Sep 01 2008

Citation managers

Published by sarcozona under Uncategorized

in my natural habitat

I have to read a lot of papers for work, and every once in awhile I write one of my own. Keeping track of all the papers and then citing them and building bibliographies can be pretty time consuming. Citation managers make the job a lot easier. I’ve been using RefWorks for the past year, but recently switched to Zotero after reading about it at Ruminations of an Aspiring Ecologist.

Zotero is much faster and easier to use.  The integration with Firefox is flawless and importing references is effortless.  For databases without automatic RefWorks export options for their citations, I had to download a citation file, then import it into RefWorks in a separate (tricky) step.  I say tricky because I had to choose several options on the import that were different for different databases and often not very intuitive.  This doesn’t happen with Zotero.

The biggest problem I have with Zotero is that it doesn’t work with Microsoft Office 2008 yet.  So I’m using both RefWorks and Zotero until the new plugin gets built.  Hopefully that will be soon.  I’m excited about not using clunky RefWorks anymore.

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May 28 2008

Increasing Carbon Dioxide Levels and Trees at High Elevations

Published by sarcozona under Uncategorized

ResearchBlogging.org

Carbon dioxide levels have been increasing since the industrial revolution and have been increasing really really fast since the 1950s. You’ve all seen the hockey stick graph.

hockey stick graph

I’ve been looking at pinyon pine tree rings for the past year and think there might be something going on with increasing CO2 and what the rings are doing. So I’ve got a stack of papers to read through and thought I’d share some of them with all of you.

Carbon dioxide is pretty good for plants because plants need carbon for photosynthesis. We’re interested in what higher levels of CO2 will do to plants because if plants are growing more and eating more carbon dioxide it could help slow down global warming. But giving most plants most places extra carbon dioxide doesn’t seem to do much in the long run because plants need lots of other things to grow, like nitrogen and water, and carbon isn’t usually the most limiting. It’s the same for you: it doesn’t matter how many vegetables you eat if there’s no water.

But what about plants where carbon might be a limiting factor for growth? Carbon can be limiting in hot, dry places because to get carbon, plants have to lose water. Plants have little tiny pores in their leaves called stomata. They have to open these to let in CO2, but water escapes whenever they’re open. A lot of plants that live in hot, dry places have evolved a different kind of photosynthesis to deal with this.

stoma

Another place carbon might be limiting is at very high elevations. Atmospheric CO2 concentrations decrease with increasing elevation. That means that in the same amount of space there’s less CO2. This happens to all gases. Flagstaff is above 2000 meters. When people move here, they have a hard time breathing for awhile because of the lower oxygen concentration.

Lamarche et al. looked at tree rings in the 1980s of bristlecone pine growing at 3100 meters. They found that the trees had increasing growth since about 1840. Initially they thought that this was due to warmer temperatures, but then when it cooled down in the 60s, the trend kept going and even accelerated. So, the faster growth wasn’t due to hotter temperatures.

bristlecone

But was it caused by higher CO2 levels? Plants can only use so much CO2, no matter how much is available. Like at Thanksgiving dinner, there’s lots of food available, but you can only eat so much. In the 1960s, CO2 was between 223 and 230 ppm at 3500 meters. For spruce, that concentration is well below what it considers CO2 saturation and so is probably well below what bristlecone considers saturation.

While the authors didn’t really have enough data from enough places to say for sure CO2 makes trees growing at high altitudes grow more, what they do have certainly suggests it.

This paper is over 20 years old, so we’ll see what more recent papers have found…

LAMARCHE, V.C., GRAYBILL, D.A., FRITTS, H.C., ROSE, M.R. (1984). Increasing Atmospheric Carbon Dioxide: Tree Ring Evidence for Growth Enhancement in Natural Vegetation. Science, 225(4666), 1019-1021. DOI: 10.1126/science.225.4666.1019

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Mar 13 2008

What I’ve noticed

Published by sarcozona under Uncategorized

Poor Brazilians figuring out who’s really screwing them over

A very addictive game

John McCain is a hypocrite

John McCain thinks I’m a baby machine

Another university goes after the people who aren’t really cheating

A song to brighten your day

It’s a computer, it’s a mouse brain!

Frida Kahlo, survival, and the stories we tell ourselves

Survivor: scientists edition

UNC drag show pictures

Poorly trained campus police + assault rifles = dead students

Pulp fiction cover art (and atheists)

A very big squid

Rapid evolution of a plant in Montpellier

US “democracy” in action

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Mar 06 2008

who’s gonna die?

Published by sarcozona under Uncategorized

ResearchBlogging.orgNothofagus dombeyi, or coihue, is a large tree that grows in the Andes. In the late 90s, northern Patagonia was hit with a pretty severe drought that killed many of these trees. So what was the difference between the trees that kicked it and the trees that are still going strong?

Some trees constantly live with higher water stress than others. This is usually due to where they’re growing. If a tree is on a particularly steep patch of ground, the water runs off before it can suck it up. If a tree is growing in shallow soil or on a very sunny slope, it’s going to be a lot thirstier than your average tree in the forest.

The authors of this study thought that these trees might be the ones to be hit hardest during the drought since they were already stressed. They also considered the possibility that the trees growing in more water stressed areas are different and better able to cope with drought. The trees used to the good life might have invested more in their tops than their roots, which could be bad news in a drought. A tree with a smaller root system might not be able to suck up enough water to support all its branches in a very dry year.

The authors also wondered if there were a way to look at a tree and use where and how its growing to predict whether or not it will survive a drought.

So, what did they find?

Continue Reading »

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Jan 12 2008

my schedule

Published by sarcozona under Uncategorized

This semester is going to be very busy, but doable. I’ve got a week where I’m going to Humboldt to do some work that could cause some problems because I’ll be missing an entire week of classes. Hopefully it’ll work out alright.

I’m taking differential equations, the second course of a three-course long physics series, and sort of a research methods course associated with my UMEB fellowship. I’m a bit worried about my physics course. I took an algebra based physics about electricity and magnetism in high school and I really struggled with some of the concepts. (I demonstrated my complete misunderstanding of said concepts by shocking the living hell out of myself every week in lab.) This semester I resolve to use the right hand rule with my right hand rather than my left. We’ll see how it goes… If I make my hair stand up, I’ll post pictures.

I’m also working about 30 hours a week. Almost all of it will be in the lab or in the field. I’m pretty excited. I get to go to a lot of beautiful old volcanoes across northern Arizona to collect tree cores. Best of all, I actually get paid (an incredibly small amount) for it! Financially, things are still pretty tight, but I’ve got enough for rent and I’m rich enough to have joined the Flagstaff CSA. Lots of vegetables every week are far better than peanut butter, peanut butter, peanut butter, ramen. I even bought a new bed with a nice firm futon mattress. I’m all grown up now, so my back hurts and a good firm mattress seems to help. Of course, presents are always welcome. Hugs and cookies too :)

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Jan 07 2008

COFECHA and file format problems

Published by sarcozona under Uncategorized

I use a program called COFECHA to help crossdate trees. COFECHA uses some old school formats developed for punch-cards. Excel, which I used to make changes to ring widths, does not like these formats. There are lots of programs for changing formats, but it’s all a bit confusing.

Many dendrochronology programs produce and use Compact/Precision formats. When crossdating trees with the program COFECHA, it is often useful to convert Compact/Precision formats to formats recognized by spreadsheet programs like Excel and then convert back to Compact/Precision formats to run through COFECHA. So for any other confused dendrochronologists out there, here’s a method that works for me.

Compact/Precision format looks like this when you open it with notepad:

ira 11946 170 200 216 755

ira 11950 529 332 405 342 384 760 647 363 556 466

ira 11960 288 431 490 124 827 282 319 248 441 1082

ira 11970 1601 498 992 1407 850 1053 1356 951 1145 1621

ira 11980 1756 1381 1397 1626 1868 2739 2447 2250 1684 1942

ira 11990 1401 1390 861 1389 1158 1421 1454 1040 -9999

Sometimes the numbers seem to run together, but each line will start with a series identifier and each series will end with -9999.

Convert file from Compact/Precision to tab delimited .txt file with program YUX. Open .txt file with Excel and make necessary changes, being sure to save as a tab delimited .txt file. Convert to Compact/Precision format with program CASE, being sure to save the new file as a .rwl. COFECHA should be able to read this file.

If you get COFECHA output that only includes the title or part of the desired output, try playing around with the print options in COFECHA.  If COFECHA produces a completely empty output file, try copying and pasting the information from your .rwl file into an existing .rwl file and saving it as a new .rwl file.

All programs can be downloaded from the Ultimate Tree Ring Web Pages run by Henri Grissino-Mayer.

tree rings

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Dec 30 2007

IGERT

Published by sarcozona under Uncategorized

I got money!  To do research!  Hooray!

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Nov 29 2007

Finished

Published by sarcozona under Uncategorized

As of 6:30 this morning, my research proposal is finished. In case you haven’t been keeping track, that’s two this month. The first one was a description of what I was going to do with money I’d already been given. The second is an attempt to convince someone to give me money for what I want to do. I really hope I get it! I really want to do this project. And I need more paid hours in the lab next semester.

Assuming I get this grant, I’ll be working on two related projects involving pinyon pine and drought. Pinyon pine are a foundation species. Unlike the forests where I grew up, there aren’t a ton of tree species out here. Pinyon grow in pinyon-juniper woodlands. There are pinyon pine and juniper. No other trees at all. And the pinyon here are dying out very very quickly. It’s been getting dryer and hotter here since the 90s and most climate models say that trend is only going to continue. In some places 90% of the pinyon have died. We have sites that have experienced 85% mortality. My research will hopefully find better drought adapted pinyon populations and help predict where other drought adapted populations may be found.

dead pinyon

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Nov 07 2007

why i haven’t written much lately (and why I won’t be writing much for awhile…)

Published by sarcozona under Uncategorized

This month:

  • Calc test on stuff I actually have to work at to understand
  • Research prospectus
  • Research proposal
  • Research presentation
  • Botany class semester long lab project due
  • Definite progress on the Goldwater application must be made
  • I kicked my non-rent paying, non-cleaning, alcoholic roommate out and must find another one/work a gazillion hours to make rent.

I’m really glad November includes Veteran’s day and Thanksgiving. With a few days off, I might be able to actually accomplish all of this…

That said, I had a fantastic cookie baking party a few days ago, a friend of mine cleaned my really and truly disgusting stove, I’ve got some awesome roommate possibilities, I’m spending far too much time thinking about a crush (and why I shouldn’t have a crush on her), and while research is intimidating and sometimes overwhelming, I love it.

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Dec 31 1969

Berry Go Round 4

Published by sarcozona under Uncategorized

The 4th edition of Berry Go Round is up at Foothills Fancies.  Go check it out!

Highlights:

This post on redbuds makes me terribly homesick.

Julia is right: this seed fern fossil discovery is very exciting.

The twists and turns of research.

Bryophytes rock my world.

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