Weblog archive
What is a Prion?
Links to Stuff

Angry Cows
WoW Comic

WoW Guides

Writing Update


Realized that the background chapter I started on was really more of the introduction to the paper. The background is supposed to be EVEN MORE BROAD! So rather than jumping into why invasion is bad (pretty broad), I'm going to talk about the causes and effects of invasion (super broad)

Should be interesting. Maybe I can keep what I have from before and use it as part of the introduction

Thursday Update: Must Update More Frequently


The field plots have been set up. I ran a bit short on pegs and used half-pegs for some of site 4, I have to go back there and check to be sure it's still in place on Sunday.

I also moved all the dirt up to the greenhouse, as well as the potting soil. I also brought the plastic pots and washed out 75 of them, but I haven't yet gotten the correct keys so I am waiting for one of two things to happen: either the keys come in, or GS ends in two weeks and after that my Tuesdays and Thursdays are completely blank. Having the greenhouse be a month behind the field should be okay I think. I hope. It's not like I have any viable alternatives anyway.

I chatted with Prof. Friedenburg who is on my committee and she is likely not going to be around next year. This was a sharp reminder that I have to finish THIS YEAR. If she goes somewhere else she can probably sit in for the thesis defense or whatever but all the final stuff has to be done this year.

If I do plant in week 8 for the greenhouse, that's four weeks (8, 9, 10, finals) where I can be around and monitor the growth and water regularly. There is a one week break where I can HOPEFULLY still get in, i.e. either I'll have the keys or Bill will still be around. Then comes Spring quarter.

Spring should be higher availability (GS and labs will be about the same, Concord will be easier because it will only be bio2020 and no chem). I can also take advantage of the wacky GS times (one class each Mon, Tues, Wed) to be on campus those three days and go to Concord Thu/Fri. Being on campus those days in a row will help me keep up with the things that need doing (e.g. if I want to do a big task and am worried I won't have enough time, splitting it across two consecutive days is workable whereas right now splitting it across the week doesn't work, only Sat/Sun)

The experiments should run for a couple months if possible (should be entirely possible, I can just overwater a bit before the break if I can't get in that week, poppies go a while without rain in the field eh). Also I shouldn't wait quite so long to ID the plants and take the pinframe data. That doesn't work as well once the grass is all dried out.

Minor point, I haven't decided how to label everything. I may see if I can steal some of Bill's green tape and a sharpie. That would probably be best.

Now to engage in some writing!



Neglectful a bit, I suppose. I have taken more time than I probably should have to adjust to the winter quarter, and the weeklong visit of old friends probably didn't help.

But I am in fact back on the wagon, and just in time! One year ago from this weekend I set up all the field plots, so I'm going to do the exact same thing this weekend! (Weather be damned, in multiple senses: I will do it regardless of weather, but also the idea of controlling for time doesn't account for any variation in rain)

I have been preparing for this eventuality, and on Thursday I sawed the pegs and made some necessary calculations.

This means on Saturday after weapons class I will go straight out to the field with a trowel, seeds in a petri dish, pegs, and notebook. The plan is to set up 5 plots each with 3 subplots each the size of a 4inx4in gardenbox like the ones I will be using in the greenhouse.

Any delay can push it to Sunday, where I have the morning completely off (I contemplated skipping Karate to get this done on Saturday but therein lies a slippery road I went down last year and don't care to revisit except in case of emergency). Sunday I would rather hold in reserve though, especially since some last-minute collecting of materials is needed in order to run the greenhouse experiment.

If I had the correct keys I would just do the greenhouse setup on Sunday to have the seeds in perfect synchronization, but sadly I do not have the necessary keys. This means I will be hassling Bill all this upcoming week to get into the greenhouse.

The steps for that are pretty simple:

Should be able to drag the dirt up on Monday after biolab or Tuesday after office hours, then do all the setup and planting on Wednesday when I have a 3-hour block available.

Writing progress: very little. Should spend time on it at Concord but I suspect I have to get really started under some other circumstances and then just proceed while there.



What do you think?

Winter Break update


Good things: started the dirt digging, plans complete for winter experiments

Less-good things: extremely unfriendly weather, dirt is really heavy.

This winter break I think I will see what I can do about writing an introduction section sketch and start filling it in. Since I won't have access to campus I won't be able to do all the literature searching but I can use my knowledge and textbooks to get started on it. Also the book Dr. Opp lent me on weed ecology will be quite helpful.

I will post an outline here once I write it.

Monday update: Catchup logging!


I missed two weeks of posting it seems. On 11/2 I was just busy putting out the stakes, taking pictures, etc. On 11/9 I had meetings all day long, so no thesis work then.

Today I plotted out the greenhouse design. Looks like 25 pots with seeds and dirt base, possibly times 2 or 3 for different seed densities, probably a total of 75. Also some uncertainty whether to still do the autoclaving and competitor seeds as different sets. Leaning against it now because I'm not sure it would add enough more value to warrant having 150 or 225 pots. 75 will already be quite a lot, though manageable.

Still, I think I will ask Sue about that next week.

Once I know my winter schedule I will plot out a scheme for when to manage the greenhouse and field plots. Those field plots need some minimal amount of planning as well, though probably not as much. I'll likely do them in one large stripe each site, rather than haphazardly putting them wherever I feel like it.

Monday update: T-0 go!


Today's accomplishments: set up the four sites with stakes, seeded them! Go me!

Seed density was 1000 seeds per square meter, or more accurately, 7.0g per 1mx5m zone.

More update later, since I'm tired.

Monday update: Rain, rain, make up your mind


I appear to be a total slave to the weather at this point. I know where I'm going to put the plots, but I don't seed until after the rainy season has started (and if any windstorms like last Tuesday are showing up, wait until after those).

I use the internet weather sources ( and have 2-week projections) to keep an eye on the weather, and it still isn't the real rainy season yet.

I fear I may need more stakes than previously thought, since I left a number out on the sites, and the wind and rain may have caused some to roll down hills (it was *awful* on Tuesday). I hope not, but I will check before buying more stakes.

So that is settled, just need to wait for the right time. In the meantime, I also need to work on the written thesis. I've sort of attempted writing a few times, but it's really hard to get started. Part of it I think is the lack of an idea as what it's supposed to end up looking and sounding like. I will probably go ask Dr. Opp to see some old masters theses next time I get a chance.

Monday update: Still No Rainy Season


Let's see here.

Picked out sites, but I'm short stakes (I think someone walked off with a few) and I decided to add a fourth site anyway. Not going to plant seeds yet since the incoming raid is just a fluke again. No more rain predicted for the rest of the month as far as I can tell, so I'll wait.

Still haven't written. Will get something done with that soon.

Monday update: Getting Ready


Things to clear with Professor Opp at next opportunity

Things to ask Prof. Ward about at some point

Also need to go on campus to read the papers Sue e-mailed me. I can't access them from here.

Also, not digging the idea of a negative control so much. Not sure of any good sites, and nothing would happen anyway. Perhaps a greenhouse positive control can be in potting soil. That might be interesting. It would give some sort of upper bound on the expected growth of poppies in competition-free environment (except maybe for intra-species competition).

After lunch I am going out to pick out some sites. We'll see how that goes!

Monday update: Some Assembly Required


Major thesis components:


Not having field control groups this time for the small plots. Also going to have higher seed density in the large plot (1000 per square meter instead of 200). For the small plots and greenhouse, seed densities will be 2, 5, and 10 seeds again.

Locations: a site on hill1 and on hill2 again, also a positive control somewhere on the top hill where poppies are known to grow. Soil analysis will be performed by proxy with the greenhouse numbers. Maybe a fourth site somewhere that would be more like a negative control due to being close to water and greenery, though I can't seem to think of a good spot off the top of my head.

Not using the sites from last year that were really hard to get to. I will check back in there at least once to see if any poppies have turned up, but I'm not holding my breath for it.

Timeframe: plots have to be located and ready, and enclosures have to be designed and assembled, before the rains come. Not counting this freakish downpour we had a couple weeks ago.

Materials: Already have the pinframe, stakes, cleats, gaters, Brunton compass, greenhouse pots, buckets, and petri dishes. Will have to get enclosure plans and the materials (probably chicken wire), more dowels probably, and new seeds from OSH. It's a short list, I'm pretty sure everything will work.

New updates expected every Monday.



Found a really cool paper on allelopathy: In Search of Allelopathy, by RW Halsey. I originally read it to deal with the experiment we're running in Bio1002, but the more I look at it the more I feel that allelopathy will factor in to my thesis. You see, like many plants, Avena has been investigated for allelopathic properties in the lab. This means that the dirt I use out there is probably filled with funny plant chemicals, in addition to its various nutritive deficiency problems.

The problem is that allelopathy is everywhere and nowhere. It is the ninja of landscape ecology. Its effects are probably overshadowed by resource depletion, but it may still pose problems. A possible experiment on this would be to mix field durt with potting soil in various proportions to see whether adding soil dirt from some sites actually has a depressant effect on the germination and growth, as compared to nutritionally deficient but unharmful sand.

However, I fear it might lead me somewhat off track, since my main goal is still to look more at whether poppies are capable of reinvading other regions, and if not, why not (it looks like if they can, it would take a much higher seed concentration than what I used last time).

The greenhouse experiment should seek to test the soils at the various locales, to try and isolate the external competition with the environmental factors.

Gonna work that out soonish.

*Brushes off dust*


Phase 1 Complete, on schedule. Summertime!

Phase 2: analyze all data, start writing, read on soil analysis. For the summer. Goal: entire methods section written. Intro will be written later and cribbed from original proposal.

(Note: also need to check to see if any of the poppies from the plots actually flower)

Phase 3: fall plantings, finish writings, collect more data.

Phase 4: Profit!

Heh. In seriousness, this is how I plan on analyzing the data:



It feels good to be on track!

Committee meeting and recon results


New game plan:

Fields stay as they are. Inspection has only been able to find any poppies growing at site 1 (which is on a different hill from the others) so that's interesting, to say the least.

Greenhouse is reduced to a simple viability test.

The original competition test is now small field quadrats. I just today cleared out five replicate zones large enough to hold four 4"x4" quadrats.

However, I've just recently had the thought that if the poppies really are only growing on Site 1, I should clear out an equal number of quadrats on the other hill and run parallel experiments. Double the work (actually more than double because that hill is FAR man) but it will be worth it to see if the soil or sunlight or slope is playing a factor or if it's competition alone that squashed the poppies on that hill.

See THIS is what research is about! That and not dying....



A first draft has been finished and looked at by Professor Opp. It needs work but it's on the right track and I am confident that my parents and Exalted will not stand in the way of finishing it by Sunday for a final set. Then it goes off to Profs Inouye and Friedenburg for further review, but some fresh eyes will make it all work out.


Brief update


Took pictures of the sites yesterday (11/29). Can't tell whether the poppies are sprouting, since the entire place is carpeted with sprouting grasses, clovers, and weeds.

Gonna reread some sections of Dr. Opp's Weed Book for additional insights I may have missed before, since I've gotten a better grip on what I'm looking for.

Have the containers for the poppies from Bill, need to make cash deposits for the keys (40 bucks! Sheesh! At least I get them back in theory). Once I do that the buckets are in place, so maybe I can do the dirt-grubbing on the upcoming weekend! It'll put the poppies at 3.5 weeks behind the wild ones. I also need to dig up some cloth for using the moisture meter. That weekend will be busy eh.

Thirteen days since seeding


Waiting on the lab key to get my dirt. I will probably also try to have poppy pots in place prior to uh... something that starts with P. I wanted to relate how I want the poppy pots at the greenhouse so that when I drag in buckets of dirt I can immediately (if I have the energy) fill up the pots and label them all so it doesn't degenerate into its own separate job that needs avoiding. Not that I every avoid work.

Back on topic, I'd been slowly going nuts over the topic of how closely the greenhouse study needs to be synchronized to the field study (short answer, it doesn't). Dr. Opp was more worried about having measurements in play for the field, but I pointed out that in the previous seeding experiments no data was taken until peak biomass (the literature will hopefully educate me on that time, another one to look up when I get a spare day eh)

Come to think of it, if I run out of things to do over Thanksgiving break I should do my literature marathon. Sooner definitely better than later. Though since I also have grading and writing to do it may not happen until Finals week (when I have comparatively few finals).

The proposal has sort of ground to a halt for lack of literature to back it up, so the sooner the better I suppose. I guess the lab papers aren't due until Finals week so I can take it easy on those for the lit marathon (which is really just the sitting down with an iPod and a water bottle in front of a computer on campus and not standing up until all relevant papers on the various topics have been found).



The major steps left for Fall are twofold: start the greenhouse section, and write the proposal (backseat'd).

The greenhouse section is still a fairly big, multistep process:

I also need to use some of the leftover dirt from each site to calibrate the moisture meter (an irritating time-suck, in that it needs to be done and done well with plenty of time but it's just a supporting move that by all rights an undergrad somewhere would do for me.... sigh, there goes that feeling of entitlement, folks, he's vicious).


What are the 9 treatments? It is a factorial combination of:
->Autoclaved, autoclaved with competitor grass added, and unautoclaved dirt
->0, 200, and 1,000 poppy seeds per square meter (in a 4in x 4in pot, that's 0, 2, and 10 seeds, see appendix A). The second treatment matches field density

So the controls of 0 poppies should show nothing (testing autoclave power), competitor grass only, and wild growth only

The tests of 200 poppies should show larger-than-field-strength poppies, poppy and grass competition, and field-equivalent poppies

The test of 1000 poppies should show the same thing only with more poppy competition.

Appendix A
1 inch = 0.0254 meters, therefore 4 inches = 0.1016 meters, therefore 4 square inches = 0.0103 square meters, and this checks out because 1 inch = approx 1/40th of a meter, so 4 inches = approx 1/10 meter, so squaring yields approx 1/100 meter. So 1/100 of 200 poppy seeds per square meter makes 2 seeds in one pot. Kinda thin, I know, but whatever.

T-11 hours


Tomorrow's agenda:


As for the seeds, I have bought a great pile of poppy seeds. At lunch break, I will measure out how much 100 seeds weighs, then measure out the mass equivalence of 5000 seeds (all the seeds for one site, hopefully have 30,000 seeds in the packets.... see appendix A). Each study plot is 5m square, so 25m x 200 seeds per square meter makes 5000 seeds, I will aliquot them into usable sizes, fit in petri dishes taped shut.

As long as it doesn't rain, I think everything will be fine! Go us.

Appendix A: I purchased 2 packets holding 1oz of seeds and 12 packets of 1g each. One ounce is 1/16th of a pound, one pound is 2.2 kgs, and 1kg is 1000 grams, so 1oz = 137.5 grams (now I feel dumb for buying the extra 12 packets...)

Anyways, 287g of seeds, where 1 poppy seed weighs about 0.0015g, so this should be approaching 200,000 seeds. Impressive eh.

Yes, I will probably be using them all, since I'll ALSO be doing greenhouse experiments in addition to simply seeding 30,000 off the bat.

As a matter of record, 1g contains about 650 seeds. Well done Alejo.

Thesis Proposal Talk


Proposal is supposed to be of some minimum length. I think my Bachelor's Thesis Proposal was like 10 pages? Over half was the introduction.

My intro is currently two full pages, but it's also marked in a bunch of places with (REFERENCE) and a couple paragraphs that need writing. Even so, not sure how long it will end up being. Brevity may be a virtue but I'm concerned about having it done done done by its due date (which is I think day 1 of Winter quarter?).

I also still have to write the methods section, but that will be easy enough on account of how I've already outlined the basic methods completely in my head.

Guess I'll work on it more today, I think I have some spare time lying around. Not having to prepare a GS class this week or next has opened up a lot of time I need to be using for writiiiiing!

Yeah, if I can add three more pages of intro and the methods + expected results + prior data takes up 5 pages I think I might be good. Right now the intro is very skeletal anyways.

Things, they need doing


As you may be aware, the third step in a good field research project is to find your suitable locations (the first two being notice something in the field and spend inordinate amounts of time reading and re-reading the literature because most of what you noticed has already been studied). I think I've gotten that down already, which brings me to my fourth step: get materials! For the most part this is just poppy seeds (already available), stakes for marking out territory (need to check OSH's website as soon as I'm somewhere with acceptable internet), and a shovel and bucket/wheelbarrow to obtain field dirt for the greenhouse (oh noes, a bucket, wherever will I get a bucket?!)

There are other materials I will need to pull this off, however. That includes a Brunton compass (fortunately already have one!) and a Moisture meter (ditto!). Amusingly enough, neither of these will be used for their *original* intended purpose, yet will still be valuable. I intend to use the Brunton Compass to make sure the angles on the test zones are 90° angles (without which, the area would be smaller than intended even if all four sides were measured rather than just two). The Moisture meter, meanwhile, will be for making greenhouse conditions mimic the field conditions.

(Originally, they were both for taking readings at existing poppy locations, to try and statistically determine via regression what sorts of things keep the poppies going. As it turns out the literature has more or less addressed this to its own satisfaction).

No problem though, eh. Anyways, I will also need a nice map to keep track of my stuff on, and I'd like to take a GPS device down there once I stake out my territory (I'll borrow it from my media pals!) so I can accurately place the zones on a google maps thing.

Speaking of media people, I need to remember to meet with them for their Master's thesis tomorrow. Yee ha.

Limitation Theory


Seed-limited and recruitment-limited *seem* to be interchangeable terms for the same thing (Seabloom uses them interchangeably and if it's good enough for him, it's now good enough for me (god I hope he doesn't read this right away... "who is this crazy stalker dude")).

The basic idea seems pretty simple: the more seeds get out there, the more plants grow. I think this runs in opposition to a situation where plants would shuck out tons of seeds but only a fixed number are even capable of sprouting, the others being too slow on the draw and failing to collect resources.

Note to self: Alejo, find more on recruitment thory, good example:
PETER CHESSON, Recruitment limitation: A theoretical perspective. Volume 23 Issue 3, Pages 234 - 240.

Sort of need that eh.

Liveblogging the Thesis!


So this is my shoestring Master's Thesis Blog, started October the 25th, 2008, mostly just for the heck of it.


So what is my thesis on? Basically, the hills around here have been thoroughly invaded by exotic plants, and the original natives have been pushed up into poor soil areas like the tops of hills. According to Seabloom et al. (2003), native annual forbs can reinvade from hummocks because they are seed-limited, and are not making any inroads because (presumably) their seed yield is lower. When heavily planted they compete nicely with the exotic annuals.

My question is whether California poppies on the hilltops around campus can do the same thing. Now poppies are perennial instead of annual so this may reduce their chances, but since the assumption this entire time has been that native plants are just inferior competitors when in fact that is not the case, this deserves some new inspection.

I am building off two studies in particular, one where native annual forbs were shown to be seed limited and another where native perennial grasses were shown to be seed limited as well. Poppies are a native perennial forb, which has not been looked at, but they are similarly found on hummocks only, and thus would seem to fall into the same broad category of marginalized native.

How am I going to test this? The same way Seabloom tested it, except without a Ph.D., a team of other postdocs, giant fields, and 5+ years to do it: Seeding experiments!

The basic concept of a seeding experiment is extravagantly simple: toss seeds into the field and see whether they sprout! The devil is in the details, like identifying test sites (check) and getting markers for these sites, choosing the right time to seed, selecting density of seeds to plant, and actually doing it (not so much).


Created: 10/25/08 By: Prions

Back to home.