tag:blogger.com,1999:blog-86780899020650823832024-03-14T08:33:46.050-07:00Phenology & Plant InvasionsIn the trenches of bioinformatics research: undergraduate and postdoc perspectivesLizziehttp://www.blogger.com/profile/09989005827839292498noreply@blogger.comBlogger26125tag:blogger.com,1999:blog-8678089902065082383.post-16510269196941135202011-06-23T16:59:00.000-07:002011-06-23T16:59:28.085-07:00At long lastIt has been a while, but I've finally found time to write up this graduation blog, *whew*<br />
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The week after I went out into the field with Lizzie was finals week, which was great! No really, it was a great week, especially since I decided that that was a good week to try and finish off items on my bucket list for UCSD before commencement while trying to remain focused on my senior research paper. There were just so many things to do before I graduated (such as running around campus at midnight finding all the art pieces in the Stuart Art Collection), though unfortunately, I didn't get to go around and finish my list. But by the time commencement rolled around, I was happy enough with where I was.<br />
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One thing I do have to say is that commencement was overrated. I thought it would have been a bit more grandiose; I was wrong, though the bagpipes that were playing while my graduating class walked in was exciting (it may have been the most exciting portion of the ceremony). Two hours later... I'm a college graduate!<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGwyWLq7Ce-oKZrzBXylsdVxQfieJQ7z6Kr5iDXui9htRJrxQpo-8F7ZqqewLJDmQ-Un0bwhXhm8QckjR345oIm6PYUH0Y2WCxPHzr9gTP1SUN8Xbico6ZuHxLpQsgVAp7LJiNRRRBRZY/s1600/SAM_2655.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGwyWLq7Ce-oKZrzBXylsdVxQfieJQ7z6Kr5iDXui9htRJrxQpo-8F7ZqqewLJDmQ-Un0bwhXhm8QckjR345oIm6PYUH0Y2WCxPHzr9gTP1SUN8Xbico6ZuHxLpQsgVAp7LJiNRRRBRZY/s400/SAM_2655.jpg" width="271" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Just smell that freedom!</td></tr>
</tbody></table>And now that I've joined the (part-time) working world, I'm think I may miss the work and schedule that comes with academia, but who knows? Maybe I'll be back in it again some time in the future. For now, I'll enjoy this summer in La Jolla and play things by ear until September rolls around, how exciting!Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-11215372055414182792011-06-04T02:27:00.000-07:002011-06-04T03:16:53.178-07:00The hills are alive...with the sound of music! Or the wind, which was more the case. However, when I was working throughout the day in the field, I barely felt the wind blowing sometimes (it was hot, but Lizzie says that it wasn't as hot as it could be...I'll take her word for it). Lizzie picked me up from the vicinity of my residence at around 7:00am, and from there, we drove about 30 minutes to the experimental site where we started our work. For about 6 hours, most of our work consisted of these steps:<br />
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<tr><td class="tr-caption" style="text-align: center;">Find the exclosure and/or sham. Sadly, I am almost completely covered by the surrounding shrubbery.</td><td class="tr-caption" style="text-align: center;"><br />
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<tr><td class="tr-caption" style="text-align: center;">First, the cable ties have to be removed before the netting on the exclosure can be taken off.</td><td class="tr-caption" style="text-align: center;"><br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbpQ1iDKYlLG4wYiTsiIYvDXuWOV6rF0zdtgmHmtVj8jBcBGMmzXZ5ESBEcBC5KMpxsoRTtanZSgBq8puorZ2NVBNdTV2TiS8YqgtfIoqQ_5dFU1QdHlsfknivMIR3siojobDYJEPixto/s1600/2011Jun2_TakedownExcl3.JPG" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbpQ1iDKYlLG4wYiTsiIYvDXuWOV6rF0zdtgmHmtVj8jBcBGMmzXZ5ESBEcBC5KMpxsoRTtanZSgBq8puorZ2NVBNdTV2TiS8YqgtfIoqQ_5dFU1QdHlsfknivMIR3siojobDYJEPixto/s400/2011Jun2_TakedownExcl3.JPG" width="300" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">This is followed by multiple strikes to the rebars to loosen them from the ground.</td></tr>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEigdWnDpTkuxT1FDUbPNHevcBDGBltZsxZgRK27DxnBlATG57pMV-NrJ3ajIB5FIY14MBNM6quNq5CcNneFOh5vQ03NsIUynfRE6SNmbIyKRzlM5o21qAPouDdNKp7Q1mTXtPdYRPL6k_4/s1600/2011Jun2_TakedownExcl8.JPG" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEigdWnDpTkuxT1FDUbPNHevcBDGBltZsxZgRK27DxnBlATG57pMV-NrJ3ajIB5FIY14MBNM6quNq5CcNneFOh5vQ03NsIUynfRE6SNmbIyKRzlM5o21qAPouDdNKp7Q1mTXtPdYRPL6k_4/s400/2011Jun2_TakedownExcl8.JPG" width="300" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">If that doesn't work the first time around, intermittently hammer while moving the bars from left to right before pulling. </td></tr>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyJhtc0BAJAvIUPlrJfJJOHCGwGugelGOVxRyjDkpgtpfO6dZ6EVHB9slIdPMK4ApzSnhnQj2jUKe-2MImoy5DuDo3K00LRXhYcPD9cKN1azIfL4gY2Peo8MC0xGv-lrWiADxfBqrwh7s/s1600/2011Jun2_TakedownExcl22.JPG" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyJhtc0BAJAvIUPlrJfJJOHCGwGugelGOVxRyjDkpgtpfO6dZ6EVHB9slIdPMK4ApzSnhnQj2jUKe-2MImoy5DuDo3K00LRXhYcPD9cKN1azIfL4gY2Peo8MC0xGv-lrWiADxfBqrwh7s/s400/2011Jun2_TakedownExcl22.JPG" width="300" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">After the rebars are removed, roll up the salvageable chicken wire to be ready for transport.</td></tr>
</tbody></table>It was pretty grueling work, but I enjoyed it for the most part, despite the fact that we had to cart everything to the car at least 3 times. I believe that was about 15 minutes downhill with equipment and 10 minutes back uphill to get to the rest of items left behind; it was like an edition of Extreme Makeover: Gardening Edition/Field Work. After all this work, Lizzie and I had a Jamba Juice smoothie, which tasted like heaven after a hard day's work. Then we drove back to campus, and dumped the rebars in a dumpster and moved the rolls of chicken wire into the lab. *whew* I didn't realize until the next morning exactly how sunburned I was, haha. I just thought it was hot, considering the weather that I'm usually used to, which is nice and breezy La Jolla. Despite the now chafed and red arms and shoulders I have, I enjoyed my time outside, and the physical labor required to do this type of work. I have to say, this is a great way to end the quarter, and a better way to end a memorable internship experience. :)Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-14651329269524479952011-05-25T14:26:00.000-07:002011-06-03T22:38:44.069-07:00Part 1 complete!Huzzah! I have finished my poster for my ESYS symposium that is tomorrow night. I do believe that I spent as much time on the alignment of my text boxes and figures as I did with the content itself...hm. But the result of that is a poster that I am very satisfied with aesthetically!<br />
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<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5dcA5m5wkbxpjgZq9ArX1LniG3Ibap6Zt4SEN3llcVBtos5v4GQ26dHnabfp9lsk7bnC2dM1tTWAd2YjdW4wO2eqeahMB3UMlqi9fabuH8-RFJyyvBX_Gjhn6_8kFfTeirHhk9fK4FfU/s1600/poster+final.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="298" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5dcA5m5wkbxpjgZq9ArX1LniG3Ibap6Zt4SEN3llcVBtos5v4GQ26dHnabfp9lsk7bnC2dM1tTWAd2YjdW4wO2eqeahMB3UMlqi9fabuH8-RFJyyvBX_Gjhn6_8kFfTeirHhk9fK4FfU/s400/poster+final.JPG" width="400" /> </a></div>I have to say though, it was difficult to figure out how to get this plotted...and I went through a somewhat complicated process of converting files, printing to two different printers (one to get the print preview/quote and one to print), and then making more minute changes to my poster. However, thank you Academic Computing Services for offering this service at a price 4 times cheaper than what Imprints offers its students. Now all that's left to do is to go through the rest of the graphs that Lizzie sent me for my paper and work on that, after I get through my poster presentation of course. I'm excited to see what my fellow ESYS classmates have been working on for their internship these past 2 quarters as well.<br />
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<br />
::post-ESYS symposium 5.27.2011::<br />
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It was great seeing everyone's posters! Everyone was dressed up very nicely as well and had good presentations of their internships, which varied from educational outreach programs to specified scientific research topics. All in all, I think the symposium went well, especially since there were many community members, alums, and other faculty and staff members that came to see everyone's internship work.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2SPdXEy_1A65F2XOL2dRW3VzeC8AO9B-P7om47QuIN5L9ZUU7iHcpdRl1sMaO_90bsi4WUbe7Z1rwntYF9_YGBMd-IthsBJnvcQcJci9WOXG4MLrvU6Z_NR1dK7XzfarPY2oAaSr5v0w/s1600/IMG_1215.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2SPdXEy_1A65F2XOL2dRW3VzeC8AO9B-P7om47QuIN5L9ZUU7iHcpdRl1sMaO_90bsi4WUbe7Z1rwntYF9_YGBMd-IthsBJnvcQcJci9WOXG4MLrvU6Z_NR1dK7XzfarPY2oAaSr5v0w/s400/IMG_1215.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Lizzie insisted I present my poster, so here I am!</td></tr>
</tbody></table>We also had a few former ESYS alumni come and speak at the reception and gave recognition to the faculty and staff that work behind the scenes and helps make the ESYS program work smoothly. The ESYS symposium concluded with a class of 2011 picture (which I've yet to receive), and it was quite sad for a few moments as we all stood there together thinking about the culmination of our project and our years at UCSD. I, for one, am glad that I came into the university with this major, not knowing what it was but leaving the school very satisfied at the road I've taken these past 4 years. Only a few more days to go!Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-79757678078584831352011-05-13T11:35:00.000-07:002011-06-06T11:02:51.729-07:00A whole new world, a new fantastic point of view<span style="background-color: transparent; color: black; font-size: small; font-style: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">It has taken about 2.5 months, but at long last, all vacuum sampled and frozen arthropods from Lizzie’s collection have been processed! There are a few minor tasks that I have left to do with them, such as comparing vouchers, but that will most likely be done in a short bit.<span style="font-family: Arial;"> </span></span><br />
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<span style="background-color: transparent; color: black; font-size: small; font-style: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Now, to say that I didn’t recognize the arthropods until more than halfway through the samples is an understatement. I had to re-familiarize myself at each sorting session what the types of arthropod were, and that in itself took a long time to become acquainted with. After many sessions of bug identification frustration, I finally decided that I was going to go and capture these bugs on camera and store them on my laptop when I sort through the rest of the samples. Here are a few pictures of some of the arthropods I caught on camera:</span><br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisWgMRZM2Qxp4XZcXT1i74XtLA8n_rVaAGc25WVjJWyZlbgUquCclI5b1L2IFPp3afkUWeV2W0R8aMKC3RROXJznhLRrqf4AfdV-ZsaAs2D4lOwR4EyxohhUrpOKdMd_2sIWuuvN6EZr0/s1600/auchbls%25283%2529_BEL10_10May2010.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisWgMRZM2Qxp4XZcXT1i74XtLA8n_rVaAGc25WVjJWyZlbgUquCclI5b1L2IFPp3afkUWeV2W0R8aMKC3RROXJznhLRrqf4AfdV-ZsaAs2D4lOwR4EyxohhUrpOKdMd_2sIWuuvN6EZr0/s320/auchbls%25283%2529_BEL10_10May2010.JPG" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">This is a one of a kind bug I found in the samples, though I'm not really sure what it is.</td></tr>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGS7lLcZolpJGAvAMIYOSvkvvc5OVUlFRzKT6AdFoXf2geonH-93HeLMJIpLAG9m12rxnjD8lgpgQQ7GejHo0rW6eFoD7rLEsUCLetW5qH8cFxuR2hqEl7SvwfUOT9dgNlNgotZdtuv1k/s1600/auchbw%25282%2529_BE%2528next+to+H8%2529_10May2010.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGS7lLcZolpJGAvAMIYOSvkvvc5OVUlFRzKT6AdFoXf2geonH-93HeLMJIpLAG9m12rxnjD8lgpgQQ7GejHo0rW6eFoD7rLEsUCLetW5qH8cFxuR2hqEl7SvwfUOT9dgNlNgotZdtuv1k/s320/auchbw%25282%2529_BE%2528next+to+H8%2529_10May2010.JPG" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">This is one of the many auchenorrhynchas (what a mouthful) that I saw while sorting. What a beauty.</td></tr>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibog_Ov8Vos5z0Bqy9Ix-BGTHK_T7hCokC4ngpPIiH6S-DihaiO7rB14TNpLIvNDvERKyyTxSBZISyCLI4b9vd-Pw2gxjQs6owmu0JGEj30xauYEgT_ccmKu5WTHUWnhrMA1gNGBpQD-U/s1600/diptrs_BEL13_10May2010.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibog_Ov8Vos5z0Bqy9Ix-BGTHK_T7hCokC4ngpPIiH6S-DihaiO7rB14TNpLIvNDvERKyyTxSBZISyCLI4b9vd-Pw2gxjQs6owmu0JGEj30xauYEgT_ccmKu5WTHUWnhrMA1gNGBpQD-U/s320/diptrs_BEL13_10May2010.JPG" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">There were many flies in the samples, this one I labeled as 'diptrs' for red stripes.</td></tr>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyDMzMo9GlEt9tTQaUyV7fJpJf5XyNFHB2_xUBs4zyB2nRtEHHACBO00FaZGYfUqkmyCrdbRu5HT7jHSz0S8Pwloedd1NzVcURiueQ91f_GcLf4bIn7-jx0ZQ2n7Q1DHfyH9WGguyeBWQ/s1600/mord_BEL1_10May2010.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyDMzMo9GlEt9tTQaUyV7fJpJf5XyNFHB2_xUBs4zyB2nRtEHHACBO00FaZGYfUqkmyCrdbRu5HT7jHSz0S8Pwloedd1NzVcURiueQ91f_GcLf4bIn7-jx0ZQ2n7Q1DHfyH9WGguyeBWQ/s320/mord_BEL1_10May2010.JPG" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">This one is my favorite since it reminds me of the alien from the movie, 'Aliens'.</td></tr>
</tbody></table><div style="background-color: transparent; font-family: Arial,Helvetica,sans-serif;"><span style="background-color: transparent; color: black; font-size: small; font-style: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">I made note to take pictures of them from as many sides as possible, since I couldn’t be sure whether or not if a single picture was enough to help me identify future samples. As it is, I feel like my pictures, which made identifying arthropods much easier later on, are not as clear as they could be since they do not capture all the details on the insect bodies. I would also have trouble with the light on the microscope and in how I centered the camera lens on the microscope lens, since it required multiple minute tweakings of both camera and microscope lenses. </span><span style="font-size: small;">I ended up zooming my camera lens to the max and the microscope to 3x the magnification and then centering the camera lens on the microscope lens before I found a middle point where I was satisfied with the quality of the photos.</span><br />
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<span style="background-color: transparent; color: black; font-size: small; font-style: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">But doing so did help me match up bugs closely, or at least, better than I did before. Now that Lizzie is back, and brought with her her vouchers of these little guys, I can match up my vouchers with hers and see how to better create a system for identification. Ta da!</span></div><div style="background-color: transparent; font-family: Arial,Helvetica,sans-serif;"><br />
<span style="background-color: transparent; color: black; font-size: small; font-style: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Happy Friday everyone, and happy Sun God! </span></div>Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-69917373584764736942011-04-26T23:24:00.000-07:002011-05-01T21:26:21.438-07:00Yay for summer! I mean, um...For weeks, I've been battling one of the seven sins...sloth. It's almost difficult to bring myself back to work, especially with the nice weather we've been having the past few weeks. However, I've finally been able to pull myself slightly back into a working mode and am now going to present to you a portion of what my ESYS paper will be talking about.<br />
<div><br />
</div><div>A majority of the data I've gathered for my paper is based off of work that involves bird exclosures experimentation. In the data that I gathered, they were 3 types of shrubs: exclosures, shams, and control shrubs. Another variable of this experiment was whether or not the shrubs were surrounded by low or high grasses. To better illustrate, here is a picture of an <i>A. californica</i> bush that Lizzie did her experiment on at Sweetwater NWR:</div><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsHLrj0BupF0T9j6s__XB9h0bIONf1gpTeW9D_GgP5QPOxoKkOI_n7KOJb7GYh1TDKmEZuO08pjgaXj17vH_wIy-EKZNDr6JHG_E0RABlbmAVOir8wROH-nLfKt06mkKp9oyjdMD9a3EE/s1600/17Feb08_Sweetwater29LowExcl.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsHLrj0BupF0T9j6s__XB9h0bIONf1gpTeW9D_GgP5QPOxoKkOI_n7KOJb7GYh1TDKmEZuO08pjgaXj17vH_wIy-EKZNDr6JHG_E0RABlbmAVOir8wROH-nLfKt06mkKp9oyjdMD9a3EE/s400/17Feb08_Sweetwater29LowExcl.JPG" width="266" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">This is a low-grass bird exclosure shrub. Cute!</td></tr>
</tbody></table><div>From these shrubs, Lizzie collected samples from the shrub itself and vacuumed arthropods pre- and post-experimental period. These samples are what I have been working with for the past few months (albeit slowly), and although there has not been much analysis done on the data gathered, in terms of herbivory, there is not much difference between the different treatment types (<a href="http://plantphenology.blogspot.com/2011/02/fin.html">previous blog post</a>). As for the post-experimental period samples gathered, I have noticed while sorting the arthropods that some shrubs would have a high quantity in the vacuumed samples. I'm not sure if this is due to the amount of actual foliage that was vacuumed, as some sample bags had more (or less) in terms of volume, but there should be more information about this answered as soon I'm able to enter in all the data concerning the types of arthropods I've sorted.</div>Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-48646596601040936402011-04-11T10:22:00.000-07:002011-04-11T10:23:31.438-07:00Questions? Comments? Concerns? ???I have many of those, especially questions that starts out with, "What the heck am I writing and how?" In brief (and frequent) moments of confusion, I ask myself that, especially when I'm beginning to carve out my outline and tentative final paper. Like I've said in the past, I find it hard to get started until I sit down and actually force myself to think about the topic at hand...but even then, I find myself at a loss for words. So, in the best possible way, I will try to translate my mumble-jumble of thoughts and ideas and translate them to a semi-understandable and logical way. Here is my still-and-must-be-continually-edited version of an abstract/summary:<br />
<blockquote style="font-family: Verdana,sans-serif;"><div style="color: #666666;"><span style="font-size: x-small;">There is a top-down control on arthropod communities by bird predation which leads to trophic cascades that affect shrub biomass. In doing bird exclosure experiments, we can determine whether removing these large predators on arthropods will affect the size and quantity of arthropods present on experimental shrubs and if this in turn, affects the amount of plant biomass. We expect there to be differences throughout the three types of experimental shrubs; the control, sham, and exclosed shrubs should contain the least </span><span style="font-size: x-small;">to the most </span><span style="font-size: x-small;">amount of arthropods, respectively. With this expectation, we will try and predict if the following are true: (P1) California sagebrush shrubs in bird exclosures contain higher amounts of larger arthropods (past a certain size), which causes trophic cascades; (P2) there is a higher new to old growth ratio on control shrubs than on shams and exclosures due to higher amounts of arthropod predation by birds. The absence or presence of birds may be used as an indication of how temporal variations of coastal sagebrush habitat are affected by fluctuating seasonal temperatures. It is important to understand how these tertiary consumers will impact trophic scales down to the plant level to see if changes in migratory patterns of these consumers would affect consumer and producer interactions within the community. </span> </div></blockquote>As of this moment, I am still trying to further flesh out and rewrite my thoughts and ideas, but for the most part, this may be my writing at its most coherent. The more difficult part of writing this was trying to figure out how I can have my readers understand why they should be interested...I'm still working on trying to find the "Wow!" factor. This is a painstakingly slow work in progress, but in the end, slow and steady wins the race (at least what we're taught to believe in Aesop's fables)? Go brain, think! And go fingers go! Write!Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-17299960385199950022011-04-04T00:43:00.000-07:002011-04-11T10:36:16.885-07:00Here comes the sun---doo do doo doooWelcome to spring (quarter)! This celebratory quarter is appropriately heralded by the wonderful and toasty sunny days that have finally arrived, and now we can really call this place sunny San Diego. This week has been quite hectic, with me being sick and all while volunteering for the Clinton Global Initiative University for the past two days. Former President Clinton is a great public speaker, and I greatly enjoyed being able to hear him discuss about various social justice issues and topics with the panelists.<br />
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<div style="text-align: left;">But to get back to the blog on hand, spring quarter also means the revisiting of bioinformatics work! To start this off, Lizzie assigned me with the task of going through a list of plant species through the Kew Royal Botanical Gardens database, which I have to say, was much easier to do than going through previous data sets in the past. This database is a mix between USDA Plants and Jepson Online Interchange in that I think it is aesthetically pleasing to view and to read the information, props to you Kew Gardens webmaster. The site in general is easy to navigate, and the database is well organized, easy to read, and contains information by category type and color-coded, something that gives it a bit of character unless the viewer is color-blind, in which case the viewer may be out of luck. I was able to obtain a majority of the information for seed mass of the species listed on the data set from this site, but I may have to poke around elsewhere to obtain other information, such as seed numbers, genome size, and any other random, but relevant information.</div><div style="text-align: left;"><br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiamPT7AASnkF9AHVx9p5WPmNx_MYjj9Qj27cqx9MBPeWmZ_0RUbYdKr7MoqLgHzS740MvUA3NHkQkzN41HSTRuyEimmdMunrBTWExh_IoglzoD_VawUfE258X1DrPBofs7QXCq4CMHEP4/s1600/map.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiamPT7AASnkF9AHVx9p5WPmNx_MYjj9Qj27cqx9MBPeWmZ_0RUbYdKr7MoqLgHzS740MvUA3NHkQkzN41HSTRuyEimmdMunrBTWExh_IoglzoD_VawUfE258X1DrPBofs7QXCq4CMHEP4/s320/map.png" width="271" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">This, by the way, is the time it takes to arrive by bike.</td></tr>
</tbody></table>While going through and viewing the Kew Gardens site, I remembered what Lizzie had said about arboretums being large plant museums and thought, "Hey, maybe I should check out the one close to home...How close is it anyway?" Thanks to Google Maps, I now know that I live approximately ~10 minutes from the Los Angeles Arboretum and Botanical Gardens (and ~10 minutes east of The Huntington Library, which also contains a botanical garden). Sadly, the LA Arboretum is only 127-acre, small when compared to the 300-acre large Kew Gardens. Maybe I should visit the next time I'm in the area...or I can simply wait for the resident peacocks that wander in the park to come visit me.<br />
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::edit 4-8::<br />
Ok, I take back a portion of what I said about this data set being "easier" to complete than the others in the past. Seed mass was easy to get, everything else however...not so much. The "everything else" includes chromosome number, ploidy level, and C-value of the plant species. This is now a familiar position that I find myself in, because searching for this information on the data base often comes up with the page that states "<b>No rows returned by this query. Try selecting different conditions.</b>" This translates to my data set being splotchy and sporadic in the information that I can find and have input into Excel, but not to worry because the search for this information will continue!<br />
<div class="separator" style="clear: both; text-align: left;"></div><div class="separator" style="clear: both; text-align: left;"></div><div class="separator" style="clear: both; text-align: left;"></div>Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-91835692863617334952011-03-21T15:17:00.000-07:002011-03-22T00:16:07.025-07:00A (brief) breakToday is officially the first day of spring break, joy! Well, technically spring break started on Saturday, but that's besides the point. The point is that everyone (most everyone?) gets a week off to relax, go someplace relaxing, and enjoy the weather...or not. I can't put my finger on it, but there's just something off Mother Nature's timing, because it is indeed raining. Again. Or maybe it's because the powers that be in the school system knew of the incoming rainfall and deliberately scheduled break so that it would coincide with these storms. I guess we'll never know.<br />
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But never fear because spring quarter is near! I'm excited for my last academic quarter, and the work/fun that the quarter will bring. Looking back, I didn't think that I had done much this past quarter, but looking back at all the work that was done, it was quite an accomplishing quarter. There was the herbivory counting on the shrub sub-samples, all 21 of them), which was followed by going through the full samples and separating them by new and old shrub growth that were dried and massed. Then work with the arthropods come in, starting with measuring the length and dry weight of larvae pre-bird exclosure experiment, and then sorting the post-experiment arthropods. *whew*<br />
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So in this upcoming quarter, I'll be continuing the lab work that I've been doing, which includes finishing the sorting of the arthropod vacuum samples and vouchering them as well as picking up the phenology work that I did during the fall. On top of that, I'll be writing my scientific research paper on this past quarter's work and present it at my ESYS symposium in May. <br />
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In the meantime, I'll enjoy my opportunity to mentally vegetate for a week and be ready to go starting next Monday!Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-90853413281454788492011-03-17T00:23:00.000-07:002011-03-19T15:12:34.417-07:00And back again<div class="separator" style="clear: both; text-align: center;"></div><div class="separator" style="clear: both; text-align: center;"></div>Hello all! Now that finals are over, for me at least, I bring you back to the dry weight of arthropod larvae that I did a while back and publish this post on the comparisons of the bug biomass to its length. But before I get started, some graphs that I ran in R to help illustrate what is going to be discussed.<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhwVMvU9ccpwWPa9Fr2xqM0NakK81WTAUH2GKHIENZfLcYoxaXgysapVpiBeAzo1beKAQi4vnzjoRNIe8LwNkI2U5-hdq64whSx6Mn9wFHd6sURbI8IrFG3bV70TZlwmepXtSm9X3C-V1M/s1600/bugbiomasslength.jpeg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="318" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhwVMvU9ccpwWPa9Fr2xqM0NakK81WTAUH2GKHIENZfLcYoxaXgysapVpiBeAzo1beKAQi4vnzjoRNIe8LwNkI2U5-hdq64whSx6Mn9wFHd6sURbI8IrFG3bV70TZlwmepXtSm9X3C-V1M/s320/bugbiomasslength.jpeg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 1: Here is the original graph when simply plotting out the length of the arthropod larvae to its biomass. Though some details escape the plot, there are 3 points on this graph that show a different type of larvae (dark red circles).</td></tr>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiGTkOqLsYg6moiMzsQVLOgoKKU_4S47MxNj5o6maoADqR4eJ38BPwa7zoxloxLDHbBxgg_bdptEZaRDVcZL8cdPzDx7NwWbx7GLKS4ZFC1rJL906H45rWc-O8dfQgltlj53z48i6oUZfo/s1600/bugbiomasslength+log.jpeg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="318" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiGTkOqLsYg6moiMzsQVLOgoKKU_4S47MxNj5o6maoADqR4eJ38BPwa7zoxloxLDHbBxgg_bdptEZaRDVcZL8cdPzDx7NwWbx7GLKS4ZFC1rJL906H45rWc-O8dfQgltlj53z48i6oUZfo/s320/bugbiomasslength+log.jpeg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 2: After doing a log transform, this is what the data looks like; much data pertaining to body size are non-linear. There is now more of a distinction between the two types of arthropod larvae. </td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpSyMe5Ho4fQgY_Kp77O7sbpAKu5zOMCLX6fBe6h_WJxXeLkqp-DToGyA8GaBEWQCO50FcfDPa_w55lLDHSYQiDNwmeV8FGErCYC2EV414p0OQnEgwiYuw6Ta5vDVYIoqqW4AafsOn3do/s1600/fit+lines+%2528log%2529.jpeg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="318" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpSyMe5Ho4fQgY_Kp77O7sbpAKu5zOMCLX6fBe6h_WJxXeLkqp-DToGyA8GaBEWQCO50FcfDPa_w55lLDHSYQiDNwmeV8FGErCYC2EV414p0OQnEgwiYuw6Ta5vDVYIoqqW4AafsOn3do/s320/fit+lines+%2528log%2529.jpeg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 3: Voila! These fit lines better help illustrate the relationship of each type of larvae length to biomass.</td></tr>
</tbody></table>And so, we get to the meat of this discussion. To start off, I had collected 37 individual arthropod larvae samples, in which they totaled to about 0.2375g in dry weight. A majority of these samples happen to be of a type of Coleoptera larvae, with the 3 exceptions that were Lepidoptera larvae, and they show that there is a significant increase in weight as their length increases. This appears to be influenced by factors such as body shape, feeding habits (herbivorous or predatory), and the metabolic rate of animals etc[1]. The general idea that can be assumed is that the more an arthropod eats (higher herbivory counts on <i>A. californica</i>), the bigger in mass it becomes, until a certain threshold point. Looking at Figure 1, there seems to be a cutoff value at around 12 mm for arthropod larvae length, which I assume is the maximum size larvae grow to before they are either consumed or pupated. This is useful to know because in such cases, species biomass may reflect functionality more accurately than abundance[2].<br />
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It might be more presumable to think that this is due to bird predation because the larger these larvae are, the more conspicuous it is on the sagebrush leaves. This leads to the possible conclusion that there could a top-down effect on the arthropod community, but only on the larvae in the earlier months, and not necessarily on the mature arthropods that appear closer to summer. Maybe the earlier hypothesis that I came up with should also include a comparison of temporal variation of herbivory; it would be interesting to see if the data changes at different times of the year.<br />
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<div class="MsoNoSpacing"><span style="font-family: Arial,sans-serif; font-size: 8pt;">1. </span><span class="Apple-style-span" style="font-family: Arial,sans-serif; font-size: 11px;">Sage, R.D. 1982. “Wet and Dry-weight Estimates of Insects and Spiders Based on Length.” <u>American Midland Naturalist</u> 108(2): 407-411.</span></div><div style="margin: 0px;"></div><span class="Apple-style-span" style="font-family: Arial,sans-serif; font-size: 11px;">2. Saint-Germain, M; Buddle, C.M.; Larrivee, M; et al. 2007. “Should Biomass be considered more frequently as a currency in terrestrial arthropod community analyses?”</span><span class="Apple-style-span" style="font-family: Arial,sans-serif; font-size: 11px;"> <u>Journal of Applied Ecology</u></span><span class="Apple-style-span" style="font-family: Arial,sans-serif; font-size: 11px;"> 44: 330-339.</span><br />
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</span></span></div>Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-8543489061271050472011-03-02T21:29:00.001-08:002011-03-22T00:17:56.917-07:00Eureka!At least, that's what I think most times I find a new type of arthropod that I haven't seen yet in Lizzie's vacuum samples. She got me started on sorting her bug samples by morphospecies by first going through them and meticulous scanning and collecting them from the trays. I find it rather like a "Where's Waldo?" book, but much more complex and more miniscule. Here are some pictures to illustrate this process:<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZOT3uGvXsh6R66LmuZPtkOIUHwKVZ7Z8Ri8hpwXxYh1GfwU3CLzZ5w6lyraP-GoYL-6z3Yf5PCu6NYbIh-djuQy5lCL4R0wvW40kt0rY2-hR-w6wtsp9TJ0JBIgvGzAx3MqDPwyTSavg/s1600/2011Feb25Morpho_04.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZOT3uGvXsh6R66LmuZPtkOIUHwKVZ7Z8Ri8hpwXxYh1GfwU3CLzZ5w6lyraP-GoYL-6z3Yf5PCu6NYbIh-djuQy5lCL4R0wvW40kt0rY2-hR-w6wtsp9TJ0JBIgvGzAx3MqDPwyTSavg/s400/2011Feb25Morpho_04.JPG" width="266" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Just keep searching, just keep searching, just keep searching searching searching...</td><td class="tr-caption" style="text-align: center;"></td></tr>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgve739Sp-pD7mhBFFlBG7yX4ucacVyHZewWp1vIoPh5AeKm5EMIedwIWoMAMapzZORO9Rv45K8NPT98QVBdJ8PquVY2fr65TNV0dU-30fiYvJPGXN_mJF6oaD4tczoc_pZ5wF-4vGklTs/s1600/2011Feb25Morpho_05.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgve739Sp-pD7mhBFFlBG7yX4ucacVyHZewWp1vIoPh5AeKm5EMIedwIWoMAMapzZORO9Rv45K8NPT98QVBdJ8PquVY2fr65TNV0dU-30fiYvJPGXN_mJF6oaD4tczoc_pZ5wF-4vGklTs/s400/2011Feb25Morpho_05.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Bug of interest has been found!</td></tr>
</tbody></table>Naturally, this is repeated many times over and it is more eyestraining than looking for herbivory on the shrub samples through the microscope, but I find it much more enjoyable. The only problem with this is that I end up spending too much time on each sample bag combing through the litter for bugs that are sometimes <1 mm large and often in a contorted shape. I am hoping to figure out a tempo for how I look for these critters soon so I can become more efficient at searching and memorizing their features. I also hope to be able to take pictures and make some sort of comprehensive pictionary of these insects, but we'll see how time will work out. There's effectively 1.5 weeks left until finals week, got to get cracking!Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com1tag:blogger.com,1999:blog-8678089902065082383.post-54472425999473902152011-02-24T00:46:00.000-08:002011-03-02T23:31:37.701-08:00Pictures are worth many words<center><embed flashvars="host=picasaweb.google.com&hl=en_US&feat=flashalbum&RGB=0x000000&feed=https%3A%2F%2Fpicasaweb.google.com%2Fdata%2Ffeed%2Fapi%2Fuser%2F106232858273422604885%2Falbumid%2F5577562418377190337%3Falt%3Drss%26kind%3Dphoto%26authkey%3DGv1sRgCMupmOnBnry7hQE%26hl%3Den_US" height="367" pluginspage="http://www.macromedia.com/go/getflashplayer" src="https://picasaweb.google.com/s/c/bin/slideshow.swf" type="application/x-shockwave-flash" width="500"></embed></center><br />
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Hopefully the flash works since I decided to try putting pictures in a slideshow for the sake of saving space. However, if it doesn't, I have provided the link to the album <a href="https://picasaweb.google.com/106232858273422604885/SortingAdventures?authkey=Gv1sRgCMupmOnBnry7hQE&feat=directlink">here</a>.<br />
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To better narrate the story, I spent a few hours sorting through the arthropod samples that Lizzie had in the fridge, measuring their lengths, drying them, and then weighing them for their mass. Later on, we hope to be able to determine whether or not there is a correlation between arthropod weight and amount of herbivory on the shrubs.<br />
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The rest of last week was dedicated the remaining shrub samples and sub-samples that were still in the fridge. I separated them into new growth and old growth bags, with new growth being anything that contained leaves and were still "green" and old growth as everything else. These bags were also popped into the dryer, which sat there for ~96 hours each before I were able to measure their weight. To account for the paper bag weight, I also included 4-5 empty paper bags which were dried as is and weighed before I took out the samples. I'll most likely be adding more information here later on to show what our analysis of the data brings us. Hopefully it's something exciting!Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-69253870684382628552011-02-13T20:59:00.000-08:002011-02-14T18:35:33.264-08:00Mas o menos fin!I'm happy to report that manual data recording of herbivory is finished! After editing the excel sheets and entering the data, Lizzie wrote up several R codes to run the data through some statistical analysis and to plot them out. I was able to run them again myself from my trusty laptop, and here are some of the charts for the data:<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhTnvfkdmTvYN5GisoYIpt57kGfr_Mjj4QR3Iw6xi0TFCRMoeV0GRvEGwwh2hMu7TlTIGhOOE6vDzLe8hkbrnollktS1gsDqdI3asUDOfHk6zgDnbEZO-jMPaEDvTtPKEs1M7JjNgJe3II/s1600/histogram.jpeg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="398" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhTnvfkdmTvYN5GisoYIpt57kGfr_Mjj4QR3Iw6xi0TFCRMoeV0GRvEGwwh2hMu7TlTIGhOOE6vDzLe8hkbrnollktS1gsDqdI3asUDOfHk6zgDnbEZO-jMPaEDvTtPKEs1M7JjNgJe3II/s400/histogram.jpeg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">This is the histogram of different shrubs to the total number of herbivory counts. Fortunately, the graph isn't right or left skewed.</td></tr>
</tbody></table><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhKAzKUsr4DmNTm7UY9FdxgDb3w8ZCGZW6Xs5dP1Z5cuLqmBFPC5E_Ph-pcR_Jhs73qdM91cy7LSuXD_OA5tXcKm8yZ_lgaBPdayaftCaxeHrymMv4AecAiXAl9B7bzJyRV741kU8KVWk/s1600/herbiv-trmt.jpeg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="398" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhKAzKUsr4DmNTm7UY9FdxgDb3w8ZCGZW6Xs5dP1Z5cuLqmBFPC5E_Ph-pcR_Jhs73qdM91cy7LSuXD_OA5tXcKm8yZ_lgaBPdayaftCaxeHrymMv4AecAiXAl9B7bzJyRV741kU8KVWk/s400/herbiv-trmt.jpeg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">This is the plot of total herbivory in relation to the type of treatment. From the looks of this, there isn't much herbivory variation between the different types.</td></tr>
</tbody></table><div class="separator" style="clear: both; text-align: center;"></div>Analysis of Variance Table<br />
<br />
Response: tot.herbiv<br />
Df Sum Sq Mean Sq F value Pr(>F)<br />
Trmt 2 3580 1790.1 0.4844 0.6239<br />
Residuals 18 66516 3695.3 <br />
<br />
<br />
In the previous post, I had hypothesized that there would be the greatest variation of herbivory counts between the control and exclosure, but the analysis and plots of the data entered shows otherwise. In the meantime, I've separated the arthropods that Lizzie vacuumed off of various shrubs from last year, measured their lengths, and have put them in the dryer, which will then be weighed to determine their mass. I will also be separating and drying new from old growth on the shrub samples to be weighed so that we can determine the ratio of herbivory to biomass. After Lizzie and I meet tomorrow, we'll be coming up with the next few steps of what's left to be done, and hopefully we'll have more conclusions to display when we finish.Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-35854176073246268992011-02-03T23:56:00.000-08:002011-02-04T00:03:15.304-08:00Short, but sweetHello everyone!<br />
<div><br />
</div><div>Shrub sub-sampling has been great so far. It took a while, but I have finally established a rhythm and method of how to count for the different signs of herbivory without having to consult the data sheet after ever observation. From the data that I've gathered so far, I would hypothesize that there would be the greatest amount of herbivory (nibbles and side-crunches) on the shrubs in the bird exclosures and the least amount on the controls. I think that this makes sense since the exclosure would keep out birds that would eat arthropods, creating a top-down control and the amount of damage arthropods would wreak. After I finish the rest of the samples, I will be inputing the data into an Excel sheet and then Lizzie and I will see if the predictions are true. To conclude this short post, I present a picture taken with my point-and-shoot camera through the microscope lens (which took me about 20 minutes to figure out how to do, James made it look so easy...)<br />
</div><div></div><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyJtdEcigVHfPUtdY9kttp3I43EcvwAoFC2hy6lCBhzEpqZaFWbzD8oyVRFk217JaeGfVuQAZ5XpE4tnE0ARELTEzF66D8yjpe9H54B0pyO709QO5nBVDsbaMcCgNYhgQ5514O5n4-UGk/s1600/bug+picture.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="303" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyJtdEcigVHfPUtdY9kttp3I43EcvwAoFC2hy6lCBhzEpqZaFWbzD8oyVRFk217JaeGfVuQAZ5XpE4tnE0ARELTEzF66D8yjpe9H54B0pyO709QO5nBVDsbaMcCgNYhgQ5514O5n4-UGk/s400/bug+picture.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Surprise!<br />
I found this cicadellid while sampling. It was very exciting, I ended up poking/playing around with it for a good 5 minutes.</td></tr>
</tbody></table><div></div><br />
Oh yes, and a Happy Chinese New Year to all. May this year bring about great discoveries and festivities in the Year of the Rabbit.Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-23451265074987181942011-01-28T00:56:00.000-08:002011-01-29T19:18:12.290-08:00Through the looking glassOn Monday, Lizzie and I worked on coming up with a procedure to determine herbivory from shrub clippings by looking at them with a microscope, which is actually harder than it sounds. Until I actually saw it in person, I had no idea how small the leaves on the <i>Artemisia californica</i> would be... *whew*. But to better illustrate the process in which we decided to try, here is "How to Determine Herbivory" in five easy steps:<br />
<br />
Step 1:<br />
Remove bagged and frozen samples from the fridge.<br />
<div class="separator" style="clear: both; text-align: left;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj-nMjuHxSaaFmFO6V6jZoq7FWlLaBwL1JICgxXKiTjzfC9X37PUeAXKshG46IBa9VYjc_pEK4GURJHJTStJXUfG_uNO7YOTVgMcppzbm91-ILGSYkXM8h7lvq6ySspDzdO1IkDHhS1loM/s1600/2011Jan_BugSorting36.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj-nMjuHxSaaFmFO6V6jZoq7FWlLaBwL1JICgxXKiTjzfC9X37PUeAXKshG46IBa9VYjc_pEK4GURJHJTStJXUfG_uNO7YOTVgMcppzbm91-ILGSYkXM8h7lvq6ySspDzdO1IkDHhS1loM/s400/2011Jan_BugSorting36.JPG" width="332" /></a></div><br />
Step 2:<br />
Sort through the clippings for evenly sized samples. Because not every bag has the same amount, use your eyes to visually judge the amount of foliage you believe is the best to sample (3-4 individual samples should be sufficient).<br />
<div class="separator" style="clear: both; text-align: left;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEii8-Nd683nxSQ6DXZhDig3JKbibZwL7GnIwop6LZpPMtOEXX7LkXe0f8OZkyfOkoKbWwr5LHwVrdQtL9_WXc0zLLNkrFVlDBfe7omM5X1ER6WwJ_QSyXEW3pm2fL38q9q-pDux4T-wjZ8/s1600/step+2.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEii8-Nd683nxSQ6DXZhDig3JKbibZwL7GnIwop6LZpPMtOEXX7LkXe0f8OZkyfOkoKbWwr5LHwVrdQtL9_WXc0zLLNkrFVlDBfe7omM5X1ER6WwJ_QSyXEW3pm2fL38q9q-pDux4T-wjZ8/s400/step+2.jpg" width="400" /></a></div><br />
Step 3:<br />
Take your small clipping and put it under the microscope. Carefully move it around to examine the sample for signs of herbivory (i.e. galls, nibbled ends, etc)<br />
<div class="separator" style="clear: both; text-align: left;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjg3nN0wrg3bOFiF0VMEXqNJi-5KE8apYzS86pMBzNC74JXah_5L-McoUoWeUpH6pG8RAOlkE5QqJVugFbz4ePP2gg0GMoH4yf6Kvaq4ZAODhf5um5zPGOlwXvFGks9b78d6WvNSs95H7M/s1600/step+3.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjg3nN0wrg3bOFiF0VMEXqNJi-5KE8apYzS86pMBzNC74JXah_5L-McoUoWeUpH6pG8RAOlkE5QqJVugFbz4ePP2gg0GMoH4yf6Kvaq4ZAODhf5um5zPGOlwXvFGks9b78d6WvNSs95H7M/s400/step+3.jpg" width="285" /></a></div><br />
Step 4:<br />
Write down results on the accompanying data sheet.<br />
<div class="separator" style="clear: both; text-align: left;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhpPomdtPW9F56edaGZrNoX5P4lIMmCZ9qUOj2jkRvUjoTKjg0LcjukrJbcWp_Lv0mpst5TQGyX7mKFOnbCpRbmcpsd_6SjApGqsJPrw90msrEXAvNjnhGzwB52f2Z0oQ4Bhafz8tZKdHI/s1600/step+4.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhpPomdtPW9F56edaGZrNoX5P4lIMmCZ9qUOj2jkRvUjoTKjg0LcjukrJbcWp_Lv0mpst5TQGyX7mKFOnbCpRbmcpsd_6SjApGqsJPrw90msrEXAvNjnhGzwB52f2Z0oQ4Bhafz8tZKdHI/s400/step+4.jpg" width="375" /></a></div><br />
Step 5:<br />
Repeat steps 1-4 until finished with day's worth of samples.<br />
<br />
So far, through our initial trial, we've found that we can classify most of the plant damage into three categories: galls, side-crunch (entire sides of leaves gnawed), and nibble (small bites into leaf or at the tip). There were the occasional anomalies, such as this cotton-ball like substance I found on a few of my samples, and the waxy exterior that some of the leaves seemed to have. But in all, these discoveries were exciting to see through the microscopes since everything looked so much better magnified.<br />
<br />
<br />
::edit 1-29::<br />
<br />
I've found that working in the Holway Lab has its perks. For example, I was able to talk to Professor Holway about some of the observations I made, such as the cotton-ball I've been seeing on some of the samples, and he said it's most likely another type of gall (Lizzie also confirmed this after emailing and asking around for answers). I was also able to talk to one of the PhD students, James, about another observation<i> </i>I made later in the day. I had asked him to look at it, but he wasn't able to view it through the microscope (which by the way, is a fantastic piece of equipment). James came up with an ingenious idea of taking a picture of what I was seeing through the microscope itself, and this is what came up:<br />
<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtKsxMKJchktk4TbVom-_dyJMt0wVrKzjNWkov9JioVclwtBiJu_CaaD3jNOCLEzyg-329Ybplfkx29_vZet1Wy6GLYmawMXtMgJB3A_gotPnMoRow1f9jIveEYLStUCrZa3ziEo9vL0c/s1600/IMG_5538.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtKsxMKJchktk4TbVom-_dyJMt0wVrKzjNWkov9JioVclwtBiJu_CaaD3jNOCLEzyg-329Ybplfkx29_vZet1Wy6GLYmawMXtMgJB3A_gotPnMoRow1f9jIveEYLStUCrZa3ziEo9vL0c/s400/IMG_5538.JPG" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;"><br />
</div><div class="separator" style="clear: both; text-align: left;">I'm not sure exactly what this is, but I have assumed that this is a may be a scale insect. Until I have further confirmation through readings (or through the power of Google search engine), I have written down these occurrences as a separate category. In the meantime, I will rest my eyes up until Monday's sample scoping adventures. New discoveries await!</div>Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-23874430153752908532011-01-24T01:06:00.000-08:002011-01-24T02:57:47.022-08:00TMI<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"></span><br />
<div class="MsoNoSpacing"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Until Lizzie told me to mentally force myself to write down hypotheses for these papers I've been reading, I have to say that I definitely had too many conflicting ideas floating around in my head, literally. Floating as in, "I think this is what the authors are saying but I'm not really sure because I'm already thinking about the other two articles I just read" kind of floating.</span><br />
<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"><br />
</span><br />
<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"></span><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">So needless to say, actually sitting down and writing 6 different hypotheses on floral reflectance in relation to phenology and pollinators was a daunting task (I had fortified myself with two delicious Klondike ice cream bars before I started). But I believe I have come up with some hypotheses, please excuse me if they are not as original or understandable as they could possibly be:</span></div><div class="MsoNoSpacing"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"><br />
</span></div><div class="MsoNoSpacing"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">1)<span style="font-size: 7pt;"> </span>Floral reflectance variability differs depending on the time of year which the plant blooms.<o:p></o:p></span></div><div class="MsoNoSpacing"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">2)<span style="font-size: 7pt;"> </span>Exotic, invasive plants have higher ranges of color spectrum variability to attract native pollinators (discriminated through human vision).<o:p></o:p></span></div><div class="MsoNoSpacing"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;"><br />
</span></div><div class="MsoNoSpacing"><span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif;">Another note, I wrote out these hypotheses before I read some more papers, one of which included<span class="apple-converted-space"><span style="color: black; font-family: Arial, sans-serif; font-size: 13.5pt;"> </span></span><i>Flower color phenology in European grassland and woodland habitats, through the eyes of pollinators</i>, written by Sarah E.J. Arnold, Steven C. Le Comber, and Lars Chitka. Fortunately (and somewhat unfortunately), their results showed that there was no trend in woodland flowers blooming in particular months to share the same color more often than expected by chance, "as one might predict if particular colors dominated at certain times of the year..." Their results (technically) nullified my first hypothesis since I do not know if this is true among other biomes, but it was a good discovery. The article in itself was a good find as well, since the authors included phenology tables for five habitats, and organized plants by family, genus, and species in regards to their flower colors (humans and bees). I'll be inputing this data into the known modes tab of the plant traits document I've been updating, but I think I'll save that for some time later during the day. So long for now!</span></div><br />
<div class="MsoNoSpacing" style="margin-left: .5in; mso-list: l0 level1 lfo1; text-indent: -.25in;"><span class="Apple-style-span" style="font-family: 'Times New Roman', serif; font-size: small;"><o:p></o:p></span></div>Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-64534051291253898812011-01-19T20:05:00.000-08:002011-01-19T20:51:54.173-08:00Hello FReD!This week, I was given the task of doing several literature reviews on floral reflectance in respect to pollinators, one of which was called <i>FReD: The Floral Reflectance Database-A Web Portal for Analyses of Flower Colour</i>. This paper, which was published and can be accessed freely on PLoS ONE, can be viewed as an instructions manual of how to access and use this database for researchers to "...download spectral reflectance data for flower species collected from all over the world." I've included a print screen to show the data that comes up when I hit the search button:<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHwd2nIdLKABYi1MAHDer0ms2x9_fM9ekonoCemC0FRlEqcMcNPKlYtHK06CMpQX8QPnJBfdh8eA91FvbTpcgf0GQmVj6gG238OdSlkGuH685YLMBjOXD_nDJ3F6Nk4QiUbSOMDT2PGiU/s1600/fred+printscreen.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="296" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHwd2nIdLKABYi1MAHDer0ms2x9_fM9ekonoCemC0FRlEqcMcNPKlYtHK06CMpQX8QPnJBfdh8eA91FvbTpcgf0GQmVj6gG238OdSlkGuH685YLMBjOXD_nDJ3F6Nk4QiUbSOMDT2PGiU/s400/fred+printscreen.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">In this screen-shot, I've categorized the entries by country of origin (where the data was collected).</td></tr>
</tbody></table><div>I think that once this database contains more information, it will be a great key tool for researchers wanting to find out what type of color (viewed through human eyes) are most likely to attract the attention of bees. However, a few problems that I have with this at the moment is that there are only 899 records on the database, which limits the amount of information that can be gathered. Second, in relation to the work that Lizzie has assigned me, this database does not provide information on plant species in the U.S., and instead has much more floral information about plants mainly in Brazil and Germany. Lastly, this database is highly focused on bees and no other types of pollination modes by animals (i.e. hummingbirds, beetles, etc.). Despite these limitations, FReD has been set up in a very user-friendly mode that makes it easy for anyone to search up information.</div><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOKaLlcltqtNq4bjwNy-SKrQ16QsmeVxpQ0GIGNndrIIOfWSYWsQH-1eHJWa30ai40-G0PpQeJ0RduTIVUOvCf2JcX5XJ292QUgl3mNCU7EBNU6qfVbwnkDhBVOBYBCbKnTfSv-RjWY2Y/s1600/advanced+search.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOKaLlcltqtNq4bjwNy-SKrQ16QsmeVxpQ0GIGNndrIIOfWSYWsQH-1eHJWa30ai40-G0PpQeJ0RduTIVUOvCf2JcX5XJ292QUgl3mNCU7EBNU6qfVbwnkDhBVOBYBCbKnTfSv-RjWY2Y/s400/advanced+search.JPG" width="357" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The drop-box selections and check boxes allow users to control what information they wish to have presented.</td></tr>
</tbody></table><div>Going back to this paper, however, the writers have brought up several interesting points about pollinators' sensitivity to different wavelengths of light, and in short, floral reflectance. The reason that FReD was developed is to provide access to flower colors are "...not inherently human-biased and which can be used when considering the interactions between floral appearance and the visual systems of pollinators." This brings up several other papers that Lizzie printed out for me to read, and a few that I've browsed on ISI Web of Science, but I've decided that I will save that post for a later time. Stay tuned for more information!</div>Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-36413788389474504992011-01-08T00:06:00.000-08:002011-01-10T00:07:02.400-08:00Happy (belated) New Year!Hello all!<br />
<br />
The holidays have come and passed, so now it's time to get back into the swing of things. Where we last left off, I had just finished the last of my assigned work that Lizzie gave me to do...and now, it's time to pick the pace up again. I'll be updating the ongoing master output list, which will hopefully also cut down on the amount of time and need-to-find info that I will be working on for these sites. Looking at it now, the list is larger than I last remember, but never fear! I'll be tackling this one location at a time, starting with the kochmer site and slowly making my way down the list Lizzie has posted.<br />
<br />
Another project that will be happening this quarter involves the Sweetwater NWR area to look in on exclosures to determine the important of interactions between arthropods and birds in the area and how they affect the fauna. However, considering that southern California received copious amounts rainfall during the holiday weeks, I think that there is a high possibility that the area could either be washed out or at the very least, inundated. Lizzie on the other hand, would like to say otherwise and disagree with my prediction; we'll be able see who is right once we head out there to check out the area.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgD52YVpXZikpw9TfB-y0QsfaWVzuqqUgZr30bOBbskRz55fH15rUvvluY74lKzkPvXH8YyG7bubazDjxMzNqb41mGyG8W4BELvV8nGJl9wmFHIB93oK5TwFQxmjAmfRS6tzocer-Fi1XM/s1600/cropped.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="276" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgD52YVpXZikpw9TfB-y0QsfaWVzuqqUgZr30bOBbskRz55fH15rUvvluY74lKzkPvXH8YyG7bubazDjxMzNqb41mGyG8W4BELvV8nGJl9wmFHIB93oK5TwFQxmjAmfRS6tzocer-Fi1XM/s400/cropped.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Exclosure! Or at least, half of it. This is also used to test the intelligence of birds (just kidding!)</td></tr>
</tbody></table>And with this said, hopefully the next update I have will include my progress on getting information for the sites listed, and have non-weather related information.Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-9807626054928521512010-12-15T13:58:00.000-08:002011-01-24T02:56:24.088-08:00In which we take a breakGreetings to all from Los Angeles!<br />
<br />
I apologize for the very long break between the last post I wrote and this current one. Finals week impeded any progress that would have been made and diverted a substantial amount of my brainpower towards viewing and reviewing my several hundred sheets of printed notes (don't worry, I chose the most eco-friendly of options and printed front and back whenever I could).<br />
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Before finals week though, I had lunch with Lizzie, where she presented me with a challenge of coming up with my own ideas of how I could use data on pollination mode and flowering time to test ideas about niches. Despite the fact that Lizzie told me it was supposed to be a somewhat fun and light-hearted question to think about, I ended up racking my brain to find some all-encompassing idea that would tie these factors together.<br />
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In my not-so-coherent thought process, I based my ideas around temperature, and a few other factors that I've learned this quarter. Since it is generally concluded that plants would flower around the times of their preferred mode of pollination, I feel that it is safe to say that perhaps during the months of mid-March onwards, plants are more frequently animal pollinated as opposed to wind pollinated since temperatures begin to warm around then. On the other hand, the earlier months (January-March) would consist more of wind pollinated species, mostly those that are forbs/herbs (I had the picture of the graph we got from running R on the Gates' phenology data in my head while I was writing this). From what I've also learned this quarter is that the degree of latitude and altitude at which plants are observed at can play a role into phenology. The fact is that as climate becomes increasingly warmer earlier in the year, plants and animal species tend to migrate towards the poles and upwards in latitude to find locations more suited for their growth and reproduction. In terms of niches, this would mean that plants that flower later in the year are likely to be more specialized since there would be more competition for limiting resources (light, water, nutrients, etc), and vice versa.<br />
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With this in mind, Lizzie said we may be able to test some of these ideas on a smaller scale next quarter (or maybe the quarter after, but that's TBD). But for now, I'll be enjoying the comforts and festivities of home before heading back to San Diego and the last chapters of my undergraduate career!<br />
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Have a safe and happy holidays everyone! =DWinnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-28286102016663571322010-11-23T22:36:00.000-08:002010-11-26T22:21:04.394-08:00The new queen of pollination modes (get it? bees, queens, pollination!)<div class="separator" style="clear: both; text-align: center;"><br />
</div>While Winny tries to catch up on all the life (and bioinformatics work) missed while she was grounded by computer woes I am blogging to wish you all a Happy American Thanksgiving. Happy American Thanksgiving all.<br />
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One of the main things Winny missed while hanging out with the computing help staff was my ebullient emails to her about her progress. After weeks of reading old books on pollination modes, new papers suggesting we know nothing about pollination and visiting many websites, transcribing many, many (I repeat, many) pollination modes, Winny had 2,228 known pollination modes (at the species, genus or family level)! I ran this through a list of 16,659 species I was hoping we could get pollination mode data for and we have it for 77% of them -- or 14,490 species. I think Winny's known modes tab is probably the most complete directory of pollination modes anywhere.<br />
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So in summary, Winny -- the best and brightest new plant traits informatician I know - you rock!<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh9BR_Eo9mGwZ37bgWE3QDKpp8Zfi1DGnAp3YncmkuBrzXML6YDZXHVJcFB4NV2nYLuEA_i3SXnkKBAcPoO5KYmve65qHUiC5ggTYTuOZrBCd37Iq1W7w-iwphzzC8FpYHgfxJu7q4w2jk/s1600/2010Oct19_rainyMuir15.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh9BR_Eo9mGwZ37bgWE3QDKpp8Zfi1DGnAp3YncmkuBrzXML6YDZXHVJcFB4NV2nYLuEA_i3SXnkKBAcPoO5KYmve65qHUiC5ggTYTuOZrBCd37Iq1W7w-iwphzzC8FpYHgfxJu7q4w2jk/s320/2010Oct19_rainyMuir15.JPG" width="213" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">That's Winny entering data buried in the <i>Principles of Pollination Ecology.</i> Back in the day when things with her computer were swell.</td></tr>
</tbody></table><br />
<br />
Winny will be back with an exciting end-of-term blog in the next week or so, so stay tuned for the final chapter of our current plant traits journey. Then I will round out the year with news from a trip to Santa Barbara for work and a visit to the Entomological Society of America, to be held right here in the happening hotel circle neighborhood of San Diego (I jest, about the 'happening,' the meeting really is in San Diego).<br />
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<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhNgM85N9gnEX8fPV8nkSfmw_HQ1a-57Kh9OgAuFLhRezoEPoQ9kA0G2rYhS33fOtOXAj3ytKgN1z92EEu73Ua2j8odGL4jUG6iLV0TbP8-_PXe90WHcEAlyZK1sbAcxXogqPpgqD0JxiQ/s1600/Lights_sm.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><span class="Apple-style-span" style="-webkit-text-decorations-in-effect: none; color: black;"></span></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiv0ENhYNJzdkbaOrOmzd_RnA4tvk0HxszgaR5nRsgckEw8cVx2xEq5lArPRliqVqHdruCJ3NwkotM4Ulgzrzl87oEbz4ZLCNMUV73JVWIYNemUoWSvXbiPV_5bqJSTdPaGdKQA66bqrEw/s1600/OB+Christmas+treesm.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiv0ENhYNJzdkbaOrOmzd_RnA4tvk0HxszgaR5nRsgckEw8cVx2xEq5lArPRliqVqHdruCJ3NwkotM4Ulgzrzl87oEbz4ZLCNMUV73JVWIYNemUoWSvXbiPV_5bqJSTdPaGdKQA66bqrEw/s320/OB+Christmas+treesm.jpg" width="240" /></a><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhNgM85N9gnEX8fPV8nkSfmw_HQ1a-57Kh9OgAuFLhRezoEPoQ9kA0G2rYhS33fOtOXAj3ytKgN1z92EEu73Ua2j8odGL4jUG6iLV0TbP8-_PXe90WHcEAlyZK1sbAcxXogqPpgqD0JxiQ/s320/Lights_sm.jpg" width="240" /></div><div class="separator" style="clear: both; text-align: center;"><span class="Apple-style-span" style="font-size: x-small;">Holiday season started this week in San Diego: The beach-ball tree at Ocean Beach and lights up el Prado at Balboa Park. I admit we're a little Christian-centric here (it's a military town!) so apologies on the uni-denomination theme.</span></div>Lizziehttp://www.blogger.com/profile/09989005827839292498noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-70637932281480888132010-11-16T19:10:00.000-08:002010-11-16T19:47:38.976-08:00I've been grounded!<div class="MsoNormal"><span style="font-family: "Arial","sans-serif";">..or at least, benched, for the past 5 days due to hard drive failure. On Sunday night, at around 1:30am, I was finally able to do a clean reinstall of Windows 7 and Ubuntu. However, I also lost many of my documents that I haven't backed up in the past month, which is very aggravating to say the least. I thought that my troubles were at an end when I received multiple notifications from my computer that I need a new hard drive. So finally, I received my hard drive today and am currently re-reinstalling Windows 7. Oh PCs, how you aggravate me so.</span></div><div class="MsoNormal"><br />
</div><div class="MsoNormal"><span style="font-family: "Arial","sans-serif";">I've also lost some nifty graphs that I saved from the R-script code that Lizzie wrote and went through with me on Tuesday. Though the scripting language still seems daunting, I can't deny that it looks very useful and helpful for sorting out a great multitude of data. Hopefully, once I am able to reinstall R and the VPN, I will be able to reconnect back to the server and run through the script again myself so I can update this post with some graphs (edit: Lizzie was awesome enough to help me upload the graphs from the R script that she wrote!).</span></div><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjboLkWaLavhIClyjXph3dKuF0DRwsF6B4ya4R-sCejPdiok_20sl8jWptmdny8rYe_XDcoXG-BLd8VBLGTKEw4irEI605wLUGFbnj0R_zw6dOPLS9weSoUm92zIYbnLZ3tkMY_w9njbjs/s1600/many+curves.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjboLkWaLavhIClyjXph3dKuF0DRwsF6B4ya4R-sCejPdiok_20sl8jWptmdny8rYe_XDcoXG-BLd8VBLGTKEw4irEI605wLUGFbnj0R_zw6dOPLS9weSoUm92zIYbnLZ3tkMY_w9njbjs/s400/many+curves.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Each color represents one species listed on Gates' records. The snazzy features of R allowed it to run the data in the excel sheet and colorfully map it out.</td></tr>
</tbody></table><span style="font-family: "Arial","sans-serif";">In the meantime, I've been reading the book that Lizzie uploaded onto the server, called R in a Nutshell, to gain a better understanding of this esoteric language. Fortunately, the author has an easygoing writing style that I like, which is similar to the books in the Dummies series. I like how it has a very nice, tutorial in the beginning accompanied by examples of the explanations and later on, provides more advanced material for readers that would like more in depth knowledge of R (in short, this book does not make me feel like such a n00b, so to speak).</span><br />
<div class="MsoNormal"><span style="font-family: "Arial","sans-serif";"> </span></div>Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-12386456747223639762010-11-04T13:07:00.000-07:002010-11-04T13:08:08.018-07:00Summer in November with numbers, tables, and rulers<style type="text/css">
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<div style="margin-bottom: 0in;">90<span style="font-family: 'Liberation Serif', 'Times New Roman', serif;">°</span>F in La Jolla? Sweet... except that it's already November. Not that I mind, but it would have been nice to have this be the other way around, where summer was actually summer and now to be autumn. It's like we're in the southern hemisphere! </div><div style="margin-bottom: 0in;"><br />
</div><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjCsrQRx38jbqhBpswClaKfLD5ZZj0djiXuatBJUH7nFhYjrgps_WXAIafMsxGj6otWsVKXDXVHBW2BtzwGVLCxIX342GqJR9_cOjYqKOUc1EFWHzkO7zleqknxRiBhgwuh43n3y3PWD8Q/s1600/SAM_0623.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjCsrQRx38jbqhBpswClaKfLD5ZZj0djiXuatBJUH7nFhYjrgps_WXAIafMsxGj6otWsVKXDXVHBW2BtzwGVLCxIX342GqJR9_cOjYqKOUc1EFWHzkO7zleqknxRiBhgwuh43n3y3PWD8Q/s400/SAM_0623.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Looks like the Sungod statue is happy as well!</td></tr>
</tbody></table><div style="margin-bottom: 0in;">I know that many phenological records we have today are from long time observations of many individuals taking time to painstakingly write down information about the species they have observed. This is exemplified by the paper that Lizzie gave me on Tuesday to peruse, called Gates' Phenological Records of 132 Plants at Manhattan, Kansas as transcribed by Lloyd C. Hulbert. In it, Hulbert talks about how most of the records started in 1929 by Dr. Gates were “...of plants around his home or seen when walking between his home and Dickens Hall on the KSU campus, a distance of about three-fourths mile” and he continued to do so until his death in 1955. Due to Gates' dedication to recording the flowering times of the species he observed, Hulbert later writes that maybe the reader will also wish to record phenological data and in doing so, can contribute useful knowledge while enjoying oneself.</div><div style="margin-bottom: 0in;"><br />
</div><div style="margin-bottom: 0in;">Also accompanying this paper is an index of all plant species that Gates encountered and recorded, along with tables of flowering dates in conjunction to the year it was observed. The following picture should be able to illustrate what are on the tables:</div><div style="margin-bottom: 0in;"><br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2IVmpr5CUDGJdnjZz5jYC-0H5cQX7uTgK8T9UpJMY-v7WuGbp15Ln5SkHP7_hWJ2myMrykgpUn2O3TAzFSx7cBmINSB7rlyHrIFvN9Rc3lGEE-3koPrYGun_7G7suyENg51WDFDEAqwI/s1600/SAM_0617.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2IVmpr5CUDGJdnjZz5jYC-0H5cQX7uTgK8T9UpJMY-v7WuGbp15Ln5SkHP7_hWJ2myMrykgpUn2O3TAzFSx7cBmINSB7rlyHrIFvN9Rc3lGEE-3koPrYGun_7G7suyENg51WDFDEAqwI/s400/SAM_0617.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Handy-dandy ruler</td></tr>
</tbody></table><div style="margin-bottom: 0in;">What I have been doing with the tables are going through each individual species listed and writing down the corresponding month, day, and year in which the species first flowered. 7 complete tables and 1450 entries later, I have to say that this is slightly eyestraining work, mostly because the tick marks that indicate the date are small, along with the years that are written down. At times, I take breaks and move my eyes around to prevent them from becoming stuck (if that's possible). The good thing about this is that I can easily fall into a routine and finish at a fairly even and rapid pace, so pretty soon, we should be able to create graphs from the data input in the excel sheet.</div><div style="margin-bottom: 0in;"><br />
</div>Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-70664389151455069562010-11-01T18:14:00.000-07:002010-11-01T21:02:30.843-07:00Aberrant phenologies<meta content="text/html; charset=UTF-8" http-equiv="Content-Type"></meta> <meta content="text/css" http-equiv="Content-Style-Type"></meta> <title></title> <meta content="Cocoa HTML Writer" name="Generator"></meta> <meta content="1038.32" name="CocoaVersion"></meta> <style type="text/css">
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<div class="p1">This weekend I got bonked on the nose by a foam surfboard while paddling out over a crazy wave -- it was that 'thhwwwamp' part where, if you're lucky, you've slammed down on the other side of the wave with most of your body still on the board. If you're less lucky, like me, you're halfway off your board and scrambling back on before the next thwampy wave, and your poor friend has lost total control of her board and it's careening quietly towards your nose.</div><div class="p2"><br />
</div><div class="p1">But of course the exciting part of my week was the previous 5 days which I spent in a conference room in Tucson. Working with the USA National Phenology Network, a couple folks and I were hammering out how plants respond to climate across sites and how constrained by evolution phenology may be. The short story is flowering time is ridiculously constrained by phylogeny and responses to climate are not -- we're working on that latter bit now. I am cleaning up code: it gets so messy written on the fly. On the way to these exciting findings we made predictions about latitudinal gradients and invented the new Whittaker plot for phenology (see picture).</div><div class="p1"><br />
</div><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi-GjHkNmj7IQw-zdIk4ODZx-uXBRGoQi267bZ59ktQkjcvhsQoIM_CAHJc35hSYTIuAUSA6Uf-e6Q5pteGwgtbl0unowRmiuYHwUkf8l_nZ-IMTUjUuMqrQ0c405qV13_7UWAUwSEx9zg/s1600/2010Oct29_WeltzinPhen03.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi-GjHkNmj7IQw-zdIk4ODZx-uXBRGoQi267bZ59ktQkjcvhsQoIM_CAHJc35hSYTIuAUSA6Uf-e6Q5pteGwgtbl0unowRmiuYHwUkf8l_nZ-IMTUjUuMqrQ0c405qV13_7UWAUwSEx9zg/s320/2010Oct29_WeltzinPhen03.JPG" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The new Whittaker Biome Plot! It took three PhDs two hours or so to come up with this work of clear genius. We're obviously taking it up a notch by adding the Atacoma desert to the plot.</td></tr>
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</div><div class="p2"><br />
</div><div class="p1">I also got out to see some aberrant phenology research in action! On Friday, Jake Weltzin, Director of the USA National Phenology network took one colleague and I out to see something other than the construction zone of Tucson (which seemed to be the part of Tucson our morning walk from hotel to office was based). </div><div class="p2"><br />
</div><div class="p1">Jake let us see some of the plants he's monitoring as part of the USA National Phenology Network's Nature's Notebook program (http://www.usanpn.org/participate/observe): a couple buffel grass (a non-native with a uncommon phenology), a barrel cactus and two totally freak saguaros: one was moving beyond some disease or such; I forget what he called it but it definitely should be 'headdress saguaro.' The other one has freak buds and is named by Jake 'baby saguaro.'</div><div class="p1"><br />
</div><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIJFN9aLDs0suv4UtK5F0g_SEv4ekczJu1oYd8HyRqLD4xCjzCAUNHo73I7B-dE6491p9EmbsUwQg9vDpesOqzeyzlHuZSytNkYW2iH9053q6oUj5F7S9uUQCHmDpXrpzfIopRaFtrfa0/s1600/2010Oct29_WeltzinPhen07sm.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIJFN9aLDs0suv4UtK5F0g_SEv4ekczJu1oYd8HyRqLD4xCjzCAUNHo73I7B-dE6491p9EmbsUwQg9vDpesOqzeyzlHuZSytNkYW2iH9053q6oUj5F7S9uUQCHmDpXrpzfIopRaFtrfa0/s400/2010Oct29_WeltzinPhen07sm.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Jake explained the current phenological state of one of the 3 buffel grasses he's monitoring. His buffel grasses seem normal but check out the crazy saguaro behind him (upper left) -- I call it 'headdress saguaro,' and he's monitoring it too.</td></tr>
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</div><div class="p2"><br />
</div><div class="p1">Of course when you're trying to use a network of people to get at mean phenological trends for different species observing the most aberrant individuals is a special approach. But you have to spice up life a little: I think that's why I like to thwamped by waves and Jake likes to monitor an adorable cactus that seems to be developing alien buds.</div><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhY8-4MUMe2FEumu1Xw97s1kIGukY8KKsydFYVTObf5yOrm-YYHE4q2Gx-8eT5CZYRBJlurF8xN_a9z67KdEoaqWidryFT2I3ESdl545JOYhrfBeG632RQwbSA11PFp8dYxrswmiqQhZhI/s1600/2010Oct29_WeltzinPhen17sm.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhY8-4MUMe2FEumu1Xw97s1kIGukY8KKsydFYVTObf5yOrm-YYHE4q2Gx-8eT5CZYRBJlurF8xN_a9z67KdEoaqWidryFT2I3ESdl545JOYhrfBeG632RQwbSA11PFp8dYxrswmiqQhZhI/s640/2010Oct29_WeltzinPhen17sm.jpg" width="419" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Jake with another saguaro he's monitoring. He calls this one 'baby saguaro' because of its freak buds (top).</td></tr>
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</div>Lizziehttp://www.blogger.com/profile/09989005827839292498noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-50209302934833232542010-10-21T11:41:00.000-07:002010-10-21T11:45:52.344-07:00Welcome to not-so-sunny San Diego<div style="margin-bottom: 0in;">Rain has arrived!...in October. I have to say, I still find the weather strange. It was only a few weeks ago that temperatures soared up into the 110+ degrees Fahrenheit, but now it's the complete opposite with storm clouds dominating every part of the sky. The weather just doesn't seem to be making up its mind as to what it wants to do, which somewhat makes me sad.</div><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjc2iPqhxNIF4fV1rNsNe_bOYFVy8T7D2G5ILVqSVJhXOh-QoduG9UNrBwzGX3TZFrWQoM9g5P2F7gAkc_1Rl5AhC4-j4yNXWt1yHU8WdW32RvrYictQTYAFeVPHnzktV94GM5NO_mKVk0/s1600/2010Oct19_rainyMuir09.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjc2iPqhxNIF4fV1rNsNe_bOYFVy8T7D2G5ILVqSVJhXOh-QoduG9UNrBwzGX3TZFrWQoM9g5P2F7gAkc_1Rl5AhC4-j4yNXWt1yHU8WdW32RvrYictQTYAFeVPHnzktV94GM5NO_mKVk0/s400/2010Oct19_rainyMuir09.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">I was told to look happy, but I was mostly laughing at the situation this picture was taken in.</td></tr>
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</div><div class="separator" style="clear: both; text-align: center;"></div><div style="margin-bottom: 0in;">Lizzie is sad too. Actually, she's mostly sad over the fact that one of the weather blogs she followed is no longer posting (<span style="color: navy;"><span lang="zxx"><u><a class="western" href="http://www.signonsandiego.com/weblogs/weather-watch/">http://www.signonsandiego.com/weblogs/weather-watch/</a></u></span></span>). I can't tell you whether or not the blog was a good one (especially since I didn't know that weather blogs existed), but I am taking it on Lizzie's word that it was the best weather blog to be created. Personally, I thought that a weather blog was somewhat strange and kept by bloggers who weren't sure of what else they should be observing or commenting on besides the weather, to which I think is fine since everyone has their own idiosyncracies. (Note from Lizzie: This weatherblog was fantastic, especially as a grad student who was based 3.5K miles from my field sites in San Diego most of the year, and whenever you thought, ‘boy, is it oddly wet’ you could check it and it would say ‘this is the wettest March since . . . . ‘ And it did a complete review of all ENSO predictions.)</div><div style="margin-bottom: 0in;"><br />
</div><div style="margin-bottom: 0in;">Anyway, the other big issue with the rain is that it’s putting a crimp in field work plans. Doing phenology work on first leaf means getting the jump on the season. But scheduling that work also means having some guesses at the seasons. Lizzie and <span style="color: black;"><span style="font-family: 'Liberation Serif', 'Times New Roman', serif;"><span style="font-size: small;"><span lang="en-US">I</span></span></span></span> were hoping to collect some coastal sage scrub high-resolution phenology data – in the winter (the winter being when things usually start growing). Now we’re going to re-assess.</div><div style="margin-bottom: 0in;"><br />
</div><div style="margin-bottom: 0in;">To take my sadness and slight displeasure to the rain, I have written an open letter to the weather, to which I will not have any responses.</div><div style="margin-bottom: 0in;"><br />
</div><div style="margin-bottom: 0in; margin-left: 0.49in;">Open letter to the storm clouds:</div><div style="margin-bottom: 0in; margin-left: 0.49in;"><br />
</div><div style="margin-bottom: 0in; margin-left: 0.49in;">Hello, how are you? Fantastic. I've noticed that you've arrived somewhat early this year, and though normally I would be glad to see you, I'm tired of you quite frankly. This year was the first summer that I spent in San Diego, and I had expected San Diego to live up to its amazingly beautiful and sunny reputation. You, however, have dashed my hopes of San Diego ever being sunny again. Don't take this personally, storm clouds, I do like you...just not at this moment. </div><div style="margin-bottom: 0in; margin-left: 0.49in;"><br />
</div><div style="margin-bottom: 0in; margin-left: 0.49in;">Fortunately, the temperature is still warm enough that your cold raindrops do not give me chills when I bike downhill heading home after a day on campus. At times, I even enjoy the rain that you bring down upon me, but I'm not here to tell you how I enjoy some of the benefits of your arrival. No, I'm writing to tell you that I am displeased, that you make places much less convenient to get to. If only you weren't so finicky as to when you decide to rain. </div><div style="margin-bottom: 0in; margin-left: 0.49in;"><br />
</div><div style="margin-bottom: 0in; margin-left: 0.49in;">And curses to you too, not-so-accurate Weather.com. You have not lived up to your services either, especially your 'hourly' tab, where you think you are so accurate as to what the chance of precipitation is and its time of arrival. I am starting to wonder whether or not you are working together with these weather forecast services, storm clouds.</div><div style="margin-bottom: 0in; margin-left: 0.49in;"><br />
</div><div style="margin-bottom: 0in; margin-left: 0.49in;">I hope you will be able to find some time to respond to me and retreat for a while, just so the days are actually days instead of a seamless evening. I do really miss the sun. Also, my tomato seedlings need sunlight too. I hope to not see you anytime soon in the next few days.</div><div style="margin-bottom: 0in; margin-left: 0.49in;"><br />
</div><div style="margin-bottom: 0in; margin-left: 0.49in;">Sincerely,</div><div style="margin-bottom: 0in; margin-left: 0.49in;"><br />
</div><div style="margin-bottom: 0in; margin-left: 0.49in;">Winny</div>Winnyhttp://www.blogger.com/profile/18134660159402981225noreply@blogger.com0tag:blogger.com,1999:blog-8678089902065082383.post-74982908562005261912010-10-21T11:14:00.000-07:002010-10-21T11:59:12.023-07:00Computers, dogs and field work<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwjBkIcKjl-Pl80aNLo4NbLJYcMlMfJTorPdqh7XnHwoqLSjhy7MYai2U_XD-cRmkW0MBL7hXE-eLnVtaulg2z0uXdIZKJCNlfcj1CrpKEn5BoUwjjno5Qsxqu-cC0_6qEYhz_8gFn0k4/s1600/2010Oct21_Willy4.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="213" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwjBkIcKjl-Pl80aNLo4NbLJYcMlMfJTorPdqh7XnHwoqLSjhy7MYai2U_XD-cRmkW0MBL7hXE-eLnVtaulg2z0uXdIZKJCNlfcj1CrpKEn5BoUwjjno5Qsxqu-cC0_6qEYhz_8gFn0k4/s320/2010Oct21_Willy4.JPG" width="320" /></a></div><br />
Doing bioinformatics work seems to mean I am always sitting in front of a computer. The good news is that also means that while other people need to go out to their field sites I am around to hang out with the dogs left behind. So today, my officemate Claire and I have Willy for companionship.<br />
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<tr><td class="tr-caption" style="text-align: center;">Nice work Claire with the tidy desk, apple and mug--looks very scholarly.</td></tr>
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</div>Lizziehttp://www.blogger.com/profile/09989005827839292498noreply@blogger.com1tag:blogger.com,1999:blog-8678089902065082383.post-21058913407735023182010-10-19T19:05:00.000-07:002010-10-19T21:38:46.770-07:00How computer-savvy do ecologists need to be?<i>Greetings from monsoonal San Diego! I am going to post every now and then as we get this blog started and in lull periods.</i><br />
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</div><div class="MsoNormal">While waiting for the bus in the pouring rain to go from campus in La Jolla to my sopping wet bike in Hillcrest (smart move of the day #1 was leaving my bike helmet attached to my bike) I read a recent article by Aaron Ellison and Brian Dennis (<a href="http://www.esajournals.org/doi/abs/10.1890/080209">http://www.esajournals.org/doi/abs/10.1890/080209</a>) suggesting that all ecologists have two terms of college-level calculus, a touch of linear algebra and several probability courses. That’s a daunting list for a good number of ecologists (and I don’t exactly measure up—though I did sit in on linear algebra in my final year of grad school—clearly the perfect time to absorb new info), with some who far exceed it and many who dreadfully avoid differential equations.</div><div class="MsoNormal"><br />
</div><div class="MsoNormal">That and a recent project re-synthesizing a >30 year dataset in plant phenology has got me wondering what the requirements should be for the more technical aspects of analyzing data. Lots of people say the future of ecology is synthesizing big datasets and asking questions on global scales, but that actually requires some key skills. I came out of grad school with a basic knowledge of R and thought I was ahead of the curve. Now that I am processing a number of long-term datasets I’m impressed by all the basics needed just to keep a decent pace, and also how much you can do with them.</div><div class="MsoNormal"><br />
</div><div class="MsoNormal">For the 30-year dataset we needed to read in and manipulate hundreds of xls files into one nice, usable csv. Despite learning a couple new coding languages in the last year I can’t do that, but luckily Jim Regetz, a rare mix of ecologist and computer programmer can (in perl mixed with R). I play backup singer and help with post-processing in R. To do just that somewhat efficiently I have: a nice monitor (because monitors >24” but <30” increase productivity: <a href="http://www.kentshaffer.com/increase-your-productivity-with-a-24-computer-monitor/">http://www.kentshaffer.com/increase-your-productivity-with-a-24-computer-monitor/</a>), a version control system to keep track of the code Jim and I share, project management software which tallies all the project issues and their someday resolutions with key notes along the way, an editor I love (emacs) that I use for all my code, including R, where I do 95% of my data work and an irc chat so Jim and I can discuss what the word 'satlks' means (since he’s in sunny Santa Barbara and I apparently live in a puddle). And this is for just one of 29 datasets (though I admit the gnarliest). <o:p></o:p></div><div class="MsoNormal"><br />
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<tr><td class="tr-caption" style="text-align: center;">My monitor today while working on one dataset (I highly recommend my new Dell Ultrasharp 27inch by the way, and I am not being paid to say that).</td></tr>
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</div><div class="MsoNormal">I am lucky to have an NCEAS working group that got the version control and project management stuff up and running but I am daunted by (well, first I am daunted that someday I need to set all these things up for myself, by myself) how much more we could get done in ecology if there were more people like Jim, slowly filtering the best resources to be productive and useful to labs and students. For most of grad school I used JMP and avoided scripting but I am no longer convinced it’s any harder to program my brain to remember to type a single word command than to remember which menu, submenu, right-click sequence to use to find the same command already pre-programmed for me. (And it’s of course immensely more useful for me to have all my code, crufty comments and all, to go back to, than to open JMP and a bunch of different, befuddled, saved file steps.)</div><div class="MsoNormal"><br />
</div>Lizziehttp://www.blogger.com/profile/09989005827839292498noreply@blogger.com0