tag:blogger.com,1999:blog-143238142024-03-07T03:36:27.920-08:00Discovering biology in a digital world (Archives)My thoughts on biology, teaching, life, and exploring the living world via the digital one. Only my opinions are represented by these postings, they do not represent the viewpoints of any funding agency or Geospiza, Inc.Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.comBlogger75125tag:blogger.com,1999:blog-14323814.post-455142413112477442008-10-17T14:44:00.000-07:002008-10-17T14:48:39.925-07:00Attention new iFinch users! Turn on your data processor!New iFinch users: <div><br /></div><div>Before you can upload data, you will need to turn on your data processor. </div><br /><div><span class="Apple-style-span" style="font-weight: bold;">Checking and starting your Finch data processor</span></div><div>1. Log into your iFinch account.</div><div>2. Find and select the <span class="Apple-style-span" style="font-weight: bold;">Data Processor</span> link in the System menu.</div><div><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.geospiza.com/finchtalk/uploaded_images/menu1-766412.gif"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://www.geospiza.com/finchtalk/uploaded_images/menu1-766410.gif" border="0" alt="" /></a></div><div><div>3. Look at the Data processor status.</div><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.geospiza.com/finchtalk/uploaded_images/finchd-704963.gif"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://www.geospiza.com/finchtalk/uploaded_images/finchd-704961.gif" border="0" alt="" /></a><br /><div>4. If the Data processor has stopped, you will need to Restart it by selecting the <span class="Apple-style-span" style="font-weight: bold;">Restart</span> button. If you are a student, you will need to have an instructor log in and do this.</div><div><br /></div><br /></div><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1151712566531414372006-06-30T17:00:00.000-07:002007-01-28T10:18:18.263-08:00Hello Kitty! or Don't Eat Me, I Study Genetics!Genetics textbooks abound with stories of European royalty and the hazards of having children after you've married one of your cousins. It struck me as an interesting parallel that the lion is such a popular symbol in so many royal coats of arms. Like the royal families of Europe, certain lion populations have also suffered from a few too many copies of certain recessive genes.<br /><br /><br /><a href="http://scienceblogs.com/digitalbio/2006/06/hello_kitty_or_dont_eat_me_i_s_1.php#more">Read the rest at the new site>></a><br /><br /><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/cats" rel="tag">cats</a>, <a href="http://technorati.com/tag/panthers" rel="tag">panthers</a>, <a href="http://technorati.com/tag/conservation+biology" rel="tag">conservation biology</a>, <a href="http://technorati.com/tag/biology" rel="tag">biology</a>, <a href="http://technorati.com/tag/genetics" rel="tag">genetics</a>, <a href="http://technorati.com/tag/population+genetics" rel="tag">population genetics</a>, <a href="http://technorati.com/tag/DNA" rel="tag">DNA</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1149870939278753732006-06-09T09:28:00.000-07:002006-06-09T09:36:35.226-07:00My new addressAs <a href="http://scienceblogs.com/clock/">Bora Zovkovic</a>, so kindly puts it, in <a href="http://themagicschoolbus.blogspot.com/">The Magic School Bus</a>, summer is starting and many of us are going to SEED. Hopefully, our readers don't have <i>too</i> many allergies.<br /><br />I will leave archives here, but you can find new postings at: <a href="http://www.scienceblogs.com/digitalbio">http://www.scienceblogs.com/digitalbio</a><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1148490855393034912006-05-24T10:08:00.000-07:002006-10-04T19:19:33.280-07:00Time to fly<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/flying.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/320/flying.jpg" alt="" border="0" /></a><br /><div style="text-align: center;">"I'm goin' where the sun keeps shinin'<br />Thru the pourin' rain,<br />Goin' where the weather suits my clothes.<br /><br />Bankin' off the northeast wind,<br />Sailin' on a summer breeze,<br />Skippin' over the ocean like a stone."<br /><br />- Fred Neil<br />Everybody's Talkin (Echoes)<br /><br /><br /><div style="text-align: left;">Where am I going?<br /><br /><span style="font-style: italic;">California?</span><br /><br />Well, there too, for a few days, but blogwise, I'm going to <a href="http://scienceblogs.com/">ScienceBlogs</a>. And you're welcome to come visit. My new link won't be functional for a few days yet, but I will post it when I'm ready for visitors.<br /><br /><br /></div></div><br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#announce" rel="tag">Announcements</a></span><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com2tag:blogger.com,1999:blog-14323814.post-1148474210168024452006-05-24T05:32:00.000-07:002006-05-24T05:54:09.480-07:00Tangled Bank #54 is up and ready<a href="http://photos1.blogger.com/blogger/7482/1292/1600/bhs_band.jpg"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;" src="http://photos1.blogger.com/blogger/7482/1292/400/bhs_band.jpg" border="0" alt="" /></a>Yet another great collection of science blogamainia is live and ready at <a href="http://sciencepolitics.blogspot.com">Science and Politics</a>. <br /><br />Hosted by Bora Zivkovic, a hard-writing science blogger extraordinare, it's <a href="http://sciencepolitics.blogspot.com/2006/05/tangled-bank-54.html">Tangled Bank #54</a>!! <br /><br />Clear some time off your schedule and grab a cup of coffee, there's lots of good reading ahead.<br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/carnivals" rel="tag">carnivals</a>, <a href="http://technorati.com/tag/tangledbank" rel="tag">Tangled Bank</a>, <a href="http://technorati.com/tag/science" rel="tag">science</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1147904095208627502006-05-17T15:13:00.000-07:002006-05-17T15:14:55.226-07:00Hurrah for Syttende Mai!<a href="http://photos1.blogger.com/blogger/7482/1292/1600/DSC00857.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://photos1.blogger.com/blogger/7482/1292/400/DSC00857.jpg" border="0" alt="" /></a><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1147627330897266632006-05-14T10:18:00.000-07:002006-05-14T17:36:39.090-07:00Hard-working birds on Mother's Day<div style="text-align: center;">At first, we thought the tent caterpillars were back for the summer.<br /></div><div style="text-align: center;"><br /></div><div style="text-align: center;"> <a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/nest.1.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/400/nest.0.jpg" alt="" border="0" /></a><br />Then, we saw a bird go into the "tent."<br /><br /></div><span style="text-decoration: underline;"></span><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/working_bird.1.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/400/working_bird.0.jpg" alt="" border="0" /></a><br />I guess you don't get Mother's Day off until <span style="font-style: italic;">after</span> you've laid your eggs.<br /></div><span style="text-decoration: underline;"><br /></span><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/bushtit_branch.1.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/400/bushtit_branch.0.jpg" alt="" border="0" /></a><br /><div style="text-align: center;">Happy Mother's Day to mothers and future mothers.<br /></div><span style="text-decoration: underline;"><br /></span><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#birds" rel="tag">Birds</a></span><br /><span style="font-size:85%;"><br />technorati tags: <a href="http://technorati.com/tag/biology" rel="tag">biology</a>, <a href="http://technorati.com/tag/birds" rel="tag">birds</a></span><br /><span style="text-decoration: underline;"><br /><br /><br /><br /></span><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1147360384135435882006-05-11T10:16:00.000-07:002006-06-19T05:56:25.476-07:00Part II. Future Shock and Selenocysteine: it's time again to update the databanksOne of the surprises (<span style="font-style: italic;">for me anyway</span>) in discovering the existence of selenocysteine (<a href="http://digitalbio.blogspot.com/2006/05/part-i-future-shock-and-selenocysteine.html">Part I. Future Shock and Selenocysteine</a>), was the corresponding discovery that it's encoded by <span style="font-weight: bold;">UGA</span>. Ordinarily, UGA is a stop codon. If a UGA is in an mRNA sequence, it tells the ribosome that the job is done. It's time to pack up all the tRNAs and elongation factors and move on to the next project.<br /><br />But in the case of selenocysteine, we have a "<span style="font-style: italic;">work-around</span>." Sometimes UGA stops everything, sometimes the UGA says "put the selenocysteine right here." (<span style="font-style: italic;">Someone in the office joked that the ID g-o-d must be a programmer since he/she is trying to fix bugs</span>.)<br /><br /><span style="font-weight: bold;">How do the ribosomes and tRNAs know whether to stop or go?</span><br /><br />They <span style="font-style: italic;">feel</span> the difference.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/rna_hairpin.0.png"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/200/rna_hairpin.png" alt="" border="0" /></a>Seriously, the sequences at the 3' end of an mRNA fold into a special hairpin shape like the one shown here (<a href="#kryukov">1</a>, <a href="#diamond">2</a>, <a href="#yoshizawa">3</a>). In bacteria, this structure is called a "selenocysteine insertion sequence" or SECIS element. Eucaryotes have similar structures at the 3' ends of mRNAs for selenoproteins.<br /><br />The RNA in the picture has a rainbow coloring scheme (<span style="color: rgb(255, 0, 0);">Red</span>, <span style="color: rgb(255, 102, 0);">Orange</span>, <span style="color: rgb(255, 255, 51);">Yellow</span>, <span style="color: rgb(51, 204, 0);">Green</span>, <span style="color: rgb(51, 51, 255);">Blue</span>, <span style="color: rgb(102, 0, 204);">Indigo</span>, <span style="color: rgb(204, 51, 204);">Violet</span>). Nucleotides at the 5' end are red, nucleotides at the 3' end are violet. You can follow the colors in the RNA backbone to see how the RNA is twisted around into a hairpin shape.<br /><br />One of the tests that we used to give job applicants was to have them write a short script for translating a DNA sequence in 6 reading frames. We would give them a mouse pad with the genetic code and put them to work.<br /><br />Selenocysteine makes this problem a whole lot harder.<br /><br />Since the recognition feature is a secondary structure, locating the coding sequences for selenocysteines presents an interesting challenge to computational biologists. Finding these sequences requires a bit more than a regular expression.<br /><br />Kryukov, et. al. describe an algorithm for doing this type of search (<a href="#kryukov">1</a>). They've refined it in the years since this publication, but it seems that the information has yet to percolate through much of the world's bioinformatics community.<br /><br /><span style="font-style: italic;">And here, I thought I was the only one who seemed to have missed this.</span><br /><br />Nope.<br /><br /><br /><span style="font-weight: bold;">Can we find selenocysteine in GenBank?</span><br />I started to wonder if the news about selenocysteine had trickled out beyond PubMed articles and into the rest of the NCBI.<br /><br />Could I find selenoprotein sequences in the <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene">Gene database</a>? I thought this would be a good place to start since the data are well curated and there are links to reference protein sequences.<br /><br />I searched and searched, and lo and behold, I found them.<br /><br /><a href="http://photos1.blogger.com/blogger/7482/1292/1600/human_selp.gif"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;" src="http://photos1.blogger.com/blogger/7482/1292/320/human_selp.3.png" border="0" alt="" /></a><br><br /><br /><br /><br />The sequence above codes for human selenoprotein P. U is the one letter symbol that represents selenocysteine. This protein contains an unusually large number of selenocysteines.<br /><br />I only looked at a few of the reference protein sequences (labeled NP---) from the Gene database, but they all seemed to have selenocysteines.<br /><br />So the NCBI Gene Database seems to be caught up, at least for the sequences that I checked out.<br /><br /><br /><span style="font-weight: bold;">Mischief and Misannotations</span><br />I followed the links to the <a href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml">Conserved Domain Database</a>. (I'm writing a book on this BTW, and the CDD is really, really cool).<br /><br />When I got to a summary page, I choose the SelP_C domain (since more U's are on that side of the protein). This gave me a page with a <a href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?ascbin=8&maxaln=10&seltype=3&uid=pfam04593&querygi=62530391&aln=6,8,258,41,50,300,17,68,318,11,80,330,14,95,345,6,102,352,14">Pfam alignment</a> between my human SelP sequence and some sequences that were chosen for Pfam. (<span style="font-style: italic;">you can take a look at this yourself by clicking the link above. Change the format to </span><span style="font-weight: bold; font-style: italic;">Hypertext</span><span style="font-style: italic;"> and click </span><span style="font-weight: bold; font-style: italic;">Show Alignment</span><span style="font-style: italic;"> to see the selenocysteines in the query sequence</span>).<br /><br />Reading downward, the Pfam sequences, in the alignment below, are from cow, my query(human), rat, another human sequence, and zebrafish.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/selp_cdd.gif"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/400/selp_cdd.png" alt="" border="0" /></a><br />Every time my query sequence has a "U," the other sequences have a "c" (<span style="font-style: italic;">purple boxes above</span>).<br /><br />This is interesting and odd. Only <span style="font-style: italic;">one</span> of the proteins with the conserved SelP domain has selenocysteine (and it's our human query sequence).<br /><br />One interpretation that Kryukov suggested in 2003 (<a href="#kryukov">1</a>), (<span style="font-style: italic;">and later regretted, I'm sure</span>), is that through evolution, cysteine was substituted for selenocysteine in organisms like the rat and mouse.<br /><br />I think the presence of the <span style="font-style: italic;">other</span> human SelP sequence argues for <span style="font-style: italic;">another</span> interpretation, especially since it's an older version of our query.<br /><br />If we click the gi links to see the database records, we find something else that's interesting.<br /><br />A note in the first sequence, from the cow, deposited in April 2006, shows that <span style="font-style: italic;">someone</span> knew about the selenocysteines,<br /><blockquote>[MISCELLANEOUS] The selenocysteines are all encoded by the opal codon, UGA.</blockquote>But apparently, no one bothered to put them in the amino acid sequence, since there aren't any selenocysteines there.<br /><br /><i>Maybe they didn't read the note.</i><br /><br />Stranger, yet, the missing selenocysteines could be rationalized away by arguing that the protein sequence is just a conceptual translation - that is, it was determined by using the standard genetic code. Except that using the standard genetic code would have generated <span style="font-style: italic;">a much</span> shorter sequence since UGA makes translation stop. So, instead of putting in the correct amino acid, the curators (Swiss prot?) typed in the <span style="font-style: italic;">wrong</span> amino acid. Instead of using the U for selenocysteine, they typed a C for cysteine.<br /><br />The rat sequence was also updated in April 2006 and we can see that the positions of selenocysteines also seem to be marked in the GenPept record (below), but, funny, there aren't any selenocysteines in the rat sequence.<br /><br /><a href="http://photos1.blogger.com/blogger/7482/1292/1600/Picture-20.gif"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;" src="http://photos1.blogger.com/blogger/7482/1292/320/Picture-20.gif" border="0" alt="" /></a><br><br /><br />The other human sequence for SelP and the zebrafish sequence show the same kinds of annotations. Yet <span style="font-style: italic;">neither one</span> contains selenocysteines in the amino acid sequence.<br /><br /><span style="font-weight: bold;">Could the source of the sequences (Pfam) be the source of the problems?</span><br />I'm not sure where the problem originates but if I search the <a href="http://www.sanger.ac.uk/Software/Pfam/">Pfam database at the Sanger Center</a>, for selenocysteine, I get a list of 31 proteins that contain it, and again, I get an annotation that indicates that someone is aware of selenocysteine.<br /><blockquote>SelP is the only known eukaryotic selenoprotein that contains multiple selenocysteine (Sec) residues...</blockquote>Yet when I do a seed alignment, <span style="font-style: italic;">none</span> of the amino acid sequences contain selenocysteine. Here is one example:<br /><blockquote>SEPP1_HUMAN/22-250 QDQSSLCKQPPAWSIRDQDPMLNSNGSVTVVALLQASCYLCIL<br />QASKLEDLRVKLKKEGYSNISYIVVNHQGISSRLKYT</blockquote>The selenocysteines are missing here, too.<br /><br />If I take this sequence and do a blastp search at the NCBI, I get quite few perfect matches. Just like Pfam, there <span style="font-style: italic;">are</span> sequences in GenBank that are not yet fixed.<br /><br /><br /><br /><span style="font-weight: bold;">What is our take home message?</span><br />The simple take-home message, of course, is to be aware the FASTA sequences for selenium-containing proteins <span style="font-style: italic;">are likely to be wrong</span>. If the annotations say there should be selenocysteine and you can't find a "u" in the sequence, it probably hasn't been fixed yet. Those of us who use the date must always be skeptical and read the literature.<br /><br />The second take-home message concerns process. The acceptance of new ideas in science generally prompts some re-evaluation of older ideas. We evaluate older concepts more critically in the electric light of new ideas. It would be helpful if these processes could be applied more quickly to sequence data and bioinformatics algorithms. These results support the need for scientific curators who can read the literature, add annotations, and even make corrections in amino acid sequences, from time to time.<br /><br />The amino acid matrices that we use for protein comparisons, were updated when more sequences became available for doing alignments. We all switched from using PAM to BLOSUM matrices. Maybe it's time to make update the Pfam domains as well.<br /><br />Selenocysteine exists.<br /><br />It's time to deal with it and get on with the work.<br /><br /><br /><span style="font-weight: bold;">References:</span><br /><a name="kryukov"></a>1. Kryukov GV, Castellano S, Novoselov SV, Lobanov AV, Zehtab O, Guigo R, Gladyshev VN. 2003. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12775843&query_hl=3&itool=pubmed_docsum">Characterization of mammalian selenoproteomes</a>.<br />Science. 300:1439-43.<br /><br /><a name="diamond"></a>2. Diamond, AM. 2004. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15353586&query_hl=8&itool=pubmed_docsum">On the road to selenocysteine</a>. Proc Natl Acad Sci U S A. 101: 13395-13396.<br /><br /><a name="yoshizawa"></a>3. Yoshizawa S, Rasubala L, Ose T, Kohda D, Fourmy D, Maenaka K. 2005. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed">Structural basis for mRNA recognition by elongation factor SelB</a>. Nat Struct Mol Biol. 12:198-203.<br /><br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#discovery" rel="tag">Doing biology with bioinformatics</a></span><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/bioinformatics" rel="tag">bioinformatics</a>, <a href="http://technorati.com/tag/selenocysteine" rel="tag">selenocysteine</a>, <a href="http://technorati.com/tag/biochemistry" rel="tag">biochemistry</a>, <a href="http://technorati.com/tag/biology" rel="tag">biology</a>, <a href="http://technorati.com/tag/blast" rel="tag">blast</a>, <a href="http://technorati.com/tag/genetics" rel="tag">genetics</a>, <a href="http://technorati.com/tag/genomics" rel="tag">genomics</a>, <a href="http://technorati.com/tag/DNA" rel="tag">DNA</a>, <a href="http://technorati.com/tag/RNA" rel="tag">RNA</a>, <a href="http://technorati.com/tag/science_education" rel="tag"> Science Education</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com16tag:blogger.com,1999:blog-14323814.post-1147352058590161452006-05-11T05:35:00.000-07:002006-05-11T05:56:18.536-07:00Carnival time<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/DSC02012.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/200/DSC02012.jpg" alt="" border="0" /></a>The carnivals are up and running.<br /><br /><a href="http://monado2.blogspot.com/2006/05/tangled-bank-53-go-climb-tree.html">Tangled Bank 53: Go climb a tree! </a>looks at the tree of life from a higher point of view.<br /><br /><a href="http://birddc.blogspot.com/">I and the bird #23</a> at birdDC asks the question, is it possible to do birding on the internet?<br /><br />Enjoy!<div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1147286773913291462006-05-10T10:54:00.000-07:002007-03-22T13:19:33.626-07:00Part I: Future Shock and Selenocysteine<span style="font-weight: bold;">Future Shock</span><br /><br />When I was in high school, we read an intriguing book by Alvin Toffler called <a href="http://www.amazon.com/exec/obidos/redirect?link_code=ur2&tag=discovebiolog-20&amp;amp;camp=1789&creative=9325&path=http%3A%2F%2Fwww.amazon.com%2Fgp%2Fproduct%2F0394425863%3Fv%3Dglance%26n%3D283155">"Future Shock."</a><img src="http://www.assoc-amazon.com/e/ir?t=discovebiolog-20&l=ur2&o=1" alt="" style="border: medium none ! important; margin: 0px ! important;" border="0" height="1" width="1" /><br /><br />Now, the book is over 30 years old but some of the predictions Toffler made were uncanny.<br /><br />One of the ideas Toffler proposed was that people could become overwhelmed and disoriented with the onslaught of new information. My field is a good example. For <a href="http://www.geospiza.com">Geospiza</a>, helping people manage large amounts of new data, while maintaining the old, is our whole raison d’être.<br /><br />But going back to Toffler, he predicted that the increasing rate of societal change would cause some people to experience symptoms of "Future Shock." One morning you might wake up in a familiar place, but everything would seem a bit different and strange. I'm channeling the ghost of Jim Morrison a bit, but the The Doors had the feeling nailed down.<br /><br />It's never bothered me though, until the other day.<br /><br />I learned something new that shook one of my core beliefs.<br /><br /><span style="font-style: italic;">We have a new amino acid in the genetic code.</span><br /><br />Sure, go ahead and laugh.<br /><br />This might <span style="font-style: italic;">seem</span> like an odd thing to be bothered by, b<span style="font-style: italic;">ut the genetic code was solved in the early 60's</span>. Some things in life are NOT supposed to change. Yeah, there are some variations in translating DNA from different species, and we <span style="font-style: italic;">expect</span> to learn new things from deciphering the genome, but <span style="font-style: italic;">no one </span>expects changes in something as fundamental as the genetic code.<br /><br />So, it was a bit jarring to find out that now there are 21 amino acids.<br /><br />And it was even a little reasurring that no one believed me.<br /><br />My husband kept insisting that this was a post-translational modification or some strange anomaly from archeabacteria.<br /><br />Naturally, I was <span style="font-weight: bold;">forced</span> to hunt down a bunch of abstracts and read them to everyone (<span style="font-style: italic;">I love PubMed!</span>).<br /><br /><br /><span style="font-weight: bold;">Selenocysteine: our 21st amino acid<br /><br /></span>It's true. The new amino acid is selenocysteine and there are even special tRNAs that can add it during translation. The translation machinary recognizes the UGA stop codon, plus special secondary structures in mRNA, and puts in a selenocysteine instead of stopping.<br /><br />This amino acid is uncommon, but GenBank has 7904 entries for selenoproteins and 3293 RefSeqs. Many are probably orthologs (<span style="font-style: italic;">the same protein in different organisms</span>) or our favorites, those wonderful "<span style="font-style: italic;">hypothetical proteins</span>," and I think some of the records represent the same sequence, but there's still a fair number to be found (<span style="font-style: italic;">except in Pfam, but more on that in part II</span>).<br /><br />Selenoproteins are pretty wide-spread, too. At least 25 selenoproteins are known in humans and I found papers describing them in mouse, fruit flies, humans, fish, bacteria, and protozoans. Most selenoproteins only contain one selenium and it's positioned at the active site. One selenoprotein contains so many seleniums that this one protein, alone, accounts for half of the selenium in a cell.<br /><br />I'm not too sure yet, about the function of these proteins. Some of the selenoproteins may be important in redox reactions, one might prevent heavy metal toxicity, and there seems to be some link to cancer, too.<br /><br /><span style="font-style: italic;">And, guess what?</span><br /><br />I'm wasn't the only one who was taken by surprise. It looks like some of our favorite bioinformaticists and genome annotators missed this one, too.<br /><br />Stay tuned.<br /><br />In <a href="http://digitalbio.blogspot.com/2006/05/part-ii-future-shock-and.html">part II</a>, we look at the infinite loop of information updates and an interesting conclusion drawn from erroneous annotations.<br /><br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#discovery" rel="tag">Doing biology with bioinformatics</a></span><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/biology" rel="tag">biology</a>, <a href="http://technorati.com/tag/bioinformatics" rel="tag">bioinformatics</a>, <a href="http://technorati.com/tag/blast" rel="tag">blast</a>, <a href="http://technorati.com/tag/genetics" rel="tag">genetics</a>, <a href="http://technorati.com/tag/genomics" rel="tag">genomics</a>, <a href="http://technorati.com/tag/DNA" rel="tag">DNA</a>, <a href="http://technorati.com/tag/RNA" rel="tag">RNA</a>, <a href="http://technorati.com/tag/science_education" rel="tag"> Science Education</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com2tag:blogger.com,1999:blog-14323814.post-1146710143925698222006-05-03T19:32:00.000-07:002006-05-04T07:55:12.480-07:00Animalcules Volume 1, Issue 7It's the 4th of May, almost summer time and time to think about microbes.<br /><br />Some of them are giant, some are just, well, ... unusual.<br /><br />I guess we'll let the procaryotes go first, since apparently they're working by the clock. And you probably thought it was simple being a single-celled organism without a nucleus. You can read about them in <a href="http://circadiana.blogspot.com/2006/04/clocks-in-bacteria-iv-clocks-in-other.html">Clocks in Bacteria IV: Clocks in other bacteria</a>, brought to you by none other than <a href="http://circadiana.blogspot.com/">Circadiana</a>.<br /><br /><a href="http://www.giantmicrobes.com/affiliates/idevaffiliate.php?id=122_0_1_8"><img src="http://www.giantmicrobes.com/affiliates/banners/GIANTmicrobe_banner_150x150.jpg" img="" style="margin: 0pt 10px 10px 0pt;" 0="" align="left" /></a>Next, in keeping with the image of pathogens as giant fluffy toys, we have a collection of <a href="http://www.microbeworld.org/htm/mam/activities.htm">Hands-on, Fun Microbiology Activities </a>from the ASM. Let's Get Small, Yeast on the Rise, and Fun with Fomites are some of the entertaining activities that you could either try at home, or use to liven up a class with the small fry, or even larger fry. <a href="http://www.microbeworld.org/mlc/gifs/activities/pgs54-57.pdf">Fun with Fomites</a> exams the wonders of things that grow on your kitchen cutting board, or even the pennies in your pockets. And there are plenty of helpful suggestions for the cognitively impaired, but since this isn't a political sort of blog, I won't go there.<br /><br />Do your bacteria keep swimming away? Isn't chemotaxis a pain? I remember when researchers studied flagella and bacterial motion by using anti-flagella antibodies to pin the little suckers to a slide and then, they would watch the bacteria twirl around and around with a microscope. Ah, torturing bacteria! The <a href="http://biocurious.com">BioCurious</a> have found a better way. "<a href="http://biocurious.com/studying-bacteria-with-atomic-force-microscopy-afm">Studying Bacteria with Atomic Force Microscopy</a>" looks far more fun than old antibody and slide method.<br /><br />Further representing the uncultured world, we have the GMO pundit asking, '<a href="http://gmopundit.blogspot.com/2006/05/is-studying-soil-dna-any-value-to.html">Is Studying Soil DNA Any Value to The Australian Farmer Part 1. About 99% of soil bacteria have never been grown.</a>" Even if they're not, my collaborators have got <a href="http://digitalbio.blogspot.com/2006/02/sequencing-campus-at-johns-hopkins.html">college biology students doing PCR and sequencing dirt</a>, so the farmers may not care, but knowing your soil bacteria, will still be important for getting a good grade in general biology.<br /><br />In the <a href="http://deepseanews.blogspot.com/">Deep-Sea News</a>, we learn about some lovely cyanobacteria, the <a href="http://deepseanews.blogspot.com/2006/03/deep-phytoplankter-prochlorococcus.html">Deep phytoplankter Prochlorococcus</a>, a "plain little mite at first site" but very productive in terms of biomass.<br /><br />Ewen Callaway from <a href="http://complexmedium.blogspot.com/">Complex Medium</a> contemplates the true meaning of diversity, in <a href="http://complexmedium.blogspot.com/2006/04/does-microbial-diversity-count.html">Does microbial diversity count</a>? Is is important to preserve the bacteria in a desert oasis?<br /><br />A carnival with bacteria, of course, would never be complete without our faithful laboratory, friend, the mouse of the microbes, the king of our colon, the one and many, <span style="font-style: italic;">E. coli</span>. In <a href="http://mikethemadbiologist.blogspot.com/2006/04/e-coli-shigella-and-creationism.html">E. coli, Shigella, and Creationism</a>, <a href="http://mikethemadbiologist.blogspot.com">Mike the Mad Biologist</a> even manages to link our fuzzy friend to creationism and Shigella, with an amazing amount of intestinal fortitude.<br /><br />Now, Mike the Mad also has me worried about cleaning my aquarium. He writes <a href="http://mikethemadbiologist.blogspot.com/2006/04/more-on-that-ny-times-article.html">More on That NY Times Article </a>about the dangers of getting Salmonella from your fish tank. And, if that wasn't enough, well, he explains why tummy aches in Australia (<a href="http://mikethemadbiologist.blogspot.com/2006/04/australia-agriculture-and-antibiotics.html">Australia, Agriculture, and Antibiotics</a>) might last longer than you'd think.<br /><br />Who knows what evil bacteria lurk in the hearts of men? The protozoa know. Inspired by the TV, <a href="http://paulorwin.blogspot.com">Paul Orwin</a> identifies a microbial influence on pop culture (<a href="http://paulorwin.blogspot.com/2006_04_30_paulorwin_archive.html#114671584557802169">Microbiology and Pop Culture</a>).<br /><br /><a href="http://www.cafepress.com/wbsmartart/1189355?pid=2865832"><img class="imageborder" alt="bird flu" src="http://logo.cafepress.com/5/1868569.1189355.jpg" style="margin: 0pt 10px 10px 0pt;" 0="" align="right" border="0" height="150" /></a>So far, we've let procaryotes have all the fun. This bird has had enough. Maybe it smelled the Campybacter. Or could it be that this chicken has read <a href="http://scienceblogs.com/aetiology/2006/04/new_swine_influenza_virus.php">Emerging Disease and Zoonoses #13--new swine influenza virus detected</a> and just wants to play it safe? Maybe this rooster watched this <a href="http://video.lisarein.com/dailyshow/oct2005/10-06-05/10-6-05-avianflu.mov">short hysterically funny video clip</a> and just isn't willing to play chicken?<br /><br />Before we go too mad, perhaps we should foam at the mouth to read this story, and accompanying links on <a href="http://sciencepolitics.blogspot.com/2006/04/rabies-novel.html">Rabies, the Novel</a>, from Bora Zivkovic of <a href="http://sciencepolitics.blogspot.com">Science and Politics</a>.<br /><br />And for one last, truly viral article, lets contemplate our friend the mosquito, one last whiny time, and read about <a href="http://www.microbeworld.org/htm/cissues/wnile/wnile_0.htm">West Nile Virus</a>, a last friendly parting thought, from our friends at <a href="http://www.microbeworld.org">MicrobeWorld</a>.<br /><br />Check out the schedule for the next episode of <a href="http://scienceblogs.com/aetiology/2006/02/announcing_new_blog_carnival_1.php">Animalcules</a>!<br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#microbiology" rel="tag">Microbiology</a></span><br /><br /><p><span style="font-size:85%;">technorati tags:<br /><a href="http://technorati.com/tag/animalcules" rel="tag">animalcules</a>, <a href="http://technorati.com/tag/biology" rel="tag">biology</a>, <a href="http://technorati.com/tag/DNA" rel="tag">DNA</a>, <a href="http://technorati.com/tag/genomics" rel="tag">genomics</a>, <a href="http://technorati.com/tag/microbiology" rel="tag">microbiology</a><br /><a href="http://technorati.com/tag/science_education" rel="tag">science education</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com2tag:blogger.com,1999:blog-14323814.post-1146237586089044372006-04-28T08:17:00.000-07:002006-04-28T19:44:53.126-07:00Powers of Ten and Shifting Perspectives on Science and SocietyI bought this book for my kids awhile back, called "<a href="http://www.amazon.com/gp/product/0716760088/104-8663694-4170365?v=glance&n=283155">Powers of Ten</a>" by Philip Morrison and Phylis Morrison. The premise (quoted from Amazon) is this:<br /><blockquote>"Starting with a view of a billion light-years, the book (like the film) moves inward, with each page being at one-tenth the scale of the previous one. In 25 steps, you're looking at a picnic by the shores of Lake Michigan, then plunging into a human hand, down through the cells inside it, the DNA inside the cells, the atoms inside the DNA, and the subatomic particles inside the atom. By the time you've gone a total of 40 steps, you're in a world of quantum uncertainty."</blockquote><br />Each shift in perspective changes the view as familiar objects are seen in new ways.<br /><br />My life has done the same thing, except in the opposite direction. For the first 25 years or so, my perspective was from the nuclear level as all the electrons revolved around me. And I would have <span style="font-style: italic;">completely</span> agreed with these opinions in the comments at <a href="http://www.epigeneticsnews.com/2006/04/26/scientists-in-training-the-experience-dilemma">Epigenetics News</a>:<br /><blockquote>"I did get a discussion about this topic going in the lab today (three postdocs, a tenured faculty member and a couple of other students). Surprisingly, there was very little sympathy for the high school students seeking biotech internships. The general consensus was that even if a student was taken on as an intern during the summer, it would take so much time to “get them up to speed” without any background knowledge coming in (and potentially no experience working a real job at all) that it just wouldn’t be worth the effort."<br /><br /></blockquote>As a 25 yr old graduate student, I <span style="font-style: italic;">still</span> would have agreed.<br /><br />I had to TA during the entire first year of graduate school and I didn't particularly like it. Why should I work hard as a TA when I had <span style="font-style: italic;">my own</span> research to do and courses to pass? Why lose my valuable research time? Why bother? It wasn't <span style="font-style: italic;">my fault</span> that students who were seniors in college couldn't do the basic algebra we asked for in our microbiology course.<br /><br />Let's fast-forward five more years to age thirty.<br /><br />Now, I'm a post-doc with a baby who goes to day-care. My non-profit research institution holds Monday afternoon post-doc research seminars at 5:15 pm that last until 6:30. But my day care provider requires that children be picked up at 5:00 pm, and since I'm making $17,000 a year as a post-doc, and my husband is a grad student, we only have one car (<span style="font-style: italic;">which I drive</span>). So I go to the scientist in charge of the weekly seminar and ask if we can move the time, only to be told "<span style="font-style: italic;">no one else considers this to be a problem.</span>" Oooh, that was a jarring shift in perspective. Maybe the nuclear model has to be replaced. I advance grimly to the cellular level.<br /><br />Five years later, my perspective shifted farther outward to the organism view. And I <span style="font-style: italic;">still</span> would have agreed with the lab in Epigenetics News. <span style="font-style: italic;">Why have high school students in the lab? What could they do?</span><br /><br />I'm teaching in a community college. I'm about the same age as many of my students (the median age is 33), and I've gone from wondering why anyone would hire a community college student to wondering why they wouldn't. I've watched community college students, many with bachelor's degrees, some with kids, go to school full-time, and work at both jobs and internships, sometimes simultaneously. And I have developed a whole new level of respect and awe for what people can do.<br /><br />I've also learned about multiple intelligences. Students can get A's on every assignment and write brilliant essays on exams and set boxes of Kimwipes on fire when they get a job in a lab. There are plenty of opposites, too, like the students who get C's on every test and become highly-valued technicians or even go on to graduate school. One of my former students, with only a two-year degree, gave a key note talk at cytokine conference and one student started his own biotech company.<br /><span style="font-style: italic;"><br /></span>Well, here we are, ten years later, and I'm starting see the world from the ecosystem perspective. I work at a bioinformatics company and have one child in high school and one in middle school. I know <span style="font-style: italic;">now</span>, how <span style="font-style: italic;">efficiently</span> the public school system - at least middle school - turns kids off of science early on. I no longer think that we can afford to wait until college - or in the case of community colleges - after college - to counteract the impressions that kids get of science and scientists.<br /><br />Not only have I come to appreciate the broad spectrum of capabilities that high school students represent, but I can stand back, <span style="font-style: italic;">now</span>, and see other goals beyond getting a nice-looking gel or cloning that fragment of DNA.<span style="font-style: italic;"><br /><br />Why do I think it's important to find science opportunities for high school students and undergraduates? </span><br /><br /><a href="http://digitalbio.blogspot.com/2006/04/re-thinking-biotech-student.html">There are many reasons</a>. But looking from an ecosystem view, internships are <span style="font-style: italic;">one</span> way to help society achieve the goals to which many scientists give lip service and <a href="http://seejanecompute.blogspot.com/2006/03/who-wants-to-help-me-carry-this-torch.html">some even work to support</a>. These are goals like a <a href="http://biology.plosjournals.org/perlserv/?request=get-document&doi=10%2E1371%2Fjournal%2Epbio%2E0040167">scientifically literate society</a>, a diverse society, and a society that doesn't view science as an elitist enterprise that's only open to rich white kids. Because, like it or not, that <span style="font-style: italic;">is</span> <a href="http://smartbrief.blogspot.com/2006/04/mama-please-let-your-babies-grow-up-to.html">how the outside world views the academy</a>.<br /><br />If we <span style="font-style: italic;">had</span> a scientifically literate society we would be working on serious issues like global warming and over-fishing and disappearing species. We wouldn't have to waste our time with silly distractions like intelligent design. I don't think there would be such an anti-science sentiment on the part of the general public <a href="#liza">(1)</a> if it were understood that strong science empowers <span style="font-style: italic;">all</span> of us.<br /><br />Of course, neither University research labs nor biotech companies are or should be charities, and my experience has been that they can't be relied on to act in a consistently charitable manner, anyway. If we are to increase diversity in science and develop a scientifically literate society, we need a <a href="http://digitalbio.blogspot.com/2006/04/re-thinking-biotech-student_24.html">workable way to open the laboratory doors</a> and let in more students.<br /><br /><br />References:<br /><a name="liza"></a>1. Liza Gross. 2006.<a href="http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040167">Scientific Illiteracy and the Partisan Takeover of Biology</a>.PLoS Biol 4(5): e167.<br /><br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#education" rel="tag">Education</a></span><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/biotechnology" rel="tag">biotechnology</a>,<br /><a href="http://technorati.com/tag/teaching-carnival" rel="tag">teaching-carnival</a><br /><a href="http://technorati.com/tag/education" rel="tag">education</a><br /><a href="http://technorati.com/tag/science education" rel="tag">science education</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com2tag:blogger.com,1999:blog-14323814.post-1146143554281877912006-04-27T06:02:00.000-07:002006-05-13T08:09:27.096-07:00Spring is in the heronThe herons have all built their nests now and are happily sitting on them. It seemed like a good time to post some pictures from the early days of nest repair.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/nesting.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/320/nesting.jpg" alt="" border="0" /></a>It's a little hard to tell but this bird is carrying a stick and coming in for a landing as you can see below.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/landing.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/320/landing.jpg" alt="" border="0" /></a>Even herons have to take a break from nest building sometimes.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/trees.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/320/trees.jpg" alt="" border="0" /></a><br /><br />What if we built a zoo and the animals just happened to show up? This heron did exactly that. It's sitting in the penguin exhibit at the Woodland Park Zoo enjoying the abundant little fish.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/zoo_heron.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/320/zoo_heron.jpg" alt="" border="0" /></a>Everyone else enjoyed watching the heron. It's a good thing herons can't read.<br /><br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#birds" rel="tag">Birds</a></span><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/biology" rel="tag">biology</a>, <a href="http://technorati.com/tag/birds" rel="tag">birds</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com2tag:blogger.com,1999:blog-14323814.post-1146057705190624032006-04-26T06:17:00.000-07:002006-04-26T11:11:09.926-07:00Carnivals, Carnivals, and more CarnivalsA long, long, time ago, in a galaxy far, far away there came ....(pause for dramatic effect)<br /><br /><br /> <a href="http://www.inoculatedmind.com/?p=38"><b>TANGLED BANK #52</b></a><br /><br /><br />And I've been promoted to Jedi trainer! Be sure to clear some time for some enjoyable reading.<br /><br />In keeping with my new role as Jedi trainer, you might also want to check out the <a href="http://educationwonk.blogspot.com/2006/04/carnival-of-education-week-64.html">Education Carnival</a> over at <a href="http://educationwonk.blogspot.com/">Education Wonk</a>.<div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1145897804703401832006-04-24T09:53:00.000-07:002006-04-28T07:37:55.586-07:00Re-thinking biotech student internships, part II<span style="font-weight: bold;">Three models for getting lab experience</span><br /><br />In <a href="http://digitalbio.blogspot.com/2006/04/re-thinking-biotech-student.html">part I</a>, I wrote about the need for both high school and college students to have learning experiences outside of school. High school students need learning experiences that open their eyes to potential careers and help them focus on education. College students need learning experiences that will open doors to jobs. Internships meet the needs of both groups but biotech companies only offer a small number of internships, if they offer any at all.<br /><br />I've now seen three different models that present interesting, and viable alternatives to the traditional view of company internships. Each model allows students to gain hands-on working experience in a company or company-like setting. And the beauty is that, in contrast to the standard practice, none of these models depends on the benevolence or transient charity of local companies.<br /><br /><span style="font-weight: bold; font-style: italic;">How do you create opportunities for students to do internships?</span><br /><br /><span style="font-weight: bold;">Model 1. Make your school program more like a research lab</span><br /><br />This model is exemplified by the biotech program at <a href="http://www.bates.ctc.edu">Bates Technical College</a> in Tacoma. At Bates, Students can start the biotech program on any given Monday and continue until they're finished. I've known about the school for a long time, but I never understood how this worked until I heard the director, Kelly Hamilton, talk at a Bio-Link conference last week. Apparently, this model works more like an apprenticeship or graduate school. Students join the program, get a customized training plan and get right to work in the lab. I don't think the Bates program entirely substitutes for a company internship, but Bates students do develop solid lab skills since they spend a considerable amount time working independently in the lab.<br /><br /><br /><span style="font-weight: bold;">Model 2. Become an incubator</span><br /><br /><a href="http://www.shoreline.edu/biotech">Shoreline Community College</a> has become an incubator. <a href="http://www.wabio.com/industry/directory/companybyid?companyid=2766">Xactagen</a>, a small biotech company, has moved in and shares some of Shoreline's lab facilities. This is truly a win-win situation. The company benefits from the infrastructure at the community college and the college benefits from the interaction between students and Xactagen employees. Having an authentic research program happening on site makes biotech lab a familiar site and Xactagen employees serve as informal instructors and role models. Xactagen has also hired graduates of the SCC biotech program and has students interns employed on their projects. The benefits are many. The greatest downside is that Xactagen is too small to hire very many student interns and those interns are all college students.<br /><br /><br /><span style="font-weight: bold;">Model 3. Start a contract-research company</span><br /><br />This model is the most intriguing and, I think, shows the most promise. Community colleges have always operated small businesses as way to educating students in both running a business and different types of careers. Some of the examples at my former school were culinary arts programs where the program operates restaurants, optician-training programs, beauty salons, and day-care facilities. So, I'm really glad these ideas are finally getting tested in the realm of biotechnology.<br /><br /><span style="font-style: italic;">Why not have a small college-based business that does a bit of contract research? </span><br /><br />Dr. Tamara Goetz at <a href="http://www.slcc.edu/">Salt Lake City Community College </a>is giving this model a try. Frustrated with the challenges of finding student internships, Dr. Goetz started <a href="http://innovabio.org/">InnovaBio</a>.<br /><br />InnovaBio is a small non-profit company that does contract research for biotech and nutraceutical companies in the Salt Lake area. InnovaBio has a few paid employees, acting as supervisors, but most of the lab work is done by high school and college interns. InnovaBio provides a low-risk opportunity for companies to try out high-risk products and train future employees at the same time. Further, this is a model that can handle large numbers of students and can accommodate high school students. Students can even work in non-lab areas of biotechnology, such as marketing and business development.<br /><br />This is a model that should be replicated.<br /><br />With all the challenges that our local high school programs and colleges face in locating student internships, and all the challenges that our local biotech industry has in finding qualified employees, I hope the educators in our state will look a bit eastward and pay attention to what's happening in Utah.<br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#education" rel="tag">Education</a></span><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/biotechnology" rel="tag">biotechnology</a>,<br /><a href="http://technorati.com/tag/teaching-carnival" rel="tag">teaching-carnival</a><br /><a href="http://technorati.com/tag/education" rel="tag">education</a>,<a href="http://technorati.com/tag/science_education" rel="tag">science education</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com3tag:blogger.com,1999:blog-14323814.post-1145838866920641382006-04-23T17:23:00.000-07:002006-04-23T17:34:26.936-07:00Upcoming carnivals<a href="http://photos1.blogger.com/blogger/7482/1292/1600/baby_ducks.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://photos1.blogger.com/blogger/7482/1292/320/baby_ducks.jpg" border="0" alt="" /></a><br /><br />This is a reminder. Animalcules will be here on May 4th. If you write about tiny things (<i>life forms that is</i>), this is the place to show off your writings. Send Animalcule submissions to sandy at geospiza dot com with Animalcules in the subject line.<br /><br />If you're not sure what an Animalcule carnival might look like like - you can take a look at <a href="http://www.biotech-weblog.com/50226711/animalcules_16_carnival_of_the_microbes.php">the last one</a> at the <a href="http://www.biotech-weblog.com">Biotech Weblog</a>. <br /><br />And the next Tangled Bank will be April 26th at <a href="http://www.inoculatedmind.com/">The Inoculated Mind</a>. Send those submissions to karl AT inoculatedmind DOT com and put "Tangled Bank Submission" in the subject line. <br /><br />TTFN!<div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1145732942001103832006-04-22T11:37:00.000-07:002006-05-07T10:35:26.316-07:00Re-thinking biotech student internships, part I<span style="font-weight: bold;">Jobs can be learning experiences, too</span><br /><br />I read an amusing story yesterday about a summer job <a href="http://suburbdad.blogspot.com/2006/04/summer-jobs.html">packaging ice in plastic bags</a>. I had jobs like that, too, when I was in high school. I waited tables, sold popcorn at a theatre, sold plants at a garden store, and did lots of babysitting. I learned something from every mindless part-time job, but mostly I learned that I didn't want to do them.<br /><br />So when I started college, I started looking for jobs that would do more than pay the rent. I wanted first-hand impressions of potential careers. As a receptionist in a veterinarian's office, I learned that small animal vets needed to be good with handling animals and even better with handling people. As an autopsy assistant, I learned about anatomy and pathology. Working as a phlebotomist in a plasma center, I learned to spot needle tracks and find good veins. My medley of part-time and volunteer jobs were eye-opening forays into the working world.<br /><br />The job that I wanted the most though, was the hardest to get. I <span style="font-style: italic;">really</span> wanted to work in a science lab. Every now and then I would go to the student employment center and look at the job postings, but I was <span style="font-style: italic;">never</span> eligible. The lab positions at my University required either work-study funding or work experience and I had neither. This was before the age of biotech, but I spent five years looking, and didn't find a lab job until the middle of my senior year in college.<br /><br /><br /><span style="font-weight: bold;">Learning about careers</span><br /><br />Making career choices as a young person is a challenge. It's hard to commit to a future and focus on education when you don't have a clue what a future job might involve. Some students never even consider that studying science could lead to an interesting job. They think that you need a Ph.D. or they get the <span style="font-style: italic;">interesting</span> notion (<span style="font-style: italic;">that I heard from one of my kids</span>) that science would be a <span style="font-style: italic;">really</span> boring job because all you did in middle-school science class was read textbooks.<br /><br />The part-time jobs that I collected were pivotal in helping me decide <span style="font-style: italic;">what</span> I wanted to do and <span style="font-style: italic;">why</span> I wanted to do it. For me, working as a lab technician convinced me to go on to graduate school and study science more seriously.<br /><br />Over the years there has been a greater and greater push, at least in our area, to find internships in science labs for both high school and college students. Teachers want their students to know that people of all sexes, shapes, colors, and sizes work in biotech companies and that studying science can lead to an interesting career.<br /><br />At the same time, internships in the biotech industry have become harder to get (<span style="font-style: italic;">especially for high school students!</span>). As the local industry has shifted from research to production, the environment has become more controlled and closely regulated. Even though some business leaders might recognize the long-term benefits of contributing to a scientifically literate society, and inspiring future employees, <span style="font-style: italic;">few</span> companies want to accept the risk of having an $80,000/year employee spend the summer babysitting a student intern. (<span style="font-style: italic;">The $80,000 yr/number comes from salary + benefits</span>).<br /><br />I'm on advisory committees for some high school biotech programs, and I've had student interns, so I <span style="font-style: italic;">know</span> these students have an excellent track record and <span style="font-style: italic;">can</span> be a great help. But, I also know how people in companies think. Hiring interns presents a risk for employers in terms of lost time and productivity.<br /><br /><br /><span style="font-weight: bold;">Learning skills</span><br /><br />Not only are internships important for investigating future careers, sometimes internship experience is <span style="font-style: italic;">essential</span> for getting a job.<br /><br />We still have the same catch 22 that I experienced in college. Biotech companies and University research labs want to hire experienced people, but they're unwilling or unable to provide that experience. Students need experience to get jobs, but they can't get jobs without experience.<br /><br />Community college biotech programs have helped and <a href="http://www.bio-link.org">Bio-Link</a> centers have been instrumental in helping schools connect with companies. By focusing on marketable lab skills, those programs have become fairly successful at getting students into the workforce.<br /><br />Many community college programs also require their students to do an internship.<br /><br />But guess what, unless you have experience, those internships are still hard to get.<br /><br /><br /><span style="font-weight: bold;">What can we do?</span><br /><br /><span style="font-style: italic;">Stay tuned. We discuss different models in <a href="http://digitalbio.blogspot.com/2006/04/re-thinking-biotech-student_24.html">part II</a>.<br /><br /><br /></span><br /><span style="font-weight: bold;"></span><br /><br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#education" rel="tag">Education</a></span><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/biotechnology" rel="tag">biotechnology</a>,<br /><a href="http://technorati.com/tag/teaching-carnival" rel="tag">teaching-carnival</a><br /><a href="http://technorati.com/tag/education" rel="tag">education</a><br /><a href="http://technorati.com/tag/science_education" rel="tag">science education</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com1tag:blogger.com,1999:blog-14323814.post-1144816379913277042006-04-11T21:31:00.000-07:002006-06-02T12:51:48.173-07:00Tangled Bank #51: the Seattle Tour!<a href="http://photos1.blogger.com/blogger/7482/1292/1600/DSC00340.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/200/DSC00340.jpg" alt="" border="0" /></a>I've been racking my brain about what to do when Tangled Bank #51 came to Seattle.<br /><br />And it hit me.<br /><br />What do I normally do with visiting nobility (<span style="font-style: italic;">like my in-laws or my parents</span>)?<br /><br />We go sightseeing.<br /><br />So come along, get your reading glasses and your walking shoes, we've got places to go and lots of scientific treats to sample along the way.<br /><br />We're going to do a circle around the center of the city, starting in a bus ride to the zoo and ending up at our local cultural hotspot, Archie McPhee's.<br /><br />Since I'm a biologist, we'll start our tour at Woodland Park Zoo. Before we're allowed in, we have to answer this riddle.<br /><br />"Who's bald head makes it easier to dive head first into dead meat?" I think we'll let <a href="http://www.10000birds.com">10,000 birds</a> answer that question and explain to us why <a href="http://www.10000birds.com/april2006.htm#4/4/06">Black is Back</a>.<br /><br />No visit to the zoo would be complete without a trip to the Tropical Rain Forest display. If we can be quiet, we might even learn from our docent, GrrlScientist, about the new species of parrot and mouse that were recently described from the small Philippine Island of Camiguin. Her enchanting display, <a href="http://scienceblogs.com/grrlscientist/2006/04/new_parrot_and_mouse_species_d.php">New Parrot and Mouse Species Discovered in Phillipines</a>, includes lovely photos and maps. It's right around the corner at <a href="http://scienceblogs.com/grrlscientist">Living the Scientific Life (Scientist, Interrupted)</a>. Woodland Park has lovely landscaping as well. Could they have saved some $$ if they bought their plants on eBay? Check out <a href="http://invasivespecies.blogspot.com/2006/04/it-came-from-ebay.html">It came from eBay</a> from the <a href="http://invasivespecies.blogspot.com">Invasive Species Weblog</a> to learn some surprising facts about those bargain basement plants.<br /><br /><a href="http://photos1.blogger.com/blogger/7482/1292/1600/DSC_2591.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/200/DSC_2591.jpg" alt="" border="0" /></a>The petting zoo is always a popular stop. But be sure to wash your hands when you're finished. Tara Smith, of <a href="http://scienceblogs.com/aetiology">Aetiology</a>, has an entire series on <a href="http://scienceblogs.com/aetiology/2006/03/emerging_disease_and_zoonoses.php">Emerging Disease and Zoonoses</a> that explains why this is a good idea.<br /><br />After we leave the zoo, we'll take a short stroll through Woodland Park and do some rabbit watching. The city plans to round-up most of the rabbits, sterilize them, and send them off to retire at a bunny farm (<span style="font-style: italic;">after Easter?</span>) but I think the city should consider another solution. After reading <a href="http://newdharmabums.blogspot.com/2006/04/another-bobcat-story.html">Another Bobcat Story</a> from the <a href="http://newdharmabums.blogspot.com">Dharma Bums</a>, I wonder if we shouldn't look into getting a Mayan Jaguar carving and let Nature take its course.<br /><br />Our next stop will be the Burke Museum of Natural History, but on the way we'll hike through Wallingford and check out one of my favorite landmarks, the Word of the Week. This week we'll fortunate to have two new words. From Bora Zivkovic at <a href="http://circadiana.blogspot.com">Cicadiana</a>, we have a word to describe that feeling when in you've been in one place too long, <a href="http://circadiana.blogspot.com/2006/04/ah-zugunruhe.html">Ah, Zugunruhe!</a>, and from <a href="http://wanderingvisitor.blogspot.com">Wandering Visitor</a> we have a photograph that might have been the model for "The Scream" and we have <a href="http://wanderingvisitor.blogspot.com/2006/04/word-of-day-pandiculation.html">Pandiculation</a>, a word guaranteed to make you very, very, sleepy.<br /><br />Before we get to the Burke, we'll also make a quick trip inside the University Book Store to check out a new book that we read about at <a href="http://scienceblogs.com/grrlscientist">Living the Scientific Life </a>on <a href="http://scienceblogs.com/grrlscientist/2006/04/darwin_discovering_the_tree_of.php">Darwin: Discovering the Tree of Life</a>.<br /><br />The Burke has lots of bones and interesting displays. We might even see some displays getting set up or moved around like the you can see in the <a href="http://ipath.blogs.com/zygotegames/2006/04/ice_age_migrati.html">Ice Age Migration</a> web cam that <a href="http://ipath.blogs.com/zygotegames">Zygote Games</a> shared.<br /><br />Naturally, there are wonderful diplays on evolution. <a href="http://science_boy.blogspot.com">Science and sensibility</a> wants to know why there's so much hoopla over a funny-looking fish. He invites you to read about the <span style="font-style: italic;">real</span> winners of the first land race in <a href="http://science_boy.blogspot.com/2006/04/when-animals-first-conquered-land.html">When animals first conquered the land</a>.<br /><br />What's that <a href="http://scienceblogs.com/pharyngula">PZ</a>? You found some interesting fossils, too? Wow! Those <span style="font-style: italic;">are</span> incredible. Take a look at the <a href="http://scienceblogs.com/pharyngula/2006/04/taphonomy_of_fossilized_embryo.php">Taphonomy of fossilized embryos</a> for some wonderful photos and interesting experiments.<br /><br />As we leave the Burke, we'll walk through the University of Washington campus and pass by the old nuclear reactor. I wonder if there any <span style="font-style: italic;">Deinnococcus</span> living close by. These radiation-resistant bacteria have been found living on the Hanford Nuclear Site in eastern Washington and seem to be ready for any type of environmental insult. But Hanford's too far away for us to visit today. We'll have to be content with reading Karmen Lee Franklin's wonderful story and looking at electron micrographs at <a href="http://chaoticutopia.com">Chaotic Utopia</a>'s <a href="http://chaoticutopia.com/wp/?p=254">Conan the Bacterium: The Ancient Microscopic Hero</a>.<br /><br />It's time now, to stop at the UW Health Sciences complex. Construction never stops in this part of campus. We can ask the Seattle SNP group about the study on aging that Jeremy Cherfas described in <a href="http://jeremycherfas.net/wp/archives/2006/04/09/why-die/">Why Die?</a> at <a href="http://jeremycherfas.net/wp/">Another Blasted Weblog</a>. A single nucleotide change in the APOC3 gene is correlated with a longer lifespan.<br /><br /><a href="http://opendotdotdot.blogspot.com">Glyn Moody</a> writes about other interesting studies in genomics in <a href="http://opendotdotdot.blogspot.com/2006/04/coughing-genomic-ink.html">Coughing Genomic Ink</a>. I was fortunate to hear the subject of this piece, David Haussler, give a wonderful seminar at the UW and Moody does a fine job describing Haussler's work to reconstruct ancestral genomes.<br /><br />Before we go on, and as long as we're talking about seminars, I have to add a story from <a href="http://scienceblogs.com/principles">Uncertain Principles</a> on writing letters to famous figures in science (<a href="http://scienceblogs.com/principles/2006/04/origin_story_1.php">Origin Story</a>). He would have been very impressed the night that<a href="http://montanakids.com/db_engine/presentations/presentation.asp?pid=259"> Jack Horner</a> talked at the UW. Kids were lined up in the aisles waiting for autographs!!!<br /><br />We might also drop by the teaching labs in the biology department and ask if they have anything informative to say about <a href="http://scienceblogs.com/transcript/2006/04/the_three_types_of_experiments.php">The Three Types of Experiments</a> that are described at <a href="http://scienceblogs.com/transcript">The Daily Transcript</a>.<br /><br />No discussion about genomics is complete without considering the ethical implications of this line of work. I wrote about how <a href="http://digitalbio.blogspot.com/2006/04/ethical-issues-in-biotechnology.html">these discussions differ a bit between classrooms and companies</a>. <a href="http://ketewere.blogspot.com">Kate Were</a> tackles a harder problem in a three part series (<a href="http://ketewere.blogspot.com/2006/03/biological-basis-of-boys-loving-boys.html">I</a>, <a href="http://ketewere.blogspot.com/2006/04/homosexuality-part-ii-what-is-it-with.html">II</a>, and <a href="http://ketewere.blogspot.com/2006/04/homosexuality-part-iii-pink-sperm-and.html">III</a>) on sperm donors and sexuality. Since Google has opened an office in the region, Hsien Hsien Lei at <a href="http://www.geneticsandhealth.com">Genetics and Health</a> wants us to ponder this idea: <a href="http://www.geneticsandhealth.com/2006/04/01/google-a-threat-to-genetic-privacy/">Google: A Threat to Genetic Privacy?</a> What if Google were to become a gigantic version of BLAST?<br /><br />Our next stop will be biotech companies and institutes near Lake Union. First, let's go to the Fred Hutchinson Cancer Research Center. I'm sure the researchers there would enjoy Charles Daney's article, from <a href="http://scienceandreason.blogspot.com/">Science and Reason</a>, <a href="http://scienceandreason.blogspot.com/2006/01/cancer-genes-tender-their-secrets.html">Cancer Genes Tender Their Secrets</a>. And they would certainly agree with Orac, from <a href="http://scienceblogs.com/insolence">Respectful Insolence</a> on Linus Pauling and clinical studies of vitamin C. (<a href="http://scienceblogs.com/insolence/2006/04/by_seed_prodded_or_theres_les_1.php">By Seed prodded, or there's less to these studies than meets the eye</a>). I have to share a funny Linus Pauling story that was told to me by a former boss. He said that he once asked Linus Pauling how he detemined the appropriate dose of vitamin C to take. He (<span style="font-style: italic;">my boss</span>) claimed that Linus said that he upped the dose until he got diarrhea and then backed off.<br /><br />Let's go on. Close by the Hutch is the Seattle Biomedical Research Institute. Perhaps we can see some trypanosomes if their outreach scientists are on duty. I have a soft spot for Tryps since I studied them as a post-doc at the aforementioned Fred Hutch. Orac tells us Tryps are also a wonderful model that illustrates how evolutionary understanding furthers our understanding of biology, overall. (<a href="http://scienceblogs.com/insolence/2006/03/medicine_and_evolution_part_3.php">Medicine and evolution, Part 3: A trypanosome shows the way</a>). It's a great article with wonderful pictures.<br /><br /><a href="http://photos1.blogger.com/blogger/7482/1292/1600/DSC_0076.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/200/DSC_0076.jpg" alt="" border="0" /></a>Time for a lunch break. <a href="http://cdavies.wordpress.com">Lab Cat</a> has an enjoyable read, <a href="http://cdavies.wordpress.com/2006/04/10/what-is-food-science">What is Food Science?</a>, that's a perfect lunch time treat. Who would have guessed that there is a Research Chefs Association? or a trademarked field, with a somewhat erotic sounding name called Culinology®?<br /><br />What better place to head after lunch than down south to the Museum of Flight? If the Museum of Flight had animal exhibits, I would suggest that they include these. From the <a href="http://www.hmnh.org">Hairy Museum of Natural History</a>, we have <a href="http://www.hmnh.org/archives/2006/04/08/sharovs-wondrous-wing">Sharov's Wondrous Wing</a>. In the art section we could include the interesting paintings from <a href="http://rigorvitae.blogspot.com">Rigor Vitae</a> and the story: <a href="http://rigorvitae.blogspot.com/2006/04/gliders-and-evolution-of-flight.html">Gliders and the evolution of flight</a>. And we can't forget the incredible <a href="http://sciencepolitics.blogspot.com/2006/04/ants-are-amazing.html">Gliding Ants</a> from <a href="http://sciencepolitics.blogspot.com">Science and Politics</a>.<br /><br />Time to head back north again. On to the Seattle Aquarium where we can see people embrace their inner fish. And the Pike Place Market where we can see the fish get embraced and then tossed around. I would like to see the guys at the Market toss Tiktaalik, the fish that <a href="http://stribs.blogspot.com">Hitched to Everything</a> writes about in <a href="http://stribs.blogspot.com/2006/04/we-hit-jackpot_06.html">We hit the jackpot</a>. But I shudder to think what would happen if they only tossed the fish halfway there, as <a href="http://whirledview.typepad.com/whirledview">Whirled View</a> explains in <a href="http://whirledview.typepad.com/whirledview/2006/04/tiktaalik_and_z.html">Tiktaalik and Zeno</a>. If the fish paid more attention, maybe they could crawl on over to the tourists, we could spend our time musing about more general issues in tetrapod evolution like <a href="http://www.indiancowboy.net">IndianCowboy</a> (<a href="http://www.indiancowboy.net/blog/?p=104">New Transitional Fish/Tetrapod Fossil And Other Thoughts</a>).<br /><br /><a href="http://photos1.blogger.com/blogger/7482/1292/1600/DSC00302.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/200/DSC00302.jpg" alt="" border="0" /></a>Only two more stops left. No trip to Seattle would be complete without a visit the Specific appliance center, no wait, the magnificent defiance penter, oh right, the Pacific Science Center! And my home base, <a href="http://www.geospiza.com">Geospiza</a> is only two blocks away.<br /><br />Pacific Science Center has one of the most wonderful collections of physics toys in the entire city. I think <a href="http://scientiaestpotentia.blogspot.com">Scientia est Potentia</a> would enjoy this place and it would be perfect for looking at <a href="http://scientiaestpotentia.blogspot.com/2006/04/physics-sex-and-people-in-box-shaped.html">Physics, Sex, and People in a Box-shaped Room</a>. Well, maybe not the sex, actually. There are quite a few kids running around. But if any creatures behave just like random particles, it's a group of kids at the science center.<br /><br />I think Stein from <a href="http://catdynamics.blogspot.com">Dynamics of Cats</a> would enjoy it too. Although it's pretty unlikely that the PSC could help fund the <a href="http://catdynamics.blogspot.com/2006/04/terrestrial-planet-finder-abc-c-first.html">Terrrestrial Planet Finder</a>, they're badly in need of funding themselves. If there is anywhere in Seattle where people might <span style="font-style: italic;">really</span> enjoy Mark Chu-Carroll's discussions on <a href="http://goodmath.blogspot.com/2006/04/dimensions.html">Dimensions</a> from <a href="http://goodmath.blogspot.com">Good Math, Bad Math</a>, it would be at the PSC.<br /><br />Now, we have to wait for the bus to Ballard and our last stop. Time goes so fast when we're having fun. Bora wonders if time moves faster at night because you're cold or because you're hungry? He'd like to have a group of undergraduates test this out (<a href="http://circadiana.blogspot.com/2006/04/chossats-effect-in-humans-and-other.html">Chossat's Effect in humans and other animals</a>), so if you teach a class, and want to do some relatively harmless human experimentation, let him know.<br /><br />If you're worried that we won't see the bus coming, check out <a href="http://scienceblogs.com/cognitivedaily">Cognitive Daily</a>, where we learn about <a href="http://scienceblogs.com/cognitivedaily/2006/04/seeing_and_awareness_or_how_fe.php">Seeing and awareness, or how fear can bypass the visual system</a>.<br /><br /><a href="http://photos1.blogger.com/blogger/7482/1292/1600/DSC02604.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/200/DSC02604.jpg" alt="" border="0" /></a>At last, the bus comes to take us to Ballard. Ballard is the Scandanavian enclave of Seattle. This part of the city boasts the largest Syttende Mai parade outside of Norway. We better not let Ballard know about the discovery of the ancient Swedes between the ice (thanks <a href="http://saltosobrius.blogspot.com">Salto Sobrius</a> for this story on the <a href="http://saltosobrius.blogspot.com/2006/04/first-people.html">First People</a>!) or we'll be finding settlements of Neanderthal Swedes down on Market Street for sure. You betcha!<br /><br />Since we're in Ballard, and it's the end of the trip, we have to visit <a href="http://www.mcphee.com/">Archie McPhee's</a>. After all, it's a cultural highlight of the city. Not only does Archie's have useful items like bacon strip bandages and the every popular Einstein and Librarian action figures, Archie's would be the type of place that would carry <a href="http://www.markarayner.com/blog/archived/501">Professor Quippy's invention</a> - the Cliffy Siren (from <a href="http://www.markarayner.com">Mark Rayner</a>). And if Archie's had pets, you could probably get an interview with a <a href="http://www.bioteach.ubc.ca/quarterly/?p=214">nude mouse</a>, just as described in the <a href="http://www.bioteach.ubc.ca/quarterly">Science Creative Quarterly</a>.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/imgsrv.fcgi.0.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/320/imgsrv.fcgi.0.jpg" alt="" border="0" /></a>Luckily, they don't sell chemicals like Bis(Chloroethyl) NitrosoUrea, otherwise known as:<br /><br />BCNU.<br /><br />Because our tour is over, and it is time for me to be BCNU.<br /><br /><span style="font-style: italic;">If you speak English, be sure to say it out loud</span><br /><br />and I'll BCNU, too!<br /><br /><br /><br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#announce" rel="tag">Announcements</a></span><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/tangledbank" rel="tag">Tangled Bank</a>, <a href="http://technorati.com/tag/science" rel="tag">science</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com8tag:blogger.com,1999:blog-14323814.post-1144368957688385982006-04-06T16:56:00.000-07:002006-04-15T11:32:46.410-07:00Ethical issues in biotechnology: contrasting companies and classroomsAbout a decade ago, I took a fascinating summer course at the UW on bioethics. We read about the Nuremburg trials and the Geneva conventions. We learned about horizon problems and eugenics. And we discussed lots of challenging scenarios with genetic testing, autonomy, family relationships, and the problems faced by people seeking to have children, trying to get insurance, or looking for a job.<br /><br />So naturally, when I started a biotechnology course for non-science majors (Biotechnology and Society) at our community college, I used many of those examples. The class had a grand time discussing all those interesting things. <span style="font-style: italic;">And they all had opinions!</span> We debated the merits of labeling GMO food, animal testing, genetic tests and all sorts of fun topics. We had a great time during the OJ trial, studying good and bad DNA fingerprinting data and the chain of custody. And considering all the vegetarians in our class, our talks on making cheese were especially enjoyable. Since many of our vegan students were also anti-GMO, it was truly enlightening for them learn about the GMO <span style="font-style: italic;">E. coli </span>used to make rennin for vegetarian cheese.<br /><br />Later, when I became a member of <a href="http://www.bio-link.org">Bio-Link</a> in 1997, one of our goals was to address teaching ethical issues related to the biotech industry.<br /><br />I decided it was time to find out what they were so, I asked members of our industrial advisory board.<br /><br /><span style="font-style: italic;">What are the most important ethical issues in your company?<br /><br /></span>These were the sorts of answers I received:<span style="font-style: italic;"></span><br /><ul><li style="font-style: italic;">Make sure your students know that they need to write down every thing in their notebooks! Even – no, especially if it didn't work. I fire people for not recording negative results!<br /></li><br /><li style="font-style: italic;">They need to take good notes and understand what they're doing. I had to testify in court, in a patent dispute, about experiments that I did many years ago as a technician.</li><br /><li style="font-style: italic;">They need to know that telling the truth is critical!</li><br /><li style="font-style: italic;">They need to know that we work with animals, people have taken shots at our building, and sometimes I've had to walk around protestors to get to work. If they have problems with animal research they should do something else.</li><br /><li style="font-style: italic;">Make sure they know that experiments cost money!</li></ul>I listened and modified my seminar course for biotech majors to better align with industry concerns. We had speakers talk about patent disputes, interpreting data, and animal research. We had speakers from the FDA talk about their role in making sure that biotech products are safe (<span style="font-style: italic;">although, I guess you want to <a href="http://seattletimes.nwsource.com/html/health/2002913893_benzene06.html">stay away from diet pop</a></span>).<br /><br />Perhaps our biotech program was a bit unusual, though, because from what I read, biotech instructors spend more time on interesting controversial topics and miss the topics that concern biotech companies.<br /><br />This gap can be seen very clearly when comparing what teachers say they teach (<span style="font-style: italic;">genetic testing, euthanasia, cloning, stem cell research, GMO foods</span>) with the top ethical topics concerning companies. According to Finegold and Moser <a href="#ethics">(1)</a>, in the March issue of Nature Biotechnology, the top ethical concerns of companies were these:<br /><ol><li>Employee behavior</li><li>Conduct of clinical trials</li><li>Sales practices</li><li>How to market products</li><li>Corporate governance</li><li>Regulatory strategy</li><li>Who to partner with</li><li>What research to conduct</li><li>What products to develop</li><li>Accounting practices</li><li>Company mission</li><li>Where to do business</li><li>Product pricing</li></ol><br />We don't do clinical trials, but I'd say this list is pretty much correct, given my limited company experience.<br /><br />Which raises an interesting point. <br /><br />Could it be that biotech instructors are biased towards picking more <span style="font-style: italic;">interesting</span> topics? <span style="font-style: italic;">Few things could be worse than lecturing on accounting issues to biotech students.</span><br /><br />Or perhaps this list is different from the standard garden-variety set of classroom biotech issues because some of the ethical stands that people might take should discourage them from working in companies that engage in those activities in the first place.<br /><br /><span style="font-style: italic;">Against animal testing?</span> Forget working in a biotech company. Almost all of them rely on animal tests somewhere down the road.<br /><br /><span style="font-style: italic;">Against GMOs?</span> That rules out any agbiotech companies, plus several other biotech companies that might be doing research to express therapeutic proteins in tobacco or corn.<br /><br /><span style="font-style: italic;">Have a problem with stem cells?</span> Many biotech companies that make or do research on developing therapeutic drugs are interested in this technology. If they're not doing this work in the U.S. they might be outsourcing this work to countries with a more enlightened view.<br /><br /><span style="font-style: italic;">Against cloning?</span> The whole industry, just about, is based on cloning something - either DNA, cells, or bigger things.<br /><br /><span style="font-style: italic;">Euthanasia</span>? Dead issue. (<span style="font-style: italic;">oh sorry! I just couldn't help it!</span>) Rest in peace, <span style="font-style: italic;">we're</span> not planning a product line around this one.<br /><br />Hmmm, on second thought, maybe the classroom topics <span style="font-style: italic;">are</span> on target after all. Could the answer be that biotech instructors want to help individuals avoid a rude shock by thinking about <span style="font-style: italic;">where</span> they want to work and why</span>, <span style="font-style: italic;">before</span> they apply for a job?<br /><br /><a name="ethics">1.</a> David Finegold & Allison Mose. 2006. <a href="http://www.nature.com/nbt/journal/v24/n3/full/nbt0306-285.html">Ethical decision-making in bioscience firms</a>. Nature Biotechnology 24:285 - 290.<br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#education" rel="tag">Education</a></span><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/biotechnology" rel="tag">biotechnology</a>,<br /><a href="http://technorati.com/tag/teaching-carnival" rel="tag">teaching-carnival</a><br /><a href="http://technorati.com/tag/education" rel="tag">education</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com1tag:blogger.com,1999:blog-14323814.post-1144168287152034142006-04-04T09:18:00.000-07:002006-04-04T09:43:27.556-07:00Tangled Bank is coming April 12th!Hey there aspiring science writers!<br /><br />Warm up your typing fingers and get to work 'cause the very famous Tangled Bank will be hosted here on April 12th.<br /><br />Your assignment is to send essays, reviews, and interesting things for me to post and the rest of the world to chew on and puzzle about.<br /><br />Weird science entries are especially welcome. : P<br /><br />Send your submissions to: sandy at geospiza.com<br /><br />or to: host at tangledbank.net<br /><br />If you'd like to see past issues of Tangled Bank, simply click the image below to go check out the archives:<br /><br /><div style="text-align: center;"><a href="http://tangledbank.net/" title="The Tangled Bank"><img src="http://pharyngula.org/images/tbbadge.gif" alt="The Tangled Bank" height="31" width="88" /></a><br /></div><br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#announce" rel="tag">Announcements</a></span><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/tangledbank" rel="tag">Tangled Bank</a>, <a href="http://technorati.com/tag/science" rel="tag">science</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1143649012541036752006-03-29T07:51:00.000-08:002006-03-29T08:34:36.300-08:00Happy Sun-Earth Day!<div style="text-align: center;"><img src="http://sunearthday.nasa.gov/2006/images/gal_010.jpg" style="width: 250px; height: 160px;" marginwidth="10" marginheight="10" frameborder="0" scrolling="no" align="middle" /><br />photo from <a href="http://sunearthday.nasa.gov/2006/multimedia/gallery.php">NASA's image gallery</a>.<br /></div><br />I guess there was a live webcast from Turkey this morning (2:00 am PST) of a total solar eclipse. Needless to say, I missed it due an earlier appointment with my pillow.<br /><br />But it doesn't matter. You can satisfy any urge to see an eclipse over the web at <a href="http://sunearthday.nasa.gov/2006/multimedia/video.php">NASA's video gallery</a>. There are 5 short videos of past eclipses that are lots of fun and even one of my favorite technologies, podcasts! I haven't listened to any yet, hopefully they'll be as good as the <a href="http://stardate.org/">Stardate radio shows on NPR</a>.<br /><br />The video gallery includes animations that describe what's happening during an eclipse. Personally, I still like the old fashioned method for teaching these ideas. Outside of seeing an eclipse in person or watching the eclipse videos, nothing beats making an eclipse with a flashlight and a couple of oranges.<br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#resources" rel="tag">Web resources</a></span><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/astronomy" rel="tag">astronomy</a>, <a href="http://technorati.com/tag/eclipse" rel="tag">eclipse</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1143252763385598382006-03-24T17:40:00.000-08:002006-11-10T09:04:55.760-08:00Sugar, Sugar ...As of March 24th, over 186 people have tested positive for the avian flu virus (H5N1) and 105 are dead (<a href="#who">1</a>).<br /><br />This is a <span style="font-style: italic;">nasty</span> kind of flu.<br /><br />Luckily, most of the cases, so far, have been in our avian friends and their human companions. Health professionals all over the world, though, are warily watching web sites and looking for signs that people are catching flu from other people. Everyone wants to know the point when it's no longer strictly for the birds.<br /><br />But for the moment, we're okay, it seems like the avian flu doesn't spread easily from one human to another.<br /><br /><span style="font-style: italic;">And now we know why.</span><br /><br />Two reports this week, in Nature from Shinya, et. al.(<a href="#shinya">2</a>), and in Science from van Niel, et. al.(<a href="#van">3</a>) provide the answer.<br /><br />Avian flu, it seems, likes to stick to a <span style="font-style: italic;">certain kind</span> of sugar. That modified sugar, is a sialic acid with an alpha 2,3 link to galactose, and is joined through other sugar residues to the surface of special kinds of cells. At one time, flu researchers didn't think humans had these specific kinds of cell-surface sugars. But both of research groups found extra-special sugar coating on the surface of cells, deep in the lungs, and confirmed that these were the cells that got infected.<br /><br />Van Reil and colleagues found this result by mixing inactivated viral particles with tissue samples. They used fluorescent antibodies to see where the virus stuck and which kinds of cells it liked.<br /><br />Shinya, et. al. stained infected tissues with lectins to see what kinds of sugars could be found on different cells. They also stained infected tissues (epithelial and alveolar) to look for viral particles.<br /><br />Since the cells that get infected are located deep in the lungs, any new viral particles produced through an infection have to travel a long distance in order to get out of the mouth and infect someone new. This would make it harder for the virus to infect a new human because it doesn't escape the body through a simple cough or casual sneeze.<br /><br /><span style="font-weight: bold;">How is this different from the current human flu? </span><br /><br />The influenza strains that are doing most of the damage, in humans <a href="http://www.cdc.gov/flu/weekly">this year</a>, bind to a different kind of sugar than the avian strain. The human flu sticks to a sugar with an alpha 2,6 link to galactose; unfortunately for us, this sugar is found on cells in the nose and upper respiratory tract. This makes the human flu more infectious (for us) since it can travel long distances with a good strong sneeze.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/HA_cell.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/320/HA_cell.jpg" alt="" border="0" /></a><br /><br />Click the drawing to make it bigger. <span style="font-style: italic;"> But be warned, I took some liberties here. Influenza is usually drawn like it comes from outer space. Typical images show lots of spikes to represent the hemagglutinin and neuraminidase molecules on the surface of the particle. Also - the cell and the virus are <span style="font-style: italic;">not</span> drawn to scale.</span><br /><br /><span style="font-weight: bold;">What does this mean? Are we safe?</span><br /><br />No one knows. Some experiments earlier this month, by Stevens, et. al.(<a href="stevens">4</a>) found that it only took two mutations, in the right positions, to change the specificity of a hemagglutinin from one kind of sugar to another. No one knows how many mutations would be needed to change the specificity of the H5 hemagglutinin. Neither do we know much about the probability that this will happen (although I'm sure this is something that <span style="font-style: italic;">could</span> and <span style="font-style: italic;">should</span> be examined by mathematical modeling).<br /><br />It <span style="font-style: italic;">could</span> happen.<br /><br /><br /><span style="font-weight: bold;">References</span>:<br /><br /><name="who">1. World Health Organization. <a href="http://www.who.int/csr/disease/avian_influenza/country/cases_table_2006_03_24/en/index.html">WHO Cumulative Number of Confirmed Human Cases of Avian Influenza A/(H5N1) Reported to WHO</a>. (www.who.int). (accessed March 24, 2006).<br /><br /><name="shinya">2. Shinya K, Ebina M, Yamada S, Ono M, Kasai N, Kawaoka Y. 2006. Avian flu: influenza virus receptors in the human airway. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16554799&query_hl=24&itool=pubmed_docsum" rev="review">Nature. Mar 23;440(7083):435-6.</a><br /><br /><name="van">3. van Riel, D., Munster, V., de Wit, E., Rimmelzwaan, G., Fouchier, R., Osterhaus, E., and T. Kuiken. 2006. H5N1 Virus Attachment to Lower Respiratory Tract. Sciencexpress. <a href="http://www.sciencemag.org/cgi/content/abstract/1125548v1" rev="review">www.sciencexpress.org</a><br /><br /><name="stevens">4. Stevens J, Blixt O, Tumpey TM, Taubenberger JK, Paulson JC, Wilson IA. 2006. Structure and Receptor Specificity of the Hemagglutinin from an H5N1 Influenza Virus. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16543414&query_hl=21&itool=pubmed_docsum" rev="review">Science. Mar 20; [Epub ahead of print] </a><br /></name="stevens"></name="van"></name="shinya"></name="who"><br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#microbes" rel="tag">Microbes</a></span><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/virus" rel="tag">virus</a>, <a href="http://technorati.com/tag/avian+infuenza" rel="tag">avian influenza</a>, <a href="http://technorati.com/tag/bird+flu" rel="tag">bird flu</a>, <a href="http://technorati.com/tag/influenza" rel="tag">influenza</a></span></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com6tag:blogger.com,1999:blog-14323814.post-1143126017589400062006-03-23T06:58:00.000-08:002006-03-23T07:01:51.476-08:00Look at the wee animalcules!A new <a href="http://sciencepolitics.blogspot.com/2006/03/animalcules-volume-1-issue-4.html">Animalcules has been posted</a>. This week's issue contains stories on Plasmodium, papilloma virus, antibiotics, influenza, and other interesting bits.<br /><br />Stop by and take a look. And, consider submitting a story to one of the next issues. It's a low pressure way to share subjects that you enjoy.<br /><br />Read away and wash those hands!<div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1142964395218929402006-03-21T09:58:00.000-08:002006-03-21T10:13:51.950-08:00Sequencing a Genome: the video<span style="font-style: italic;">Have you ever wondered how people actually go about sequencing a genome? </span><br /><br />If they're sequencing a chicken genome, do they raise chickens in the lab and get DNA from the eggs? Does the DNA sequence come out in one piece? Why is there so much talk about computers? What are Phred, Phrap, and Consed? What is the Golden Path?<br /><br /><span style="font-weight: bold;">Wonder no more!</span><br /><br />You too, can take a <a href="http://www.nslc.wustl.edu/elgin/genomics/tour/html/genome_video.htm">virtual tour of the Washington University Genome Center</a>.<br /><br />I found this really excellent series of short videos that follows two genetics students, Libby and Bryce, as they meet on the bus to the Genome Center and learn about all the steps involved in sequencing a genome.<br /><br />A kindly tour guide takes Libby and Bryce through an amazing number of core labs, where they see gallons of media getting made. Among other things, they watch robots pick colonies of bacteria and inoculate broth. They see capillary tubes transport sequencing reactions into genetic analyzers and they see lots of people sitting in front of computers. All the steps are presented nicely and there a number of short animations to help visualize concepts such as growing <span style="font-style: italic;">E. coli</span> that contain BACS (Bacterial Artificial Chromosomes), restriction mapping, and PCR.<br /><br />Not only are these videos helpful for students who want to learn about biotechnology, these videos are helpful for bioinformatics groups and software companies like ours. Although some of us grew up sequencing DNA, a large fraction of the programmers and software engineers at Geospiza, did not. We routinely send our development team on field trips to a local genome center so they can learn what technicians do. Now, we can refer developers to the genome video to see where the samples go and learn how people work with all those robots.<br /><br />I like this video, too, because it shows scientific careers that do not require a Ph.D. All too often, people think the <span style="font-style: italic;">only</span> jobs in science involve heading up a laboratory, and they forget that industrial-scale science requires many different kinds of abilities and offers several different opportunities. In fact, a large number of the people working in facilities like genome centers have bachelor's degrees or 2-year degrees from community college biotechnology programs.<br /><br />Even if you've done some sequencing yourself, it's still interesting to see how the Wash. U. genome center has turned DNA sequencing into an industrial scale process.<br /><br /><span style="font-style: italic;">I, for one, never knew that so many genome technicians wore baseball caps at work.<br /></span><br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#resources" rel="tag">Web resources</a></span><br /><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/biotechnology" rel="tag">biotechnology</a>, <a href="http://technorati.com/tag/genomics" rel="tag">genomics</a></span>, <a href="http://technorati.com/tag/DNA_sequencing" rel="tag">DNA sequencing</a></span><br /></p><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0tag:blogger.com,1999:blog-14323814.post-1142529976447735452006-03-16T09:04:00.000-08:002006-03-29T10:47:45.840-08:00When Mt. St. Helens moves her bowels ...<a href="http://www.2theadvocate.com/news/suburban/2440071.html">brown water flows out of faucets in Arkansas</a>.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/7482/1292/1600/08Aug.0.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="http://photos1.blogger.com/blogger/7482/1292/320/08Aug.0.jpg" alt="" border="0" /></a><span style="color: rgb(0, 0, 0);">A simple little earthquake on March 7th, 2006, and 22 hours later, there were calls about brown water in the Feliciana Parish.</span><br /><blockquote style="color: rgb(102, 102, 102);"><br /><br /><br />“People don’t want to believe me when I say an earthquake caused their brown water, but it’s true,” John Hashagen said.</blockquote><blockquote><span style="color: rgb(102, 102, 102);">Hashagen said he began looking into the possible effects of seismic waves on the Laurel Hill wells after reading an article in WaterWorld, a magazine for the municipal water industry, on the effects the March 1964 Alaskan earthquake had on water systems across the country.</span><br /></blockquote><span style="color: rgb(0, 0, 0);">Not only did the utilities chief uncover a possible connection between west coast earthquakes and discolored water, he found a way to use that information.</span><br /><br /><span style="color: rgb(0, 0, 0);">Apparently there are only two wells in the area that are sensitive to seismic activity.</span><br /><blockquote style="color: rgb(102, 102, 102);">Hashagen said he and water district employees can prevent the wells from pumping the discolored water if they learn about an earthquake hundreds or thousands of miles away in time to temporarily shut down the wells.</blockquote><span style="color: rgb(0, 0, 0);">So, he signed up for earthquake alerts, via e-mail, from the U.S. Geological Survey. Whenever a quake occurs that measures over 5.0 on the Richter scale, he gets the message and shuts down the wells.</span><br /><br /><span style="color: rgb(0, 0, 0);">The brown water happened on March 8th because the March 7th earthquake was too small to trigger the e-mail alert (only 3.1 on the Richter scale).</span><br /><br /><span style="color: rgb(0, 0, 0);">I think if Dave Barry were a science teacher, this is the kind of stuff he would love.</span><br /><br />Thanks are due to the <a href="http://wsta.net/html/">WSTA</a> for sharing the fun!<br /><br /><br /><span style="font-size:85%;"><span style="font-weight: bold;">Subject</span>: <a href="http://digitalbio.blogspot.com/2006/02/subjects.html#silly" rel="tag">Weird Science</a></span><br /><p><span style="font-size:85%;">technorati tags: <a href="http://technorati.com/tag/geology" rel="tag">geology</a>, <a href="http://technorati.com/tag/earthquake" rel="tag">earthquake</a></span></p><br /><span style="color: rgb(0, 153, 0);">3/39/2006 </span><span style="color: rgb(0, 153, 0);">Update: <span style="color: rgb(0, 0, 0);">It should be noted that the geological jury is not convinced that Mr. Hashagen is correct. <span style="font-style: italic;">He might</span> be right, Mt. St. Helen's movements <span style="font-style: italic;">might</span> truly be connected with the funny colored water, but a bit more science needs to be done before geologists will believe that the connection is real. <br /><br />How would <span style="font-style: italic;">you</span> test this? What sorts of data do <span style="font-style: italic;">you</span> think need to be collected and analyzed in order to test Mr. Hashagen's hypothesis?<br /></span></span><div class="blogger-post-footer"><script language="javascript"><!--
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<script type="text/javascript" src="http://promo.cafepress.com/ad.js"></script></div>Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.com0