tag:blogger.com,1999:blog-5024201174581371822024-03-18T17:05:00.680-04:00The Obligate ScientistPaulhttp://www.blogger.com/profile/13292217467465413191noreply@blogger.comBlogger314125tag:blogger.com,1999:blog-502420117458137182.post-41711701693646997852014-02-04T15:57:00.000-05:002014-02-04T15:57:45.748-05:00Evolution vs Religion, tonight at 7pm!Greetings! It's been a VERY long time since I've posted to this blog, but it's nice to see posts are still getting read from time to time. Yay, google! <br />
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So, what has drawn me out of my blogging hiatus and compelled me to post something? Why, <b>Bill Nye the Science Guy</b>, of course!<br />
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You knew he was debating Ken Ham at the <a href="http://ncse.com/taking-action/aig-creation-museum" rel="nofollow" target="_blank">Creation Museum</a> tonight, right? And that you could watch the debate live online?<br />
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<a href="http://media.npr.org/assets/img/2014/02/04/debate042way-65adeddb11ca3a0c8c9482384218de57694a0362.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://media.npr.org/assets/img/2014/02/04/debate042way-65adeddb11ca3a0c8c9482384218de57694a0362.jpg" height="297" width="400" /></a></div>
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For more details, hop on over <a href="http://www.npr.org/blogs/thetwo-way/2014/02/04/271383099/creationism-vs-evolution-the-debate-is-live-tonight" rel="nofollow" target="_blank">to this post at NPR</a>, and/or tune in <a href="http://www.youtube.com/watch?v=z6kgvhG3AkI&feature=share" rel="nofollow" target="_blank">here</a> to catch the debate live. If you've never heard of the Creation Museum (technically, it's a Christian ministry) check out the link on the sidebar.Paulhttp://www.blogger.com/profile/13292217467465413191noreply@blogger.com63tag:blogger.com,1999:blog-502420117458137182.post-67891343537644712882011-05-20T13:00:00.000-04:002011-05-20T13:00:00.987-04:00The end of the world... and I feel fine!The end is very nigh. May 21<sup>st</sup> is upon us and as you've probably already heard <a href="http://www.denverpost.com/news/ci_18070758" target="_blank">in the news</a> or <a href="http://www.dailymail.co.uk/news/article-1363837/Doomsday-campers-Project-Caravan-say-world-end-May-21.html" target="_blank">elsewhere</a> that means it's time for <strike>the rapture</strike> The Rapture! <br />
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<center><iframe allowfullscreen="" frameborder="0" height="405" src="http://www.youtube.com/embed/Z0GFRcFm-aY" width="500"></iframe></center><br />
Predictions like these have <a href="http://www.google.com/search?q=history+of+end+of+the+world+predictions+failed&hl=en&safe=off&prmd=ivns&tbs=tl:1&tbo=u&ei=6RTRTaLqEYLcgQfPmo3BDA&sa=X&oi=timeline_result&ct=title&resnum=11&sqi=2&ved=0CGQQ5wIwCg#q=history+of+end+of+the+world+predictions+failed&hl=en&safe=off&sa=X&tbs=tl:1,tl_num:100&prmd=ivns&ei=XhXRTaaDDdDqgQer6NG-DA&ved=0CHcQywEoBA&bav=on.2,or.r_gc.r_pw.&fp=c4b94ef403c105f7" target="_blank">a long track record of being correct</a>, so best of luck to you come judgement and until then be vigilant for unmanned cars whizzing down the road, anyone <a href="http://www.facebook.com/event.php?eid=198820600156074" target="_blank">flying up into the air</a>, or any <a href="http://www.biblegateway.com/passage/?search=Revelation+4&version=NIV">six-winged creatures covered in eyeballs</a>. If you happen to see any of these things, do leave a comment below! <br />
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<b>PS</b>: if you're still here on the 22<sup>nd</sup> consider opening your home to your ex-neighbors' <a href="http://eternal-earthbound-pets.com/" target="_blank">earth-bound pets</a>!Paulhttp://www.blogger.com/profile/13292217467465413191noreply@blogger.com21tag:blogger.com,1999:blog-502420117458137182.post-62994153995126179692011-05-08T13:57:00.000-04:002011-05-08T13:57:50.454-04:00Happy Mother's Day!!If you were planning on sending your mom a nerdy video, make sure you don't go overboard on the nerdiness -- unless you're mom's a super nerd, then go for it! For example, this is an excellent choice<br />
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<div style="text-align: center;"><object height="340" width="560"><param name="movie" value="http://www.youtube.com/v/osWuWjbeO-Y&hl=en_US&fs=1&color1=0x2b405b&color2=0x6b8ab6"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/osWuWjbeO-Y&hl=en_US&fs=1&color1=0x2b405b&color2=0x6b8ab6" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="560" height="340"></embed></object></div><br />
while this one -- although both nerdy and relevant to motherhood -- might not quite be the best choice...<br />
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<div style="text-align: center;"><object height="340" width="560"><param name="movie" value="http://www.youtube.com/v/nLmg4wSHdxQ&hl=en_US&fs=1&color1=0x2b405b&color2=0x6b8ab6"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/nLmg4wSHdxQ&hl=en_US&fs=1&color1=0x2b405b&color2=0x6b8ab6" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="560" height="340"></embed></object></div>Unknownnoreply@blogger.com67tag:blogger.com,1999:blog-502420117458137182.post-80747851508855310372011-03-14T23:15:00.000-04:002011-03-14T23:15:00.542-04:00Happy π Day!!! No, wait, scratch that...Lets face it -- π sucks. Not pie, pie is genuinely awesome and so is the fact that "pie" sounds like "π", so we can have fun with things <a href="http://theobligatescientist.blogspot.com/2010/03/how-to-make-pi-using-r.html" target="_blank" title="How to make pi... using R">like this</a>. But seriously... π? It's <b>totally</b> off by a factor of 2! <br />
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<div style="text-align: center;"><iframe allowfullscreen="" frameborder="0" height="443" src="http://www.youtube.com/embed/jG7vhMMXagQ" title="YouTube video player" width="550"></iframe></div><br />
For more on τ day, check out the Tau Manifest at <a href="http://tauday.com/" target="_blank">http://tauday.com/</a> and of course <a href="http://halftauday.com/" target="_blank">http://halftauday.com/</a> if you're still a fan of π.Unknownnoreply@blogger.com32tag:blogger.com,1999:blog-502420117458137182.post-61743001281866728722011-03-11T16:54:00.002-05:002011-03-14T23:28:25.899-04:00A request: I need your comments!I need your help! A reader recently tried to leave a comment on this blog, and despite the fact that I received an email notifying me of the new comment, it never appeared on the blog post...<br />
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<div class="separator" style="clear: both; text-align: center;"><img border="0" height="244" src="http://2.bp.blogspot.com/_Q2P0_syupDE/TN3BC4H_7eI/AAAAAAAABDk/ppenRC-2_AU/s320/kid-confused-about-buying-a-new-home-300x244.jpg" width="300" /></div><div style="text-align: center;"><b>Figure 1</b>: I'm about this confused, if not more.</div><br />
So, if you can spare a few moments, please head over to <a href="http://theobligatescientist.blogspot.com/2010/10/home-birth-death-toll-rising-in.html" target="_blank">this post</a> (and/or leave a comment below) and let me know the following:<br />
<blockquote>Operating System:<br />
Browser:<br />
Comment type (Anonymous, Google, etc.):<br />
Link to your favorite recipe<sup>**</sup>:</blockquote><span style="font-size: x-small;"><i>** Totally unrelated, optional, but potentially delicious and therefore worth requesting. ;)</i></span><br />
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If the comment submission process seemed to work but your comment doesn't show up on the post, please drop me an email letting me know what happened.<br />
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Thanks! ~ PaulPaulhttp://www.blogger.com/profile/13292217467465413191noreply@blogger.com187tag:blogger.com,1999:blog-502420117458137182.post-28369196451440749352011-03-03T01:26:00.000-05:002011-03-03T01:26:00.262-05:00Evolution is a pain in the ass, especially for herpetologists and ornithologistsThe reason? Imagine you have a kid, and your neighbor has 2 kids, then you both find out that really, one of their kids is sort of... yours. (-- awkward pause --) That's basically the problem <a href="http://xkcd.com/867/">here</a>:<br />
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<div class="separator" style="clear: both; text-align: center;"><a href="http://xkcd.com/867/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img border="0" height="280" src="http://imgs.xkcd.com/comics/herpetology.png" title="Birds are Aves, which is part of the clade Theropoda, which is in Saurischia, which is in Dinosauria. Those birds outside our windows are dinosaurs. We can clear out the rest of our brains because we now have the best fact." width="640" /></a></div><br />
Herpetology is the study of reptiles and amphibians, however unraveling the evolutionary history of these two groups (along with birds) has shown us that birds are actually nested in among reptiles. <br />
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Now, to be fair, I think the comic has it wrong: I mean, shouldn't this justify lumping ornithology in a sub-discipline of herpetology?Unknownnoreply@blogger.com25tag:blogger.com,1999:blog-502420117458137182.post-73833737006770622072011-03-02T14:28:00.000-05:002011-03-02T14:28:51.753-05:00Thesis writing...... has pulled me away from blogging the past couple of months. BUT, I'll hopefully be done and back to a regular posting schedule later this spring!<br />
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<div class="separator" style="clear: both; text-align: center;"><a href="https://lh4.googleusercontent.com/-f4fa3zTbSp8/SrmQSVCFzZI/AAAAAAAAEM8/z4KfRYEK0F0/s1600/snapper_sept2008.jpg" target="_blank" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="110" src="https://lh4.googleusercontent.com/-f4fa3zTbSp8/SrmQSVCFzZI/AAAAAAAAEM8/z4KfRYEK0F0/s320/snapper_sept2008.jpg" width="320" /></a></div><div style="text-align: center;"><span style="font-size: x-small;"><b>Figure 1</b>: Mascot for my recent rate of new blog posts.</span></div><br />
In the meantime, you should check out <a href="http://www.r-bloggers.com/" target="_blank">R-bloggers.com</a> and "like" <a href="http://www.facebook.com/pages/R-bloggers/191414254890" target="_blank">their facebook page</a> to get regular updates on your news feed.Unknownnoreply@blogger.com223tag:blogger.com,1999:blog-502420117458137182.post-83312284879315216072011-01-17T14:25:00.003-05:002011-01-17T14:32:11.243-05:00Shame on you, R... again! (But not really...)Remember how a few months ago <a href="http://theobligatescientist.blogspot.com/2009/10/shame-on-you-r.html" target="_blank">I lamented</a> the fact that the <span style="font-family: "Courier New",Courier,monospace;">round()</span> function in R uses a non-standard rule for rounding to the nearest integer? Instead of rounding k+0.5 to k+1 (k being an integer) R rounds to whichever integer k or k+1 is even. Well <a href="http://4dpiecharts.com/2011/01/16/when-1-x-x/" target="_blank">here's another example</a> of R offending our mathematical sensibilities... R seems to think that even though<br />
<div style="text-align: center;"><span style="font-family: "Courier New",Courier,monospace;">1 * Inf = Inf</span></div>somehow it can get away with telling us that<br />
<div style="text-align: center;"><span style="font-family: "Courier New",Courier,monospace;">1 * (Inf + 0<b>i</b>) = Inf + NaN</span><b><span style="font-family: "Courier New",Courier,monospace;">i</span><span style="font-family: "Courier New",Courier,monospace;">?</span></b></div><br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://scienceblogs.com/ethicsandscience/upload/2006/09/sad_puppy.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img border="0" height="239" src="http://scienceblogs.com/ethicsandscience/upload/2006/09/sad_puppy.jpg" title="OK, not really... keep reading!" width="320" /></a></div><br />
"Gasp!" I know, insane, right? What's going on here? Whatever happened to "anything times one is equal to that same number"? Granted, infinity isn't <i>really</i> a number so sometimes we can't assign a value to an expression like <span style="font-family: "Courier New",Courier,monospace;">Inf*0</span>, but deep down inside I can't shake the feeling that <span style="font-family: "Courier New",Courier,monospace;">1 * Inf</span> really should be <span style="font-family: "Courier New",Courier,monospace;">Inf</span>! <br />
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It turns out that R and I are both right - we're just making different assumptions about how we interpret all these <span style="font-family: "Courier New",Courier,monospace;">1</span>s, <span style="font-family: "Courier New",Courier,monospace;">0</span>s and <span style="font-family: "Courier New",Courier,monospace;">Inf</span>s in these two statements. Let me explain...<br />
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Despite using sound, puppy-approved logic in this case, R gives the offending result because of how it implements everyone's favorite section in Calculus class: computing limits. To understand why, take a closer look at how the multiplication is happening in each case above. The first case is hopefully straightforward. In the second case 1 is treated as a complex number instead of a scalar which gives <br />
<div style="text-align: center;"><span style="font-family: "Courier New",Courier,monospace;">1*(Inf+0<b>i</b>) = </span><span style="font-family: "Courier New",Courier,monospace;">(1+0<b>i</b>)*(Inf+0<b>i</b>) = </span></div><div style="text-align: center;"><span style="font-family: "Courier New",Courier,monospace;"> = </span><span style="font-family: "Courier New",Courier,monospace;">Inf + (0*Inf+0)<b>i</b> = Inf + NaN<b>i</b></span></div><br />
We could also throw in a third case and multiply these two complex numbers in the more natural context of polar coordinates. Writing each in terms of their <i>modulus</i> <span style="font-family: "Courier New",Courier,monospace;">r</span> (distance from the origin) and <i>argument</i> <span style="font-family: "Courier New",Courier,monospace;">θ</span> (angle off of the positive real axis) instead of in terms of their real and imaginary parts, we have<br />
<div style="text-align: center;"><span style="font-family: "Courier New",Courier,monospace;"> 1*(Inf+0<b>i</b>) = </span><span style="font-family: "Courier New",Courier,monospace;">(1+0i)*(Inf+0<b>i</b>) </span></div><div style="text-align: center;"><span style="font-family: "Courier New",Courier,monospace;"> = 1exp(i</span><span style="font-family: "Courier New",Courier,monospace;">0)* Inf exp(</span><b><span style="font-family: "Courier New",Courier,monospace;">i</span></b><span style="font-family: "Courier New",Courier,monospace;">0)</span></div><div style="text-align: center;"><span style="font-family: "Courier New",Courier,monospace;"> = (1*Inf) exp (<b>i</b>0)</span></div><div style="text-align: center;"><span style="font-family: "Courier New",Courier,monospace;"> = Inf exp(<b>i</b>0)</span></div><div style="text-align: center;"><span style="font-family: "Courier New",Courier,monospace;">= Inf + 0<b>i</b></span></div>Whew! So what's "wrong" with multiplying things in <span style="font-family: "Courier New",Courier,monospace;">x+y<b>i</b></span> form??<br />
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R recognizes that any computations involving infinity really require the algebra of limits, and acts appropriately (albeit conservatively) to evaluate such expressions. This discord then comes from what R assumes is <b>the result of taking some limit</b> and <b>what is to be treated as a constant</b>. Unless you've taught a calculus class recently some explanation might be in order. <br />
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In general, expressions involving infinity are treated as limits where some unspecified variable is going to infinity: For example, statements like <span style="font-family: "Courier New",Courier,monospace;">Inf*0</span> can't be assigned a value because in it's most general interpretation we're asking "What is the limit of the product of <span style="font-family: "Courier New",Courier,monospace;">x*y</span> as <span style="font-family: "Courier New",Courier,monospace;">x→Inf</span> and <span style="font-family: "Courier New",Courier,monospace;">y→0</span>?" Here, whether <span style="font-family: "Courier New",Courier,monospace;">y</span> goes to <span style="font-family: "Courier New",Courier,monospace;">0</span> from above (e.g. <span style="font-family: "Courier New",Courier,monospace;">y=1/x</span>) or below (<span style="font-family: "Courier New",Courier,monospace;">y=-1/x</span>) or neither will determine where the limit of the product goes to zero, some non-zero number, plus or minus infinity, or will have no limit at all. (Open any calculus text to the sections on limits for examples leading to these different outcomes). Note this example does have an answer if <span style="font-family: "Courier New",Courier,monospace;">y</span> is always assumed to be 0, since it's always the case that <span style="font-family: "Courier New",Courier,monospace;">x*0=0</span>.<br />
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That means that, depending on how we interepret the zero, our example might equal either<br />
<div style="text-align: center;"><span style="font-family: "Courier New",Courier,monospace;"> Inf*0=NaN</span></div><div style="text-align: center;"><span style="font-family: "Courier New",Courier,monospace;">Inf*0=0</span><span style="font-family: "Courier New",Courier,monospace;"> </span></div>This is exactly what's going on above.<br />
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Returning to the two statements at the top of this post, we can now understand why R gives these two different answers. By making the zero implicit vs. explicit R treats these expressions differently. R interprets <span style="font-family: "Courier New",Courier,monospace;">Inf</span> as "the limit of <span style="font-family: "Courier New",Courier,monospace;">x + 0<b>i</b></span> as <span style="font-family: "Courier New",Courier,monospace;">x→Inf</span>," allowing for the result that <br />
<div style="text-align: center;"><span style="font-family: "Courier New",Courier,monospace;">1 * Inf = Inf</span></div>whereas in the second case R treats <span style="font-family: "Courier New",Courier,monospace;">Inf + 0<b>i</b></span><span style="font-family: inherit;"> </span>as "the limit of <span style="font-family: "Courier New",Courier,monospace;">x + y<b>i</b></span> as <span style="font-family: "Courier New",Courier,monospace;">x → Inf</span> and <span style="font-family: "Courier New",Courier,monospace;">y → 0</span>" which has no general answer and therefore gets assigned a value of <span style="font-family: "Courier New",Courier,monospace;">NaN</span>.<br />
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The take-home message: <b>as soon as there's an <span style="font-family: "Courier New",Courier,monospace;">Inf</span> in an expression, R proceeds assuming <i>everything</i> is a limit</b>, even though it might be clear to the user that some of those key 1s and 0s should be treated as constants.Unknownnoreply@blogger.com14tag:blogger.com,1999:blog-502420117458137182.post-47047789205542566222011-01-14T15:26:00.000-05:002011-01-14T15:26:36.827-05:00Data Visualization in R: Part... 0I haven't forgotten that <a href="http://theobligatescientist.blogspot.com/2010/12/data-visualization-200-years-of-health.html" target="_blank">I promised to do a series of posts on data visualization using R</a> - just a bit busy catching up after some excellent holiday R&R. Hopefully I'll get a post out soon!<br />
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In the mean time, check out <a href="http://www.r-bloggers.com/visualizing-the-haiti-earthquake-with-r/">these</a> <a href="http://www.r-bloggers.com/winners-of-mozilla-open-data-competition-announced/">two</a> posts from the <a href="http://www.r-bloggers.com/" target="_blank">R-bloggers</a> network.Unknownnoreply@blogger.com24tag:blogger.com,1999:blog-502420117458137182.post-39245767463497924532010-12-15T22:48:00.004-05:002010-12-15T23:13:57.644-05:00Data Visualization: 200 Years of Health and WealthThis video is super awesome! It's part of BBC 4's program <a href="http://www.bbc.co.uk/programmes/b00wgq0l" target="_blank">The Joy of Stats</a> and you can learn a little more about the data <a href="http://www.gapminder.org/data/" target="_blank">here</a> or play with it using <a href="http://www.gapminder.org/world/" target="_blank">this web app</a> on <a href="http://www.gapminder.org/" target="_blank">http://www.gapminder.org/</a>. Now don't you wish <i><b>you</b></i> could do that with data?<br />
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<div style="text-align: center;"><object height="362" width="600"><param name="movie" value="http://www.youtube.com/v/jbkSRLYSojo?fs=1&hl=en_US&color1=0x2b405b&color2=0x6b8ab6"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/jbkSRLYSojo?fs=1&hl=en_US&color1=0x2b405b&color2=0x6b8ab6" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="600" height="362"></embed></object></div><br />
The reason I wanted to share this video (beyond the fact that it's so amazingly awesome) is to let you in on a little secret... are you ready? Here it comes...<br />
<div style="text-align: center;"><blockquote><i>Data visualization is easy, and <b>anyone</b> with a computer can do it!</i></blockquote></div>Seriously, it is not that hard! <i><b>YOU</b></i> can make cool little wobbling bubble graphs just like in the video! Aren't you excited to learn how?! Yeah? Fantastic!<br />
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Now that you're all psyched to visualize some data, I should mention that I am being a bit misleading here... because it <i><b>does</b></i> require a bit of computer know-how, and <i>sometimes</i> (ok, <i>almost always</i>) takes a bit of tinkering with the data to find the best ways of boiling down to just the relevant information. But frankly, these things aren't all that hard to learn and aren't always necessary if we're just poking around to get a feel for the data, so none of these words of caution should give you much pause. Add to that the fact you can always hit up the internet for examples to <strike>download and use</strike> study and learn from and many of these obstacles are reduced to mere speed bumps. If you've got a computer, we can get it to plot some data.<br />
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</div><div class="separator" style="clear: both; text-align: center;"><a href="http://flowingdata.com/2010/12/14/10-best-data-visualization-projects-of-the-year-%E2%80%93-2010/" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img border="0" src="http://flowingdata.com/wp-content/uploads/2010/12/tourists-in-sf-575x374.png" /></a></div><div style="text-align: center;"><span style="font-size: x-small;">Figure 1. Tourist hot spots based on Flickr data. #1 of flowingdata's <a href="http://flowingdata.com/2010/12/14/10-best-data-visualization-projects-of-the-year-%E2%80%93-2010/" target="_blank">Top Ten Data Visualization Projects of 2010</a>.</span></div><br />
So here's the deal... there are some <a href="http://www.gapminder.org/data/" target="_blank">really cool data available</a> from <a href="http://www.gapminder.org/" target="_blank">http://www.gapminder.org/</a>, and I'm going to have a little free time these next few weeks in between birding trips, visiting family and friends, and doing thesis work. Assuming that free time stays free, I'm going to walk through an example or two of plotting some of this data in <a href="http://www.r-project.org/">R</a>. If you'd like to follow along, you'll need to <a href="http://theobligatescientist.blogspot.com/2010/04/software-for-science-math-r-and-maxima.html">download and install R</a> on your computer, and if you don't already have software that can open excel spreadsheets, you'll also want to install something (free) like <a href="http://www.openoffice.org/" target="_blank">OpenOffice</a>.<br />
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Sound good? Excellent! Feel free to share any questions or suggestions in the comments section below. Now hurry along and go <a href="http://www.r-project.org/" target="_blank">install R</a>! <img border="0" src="http://us.i1.yimg.com/us.yimg.com/i/mesg/emoticons7/1.gif" />Unknownnoreply@blogger.com45tag:blogger.com,1999:blog-502420117458137182.post-15255979069339445452010-12-13T14:55:00.000-05:002010-12-13T14:55:11.773-05:00Support Wildlife Conservation in OhioBuy an Ohio Wildlife Legacy stamp!<br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://www.dnr.state.oh.us/Portals/9/Images/diversity/OWLS/luggage-tag.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="257" src="http://www.dnr.state.oh.us/Portals/9/Images/diversity/OWLS/luggage-tag.jpg" width="320" /></a></div><br />
While hunters automatically contribute funds towards the conservation coffers each time they purchase a hunting licenses, wildlife watchers (like birders and herpers) and native plant aficionados <i>aren't</i> required to make such contributions when they go outside to enjoy their favorite organisms. The result? Less money for habitat and wildlife conservation.<br />
<br />
The Ohio Wildlife Legacy stamps are an attempt to fix this problem, by inviting all those non-hunters to contribute. With the holidays coming up, and at only $15 each, they make great gifts for that outdoorsy guy or gal on your gift list. Even for those who do hunt or fish, and already buy licenses (which I believe can't be purchased as a gift) the Wildlife Legacy stamp might still be a much appreciated gift.<br />
<br />
To purchase one (or more!), you can buy them online from the ODNR <a href="http://www.dnr.state.oh.us/Home/ExperienceWildlifeSubHomePage/ohiowildlifelegacystamp/buystamp/tabid/22506/Default.aspx" target="_blank">website</a>, the Columbus Audubon Society's <a href="http://columbusaudubon.org/" target="_blank">website</a>, or you can buy them in person at the nearest <a href="http://www.dnr.state.oh.us/Home/ContactUs/tabid/18270/Default.aspx" target="_blank">ODNR Wildlife District Office</a>.Unknownnoreply@blogger.com7tag:blogger.com,1999:blog-502420117458137182.post-38043125069107545232010-12-08T09:12:00.000-05:002010-12-08T09:12:24.299-05:00Knotty Doodles<center><object width="550" height="437"><param name="movie" value="http://www.youtube.com/v/heKK95DAKms?fs=1&hl=en_US&color1=0x2b405b&color2=0x6b8ab6"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/heKK95DAKms?fs=1&hl=en_US&color1=0x2b405b&color2=0x6b8ab6" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="550" height="437"></embed></object></center>Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-502420117458137182.post-76350950728105813062010-12-04T15:21:00.001-05:002010-12-04T15:35:33.773-05:00Fast and Sloppy Root Finding<i>Disclaimer: While the approach to root finding mentioned below is both slow and imprecise, it's also a cheap and incredibly handy approach when all you need to do is get "close enough". If you like <A HREF="http://www.r-project.org/" target="_blank">R</A> quick and dirty (hey now, get your mind out of the gutter...) this is totally the root finding method for you!</i> <br />
<br />
I just read a post on <a href="http://www.r-bloggers.com/root-finding/" target="_blank">Root Finding</a> (original <a href="http://ygc.cwsurf.de/2010/12/04/root-finding/" target="_blank">here</a>) by way of <a href="http://www.r-bloggers.com/about/" target="_blank">R-bloggers.com</a> which was timely given that only yesterday I'd needed to do some root finding in <a href="http://www.r-project.org/" target="_blank">R</a> to make a figure for a manuscript -- something like the following image.<br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://4.bp.blogspot.com/_COnkiDzcPPA/TPqfztOW81I/AAAAAAAAEr0/IJQLaKX7aLk/s1600/rootfinding.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img border="0" src="http://4.bp.blogspot.com/_COnkiDzcPPA/TPqfztOW81I/AAAAAAAAEr0/IJQLaKX7aLk/s1600/rootfinding.gif" /></a></div>The blog post prompted me to mention here how I did my root finding for two reasons:<br />
<ol><li><b>Precision</b> and <b>computation time</b> sometimes <b>don't matter</b> all that much; and</li>
<li>The way I did my root finding was <b>way easier</b> to implement than convergence-based methods described in the post above.</li>
</ol>So here's what I was aiming for, and how I implemented it in R.<br />
<br />
<b>The Task:</b> Suppose you're plotting two curves (say, <span style="font-family: "Courier New",Courier,monospace;">y=f(x)</span> and <span style="font-family: "Courier New",Courier,monospace;">y=g(x)</span>) and would like to indicate their intersection with an empty circle (i.e. <a href="http://www.harding.edu/fmccown/r/#misc" target="_blank"><span style="font-family: "Courier New",Courier,monospace;">pch=21</span></a>). In my case, the intersection of these two curves was equilibrium point for a dynamic model, and I wanted to indicate it as such.<br />
<br />
If you can find their intersection mathematically (i.e. set <span style="font-family: "Courier New",Courier,monospace;">f(x)=g(x)</span> and solve for <span style="font-family: "Courier New",Courier,monospace;">x</span>) then awesome -- do that if you can. But if for some reason you can't, and you know a single root exists in some interval <span style="font-family: "Courier New",Courier,monospace;">a≤x≤b</span>, you can find that root quickly using some straightforward vector tricks.<br />
<br />
<b>The Solution:</b> Lets use the example of finding the intersection of <span style="font-family: "Courier New",Courier,monospace;">f(x) = x/(1+x)</span> and <span style="font-family: "Courier New",Courier,monospace;">g(x) = (5-x)/5</span> over the interval <span style="font-family: "Courier New",Courier,monospace;">(0,5)</span>.<br />
<br />
<b>Step 1</b>: Define an x vector full of values between a and b. The smaller the step size (or, the longer the list) the better. <br />
<blockquote><span style="font-family: "Courier New",Courier,monospace;">> x = seq(0, 5, length=5000);</span></blockquote><b>Step 2</b>: Compute the square of the difference of your two functions over that interval using x. This is as simple as the line of code...<br />
<blockquote style="font-family: "Courier New",Courier,monospace;">> fgdiff = ( x/(1+x) - (5-x)/5 )^2;</blockquote><b>Step 3</b>: Using the which() function, we can pick out the index for the smallest value in our list of squared differences... Once we know this index (call it j) we know the intersection occurs at, or very near, the x value x[j], and we're basically done! <br />
<blockquote style="font-family: "Courier New",Courier,monospace;">> j = which(fgdiff==min(fgdiff))[1]; <br />
> j; x[j]; ## show the value of j, x[j] </blockquote>For a closer look at what's going on with that <span style="font-family: "Courier New",Courier,monospace;">which()</span> statement, check out the help for <span style="font-family: "Courier New",Courier,monospace;">which()</span> and following example. <br />
<blockquote style="font-family: "Courier New",Courier,monospace;">## A Closer look at the which(fgdiff==min(fgdiff))<br />
> ?which<br />
> which(c(F,F,T,T,F))<br />
[1] 3 4<br />
> which(c(F,F,T,T,F))[1]<br />
[1] 3<br />
> xample = c(5:1,2:5); xample<br />
[1] 5 4 3 2 1 2 3 4 5<br />
> min(xample)<br />
[1] 1<br />
> xample==min(xample)<br />
[1] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE<br />
> which(xample==min(xample))<br />
[1] 5<br />
> which(xample==min(xample))[1] <br />
[1] 5</blockquote><b>Step 4</b>: Since both functions are (approximately) equal at this x value, it only remains to decide whether you want to indicate the point of intersection using (x, f(x)) or (x, g(x)).<br />
<blockquote style="font-family: "Courier New",Courier,monospace;">> points(x[j], x[j]/(1+x[j]), pch=19, cex=2)</blockquote>All done! <br />
<br />
If you'd like to tinker with this example, here's the code to produce the image above.<a name='more'></a><blockquote><pre class="code">win.graph(5,4) ## Open a new window, 5in x 4in.
## Plot the two functions
curve(x/(1+x), from=0, to=5, lwd=3, ylab="f(x), g(x)",
ylim=c(0,1), cex.lab=1.5)
curve((5-x)/5, from=0, to=5, lwd=3, lty=2, add=T)
## Find their intersection the quick n' dirty way
x=seq(0,5,length=1000)
fgdiff = (x/(1+x) - (5-x)/5)^2;
j = which(fgdiff==min(fgdiff))[1]; # Only 1st, in case of 2 mins
j; x[j]
## Plot an empty circle at the intersection, and label curves.
points(x[j], x[j]/(1+x[j]), pch=21, col="black", bg="white", lwd=3, cex=1.7)
text(4.5, 0.65, expression(f(x)==frac(x,1+x)), cex=1)
text(3, 0.15, expression(g(x)==frac(5-x,5)), cex=1)
</pre></blockquote>Unknownnoreply@blogger.com8tag:blogger.com,1999:blog-502420117458137182.post-56811672590245714252010-11-27T13:17:00.001-05:002010-11-27T13:17:23.162-05:00New Rule for Science Journalism...Agreed!<br />
<br />
<br />
<center><a href="http://scienceblogs.com/pharyngula/2010/11/i_like_this_rule.php" target="_blank" title="Or make it a cover story..."><img src="http://scienceblogs.com/pharyngula/upload/2010/11/i_like_this_rule/scijournalism.jpeg" target="_blank" /></a></center><br />
<i>[Hat tip to <a href="http://scienceblogs.com/pharyngula/2010/11/i_like_this_rule.php" target="_blank">PZ Myers</a>]</i>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-502420117458137182.post-75987989590163824112010-11-25T09:46:00.008-05:002010-11-25T09:58:25.843-05:00Happy Turkey Day!<div class="separator" style="clear: both; text-align: center;"><a href="http://upload.wikimedia.org/wikipedia/commons/thumb/a/a3/Thanksgiving_Turkey.jpg/800px-Thanksgiving_Turkey.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;" target="_blank"><img border="0" height="150" src="http://upload.wikimedia.org/wikipedia/commons/thumb/a/a3/Thanksgiving_Turkey.jpg/800px-Thanksgiving_Turkey.jpg" width="200" /></a></div>There's a Turkey in my fridge waiting to be cooked, but I couldn't resist writing a quick post full of links on today's official bird. Enjoy!<br />
<br />
<h3>On this blog</h3><ul><li><a href="http://theobligatescientist.blogspot.com/2009/11/mid-week-reptilian-happy-turkey-day.html" target="_blank">Mid-week Reptilian #8: Wild Turkey</a></li>
<li><a href="http://theobligatescientist.blogspot.com/2009/12/dinosaur-on-christmas-table.html" target="_blank">A Dinosaur on the Christmas Table</a></li>
</ul><h3>External Links</h3><ul><li><a href="http://channel.nationalgeographic.com/series/morphed/3002/Overview" target="_blank">From Dinosaur to Turkey</a> | NatGeo (Jump to <a href="http://channel.nationalgeographic.com/series/morphed/3002/facts#tab-Videos" target="_blank">Video</a>, <a href="http://channel.nationalgeographic.com/series/morphed/3002/facts" target="_blank">Facts</a>)</li>
<li><a href="http://www.ucmp.berkeley.edu/museum/events/bigdinos2005/turkey.html" target="_blank">Your Holiday Dinosaur</a> | Berkeley's UC Museum of Paleontology</li>
<li><a href="http://www.werc.usgs.gov/outreach.aspx?RecordID=17" target="_blank">Turkey Day Science: What Do Gobblers Gobble?</a> | USGS Western Ecological Research Center Blog </li>
<li><a href="http://blogs.smithsonianmag.com/dinosaur/2010/11/24/this-thanksgiving-make-a-wish-on-a-dinosaur/" target="_blank">This Thanksgiving, Make a Wish on a Dinosaur</a> | Smithosonian Blog </li>
</ul> <br>Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-502420117458137182.post-71628339931983280902010-11-22T12:57:00.000-05:002010-11-22T12:57:17.673-05:00Sex, Life, Death and the Scientific MethodWhy do women live longer than men? That question caught my eye when it popped up in my twitter feed, so I followed the link over to <a href="http://www.scientificamerican.com/podcast/episode.cfm?id=why-do-women-live-longer-than-men-10-11-19" target="_blank">a podcast on the Scientific American website</a>. Before I could even listen to the podcast I noticed that someone posted the following in the <a href="http://www.scientificamerican.com/podcast/episode.cfm?id=why-do-women-live-longer-than-men-10-11-19#comment-02">comments section</a>:<br />
<blockquote>"I have a possible explanation of why women live longer than men. Men have an XY sex chromosome while women have an XX sex chromosome. This results in both the greater potential for genetic (chromosomal) variation in men that successfully adapts to the environment (and passes the same to succeeding generations) and genetic mutation which results in both chromosomal deleterious deterioration and maladaptation that results in early cell and male human death (and which, therefore, is less likely to pass the deleterious chromosomal variation to succeeding generations). Thus, men, in general, live shorter lives than women because their environmental success has a significantly more profound influence on how appropriate their genetic make up is to adapting to the same. At the same time, men's genetic make up (XY vs XY) is much more susceptible to deleterious genetic aberrations and maladaptations. Of course, the aforementioned is simply theory."</blockquote><br />
Viewed through the lens of science, this suggestion makes a great hypothesis, so I thought I'd mention it here (total avoidance behavior, by the way - I've got a thesis to write!!). So why is it a good hypothesis? Because <b>a good hypothesis is (among other things) one that suggests practical ways to challenge it's own validity</b>. Using claims that logically follow from the original hypothesis, we can test those claims with experimental or observational data. In this case, our hypothesis is: <br />
<blockquote>XY individuals lead shorter lives (on average) than do XX individuals because (on average) mutations in either the X or Y chromosome have the potential to result in greater phenotypic change.</blockquote>So what statements or predictions follow from this claim <i>that we can test empirically</i>? <i>How can we try and falsify this idea</i>? In this case, we need to look beyond humans for the answer to that questions...<br />
<br />
Now, before we get all myopic and try and pretend all gender differences in all species boil down to this single hypothesis, we should be mindful of the myriad other differences between males and females that contribute to longevity. For example, in humans...<br />
<br />
<div style="text-align: center;"><object height="385" width="480"><param name="movie" value="http://www.youtube.com/v/lVruzrZmgN4?fs=1&hl=en_US"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/lVruzrZmgN4?fs=1&hl=en_US" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="385"></embed></object></div><br />
But hey, <b>nothing in science would ever get done if we didn't take things one step at a time</b>, so lets take a closer look at the hypothesis at hand.<br />
<br />
I just so happens that here are other mechanisms of sex determination than the XX/XY system found in humans and other mammals. Many reptiles and birds, for example, have a <a href="http://en.wikipedia.org/wiki/ZW_sex-determination_system" target="_blank">ZW/ZZ system</a> where unlike the mammalian system, ZZ=male and ZW=female. So putting this fact together with our summary statement above, we've come up with a quick prediction: <b>that in birds and reptiles with ZW/ZZ sex determination, the females should be the shorter-lived sex</b>.<br />
<br />
So what's the story in birds? A quick web search (sorry - I need to get back to work!) revealed that people have actually considered this hypothesis before and done some of the leg work for us already. For example, in Austad 2006 (reference below) the author writes:<br />
<blockquote>Another way to investigate the hypothesis that the sex possessing the heterogametic chromosomes is going to be longer-lived is to consider birds, because the sex-chromosome situation is reversed compared with mammals. In birds, it is the female that has 1 short and I long sex chromosome, and therefore does not have the backup of the 2 long sex chromosomes (the Z chromosomes) that the male has. The prediction is that if heterogametic sex is a key factor, then male birds should be longer-lived. In fact, in 3 species of birds, including budgerigars, zebra finches, and Japanese quail, males outlive females, at least in captivity. For every bird species that I have been able to find in which there is good captive data, males outlive the females. Certainly, this is provocative evidence that would seem to favor the heterogametic sex hypothesis. It is of concern, however, that in some avian species, the female has been reported to outlive the male, but all of these reports were from field studies and are thus difficult to interpret for the reasons discussed previously.<br />
<br />
I like the heterogametic sex hypothesis because it is biologically interesting. Unfortunately, that does not mean it is true. There are some problems with this hypothesis that can be illustrated with Brandt's bat, a small bat that weighs about 7 grams and is a third to a quarter the size of a mouse... [author cites a study that found males appeared to be longer lived.] We just don't know the answers to these questions because we do not know what the underlying physiology is and whether behavioral differences or physiological differences are responsible for this remarkable observation in a Siberian cave.<br />
<br />
We are also aware of some mammals in which the males are significantly longer-lived than the females; we have very good captive data for 2 of these species, the guinea pig and the golden hamster. In both species, the males live substantially longer than the females, thereby contradicting the heterogametic sex and estrogenic hypotheses. Again, this is a problem in a general biological sense; it may very well be that one of these hypotheses is absolutely valid for humans but is just not generalizable to the rest of mammals. I would like a general explanation, and that is something we currently do not have.</blockquote><br />
So strictly speaking, this hypothesis is toast. Plenty of <b>evidence to the contrary</b> is floating around out there, <b>so we can rule it out as an accurate summary of reality</b>. But does that mean we just throw it out? Heck no! Instead of viewing hypotheses as a black and white question of "true vs. false," we instead seek to <b>refine the statement (if possible)</b> and make a <b>new hypothesis</b> consistent with this new information. <br />
<br />
For example, we may include the caveat that other processes might matter more in some species than accumulated deleterious effects, thus restricting the kinds of organisms we can apply our hypothesis to. Also, better experimental investigations could better challenge the core idea behind our hypothesis: genetic changes in the sex chromosomes and their resulting phenotypic changes. As you can see, all this hypothesizing and testing can snowball into an entire career of work fairly quickly.<br />
<br />
As much as I'd love to continue probing the world of longevity and gender genetics, I'm afraid I've got work to do (thesis work!). If I've piqued your interest and you turn up any other interesting studies on the subject, feel free to share in the comments below.<br />
<br />
<h3>References</h3><ul><li>Austad, Steven N. 2006 "<i>Why women live longer than men: Sex differences in longevity.</i>" Gender Medicine 3(2). <a href="http://dx.doi.org/10.1016/S1550-8579%2806%2980198-1" target="_blank">doi:10.1016/S1550-8579(06)80198-1</a> </li>
</ul>Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-502420117458137182.post-54558106932585167212010-11-17T20:37:00.001-05:002010-11-17T22:28:01.778-05:00U.S. Math & Science Students Need Our HelpThe U.S. ranks very low in math and science compared to other nations -- 35th in Math and 29th in Science. That's embarrassingly low, a threat to the future of our nation's economy, and most importantly <b>it's a problem we can solve</b>. So why are we so far behind? <br />
<br />
While digging through <a href="http://nces.ed.gov/timss/" target="_blank">TIMMS results</a> can be thought provoking, <b>you must, must, must <a href="http://www.connectamillionminds.com/campaigns/cammww/" target="_blank">watch this video</a></b> which provides a sobering comparison between US student attitudes towards math and science with those of their counterparts from some of the top ranked countries. So <a href="http://www.connectamillionminds.com/campaigns/cammww/" target="_blank">click here</a> if you can spare 3 minutes -- it's worth it! The video was produced as part of the <a href="http://www.connectamillionminds.com/campaigns/cammww/about/" target="_blank">Connect A Million Minds (CAMM)</a> campaign, "Time Warner Cable’s philanthropic commitment to connect youth to ideas, people and opportunities that will inspire them to become the problem solvers of tomorrow."<br />
<br />
<div style="text-align: center;"><object height="360" width="600"><param name="movie" value="http://www.youtube.com/v/TobtxNyerUw&hl=en_US&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/TobtxNyerUw&hl=en_US&fs=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="640" height="385"></embed></object></div><br />
You can see more CAMM videos <a href="http://www.connectamillionminds.com/videos.php">here</a>. For more information, look <a href="http://www.connectamillionminds.com/campaigns/cammww/discuss/" target="_blank">here</a>, <a href="http://www.connectamillionminds.com/campaigns/cammww/town-hall/after.php" target="_blank">here</a>, <a href="http://current.com/bfd/92804057_why-are-so-many-countries-ahead-of-the-us-in-math-and-science.htm" target="_blank">here</a> and <a href="http://urban-science.blogspot.com/2010/11/connecting-minds-to-science.html" target="_blank">here</a>. <br />
<br />
<i>[Hat tip to <a href="http://urban-science.blogspot.com/2010/11/connecting-minds-to-science.html" target="_blank">DNLee</a>]</i>Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-502420117458137182.post-50331716551809680692010-11-11T23:33:00.002-05:002010-11-11T23:35:45.293-05:00Do Reptiles Hibernate or Brumate?<a href="http://www.globalanimal.org/2010/11/08/snakes-mate-by-the-thousands-non-squeamish-humans-watch-in-awe/21615/" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;" target="_blank"><img border="0" height="240" src="http://www.globalanimal.org/wp-content/uploads/2010/11/DSCN5011.jpg" title="Click for image source..." width="320" /></a>Nearly everyone knows what <i>hibernation</i> means, but when speaking of reptiles the term <i>brumation</i> seems to reign supreme. Why? Is one term more correct than the other? To try make sense of these competing terms, I recently did some digging into the history of the word <i>brumation</i> which brought me to the following conclusions:<br />
<b><ol><li><b>The term <i>brumation</i> is (mostly) unnecessary jargon. </b></li>
<li><b>Both <i>hibernation</i> and <i>brumation</i> should be acceptable terms to use in most (if not all) situations, however <i>hibernation</i> is the better term to use in a public forum.</b></li></ol></b><br />
As for <i>why</i> I've arrived at these conclusions, we need to look back a few decades to see where this word "brumation" came from, what we knew about hibernation way back then, and what we've learned about since.<a name='more'></a><br />
<br />
If you happen to call that thing that snakes do each winter "hibernating" in front of an avid snake enthusiast, what usually follows is debate over whether the proper term is <i>hibernate</i> or <i>brumate</i>. Often, the rational for using the latter is that reptiles spend the winter in a different physiological state than mammals (i.e. somewhat awake instead of unconscious) which therefore necessitates a new term to make the distinction. So where does all this come from?<br />
<br />
Searching online journal articles for the word "brumation" leads to an article by Wilber W. Mayhew (1965) on hibernation in horned lizards (see below for references). The final point of the abstract reads...<br />
<blockquote>The term <i>brumation</i> is proposed to indicate winter dormancy in ectothermic vertebrates that demonstrate physiological changes which are independent of body temperature.</blockquote>Searching for <a href="http://scholar.google.com/scholar?hl=en&q=brumation&as_sdt=100000000001&as_ylo=1965&as_yhi=1975&as_vis=0" target="_blank">journal articles including the word "brumation" from 1965-1975</a> validates Mayhew (1965) as the origin of the term, as these later references usually cite Mayhew (1968) as the source. In the final paragraph of that article, Mayhew gives is a more clear version of his intended meaning of the word (emphasis mine):<br />
<blockquote>Results to date show that relatively complex physiological changes occur during or immediately preceding winter dormancy in some ectothermic vertebrates. To this extent, these animals are similar to hibernating birds and mammals. However, they differ from these heterotherms (see <a href="http://dx.doi.org/10.2307/1932207" target="_blank">Cowles, 1962</a>) in their inability to control their body temperatures. Consequently, <b>it seems advisable to have one term to designate winter dormancy in heterotherms and another for such ectotherms</b>. Hibernation has been used to denote this condition in heterotherms particularly, so it seems best to retain this term for that group of vertebrates. Therefore, <b>I propose the term <i>brumation</i> (from <i>bruma</i>, L. winter) to indicate winter dormancy in ectothermic vertebrates that demonstrate physiological changes which are independent of body temperature</b>.</blockquote>Clearly the term gained footing, but from the beginning some considered Mayhew's distinctions to be unnecessary. They simply saw no real need for the new terminology, leaving those looking to keep abreast of the latest jargon wondering what they should be calling... you know... that thing reptiles do during winter.<br />
<br />
As relevant today as they were a few decades ago, some authors were kind enough to share their concerns about this new terminology in their publications. So lets have a look at a few of these objections.<br />
<br />
The early references I dug up simply equate the two terms. For example in Gatten (1978)...<br />
<blockquote>In this paper, <b>hibernation will be used in a broad sense to refer to the general reduction in activity </b>in snapping turtles following cold-acclimation or cold-acclimatization. <b>As such, it is equivalent to the term "brumation"</b> as originated by Mayhew (1965).</blockquote>The two terms were equated elsewhere (e.g. Dunham 1980, Bauwens 1981) although some took it a step further and took issue with Mayhew's original definition of the term.<br />
<br />
One early example comes from Ultsch (1989), who basically gives the term brumation a pretty solid beatdown (emphasis mine):<br />
<blockquote>There has been some concern, particularly among physiologists, about using the term ‘hibernation ’ to denote the state of ectotherms during the winter. <b>The argument is that the term should be reserved for the state of controlled torpor typical of ‘true’ mammalian hibernators,</b> with body temperature regulated at a low level at which the animal is torpid, and with arousal characterized by an energetically expensive and relatively rapid increase in body temperature to its normal operative range. <b>Any other pattern, it is argued, is something other than hibernation and should be given another name</b>. In particular, cold ectotherms, although their activity and responsiveness are often greatly reduced, are usually not torpid, their body temperature is close to or at that of their microenvironment, and they do not warm themselves endogenously during arousal. Hence <b>a variety of other terms have been used to describe the condition of wintering ectotherms ; dormancy, cold torpidity, overwintering, and brumation (Mayhew, 1965) are among them</b>.<br />
<br />
Hibernation is derived from the Latin for wintering quarters, and to hibernate therefore simply means to spend the winter in sequestration ; <b>there is no implication in the etymology about the physiological state of the animal. As such, hibernation is a general term applicable to all animals that seek a local refuge (a hibernaculum) in which to overwinter</b>. Attempts to restrict its use to mammals may be mostly a reflection of the fact that most of the early and extensive physiological studies were done with that taxon. <b>I see no pressing reason to develop an array of jargon concerning the physiology of overwintering</b>. Therefore <b>‘hibernation’ will be used throughout this review, with the understanding that hibernation strategies vary among and within taxa</b>. ‘Overwintering’ is viewed as a more general term that means only what animals do in passing the winter; possible strategies include remaining active, migration and hibernation. </blockquote>There are two fantastic points here that deserve reiteration:<br />
<ol><li>The term hibernation asserts no specifics about the physiological details of the hibernating organism.</li>
<li>One can use the term <i>hibernation</i> while recognizing that the underlying details vary among and within taxa.</li>
</ol>Why is this important? Because in reality, there really is a lot of variation in how different organisms deal with shutting down during winter. You can read more about them <a href="http://www.daviddarling.info/encyclopedia/H/hibernation.html">here</a>, <a href="http://scholar.google.com/scholar?hl=en&q=hibernation+in+reptiles" target="_blank">here</a>, <a href="http://scholar.google.com/scholar?hl=en&q=hibernation+in+mammals" target="_blank">here</a>, <a href="http://www.wired.com/wiredscience/2008/03/researchers-fin/" target="_blank">here</a>, <a href="http://en.wikipedia.org/wiki/Insect_winter_ecology" target="_blank">here</a>, <a href="http://books.google.com/books?id=oBw3U2916qQC&printsec=frontcover" target="_blank">here</a> and <a href="http://en.wikipedia.org/wiki/Hibernation" target="_blank">here</a>. Using the term "brumation" implies that reptiles have some special way of doing this, and that interpretation of the term runs the risk of whitewashing over a lot of that variation. That is, to some it gives the false notion that we have all the details worked out and summarized nicely by these two categories.<br />
<br />
Here's my advice: upwards of 99% of the time you should use the term <i>hibernate</i>/<i>hibernation</i>, although if someone else uses <i>brumate</i>/<i>brumation</i> (appropriatly) you probably shouldn't bother trying to correct them. Both terms suffice to get the point across, although <i>hibernate</i>/<i>hibernation</i> makes sense to a much wider audience making it the more appropriate choice in a public forum.<br />
<br />
<h3>References</h3><ol><li>Mayhew, Wilber W. 1965. <i>Hibernation in the Horned Lizard, <u>Phrynosoma m'calli</u></i>. Comparative Biochemical Physiology. Vol 16, pp. 103-119. doi: <a href="http://dx.doi.org/10.1016/0010-406X%2865%2990167-2" target="_blank">10.1016/0010-406X(65)90167-2</a></li>
<li>Gatten Jr., Robert E. 1978. <i>Aerobic metabolism in snapping turtles, Chelydra serpentina, after thermal acclimation</i>. Comparative Biochemistry and Physiology Part A: Physiology. 61(2), pp. 325-337. doi: <a href="http://dx.doi.org/10.1016/0300-9629%2878%2990116-0" target="_blank">10.1016/0300-9629(78)90116-0</a> </li>
<li>Dunham, Arthur E. 1980. <i>An Experimental Study of Interspecific Competition Between the Iguanid Lizards <u>Sceloporus Merriami</u> and <u>Urosaurus Ornatus</u></i>. Ecological Monographs 50(3), pp. 309-330. (<a href="http://www.jstor.org/stable/2937254" target="_blank">JSTOR</a>)</li>
<li>Bauwens, Dirk. 1981. <i>Survivorship during Hibernation in the European Common Lizard, <u>Lacerta vivipara</u></i>. Copeia 3 (Aug), pp714-744. (<a href="http://www.jstor.org/stable/1444592" target="_blank">JSTOR</a>)</li>
<li> Ultsch, Gordon R. 1989. <i>Ecology and Physiology of Hibernation and Overwintering Among Freshwater Fishes, Turtles, and Snakes</i>. Biological Reviews 64(4), pp. 435-515. doi:<a href="http://www.blogger.com/10.1111/j.1469-185X.1989.tb00683.x" target="_blank">10.1111/j.1469-185X.1989.tb00683.x</a></li>
</ol>Unknownnoreply@blogger.com12tag:blogger.com,1999:blog-502420117458137182.post-71239642253489242942010-11-09T23:15:00.001-05:002010-11-11T01:32:12.246-05:00Fascism, Communism and Socialism and Other Awesome SignsThere are some great <a href="http://www.huffingtonpost.com/2010/10/30/the-funniest-signs-at-the_n_776490.html#s170117" target="_blank">signs from the Rally to Restore Sanity</a> up on HuffPo. Here are a few of the 800+ of them available for your browsing pleasure.<br />
<br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_170144_large.jpg?1289359270316" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="400" src="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_170144_large.jpg?1289359270316" width="550" /></a></div><div style="text-align: center;">If you aren't already in that club...</div><div style="text-align: center;"><br />
</div><b><u><a href="http://www.merriam-webster.com/dictionary/fascism" target="_blank">Fascism</a></u></b> a political philosophy or movement "that <b>exalts nation and often race above the individual</b> and that stands for a centralized autocratic government headed by a <b>dictatorial leader</b>, severe economic and social regimentation, and <b>forcible suppression of opposition</b>."<br />
<br />
<a href="http://www.merriam-webster.com/dictionary/communism"><u><b>Communism</b></u></a> is a social structure <span class="ssens">advocating <b>elimination of private property</b>. </span><br />
<br />
<b><u><a href="http://www.merriam-webster.com/dictionary/socialism" target="_blank">Socialism</a></u></b> includes any of "various economic and political theories advocating <b>collective or governmental ownership</b> and administration of the means of production and distribution of goods."<br />
<br />
Moving on...<br />
<br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_171920_large.jpg?1289360921731" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_171920_large.jpg?1289360921731" /></a></div><br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_169459_large.jpg?1289360990888" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_169459_large.jpg?1289360990888" /></a></div><br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_169783_large.jpg?1289361428432" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_169783_large.jpg?1289361428432" /></a></div><br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_169570_large.jpg?1289361181033" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_169570_large.jpg?1289361181033" /></a></div><br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_171066_large.jpg?1289362039208" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_171066_large.jpg?1289362039208" /></a></div><br />
and the oh-so-appropriate...<br />
<br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_171493_large.jpg?1289362229174" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://i.huffpost.com/gadgets/slideshows/12644/slide_12644_171493_large.jpg?1289362229174" /></a></div>Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-502420117458137182.post-35409347425370421002010-11-09T20:31:00.001-05:002010-11-09T20:36:16.947-05:00Consider HumanismThe <a href="http://www.americanhumanist.org/" target="_blank">American Humanist Association</a> has launched <a href="http://www.considerhumanism.org/" target="_blank">a huge ad campaign</a> today, which "will include a spot on NBC Dateline on Friday, November 12, as well as other television ads." Fund raising for the campaign <a href="http://secure.americanhumanist.org/Page.aspx?pid=303" target="_blank">is ongoing</a>, and is up to $200K as of today.<br />
<blockquote>The Stiefel Freethought Foundation was the primary sponsor of the Consider Humanism campaign with a $150,000 donation. Another $50,000 was raised from supporters of the American Humanist Association for the launch of this campaign, bringing the total ad buy to $200,000 so far.</blockquote>You can read more in <a href="http://www.americanhumanist.org/news/details/2010-11-humanists-launch-largest-national-advertising-campai" target="_blank">the press release</a>, watch the <A HREF="http://vimeo.com/americanhumanist/videos" target="_blank">AHA's videos on vimeo</A>, by visiting <a href="http://www.considerhumanism.org/" target="_blank">http://www.considerhumanism.org</a> and by clicking the images below for higher resolution PDFs.<br />
<blockquote><br />
<center><a href="http://www.considerhumanism.org/ads/Women.pdf" target="_blank"><img alt="" height="216" src="http://www.considerhumanism.org/ads/Women.jpg" width="550" /></a></center><a name='more'></a><br />
<center><a href="http://www.considerhumanism.org/ads/Slavery.pdf" target="_blank"><img alt="" height="229" src="http://www.considerhumanism.org/ads/Slavery.jpg" width="550" /></a></center><br />
<center><a href="http://www.considerhumanism.org/ads/War.pdf" target="_blank"><img alt="" height="218" src="http://www.considerhumanism.org/ads/War.jpg" width="550" /></a></center><br />
<center><a href="http://www.considerhumanism.org/ads/Intelligence.pdf" target="_blank"><img alt="" height="215" src="http://www.considerhumanism.org/ads/Intelligence.jpg" width="550" /></a></center><br />
<center><a href="http://www.considerhumanism.org/ads/Homosexuality.pdf" target="_blank"><img alt="" height="251" src="http://www.considerhumanism.org/ads/Homosexuality.jpg" width="550" /></a></center><br />
<center><a href="http://www.considerhumanism.org/ads/Fear.pdf" target="_blank"><img alt="" height="251" src="http://www.considerhumanism.org/ads/Fear.jpg" width="550" /></a></center><br />
<center><a href="http://www.considerhumanism.org/ads/Hatred.pdf" target="_blank"><img alt="" height="251" src="http://www.considerhumanism.org/ads/Hatred.jpg" width="550" /></a></center><br />
<center><a href="http://www.considerhumanism.org/ads/Punishment.pdf" target="_blank"><img alt="" height="219" src="http://www.considerhumanism.org/ads/Punishment.jpg" width="550" /></a></center><br />
<center><a href="http://www.considerhumanism.org/ads/Genocide.pdf" target="_blank"><img alt="" height="251" src="http://www.considerhumanism.org/ads/Genocide.jpg" width="550" /></a></center><br />
<center><a href="http://www.considerhumanism.org/ads/Violence.pdf" target="_blank"><img alt="" height="219" src="http://www.considerhumanism.org/ads/Violence.jpg" width="550" /></a></center></blockquote><br />
[Hat tip to <a href="http://friendlyatheist.com/2010/11/09/consider-humanism-the-largest-atheist-ad-campaign-ever-2/" target="_blank">Hemant Mehta</a>]Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-502420117458137182.post-21012779495235840142010-11-08T20:20:00.000-05:002010-11-08T20:20:00.578-05:00Using Reptiles For Public Education, OutreachMelissa Kaplan has a great website regarding <a href="http://www.anapsid.org/" target="_blank">reptiles in captivity</a>, and included among her writing is <a href="http://www.anapsid.org/repsineduc.html" target="_blank">some great advice for using animals in public outreach and education</a>. Though geared towards reptiles, the comments I think apply broadly -- check it out!Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-502420117458137182.post-8462816863566568152010-11-02T20:22:00.001-04:002010-11-02T20:48:22.457-04:00The Power of Data Visualization & Comparison<div style="text-align: center;"><object height="340" width="560"><param name="movie" value="http://www.youtube.com/v/pLqjQ55tz-U?fs=1&hl=en_US"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/pLqjQ55tz-U?fs=1&hl=en_US" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="560" height="340"></embed></object><br />
<i>David McCandless: The beauty of data visualization</i> (<a href="http://www.youtube.com/watch?v=pLqjQ55tz-U" target="_blank">TED Talk</a>)</div><br />
Computational statistics and computer programming abilities are -- and will continue to be -- valuable skills in the job market (and in the sciences). If I could offer any career advice to students, it is to work hard to learn these two things well!Unknownnoreply@blogger.com2tag:blogger.com,1999:blog-502420117458137182.post-75284642174491207252010-11-01T23:16:00.000-04:002010-11-01T23:16:17.724-04:00Why Not Vote Republican?<div style="text-align: center;"><object height="306" width="500"><param name="movie" value="http://www.youtube.com/v/8BJfMPxQuiU?fs=1&hl=en_US"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/8BJfMPxQuiU?fs=1&hl=en_US" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="500" height="306"></embed></object></div><br />
While some of those claims need fact checking, there are excellent lines in there! Feel free to quote any favorites in the comments below.Unknownnoreply@blogger.com6tag:blogger.com,1999:blog-502420117458137182.post-807547291230568162010-10-31T23:34:00.001-04:002010-10-31T23:35:55.903-04:00Do Night Shifts Cause Breast Cancer?According to <a href="http://ehp03.niehs.nih.gov/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1289%2Fehp.0901828" target="_blank">this review article</a>, the answer appears to lie somewhere between <i>maybe</i> and <i>probably</i>. While there seems to be a <i>correlation</i> between the two, more research is needed to determine whether or not there is a <i>causal</i> link as other plausible reasons for the correlation haven't yet been ruled out.<br />
<blockquote>...Shift work. Excess incidence of breast cancer has been observed consistently in studies of women with prolonged exposure to shift work involving exposure to light at night (<a href="http://ehp03.niehs.nih.gov/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1289%2Fehp.0901828#r54" target="_blank">Kolstad 2008</a>; <a href="http://ehp03.niehs.nih.gov/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1289%2Fehp.0901828#r92" target="_blank">Stevens 2009</a>). Research needs in this area include <i>a</i>) a better definition of what is meant by shift work and related exposure metrics; <i>b</i>) studies of markers of circadian disruption in non–day workers; <i>c</i>) better descriptions of controls and their exposure to light at night; and <i>d</i>) investigation of the effect of variations in expression of circadian genes on cancer in shift workers. An emerging area of interest is the relative toxicity of occupational chemical exposure depending on time of day of that exposure. The marked circadian variations in cell division and DNA repair during the daily cycle are controlled by the circadian genes (<a href="http://ehp03.niehs.nih.gov/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1289%2Fehp.0901828#r35" target="_blank">Haus and Smolensky 2006</a>; <a href="http://ehp03.niehs.nih.gov/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1289%2Fehp.0901828#r93" target="_blank">Stevens et al. 2007</a>). Therefore, non–day workers may have very different susceptibility to occupational exposures compared with day workers. Studies are also needed to determine if shift work is associated with other cancers, especially hormonally related cancers, and prostate cancer in particular. If further experimental and epidemiologic evidence confirms a causal association between exposure to light at night and breast cancer, it will be important to develop interventions to reduce the risk.</blockquote><br />
You can read more <a href="http://www.scienceline.org/2010/10/night-shift%E2%80%99s-possible-link-to-cancer/" target="_blank">here</a>. For details, see the article and relevant references.<br />
<br />
<h3>Reference</h3><div class="intro"><ol><li>Ward EM, Schulte PA, Straif K, Hopf NB, Caldwell JC, et al. 2010 <i>Research Recommendations for Selected IARC-Classified Agents</i>. Environ Health Perspect 118(10): doi:<a href="http://dx.doi.org/10.1289/ehp.0901828">10.1289/ehp.0901828</a></li>
</ol><ol></ol></div>Unknownnoreply@blogger.com5tag:blogger.com,1999:blog-502420117458137182.post-35228236924197570002010-10-30T17:46:00.001-04:002010-10-30T18:13:47.058-04:00Fluffy the Python Dies<div class="separator" style="clear: both; text-align: center;"><a href="http://news.uk.msn.com/photos/photos.aspx?cp-documentid=154691184&page=5" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;" target="_blank"><img border="0" src="http://estb.msn.com/i/4F/27E459AFF747C9C6CB944ADE977B.jpg" title="Click for source" /></a></div>The Columbus Zoo's famed Reticulated Python (<i>Python reticulatus</i>) <a href="http://www.colszoo.org/news_room/press_releases/big_loss_for_the_columbus_zoo_and_aquarium.aspx" target="_blank">died this week</a> at the ripe old age of 18.<br />
<br />
According to the <a href="http://www.dispatch.com/live/content/local_news/stories/2010/10/28/crowd-pleasing-fluffy-dies-at-zoo.html?sid=101#story-continues" target="_blank">Columbus Dispatch</a>:<br />
<blockquote>...Fluffy died Tuesday night, apparently of a tumor.<br />
<br />
The 18-year-old reticulated python was 24 feet long and held the Guinness World Records title of longest snake in captivity. She weighed 300 pounds, according to a news release from the zoo.</blockquote>Sad news, but this made me <i>even more sad</i> ... <br />
<blockquote><b>The snake will be cremated</b>, zoo spokeswoman Patty Peters said.</blockquote>Cremated?! Why not <i><b>preserved</b></i>? <b>Let Fluffy break another record</b> and become <a href="http://www.news.cornell.edu/stories/april06/python.giant.kr.html" target="_blank">the world's longest snake <i>skeleton</i></a>! Surely there are <a href="http://mbd.osu.edu/faculty.htm" target="_blank">people in the area</a> that <a href="http://asm.wku.edu/faculty/huskey/" target="_blank">could prepare the specimen</a>, it it really would make for an awesome display at the zoo. Beyond the immediate future, Fluffy's passing no doubt brings up another big question...<br />
<br />
<h3>Will Fluffy Be Replaced?</h3>I certainly hope so, and I'll go one step further and encourage the Columbus Zoo to not only replace Fluffy but to do so by doing one (or both!) of the following:<br />
<ol><li><b>Get a "normal" Reticulated Python</b>. If I'm not mistaken, Fluffy was a "<a href="http://www.bobclark.com/d_learn.asp?id=23" target="_blank">tiger</a>" morph - a pattern mutant commonly bred in captivity that looks <a href="http://commons.wikimedia.org/wiki/File:Reticulated_python_MP1.JPG" target="_blank">like this</a> instead of <a href="http://www.reticulatedpython.info/images/sulaweysi/sulaweysi01.jpg" target="_blank">this</a> or <a href="http://www.reticulatedpython.info/images/java/java06.jpg" target="_blank">this</a>.</li>
<li><b>Exhibit this species' natural variation</b> by acquiring (and breeding) some of the diminutive individuals that can be found in <a href="http://www.reticulatedpython.info/variety10.html" target="_blank">the pet trade</a>, or at least individuals from (and representative of) a known locality. These island "dwarfs" (see <a href="http://www.constrictors.com/Collection/ReticulatedPythons/SuperDwarfReticulatedPython.html" target="_blank">here</a>, <a href="http://www.constrictors.com/Collection/ReticulatedPythons/JampeaDwarfReticulatedPython.html">here</a> and <a href="http://www.springerlink.com/content/bv8nny7e8k8lv8nv/" target="_blank">here</a>[<a href="http://www.springerlink.com/content/bv8nny7e8k8lv8nv/fulltext.pdf" target="_blank">PDF</a>]) seem to only reach about 6'-10' long (tiny!) instead of 20'+ like individuals from other populations.</li>
</ol>Why a normal looking reticulated python and these tiny island dwarfs? To quote <a href="http://www.anapsid.org/aboutmk/bio.html">Melissa Kaplan</a>'s article <a href="http://www.anapsid.org/repsineduc.html" target="_blank">The Use of Reptiles in Public Education</a> (emphasis mine):<br />
<blockquote>...The education animal <b>should be representative of a normal form of the species</b> (Gibson, 1994a; San Francisco Zoological Society, 1983). One of the goals of reptile education is to teach not only about the reptile itself but how that species lives in its environment, including how it is camouflaged from predator and prey. In the case of indigenous species, normal forms will help the audience identify the species when they see it in their yards, parks or in wild areas. Captive-bred color and pattern morphs are best saved for use in teaching the basics of genetics and heredity or in lectures addressing reptiles as pets rather than where the focus is on creating an awareness of wildlife and conservation.</blockquote><br />
[Hat tip to <a href="http://kingsnake.com/blog/archives/260-Fluffy,-the-longest-captive-snake-in-the-world,-dies.html" target="_blank">Cindy Steinle via Kingsnake.com</a>]Unknownnoreply@blogger.com145