Wednesday, December 30, 2009

(Belated) Trip Report part 2 - North Cascades, Yellowstone, Grand Tetons, Badlands

North Cascades National Park

North Cascades National Park photos.

9/4/2009

  • Just woke up after 2nd night in North Cascades National Park. Camped at Hidden Meadows - one of the most spectacular places I've ever been.
  • Last night I climbed to a saddle in one of the surrounding ridges to see the view of the other side. Saw pikas, 2 different species of ground squirrel, and a (then) unidentified bird (which, when I had access to a field guide I later identified as a Clark's Nutcracker), as well as some kind of falcon (somewhat large, nearly the size of an accipiter, with rusty coloring).
  • Pack is HEAVY for this trip. Need to strip down base weight and food weight (a food dehydrator would be helpful).
  • 1st night was at Fireweed Camp - T-storm.
9/4/2009, 2nd entry

  • Left Hidden Meadows today. The hike to Dee Dee Lakes was GORGEOUS! Walked slowly, elation so great I didn't even feel my pack.
  • Went swimming in upper lake. In attempt to cross lake I seriously almost died. Cold froze my muscles up, and I couldn't fully expand lungs.
  • Now it's raining again. Bed early.

Badlands (also Yellowstone and Grand Tetons in retrospective)

Photos from Yellowstone, Grand Tetons, and Badlands.

9/14/2009 (?)

  • Left N. Cascades early - more rain and colder according to hiker with updated forecast.
  • Drove to rest stop in eastern WA, watched stupid middle aged couple try to get dog into truck (45 min?)
  • Spent next night in Moscow, Idaho, then stayed in Bozeman, Montana the night after that. Drank lots of Moose Drool.
  • Yellowstone 1 night in campground outside park, 3 nights in Lamar Valley. Heard wolf howls and saw tracks and scat, but didn't see any.
  • I did a solo day hike up the Lamar River in my keens on the second day. Beautiful river.
  • 1 night in national forest outside of Grand Tetons. Day hike up to Amphitheater Lake (~9600 ft.); highest elevation I've been so far.
  • Drove for hours, stayed half night at rest stop. Arrived in Badlands this morning. Saw Bighorn sheep. Waiting out mid-day heat right now.
So there you have it. Not the most detailed notes, but one doesn't usually feel like writing a long narrative while backpacking. Anyways, I think that the pictures are more telling, though even those don't come close to replicating the experience. Still, it's a nice reminder for myself, and hopefully it whets the appetite of readers who may be interested in hiking/backpacking.

(Belated) Trip Report - Mt. St. Helens and Olympic NP

Wow, I meant to do this a while ago, but I was just organizing some magazines and found the notebook that I was going to use as a journal for my road trip back home from WA. It has exactly one entry, at which point I switched to my little 4x2 Rite in the Rain notebook (meaning that entries are fairly short, but it was much more portable for backpacking). For those that don't know, my friend Julie and her boyfriend Justin met me in Everett, where I'd been living (they had spent the past month in San Francisco), and we began our journey back east (backpacking a lot along the way). So here is a trip summary copied (with some editing) from my journal entries!

Mount St. Helens

Mt. St. Helens photos

8/25/2009

The evening before our climb, a large man with a sweat-stained shirt and an extremely large external frame backpack emerged from the trailhead, loudly stating "That was bullshit, I'm never doing that again!" We all started laughing. I slept outside that night, despite having set the tent up, and I woke up in the middle of the night to a good view of the night sky (clear, lots of stars).

Left for the climb at 7 a.m. and finished at 1! Six hours is actually really good time for a hike to the crater and back, especially considering that my knees were really starting to crap out. Worse than they ever have before, actually. It was a combination of joint, tendon, and muscle pain which main moving my leg to take a step awkward and painful no matter how I altered my stride. I'm hoping that they strengthen up as I continue hiking more. Note: A couple of days before, on my last day of work, I had slipped while walking in Canyon Creek and landed hard on (just) my right knee on a large boulder. This injury wouldn't have normally been all that bad, but it was very inconvenient considering that I was going to be hiking with a heavy pack for the next month or so. In the case of Mt. St. Helens and later in Olympic NP, I favored my left leg while hiking to help the right knee heal, with the result that my left leg soon became strained. So for about a week I had 2 bad legs, especially for the downhill hiking.

The first 2/3 of the summit hike was great. Started out in fir forest with Vaccinium understory, then after timberline there were various rocky specialist herbacious plants that I was not familiar with (though I did notice Fireweed and elderberry, as well as one willow fairly high up). Then the hike become rockier (with large boulders being the dominant feature), and it was officially a scramble. After the large boulders the substrate was mostly ashy, and it got cold and VERY windy. By this point, we'd pretty much gone into a cloud. The crater was anti-climactic, as visibility was only about 30 feet so we couldn't see down into it. Oh well. Currently at a free campsite along the Hoh River Road in Olympic National Park.

Olympic National Park

Olympic National Park photos

8/27/2009

  • Woke up to the sound of Roosevelt Elk crossing the Hoh River. Camped at bank (5 mile island). Occurred about 45 min to an hour before sunrise.
  • Went to get water shortly after, encountered the herd near the trail. They ran toward the open gravel bar before I saw them, and we watched each other from about 75 ft away. I cautiously passed. Several bulls. About 25-30 individuals.
  • Back at camp I watched crossbills for about 20 minutes. I'd never seen them before.
8/29/2009

  • Hike on 27th was brutal. 10ish miles to Elk Lake, the last half steep upill. Put moleskin on defective toe without noticing that blister had already formed. Hurt like bitch!
  • Elk Lake productive (aka mosquito infested). Constructed "armor" out of clothing and referred to myself as a Bedoin woman (all but eyes covered).
  • Yesterday hiked 2 miles (with ~1500 ft elevation gain) to Glacier Meadows. Resident doe and 2 point buck were very acclimated to humans. Saw small owl (Western Screech?) at dusk.
  • Day hiked to terminal moraine of Blue Glacier. Beautiful views! Then hiked to lateral moraine, down the inner scree slope (there was a "trail"), and then stood on the glacier! Drank refreshing glacier water. Julie did this all in flip flops.
  • Today hiked downhill to Olympus Ranger station. Park-like campsite with alders along Hoh river. Lots of bees and hornets.

8/30/2009

  • Hiked 9 miles out from Olympus Ranger Station to VC (visitor center). Very fast pace (est. 3 mph average)
  • Drove through Forks, not realizing that it was the center of Twilight madness. Showered at small motel that "smelled and looked like old lady." Then ate pizza and drank beer at small diner-like restaurant.
  • Drove to Lake Ozette, found $12/night campsite. About to go to bed before sunset.

To be continued in later post, probably later today.

Monday, December 28, 2009

Limb regeneration in Axolotls

From the 12/21 issue of HerpDigest:

7) How Do Salamanders Grow a New Leg? Protein Mechanisms Behind Limb Regeneration

ScienceDaily (Dec. 15, 2009) — The most comprehensive study to date of the proteins in a species of salamander that can regrow appendages may provide important clues to how similar regeneration could be induced in humans.

Researchers at the School of Science at Indiana University-Purdue University Indianapolis and colleagues investigated over three hundred proteins in the amputated limbs of axolotls, a type of salamander that has the unique natural ability to regenerate appendages from any level of amputation, with the hope that this knowledge will contribute to a better understanding of the mechanisms that allow limbs to regenerate.

"In some ways this study of the axoltol's proteins was a fishing expedition. Fishing expedition can be a derogatory term in biology but for us it was positive, since we caught some important "fish" that enable us to formulate hypotheses as to how limb regeneration occurs," said David L. Stocum, Ph.D., professor of biology and director of the Indiana University Center for Regenerative Biology and Medicine, both in the School of Science at IUPUI, who led the study.

"Comparison of these proteins to those expressed in the amputated frog limb, which regenerates poorly, will hopefully allow us to determine how we might enhance limb regeneration in the frog and ultimately in humans, Dr. Stocum said.

With few exceptions -- notably the antlers of moose, deer and their close relatives, the tips of the fingers and toes of humans and rodents, and the ear tissue of certain strains of mice and rabbits -- the appendages of mammals do not regenerate after amputation.

Limb regeneration in the axolotl occurs when undifferentiated cells accumulate under the wound epidermis at the amputation site, a process known as the establishment of a blastema. These cells are derived by the reprogramming of differentiated cells to a less specialized state, and from resident stem cells.

"We found proteins that point to several areas that need to be studied closely to give us vital information about the mechanisms that operate to form a blastema that then goes on to regenerate the missing parts of the limb," said Dr. Stocum, an internationally respected cell and developmental biologist who has studied limb regeneration for over three decades.

Investigating the proteins found in the axolotl limb, the researchers noted three findings that appear to have significance in reprogramming cells to grow new limbs:

1.Quantities of enzymes involved in metabolism decreased significantly during the regeneration process.
2.There were many proteins that helped cells avoid cell death. Because amputation is very traumatic, this is critical.
3.A protein which appears to keep cells from dividing until they are fully dedifferentiated and reprogrammed to begin forming a new limb was expressed at high levels throughout blastema formation.

Findings were published online in the journal Biomedical Central Biology on November 30 (BMC Biology 7:83, 2009). Co-authors of the study, which was funded by the W. M. Keck Foundation, are Nandini Rao, Ph.D. and graduate student Behnaz Saranjami of the School of Science; graduate student Deepali Jhamb and Mathew Palakal, Ph.D. of the IU School of Informatics; Fengyu Song, D.D.S., M.S., Ph.D. of the IU School of Dentistry; Mu Wang, Ph.D. and Michael W. King, Ph.D. of the IU School of Medicine; Bingbing Li, Ph.D. of Central Michigan University; S. Randal Voss, Ph.D. of the University of Kentucky; and Derek J. Milner, Holly L. D. Nye and Jo Ann Cameron, Ph.D. of the University of Illinois. All except the final four are also affiliated with the IU Center for Regenerative Biology and Medicine.

The School of Science, IU Center for Regenerative Biology and Medicine, IU School of Dentistry, IU School of Informatics, and IU School of Medicine are all located on the IUPUI campus.

Interesting article overall, though I wish they'd gone into more specific detail.

EDIT: I also ran into this article on ScienceDaily, which elaborates on the subject of Axolotl limb regeneration. Cool stuff! Especially the bits about salamanders being able to regenerate a sliced spinal cord and pieces of brain tissue that had been removed. I wasn't aware of that.

References:

HerpDigest (email Listserve), Vol. 9, Issue 56, 12/21/09, as appeared on Science Daily, How Do Salamanders Grow a New Leg? Protein Mechanisms Behind Limb Regeneration.

University of Florida (2009, July 2). Salamanders, Regenerative Wonders, Heal Like Mammals, People. ScienceDaily.

Friday, December 25, 2009

2009 New Years Predictions: Commentary

It's almost that time of year again! In case you aren't aware, Reyan, David and I started this tradition in college (I don't remember which year, Junior year maybe?) of coming up with 10 predictions for the upcoming year instead of doing New Years resolutions. In anticipation of the 2010 predictions, I'd like to review/comment on the predictions that I made for 2009.

1.Winter and spring in WA will be dull, but the summer will make it worthwhile.
Hmm, I'm not entirely sure what I meant by this. Weather-wise, this was definitely true. I guess in general it was true, too. In June I went backpacking in the N. Cascades, and I started my road trip back home in late August (much of which was backpacking in WA). And the summer field season at the Task Force was definitely good; Tychman Slough assessment, Knotweed surveys, and monitoring/maintenance (which included me getting supervisory experience, and with a Dept. of Corrections field crew, no less!). Overall I'd say I nailed this one.

2.President Obama will assume a major role in addressing climate change, but will fall short with energy policies.
Hmm, I honestly haven't been paying very much attention to what Obama's been up to. I know he got a dog, lol. Not sure if he's still plugging "clean coal," but if so that's definitely some major points docked right there. As for climate change, from what I understand there's been a lot of talk but not much meaningful regulation. Seems like climategate didn't really make a dent in the perceptions of most educated people, as the subject just sort of died down. I've only read a couple of blogs on Copenhagen, but from what I gather it was pretty much a failure. Seems like Tuvalu is making more strides than the U.S.A. So, prediction tentatively failed?

3.Reyan will get another job writing about sports :)
As far as I know this didn't happen, but he did get to interview Seth Green, which is far more impressive.

4.I will get a sub-par job, but I will actually be making money (which I will then save up for travel/grad school)
Yeah...tried and failed. To be fair I only had from late September to really begin this, and then that whole recession thing was kind of unforseen. I need to get on that in January though. Need some income!

5.While in WA, I will consistently follow a self-education program which I began this very day by checking out a geology textbook from the library. Genetics is next.
I didn't do too bad with this. I actually got through the majority of the Geology book, but only a few chapters of Genetics. I just had no focus, especially considering the subject matter. Genetics is broadly interesting to me, but I was mostly brushing up on basics, which I needed to do but it was still dull. I did read a decent amount after that; just not necessarily textbooks (though I'd call some natural history books of the area"self education."). So...prediction successful, if not to the degree that I'd hoped for.

6.Erin and I will coordinate a really awesome camping trip for this summer.
Oh yes, North Cascades in June! Her roommate, Kelly, came along too. It was a great area and the weather was wonderful, and my only complaint is that the mosquitoes were AWFUL!!! Click on my shutterfly page and scroll down to North Cascades June 09 for pics!

7.At least one more of my friends will get engaged.
I'm fairly sure that Jimmy and Amanda were engaged in '09 (my conception of time has been somewhat impaired since graduating from Denison). So I'm counting it. In any case, both David and Jimmy asked me to be a groomsman in their weddings, so it was definitely a marriage-centric year.

8.I will once again remain single this year.
Is this really a surprise? Well, at least I'm fairly comfortable with being single.

9.I will NOT get poison ivy or stung by bees at all this year!
I will never make this prediction again, lol. Talk about doomed to failure. No poison ivy (surprisingly!), but I was stung by yellow jackets once in WA. The yellow jackets there are much less painful than the ones here though. Also got bitten by a ton of mosquitoes. And actually, I revise the "no poison ivy" comment because I may have had a very mild case after walking Angel in the park when I was home for Laura's wedding. Just a few itchy spots which could have been bug bites, but seemed more like poison ivy to me.

10.I will find $5.
I honestly don't remember if I ever found $5 this year. I think this was a joke prediction because I couldn't think of anything else. I'm going to assume that I didn't.

Total Sco
re: 5/10. Not too bad, especially since #5 was the only one that I had complete control over.

P.S. I'd also like to point out prediction #2 from 2007, which I just noticed as I was giving all of the previous prediction posts tags: " I or one of my close friends will have a near death experience." I actually fulfilled that one this year (yes, I realize that it doesn't count because it's the wrong year, but I still wanted to mention it). Word of advice: the extremely cold temperature of alpine lakes severely impairs swimming ability. Cold muscles not liking to work and all. Stay close to the shore ;)

Wednesday, December 23, 2009

Ancient DNA preserved in permafrost

I just read a post on the blog Laelaps on the extinction of mammoths and horses in the Alaskan interior. The discussion refers to this paper, which I haven't read yet but will hopefully get around to it soon. Instead of looking for fossilized hard tissues (bones, teeth), the researchers instead recovered mitochondrial DNA (mtDNA) from the permafrost (in this form, it's known as sedimentary ancient DNA, or sedaDNA). Conditions for fossilization of bones are rare, and thus once a species becomes rare the likelihood of an individual becoming fossilized is low. However, these animals still bleed, urinate, defecate, shed hair, etc, and these activities are not rare (indeed, they occur daily). Thus, it may be easier to pinpoint a more exact timeline for extinction using these methods.

I'm not going to reiterate what's in the blog, so if you're interested in the subject just click on the link above. I will, however, add that global climate change poses a great threat to this type of research in the future. Permafrost is by far the best environment to find sedaDNA, but once it melts and the meltwater leaches through the soil that DNA will be lost forever. It's tragic, as this is an incredibly fascinating (not to mention informative) technique, and I hope that emphasis is placed on funding additional expeditions sooner rather than later. Information on different species and from different sites would be an extremely useful tool in piecing together the natural prehistory of the Pleistocene megafauna (possibly even shedding light on the cause of the extinction event).


References:

Haile, J., Froese, D., MacPhee, R., Roberts, R., Arnold, L., Reyes, A., Rasmussen, M., Nielsen, R., Brook, B., Robinson, S., Demuro, M., Gilbert, M., Munch, K., Austin, J., Cooper, A., Barnes, I., Moller, P., & Willerslev, E. (2009). Ancient DNA reveals late survival of mammoth and horse in interior Alaska Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0912510106

Monday, December 21, 2009

Northern Mockingbirds

This morning while I was walking Angel around the neighborhood I noticed a bird that I hadn't seen around here before. There were two of them, and I got a good, fairly close look at them perching from several different angles and also in flight. I assume they were a pair, as they followed each other around in flight. I got back home and looked it up in my field guides, and they were indeed Northern Mockingbirds (Mimus polyglottos). Northern OH is within their summer range according to Sibley and the National Geographic field guide (5th edition), though Peterson does have their year-round range going all the way up to Lake Erie.

I find it odd that a bird which I've seen only very rarely around here was overwintering in a suburban neighborhood. I emailed my grandparents to see if they'd ever seen mockingbirds at their feeders, and they said that they haven't.

Perhaps they were just vagrants, but I also wouldn't be surprised if their range is shifting northward.

Tuesday, December 15, 2009

Thoughts on Environmental Consulting

I'd like to preface this post by noting that my knowledge of the environmental consulting business is relatively poor. Thus, I shall keep my thoughts extremely general. The first general problem that I've always had with the process of hiring an environmental consultant was the fact that the developer, etc. is the one that does the hiring. Environmental assessments are required by law, to ensure that the damage a proposed project would have is not too severe. Obviously, from the point of view of the developer the consultant's job is to give the project the green light, determining that the environmental damage would not be so great as to preclude the development of the project. In other words, the burden of proof is on the developer, which is all great and consistent with the Precautionary Principle.

However, problems often arise due to the fact that, to the best of my knowledge, environmental consulting firms are privatized. There is good old capitalist competition between different consulting firms, and this often gets in the way of scientific integrity. After all, how do we determine how much environmental damage is acceptable? Setting the bar higher is an obvious goal for environmentalists, as it reduces development to more marginal areas while protecting a greater amount of land. But that's not what the developer's want. They want it to be easier to develop in the most convenient locations regardless of the environmental impact, all the while negotiating the least amount of red tape. So if there's a specific consulting firm that's known for setting the bar a little lower, developer's are going to want to hire them. Disproportionately more than competing firms. That is, until other firms start to lower the bar just to prevent themselves from being run out of business. Free market competition is antithetical to the ultimate goals of the environmental laws that require consulting firms to be hired. But it's a balancing act, because clearly having successful firms with some standards (albeit standards that lean toward favoring developers) is better than letting developers run rampant, unchecked. After all, the most damaging projects won't be approved because any consulting firm that approves it will have its reputation completely tarnished, and will likely be harassed by environmental groups until their forced out of business. After all, developers won't want to hire a firm that gets such negative press, either.

It logically follows that projects near the border will be skewed in favor of development, because you can make an argument that the benefits outweigh the costs while still sounding reasonable. Thus, your reputation as an environmental firm isn't tarnished, but the developers that hire you can still appreciate your pro-development slant (even if the slant only exists to stay in business, not necessarily representing the personal convictions of the employees). I worry that this pattern results in the bar being discretely and incrementally set lower, especially in the face of a growing population and more land use "requirements."

My solution would be to remove environmental consulting from the free market and give it some sort of government oversight. I recognize that this could also be problematic, as large firms interested in development hold a lot of political influence. However, it's still better than having the developers hire consultants directly, in part because politicians - who need to be re-elected - are subject to more public scrutiny than private businessmen (after all, it's a free, capitalist country, and if you've built a business up you can't get voted out). Essentially, a developer would pay a mandatory consulting fee, probably commensurate with the scale of the project. Government consultants would then be sent to do the assessments. Employees from the disbanded private consulting firms could be hired as government workers, and the funding would come from the consulting fees. Without competition between firms, there would be no incentive to compromise scientific integrity, thus ensuring more objective assessments.

Saturday, December 5, 2009

Summer Glau on Dollhouse!

Beware, there be Spoilers!


Dollhouse returned last night for a two hour "event." Which is pretty much the schedule it's going to have all December, as Fox rushes to get rid of another Joss Whedon show as quickly as possible to make room for more of the senseless drivel that comprises most television shows. But at least Joss Whedon got pretty advanced notice that the show would be cancelled, and at least it got to its second season (unlike Firefly). I'm guessing that the remaining episodes will be thematically rich, as Joss and Eliza try to shove all of their ideas for what they wanted to explore in before the (series) finale.

Still wondering where Whiskey/Dr. Saunders (played by the wonderful Amy Acker) is, but I've read that she will be back. For that matter, Sierra/Priya (Dichen Lachman) was also absent for both episodes. But, as the title of my post indicates, we got Summer Glau as the D.C. Dollhouse's version of Topher (the character's name is Bennet Halverson). Bennet's an interesting character, but I'm not quite sure what to think of her. She seems more "evil" than Topher (who is just amoral; well, mostly), but she also got royally screwed by Caroline, which is how she got her dead arm. They didn't go into this backstory much, as we really only saw the imprinted memory that she gave Echo of her laying on the ground, pinned (by her arm, obviously) by a large concrete pillar. Seems like she was working some sort of job with Caroline (not Echo?!), and that Caroline left her there. Seems a bit out of character for Caroline. I'm sure there's more to this story, so I expect to see Summer Glau return (speaking of which, Alan Tudyk, another Firefly veteran, will return next week as Alpha!).

Perhaps my favorite part of these two episodes (technically only the second episode) was when Topher imprinted Viktor (Enver Gjokaj) with his own personality (so that when Topher went to D.C., he could leave "himself" behind). I was extremely impressed with Enver's acting here, as he played Topher perfectly (just as well as Fran Kranz). I've liked Enver throughout the series, but this was definitely the highlight (even better than when he accidentally got imprinted with Echo's imprint, Kiki!). It's something that you really just have to see.

And finally, there's the Senator Perrin (Alexis Denisof) storyline. The fact that he's a doll and his wife is his handler was certainly an unexpected twist. It's also an interesting concept that they didn't wipe his original personality, but rather improved it to create the perfect politician to use as a tool for Rossum. In hindsight, it makes perfect sense that Rossum would need allies in politics to ensure that laws get passed, allowing them to do whatever else they plan on doing. However, I see a flaw in this plan. They have one Senator that's a doll (that we know of). Obviously, some stuff hinted at in Epitaph One (last season's dystopian future season finale) would require some pretty major laws to make legal. I'm a little skeptical that proposed laws could be spun in such a way as to make them seem like a good idea to the majority of Senators and Representatives. There's only so much one person (even a person so "improved" by Rossum) could do. Given the political controversy over something like stem cells, the technology employed by the Dollhouses (which is shown to be under the radar of most politicians) wouldn't stand a chance at being legalized. But yes, it's a show and some suspension of disbelief is required to enjoy it. And regardless, it allows Joss to tell some good stories.

Thursday, December 3, 2009

Where are you, snow?

A couple of days ago I put up the Christmas tree, and for that matter I've been drinking Great Lakes Brewery Christmas Ale for about a month already, but it still doesn't feel like Christmas. Obviously the lack of snow is contributing to this. I'm especially anxious since I spent last winter in western WA, where it rarely snows. A larger factor is probably the shift in my perspective compared to when I was a child. I never attached much religious meaning to the holiday, which works out just fine for me now being an atheist. Even when I was being brought up Catholic, however, the rampant materialism pretty much overshadowed everything. I was excited about getting new toys, and of course getting a break from school was nice too. Since I've become increasingly less materialistic (coming up with a X-mas list is a chore now, and one that I haven't really begun working on this year), this aspect of the holiday has not only lost its luster, but become extremely annoying to me. Fortunately there was always something else about the Christmas season, the aesthetic values of the decorations, and the lights, and the Christmas tree. That's still there. And just last night I watched the old Rankin-Bass Rudolph the Red Nosed Reindeer, and despite being for kids it was still enjoyable (same with Charlie Brown Christmas). Then there's other movies, like Home Alone, etc. which I still enjoy, but the effect of instilling in me the "Christmas spirit" is short-lived. I guess I sometimes get nostalgic because Christmas used to be such a big deal, and now it's just merely a nice time of year with pretty lights when the first snow begins to fall. Oh well, it is what it is.