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	<title>KQED QUEST &#187; dna</title>
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	<link>http://science.kqed.org/quest</link>
	<description>Explore science, nature and environment stories from Northern California and beyond with KQED’s multimedia series</description>
	<lastBuildDate>Thu, 09 Feb 2012 23:37:04 +0000</lastBuildDate>
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		<item>
		<title>The Benefits of Radioactive Fallout</title>
		<link>http://science.kqed.org/quest/2012/01/09/the-benefits-of-radioactive-fallout/</link>
		<comments>http://science.kqed.org/quest/2012/01/09/the-benefits-of-radioactive-fallout/#comments</comments>
		<pubDate>Mon, 09 Jan 2012 15:44:23 +0000</pubDate>
		<dc:creator>Dr. Barry Starr</dc:creator>
				<category><![CDATA[Biology]]></category>
		<category><![CDATA[Environment]]></category>
		<category><![CDATA[Partners]]></category>
		<category><![CDATA[Chernobyl]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[DNA damage]]></category>
		<category><![CDATA[genetics]]></category>
		<category><![CDATA[nuclear fallout]]></category>
		<category><![CDATA[Radioactive Wolves]]></category>
		<category><![CDATA[radioactivity]]></category>

		<guid isPermaLink="false">http://science.kqed.org/quest/?p=29086</guid>
		<description><![CDATA[Wildlife seems to be thriving in the radioactive areas around Chernobyl.  For now it looks like if animals had to choose, they'd choose radioactivity over humans.]]></description>
			<content:encoded><![CDATA[<div id="attachment_29087" class="wp-caption alignnone" style="width: 650px"><a href="http://science.kqed.org/quest/2012/01/09/the-benefits-of-radioactive-fallout/wolves/" rel="attachment wp-att-29087"><img src="http://science.kqed.org/quest/files/2012/01/Wolves.jpg" alt="" title="Wolves" width="640" height="362" class="size-full wp-image-29087" /></a><p class="wp-caption-text">Animals are doing surprisingly well in the radioactive areas around Chernobyl.</p></div>
<p>Imagine people’s worst fears are realized and the nuclear power plant at <a href="http://www.pge.com/myhome/edusafety/systemworks/dcpp/">Diablo Canyon</a> here in California has a Chernobyl-style meltdown.  The effects on people are obvious: high rates of thyroid and other cancers, permanent resettlement elsewhere, increased rates of birth defects and so on.  But as the area around Chernobyl is showing, the effects on the environment may be more subtle.</p>
<p>Over the break I watched a Nature special called, "<a href="http://www.pbs.org/wnet/nature/episodes/radioactive-wolves/introduction/7108/">Radioactive Wolves</a>".  This is a documentary about wildlife in a radioactive exclusion zone around Chernobyl.</p>
<p>Even though the area around Chernobyl is still so contaminated that humans can only go in for limited amounts of time, the wildlife appears to be doing surprisingly well.  Birth defects are higher than in surrounding areas but life is thriving.  Wolves are doing great, beavers have returned and everything looks hunky dory.</p>
<p>This seemed strange to me.  I would think that so much radiation should be having pretty severe effects on these animals.  And as noted in this <a href="http://www.ncbi.nlm.nih.gov/pubmed/20002049">in this NIH study</a>, for certain individuals it definitely is.</p>
<p>The difference is in perspective.  For the individual, the area around Chernobyl is terrible.  Your kids have a higher rate of being stillborn or having birth defects, you have a much higher rate of developing various cancers, and so on.  But for the species as a whole, things aren’t so bad.  The higher background radiation appears to hardly be affecting their numbers at all.</p>
<p>Now this isn’t to say that the initial fallout wasn’t catastrophic to wildlife.  It was.  Untold numbers of animals died a terrible death in Chernobyl’s aftermath.</p>
<p>For the lucky survivors and new immigrants, though, Chernobyl is a different story.  It is a chance to live a life without human interference.  At least for now it looks like the high background radiation is preferable to man for these animals. </p>
<p>It is important that scientists keep studying this ecosystem though.  The DNA of the animals in this area are under constant attack from the radiation.  There may come a tipping point where the genetic burden becomes too high and populations start to crash.  We’ll have to wait and see.</p>
<p>Additional Reading: <a href="http://tv.nytimes.com/2011/10/19/arts/television/radioactive-wolves-on-pbs-review.html">NY Times Review of Radioactive Wolves</a></p>

	Tags: <a href="http://science.kqed.org/quest/tag/chernobyl/" title="Chernobyl" rel="tag">Chernobyl</a>, <a href="http://science.kqed.org/quest/tag/dna/" title="dna" rel="tag">dna</a>, <a href="http://science.kqed.org/quest/tag/dna-damage/" title="DNA damage" rel="tag">DNA damage</a>, <a href="http://science.kqed.org/quest/tag/genetics/" title="genetics" rel="tag">genetics</a>, <a href="http://science.kqed.org/quest/tag/nuclear-fallout/" title="nuclear fallout" rel="tag">nuclear fallout</a>, <a href="http://science.kqed.org/quest/tag/radioactive-wolves/" title="Radioactive Wolves" rel="tag">Radioactive Wolves</a>, <a href="http://science.kqed.org/quest/tag/radioactivity/" title="radioactivity" rel="tag">radioactivity</a><br />
]]></content:encoded>
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		<slash:comments>0</slash:comments>
	<georss:point>37.331855 -121.890129</georss:point><geo:lat>37.331855</geo:lat><geo:long>-121.890129</geo:long>
		<media:thumbnail url="http://science.kqed.org/quest/files/2012/01/Wolves.jpg" />
		<media:content url="http://science.kqed.org/quest/files/2012/01/Wolves.jpg" medium="image">
			<media:title type="html">Wolves</media:title>
		</media:content>
		<media:content url="http://science.kqed.org/quest/files/2012/01/Wolves.jpg" medium="image">
			<media:title type="html">Wolves</media:title>
			<media:description type="html">Animals are doing surprisingly well in the radioactive areas around Chernobyl.</media:description>
			<media:thumbnail url="http://science.kqed.org/quest/files/2012/01/Wolves-300x169.jpg" />
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		<item>
		<title>Turning Chickens into Dinosaurs</title>
		<link>http://science.kqed.org/quest/2011/09/12/turning-chickens-into-dinosaurs/</link>
		<comments>http://science.kqed.org/quest/2011/09/12/turning-chickens-into-dinosaurs/#comments</comments>
		<pubDate>Mon, 12 Sep 2011 15:00:01 +0000</pubDate>
		<dc:creator>Dr. Barry Starr</dc:creator>
				<category><![CDATA[Biology]]></category>
		<category><![CDATA[bioengineer]]></category>
		<category><![CDATA[chickenosaurus]]></category>
		<category><![CDATA[dinochicken]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[DNA sequence]]></category>
		<category><![CDATA[evolution]]></category>
		<category><![CDATA[extinct species]]></category>
		<category><![CDATA[genes]]></category>
		<category><![CDATA[genetics]]></category>
		<category><![CDATA[hen's teeth]]></category>
		<category><![CDATA[jurassic park]]></category>
		<category><![CDATA[reverse evolution]]></category>

		<guid isPermaLink="false">http://science.kqed.org/quest/?p=24027</guid>
		<description><![CDATA[If we are ever going to resurrect dinosaurs, it probably won't be like in the movie Jurassic Park. Instead, we'll have to throw evolution into reverse and turn a bird back into a dinosaur.]]></description>
			<content:encoded><![CDATA[<div id="attachment_24035" class="wp-caption alignright" style="width: 310px"><a href="http://science.kqed.org/quest/files/2011/09/dinochicken3.jpg" rel="lightbox[24027]" title="dinochicken3"><img src="http://science.kqed.org/quest/files/2011/09/dinochicken3-300x169.jpg" alt="" title="dinochicken3" width="300" height="169" class="size-thumbnail wp-image-24035" /></a><p class="wp-caption-text">By reversing evolution, scientists may be able to transform chickens into dinosaurs one step at a time.</p></div>
<p>You may remember that in Jurassic Park, scientists sequenced some dinosaur DNA from a mosquito trapped in amber.  They made a copy of this DNA, filled in the gaps with frog DNA and then created a dinosaur.</p>
<p>Although cool, we're not likely to get dinosaurs this way in the near future for a bunch of different reasons.  The biggest for now (besides not having any dinosaur DNA) is that we can’t <a href="http://www.thetech.org/genetics/news.php?id=129">clone anything bigger than a bacterium</a> with just a piece of DNA.  To clone a multi-celled creature like a dinosaur, we need frozen or even better, live cells.</p>
<p>While this might be possible for some extinct animals including <a href="http://science.kqed.org/quest/2008/11/10/mammoth-resurrection/">mammoths</a>, 65 million years is just too long to find any frozen or viable cells.  But there may be another way to one day create Jurassic Park.  By messing with a chicken’s genes.</p>
<p>Current theories are that birds evolved from dinosaurs.  This means that all the information for making a dinosaur was contained in bird DNA at one time.  The trick is to figure out what this dinosaur DNA looked like and to change bird DNA accordingly and/or to unlock any hidden dinosaur DNA that may still be in bird DNA.</p>
<p>After 65 million years you might think all traces of dino-DNA would be lost in birds.  Surprisingly, you’d be wrong.  It looks like there is still some T-rex lurking in a chicken’s DNA.</p>
<p>In the last decade, scientists have been able to make chickens look a bit more dinosaur-like by changing how the chickens use the genes they already have.   For example, they have been able to make a chicken’s tail look a bit more like a dinosaur’s.</p>
<p>A big difference between birds and dinosaurs is that dinosaurs have much longer tails.   But this doesn’t hold up in a chicken embryo.</p>
<p>At a very early stage of development, chicken embryos have what looks like a very reptilian tail with 16 vertebrae.  Later in development, though, most of the vertebrae disappear until only five are left.</p>
<p>What this means is that if scientists can figure out how to keep the vertebrae from disappearing, they might end up with a long tailed chicken.  And they’ve actually managed to sort of do this already.</p>
<p>By changing when certain genes are turned on or off, they have managed to <a href="http://www.dailymail.co.uk/sciencetech/article-1026340/Jurassic-Park-comes-true-How-scientists-bringing-dinosaurs-life-help-humble-chicken.html">create a chicken</a> with a tail that has eight vertebrae.  Not quite a dinosaur but a step in that direction.</p>
<p>They have also been able to create a <a href="http://dml.cmnh.org/2011Aug/msg00313.html">chicken with teeth</a>.  And even a <a href="http://www.dailymail.co.uk/sciencetech/article-1026340/Jurassic-Park-comes-true-How-scientists-bringing-dinosaurs-life-help-humble-chicken.html">snout</a>!  All of this without fundamentally changing a chicken’s genes but instead changing how they are used.  </p>
<p>Now they probably won’t be able to make the chicken-dinosaur transition simply by changing how chicken genes are used.  There are bound to have been some significant changes in certain key genes that will have to be replicated to really make a dinosaur.  And for that we’ll need to figure out what dinosaur DNA looked like.</p>
<p>But still, we can make a lot of progress towards making a dinosaur by simply using the toolkit of current bird genes.  In the end, we’ll probably be able to recreate something very much like a dinosaur.  The question will then become whether we should.  </p>
<p><embed src='http://science.kqed.org/quest/files/jw-player-plugin-for-wordpress/player/player.swf' height='360' width='640' allowscriptaccess='always' allowfullscreen='true' flashvars='&amp;bandwidth=2841&amp;controlbar=over&amp;dock=false&amp;file=117b_evolution.flv&amp;image=http%3A%2F%2Fscience.kqed.org%2Fquest%2Fwp-content%2Fuploads%2Fposter_frames%2F117c_evolution300.jpg&amp;gapro.accountid=UA-1538528-1&amp;gapro.height=360&amp;gapro.pluginmode=FLASH&amp;gapro.trackpercentage=true&amp;gapro.trackstarts=true&amp;gapro.tracktime=true&amp;gapro.visible=true&amp;gapro.width=640&amp;gapro.x=0&amp;gapro.y=0&amp;plugins=gapro-1&amp;skin=http%3A%2F%2Fscience.kqed.org%2Fquest%2Fwp-content%2Fplugins%2Fjw-player-plugin-for-wordpress%2Fskins%2Fglow.zip&amp;streamer=rtmp%3A%2F%2Fkqed-flash02.streamguys.us%2Fquest%2F&amp;viral.allowmenu=true&amp;viral.bgcolor=0x333333&amp;viral.fgcolor=0xffffff&amp;viral.functions=embed&amp;viral.matchplayercolors=true&amp;viral.oncomplete=false&amp;viral.pluginmode=FLASH' /></p>
<p><em>QUEST story on how scientists can figure out ancient DNA from modern DNA.</em></p>

	Tags: <a href="http://science.kqed.org/quest/tag/bioengineer/" title="bioengineer" rel="tag">bioengineer</a>, <a href="http://science.kqed.org/quest/tag/chickenosaurus/" title="chickenosaurus" rel="tag">chickenosaurus</a>, <a href="http://science.kqed.org/quest/tag/dinochicken/" title="dinochicken" rel="tag">dinochicken</a>, <a href="http://science.kqed.org/quest/tag/dna/" title="dna" rel="tag">dna</a>, <a href="http://science.kqed.org/quest/tag/dna-sequence/" title="DNA sequence" rel="tag">DNA sequence</a>, <a href="http://science.kqed.org/quest/tag/evolution/" title="evolution" rel="tag">evolution</a>, <a href="http://science.kqed.org/quest/tag/extinct-species/" title="extinct species" rel="tag">extinct species</a>, <a href="http://science.kqed.org/quest/tag/genes/" title="genes" rel="tag">genes</a>, <a href="http://science.kqed.org/quest/tag/genetics/" title="genetics" rel="tag">genetics</a>, <a href="http://science.kqed.org/quest/tag/hens-teeth/" title="hen&#039;s teeth" rel="tag">hen&#039;s teeth</a>, <a href="http://science.kqed.org/quest/tag/jurassic-park/" title="jurassic park" rel="tag">jurassic park</a>, <a href="http://science.kqed.org/quest/tag/reverse-evolution/" title="reverse evolution" rel="tag">reverse evolution</a><br />
]]></content:encoded>
			<wfw:commentRss>http://science.kqed.org/quest/2011/09/12/turning-chickens-into-dinosaurs/feed/</wfw:commentRss>
		<slash:comments>5</slash:comments>
	<georss:point>37.331855 -121.890129</georss:point><geo:lat>37.331855</geo:lat><geo:long>-121.890129</geo:long>
		<media:thumbnail url="http://science.kqed.org/quest/files/2011/09/dinochicken3.jpg" />
		<media:content url="http://science.kqed.org/quest/files/2011/09/dinochicken3.jpg" medium="image">
			<media:title type="html">dinochicken3</media:title>
		</media:content>
		<media:content url="http://science.kqed.org/quest/files/2011/09/dinochicken3.jpg" medium="image">
			<media:title type="html">dinochicken3</media:title>
			<media:description type="html">By reversing evolution, scientists may be able to transform chickens into dinosaurs one step at a time.</media:description>
			<media:thumbnail url="http://science.kqed.org/quest/files/2011/09/dinochicken3-300x169.jpg" />
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		<title>The High Cost of Sex</title>
		<link>http://science.kqed.org/quest/2011/08/01/the-high-cost-of-sex/</link>
		<comments>http://science.kqed.org/quest/2011/08/01/the-high-cost-of-sex/#comments</comments>
		<pubDate>Mon, 01 Aug 2011 16:36:54 +0000</pubDate>
		<dc:creator>Dr. Barry Starr</dc:creator>
				<category><![CDATA[Biology]]></category>
		<category><![CDATA[asexual]]></category>
		<category><![CDATA[asexual reproduction]]></category>
		<category><![CDATA[cancer]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[DNA repair]]></category>
		<category><![CDATA[evolution]]></category>
		<category><![CDATA[genetics]]></category>
		<category><![CDATA[meiosis]]></category>
		<category><![CDATA[Muller ratchet]]></category>
		<category><![CDATA[recombination]]></category>
		<category><![CDATA[sex]]></category>
		<category><![CDATA[sexual]]></category>
		<category><![CDATA[sexual reproduction]]></category>

		<guid isPermaLink="false">http://science.kqed.org/quest/?p=21587</guid>
		<description><![CDATA[Biologically speaking, sex is ungodly expensive.  One reason it may have evolved in to keep our genomes stable and intact.]]></description>
			<content:encoded><![CDATA[<div id="attachment_21594" class="wp-caption alignleft" style="width: 650px"><a href="http://science.kqed.org/quest/files/2011/07/CoupleOnBeach1.jpg" rel="lightbox[21587]" title="CoupleOnBeach"><img src="http://science.kqed.org/quest/files/2011/07/CoupleOnBeach1.jpg" alt="" title="CoupleOnBeach" width="640" height="362" class="size-full wp-image-21594" /></a><p class="wp-caption-text">Sex may have evolved to cut down on genetic variation.</p></div>
<p>No, I don’t mean in the red light district of Amsterdam or at Mustang Ranch.  What I am talking about is the high biological cost of sex.  In fact, it is so expensive it can be hard to imagine how it ever evolved in the first place.  </p>
<p>The main reason sex is so costly is it takes two parents to have a kid.  Asexual creatures can do it on their own.</p>
<p>This doesn’t sound like much of an advantage, but it is.  Some <a href="http://www.indiana.edu/~curtweb/Research/cost%20of%20males.html">computer simulations</a> show that a single asexual individual can overtake a population of one million sexual creatures in about 50 generations.  That is about 1000 years for people and only 8 years for mice.</p>
<p>So sex needs to have some pretty big advantages to have ever evolved in the first place.  Otherwise the first sexual creature would have been quickly swamped out by all of its asexual brethren as soon as it appeared.  </p>
<p>In the past, scientists have pointed to variation as one of sex’s big advantage.  This probably isn’t the whole story though.  Or even most of it.</p>
<p>Sex does create additional variety through the mixing of genes but it probably isn’t enough to explain the rise of sex.  You’d have to live in some pretty chaotic times for this variation to offer enough an advantage to an individual to overcome its cost.  Eight or a thousand years just isn’t that long in an evolutionary time scale.</p>
<p>A new <a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2010.01173.x/abstract">review</a> out is bringing up an old idea that Muller came up with <a href="http://www.jstor.org/sici?sici=0003-0147%28193203/193204%2966:703%3C118:SGAOS%3E2.0.CO;2-B&amp;">back in 1932</a>.  The main advantage of sex is to provide a safe time to recombine our DNA.</p>
<p>Recombination is simply the swapping of DNA between two identical (or nearly identical) pieces of DNA.  For us that means swapping between the chromosomes we got from mom and dad.  So DNA is swapped between our two chromosome 1’s our two chromosome 2’s and so on.   </p>
<p>This is where part of that variation we were talking about earlier comes from.  But more importantly, recombination actually helps repair DNA damage.  You can see the effects of no recombination by looking at our <a href="http://www.thetech.org/genetics/ask.php?id=51">sad little Y chromosome</a> which is slowly disappearing because it has no one to recombine with except itself.</p>
<p>But recombination is a double edged sword.  Cells need it to repair their DNA but it can cause lots of DNA damage if it isn’t controlled.  For example, even with all of our controls in place, 1 in 1000 humans still ends up with one chromosome stuck to another.  </p>
<p>You can see what happens with uncontrolled recombination by looking at cancer cells.  These cells end up with extra chromosomes, chromosomes stuck together, and lots of other chromosomal problems because they recombine willy-nilly.  They do well for themselves but are definitely bad for the individual. </p>
<p>So it makes sense to contain recombination to some easily controlled time.  Sex may have arisen and took over the world because it provides a safer way to keep harmful DNA damage in check.  The variation that everyone goes on about may simply have been a beneficial side effect.</p>
<div id="attachment_21653" class="wp-caption aligncenter" style="width: 437px"><a href="http://science.kqed.org/quest/2011/08/01/the-high-cost-of-sex/sexasexcomparison/" rel="attachment wp-att-21653"><img src="http://science.kqed.org/quest/files/2011/07/SexAsexComparison-427x360.jpg" alt="" title="SexAsexComparison" width="427" height="360" class="size-large wp-image-21653" /></a><p class="wp-caption-text">After just nine generations, the sexual beasts on the left are already being swamped out by the asexual ones on the right.</p></div>
<p><strong>See the following for more information:</strong></p>
<p><a href="http://www.evolutionary-research.net/science/mullers-ratchet/principle">Muller’s Ratchet</a><br />
<a href="http://science.kqed.org/quest/2010/03/01/and-then-there-were-44/">Extra chromosomes and new species</a>  </p>

	Tags: <a href="http://science.kqed.org/quest/tag/asexual/" title="asexual" rel="tag">asexual</a>, <a href="http://science.kqed.org/quest/tag/asexual-reproduction/" title="asexual reproduction" rel="tag">asexual reproduction</a>, <a href="http://science.kqed.org/quest/tag/cancer/" title="cancer" rel="tag">cancer</a>, <a href="http://science.kqed.org/quest/tag/dna/" title="dna" rel="tag">dna</a>, <a href="http://science.kqed.org/quest/tag/dna-repair/" title="DNA repair" rel="tag">DNA repair</a>, <a href="http://science.kqed.org/quest/tag/evolution/" title="evolution" rel="tag">evolution</a>, <a href="http://science.kqed.org/quest/tag/genetics/" title="genetics" rel="tag">genetics</a>, <a href="http://science.kqed.org/quest/tag/meiosis/" title="meiosis" rel="tag">meiosis</a>, <a href="http://science.kqed.org/quest/tag/muller-ratchet/" title="Muller ratchet" rel="tag">Muller ratchet</a>, <a href="http://science.kqed.org/quest/tag/recombination/" title="recombination" rel="tag">recombination</a>, <a href="http://science.kqed.org/quest/tag/sex/" title="sex" rel="tag">sex</a>, <a href="http://science.kqed.org/quest/tag/sexual/" title="sexual" rel="tag">sexual</a>, <a href="http://science.kqed.org/quest/tag/sexual-reproduction/" title="sexual reproduction" rel="tag">sexual reproduction</a><br />
]]></content:encoded>
			<wfw:commentRss>http://science.kqed.org/quest/2011/08/01/the-high-cost-of-sex/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
	<georss:point>37.331855 -121.890129</georss:point><geo:lat>37.331855</geo:lat><geo:long>-121.890129</geo:long>
		<media:thumbnail url="http://science.kqed.org/quest/files/2011/07/CoupleOnBeach1.jpg" />
		<media:content url="http://science.kqed.org/quest/files/2011/07/CoupleOnBeach1.jpg" medium="image">
			<media:title type="html">CoupleOnBeach</media:title>
		</media:content>
		<media:content url="http://science.kqed.org/quest/files/2011/07/CoupleOnBeach1.jpg" medium="image">
			<media:title type="html">CoupleOnBeach</media:title>
			<media:description type="html">Sex may have evolved to cut down on genetic variation.</media:description>
			<media:thumbnail url="http://science.kqed.org/quest/files/2011/07/CoupleOnBeach1-300x169.jpg" />
		</media:content>
		<media:content url="http://science.kqed.org/quest/files/2011/07/SexAsexComparison.jpg" medium="image">
			<media:title type="html">SexAsexComparison</media:title>
			<media:description type="html">After just nine generations, the sexual beasts on the left are already being swamped out by the asexual ones on the right.</media:description>
			<media:thumbnail url="http://science.kqed.org/quest/files/2011/07/SexAsexComparison-200x169.jpg" />
		</media:content>
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		<title>Patient-Specific DNA Sequencing Finally Paying Off</title>
		<link>http://science.kqed.org/quest/2011/07/04/patient-specific-dna-sequencing-finally-paying-off/</link>
		<comments>http://science.kqed.org/quest/2011/07/04/patient-specific-dna-sequencing-finally-paying-off/#comments</comments>
		<pubDate>Mon, 04 Jul 2011 15:24:24 +0000</pubDate>
		<dc:creator>Dr. Barry Starr</dc:creator>
				<category><![CDATA[Biology]]></category>
		<category><![CDATA[Partners]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[DNA sequencing]]></category>
		<category><![CDATA[DRD]]></category>
		<category><![CDATA[gene]]></category>
		<category><![CDATA[genetics]]></category>
		<category><![CDATA[IBD]]></category>
		<category><![CDATA[L-dopa]]></category>
		<category><![CDATA[personalized medicine]]></category>
		<category><![CDATA[sequencing]]></category>

		<guid isPermaLink="false">http://www.kqed.org/quest/blog/2011/07/04/patient-specific-dna-sequencing-finally-paying-off/</guid>
		<description><![CDATA[Here Dr. Starr talks about three patients who have dramatically improved lives because scientists sequenced their DNA and correctly interpreted the results.  The dream of helping individual patients using data from the human genome project is finally being realized.]]></description>
			<content:encoded><![CDATA[<p><span class="left"><a href="http://www.kqed.org/quest"><img src="http://science.kqed.org/quest/files/2011/06/ColorfulChromosomes1.jpg" alt="" /></a><em>Scientists are finally unraveling enough of the mystery of<br />human DNA to help individual patients.</em></span></p>
<p>In the last few months, a couple of stories have come out that show the promise of the upcoming genetic revolution.  In each case, doctors found a patient’s best treatment by looking at every last letter of that patient’s DNA.  </p>
<p>In the first <a href="http://www.thetech.org/genetics/news.php?id=140">case</a>, a young boy had all the hallmarks of an immune problem but there was no conclusive diagnosis.  Without knowing for sure what was wrong, doctors weren’t comfortable treating the boy with a risky bone marrow transplant.</p>
<p>Then scientists sequenced the boy’s DNA.  Lo and behold there was a never-before-seen mutation in a known gene.  This nailed down the diagnosis of a potentially life-threatening form of irritable bowel disease (IBD).</p>
</p>
<p>The doctors went ahead with the bone marrow transplant.  The boy not only survived the treatment, but his symptoms cleared up as well.  He is now essentially cured because he had his DNA sequenced.</p>
<p>The second <a href="http://www.thetech.org/genetics/news.php?id=142">case </a>involves a set of boy-girl twins.  They suffer from a movement disorder called dopamine-responsive dystonia (<a href="http://www.dystoniacanada.org/about-dystonia/dopa-responsive-dystonia">DRD</a>).  </p>
<p>Patients with DRD are usually treated with L-dopa.  This can often clear up most symptoms but didn’t seem to help these twins as much.  In particular, the twin sister still suffered severe enough symptoms to greatly diminish her quality of life.  </p>
<p>Scientists sequenced the twins’ DNA and found out that they had a kind of DRD that responds best to both L-dopa and a medicine called 5-HTP.  Once they both received this new treatment, their symptoms improved dramatically.</p>
<p>For example, the girl used to suffer from something called layngospasms that usually ended in vomiting.  With the new treatment, this went away.  An obvious improvement to her life!</p>
<p>Assuming prices keep dropping for sequencing and Congress keeps allocating money for basic research, there may come a day in the not too distant future when many more patients like these will be helped.  People will have better lives because doctors can figure out what is wrong by looking at their DNA.  As long as doctors have the tools they need to help patients that is.</p>
<p>Right now the information is so scattered and so specialized that most doctors can’t help without a scientist’s intervention.  This greatly limits the number of patients who can be helped.</p>
<p>Getting this whole process streamlined enough so that more than just the wealthy, connected, or lucky can benefit won’t be easy.  We need to generate lots more data.  But we also need to collect and organize the data so doctors can take a patient’s DNA data and translate it into the right treatment without the help of a genetic scientist.  </p>
<p>This last part is not exciting work but is absolutely necessary if the promise of the genomic revolution is to be fully realized.  Here’s hoping someone funds something like this.</p>
<p><iframe width="425" height="349" src="http://www.youtube.com/embed/jxFO-SjA-P4" frameborder="0"></iframe></p>
<p><i>Great story about DRD and how L-dopa can help.</i></p>
<p> 37.3393857 -121.8949555</p>

	Tags: <a href="http://science.kqed.org/quest/tag/dna/" title="dna" rel="tag">dna</a>, <a href="http://science.kqed.org/quest/tag/dna-sequencing/" title="DNA sequencing" rel="tag">DNA sequencing</a>, <a href="http://science.kqed.org/quest/tag/drd/" title="DRD" rel="tag">DRD</a>, <a href="http://science.kqed.org/quest/tag/gene/" title="gene" rel="tag">gene</a>, <a href="http://science.kqed.org/quest/tag/genetics/" title="genetics" rel="tag">genetics</a>, <a href="http://science.kqed.org/quest/tag/ibd/" title="IBD" rel="tag">IBD</a>, <a href="http://science.kqed.org/quest/tag/l-dopa/" title="L-dopa" rel="tag">L-dopa</a>, <a href="http://science.kqed.org/quest/tag/personalized-medicine/" title="personalized medicine" rel="tag">personalized medicine</a>, <a href="http://science.kqed.org/quest/tag/sequencing/" title="sequencing" rel="tag">sequencing</a><br />
]]></content:encoded>
			<wfw:commentRss>http://science.kqed.org/quest/2011/07/04/patient-specific-dna-sequencing-finally-paying-off/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
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		<title>Secretive Openness</title>
		<link>http://science.kqed.org/quest/2011/03/14/secretive-openness/</link>
		<comments>http://science.kqed.org/quest/2011/03/14/secretive-openness/#comments</comments>
		<pubDate>Mon, 14 Mar 2011 18:00:06 +0000</pubDate>
		<dc:creator>Dr. Barry Starr</dc:creator>
				<category><![CDATA[Biology]]></category>
		<category><![CDATA[Partners]]></category>
		<category><![CDATA[Albino redwood trees]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[mutation]]></category>
		<category><![CDATA[open source]]></category>
		<category><![CDATA[public science]]></category>
		<category><![CDATA[publish or perish]]></category>
		<category><![CDATA[redwood]]></category>
		<category><![CDATA[science funding]]></category>
		<category><![CDATA[scientific method]]></category>

		<guid isPermaLink="false">http://www.kqed.org/quest/blog/2011/03/14/secretive-openness/</guid>
		<description><![CDATA[It will take a long time for scientists to figure out why those redwoods in Henry Cowell Redwoods State Park are albino.  And because of the way science is set up, it will take the public even longer to find out the answer.]]></description>
			<content:encoded><![CDATA[<div class="wp-caption aligncenter" style="width: 560px"><a href="http://www.kqed.org/quest"><img src="http://science.kqed.org/quest/files/2011/03/AlbinoBranch3.jpg" alt="" width="600" height="402" /></a>
<p class="wp-caption-text"><em>It'll be a long time before scientists figure out why this branch is white.<br />And even longer before the public finds out.</em></p>
</div>
<p></br></p>
<p><strong>Is there any place to check in for updates on this research?</strong></p>
<p>Timothy Jordan asked this question on Chris Bauer’s <a href="http://science.kqed.org/quest/wp-admin/post.php?action=edit&#038;post=12636">blog</a> about figuring out the genetics of redwood albinism.  Unfortunately, the answer is that there really isn’t any place to see how the research is going.</p>
<p>This is because science is this weird combination of secrecy and openness.  Research projects start out as proprietary but once finished, they become open source.</p>
<p>What this means is that no results will be released until a good chunk of the research is done and it has been published in a peer-reviewed journal.  This usually takes a year or more and albino redwoods will probably take even longer.</p>
</p>
<p>Part of the reason for this is simple caution on the part of scientists.  No one wants to release results so early that that they have to retract them later.  Like everyone else, scientists don’t like to be proven wrong in public.</p>
<p>But this only explains not communicating <em>preliminary </em>results.  Once a result is pretty solid, it should be OK to broadcast publicly.  Except that it still isn’t.</p>
<p>This isn’t the fault of many of the scientists doing the research.  I remember wanting to shout my latest results from the mountaintops as soon as I got them.  Lots of scientists I have talked to feel the same way.</p>
<p>The problem has more to do with how science is funded.  It simply isn’t designed to allow incremental progress to become public.</p>
<p>Scientists rely on the federal government for most of their funding.  The NIH, NSF, DOE, and a few other agencies supply the lion’s share of research dollars.</p>
<p>Labs are awarded these grants based on the work they have done.  There is absolutely no incentive for sharing their work early.  In fact, sharing work too soon can cost you grant money and maybe even (eventually) your lab.</p>
<p><span class="right"><img src="http://science.kqed.org/quest/files/2011/03/Graveyard2.jpg" alt="" /></a><em>The graveyard of the scientific careers of those scientists who released their data too soon. Photo by <a href="http://commons.wikimedia.org/wiki/File:Unrelated_Tombstone.jpg">Corpse Reviver.</a></em></span></p>
<p>To be credible, scientific results must be published in a peer-reviewed journal.  This is the “coin of the realm” in the scientific world.  To succeed as a scientist, you need lots of these in the top journals and of course, successful scientists are the ones who get funded.</p>
<p>These journals frown on releasing data before that data can make a big splash for their journal.  This forces scientists to not release information to the general public (although they can talk about it at some point at scientific meetings).  To keep from perishing, scientists need to keep their results under wraps.  </p>
<p>Not only that, but scientists are not above stealing someone’s data and using it to get to the full story first.  Smaller labs in particular are vulnerable to this sort of predation.  Again, this forces scientists to keep their results to themselves rather than broadcasting it far and wide.  Otherwise, they’ll have nothing to show for their work and they won’t get funded.</p>
<p>The only way to overcome these barriers and get results presented to the public in a more timely manner would be to change how science gets funded.  Make it so there is lots of money to go around so that scientists will get money whether their lab makes the breakthrough or someone else uses your preliminary results to make the breakthrough.</p>
<p>Of course this won’t happen.  For one thing, you wouldn’t be able to screen out the bad and/or lazy scientists nor reward the true go-getters.  And besides, there are already way too many labs chasing way too few grants.  Given that our government is sliding into insolvency, it is very unlikely that they will throw any more money at science so the public can get information any sooner.</p>
<p>A new way to fund science also wouldn’t change other aspects that keep our current system in place.  For example, many scientists like to get a result first and beat the other guys.  No funding tweaks are going to change this competitiveness.</p>
<p>Looks like we’ll have to stick with the current way that science is set up.  It has done a great job of explaining our world and how it works.  We just need to be patient and wait for the findings to eventually be released. As soon as they are, I’ll update you right here.</p>
<p> 37.7749295 -122.4194155</p>

	Tags: <a href="http://science.kqed.org/quest/tag/albino-redwood-trees/" title="Albino redwood trees" rel="tag">Albino redwood trees</a>, <a href="http://science.kqed.org/quest/tag/dna/" title="dna" rel="tag">dna</a>, <a href="http://science.kqed.org/quest/tag/mutation/" title="mutation" rel="tag">mutation</a>, <a href="http://science.kqed.org/quest/tag/open-source/" title="open source" rel="tag">open source</a>, <a href="http://science.kqed.org/quest/tag/public-science/" title="public science" rel="tag">public science</a>, <a href="http://science.kqed.org/quest/tag/publish-or-perish/" title="publish or perish" rel="tag">publish or perish</a>, <a href="http://science.kqed.org/quest/tag/redwood/" title="redwood" rel="tag">redwood</a>, <a href="http://science.kqed.org/quest/tag/science-funding/" title="science funding" rel="tag">science funding</a>, <a href="http://science.kqed.org/quest/tag/scientific-method/" title="scientific method" rel="tag">scientific method</a><br />
]]></content:encoded>
			<wfw:commentRss>http://science.kqed.org/quest/2011/03/14/secretive-openness/feed/</wfw:commentRss>
		<slash:comments>4</slash:comments>
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		<media:thumbnail url="http://science.kqed.org/quest/files/2010/11/albino3001.jpg" />
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		<title>All (U.S.) Children Left Behind</title>
		<link>http://science.kqed.org/quest/2011/02/14/all-u-s-children-left-behind/</link>
		<comments>http://science.kqed.org/quest/2011/02/14/all-u-s-children-left-behind/#comments</comments>
		<pubDate>Mon, 14 Feb 2011 17:30:42 +0000</pubDate>
		<dc:creator>Dr. Barry Starr</dc:creator>
				<category><![CDATA[Biology]]></category>
		<category><![CDATA[Partners]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[genetics]]></category>
		<category><![CDATA[genome]]></category>
		<category><![CDATA[personal genetics]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[science education]]></category>
		<category><![CDATA[Web resource]]></category>

		<guid isPermaLink="false">http://www.kqed.org/quest/blog/2011/02/14/all-u-s-children-left-behind/</guid>
		<description><![CDATA[New test results confirm what many of us have feared: U.S. students suck at science.]]></description>
			<content:encoded><![CDATA[<p><span class="left"><a href="http://www.kqed.org/quest"><img src="http://science.kqed.org/quest/files/2011/02/china2.jpg" alt="" /></a><em>These Chinese students are kicking our butts in science.</em></span></p>
<p>New test results confirm what many of us have feared: U.S. students suck at science. These new numbers are not only bad for our reputation, they spell trouble for the future U.S. economy and possibly the world.  Maybe President Obama is right and we are in the middle of another “Sputnik” moment. </p>
<p>The most <a href="http://nces.ed.gov/pubsearch/pubsinfo.asp?pubid=2011451">recent test results</a> put us on par with France, the Czech Republic and Hungary and miles away from the likes of China, South Korea, Finland and Australia.  The top countries will be producing the best scientists who will drive economies forward.  Those of us in the middle of the pack will either fall behind economically or stay competitive either by attracting good scientists from elsewhere or by changing our education system to match the Finns or the Aussies.  </p>
<p>Of course this is only true if these results hold for top performing students, too.  Since most scientists come from this group, if the top performing students in the U.S. hold their own against their counterparts in other countries, then we may be OK.</p>
<p>The testing folks provide this great tool,<a href="http://nces.ed.gov/surveys/international/ide/"> the International Data Explorer</a>, that lets you parse the data in lots of different ways. And no matter how I sliced the data, we are in the middle of the pack. If I look at wealthy folks, or students who have educated parents or students that have scientists as parents, each category is still behind lots of different countries. </p>
<p>So we can’t blame the test results on immigrants, the poor or any of our usual convenient scapegoats.  We are simply doing a poor job of teaching science.  Such a poor job that our economy is going to be in real trouble in the not so distant future.</p>
<p>And it isn’t just our economy that is threatened.  A general U.S. public that is not up to snuff scientifically might just put our world at risk too.  </p>
<p>A scientifically illiterate public will fear vaccines and GM foods, won’t understand and so won’t believe in global warming and so on.  This could mean a spread of disease, starvation and environmental catastrophes just to name a few.    </p>
<p>It is important to remember that none of this is inevitable.  We can ramp up our science education so that we train the best scientists in the world and maybe even create a scientifically informed and savvy public in the process.  </p>
<p>In fact, Massachusetts has done just that in the last 15 or 20 years.  If it were a country, Massachusetts would now be in the upper ranks of countries.  We need to look to Massachusetts for how to improve other states' failing education systems.  </p>
<p>Massachusetts shows that with the will and money to do it, we can turn our educational system around.  Sadly, though, I am not sure most of the country will.  Sputnik came with the fear of nuclear holocaust.  Our current crisis comes with the fear of future irrelevance and a decreased standard of living.  </p>
<p>The current risks are not life and death and so it will be much harder to mobilize the government, the public, and the unions to transform our education system.  I guess our dominance economically and scientifically was good while it lasted. </p>
<p><a href="http://www.theatlantic.com/national/archive/2010/11/your-child-left-behind/66069/">A fun interactive that lets you compare math, science and reading scores between states and different countries.</a></p>
<p><a href="http://www.theatlantic.com/magazine/archive/2010/12/your-child-left-behind/8310/">State by state math scores compared to other countries.</a></p>
<p><a href="http://www.slate.com/id/2281847/">Why this crisis will be harder to overcome than the Sputnik crisis.</a></p>
<p> 37.7749295 -122.4194155</p>

	Tags: <a href="http://science.kqed.org/quest/tag/dna/" title="dna" rel="tag">dna</a>, <a href="http://science.kqed.org/quest/tag/genetics/" title="genetics" rel="tag">genetics</a>, <a href="http://science.kqed.org/quest/tag/genome/" title="genome" rel="tag">genome</a>, <a href="http://science.kqed.org/quest/tag/personal-genetics/" title="personal genetics" rel="tag">personal genetics</a>, <a href="http://science.kqed.org/quest/tag/science/" title="Science" rel="tag">Science</a>, <a href="http://science.kqed.org/quest/tag/science-education/" title="science education" rel="tag">science education</a>, <a href="http://science.kqed.org/quest/tag/web-resource/" title="Web resource" rel="tag">Web resource</a><br />
]]></content:encoded>
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		<slash:comments>4</slash:comments>
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		<title>Reliable Science Web Resource: Scitable</title>
		<link>http://science.kqed.org/quest/2011/02/03/reliable-science-web-resource-scitable/</link>
		<comments>http://science.kqed.org/quest/2011/02/03/reliable-science-web-resource-scitable/#comments</comments>
		<pubDate>Thu, 03 Feb 2011 18:01:24 +0000</pubDate>
		<dc:creator>Dr. Barry Starr</dc:creator>
				<category><![CDATA[Biology]]></category>
		<category><![CDATA[Partners]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[genetics]]></category>
		<category><![CDATA[genome]]></category>
		<category><![CDATA[personal genetics]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[science education]]></category>
		<category><![CDATA[Web resource]]></category>

		<guid isPermaLink="false">http://www.kqed.org/quest/blog/2011/02/03/reliable-science-web-resource-scitable/</guid>
		<description><![CDATA[An interview with Vikram Savkar, the man who runs a reliable web resource for science called Scitable.]]></description>
			<content:encoded><![CDATA[<p><span class="left"><a href="http://www.kqed.org/quest"><img src="http://science.kqed.org/quest/files/2011/02/scitable.jpg" alt="" /></a><em>Finally a reliable scientific resource on the web.</em></span></p>
<p>A really interesting project called <a href="http://www.nature.com/scitable">Scitable</a> recently came to my attention. This site is sponsored by the same folks who publish <a href="http://www.scientificamerican.com/">Scientific American</a>, <a href="http://www.nature.com/">Nature</a>, and many other scientific journals and magazines. It is intended to provide students, teachers, professors and the public with easy to read, understandable materials about science.  </p>
<p>From a quick look, it looks like a great website for advanced high school students, undergraduate and graduate students, scientists, and the well educated. If this is you, take a look <a href="http://www.nature.com/scitable">here</a> and let me know what you think.</p>
</p>
<p>Below is an email interview I did with the guy who runs the site, Vikram Savkar. It focuses on what Scitable offers and some ways to heal our ailing science education system.  </p>
</p>
<p><img src="http://science.kqed.org/quest/files/2011/02/VAsmall.jpg" align="right"></p>
<p><strong>Many of our readers will not have heard of Scitable before.  Can you please give a brief history of the group and what you hope to accomplish.</strong></p>
<p><em>Scitable is an open, high quality science teaching and learning site from Nature Publishing Group, publishers of Nature, Scientific American, and a number of other science journals and magazines.  We launched Scitable because we feel strongly that inspiring and enabling today’s students to immerse themselves in science is crucial for the future of the planet. Without dedicated scientific researchers, or at least a science-literate population, we won’t be able to make the progress we need as a global community on sustainability, food security, diseases, and so on. Our goal is to make access to very high quality science education information and compelling scientific experiences a common denominator for students regardless of their socioeconomic or geographic background.</em></p>
<p><strong>Can you please tell our readers who the sources are for the information on your site and how often information is updated?  Do you see it as a more reliable source for people compared to what else is out there on the web (e.g. Wikipedia)?</strong></p>
<p><em>We actively commission the pieces you see on the site from leading scientists, faculty, or science journalists, depending on the subject matter, and every piece is put through a formal review by other experts in the field.  The result is that the information is high quality: current, carefully thought through, scientifically accurate, and designed explicitly for use by teachers and students. We update our pieces on average once a month . . . often when a member of the community points out a topic they think we should have covered but didn’t; we’ll route the opinion to our reviewers and if everyone agrees, we will update the article.  Yes, our intention is very much for Scitable to be a marriage of the reliability and quality of information that we’re all familiar with from journals and formal publications with the ease of discovery of use that’s characteristic of sites like Wikipedia.</em></p>
<p><strong>What is your favorite feature of Scitable?  Why?</strong></p>
<p><em>I sometimes use the search box in the People area of Scitable to figure out whether we have any student or faculty users from far-flung parts of the world . . . and usually find that we do.  (Mauritius: yes.  Swaziland: no.  We’ll have to work on that.)  We’re really trying to create a kind of global classroom – a place where students from any part of the world can collaborate with researchers, teachers, and fellow students who are interested in the same subject but potentially thousands of miles away.<br />
</em><br />
<strong>Can you tell us a little bit about the resources that are available for the public, students, and/or teachers at your site?  How easy is it for these people to access and use these resources?</strong></p>
<p><em>The heart of Scitable is the extensive (and growing) content library.  We have more than 600 readings in genetics, cell biology, and ecology right now, and we’re adding more across the life and physical sciences this year.  We have mini-textbooks in the life sciences as well as on special topics like scientific communication and career planning. And our learning paths allow students to progress through “hot” issues like biotechnology at their own pace.  We also have a strong set of classroom tools, which teachers can use to run private online research spaces for their students.  In just five or ten minutes, a teacher can create a customized reading list (using content from Scitable or from anywhere on the web) and enroll students in discussions, news feeds, and so on.   All of this is free.  The bulk of the content doesn’t require registration; people do have to register to build or join a classroom or take a learning path.  Overall, it’s really easy for people to learn through the site . . . our users are growing rapidly every month, and they come from all walks of life: students, teachers, researchers, parents, veterinarians (yes, I’ve noticed a lot of these!), genetic counselors, and more.</em></p>
<p><strong>What do you see as the primary problem with science education today?  If you had a magic wand and could fix science education, what would you do?  Would it differ between K-12 and undergraduate education?</strong></p>
<p><em>I don’t think there is a primary problem, I think that the overall quality of science education is driven by the convergence of a lot of factors: Do parents encourage kids to tinker with nature and science? Are there enough well trained science teachers, and are they incentivized to stay at tough schools? How widely available are good lab equipment and other learning materials?  How successful are college instructors at reminding students of the “magic” behind the memorization?  If I had a magic wand, I would wave it at all of these.  If I had to pick one . . . that’s tough . . . I would probably work on ensuring that there are highly qualified teachers (which means not only understanding science but having a solid background in teaching methods) in all schools, including and particularly under resourced ones. But, really, the key point for me is that there isn’t just one thing to focus on, we must take a holistic approach.</em></p>
<p><strong>Who is the primary audience for Scitable?  K-12 students, K-12 educators, undergraduates, the general public, graduate students, etc.?<br />
</strong><br />
<em>The audience in formal education ranges from advanced high school classes to junior/senior level undergraduate classes . . . we have a broad set of content in the site, so there is much there for everyone within that range.  The audience among the general public seems to be encouragingly varied, there are so many different kinds of people whom I have seen find their way to the site.  People really do instinctively get excited by science; when we provide a way for them to easily find good answers to their questions, they will take advantage of it.</em></p>
<p><strong>Do you see Scitable as a resource for that day in the not too distant future when everyone knows their own DNA sequence?  Are there any resources available and accessible for the average person at your site?  Or is it mostly focused right now on aspiring or actual scientists?<br />
</strong><br />
<em>There are many resources for the average person, and we plan to publish more. A good example is our growing collection of Spotlights, which are essentially “home pages” for topics like Alternative Energy and Acoustic Pollution, intended specifically to help general learners go beyond the newspaper headlines and learn the actual science behind hot-button issues. I don’t see us ever helping people to make medical judgments of any kind, but I do see us helping a broad set of citizens to understand something substantial about the fields of research that can lead to a vastly improved quality of life for all of us.  And to vote in ways that help make this future a reality.</em></p>
<p><a href="http://science.kqed.org/quest/2010/01/18/the-wild-wild-web/">A previous blog on the difficulties of finding good scientific information on the web.</a></p>
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	Tags: <a href="http://science.kqed.org/quest/tag/dna/" title="dna" rel="tag">dna</a>, <a href="http://science.kqed.org/quest/tag/genetics/" title="genetics" rel="tag">genetics</a>, <a href="http://science.kqed.org/quest/tag/genome/" title="genome" rel="tag">genome</a>, <a href="http://science.kqed.org/quest/tag/personal-genetics/" title="personal genetics" rel="tag">personal genetics</a>, <a href="http://science.kqed.org/quest/tag/science/" title="Science" rel="tag">Science</a>, <a href="http://science.kqed.org/quest/tag/science-education/" title="science education" rel="tag">science education</a>, <a href="http://science.kqed.org/quest/tag/web-resource/" title="Web resource" rel="tag">Web resource</a><br />
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		<title>Meet Our Newest Relative</title>
		<link>http://science.kqed.org/quest/2011/01/17/meet-our-newest-relative/</link>
		<comments>http://science.kqed.org/quest/2011/01/17/meet-our-newest-relative/#comments</comments>
		<pubDate>Mon, 17 Jan 2011 16:09:39 +0000</pubDate>
		<dc:creator>Dr. Barry Starr</dc:creator>
				<category><![CDATA[Biology]]></category>
		<category><![CDATA[Partners]]></category>
		<category><![CDATA[Denisova cave]]></category>
		<category><![CDATA[diversity]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[genome]]></category>
		<category><![CDATA[Home sapien]]></category>
		<category><![CDATA[hominid]]></category>
		<category><![CDATA[mitochondria]]></category>
		<category><![CDATA[Neanderthal]]></category>
		<category><![CDATA[out of africa]]></category>
		<category><![CDATA[paleontology]]></category>
		<category><![CDATA[related]]></category>
		<category><![CDATA[relative]]></category>
		<category><![CDATA[Siberia]]></category>

		<guid isPermaLink="false">http://www.kqed.org/quest/blog/2011/01/17/meet-our-newest-relative/</guid>
		<description><![CDATA[Scientists identified a new human relative just using DNA from a fossilized finger.  Using this DNA they showed more non <i>Homo sapien</i> DNA in modern humans.  First Neanderthals, now Denisovans.  Who knows what DNA we'll find next.]]></description>
			<content:encoded><![CDATA[<p><span class="left"><a href="http://www.kqed.org/quest"><img src="http://science.kqed.org/quest/files/2011/01/DenisovaCave1.jpg" alt="" /></a><em>Our newest relatives hailed from around this cave in Siberia.</em></span></p>
<p>In 2008, scientists found a fossil of a humanoid finger in the Denisova Cave in Siberia.  The finger was probably from someone (or something) that had been running around Siberia forty thousand years ago.</p>
<p>Until recently, the scientists would have been stuck until they found additional fossils to build up a more complete skeleton.  Once they had the skeleton, they could then compare it to other fossils and figure out how it related to modern humans.  Of course this might never happen—it would be totally dependent on finding more fossils.</p>
</p>
<p>Rather than waiting around, these scientists decided to bring in a geneticist.  Nowadays geneticists can sometimes read every base of a fossilized beast’s DNA.  In other words, they can read its whole genome.</p>
<p>When geneticists did this, <a href="http://www.thetech.org/genetics/news.php?id=136">they found</a> that the finger did not come from a modern human or a Neanderthal.  This Denisovan (as scientists named it) probably came from a previously unknown relative that was more closely related to Neanderthals than humans.  And surprisingly, their legacy lives on in some modern humans.</p>
<p>By comparing the DNA of the Denisovan and various modern ethnic groups, scientists could see Denisovan DNA in modern Melanesians.  Apparently the ancestors of Melanesians and Denisovans had babies before the Denisovans went extinct.</p>
<p>The data suggest that Denisovans might have contributed up to 4-5% of their DNA to modern Melanesians.  Add the <a href="http://www.thetech.org/genetics/news.php?id=128">1-2% Neanderthal DNA</a> found in non-Africans and you get up to 7% of Melanesian DNA coming from nonhuman sources.  And that is just based on the two extinct species whose DNA we’ve been able to read so far.</p>
<p>Who knows how much DNA of other ethnic groups comes from relatives whose DNA we haven’t looked at yet.  I bet someone is taking a good hard look at various groups’ DNA to see if they can answer this question without having to figure out more fossil DNA.</p>
<p>This all points to an exciting new twist to paleontology…the ability to look at DNA from fossils and to compare that DNA to modern humans and any other close relatives whose DNA has been sequenced.  This new avenue of research should provide extra information that scientists didn’t have before and allow them to figure some things out with just a single finger bone.  </p>
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<p><i>BBC story on the find.</i></p>
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	Tags: <a href="http://science.kqed.org/quest/tag/denisova-cave/" title="Denisova cave" rel="tag">Denisova cave</a>, <a href="http://science.kqed.org/quest/tag/diversity/" title="diversity" rel="tag">diversity</a>, <a href="http://science.kqed.org/quest/tag/dna/" title="dna" rel="tag">dna</a>, <a href="http://science.kqed.org/quest/tag/genome/" title="genome" rel="tag">genome</a>, <a href="http://science.kqed.org/quest/tag/home-sapien/" title="Home sapien" rel="tag">Home sapien</a>, <a href="http://science.kqed.org/quest/tag/hominid/" title="hominid" rel="tag">hominid</a>, <a href="http://science.kqed.org/quest/tag/mitochondria/" title="mitochondria" rel="tag">mitochondria</a>, <a href="http://science.kqed.org/quest/tag/neanderthal/" title="Neanderthal" rel="tag">Neanderthal</a>, <a href="http://science.kqed.org/quest/tag/out-of-africa/" title="out of africa" rel="tag">out of africa</a>, <a href="http://science.kqed.org/quest/tag/paleontology/" title="paleontology" rel="tag">paleontology</a>, <a href="http://science.kqed.org/quest/tag/related/" title="related" rel="tag">related</a>, <a href="http://science.kqed.org/quest/tag/relative/" title="relative" rel="tag">relative</a>, <a href="http://science.kqed.org/quest/tag/siberia/" title="Siberia" rel="tag">Siberia</a><br />
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			<media:title type="html">DenisovaCave</media:title>
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		<title>A Dangerous Blush</title>
		<link>http://science.kqed.org/quest/2010/12/20/a-dangerous-blush/</link>
		<comments>http://science.kqed.org/quest/2010/12/20/a-dangerous-blush/#comments</comments>
		<pubDate>Mon, 20 Dec 2010 16:20:50 +0000</pubDate>
		<dc:creator>Dr. Barry Starr</dc:creator>
				<category><![CDATA[Biology]]></category>
		<category><![CDATA[Partners]]></category>
		<category><![CDATA[acetaldehyde]]></category>
		<category><![CDATA[alcohol]]></category>
		<category><![CDATA[alcohol flushing response]]></category>
		<category><![CDATA[ALDH2]]></category>
		<category><![CDATA[Asian glow]]></category>
		<category><![CDATA[cancer]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[DNA damage]]></category>
		<category><![CDATA[esophageal cancer]]></category>
		<category><![CDATA[mutation]]></category>

		<guid isPermaLink="false">http://www.kqed.org/quest/blog/2010/12/20/a-dangerous-blush/</guid>
		<description><![CDATA[Some sobering thoughts on alcohol, cancer, and the Asian glow.]]></description>
			<content:encoded><![CDATA[<p><span class="left"><img src="http://science.kqed.org/quest/files/2010/12/AsianGlow1.jpg" alt="" /></a><em>If he drinks a lot, he can be up to 56 times more likely to<br />end up with esophageal cancer compared to a nondrinker.</em></span></p>
<p>Many people of East Asian descent react to alcohol with a red face, a racing heartbeat and a slight sick feeling in their stomach.  This “Asian glow” is more than just annoying though.  If they keep drinking anyway, it can be downright dangerous.</p>
<p>In addition to its obvious charms, drinking alcohol definitely has some drawbacks (besides beer goggles and nasty hangovers).  One of these is an increased risk for getting cancer of the esophagus.  One study I saw claimed that heavy drinkers are 18 times more likely to end up with esophageal cancer compared to teetotalers.  </p>
</p>
<p>The risk is even higher for blushers.  They are 56 times more likely to end up with this particular cancer if they are heavy drinkers.  And even if they just have a couple of drinks a day, they are still at a 5 times higher risk.  </p>
<p>Unfortunately, the alcohol flushing response is pretty common.  Scientists estimate that 36% of people of East Asian descent respond to alcohol this way.  That’s over 500 million people worldwide.    </p>
<p>All of these statistics are especially scary because esophageal cancer is so common. For example, it is the 7th leading cause of cancer death worldwide and the 7th most common cancer in men in the U.S.  In some parts of Russia and China, the rates of this cancer range from 30-800 cases per 100,000 people.  The rate in the U.S is 3-6 per 100,000.</p>
<p>Many if not most of these cancers happen because the patients drank too much alcohol and smoked too many cigarettes.  One review article estimated that if heavy drinking blushers from Japan switched to just two drinks per day, the number of cases of esophageal cancer there would be cut in half.  Undoubtedly the same thing is true elsewhere.</p>
<p>Everyone is at a higher risk for esophageal cancer when they drink because of how alcohol is broken down in the body.  On the way to converting alcohol to the safer acetic acid, our bodies first turn it into acetaldehyde.  And that is some nasty stuff!</p>
<p>Acetaldehyde likes to stick to and damage our DNA.  Not only that, it also keeps our cells from repairing the damage.  Since cancer happens because of DNA damage, it isn’t surprising that alcohol causes an increased risk for cancer.</p>
<p>People who blush from alcohol have a certain version of the ALDH2 gene that has <a href="http://www.thetech.org/exhibits/online/ugenetics/BDETechDec/Screen3b.html">trouble converting</a> alcohol into acetaldehyde.  The end result is a build up of acetaldehyde that can damage DNA and so cause esophageal cancer.</p>
<p>Again, there is no increased risk if they don’t drink.  In the absence of alcohol, they are just like anyone else.  They just need to lay off the liquor.</p>
<p>Maybe these people need to find a new social lubricant.  I guess it's too bad Prop 19 didn’t pass…</p>
<p><a href="http://www.thetech.org/exhibits/online/ugenetics/BDETechDec/">A fun activity to learn more about the genetics and biology of the alcohol flushing response.</a></p>
<p><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2659709/pdf/pmed.1000050.pdf">A review article that raises an alarm about the risks of drinking alcohol as a blusher.</a></p>
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	Tags: <a href="http://science.kqed.org/quest/tag/acetaldehyde/" title="acetaldehyde" rel="tag">acetaldehyde</a>, <a href="http://science.kqed.org/quest/tag/alcohol/" title="alcohol" rel="tag">alcohol</a>, <a href="http://science.kqed.org/quest/tag/alcohol-flushing-response/" title="alcohol flushing response" rel="tag">alcohol flushing response</a>, <a href="http://science.kqed.org/quest/tag/aldh2/" title="ALDH2" rel="tag">ALDH2</a>, <a href="http://science.kqed.org/quest/tag/asian-glow/" title="Asian glow" rel="tag">Asian glow</a>, <a href="http://science.kqed.org/quest/tag/cancer/" title="cancer" rel="tag">cancer</a>, <a href="http://science.kqed.org/quest/tag/dna/" title="dna" rel="tag">dna</a>, <a href="http://science.kqed.org/quest/tag/dna-damage/" title="DNA damage" rel="tag">DNA damage</a>, <a href="http://science.kqed.org/quest/tag/esophageal-cancer/" title="esophageal cancer" rel="tag">esophageal cancer</a>, <a href="http://science.kqed.org/quest/tag/mutation/" title="mutation" rel="tag">mutation</a><br />
]]></content:encoded>
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		<slash:comments>4</slash:comments>
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		<title>Meditation Training Improves Markers Of Cellular Health and Psychological Well-Being</title>
		<link>http://science.kqed.org/quest/2010/11/05/meditation-training-improves-markers-of-cellular-health-and-psychological-well-being/</link>
		<comments>http://science.kqed.org/quest/2010/11/05/meditation-training-improves-markers-of-cellular-health-and-psychological-well-being/#comments</comments>
		<pubDate>Fri, 05 Nov 2010 16:06:56 +0000</pubDate>
		<dc:creator>Darya Pino</dc:creator>
				<category><![CDATA[Health]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[Elizabeth Blackburn]]></category>
		<category><![CDATA[meditation]]></category>
		<category><![CDATA[Shamatha Project]]></category>
		<category><![CDATA[Telomerase]]></category>
		<category><![CDATA[Telomeres]]></category>

		<guid isPermaLink="false">http://www.kqed.org/quest/blog/?p=10162</guid>
		<description><![CDATA[Intensive meditation training increases psychological well-being and telomerase activity in immune cells.]]></description>
			<content:encoded><![CDATA[<p><span class="left"><img src="http://science.kqed.org/quest/files/2010/11/mediation.jpg" alt="" /></a><em>Intensive meditation training increases psychological well-being and telomerase activity in immune cells. Image courtesy of <a href="http://commons.wikimedia.org/wiki/User:Tevaprapas/">Tevaprapas</a>.</em></span></p>
<p>Well-being and psychological health are known to be closely associated with physical health, but the mechanistic links between the two are still relatively unknown.</p>
<p>New research from scientists at UC Davis and UC San Francisco shows that intensive meditation training improves several measures of psychological health, which in turn leads to an increase in the activity of an enzyme called <a href="http://en.wikipedia.org/wiki/Telomerase">telomerase</a>, a known marker of cellular health.</p>
</p>
<p>Telomeres are DNA sequences at the end of chromosomes that shorten every time a cell divides or is exposed to oxidative stress. When telomeres become too short, the ability of a cell to replicate is diminished along with the health of the cell. Telomerase is an enzyme that increases the length of telomeres by adding additional DNA to the end of chromosomes and stabilizing genetic structure.</p>
<p>Stress and pychological distress are known to negatively impact telomerase activity, and are also associated with deteriorating health. But previous research has not shown that improving psychological health could reverse the effect and increase the action of telomerase.</p>
<p>The current study investigated the effect of intense meditation on measures of both pscyhcological well-being and telomerase activity in immune cells. Thirty participants underwent meditation training at a three month intensive meditation retreat called the <a href="http://www.shambhalamountain.org/shamatha/">Shamatha Project</a>. The participants were evaluated for Perceived control (over one's life), Neuroticism, Mindfulness and Purpose in life both before and after the retreat. Telomerase activity was also measured before and after. The particpants were compared to 30 matched control subjects.</p>
<p>Retreat participants had statistically significant increases in measures of Perceived control, Purpose, Mindfulness, and decreases in Neuroticism. They also showed a 30% increase in telomerase activity after the retreat. Age and BMI were factored into the analysis as potential covariates. According to regression analysis, the psychological changes of Perceived control and Neuroticism mediate group differences observed in telomerase activity. Further, Mindfulness and Purpose of life significantly mediated changes in Perceived control and Neuroticism.</p>
<p>The current study does not imply that meditation directly affects telomerase activity, but that it can increase one's ability to cope with and counteract stress that may interfere with physical health.</p>
<p>Though the sample size is small and more studies are needed to confirm the ability of meditation to improve telomerase activity, this is one of the first well-designed studies to directly associate psychological training with measures of cellular health.</p>
<p>The work done by researchers at UC Davis and UC San Francisco and is currently in press at <em><a href="http://www.news.ucdavis.edu/search/news_detail.lasso?id=9669">Psychoneuroendocrinology</a></em>. Contributing author and professor of biology and physiology at UCSF, Elizabeth Blackburn, won the 2009 Nobel Prize in medicine for her discovery of telomeres and telomerase.</p>
<p>The Shamatha Project is a meditation study and collaboration between UC Davis, The Santa Barbara Institute For Consciousness and the Shambhala Mountain Center.</p>
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	Tags: <a href="http://science.kqed.org/quest/tag/dna/" title="dna" rel="tag">dna</a>, <a href="http://science.kqed.org/quest/tag/elizabeth-blackburn/" title="Elizabeth Blackburn" rel="tag">Elizabeth Blackburn</a>, <a href="http://science.kqed.org/quest/tag/meditation/" title="meditation" rel="tag">meditation</a>, <a href="http://science.kqed.org/quest/tag/shamatha-project/" title="Shamatha Project" rel="tag">Shamatha Project</a>, <a href="http://science.kqed.org/quest/tag/telomerase/" title="Telomerase" rel="tag">Telomerase</a>, <a href="http://science.kqed.org/quest/tag/telomeres/" title="Telomeres" rel="tag">Telomeres</a><br />
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