles made five movies, each of which had an album associated with it. Which of those albums was the last to be released in England? Bonus points if you can tell me which year.

Creativity, genius and toilet repair

Interesting juxtaposition in yesterday's newspaper here. On the front page was a big article about the deplorable state of the studio art teaching building here at Big State U. Apparently the building itself is considered ideal for studio art in that it has loads of space and abundant natural light. Problem is, the building is in such bad shape it's close to condemnation. There is not ventilation system (studio arts often require use of noxious chemicals and/or produces significant amounts of dust), no air-conditioning (the temperature inside can exceed 100F in the Summer), most windows won't open, the electrical wiring is out of code and insufficient to power all the equipment in the building, the internal stairs are in danger of collapse and the plumbing bursts on a regular basis leading to flooding. Renovation estimates run from $30 million upwards. The administration here at Big State U. are in hot pursuit of the state government-mandated Top 20 status and have decided that science and technology should be the focus. So there are no plans to properly fix the studio art building.

In the same newspaper there was a very cool column (also featured here in the LA Times) written by Walter Isaacson, author of the Einstein biography "Einstein: His Life and Universe". In this column Isaacson makes the point that genius is a combination of smarts, rebelliousness and creativity. Creativity. That makes a lot of sense to me. Many of the best scientists I know have a very creative side. My good friend DocStymie springs to mind. A great scientist who happens to also be a musician with the great American novel inside of him (have you started writing it yet Doc?). Other scientists I know paint, sing, play muscial instruments, write and/or lose themselves in fantasy-based computer games. Creativity is key to good science.

So, Big State U., you want to be Top 20? I think perhaps you should fix the studio art building. Pronto.


Now, dear readers, on to toilet repair. Go on, admit it, that's the real reason you're bothering to read this, isn't it. You just want to hear all about my exploits with the poo pipeage. So, in our kids playroom downstairs there's this water stain on the ceiling. It's more or less below the upstairs porcelain throne. It's been there for a while and is slowly getting worse. I recently (Friday night) read an article in a home improvement magazine that pointed out that slow leaks like this one can cause extensive damage to the flooring and joists if left unrepaired. I decided maybe it was time to do something. My first step was to do some internet research. This confirmed what I thought might be the case - the most likely cause of the leak was the wax ring that seals the bottom of the toilet to the waste pipe. This seal is compressed by the weight of the toilet, plus user, forming a tight waterproof ring around the pipe. If however, it wasn't installed correctly, the bolts holding the toilet to the flange that connects to the waste pipe were tightened too much or were too loose, and/or the toilet could rock, this wax seal could develop a leak. Replacing the wax ring is, in principle, very straightforward. Most difficult step appeared to be putting the toilet back with a new ring attached. This has to be done by lining up the two small bolt holes over the bolts in the floor while keeping the toilet fairly level. Step two was to talk to a friend who is something of a home handyman. My main question was could I do this by myself. His answer was maybe, but you're better off with help. So he ended up spending much of the afternoon helping me. Pulling out the toilet was very easy (I remembered to empty all the water first!). That revealed that the old wax ring was in pretty bad shape. That wasn't the worst of it though. Whoever had installed the wax ring had overtightened the bolts holding the toilet down. This had caused the flange to bend and separate from the waste pipe, bending and putting a small hole in the pipe in the process (the likely cause of the leak). The subfloor looked fine though, which is good because that would be a very major repair job (although my friend claims we could handle it over a couple of weekends).

By the way, this isn't as yucky as it might sound. You flush a lot of clean water down that waste pipe, so it's actually pretty clean looking. Thomas Crapper was a clever man. I bet he had a creative side.

Anyway, we ended up having to cut and file the top of the waste pipe to get it level again. We then installed a replacement flange (thank goodness I had help from someone with a clue), and a new wax ring. All in all a very satisfying three hours work. Now we just have to wait a couple of weeks for the ceiling below to properly dry out before I dig out the damaged plaster, patch and seal it. Then we'll have to wait a few more weeks to be absolutely sure there isn't still a slow leak. My friend and I are pretty confident we fixed it though.

Yes, I did wash up. Thoroughly. Several times.


Word of the post:

jux·ta·po·si·tion [juhk-stuh-puh-zish-uhn]
–noun

1. an act or instance of placing close together or side by side, esp. for comparison or contrast.
2. the state of being close together or side by side.
[Origin: 1655–65; < F < L juxtā side by side + F position position]

—Related forms
jux·ta·po·si·tion·al, adjective

For an example, read the above post again.


And now for a music trivia question:

What was Nancy's real name in Rocky Racoon by the Beatles?
(Yes, I'm still on my Beatles kick.)

Sweet Loretta Fat, she thought she was a cleaner, but she was a frying pan.

I'm currently suffering from blog block. It's not that I can't think of things to write. It's that I can't think of things to write when I have the time to sit and write. Bit of a bummer really. Especially when my blog is approaching 3000 hits.

So here's some randomness...

Thanks to my little brother, I now have all of the Beatles' albums. They all fit on my 2G iPod nano. With lots of room to spare.

I was listening to Beatles tunes while following the Australia-England one day cricket match on Sunday. Fittingly, the song "Help!" came on half way through England's innings. It didn't help them.

"'I dig a pygmie' by Charles Hortree and the Deaf Aids" is the opening line to which album? (Little brother you're not eligible to answer.)

Who played lead guitar on "While My Guitar Gently Weeps"? I know the answer. Do you?

Twenty years ago I was a graduate (postgraduate) student. My research involved long computer simulations. I used the university mainframe. It filled a large room and had disk drives that looked like oversized washing machines. My current PDA fits in my pocket. It is faster and has more memory than that mainframe.

And finally, do any of you know someone who owns a Zune? I've seen them in stores, but never one out in the wild.


Word of the post:

magniloquent \mag-NIL-uh-kwent\
-adjective

Lofty or grandiose in speech or expression; using a high-flown style of discourse; bombastic.

Of applications and white supremacy

Regular readers (both of you) might recall that I'm heading up a program to have a bunch of undergraduates do research in our department over the summer. Last Friday was the deadline for applications. Here are some interesting tidbits from that process:

We received about 60 applications. Not bad at all. I am told by people with similar programs that next year we will receive up to 300! We got the grant money to run this program in mid-February which is when most programs have their deadlines. Many students would have already arranged something for the summer before we got going this year. I'm not sure I can handle 300 applications...

Of the 60 applications we have about 10 that consist only of one or two letters of recommendation. No application form, transcript etc. as required. What's with that? It takes a lot of time and effort to write a letter of recommendation. I think it's disgusting that so many students would ask faculty to write such letters and then not even bother to apply. Okay, one or two applications might have got lost in the mail, but 10?

Apparently some foreign students are blind to the stipulation that applicants be US citizens or permanent residents (a requirement of the NSF who is funding this program). Despite this being in big bold red letters on the home page of our web site. And stated in at least two other places on the web site. And on the application forms. I haven't counted those students in the 60 apllications.

One young lady from Romania emailed me to see if she was eligible. When I replied that she was not, she promptly invited me to be her "friend" on Facebox (apparently a Romanian version of the very popular US Facebook). I haven't replied to that, or the following three invitations... She's on my junkmail list.

Here's a copy of an email I received late Thursday night (keep in mind the deadline was Friday)-
"I was thinking of applying to the program but I thought the deadline was later than tomorrow until I just saw on the website. I can send in all required application materials by tomorrow except for the recommendations. I have told my professors they can have another week to send their recommendations. I hope that's okay." [Emphasis mine]

My reply-
"No, it's not okay."

Finally on applications, while I was typing this I received three express mail envelopes with more application materials and a phone call from some student's mother who wants to hand deliver an application... Oy.



And white supremacy? DocStymie, this is one you'll really like:

Rep. Charlie Rangle, D-N.Y. (remember he's black) when asked on public TV what he thought about the President, replied, "Well, I really think that he shatters the myth of white supremacy once and for all".



Word of the post:

sang-froid \sang-FRWAH\
-noun;

Freedom from agitation or excitement of mind; coolness in trying circumstances; calmness.

Example: It takes remarkable level of sang-froid to catch a Matthew Hayden six with one hand while not spilling the beer held in the other. (See here, although I'm afraid it will be lost on Americans.)

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.