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    <title>This Week in Evolution</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/" />
    <link rel="self" type="application/atom+xml" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/atom.xml" />
    <id>tag:blog.lib.umn.edu,2013-04-24:/denis036/thisweekinevolution//5625</id>
    <updated>2013-05-17T18:19:48Z</updated>
    <subtitle>See also my &quot;Darwinian Agriculture Blog.&quot; </subtitle>
    <generator uri="http://www.sixapart.com/movabletype/">Movable Type Enterprise 4.31-en</generator>

<entry>
    <title>Cooperation =&gt; deception?</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/05/cooperation_deception.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.395815</id>

    <published>2013-05-17T17:56:30Z</published>
    <updated>2013-05-17T18:19:48Z</updated>

    <summary>Cooperation creates selection for tactical deception [Open Access] &quot;cooperation can create selection pressures favouring the evolution of... deception weakening cheater detection in conditional cooperators&quot; They present a model and supporting data showing a positive correlation between cooperativeness and deception in...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p><a href="http://rspb.royalsocietypublishing.org/content/280/1762/20130699.abstract">Cooperation creates selection for tactical deception [Open Access]</a>  <em>"cooperation can create selection pressures favouring the evolution of... deception weakening cheater detection in conditional cooperators"</em><br />
They present a model and supporting data showing a positive correlation between cooperativeness and deception in nonhuman primates.  With a broader definition of deception, this could apply to species without brains.  For example, rhizobia bacteria that simply fail to provide their legume hosts with nitrogen get hit with <a href="http://rspb.royalsocietypublishing.org/content/278/1718/2698.short">plant sanctions</a> that reduce their fitness, but rhizobia that interfere with a plant's internal signaling can <a href="http://www.nature.com/ismej/journal/v3/n7/abs/ismej200938a.html">get away with cheating</a>.  </p>

<p><strong>Also this week:</strong></p>

<p><a href="http://www.pnas.org/content/110/20/8020.abstract" ">Nanoscale analysis of pyritized microfossils reveals differential heterotrophic consumption in the ∼1.9-Ga Gunflint chert</a><em> "Three-dimensional nanotomography reveals additional pyritized biomaterial, including hollow, cellular epibionts and extracellular polymeric substances, showing a preference for attachment to Gunflintia over Huroniospora and interpreted as components of a saprophytic heterotrophic, decomposing community. "</em>  1.9-billion-year-old fossils?  Isn't that 1.899994 billion years before the earth was created?</p>

<p><a href="http://www.nature.com/nature/journal/v497/n7449/full/nature12142.html">Adaptive dynamics under development-based genotype-phenotype maps" </a><br />
<a href="http://www.nature.com/nature/journal/v497/n7449/full/nature12099.html">Evolution: Stuck between the teeth" </a><br />
<em>"developmental complexity often prevents natural selection from reaching optimal fitness when fitness is directly linked to attaining a particular phenotype, but that these 'adaptive peaks' can be reached when fitness is instead linked to functional properties of the phenotype.</em></p>]]>
        
    </content>
</entry>

<entry>
    <title>Sampling Daphnia from a canoe, in the snow, May 3...</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/05/sampling_daphnia_in_the_snow_m.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.394812</id>

    <published>2013-05-03T19:36:06Z</published>
    <updated>2013-05-03T19:52:00Z</updated>

    <summary>...for our research on the evolution of aging. Sandra Brovold is sampling, I&apos;m trying to remember the J stroke, and Bob Sterner took the video....</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
        <category term="Careers in science" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="aging" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>...for our research on the <a href="http://blog.lib.umn.edu/denis036/thisweekinevolution/applications/aging/">evolution of aging</a>.  Sandra Brovold is sampling, I'm trying to remember the J stroke, and Bob Sterner took the <a href="http://www.youtube.com/watch?v=42xxjFd_2Ko&feature=youtu.be">video</a>.</p>]]>
        
    </content>
</entry>

<entry>
    <title>Handwritten data to CSV file without typing</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/05/handwritten_data_to_csv_file_w.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.394503</id>

    <published>2013-05-01T21:26:43Z</published>
    <updated>2013-05-01T21:44:37Z</updated>

    <summary>Tired of typing data from lab notebooks into spreadsheets? * Record data using a Livescribe pen, in one of their microdot notebooks. * Put a comma after each entry, including last entry in each line. * Use MyScript to convert...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
        <category term="Careers in science" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>Tired of typing data from lab notebooks into spreadsheets?</p>

<p>* Record data using a <a href="http://www.livescribe.com/en-us/smartpen/echo/">Livescribe pen</a>, in one of their microdot notebooks.  <br />
* Put a comma after each entry, including last entry in each line.<br />
* Use <a href="http://www.livescribe.com/store/20070723002/myscript-for-livescribe/p-512.htm">MyScript</a> to convert page to text, using Rich Text option.<br />
* Select (highlight) table data, including comma-separated heading. <br />
* Open a blank<a href="http://www.libreoffice.org/"> Libre-Office</a> Calc (spreadsheet) document.<br />
* Edit / Paste Special, using "Unformatted text'' and comma-separated options.<br />
* Edit if needed.<br />
* Save as .CSV file using defaults.</p>

<p>The result can be opened in Excel, if you insist.  When I tried pasting the data directly into Excel, values weren't separated properly, but there may be a way to do it.</p>

<p>I have only tested this with Livescribe 4 GB Echo Smartpen.<br />
 <br />
I got this idea <a href="http://www.livescribe.com/store/20070723002/myscript-for-livescribe/p-512.htm">here</a>.<br />
</p>]]>
        
    </content>
</entry>

<entry>
    <title>Eukaryote origins, cicadas, and silkworm sex </title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/04/eukaryote_origins_cooperation.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.393907</id>

    <published>2013-04-26T16:37:38Z</published>
    <updated>2013-04-26T16:53:41Z</updated>

    <summary>Gene similarity networks provide tools for understanding eukaryote origins and evolution &quot;multiple signatures of the chimerical origin of Eukaryotes as a fusion of an archaebacterium and a eubacterium that could not have been observed using phylogenetic trees... archaebacterial repertoire has...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p><a href="http://www.pnas.org/content/110/17/E1594.abstract" ">Gene similarity networks provide tools for understanding eukaryote origins and evolution </a> <br />
"multiple signatures of the chimerical origin of Eukaryotes as a fusion of an archaebacterium and a eubacterium that could not have been observed using phylogenetic trees... archaebacterial repertoire has a similar size in all eukaryotic genomes whereas the number of eubacterium-derived genes is much more variable"</p>

<p><a href="http://www.pnas.org/content/110/17/6919.abstract" ">Independent divergence of 13- and 17-y life cycles among three periodical cicada lineages </a> "at any given location, up to three distinct species groups (Decim, Cassini, Decula) with synchronized life cycles are involved... life-cycle synchronization of invading congeners to a dominant resident population enabled escape from predation" [OK, but why not 7 and 11 years?]</p>

<p><a href="http://www.pnas.org/content/110/17/6766.abstract" ">Transgene-based, female-specific lethality system for genetic sexing of the silkworm, Bombyx mori </a></p>

<p><a href="http://www.pnas.org/content/110/17/6931.abstract" ">Neo-sex chromosomes and adaptive potential in tortricid pests </a> "fusion between an ancestral Z [sex] chromosome and an autosome corresponding to chromosome 15 in the Bombyx mori reference genome...  conferring insecticide resistance and clusters of genes involved in detoxification of plant secondary metabolites under sex-linked inheritance"</p>

<p><br />
</p>]]>
        
    </content>
</entry>

<entry>
    <title>High-school student undermines our &quot;famine-food longevity&quot; hypothesis, maybe</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/04/high-school_student_undermines.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.392679</id>

    <published>2013-04-17T18:37:56Z</published>
    <updated>2013-04-17T19:00:40Z</updated>

    <summary>Back in 2009, I suggested that, to the extent that organic foods provide greater health benefits, this might be due to tradeoffs with reproduction. See my original post for a more-detailed explanation. Since then, I&apos;ve seen at least one paper...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
        <category term="* Darwinian Agriculture" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="aging" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="agriculture" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>Back in 2009, I suggested that, to the extent that organic foods provide greater health benefits, this might be due to tradeoffs with reproduction.  See my <a href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2009/06/the_bitter_fountain_of_youth.html">original post</a> for a more-detailed explanation.  Since then, I've seen at least one paper on a diet that increases both longevity and reproduction in some species, but there were no data on the <em>timing </em>of reproduction, which is key to our hypothesis.</p>

<p>This week, however, high school student Ria Chhabra and colleagues published a <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0052988">paper in PLoS One</a> reporting both greater longevity and increased egg-laying at all ages, in fruit flies fed various organic foods.  It's not inconceivable that some conventionally-grown produce could be so poor, nutritionally, that it would reduce both lifespan and reproduction.  But their data seem inconsistent with our hypothesis that organic-vs-conventional differences were mainly differences in toxins (synthetic in conventional, natural in organic) and that natural toxins mainly acted as environmental cues, switching physiology towards longevity at the expense of reproduction.</p>

<p>I'd like to see this experiment repeated by a different lab, however, before drawing firm conclusions.  There are a couple of strange things in their data.  First, as noted in the paper, survival curves for Drosophila are usually sigmoidal, whereas theirs are more linear.   Also, their peak egg-laying rate was reportedly at an age of 1 day.  Other studies I've seen show essentially no egg-laying that early, with peaks at day 5 or so.  See <a href="http://www.jstor.org/stable/4216698?origin=JSTOR-pdf">this</a> paper or <a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000356">this open-access one</a>.</p>]]>
        
    </content>
</entry>

<entry>
    <title>YouTube videos go fungal...</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/04/youtube_videos_go_fungal.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.392354</id>

    <published>2013-04-15T18:13:12Z</published>
    <updated>2013-04-15T21:48:15Z</updated>

    <summary>...or whatever we call over 100 but fewer than 1000 views. This page has links to an interview Michael Joyce did with me at the end of my week-long visit to the International Rice Research Institute, as well as the...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
        <category term="* About this blog and me" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>...or whatever we call over 100 but fewer than 1000 views.  </p>

<p><a href="http://www.youtube.com/playlist?list=PLNowyW0S1hI8GsRZ_RZNcECgH-TPJhrjt">This page</a> has links to an interview Michael Joyce did with me at the end of my week-long visit to the International Rice Research Institute, as well as the five lectures I gave there (plus audience questions and discussion).</p>

<p>Also still available are:<br />
* a <a href="http://www.plantsciences.ucdavis.edu/denison/AAASupdate.mp3">60-second AAAS story</a> on my most-cited paper.<br />
* a video of my <a href="http://instituteforcontemporaryevolution.org/01_cms/details.asp?ID=87">keynote talk at the Applied Evolution Summit</a><br />
* a lower-quality video of a talk on <a href="http://mediamill.cla.umn.edu/mediamill/embedqt/180950">Evolutionary Tradeoffs as Agricultural Opportunities</a><br />
* an <a href="http://www.microbeworld.org/index.php?option=com_content&view=article&id=650:mts50-ford-denison-darwin-on-the-farm&catid=37:meet-the-scientist&Itemid=155">audio interview</a> with science writer Carl Zimmer</p>

<p>Or, you can find an updated list of <strong>my publications</strong>, with links to many of them, <a href="http://scholar.google.com/citations?user=WcySQHIAAAAJ&hl=en&oi=ao">here</a>.</p>]]>
        
    </content>
</entry>

<entry>
    <title>This week&apos;s picks</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/04/this_weeks_picks_33.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.392026</id>

    <published>2013-04-12T16:32:09Z</published>
    <updated>2013-04-15T18:13:00Z</updated>

    <summary>Here are some papers that look interesting this week. See also my Darwinian Agriculture blog . Stable isotope evidence of meat eating and hunting specialization in adult male chimpanzees &quot;sex differences in food acquisition and consumption may have persisted throughout...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
        <category term="agriculture" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="bacteria" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="humans" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>Here are some papers that look interesting this week.  See also my <a href="http://blog.lib.umn.edu/denis036/darwinianagriculture/">Darwinian Agriculture blog<br />
</a>.</p>

<p><a href="http://www.pnas.org/content/110/15/5829.abstract" ">Stable isotope evidence of meat eating and hunting specialization in adult male chimpanzees </a> "sex differences in food acquisition and consumption may have persisted throughout hominin evolution, rather than being a recent development"</p>

<p><a href="http://www.pnas.org/content/110/15/E1398.abstract" ">New World cattle show ancestry from multiple independent domestication events </a> "pre-Columbian introgression of genes from African cattle into southern Europe"</p>

<p><a href="http://www.pnas.org/content/110/15/5812.abstract" ">Key role for a glutathione transferase in multiple-herbicide resistance in grass weeds </a> "When the black-grass A. myosuroides (Am) AmGSTF1 was expressed in Arabidopsis thaliana, the transgenic plants acquired resistance to multiple herbicides"</p>

<p><a href="http://www.pnas.org/content/110/15/5806.abstract" ">Potential shortfall of pyramided transgenic cotton for insect resistance management </a> "results from 21 selection experiments with eight species of lepidopteran pests indicates that some cross-resistance typically occurs between Cry1A and Cry2A toxins."</p>

<p><a href="http://www.sciencemag.org/content/340/6129/1233477.abstract">The Upper Limb of <em>Australopithecus sediba</em> </a> "use of the forelimb primarily for prehension and manipulation appears to arise later, likely with the emergence of Homo erectus" [There are several articles on A. sediba in this issue.]</p>

<p><a href="http://www.pnas.org/content/110/15/6229.abstract" ">Achieving the triple bottom line in the face of inherent trade-offs among social equity, economic return, and conservation</a> "three very different case studies in California (United States), Raja Ampat (Indonesia), and the wider Coral Triangle region (Southeast Asia). We show that equity tends to trade off nonlinearly with the potential to achieve conservation objectives, such that similar conservation outcomes can be possible with greater equity, to a point."</p>

<p><a href="http://www.pnas.org/content/110/15/5999.abstract" ">Decreased water flowing from a forest amended with calcium silicate </a> "An unexpected outcome of the Ca amendment was a change in watershed hydrology; annual evapotranspiration increased by 25%, 18%, and 19%, respectively, for the 3 y following treatment before returning to pretreatment levels. "</p>

<p><a href="http://www.pnas.org/content/110/15/5945.abstract" ">Responses of Mn2+ speciation in Deinococcus radiodurans and Escherichia coli to γ-radiation by advanced paramagnetic resonance</a> "extreme radiation resistance of D. radiodurans cells cannot be attributed to SodA"<br />
</p>]]>
        
    </content>
</entry>

<entry>
    <title>Fake journals and conferences in NYT</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/04/fake_journals_and_conferences.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.391490</id>

    <published>2013-04-08T22:24:53Z</published>
    <updated>2013-04-08T22:40:54Z</updated>

    <summary>Conferences that invite people at random, for money, are bad enough. Those that mimic real conferences are worse. The New York Times reports that people signed up for Entomology-2013, sponsored by &quot;The OMICS Group&quot;, mistaking it for the scientific-society-sponsored Entomology...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
        <category term="Careers in science" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>Conferences that invite people at random, for money, are bad enough.  Those that mimic real conferences are worse.  The New York Times <a href="http://www.nytimes.com/2013/04/08/health/for-scientists-an-exploding-world-of-pseudo-academia.html?src=me&ref=general">reports</a> that people signed up for Entomology-2013, sponsored by "<a href="http://phylogenomics.blogspot.com/2012/01/scary-and-funny-functional-researcher.html">The OMICS Group</a>", mistaking it for the scientific-society-sponsored Entomology 2013.  I've <a href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2011/05/fake_scientific_conferences_in.html">discussed</a> this problem before.  The NYT article also discusses fake "scientific journals" that publish garbage for money.  Since real journals vary in quality, and many charge authors for some of the cost of publication, it may sometimes be hard for people outside the field to tell the difference.</p>

<p>Real scientists publish in journals with scientific-sounding names, but publication in a scientific-sounding journal is no guarantee that the conclusions are correct or that the author is a real expert.</p>

<p><br />
</p>]]>
        
    </content>
</entry>

<entry>
    <title>Tradeoff-free longevity?</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/04/tradeoff-free_longevity.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.391122</id>

    <published>2013-04-05T21:29:12Z</published>
    <updated>2013-04-05T22:42:50Z</updated>

    <summary>I have argued that understanding evolutionary tradeoffs is key to improving agriculture and increasing longevity. For example, in 2009 I discussed a paper showing that food deprivation extends lifespan of C. elegans nematode worms by delaying their reproduction. I&apos;ve seen...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
        <category term="Applied evolution" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="aging" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>I have argued that understanding evolutionary tradeoffs is key to <a href="http://press.princeton.edu/titles/9777.html">improving agriculture</a> and <a href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2011/01/modeling_reproductionlongevity.html">increasing longevity</a>.  </p>

<p>For example, in 2009 I <a href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2009/12/delaying_reproduction_the_disp.html">discussed</a> a paper showing that food deprivation extends lifespan of <em>C. elegans</em> nematode worms by delaying their reproduction.  I've seen other papers claiming to extend lifespan without reducing reproduction, but those papers have ignored possible effects on <em>timing</em> of reproduction.  In a growing population, reproducing later reduces fitness, because your offspring are added to a larger gene pool.  On the other hand,<a href="http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0006055"> if the population is decreasing...</a>  </p>

<p>But a <a href="http://www.pnas.org/content/110/14/5522.abstract">recent paper in PNAS</a> reports that chemicals called <strong>ascorides</strong> (thought to be used as a crowding cue) increase the lifespan of <em>C. elegans</em>, without an apparent reproductive cost.  Treated animals produced at least as many offspring as controls, <em>at all ages</em>.  I don't understand this result.  If there's no tradeoff, why haven't they evolved to turn on this response <em>all the time</em>, even without the crowding cue?</p>

<p>In humans, though, "<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273900/">Exceptional longevity is associated with decreased reproduction</a>."  That was the conclusion of a 2011 paper.  They found that Ashkenazi Jewish centenarians (average age ~100 years) averaged 2.0 children, while a control group (parents of their children's spouses and friends, who died in their 70's) averaged 2.5 children.  The centenarians also reproduced later in life (28-32 vs. 26-30).  So, is it worth having 0.5 fewer children, to live 30 more years?  Natural selection apparently doesn't think so.<br />
   </p>]]>
        
    </content>
</entry>

<entry>
    <title>Carnival of Evolution</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/04/carnival_of_evolution_10.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.390686</id>

    <published>2013-04-02T19:51:02Z</published>
    <updated>2013-04-02T19:58:08Z</updated>

    <summary>Interesting stuff at Synthetic Daisys, but links would be good!...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>Interesting stuff at <a href="http://syntheticdaisies.blogspot.com/2013/04/carnival-of-evolution-58-visions-of.html">Synthetic Daisys</a>, but links would be good!</p>]]>
        
    </content>
</entry>

<entry>
    <title>Persistent polymorphisms, enhancing mutation, new fossils, cooperation &amp; conservation</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/03/persistent_polymorphisms_enhan.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.390203</id>

    <published>2013-03-29T17:42:27Z</published>
    <updated>2013-03-29T18:22:07Z</updated>

    <summary>All five of my Darwinian Agriculture lectures at the International Rice Research Institute are now available on YouTube. Here are some interesting papers published this week. Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees &quot; In addition...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
        <category term="* Darwinian Agriculture" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="bacteria" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="birds and reptiles" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="evolution of cooperation" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="publications &amp; publicity " scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>All five of my Darwinian Agriculture lectures at the International Rice Research Institute are now <a href="http://www.youtube.com/playlist?list=PLNowyW0S1hI8GsRZ_RZNcECgH-TPJhrjt">available on YouTube</a>.  </p>

<p>Here are some interesting papers published this week.</p>

<p><a href="http://www.sciencemag.org/content/339/6127/1578.abstract">Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees </a> " In addition to the major histocompatibility complex, we identified 125 regions in which the same haplotypes are segregating in the two species <em>[neither version has displaced the other in either species in 6 million years]</em>, all but two of which are noncoding <em>[i.e., they probably control other genes rather than coding for a protein]</em>."  <em>The most likely explanation for such prolonged co-existence is that individuals with less-common alleles may be resistant to pathogens that have evolved to attack those with more-common alleles.</em></p>

<p><a href="http://www.nature.com/nature/journal/v495/n744/full/nature11989.html">Accelerated gene evolution through replication-transcription conflicts" </a> "We propose that bacteria, and potentially other organisms, promote faster evolution of specific genes through orientation-dependent encounters between DNA replication and transcription."</p>

<p><a href="http://www.nature.com/nature/journal/v495/n7442/full/nature11963.html">Palaeontology: Tubular worms from the Burgess Shale" </a></p>

<p><a href="http://www.nature.com/nature/journal/v495/n7442<br />
/full/nature11985.html">Preservation of ovarian follicles reveals early evolution of avian reproductive behaviour" </a></p>

<p><a href="http://www.pnas.org/content/110/13/5263.abstract" ">Both information and social cohesion determine collective decisions in animal groups </a></p>

<p><a href="http://www.pnas.org/content/110/13/4956.abstract" ">Governance regime and location influence avoided deforestation success of protected areas in the Brazilian Amazon </a></p>

<p><a href="http://www.sciencemag.org/content/339/6127/1608.abstract">Wild Pollinators Enhance Fruit Set of Crops Regardless of Honey Bee Abundance </a><br />
</p>]]>
        
    </content>
</entry>

<entry>
    <title>Darwinian Agriculture at the International Rice Research Institute</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/03/darwinian_agriculture_at_the_i.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.389522</id>

    <published>2013-03-23T13:53:01Z</published>
    <updated>2013-03-23T14:23:22Z</updated>

    <summary>I&apos;m at the International Rice Research Institute (IRRI) in the Philippines this week, for a series of lectures on my book, Darwinian Agriculture. IRRI is posting my talks on YouTube. For links, and some notes on my discussions with IRRI...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>I'm at the <a href="http://www.irri.org/">International Rice Research Institute</a> (IRRI) in the Philippines this week, for a series of lectures on my book, <a href="http://press.princeton.edu/titles/9777.html">Darwinian Agriculture</a>.  IRRI is posting my talks on YouTube.  For links, and some notes on my discussions with IRRI staff, see my <a href="http://blog.lib.umn.edu/denis036/darwinianagriculture/">Darwinian Agriculture blog</a>.</p>]]>
        
    </content>
</entry>

<entry>
    <title>More conference spam... from Nature</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/03/more_conference_spam_from_natu.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.389245</id>

    <published>2013-03-18T18:54:05Z</published>
    <updated>2013-03-18T19:00:58Z</updated>

    <summary>I&apos;ve complained in the past about fake scientific conferences organized by BIT Life Sciences and IEEE. Now Nature Publishing Group is getting into the act, with TEDMED: &quot;meet a Nobel laureate or two, talk informally with the heads of the...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
        <category term="Careers in science" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>I've complained in the past about <a href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/02/more_fake-scientific-conferenc.html">fake scientific conferences</a> organized by BIT Life Sciences and IEEE.  Now Nature Publishing Group is getting into the act, with TEDMED:  <br />
<blockquote>"meet a Nobel laureate or two, talk informally with the heads of the FDA, NIH..."</blockquote> If I did medical research, I might be fooled into thinking the invitation had something to do with my expertise.  The $4950 registration fee gives the game away, though.</p>]]>
        
    </content>
</entry>

<entry>
    <title>This week&apos;s picks</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/03/this_weeks_picks_32.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.389066</id>

    <published>2013-03-15T23:11:12Z</published>
    <updated>2013-03-15T23:13:33Z</updated>

    <summary>I&apos;m off to the International Rice Research Institute to give a series of five lectures on Darwinian Agriculture. Here are some papers that look interesting this week. Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene Hind...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
        <category term="* Darwinian Agriculture" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="publications &amp; publicity " scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>I'm off to the International Rice Research Institute to give a series of five lectures on Darwinian Agriculture.  Here are some papers that look interesting this week.</p>

<p><a href="http://www.sciencemag.org/content/339/6125/1312.abstract">Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene </a><br />
<a href="http://www.sciencemag.org/content/339/6125/1309.abstract">Hind Wings in Basal Birds and the Evolution of Leg Feathers </a><br />
<a href="http://www.pnas.org/content/110/11/4374.abstract" ">Lifespan of neurons is uncoupled from organismal lifespan </a><br />
<a href="http://www.nature.com/nature/journal/v495/n7440/full/nature11912.html">Naturally occurring allele diversity allows potato cultivation in northern latitudes" </a><br />
<a href="http://www.pnas.org/content/110/11/4230.abstract" ">Water-controlled wealth of nations </a><br />
</p>]]>
        
    </content>
</entry>

<entry>
    <title>Cooperation, inducible defense, cancer, and more</title>
    <link rel="alternate" type="text/html" href="http://blog.lib.umn.edu/denis036/thisweekinevolution/2013/03/cooperation_defense_cancer_and.html" />
    <id>tag:blog.lib.umn.edu,2013:/denis036/thisweekinevolution//5625.388022</id>

    <published>2013-03-08T16:25:08Z</published>
    <updated>2013-03-08T16:38:16Z</updated>

    <summary>Here are some papers that look interesting this week. Prairie Dogs Disperse When All Close Kin Have Disappeared &quot;cooperation among kin is more important than competition among kin for young prairie dogs&quot; Variants at serotonin transporter and 2A receptor genes...</summary>
    <author>
        <name>R. Ford Denison</name>
        <uri>http://micropop.cbs.umn.edu/people/denison-r-ford.html</uri>
    </author>
    
        <category term="agriculture" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="ancestral-state reconstruction" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="behavior" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="evolution of cooperation" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="humans" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="mammals" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="plants" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://blog.lib.umn.edu/denis036/thisweekinevolution/">
        <![CDATA[<p>Here are some papers that look interesting this week.</p>

<p><a href="http://www.sciencemag.org/content/339/6124/1205.abstract">Prairie Dogs Disperse When All Close Kin Have Disappeared </a> "cooperation among kin is more important than competition among kin for young prairie dogs"</p>

<p><a href="http://www.pnas.org/content/110/10/3955.abstract" ">Variants at serotonin transporter and 2A receptor genes predict cooperative behavior differentially according to presence of punishment </a> "Participants with a variant at the serotonin transporter gene contribute more, leading to group-level differences in cooperation, but this effect dissipates in the presence of punishment." </p>

<p><a href="http://www.pnas.org/content/110/10/3973.abstract" ">Plant mating system transitions drive the macroevolution of defense strategies </a><br />
the repeated, unidirectional transition from ancestral self-incompatibility (obligate outcrossing) to self-compatibility (increased inbreeding) leads to the evolution of an inducible (vs. constitutive) strategy of plant resistance to herbivores." </p>

<p><a href="http://www.pnas.org/content/110/10/4009.abstract" ">Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics </a> "we reconstructed the phylogeny of the fragments for each patient, identifying copy number alterations in EGFR and CDKN2A/B/p14ARF as early events, and aberrations in PDGFRA and PTEN as later events during cancer progression"</p>

<p><a href="http://www.nature.com/nature/journal/v495/n7439/full/nature11942.html">Non-optimal codon usage is a mechanism to achieve circadian clock conditionality" </a><br />
"natural selection against optimal codons to achieve adaptive responses to environmental changes"</p>

<p><a href="http://www.sciencemag.org/content/339/6124/1207.abstract">Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote </a> "> 5% of protein-coding genes of G. sulphuraria were probably acquired horizontally"</p>

<p><a href="http://www.pnas.org/content/110/10/4134.abstract" ">Recent land use change in the Western Corn Belt threatens grasslands and wetlands </a><br />
"a recent doubling in commodity prices has created incentives for landowners to convert grassland to corn and soybean cropping... onto marginal lands characterized by high erosion risk and vulnerability to drought." </p>]]>
        
    </content>
</entry>

</feed>
