Liz's Bloglet - Sunday 27 January 2008

This sounds like a good possibility for what I want to do next Basically, it's a post-doc program in which one does research in a lab at UNC and teaches at one of the historically black colleges and universities (HBCU) in the area. Most post-docs are either teaching or research, and few of the teaching ones are at schools I'd like to teach at (Dartmouth is one several people I know have done--I have no interest in the Ivy League or the Pseudo Ivy League ever again). Now I just need to find out what else I need to do to make sure I get there. _
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06:04:46 PM, Sunday 27 January 2008

This looks promising and surprisingly reasonably priced (posted here mostly so I can find it again). _
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01:37:28 PM, Sunday 27 January 2008

OH NO!!1! _
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01:05:47 PM, Sunday 27 January 2008

Memorable NPR moment of the week: Yesterday on Day to Day they were discussing today's SC primary. They talked to African-American women who are having trouble choosing between Clinton and Obama. Then they spent a couple seconds discussing the fact that Edwards is still doing quite well in the state. For a moment I got excited. Were they actually going to talk about his platform and his policy proposals?

No. They spent the whole time talking about why white people in SC don't like Obama and whether Obama is "going to have trouble getting white votes in the South." Because the only reason somebody might support Edwards is because they are racist (as all white southerners are, of course) and not because Edwards gives speeches they like or is actually talking about ending poverty, bringing jobs back to areas which have completely lost their manufacturing base, and trying to fix healthcare, instead of unspecified hope and/or change and/or whose former employer was a bigger scumbag and/or who likes Ronald Reagan. _
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07:09:42 AM, Saturday 26 January 2008

I realized I've never actually written anything about Juno here, although I've commented on other people's threads. No movie has stuck with me that much in years. Part of it is just Ellen Page. Part of it is the dialogue, which to me sounds actually pretty natural, especially among the teenagers, and I'm constantly amazed by people who were put off by it. And part of it is the writing. And part of it is the soundtrack. It's a movie that needed to be made, to say that teen moms are not stupid, and pregnancy is not an easy choice for anybody, and figuring out who you are and what it means to be an adult are hard things that nobody ever completely achieves. _
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03:51:32 PM, Wednesday 23 January 2008

This happened in our neighborhood Sunday The pain inside people is horrible. _
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08:23:33 PM, Tuesday 22 January 2008

Last week I got to one of my sites at the right moment to see one of the beavers who had been living there for a couple of months. They currently live at three of my sites, but I rarely get to see them, because of course they go underwater when they hear me coming. They are amazing creatures. They're bigger than most people imagine--larger than a cat or a raccoon. Their fur is thick and shiny and keeps them warm even when there is ice on the stream as there has been lately. Their tails are these truly remarkable things--not furry like in the cartoons but perfectly etched, tough, black skin to serve all of their many purposes. Their swimming and chewing and engineering are effortless but every step on land is comical right to the point where they slide down the bank back into the water. They are vital parts of the ecosystems I study--restoring woody debris to the channel to provide food and habitat; building structures that retain sediment and help keep the channel active for the benefit of the other creatures that live there; and eventually creating openings in the forest that provide first vital wetland and then vital meadow habitat. I don't even mind when they cut down the trees my equipment is chained to.

Today there was a beaver lying dead in exactly the place I saw one last week. Somebody had cleared some trees out of the culvert upstream. The trees were not a beaver dam--they had been there for the two years I've been working at this site and did not in any way look like a beaver dam. The beavers living at my site did not seem to be dam builders anyway (some beavers prefer to live in stream banks rather than dams).

Perhaps the beaver was in the area when the equipment was used and was accidentally injured at the time. Maybe it got disoriented by the noise and drowned (I understand this can happen to them). Maybe disease or age combined with the recent very cold weather lead to a natural death. Or maybe some idiot who didn't know what a beaver dam looked like anyway decided to kill the beaver thinking that would keep the culvert clear.

So now I have to make sure that no poison, traps, or guns are likely to appear at this place I work. And that whoever in charge understands that this is a research forest and removing wood from the stream is disruptive to my research (and that I've been monitoring the site for two years and the water has never approached the road in even the biggest tropical storms we've had). And I have to remove this body from my research site because I won't be able to bear watching it slowly decompose in the stream. And wonder about its mate. _
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07:43:02 PM, Tuesday 22 January 2008

Happy Right-To-Privacy-Bodily-Autonomy-Make-Your-Own-Medical-Decisions-Reproductive-Freedom-Blog-For-Choice Day!

Read this post by a UCC minister whose own choice made her finally comfortable with making that choice available to all women _
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09:04:31 AM, Tuesday 22 January 2008

Tara Baker was murdered a few months before we moved to Athens I can't believe that 7 years later it's still unsolved. I have always been a fan of detective fiction and thrillers, but I've slowly lost my taste for the more gory parts of that genre (Jonathan Kellerman, Robin Cooke, slasher movies), and I think things like this murder and this other Georgia case are the reasons. My ability to detach my empathy from the fictional subject matter has really declined. _
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10:45:07 AM, Friday 18 January 2008

How Not To Be Insane When Accused Of Racism (A Guide For White People) _
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11:28:53 AM, Monday 14 January 2008

sweetjesusihatechrismatthews _
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08:41:51 AM, Sunday 13 January 2008

PCR--when you need to find out who the daddy is... Never has a scientific supply company gone to this much trouble to make nerds laugh in order to sell equipment.

You could read the Wikipedia article about PCR or I could just say in the past couple of decades that it has become basically what molecular, microbial, and geneticist types spend the vast majority of their time doing. As it says in the song, you really do add a bunch of raw materials and heat and cool in succession a few times and end up with amplified DNA. And this song is the funniest thing this biologist has seen in a very long time _
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09:39:15 PM, Friday 11 January 2008

The Wire first 4 seasons in 4 minutes. Spoilers galore. Yes, it's YouTube. Yes, it's an HBO promotional. Yes, it's awesome. _
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08:26:15 AM, Thursday 10 January 2008

I am not less than Melissa McEwan totally gets her feminist rant on. _
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09:27:13 AM, Saturday 5 January 2008

In the interest of not talking about politics, I realize that it's been a month and I should tell you all about my experience switching from mostly windows to all mac all the time.

First, my computer goes to sleep and wakes up pretty much instantaneously. That by itself has made me much more productive. It's also a lot lighter, so I'm taking it home more nights.

Second, Papers is the coolest thing I've ever seen. Obviously, it's aimed at a small subset of the world, but it solves a real problem (search for an article in Firefox, open it in Acrobat, save it in some folder somewhere, manage the citation in EndNote) in a novel way and once again saves a huge amount of time. These same folks developed some great software for macs used by most genetics researchers.

I still haven't installed Windows, which I'll have to do eventually to run ArcGIS and HEC-RAS, so I can't say for sure how easy and well Bootcamp will do (although I've heard with Leopard it's great). I still haven't solved the database issue: a)install Office for Windows and use Access, b)some Mac-specific database software, c)MySQL. All have pros and cons and none is really the perfect solution.

Overall, things are great. I'm glad I've made the switch, as they say. _
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06:39:10 PM, Friday 4 January 2008

So, here's the thing that gets me. Howard Dean's third place finish in Iowa in 2004 was enough for pundits to declare his campaign dead in the water. John Edwards second place finishes in both 2004 and 2008 are enough for them to talk about how he never really had much popular support. (Can't the rest of us be allowed to vote before we declare how popular candidates are? I know several people who liked Dodd--but their votes no longer count.)

But Hillary Clinton comes in third, and all the talk is about what a big threat she still is to Obama.

It really seems like whoever it is wrote the story last year and now they are carefully doctoring the facts to fit their plotline.
_
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02:05:16 PM, Friday 4 January 2008

David Simon stopped by Matthew Yglesias' blog to respond to a discussion of The Wire _
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02:24:30 PM, Thursday 3 January 2008

The problem is not 'partisanship', the problem is that one group of partisans, known as Republicans, are staggeringly wrong.

Mike the Mad Biologist makes a new years resolution to continue being partisan _
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05:00:22 PM, Wednesday 2 January 2008

It's snowing! It will do so for two or three more minutes, I'm sure. _
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11:51:45 AM, Wednesday 2 January 2008

I still think letting Iowa and New Hampshire determine things for the rest of us is pretty dumb. The good news is any of the leading Democrats will do a good job, so at least they can't screw things up the way they did in 2004. For those Iowa Republicans, maybe this will help you decide which incompetent bit of evil to caucus for: The GOP primary field as Buffy villians
_
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11:34:19 AM, Wednesday 2 January 2008

The school board in Rockland, ME recently refused a student group request to travel to New Orleans to help with rebuilding, calling it a "war zone". You've seen my pictures. It's sad. It's easy to lose hope. But it's not even mildly scary. People recognize volunteers and offer nothing but love and welcome. Total strangers stopped in front of the house we were working on to find out where we were from and chat with us. (The scariest place in New Orleans for a woman alone at night is still Bourbon Street.)

The greatest divide in America is still caused by ignorance and fear of places and people different from us and ours. _
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10:18:03 AM, Sunday 30 December 2007

For some reason this really got to me I have a friend whose little brother spent Christmas outside of Baghdad. I hope he gets to cuddle with a lab. _
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08:29:20 AM, Sunday 30 December 2007

If someone hits you over the head with a banjo that�s assault, not bluegrass. You can offer the victim all the music appreciation classes in the world. Music appreciation is a fine thing. But it won�t change the culture of violence that allowed the attack.

Chris Clarke deserves an award both for best metaphor and most impressive pro-feminist male on the internet (again) _
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06:40:44 AM, Friday 28 December 2007

I finally got my New Orleans pictures up from last month. Here is the street we worked on full of FEMA trailers and some still untouched houses:

I can lie to you to make you feel better, or I can say that the need is still enormous and you've got 3 more days to donate this year. _
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06:38:34 PM, Thursday 27 December 2007

I can't find The Dark is Rising. I will find it before we leave this afternoon. Or I'll probably end up buying another copy. This is a Christmas I really need it. _
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06:52:20 AM, Sunday 23 December 2007

The Lakota have declared their independence from the US If nothing else comes of it, maybe this will remind people of our continued crime against the native people of this continent. _
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11:35:03 AM, Thursday 20 December 2007

Some good posts about how, once again, mainline Christian beliefs are being defined out of Christianity in the popular mind:
Dwight of Religious Liberal Blog on how the "defense of Christmas resolution" carefully defines Christians as only those who believe in literal substitutionary atonement

Philocrites on how Romney's pluralism doesn't even extend to non-conservative Christians, let alone people of other religions, the non-religious, or atheists as has been pointed out elsewhere. What he admires about other religions and, by extension, what he seems to be saying deserves toleration is conservative traditionalism. But millions of Americans, and not simply atheists and "seculars," are excluded by this definition. Romney isn't defending religious pluralism; he's defending conservatism.

Finally, from my favorite "True Child of the Enlightenment" (this is an insult in some circles. who knew?), Presbyterian minister John Shuck comes Jesus: Too Liberal for America _
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07:11:28 AM, Thursday 20 December 2007

Paul Krugman on the Democratic candidates I don't really have anything to add... _
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05:16:32 PM, Wednesday 19 December 2007

No. No, I did not. _
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06:10:54 PM, Monday 17 December 2007

Speaking of problems with campus culture at Pseudo-Ivy University... _
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04:26:09 PM, Monday 17 December 2007

Last night I went Christmas caroling at a local retirement home. I met Juanita Kreps, Secretary of Commerce under President Carter and the first woman to hold that cabinet position (she was on the Duke faculty and eventually vice president of the university). There was also as a woman who had been a champion golfer and a couple who had been married for 70 years. It was pretty amazing, and also sad. Medical care is so good now in terms of physical health, but we still don't know how to care for our aging minds. _
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10:58:53 AM, Monday 17 December 2007

I can't do what I really want to do Because nothing serves our country better than preventing smart kids from getting an education. _
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10:51:24 AM, Monday 17 December 2007

St. John's' complete lack of diversity in the news I'm just so frustrated by this. I want there to be a place that offers the Program but that really is welcoming to a variety of viewpoints. Maybe it needs to be a place like Berea where the children of the rich and powerful simply aren't welcome, because goodness knows they aren't very welcoming to other sorts of people at St. John's. _
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09:26:16 AM, Monday 17 December 2007

I've turned a previous blog entry into my final essay for our Epistemologies of Biology reading group. It's been through peer review and everything. We are going to publish a zine and pass it out in the department! I would love to know what my faithful readers think:

Accounts and Metaphors
Scientists deal every day with the ways that our descriptions and understanding of the world fall short of the world, and the ways we feel unable to access what is real. We do this almost instinctively, most of us without having read Fleck or Popper. Nor do we necessarily think of the act of doing science as fitting within anything that could be called an epistemology. We speak the same language and use the same metaphors, and understand the layers of meaning within those metaphors in similar ways, but we frequently do this without examining the framework of science that we are giving to other scientists, or the public.

Differences in our accounting of science become clear, however, when reading, for instance, Susan Oyama's Evolution's Eye. Her basic contention is that biological programming by genes has come to completely dominate our understanding of life, at the expense of the many other factors that determine the appearance and behavior of organisms. Further, she argues that nature/nurture duality is useless because it paints things as a simple one-dimensional continuum--every "trait" can be said to be determined from some basic combination of nature and nurture, whether it's 100:0, 50:50, or 20:80.

Oyama�s argument is that we must look at every trait of every organism as the culmination of everything that's come before it, every phase of development, every chemical, every interaction with another organism, every behavior and experience. For this reason, she argues that immature/mature is a duality equally as useless as nature/nurture because one can no more say that an organism is "mature", that all traits are now expressed as they will be through the life of the organism, than one can separate nature from nurture. One can no more pinpoint a gene that leads to a complex trait, whether it�s schizophrenia or aggressive behavior, than one can pinpoint a single day in kindergarten that leads to that trait. While there are limits to this in some ways (e.g., trisomy 21 causes Down�s Syndrome) we must be careful both as scientists and people to understand that while we can predict the likely range of effects of a profound genetic abnormality, environmental and developmental effects still work in concert with the genetic effects to bring us the traits of a whole organism.

Biologists will have varying comfort levels with this. Ecologists, evolutionary, cell, and molecular biologists all have varying understandings of the roles and importance of genes in their work. An explanation like Oyama�s can be hard to wrap one�s head around, regardless of how many hours a day one spends studying genes or natural environments. On further consideration, however, many scientists will see the usefulness of reframing this discussion in this way. Even those who find this particular thought collective less than useful would agree that terms like �genetic programming� are constructions, i.e., useful metaphors. How far a scientist is willing to take such a metaphor and where he or she thinks it breaks down, generally depends on their area of study.

The correct use of metaphors is, ultimately, one of the real dilemmas in our scientific discussion. A good metaphor used at the right time with the right audience can illuminate a difficult concept or brighten up a dull discussion�both worthy aims. Metaphors can even be a key facet of our scientific epistemology, whether it�s genes as programs or rivers as networks. Thinking metaphorically about complex matters can alter paradigms and further scientific progress.

It is likely, however, that a scientific audience and a popular one require different metaphors. Because, in the process of translating the literature for the public, popular science writing is very good at taking out qualifiers and turning similes into metaphors and metaphors into statements of fact, most of the non-scientific public is comfortable with the idea that genes alone determine who we are. The discomfort scientists feel when reading Oyama�s writing is minimal compared to that of someone with minimal scientific education�it goes against all popular science paradigms that they read in the newspaper or see in movies (with the exception of Gattaca). We must become better communicators�with each other, the media, and regular people. We must not sacrifice truth to oversimplification, and we must not be so trapped in a single worldview and comfortable with our own metaphors that we can�t recognize when they have become a barrier to rather than a facilitator of communication. _
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10:54:22 AM, Friday 14 December 2007

Am I wrong in thinking the Mike Huckabee being in the race is the best thing for our country? If he doesn't get the nomination, many of the religious right will not vote because no other candidate meets their religious litmus test. If he does get the nomination, many Republicans who are not members of the religious right will stay home or vote for another candidate. Either way, the Democratic candidate wins and the political power of the religious right is broken. They can go back to practicing their faith and doing good works and, I don't know, feeling superior to the rest of us, instead of trying to bring about theocracy. _
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07:48:48 AM, Friday 14 December 2007

The day it snowed in San Diego _
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01:03:55 PM, Thursday 13 December 2007

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