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Lakeshore
An author of no particular popularity

Jay Lake
Date: 2008-04-17 06:10
Subject: [links] Link salad for a Thursday
Security: Public
Location:Nuevo Rancho Lake
Mood:morningish
Music:the day breaking outside
Tags:cool, funny, links, personal, politics, science, tech, writing
Suspect caught with gator in his car — Life imitates one of my short stories.

Grunt Work: Scientists Re-Create Neanderthal Speech — Cool anthropology.

Evernote: Software to help you remember everything, forever — Externalizing your mind. Apple's Spotlight + gmail already do a significant amount of this for me. The ability to freely and powerfully search unstructured data has significantly improved some important aspects of my life. (Thanks to my Aunt M.)

The sign of the long now — The art and science of making a 10,000 year "keep out" notice. (Thanks to danjite.)

Video: Water Balloon Exploding at 2,000 Frames per Second — This is pretty darned cool. Story is a brief squib about high speed cameras, not the properties of water, fyi.

Ringing the Stellar BellCentauri Dreams on astroseismology and overmetallicity. Worth reading for any of you hard sf or science geek types.

The $100 Genome — If that's not a story title, I don't know what is.

De-debunking the recent NASA asteroid collision story — Maybe they can keep English and metric straight. Rocket scientists...sheesh...

Talking Points Memo with an interesting letter from a conservative reader — One of the underlying arguments is that conservatism is not equivalent to support for the Bush administration, its policies and actions. I find this argument grossly self-serving. Much like moderate Christians silently riding the Evangelical political wave over the past 25 years, moderate conservatives (such as they are) have remained silent on the election fraud in 2000, the wholesale assault on civil liberties post-9/11, the disaster of the Iraq war, the siamese twin disasters of the budget and the deficit. Somehow the last eight years would have been worse with Democrats in charge, I guess. This is another version of the nascent "But Bush isn't a real conservative" meme. Confidential to conservatives in America: Tough shit, guys. You got in on the cult of Bush when the getting was good, you can fucking live with the consequences now. The rest of us are sure as hell stuck with them.




4/17/08
Time in saddle: 19 minutes
Last night's weigh-out: n/a
This morning's weigh-in: 271.4
Currently reading: Blue Highways by William Least Heat-Moon Powell's | Amazon ]


Post A Comment | 16 Comments | | Flag | Link






Edward Greaves
User: temporus
Date: 2008-04-17 13:28 (UTC)
Subject: (no subject)
I don't know why, but I keep misreading the link salad entries recently.

Yesterday it was: Why we shout into the darkness. (Instead of Should we shout into the darkness.)

Today it was: The $100 Gnome

I think I need more coffee.
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Jay Lake
User: jaylake
Date: 2008-04-17 13:31 (UTC)
Subject: (no subject)
If he spent enough time on the Paris subway, he'd be the $100 metro gnome
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biomekanic
User: biomekanic
Date: 2008-04-17 13:34 (UTC)
Subject: (no subject)
*groan*

That also applies to the DC subway.
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Edward Greaves
User: temporus
Date: 2008-04-17 13:39 (UTC)
Subject: (no subject)
You mean like the one from Amelie?
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Jay Lake
User: jaylake
Date: 2008-04-17 13:49 (UTC)
Subject: (no subject)
How come your replies thread and mine don't?
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mcjulie
User: mcjulie
Date: 2008-04-17 13:59 (UTC)
Subject: I agree with you!
Much like moderate Christians silently riding the Evangelical political wave over the past 25 years, moderate conservatives ... . You got in on the cult of Bush when the getting was good, you can fucking live with the consequences now.

I sometimes run into Christians who are upset at being stereotyped as intolerant bigots, but at the same time, most of them haven't done much to speak out against religious bigotry. I don't just mean in the major media, where access is an issue, I mean in everyday life.

Similarly, I get fed up when I'm around somebody, often a self-described libertarian, who complains about Bush but at the same time parrots only Republican talking points. So they can complain bitterly about Bush, but the merest suggestion that Gore might have done better -- or that Clinton *did* better -- is laughed off the table.
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User: ellameena
Date: 2008-04-17 14:03 (UTC)
Subject: (no subject)
LOL. I reported on the $1000 genome for Nature Biotechnology over a year ago. There were a couple of companies rolling out technologies for a $1000 genome at that time--not Applied Biosystems. One "trick" is that the genome is mostly introns, which we don't know what the heck they are. Even if you were to speculate that all of the introns or "junk" have some mysterious purpose, we don't know what that purpose might be, so it's not useful to sequence it. By sequencing only the exons, or the most relevant 10%, you can reduce any sequencing effort by a factor of ten.
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Jay Lake
User: jaylake
Date: 2008-04-17 14:07 (UTC)
Subject: (no subject)
Which reminds me of a question I once asked frankwu (who in his spare time is a Ph.D. geneticist). What would you have if you edited all the repeats, stutters and junk out of the human genome? Could you still have a human being?
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biomekanic
User: biomekanic
Date: 2008-04-17 14:30 (UTC)
Subject: (no subject)
Since you work in a corporate environment as well, I thought you'd be interested in this one:
Nasty memoes fired off for taking to many sick days, misplacing supplies, and not turning in your your vouchers. Just another day at Al Qaeda.
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User: ellameena
Date: 2008-04-17 14:54 (UTC)
Subject: (no subject)
That's a tricky question because it depends on how you define "junk." Obviously, once a function is identified, it is no longer junk, so theoretically, a genome with zero junk would produce a human being indistinguishable from normal. That's the theory behind junk DNA. The reality is that we have not yet investigated every nucleotide of the genome. Far from it. Until it's all characterized, we can't know what is going in in the presumptive junk sequences. Recently, a number of surprising discoveries have been made in areas once thought to be junk. These are DNA sequences which are known not to code for any protein, and it was originally assumed that this meant they did not have any organismic function. Some of these sequences we now know code for special RNAs which have function in the body--mostly regulatory function. It looks like the mysteries of embryonic development are all about RNA, which is really exciting! Do you know how frustrated scientists have been trying to figure out what makes one embryonic cell turn into, say, a brain cell, and another into a toe? So that's great, but it means we can't really answer this question. I believe some experiments have been done on simpler eukaryotic organisms, perhaps something like c. elegans (a worm), but I can't immediately track down the references. My vague recollection is that the experiment was inconclusive, but if I find it, I'll let you know.

Another fascinating thing is the "repeats and stutters" that you mention. A couple of years ago, in 2006, I think, the big genetic news of the year was a set of several papers published simultaneously about genome size. This was fascinating information where we found that there is a "normal range" of repeats in genes that in some cases is very broad, and in some cases not so much. So traditionally we think of each gene having one copy, and other regulatory mechanisms controlling "how much" of the gene gets turned into protein. But it turns out that some genes have hundreds of repeats, and that an abnormally small number of repeats will result in a genetic abnormality, even though the code is there. Conversely, and abnormally large number of repeats can function sort of like a chromosomal trisomy (think down syndrome) pumping way too many copies of the protein into cells. For that reason, it would probably be disastrous to get rid of all repeats. There's a new project/consortium that is getting researchers together to explore the implications of gene copy number.

(Okay, can you tell that I am working on a book on genetics and molecular biology?)

(What was Frank's answer?)
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User: ellameena
Date: 2008-04-17 14:54 (UTC)
Subject: (no subject)
This was meant to be a reply, above.
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daveraines
User: daveraines
Date: 2008-04-18 02:26 (UTC)
Subject: (no subject)
>> Much like moderate Christians silently riding the Evangelical political wave over the past 25 years

OK, I'll rise to the bait here at the Lakeshore. I'm a moderate Christian, and I don't recall riding any political wave. I recall people leaving my churches because I've defended your right to bitch at us, and I recall people who've stopped coming for a while because I thought it was OK not to have prayer in schools, and I recall people leaving my churches when I talked about non-violent resistance to evil in the run-up to Iraq. I recall a delegation of bishops from our 9-million member denomination going to one of our own members (Mr. Bush) with a message that invading Iraq is against everything we believe in; and being turned away. In fact, in about a week, you'll start reading stuff about our General Conference, and how the United Methodist Church is debating language about homosexuality, and how fierce the division is. That's because I have a lot of company, and the moderates aren't being silent.

So that's my evidence. Where's yours?
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Jay Lake
User: jaylake
Date: 2008-04-18 13:23 (UTC)
Subject: (no subject)
Specifically what I was thinking of when I wrote that was the voting patterns of Catholics and some mainline Protestants, who got co-opted into voting very conservatively as single-issue voters on abortion. That was one of the GOP's greatest political maneuvers of the last quarter of the 20th century, because it got millions of otherwise quite reasonable-minded Christians to go along with their rest of their BS.
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daveraines
User: daveraines
Date: 2008-04-18 14:33 (UTC)
Subject: (no subject)
Ah! thank you, that sets some context. I agree with everything you said in your reply, though I think I have more sympathy with "single-issue voters on abortion." I try to put myself in their shoes and ask, is there one issue that for me would override all others? and answer "maybe" - the Iraq war. So is it a proper analogy to say THEY feel about abortion as I feel about Iraq? Would I simply dismiss any political party that scorned my view on Iraq, as the Democrats scorned the pro-life voters?

All this is, of course, hopelessly moderate.
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Jay Lake
User: jaylake
Date: 2008-04-18 12:29 (UTC)
Subject: (no subject)
(Trying to reply here...not sure if that's working correctly.)

Frank (who's dissertation was on the redundancy of a specific enzyme-related gene site in E. coli) gave essentially the same answer you did. He told me the "junk" DNA wasn't really junk, and the redundant genes were redundant for a reason, then launched into a long and interesting discussion of the whys and hows of that redundancy.
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A large duck
User: burger_eater
Date: 2008-04-18 18:06 (UTC)
Subject: (no subject)
"But Bush isn't a real conservative"

Actually, judging by the evidence of the last couple decades, Bush is what you get when you put a conservative in the White House. They talk about small government on the way into office, but that's not what you get when you elect one.

They're like communists that way: The theory is all Karl Marx and government falling away but the practice is Stalin, Mao and other totalitarians.
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