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stevestory



Posts: 9021
Joined: Oct. 2005

(Permalink) Posted: Oct. 15 2008,00:39   

A Guiding Glow to Track the Movement of Proteins

   
Lou FCD



Posts: 5379
Joined: Jan. 2006

(Permalink) Posted: Oct. 17 2008,05:52   

Quote (stevestory @ Oct. 15 2008,01:39)
A Guiding Glow to Track the Movement of Proteins

That's just cool.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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J-Dog



Posts: 4369
Joined: Dec. 2006

(Permalink) Posted: Oct. 19 2008,11:41   

Dude...

http://www.telegraph.co.uk/news....ts.html

Far out.

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Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

UD is an Unnatural Douchemagnet. - richardthughes 7/11

  
stevestory



Posts: 9021
Joined: Oct. 2005

(Permalink) Posted: Oct. 21 2008,18:36   

Unsustainable resource depletion began 10,000 years ago.

Interesting article. Not sure how valid the argument is.

   
stevestory



Posts: 9021
Joined: Oct. 2005

(Permalink) Posted: Oct. 21 2008,18:58   

I think i'm going to give that its own thread for visibility. I'm curious what some people here have to say about it.

   
Timothy McDougald



Posts: 1016
Joined: Dec. 2006

(Permalink) Posted: Nov. 06 2008,21:19   

Copy number variation and evolution in humans and chimpanzees. Here is the abstract:

Quote
Copy number variants (CNVs) underlie many aspects of human phenotypic diversity and provide the raw material for gene duplication and gene family expansion. However, our understanding of their evolutionary significance remains limited. We performed comparative genomic hybridization on a single human microarray platform to identify CNVs among the genomes of 30 humans and 30 chimpanzees as well as fixed copy number differences between species. We found that human and chimpanzee CNVs occur in orthologous genomic regions far more often than expected by chance and are strongly associated with the presence of highly homologous intrachromosomal segmental duplications. By adapting population genetic analyses for use with copy number data, we identified functional categories of genes that have likely evolved under purifying or positive selection for copy number changes. In particular, duplications and deletions of genes with inflammatory response and cell proliferation functions may have been fixed by positive selection and involved in the adaptive phenotypic differentiation of humans and chimpanzees.


Initial sequence of the chimpanzee
genome and comparison with the human genome
. Here is the abstract:

Quote
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.


--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
J-Dog



Posts: 4369
Joined: Dec. 2006

(Permalink) Posted: Nov. 07 2008,07:27   

Quote (afarensis @ Nov. 06 2008,21:19)
Quote
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting  We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.


It's good to see that under the New Administration, scientists are trying to find out exactly why, and what happened, to make DaveScot the way he is - so no human has to go there ever again.

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Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

UD is an Unnatural Douchemagnet. - richardthughes 7/11

  
stevestory



Posts: 9021
Joined: Oct. 2005

(Permalink) Posted: Nov. 08 2008,21:12   

http://www.guardian.co.uk/environ....-alamos

I knew mini nuke plants were coming, i didn't know they were coming so soon.

   
stevestory



Posts: 9021
Joined: Oct. 2005

(Permalink) Posted: Nov. 10 2008,23:16   

Good Basic Carl Zimmer Article on Genes

   
Henry J



Posts: 4112
Joined: Mar. 2005

(Permalink) Posted: Nov. 13 2008,14:11   

Endeavour set for launch tomorrow

  
Lou FCD



Posts: 5379
Joined: Jan. 2006

(Permalink) Posted: Nov. 14 2008,06:11   

Got this message on FaceBook this morning, from the Royal Society:

Quote
R. Soc. Journals
Today at 6:21am
Reply
The complete Royal Society journal archive, dating back to 1665, is FREE to access until 1 February 2009 - see http://publishing.royalsociety.org/index.cfm?page=1600 for further information.

The Archive provides a record of some key scientific discoveries from the last 340 years including: Halley's description of 'his comet' in 1705; details of the double Helix of DNA by James Watson and Francis Crick in 1954; and Edmond Stone's breakthrough in 1763 that willow bark cured fevers, leading to the discovery of salicylic acid and later the development of aspirin.

A personal favourite is the description by Captain James Cook of how he preserved the health of his crew aboard the HMS Endeavour. Have a look and see what other treasures you can find!


We've been discussing DNA in Biology class, and what led up to and followed the Watson and Crick paper, so the timing is simply lovely.

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
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Bob O'H



Posts: 1994
Joined: Oct. 2005

(Permalink) Posted: Nov. 17 2008,01:25   

This is just stupidly cool.

In the last few years biologists have been studying gene expression with micro-arrays, which are horribly high-tec.  Well, some guys worked out how to do the same thing . . . on a CD.  Then you just need to play the CD to get the data off it.

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It is fun to dip into the various threads to watch cluelessness at work in the hands of the confident exponent. - Soapy Sam (so say we all)

   
stevestory



Posts: 9021
Joined: Oct. 2005

(Permalink) Posted: Nov. 17 2008,01:38   

Quote (Bob O'H @ Nov. 17 2008,02:25)
This is just stupidly cool.

In the last few years biologists have been studying gene expression with micro-arrays, which are horribly high-tec.  Well, some guys worked out how to do the same thing . . . on a CD.  Then you just need to play the CD to get the data off it.

I like what the nature blogger said, "They did what!?!".

Occasionally you run across an idea in science so cool all you can do is grin. This is one of those ideas.

   
Timothy McDougald



Posts: 1016
Joined: Dec. 2006

(Permalink) Posted: Nov. 18 2008,21:10   

Cave Bears!

Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet

Here is the abstract:

Quote
Retrieving a large amount of genetic information from extinct species was demonstrated feasible, but complete mitochondrial genome sequences have only been deciphered for the moa, a bird that became extinct a few hundred years ago, and for Pleistocene species, such as the woolly mammoth and the mastodon, both of which could be studied from animals embedded in permafrost. To enlarge the diversity of mitochondrial genomes available for Pleistocene species, we turned to the cave bear (Ursus spelaeus), whose only remains consist of skeletal elements. We collected bone samples from the Paleolithic painted cave of Chauvet-Pont d'Arc (France), which displays the earliest known human drawings, and contains thousands of bear remains. We selected a cave bear sternebra, radiocarbon dated to 32,000 years before present, from which we generated overlapping DNA fragments assembling into a 16,810-base pair mitochondrial genome. Together with the first mitochondrial genome for the brown bear western lineage, this study provides a statistically secured molecular phylogeny assessing the cave bear as a sister taxon to the brown bear and polar bear clade, with a divergence inferred to 1.6 million years ago. With the first mitochondrial genome for a Pleistocene carnivore to be delivered, our study establishes the Chauvet-Pont d'Arc Cave as a new reservoir for Paleogenetic studies. These molecular data enable establishing the chronology of bear speciation, and provide a helpful resource to rescue for genetic analysis archeological samples initially diagnosed as devoid of amplifiable DNA.


--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Henry J



Posts: 4112
Joined: Mar. 2005

(Permalink) Posted: Nov. 25 2008,17:05   

From nasa.gov website:

Quote
Mission managers gave the astronauts of space shuttle Endeavour an extra day in space as the crews of the shuttle and International Space Station continue transferring supplies and setting up new equipment inside the station.

Endeavour and seven astronauts are scheduled to return to Earth on Sunday at 12:55 p.m. EST. Endeavour is to land at NASA's Kennedy Space Center in Florida.

  
Lou FCD



Posts: 5379
Joined: Jan. 2006

(Permalink) Posted: Nov. 26 2008,20:14   

Dude has a new technique for genome sequencing, can do an entire human genome in about an hour.

Science Magazine Weekly Podcast

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
NSFW photography

   
Henry J



Posts: 4112
Joined: Mar. 2005

(Permalink) Posted: Nov. 26 2008,21:46   

Quote
Dude has a new technique for genome sequencing, can do an entire human genome in about an hour.


And the people who a few years ago spent years doing it, are they laughing or crying? :)

Henry

  
Lou FCD



Posts: 5379
Joined: Jan. 2006

(Permalink) Posted: Nov. 29 2008,11:47   

Quote
Most Planets May Be Seeded With Life

By Phil Berardelli
ScienceNOW Daily News
26 November 2008
Astronomers have detected a building block of RNA floating within the hot, compact core of a massive star-forming region in the Milky Way. The molecule appears to have formed with all of the other stuff that makes up planets, suggesting that many other worlds are seeded with some of life's ingredients right from birth.

Two of the greatest questions of existence--Are we alone? and How did we get here?--remain unanswered. Clues keep coming, and they are tantalizing. Over the past decade, astronomers have detected organic molecules inside meteorites and even in space (ScienceNOW, 28 March). But these latter substances have not been found in the clouds of dust and gas around new stars that can form planets, making their link to life tenuous.

The new find, described this week in the journal Astro-ph, is stronger. Using the IRAM radio dish array in France, a team of European astronomers has detected glycolaldehyde--a simple sugar that makes up ribose, one of the constituents of RNA--within the core of what appears to be a coalescing disk of dust and gas in a star-forming region called G31.41+0.31, about 26,000 light-years away. The sugar molecule can apparently form in a simple reaction between carbon monoxide molecules and dust grains.


More, at Science.

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
NSFW photography

   
stevestory



Posts: 9021
Joined: Oct. 2005

(Permalink) Posted: Nov. 30 2008,12:21   

could drinking heavy water extend your life?

   
Henry J



Posts: 4112
Joined: Mar. 2005

(Permalink) Posted: Nov. 30 2008,17:16   

Quote
could drinking heavy water extend your life?


The article that BWE referenced here seemed to have a different opinion.

Henry

  
Kristine



Posts: 3046
Joined: Sep. 2006

(Permalink) Posted: Dec. 04 2008,00:20   

I posted this jokingly at TBW but it would be my dream to work on this! :)
 
Quote
During his career, Gould wrote 300 consecutive essays for Natural History, the monthly magazine of the American Museum of Natural History, and more than 20 books, many of them bestsellers. He also assembled what he believed was a definitive library of the history of early paleontology, said Rhonda Shearer, Gould's widow.

Now, the collection of books, papers and artifacts that helped inform his writing and teaching is, for the most part, in the Stanford University Libraries, with the balance expected to arrive soon. It is an immense amount of material.

They're going to digitize much of it and make it available online!
 
Quote
Perhaps even more surprising than the books he collected is what he did with them.

"He actually used them, and he annotated on many of them in pencil, in the margins," Trujillo said. "He didn't really treat them as artifacts, he treated them as a working research library, and it is clear that is what he did, even though they're really quite amazing rare books."

Eek!  :O

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Which came first: the shimmy, or the hip?

AtBC Poet Laureate

"I happen to think that this prerequisite criterion of empirical evidence is itself not empirical." - Clive

"Damn you. This means a trip to the library. Again." -- fnxtr

  
midwifetoad



Posts: 3606
Joined: Mar. 2008

(Permalink) Posted: Dec. 04 2008,08:59   

As a hevy user of OmniPage, I have to say that hand notations in books make OCR a difficult thing.

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”let’s not make a joke of ourselves.”

Pat Robertson

  
Kristine



Posts: 3046
Joined: Sep. 2006

(Permalink) Posted: Dec. 04 2008,09:08   

Quote (midwifetoad @ Dec. 04 2008,08:59)
As a hevy user of OmniPage, I have to say that hand notations in books make OCR a difficult thing.

I'd hate to think of the EAD (encoded archival description) involved, too.

They may just go to PDFs, which wouldn't help you.

--------------
Which came first: the shimmy, or the hip?

AtBC Poet Laureate

"I happen to think that this prerequisite criterion of empirical evidence is itself not empirical." - Clive

"Damn you. This means a trip to the library. Again." -- fnxtr

  
qetzal



Posts: 309
Joined: Feb. 2006

(Permalink) Posted: Dec. 05 2008,14:53   

Quote (stevestory @ Nov. 30 2008,12:21)
could drinking heavy water extend your life?

The sidebar at the end of that article contains the following quote:

Quote
"Every single atom in the DNA of the brain of a 100-year-old man is the same atom as when he was 15 years old," says Shchepinov (BioEssays, vol 29, p 1247).


That's a stunningly incorrect claim, especially from someone who supposedly has expertise in isotope effects and their potential impact on free radical damage.*

If that quote is accurate (I can't access the original citation), it wouldn't encourage me to trust much of what Shchepinov says.

----

*For one thing, some of the protons (H atoms) on the DNA bases are sufficiently acidic to exchange with water at appreciable rates. Plus there are many spontaneous acid/base catalyzed reactions that alter the atoms in DNA, including cytosine deamination and depurination, to name two that are especially prevalent.

More important, the guy claims that the isotope effect will help us live longer by slowing damage from free radicals. Surely he realizes that free radical damage often changes the atoms in an affected biomolecule. Does he think DNA in the brain is somehow exempt from such alterations?

I sure hope that's a misquote.

  
Reed



Posts: 274
Joined: Feb. 2008

(Permalink) Posted: Dec. 09 2008,23:16   

Neanderthal genome half sequenced http://www.newscientist.com/article....ts.html

John Hawks has some commentary http://johnhawks.net/weblog....08.html

  
Lou FCD



Posts: 5379
Joined: Jan. 2006

(Permalink) Posted: Dec. 14 2008,11:16   

Jeremy Mohn of Stand Up for Real Science does a nice video on the chromosome 2 fusion in humans  on TeacherTube.

A little over 7 minutes long.

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
NSFW photography

   
Paul Flocken



Posts: 290
Joined: Dec. 2005

(Permalink) Posted: Dec. 16 2008,08:59   

Need a physics question answered.  I am trying to contribute to a game that I play and am making my scienc-y background text for it.

Since matter warps space into positive curvature, creating gravity, is it correct to say that the cosmological constant unwarps space negatively, and that the 'natural' state of rest for space is flat?  Or am I not even wrong?

Thanks in advance.
Paul

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"The great enemy of the truth is very often not the lie--deliberate, contrived, and dishonest, but the myth, persistent, persuasive, and unrealistic.  Belief in myths allows the comfort of opinion without the discomfort of thought."-John F. Kennedy

  
midwifetoad



Posts: 3606
Joined: Mar. 2008

(Permalink) Posted: Dec. 16 2008,09:39   

I'm pretty ignorant in this area, but my understanding is the "cosmological constant" is just the gravitational effect of dark matter and dark energy. The effect would be the same if the matter was visible.

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”let’s not make a joke of ourselves.”

Pat Robertson

  
Dr.GH



Posts: 1969
Joined: May 2002

(Permalink) Posted: Dec. 16 2008,10:41   

I have no idea, Paul. But, I like that image.

Edited by Dr.GH on Dec. 16 2008,08:42

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"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
nuytsia



Posts: 131
Joined: June 2006

(Permalink) Posted: Dec. 17 2008,02:39   

Great article here on recent work on Hawai'ian Honeyeaters and there origins.

But check out the comments.
Ugh!

   
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