Ecology Blog of Daren Eiri

I’ve been missing in action for a good amount of weeks, so a lot has been going on with my field research that I’m currently working on with my professor.

As I mentioned earlier in a previous post, I am collecting flowering plants that are visited by honey or bumble bees and creating an herbarium.  This requires going out with a GPS and marking points where I collect plants and collecting pollen samples for future protein analysis.  I also take pictures of the area and of the bee visiting the plant.  You can see a sample below.

Eventually, these pictures go onto acid-free paper where dried samples of the plant are placed, as well as information about the plant (e.g., lat, long, weather conditions at the time, plant and location description) and pictures.

These of course aren’t done yet since I’m still in the process of organizing the information.  When this is complete, a satellite image of the campus as well as where I’ve been walking and taken specimens will be available.  Here’s what I have so far, which is half of the campus, and 20 specimen locations.

That’s it for now.  Hopefully I’ll be back soon for another update.

A while back I posted a paper I wrote about the Eastern Garbage Patch. At that time there hadn’t been too much video coverage on the issue.
Thomas Morton of vbs.tv now has 12 episodes, 6 minutes each, detailing his adventure with Captain Charles Moore as they sailed to the Eastern Garbage Patch. You can see the episodes by going to the site here.

I’m watching the third episode right now, and it’s definitely worth watching, especially if you want to be aware of the huge amounts of trash currently in the Pacific Ocean but don’t want to read an essay about it. It’s pretty amature, and it’s not an official documentary and goes off on tangents every now and then.

But still, I really encourage you to watch it.

Hint: Skip to Part 9 to get to the issue.

A while back I originally posted a paper I wrote about plastics in the ocean and its detrimental effects on the environment.  A few days ago I read a paper from Economist about recycling efforts, in general, and what the future of recycling looks like.  

I think that most people who do recycle aren’t exactly sure where their recycled items go, more so whether or not it actually gets recycled (this goes back to the fact that less than 5% of all plastics get recycled).  The good thing that material like aluminum is very much recycled through recycling plants.  

The article also discusses how recycling actually work, illustrating two methods for sorting out recycling items.  It’s actually very interesting, very close to watching How it’s Made on Discovery Channel.   

Anyways, I have a direct link to the Economist website, but I will also provide a PDF on my website just in case the Economist website changes the URL at all.  Get it below.

The Truth About Recyling

I’m currently applying for a scholarship at UCSD to help pay for my summer research with Professor Nieh.  I thought I would post my description of my proposed project online in case anyone had something to comment on, or was just curious exactly what I’m doing this summer. I have a shortened version under the Research tab. 

Bacillus thuringiensis (Bt) is a toxin that can be expressed in genetically modified plants, such as cotton and corn. The use of Bt in genetically modified plants in the past ten years has benefited many farmers in resource-poor and developing countries, as well those in industrialized countries, where farmers have gained close to $10 billion worth of extra farm income. This is possible due to the high toxicity of Bt and replacement of synthetic pesticides. One advantage of using genetically modified Bt is that only insects that feed on the crop are affected, studies show. The genetically modified crops seem to have had no harmful affects to consumers and specific types of Bt can be manufactured to affect targeted insects. 

The effect Bt may possibly have on honeybee foragers has been independently tested by other researchers (Malone & Pham-Delégue, 2000[1]; Ramirez-Romero et. al, 2004[2]). The majority has concluded that there does not seem to be any direct adverse impacts on them (Liu et al., 2004[3], Mohr & Tebbe, 2007[4]). However, it is possible that long-term exposure may have adverse effects and thus it is important to quantify the effects of Bt on overall colony development and productivity.

This project will have two phases: (1) to create a map of where bees forage around the UCSD campus, (2) to determine the species of plants that honey bees visit in the local area to collect pollen, and (3) to determine if any of the collected pollen contains Bt toxin.

Creating a map using GPS technology and GIS (geographic information system) software such as ArcGIS will allow me (and possibly other students who will find the information useful for their own research projects) to analyze the data I collect while out in the field. This includes the exact coordinates of the foraging activity, the dimensions of the plant body, and the species of the plant. Each foraging spot will include a picture of the area and a voucher sample of the flowering plant. Samples will also be taken and recorded down in a lab notebook. Plant samples will be identified with the help of botanists and the morphological characteristics of pollen from the plants will be identified (along with microscope slides of the identified pollen) Other data such as current weather, rainfall (if any), time of data collection, and presence of bees will be recorded. To determine the locations that pollen collecting bees are visiting, I will record the locations visited by waggle dancing bees inside the hive (this provides the polar coordinates of the food source relative to the nest) and transform this data into GPS coordinates for ground-truthing verification.

Once the first phase of the research is complete, I will collect pollen from honey bees returning to their nest using an automated pollen collector that scrapes pollen off the legs of returning bees, stores it sequentially on a tape, and records the collection time.

Finally, I will use the ELISA technique to determine if the bee-collected pollen contains Bt toxin.  ELISA (enzyme-linked immunosorbant assay) is a biochemical technique to detect an antibody or antigen in a sample, depending on what type of ELISA technique (“indirect” or “sandwich”) the person uses. A previous study of analyzing the phloem sap on Bt corn crops used the ELISA “sandwich” technique using a purchased kit[5], customized for detecting antigens (Raps et.al., 2001[6]). 

The process of using a sandwich ELISA is to first prepare a surface (plate) with a known quantity of antibody, in this case, captured pollen. An antigen-containing sample is then added to bind to the antibody.  The plate is then washed to remove excess antigen.  A color-development step then allows the person to measure the fluorescence to determine the presence and quantity of the antigen.  Computer software also assists in reading the concentrations of the antigen.  No color will develop if Bt is not detected.

Macaws, Muscovy ducks, guinea pigs and turkeys.  They were all named after Macao, Moscow, Guinea and Turkey, but they all originated from the Americas. 

I just thought it was a fun fact to know.  I’m currently reading A Different Nature by David Hancocks.  Just finished the first chapter, where Hancocks discusses the history of zoos. I can’t believe how blood thirsty Romans were.  They killed thousands of animals just for entertainment.  Elephants, lions cheetahs, bears.  They drove some species to extinction in some areas.  I guess I shouldn’t be surprised, but still.  

During Winter quarter I was enrolled in a writing class — a science writing class.  Our only assignment was to focus on our style in one 10-page minimum paper.  I was going to write about the honeybee colony collapse disorder (CCD), but decided to research something I have little knowledge about.  I’m not saying I know a lot of about CCD but during this summer I will have an idea as my summer research revolves around it.  

So I decided to write about plastics in the ocean, and how there’s a big chunk of plastic floating in the middle of the Pacific Ocean about the twice the size of Texas.  In the next few days, if time permits, I will put a text version on my website, but for now here is a pdf document if you are interested about the topic.  

I’m happy to be here today to take the time to write in my almost-forgotten blog. ¬†A few days ago I went out in my backyard (I’m home in Sacramento for the holidays) and stood outside for about 15 minutes and used my mom’s DSLR camera to take some pictures of birds. ¬†I’m fascinated with a lot of things nature has to offer, but I really think birds are interesting because of their mass migrations. ¬†Marine mammals may travel the same distance as some birds, depending on the species, but it’s not something everyone can really enjoy. ¬†I have yet to see a migration¬†occurring¬†in the oceans, but I can witness hundreds of birds in the sky just by driving around town. ¬†¬†So I was able to get a picture of three different birds, all which are common around my area this time around. ¬†¬†¬†This first one I believe is Anna’s hummingbird. ¬† What led to me believe this is its white chest and green upperparts. ¬†Typically the throat will be a bright red but in low light (like this picture), it may appear dark purple or even black. ¬†¬†This next one is a White-crowned sparrow. ¬†It may be a little difficult to see; it was hiding in my next door neighbor’s tree. ¬†There must’ve been quite a few sparrows there but on the opposite side where I was. ¬†I tried going upstairs and taking a picture from my window but that view didn’t work out so well either. ¬†These sparrows have a really high pitched song. ¬†You can listen to it at this¬†website¬†and clicking on Listen to Call.¬†¬†This last one is a White Scrub-jay, sitting on my other neighbor’s rooftop. ¬†If there were a bunch of them you could call them a ‘party of jays,’ but I think the collective noun for crows (a murder of crows) or ravens (unkindness of ravens) are more interesting. So what’s different about this White Scrub-jay than the common blue jay that most people know about? ¬†Pretty much everything. ¬†They don’t even look remotely similar except for being a shade of blue. ¬†You can look at the differences between Blue Jays¬†and¬†White Scrub-jays¬†here. ¬†¬†Hopefully it won’t be too long when I post up next time.¬†

Temperature fluctuations and climate pattens arise mainly due to the variations of the physical environment and our star, the sun. It’s what makes our climate in California Mediterranean, with rainy winters and sunny summers and the tropics humid and full of rain.

Most of us are probably aware that the earth’s tilt (approximately 23.5 degrees) is what gives rise to seasonal variation on our planet. It is sometimes believed that the distance of the earth from the sun contributes to our seasons, but this is not true. Also, the earth stays at a constant tilt in the same direction. The area that receives the most sun is due to the earth’s rotating orbit around the sun. Unfortunately, I cannot find a picture that illustrates this concept clearly.

During the northern hemisphere’s winter solstice, the sun’s energy is more spread out and the intensity of the energy is less. A the same time, the southern hemisphere receives more energy from the sun, creating summer-time temperatures.

Likewise, during the summer solstice, the earth will now be tilted toward the sun (during the winter it is tiled away from the sun) and receives more energy than the southern hemisphere. It is also during this time that the North Pole has sunlight for the majority of the day.

So why does the tropics receive such large amounts of rain? This is largely due to what’s called Hadley cells. Near the equator, systems of vertical air movement occurs. As the sun heats up the air near the equator, surface currents meet near the equator (the intertropical convergence) and rises up. It rises because warm air expands and rises. Warming up, air can pick up more moisture. As it rises up to the atmosphere, it cools and starts to condense and thus rain falls.

Once it has rained, the cool air drops back down to about 30 degrees north and south of the equator. Once on the surface, air picks up moisture on the surface, essentially creating arid climates like the Sahara desert, or Mojave. This is the subtropical high pressure belt, where little rain fall occurs. When the air gets to the equator again, the whole process repeats.

So going back to the original question of why the tropical areas receive more rain. Hadley cells occur at 30 and 60 degrees north and south of the equator, but what makes the equator have more rain? It’s because water cycles more rapidly through the tropical atmosphere.

Of course, this is all generally speaking. If you look at a map of annual precipitation for earth, you’ll notice that more rain occurs more below the equator than above it. This is because there’s more water mass in the southern hemisphere, thus more moisture available to be picked up.

Wind patterns also contribute to variations in climate due to physical changes on the environment.  You may notice that for example, if you live in the northern hemisphere, like in California, that mountains create a dividing line between forests and deserts-like environments.  This is because wind flows west, blowing air up to the mountain.  As the air climbs up the mountain, air cools.  Assuming that this air has picked up moisture along the way, precipitation occurs when the air gets cold enough and showers on the slops west of the mountain.  At the peak, all the moisture from the air current is gone and starts picking up moisture east of the mountain, creating arid environments.  These environments are called rain shadows. Sierra Nevada is a good example of this.

Ocean currents play a role as well. ¬† They’re driven by the surface winds and the rotation of the earth. If you’ve ever been in the Atlantic ocean on the eastern coast of United States, you know that the water is very warm compared to the Pacific ocean.¬† This is due to cycling ocean currents.¬† In the Pacific, water from the areas like Alaska move down the coasts of Oregon, Washington and California.¬† So cold water from the north is moving down toward the equator. It’s not until this current meets near the equator that is starts warming up again, giving Japan warm ocean currents.

There’s a few exceptions to this pattern,¬† and they’re called upwellings.¬† Upwellings occur when surface currents diverge, and as they move apart, deep waters tend to rise up vertically.¬† They also occur when strong ocean currents move toward the equator.¬† The cycling of water in upwelling actually creates high areas of biological productivity, producing an area full of rich fisheries.

Ocean currents, wind patterns, intensity of sunlight — they all contribute to our global climate.¬† In some cases, they create seasonal events such as El Nino or El Nina (which follows after El Nino).¬† They’re known as ENSO (El Nino- Southern Oscillation) events.

El Nino occurs when air pressure changes in certain areas.  This in effect causes trade winds to be weakend, allowing warmer water to move east.  This warm water, as well as moisture being carried over decreases development of Atlantic hurricanes.  However, they also create higher rainfall averages to occur in Western United States.

We’re currently in a somewhat El Nina event which is just reverse of El Nino.¬† The winds that were once weak are now strong and warm water is pushed west instead of flowing east.¬† This creates a more drier climate in Eastern United States and tends to increase the development of Atlantic hurricanes.

Starting today, I will be writing a “series” (for a lack of a better word) about introductory ecology. It’s really my class and the main point of this series is to help me study. But what I really hope is that I can present this material (unless otherwise noted, most of it will be from my textbook, The Economy of Nature by Ricklefs) in such a way that is engaging for you and consequently, learn a little more about our environment.

I also have a midterm coming up and by writing content here and presenting the ideas in The Economy of Nature, I’m being quite productive by doing both at once.

I know that I previously mentioned that I’d be writing about how some plants use the pheramones of a female bee to attract male bees. I think it’s pretty cool, but that will have to wait.

All organisms have evolved and adapted to their local environment. The following two plants have adapted to the arid and extreme dryness of desert ecosystems. In the case of Mesquite (prosopis) leaves (pictured left), they’re structured to be divided individually, allowing heat to be dissipated more easily.

Plants can also evolve little tiny hairs, producing a boundary layer that traps in moisture and reduces evaporation. Encelia farinosa, also known as the brittlebush. You’ll notice on the picture to the left that this plant has an off-white color on its leaves. This white color allows more light to be reflected and thus retains more of its moisture.

It’s easy to relate to E. farinosa and how it adapts to its environment. On a hot summer day, some of us may consider wearing a lighter colored shirt, like white, than a dark colored shirt. All the running shirts that I have collected from fun runs (5k races that support various causes like breast cancer or local food bank) have been white, with an exception of a race that took place in October. It was black.

Continuing on plants, the environment plays a critical role on where the plant allocates its resources and nutrients. Ricklefs points out that when a plant is located in an area where soil nutrients are low, the plant will spend more energy creating a deeper root system. This comes at the expense of reducing shoot (leaves and stem) growth. Plants can also form symbiotic relationships with fungi (mycorhizzae).

Animals as well have adapted to their environments, and it is best illustrated in extreme environmental areas. Kangaroo rats, many which live in California’s arid climates, have adapted so well to nearly waterless environments. Ricklefs discusses how kangaroo rats can pretty much go without water for a whole year thanks in part to its ability to the dry seeds they eat into water, production of dry feces and most importantly, their respiratory system.

This rat’s respiratory system allows the organism to recover

much of the water that evaporates from their lungs by condensation in their enlarged nasal passages. When the rat inhales dry air, moisture in the nasal passages evaporates, cooling the nose and saturating the inhaled air with water. When moist air is exhaled from the lungs, much of the water vapor condenses on the cool nasal surfaces.

In other words, the hot air comes in, cools down and water vapor forms. During the exhalation process, warm air turns into cold air from the cool respiratory walls. Remembering that cold air holds less water than warm air, they’re cooling their body and reducing potential water loss.

They’re also active mostly at night, but that’s not anything special really. Not as cool as self regulating body thermostats.

I also have to add that they’re pretty darn cute-looking. I tried looking up online to see if I could get one as a pet, but it seems like no one really sells them. It’s unfortunate, really.

Thermobody regulation can occur at the respiratory level, like the kangaroo rat, or it can occur through the circulatory system. When you think about birds, how do you think they keep their feet warm? Birds can use countercurrent heat exchange to keep their body temperatures regulated. Illustrated in the picture to the right, arteries carrying warm blood flow down to the feet, and during this process, warms up the venous blood flowing back up from the feet to the core body. In this process, heat loss to the environment is minimal and is instead transferred to countercurrent blood flow.

I hope that you got a few interesting facts from reading this, and hopefully most of what I wrote down I will be able to retain in my head. Tomorrow, I’ll be discussing how variations in the physical environment affect global climate patterns and understand what El Nino really is!

Once again, I’ve been pretty busy with school and work, leaving me with little time to keep this updated.

I recently stumbled upon this one website hosting a program called Virtual Microscope.¬† It’s actually a really cool program.¬† It’s available for Mac and PC, so most people will be able to use it.

Here’s a little snip from their website: ¬† The Virtual Microscope is a NASA-funded project that provides simulated scientific instrumentation for students and researchers worldwide as part of NASA’s Virtual Laboratory initiative. This site serves as home base for the Imaging Technology Group’s contributions to that project‚Äînamely virtual microscopes and the multi-dimensional, high-resolution image datasets they view. Currently we provide 90 samples totaling over 62 gigapixels of image data. The Virtual Microscope, which is available for free download supports functionality from electron, light, and scanning probe microscopes, datasets for these instruments, training materials to learn more about microscopy, and other related tools. The project is open source and the code is available on Sourceforge.

They even have documentation and videos about how the device that captures the digital images works and the science behind id.¬† Go check it out.¬† You’ll have to download the program first before you can view the images, and each image is about 40mb large.