Jeremy B. Yoder: web log

No further updates forthcoming

noreply@blogger.com (Jeremy) — Wed, 20 Jan 2010 16:26:00 +0000

For all practical purposes, I've stopped posting to this blog. This is partly because I've now been writing quite a lot over at Denim and Tweed for some time, including notes about scientific papers I've read and updates about the most recent results of my own research. That site, not this, will probably be the forum I use for the foreseeable future. With that in mind, I'm retaining this blog on my personal site purely as a record of previous posting.

Finding Joshua tree's niche

noreply@blogger.com (Jeremy) — Thu, 23 Jul 2009 05:07:00 +0000

A new Joshua tree study is just out in the current issue of New Phytologist, presenting an analysis of the environments occupied by the two different types of Joshua tree. The results demonstrate that the two tree types mostly grow in similar climatic conditions [PDF], which suggests that coevolution with its pollinators, not natural selection from differing environments, is responsible for the evolution of the two different tree types.

The Pellmyr Lab has been studying the two types of Joshua tree, which are pollinated by two separate, highly specialized moths, for several years now. Previous papers have shown that the two types of Joshua tree, first described in the 1970s based only on their vegetative features, are most strongly differentiated by the shape of their flowers [$-a]; and that, although the two moths are separate species, the two tree types are not fully genetically differentiated [PDF].

Hey, those Joshua trees look kinda
different.
Photo by jby.

The latest paper is a chapter from the dissertation of Will Godsoe, who just received his doctorate last week. It presents an analysis that sidesteps a fundamental problem with studying long-lived, specialized organisms -- they're hard use in fully controlled experiments. To determine whether the two types of Joshua tree really evolved as a result of coevolution with their pollinators, we'd like to be able to eliminate the alternative hypothesis that the two types evolved in response to different environmental conditions. Except for a small contact zone in central Nevada, each tree type occurs in a different part of the Mojave desert, and the two regions do have some broad-scale differences in when they receive precipitation.

Ideally, to determine whether two plants have different environmental needs, you just perform an experimental transplant, growing each plant in the other's environment to see whether it fares as well as it does at home. This isn't really possible with Joshua trees, which are pretty tricky to sprout from seeds (I've tried), and which, in any event, take something like twenty years to mature. So Will proposed to use niche modeling methods instead. Niche models are statistical descriptions of environments where an organism is known to live, often used to predict where it could live. To build niche models for each type of Joshua tree, Will assembled location data we'd collected over several field seasons in the Mojave, then spent another field trip driving around the desert some more to fill in the gaps -- he wanted locations where Joshua trees were definitely growing and where they definitely weren't, to fully "inform" the models.

Using the location data, it was possible to determine what kinds of climates each Joshua tree type tended to occupy by cross-referencing with existing climate databases, then fitting statistical models to the results. The models produced for each tree type could then be compared -- and, for the most part, they're similar. That is, if you collected seeds from one tree type, planted them where the other type grows, and waited around for a few decades to check the result, you'd probably find that it grew as well as it did in its home range.

So, if differing climates don't explain the origin of the two types of Joshua tree, does that leave no other possibility but the pollinating moths? Not exactly -- there are lots of environmental variables that weren't available for Will's niche models, for instance, or there could be a third, completely unknown factor. But this does make coevolution with the moths a more plausible explanation. In light of some of our very latest results -- which should be going to press fairly soon -- coevolution is looking like a better and better possibility.

Reference

Godsoe, W., Strand, E., Smith, C.I., Yoder, J.B., Esque, T., & Pellmyr, O. (2009). Divergence in an obligate mutualism is not explained by divergent climatic factors New Phytologist, 183 (3), 589-99 DOI: 10.1111/j.1469-8137.2009.02942.x

Godsoe, W., Yoder, J.B., Smith, C.I., & Pellmyr, O. (2008). Coevolution and divergence in the Joshua tree/yucca moth mutualism The American Naturalist, 171 (6), 816-23 DOI: 10.1086/587757

Smith, C.I., Godsoe, W., Tank, S., Yoder, J.B., & Pellmyr, O. (2008). Distinguishing coevolution from covicariance in an obligate pollination mutualism: Asynchronous divergence in Joshua tree and its pollinators. Evolution, 62 (10), 2676-87 DOI: 10.1111/j.1558-5646.2008.00500.x

Mennonites in pink

noreply@blogger.com (Jeremy) — Fri, 22 May 2009 04:21:00 +0000

Pink Menno Campaign is organizing people to support broader (and officially-sanctioned) inclusion of LGBTQ people in the Mennonite Church by wearing pink at the upcoming biennial convention of Mennonite Church USA.

Mennonites are in a slightly unusual position w/r/t sexual orientation -- the Confession of Faith in a Mennonite Perspective accepts only heterosexual marriage -- but the CoF is more a descriptive than a prescriptive document, and because MCUSA lacks some sort of centralized doctrinal enforcement, a few individual congregations do welcome LGBTQ folks and even perform same-sex marriage ceremonies. Sometimes such congregations and/or their pastors are "disciplined" in various ways by the local-level church authorities that can do such things, and the results are never happy.

I thought it was a big deal when, as a delegate at the last MCUSA conference, I was involved in preparing a statement on behalf of young Mennos that included a very brief nod to broader inclusion; much more recently, a group of Mennonite pastors signed an open letter to the church calling for an end to the exclusion of LGBTQ folks. (An article in Mennonite Weekly Review covers both the letter and its context.) Progress? Hard to say. A Delegate Assembly full of pink t-shirts is a mighty appealing image, though.

(Cross-posted at Denim and Tweed.)

Field trip

noreply@blogger.com (Jeremy) — Sun, 29 Mar 2009 04:33:00 +0000

Just back from a week and a half of attempted fieldwork in Nevada, with a hiatus to Southern California for a lecture to a Desert Institute class. Very few Joshua trees were in flower; so the trip was kind of a bust. But still a nice break.

If it's online, it must be for real

noreply@blogger.com (Jeremy) — Thu, 11 Dec 2008 00:30:00 +0000

The website for the Evolution 2009 meetings, to be held right here at the University of Idaho this spring, is officially live, although issues remain with our domain registration (eventually, evolutionmeetings09.org is supposed to forward to this page). Graphic design for the conference logo is by Christian Blackman, a UI Art and Design student; HTML coding and layout by yours truly.

Conscientious objection in Israel

noreply@blogger.com (Jeremy) — Thu, 04 Dec 2008 20:45:00 +0000

All Israelis, men and women, are required to serve in the national military when they turn 18. That's a hard social background within which to be a conscientious objector, even before you account for the fact that refusal to serve means jail time. Yet there are Israeli COs. On the God's Politics blog, Howard Zinn introduces a campaign on behalf of one cohort of teenage COs, the Shministim. (That's Hebrew for "twelfth-grader" - can you imagine going to jail for your beliefs as a high school senior? Yeah, neither can I.) The American-based Jewish Voice for Peace is looking for people to sign a statement calling for the Shminstim to be released, to be delivered to the Israeli Minister of Defense as one big pile of postcards on 18 December. Sign the statement here.

Fall break: Seattle

noreply@blogger.com (Jeremy) — Mon, 01 Dec 2008 03:00:00 +0000

Powell endorses Obama, defends Muslim Americans

noreply@blogger.com (Jeremy) — Sun, 19 Oct 2008 18:41:00 +0000

Former Secretary of State Colin Powell officially endorsed Barack Obama for President on Meet the Press this morning. But, incredibly, that's not the most important thing he had to say in the interview. Referring to the Republican whisper campaign that claims Obama is a crypto-Muslim, Powell said (around 4:38 in the embedded video below):

Well, the correct answer is, he is not a Muslim, he's a Christian. He's always been a Christian. But the really right answer is, "What if he is?" Is there something wrong with being a Muslim in this country? The answer is no, that's not America. Is there something wrong with some seven-year-old Muslim American kid believing that he or she could be President? Yet I have heard senior members of my own party drop this suggestion, "He's a Muslim, and he might be associated with terrorism." This is not the way we should be doing it in America.

Powell puts his finger on the ugly nature of the Muslim Obama rumors, which has bothered me basically from the first time I heard it, but hasn't been much discussed in any major media outlet: why should it make a difference if Barack Obama is Muslim? As long as he's an American citizen, his religion shouldn't matter in a run for the Presidency. On the Media only picked it up last week - though once they did, they dissect the issue with the acumen you'd expect. More even then the endorsement, which is a big deal, I hope Powell's MTP appearance starts a conversation about this.

I had a great weekend

noreply@blogger.com (Jeremy) — Mon, 06 Oct 2008 15:19:00 +0000

Turns out Glacier National Park is spectacular even when it rains all day.

The anti-rumor

noreply@blogger.com (Jeremy) — Mon, 06 Oct 2008 13:17:00 +0000

You won't hear it from the mainstream media, but Barack Obama is a really nice guy. Best part is, it's true.

Joshua tree genetics suggest coevolutionary divergence

noreply@blogger.com (Jeremy) — Thu, 02 Oct 2008 22:41:00 +0000

The latest results from the Pellmyr Lab's ongoing study of Joshua tree and its pollinators are online as part of the new October issue of Evolution. It's the cover article, no less. The study, whose lead author is Chris Smith (now on the faculty at Willamette University) compares patterns in the population genetics of Joshua trees and the moths that pollinate them, and shows that although the moths have become two separate species, the trees may not have followed suit [PDF].

Evolution cover
Photo by Chris Smith.

As I've probably written about before, Joshua trees are exclusively pollinated by yucca moths. Female yucca moths carry pollen between Joshua tree flowers in special mouthparts. When she arrives at a new flower, the female moth lays her eggs inside it, then deliberately applies pollen to the flower's receptive surface. When the fertilized flower develops into a fruit, the moth eggs hatch, and the larvae eat some of the seeds inside the fruit.

Among the yuccas, Joshua trees are unique because they're pollinated by two species of moths, which are each other's closest evolutionary relative. One species is found in the eastern part of Joshua tree's range, the other in the west. Joshua trees from the east and west have differently-shaped flowers [PDF], which is consistent with the hypothesis that coevolution between moths and trees has driven both toward an evolutionary split.

"Western" Joshua trees at Joshua Tree
National Park. Photo by me.

The new study goes deeper to look at genetic relationships between different populations of the moths and the trees, and what it finds isn't as tidy as the earlier work might suggest: While Joshua trees' morphology corresponds nicely to the split in the pollinators, the patterns visible in their chloroplast DNA does not. In some populations, trees look "eastern," but have chloroplast DNA more closely related to "western" populations. This suggests that, although the moths have become separate species, they're still moving between the two kinds of Joshua tree frequently enough that the trees haven't quite split. Why do the two tree types look different, then? One possibility is coevolution with the two moth species, which might exert selection the trees in different ways.

There's still a lot of work to do before we fully understand what's going on here. Will Godsoe, the other doctoral student in our lab, is doing some intensive niche modeling to see how much environmental differences might be contributing to the patterns we see here. My own dissertation will look at whether the same incongruities turn up in nuclear DNA, which can have a different evolutionary history than that in the chloroplast.

References

W. Godsoe, J.B. Yoder, C.I. Smith, O. Pellmyr (2008). Coevolution and Divergence in the Joshua Tree/Yucca Moth Mutualism The American Naturalist, 171 (6), 816-23 DOI: 10.1086/587757

C.I. Smith, W.K.W. Godsoe, S. Tank, J.B. Yoder, O. Pellmyr (2008). Distinguishing coevolution from covicariance in an obligate pollination mutualism: asynchronous divergence in Joshua tree and its pollinators. Evolution, 62 (10), 2676-87 DOI: 10.1111/j.1558-5646.2008.00500.x

The best Maureen Dowd columns

noreply@blogger.com (Jeremy) — Sun, 21 Sep 2008 21:49:00 +0000

... are not written by Maureen Dowd. Today, she has Aaron Sorkin guest-write a fictional meeting between Barack Obama and Jed Bartlett, the president from Sorkin's excellent TV series "The West Wing." I guess there's pretty strong demographic overlap between Obama supporters and "West Wing" fans, both of which categories include me.

Summer Vacation

noreply@blogger.com (Jeremy) — Wed, 13 Aug 2008 04:25:00 +0000

I'm back from time with the family in Bar Harbor and Acadia National Park, plus an afternoon at the New England Aquarium and a weekend visiting an old high school buddy in Chicago. It was good, at least until the flight home, which was canceled. (I got home only a day late, but my luggage still hasn't caught up.) Highlights: climbing Dorr Mountain, whale (and bird) watching, visiting the Field Museum and the Lincoln Park Zoo in Chicago. Much bio-geeking, but nothing work-related. Although it turns out that the Field Museum has a fishbowl genetics lab in the middle of one exhibit, where you can watch actual scientists do basically what I do all day. Kinda creepy. Anyway, time for photos:

Photo by Jeremy B. Yoder.

Snow in June

noreply@blogger.com (Jeremy) — Tue, 10 Jun 2008 17:06:00 +0000

2008.06.10 - snow in June
Originally uploaded by Jeremy B. Yoder.

Science 2.0

noreply@blogger.com (Jeremy) — Thu, 05 Jun 2008 23:10:00 +0000

Back in March, Science ran a Perspectives piece in which computer scientist Ben Shneiderman suggested that the wealth of new data on human interactions provided by the Internet (Facebook, Amazon.com customer records, &c.) would require a new approach to science, which he called "Science 2.0" [subscription]:

... the Science 2.0 challenges cannot be studied adequately in laboratory conditions because controlled experiments do not capture the rich context of Web 2.0 collaboration, where the interaction among variables undermines the validity of reductionist methods (7). Moreover, in Science 2.0 the mix of people and technology means that data must be collected in real settings ... Amazon and Netflix became commercial successes in part because of their frequent evaluations of incremental changes to their Web site design as they monitored user activity and purchases.

Science 2.0 sounded, to me, a lot like what ecologists and evolutionary biologists often do - hypothesis testing based on observations, manipulations of whole natural systems in the field, and the clever use of "natural experiments" sensu Diamond [subscription]. I said as much in a post shortly after Shneiderman's article ran, and also wrote a brief letter to Science.

And now it turns out they've published it! My letter, along with a response from Shneiderman, is in the 6 June issue [subscription]. You can read it in PDF format here. In very short form, I say:

... what Shneiderman calls Science 1.0 has always included methods beyond simple controlled experiments, such as inference from observation of integrated natural systems and the careful use of "natural experiments" (1) to test and eliminate competing hypotheses.

Shneiderman's response concedes the point on natural experiments, but says he was actually talking about manipulative experiments conducted on large online social networks

Amazon and NetFlix designers conduct many studies to improve their user interfaces by making changes in a fraction of accounts to measure how user behaviors change. Their goal is to improve business practices, but similar interventional studies on a massive scale could develop better understanding of human collaboration in the designed (as opposed to natural) world ...

That still sounds to me like ecological experimentation, but with people's Facebook accounts instead of (to pick an organism at random) yucca moths. Maybe I'm just not getting it, but I don't see anything in Shneiderman's description that qualifies as a new kind of science.

References
Shneiderman B. 2008. Science 2.0. Science 319:1349-50.

Diamond J. 2001. Dammed experiments! Science 294:1847-8.

Yoder, JB, and B Shneiderman. 2008. Science 2.0: Not So New? Science 320:1290-1.

Guilt is good

noreply@blogger.com (Jeremy) — Fri, 23 May 2008 05:29:00 +0000

Slate's Ron Rosenbaum makes the case that liberal guilt is no cause for shame - and calls out "moralistic" conservatism on its weird disdain for guilt:

Shouldn't conservatives feel guilty about slavery and racism and the consequences thereof, or must they disdain such feelings, however moral, because they are associated with liberals? Do they choose their moral priorities because of their popularity among others? That doesn't seem like a conservative way of thinking about moral values. It sounds like a form of relativism. It's the kind of thinking that treats values as a brand identity. Guilt over racism is not part of the conservative brand identity. The more shame if that be the case.

Mennonites = Obama-friendly

noreply@blogger.com (Jeremy) — Thu, 15 May 2008 04:52:00 +0000

... If they're young and college-educated, anyway. The Chicago Tribune has a pretty good piece on the political leanings of Goshen College students, which mainly focuses on increasing Mennonite willingness to participate in politics at all, but also addresses Goshenites' preference for Barack Obama.

I think there's an actual trend here. In the last primaries in states with historical Mennonite population centers, Indiana and Pennsylvania, Obama lost everywhere but big cities -- and the Mennonite-heavy counties. Seriously. Check out the county-by-county results for Indiana, and Pennsylvania - both Elkhart County, Indiana (home to Goshen College) and good ol' Lancaster County are in the Obama column.

Vengeance and the role of the state

noreply@blogger.com (Jeremy) — Thu, 01 May 2008 16:54:00 +0000

The New Yorker has a great essay by Jared Diamond on the role of revenge in tribal societies. It's more story-telling than the sort of rigorous comparative anthropology on display in Guns, Germs, and Steel, but it's fascinating.

First Joshua tree article online

noreply@blogger.com (Jeremy) — Wed, 23 Apr 2008 17:20:00 +0000

The first publication from the Pellmyr Lab's study of Joshua trees and their pollinators, in which we demonstrate significant, potentially coevolved, morphological differences in Joshua trees pollinated by different species of yucca moths, is now online at the American Naturalist's website. My understanding is that it'll be in the print edition this June.

Godsoe W, JB Yoder, CI Smith, and O Pellmyr. 2008. Coevolution and Divergence in the Joshua Tree/Yucca Moth Mutualism. The American Naturalist 171.

Another slack weekend

noreply@blogger.com (Jeremy) — Thu, 17 Apr 2008 14:40:00 +0000

After blowing the last two weekends in an undistinguished collegiate cycling career, I'm now off to the EVO-WIBO biology conference in Port Townsend, Washington. It's a smallish, regional conference, but the Pacific Northwest includes some great biology departments (UBC, anyone?). And, if I go out a day early, there's supposed to be good birding in the vicinity.

And more testing

noreply@blogger.com (Jeremy) — Thu, 17 Apr 2008 06:31:00 +0000

Does the Blog It application handle embedded images?

Testing ...

noreply@blogger.com (Jeremy) — Wed, 16 Apr 2008 22:16:00 +0000

So I just found a post on Wired.com about Blog It, a Facebook application that lets you compose posts, then send them to multiple locations (i.e. separate blogs, your Facebook news feed) from one unified interface. Naturally, I've installed it.

Publication

noreply@blogger.com (Jeremy) — Mon, 17 Dec 2007 04:49:00 +0000

CV update: my first paper on the Joshua tree-yucca moth mutualism, which documents phenotype matching between Joshua tree and its two pollinator species, is accepted at The American Naturalist, pending revision.

Viva Al

noreply@blogger.com (Jeremy) — Sat, 13 Oct 2007 16:26:00 +0000

Gore Shares Peace Prize for Climate Change Work - New York Times

"I don't think there is another system that is more consistent with the teachings of Jesus Christ."

noreply@blogger.com (Jeremy) — Tue, 14 Aug 2007 16:05:00 +0000

Colorado Christian University has apparently fired a teacher for undermining the school's commitment to capitalism. The title quote is from the university's president, although he does concede that "a belief in free enterprise is not linked to salvation."

Apparently CCU adheres to the Gospel of Supply-Side Jesus.