So it seems that Joe and I are going to Indian Creek. Joe only has about 10 days, and the first two I'll be in Redding for the Cal-Neva AFS conference. Part of me wants to not go, but another part knows that it will be fun. Lots of talks that are interesting to me, fun folks from the Moyle lab, and a collaborator who's presenting on my Paiute cutthroat trout project (and who I'm going to ambush with a post-doc proposal).
Initially I wasn't too psyched on going back to the creek. I was there for 4 weeks last spring, and wasn't climbing that well. On the other hand, I wasn't climbing well at all last year. Hangover from the whole MS thing I suppose.
At any rate, I'm feeling much better now, climbing strong (for me), and I'd have a solid partner who I'm comfortable climbing with...which is what I really wanted last year when I had more time. Such is life.
So here is the tick list. Bold indicates Joe's choices, both of which require a second since they are more than a pitch. I'm going to get worked...This is merely a rough guide. I tend to balk at the rigidity of a true tick list.
Six star crack
Slot Machine
Ziji (I'm pretty sure I got lowered off of this as a blubbering mess the first year I was in IC...good times)
Pente
Slice and Dice (maybe this year?)
anything new and onsight-able
Broken Brain
T Bones tonight?
anything on any wall I haven't been to
On an unrelated note, a post-doc advert came through the grapevine in Corvallis, OR (OSU). It would be a pretty sweet post-doc: landscape genetics of aquatic inverts and amphibians in desert streams in AZ, but I'd be in Corvallis, and I don't know anything about the town. I did do a googlemaps search and learned that Corvallis is 169 miles from Terrebonne, the gateway town to Smith...which is almost exactly the distance from Davis to the valley. I think another part of the post-doc would be in Seattle as well.
John was making a pretty good case for leaving Davis when I finish, but I don't really know what I want. I'm really interested in California salmonids and the delta issues, and as I've lived here I've definitely become more invested in the issues here. I know that wherever I go I'll there will be many other interesting issues. Sometimes it's just hard to imagine what something will be like until you get there and get started.
It doesn't matter anyway about the Corvallis post-doc - they want someone to start in May 2010, and I probably won't be done until summer 2011. Plus I have this SCEP thing going on here, and I have to put in 640 hours to be guaranteed a job. The work schedule is flexible, but the 640 needs to happen. then again I might work with FWS and decide I don't want to work for a federal agency. Which is the whole point of the SCEP: get your feet wet with an agency without the commitment of a full-time job.
I might float the idea to the PI in Corvallis (I actually met the guy and hung out with him a little bit in Death Valley at the last Desert Fishes Council meeting, he seemed super cool, another reason I'd consider Corvallis) that I'd be interested in a post-doc in a year or two. Sometimes things are more flexible than you think.
There's another guy I'd be interested in working with at Colorado State in Ft. Collins. I haven't met or corresponded with him yet though, but his research is interesting and apparently he is "super cool" according to a former labmate who works at CSU now.
I haven't done an extensive faculty search, but I primarily am looking at Boulder, Ft. Collins or Salt Lake City. I'd also consider looking at faculty at Berkeley. If something amazing comes along, I'd look at other locations like the Corvallis outreach.
In other work-related news, I'm going to try to extract some DNA from ancient samples of pupfish, which requires going to another lab. Ancient DNA samples (anything older than a couple of decades is considered "ancient") are often so degraded (DNA degrades over time) that the quantities are very small (compared to tissue samples that were collected more recently, with more modern techniques that are probably guaranteed to get you gorgeous DNA). So the quantities are small, and there's fish DNA floating all over the place and covering every surface in our lab, so contamination is going to be an issue (this is standard for aDNA). So I gotta go to another lab. yay. Plus I have to be super meticulous and patient, neither of which I'd rate as my greatest skills. Anyway, there are likely to be some ranting posts about this work in the future, assuming the Cal Academy can part with 10 cubic mm of caudal fin from 20 samples from the 1930s. Fortunately I have contacts at Cal, so hopefully this is something that will happen.
Phew. wow this post isn't accurately named...like the glooove compaaaartmeeent....and everybody knows it...cause behind it's door....there's nothing to keep my fingers warm...
Wednesday, March 3, 2010
More good little things.
Sometimes I'm really happy I work on fish. I mean, I could be working on poop.
If life gives me lemons...
I'll bake the shit out of them.
My housemate took care of a meyer lemon tree at her old house, and went back on a stealth mission to gather them.
In the last couple of weeks, I've made a lemon-lemon loaf (from Baked), a lemon-yogurt cake, two batches of lemon bars (Karen DeMasco)...and I still have a few left.
I'm thinking about preserving some, or maybe getting more and then making limoncello...or making a lemon-olive oil cake. Not sure.
Or lemon sables, or a lemon-coconut cake, or a lemon-ricotta cheesecake...
Monday, March 1, 2010
It's the little things
Sometimes it's the littlest things that make me happy. Like cleaning something that's really dirty. Sometimes it's nice being a slob not a great housekeeper, because when I clean something, it's so dramatically different that it transcends clean and becomes awesome. Like when I cleaned my refrigerator. Or windexed my windows. Or scrubbed the shit out of my shower...or cleaned and detailed the leather seats in my car. These things make me feel so accomplished.
Fixing something that's broken is rad too. Like patching a thermarest, or a pair of pants.
Or simply maintaining something. Lubricating my bike chain pretty much made my February. You never realize how crappy it was until you fix it.
Finishing something is also good. I can't WAIT to turn in this trout manuscript. It's like the manuscript that won't die. I started this project the first year I was in grad school, started writing the paper before I got MS (to be more accurate, knew I had MS), and it's still NOT DONE. I did turn in a draft to Karrigan today though, so hopefully I'll get rid of this albatross soon. Then it bounces back to me, then to Molly (for her characteristic eviscerating editing...I shudder to think about it), then back to me, then to Eric, back to me, and hopefully THEN to Molecular Ecology...and then back to me, and then back to Molly and Karrigan, and then back to Molecular Ecology hopefully FOREVER.
Until then, all of the cleaning and fixing and maintaining is just a form of "productive procrastination."
and of course, this:
Fixing something that's broken is rad too. Like patching a thermarest, or a pair of pants.
Or simply maintaining something. Lubricating my bike chain pretty much made my February. You never realize how crappy it was until you fix it.
Finishing something is also good. I can't WAIT to turn in this trout manuscript. It's like the manuscript that won't die. I started this project the first year I was in grad school, started writing the paper before I got MS (to be more accurate, knew I had MS), and it's still NOT DONE. I did turn in a draft to Karrigan today though, so hopefully I'll get rid of this albatross soon. Then it bounces back to me, then to Molly (for her characteristic eviscerating editing...I shudder to think about it), then back to me, then to Eric, back to me, and hopefully THEN to Molecular Ecology...and then back to me, and then back to Molly and Karrigan, and then back to Molecular Ecology hopefully FOREVER.
Until then, all of the cleaning and fixing and maintaining is just a form of "productive procrastination."
and of course, this:
Sunday, February 28, 2010
Human evolution
"I suspect in many ways humans are themselves "self-domesticated," and the protean nature of the selection regimes shaped by rapidly changing culture makes it more likely than not that we adapt through tweaking standing genetic variation."
- Gene Expression
Current Biology has a special review issue out now on global genetic history of Homo sapiens. I guarantee you that your favorite geographic area is covered (Africa, Oceania, south Asia, east Asia, Europe, and the Americas), and your favorite sex chromosome (i.e. X and Y are discussed).
I've cut and pasted the abstracts for my reference and your convenience. Let me know if any of you actually read any of this stuff. If nothing else, click on the links and look at some of the rad-ass figures.
Open access - yay!
Archaeogenetics — Towards a ‘New Synthesis’?
It seems a timely moment to review human population history of the five continents as it emerges from recent archaeogenetic studies, as summarised in the reviews of this special issue of Current Biology. Has the ‘new synthesis’ — between genetics, archaeology and linguistics — arrived which I, perhaps incautiously, heralded a few years ago [1]? These highly informative reviews document, it seems to me, both achievement and uncertainty: the achievement relates to the remarkably consistent picture which has now emerged about the out-of-Africa emergence of our own species Homo sapiensand the initial peopling of the Earth. The uncertainty involves the application of archaeogenetics to the more recent, Holocene period, when most of the planet was already peopled — except much of Oceania — and sedentary, farming-based communities emerged. Here, it appears that much of our current understanding still depends on archaeological or, sometimes, linguistic evidence. And, with a few exceptions, the archaeogenetic evidence has not yet been assimilated into a genuine synthesis; but, let us begin with the good news.
The Evolution of Human Genetic and Phenotypic Variation in Africa
- Gene Expression
Current Biology has a special review issue out now on global genetic history of Homo sapiens. I guarantee you that your favorite geographic area is covered (Africa, Oceania, south Asia, east Asia, Europe, and the Americas), and your favorite sex chromosome (i.e. X and Y are discussed).
I've cut and pasted the abstracts for my reference and your convenience. Let me know if any of you actually read any of this stuff. If nothing else, click on the links and look at some of the rad-ass figures.
Open access - yay!
Archaeogenetics — Towards a ‘New Synthesis’?
It seems a timely moment to review human population history of the five continents as it emerges from recent archaeogenetic studies, as summarised in the reviews of this special issue of Current Biology. Has the ‘new synthesis’ — between genetics, archaeology and linguistics — arrived which I, perhaps incautiously, heralded a few years ago [1]? These highly informative reviews document, it seems to me, both achievement and uncertainty: the achievement relates to the remarkably consistent picture which has now emerged about the out-of-Africa emergence of our own species Homo sapiensand the initial peopling of the Earth. The uncertainty involves the application of archaeogenetics to the more recent, Holocene period, when most of the planet was already peopled — except much of Oceania — and sedentary, farming-based communities emerged. Here, it appears that much of our current understanding still depends on archaeological or, sometimes, linguistic evidence. And, with a few exceptions, the archaeogenetic evidence has not yet been assimilated into a genuine synthesis; but, let us begin with the good news.
The Evolution of Human Genetic and Phenotypic Variation in Africa
Africa is the birthplace of modern humans, and is the source of the geographic expansion of ancestral populations into other regions of the world. Indigenous Africans are characterized by high levels of genetic diversity within and between populations. The pattern of genetic variation in these populations has been shaped by demographic events occurring over the last 200,000 years. The dramatic variation in climate, diet, and exposure to infectious disease across the continent has also resulted in novel genetic and phenotypic adaptations in extant Africans. This review summarizes some recent advances in our understanding of the demographic history and selective pressures that have influenced levels and patterns of diversity in African populations.
A new timescale has recently been established for human mitochondrial DNA (mtDNA) lineages, making mtDNA at present the most informative genetic marker system for studying European prehistory. Here, we review the new chronology and compare mtDNA with Y-chromosome patterns, in order to summarize what we have learnt from archaeogenetics concerning five episodes over the past 50,000 years which significantly contributed to the settlement history of Europe: the pioneer colonisation of the Upper Palaeolithic, the Late Glacial re-colonisation of the continent from southern refugia after the Last Glacial Maximum, the postglacial re-colonization of deserted areas after the Younger Dryas cold snap, the arrival of Near Easterners with an incipient Neolithic package, and the small-scale migrations along continent-wide economic exchange networks beginning with the Copper Age. The available data from uniparental genetic systems have already transformed our view of the prehistory of Europe, but our knowledge of these processes remains limited. Nevertheless, their legacy remains as sedimentary layers in the gene pool of modern Europeans, and our understanding of them will improve substantially when more mtDNAs are completely sequenced, the Y chromosome more thoroughly analysed, and haplotype blocks of the autosomal genome become amenable to phylogeographic studies.
South Asia — comprising India, Pakistan, countries in the sub-Himalayan region and Myanmar — was one of the first geographical regions to have been peopled by modern humans. This region has served as a major route of dispersal to other geographical regions, including southeast Asia. The Indian society comprises tribal, ranked caste, and other populations that are largely endogamous. As a result of evolutionary antiquity and endogamy, populations of India show high genetic differentiation and extensive structuring. Linguistic differences of populations provide the best explanation of genetic differences observed in this region of the world. Within India, consistent with social history, extant populations inhabiting northern regions show closer affinities with Indo-European speaking populations of central Asia that those inhabiting southern regions. Extant southern Indian populations may have been derived from early colonizers arriving from Africa along the southern exit route. The higher-ranked caste populations, who were the torch-bearers of Hindu rituals, show closer affinities with central Asian, Indo-European speaking, populations.
East Asia encompasses a wide variety of environments, peoples, cultures and languages. Although this review focuses on East Asia, no geographic region can be considered in isolation in terms of human population history, and migrations to and from East Asia have had a major impact. Here, we review the following topics: the initial colonization of East Asia, the direction of migrations between southeast Asia and northern Asia, the genetic relationships of East Asian hunter-gatherers and the genetic impact of various social practices on East Asian populations. By necessity we focus on insights derived from mitochondrial DNA and/or Y-chromosome data; ongoing and future studies of genome-wide SNP or multi-locus re-sequencing data, combined with the use of simulation, model-based methods to infer demographic parameters, will undoubtedly provide additional insights into the population history of East Asia.
The human history of Oceania is unique in the way that it encompasses both the first out-of-Africa expansion of modern humans to New Guinea and Australia as well as the last regional human occupation of Polynesia. Other anthropological peculiarities of Oceania include features like the extraordinarily rich linguistic diversity especially of New Guinea with about 1,000 often very distinct languages, the independent and early development of agriculture in the highlands of New Guinea about 10,000 years ago, or the long-term isolation of the entire region from the outside world, which lasted as long as until the 1930s for most of the interior of New Guinea. This review will provide an overview on the genetic aspects of human population history of Oceania and how some of the anthropological peculiarities are reflected in human genetic data. Due to current data availability it will mostly focus on insights from sex-specifically inherited mitochondrial DNA and Y-chromosomal DNA, whereas more genome-wide autosomal DNA data are soon expected to add additional details or may correct views obtained from these two, albeit highly complex, genetic loci.
The Americas, the last continents to be entered by modern humans, were colonized during the late Pleistocene via a land bridge across what is now the Bering strait. However, the timing and nature of the initial colonization events remain contentious. The Asian origin of the earliest Americans has been amply established by numerous classical marker studies of the mid-twentieth century. More recently, mtDNA sequences, Y-chromosome and autosomal marker studies have provided a higher level of resolution in confirming the Asian origin of indigenous Americans and provided more precise time estimates for the emergence of Native Americans. But these data raise many additional questions regarding source populations, number and size of colonizing groups and the points of entry to the Americas. Rapidly accumulating molecular data from populations throughout the Americas, increased use of demographic models to test alternative colonization scenarios, and evaluation of the concordance of archaeological, paleoenvironmental and genetic data provide optimism for a fuller understanding of the initial colonization of the Americas.
There has long been interest in understanding the genetic basis of human adaptation. To what extent are phenotypic differences among human populations driven by natural selection? With the recent arrival of large genome-wide data sets on human variation, there is now unprecedented opportunity for progress on this type of question. Several lines of evidence argue for an important role of positive selection in shaping human variation and differences among populations. These include studies of comparative morphology and physiology, as well as population genetic studies of candidate loci and genome-wide data. However, the data also suggest that it is unusual for strong selection to drive new mutations rapidly to fixation in particular populations (the ‘hard sweep’ model). We argue, instead, for alternatives to the hard sweep model: in particular, polygenic adaptation could allow rapid adaptation while not producing classical signatures of selective sweeps. We close by discussing some of the likely opportunities for progress in the field.
Saturday, February 27, 2010
Maladapive behavior is sexually selected?
I just thought of another angle on the death-defying sports line of thinking.
If, in the hypothetical scenario outlined in the previous post (death-defying, risk taking athlete has lots of progeny before dying), then maybe sexual selection is going on.
Think of the peacock. Its crazy flashy tail makes it far more likely to get picked off by a predator, so any male peacocks that survive must have higher fitness and produce higher quality offspring (according to female choice). There's debate about whether or not the male peacock is actually displaying anything of value (like fewer parasites, healthier sperm, whatever), or if he's just responding to some innate female choice preference.
Anyway, perhaps death defying athletes that actually survive and do well enough go gain prestige have superior fitness in some way, or they are simply taking advantage of the fact that women are social learners as well, programmed to be swayed by cultural prestige regardless of whether or not the athletes have superior fitness. Think of rock stars who do a bunch of drugs but have a ton of sex and have lots of kids all over the world. Rock stars might leave a lot more offspring, but only because of the "groupie" effect of female choice.
Eh. none of this shit is probably happening enough to really cause any kind of large-scale evolution in humans, but it's fun to think about. Then again, differences in gender must be adaptive somehow (males are stronger, bigger, have all kinds of weird social tests in many cultures to become "men", leaders and rulers having access to far more women...).
Gah. I should probably go to the primary literature and back up my ramblings. I'm probably wrong all over the place.
If, in the hypothetical scenario outlined in the previous post (death-defying, risk taking athlete has lots of progeny before dying), then maybe sexual selection is going on.
Think of the peacock. Its crazy flashy tail makes it far more likely to get picked off by a predator, so any male peacocks that survive must have higher fitness and produce higher quality offspring (according to female choice). There's debate about whether or not the male peacock is actually displaying anything of value (like fewer parasites, healthier sperm, whatever), or if he's just responding to some innate female choice preference.
Anyway, perhaps death defying athletes that actually survive and do well enough go gain prestige have superior fitness in some way, or they are simply taking advantage of the fact that women are social learners as well, programmed to be swayed by cultural prestige regardless of whether or not the athletes have superior fitness. Think of rock stars who do a bunch of drugs but have a ton of sex and have lots of kids all over the world. Rock stars might leave a lot more offspring, but only because of the "groupie" effect of female choice.
Eh. none of this shit is probably happening enough to really cause any kind of large-scale evolution in humans, but it's fun to think about. Then again, differences in gender must be adaptive somehow (males are stronger, bigger, have all kinds of weird social tests in many cultures to become "men", leaders and rulers having access to far more women...).
Gah. I should probably go to the primary literature and back up my ramblings. I'm probably wrong all over the place.
Friday, February 26, 2010
Maladaptive behavior
I had Vicken, Tim and John over to watch the Canada vs. Slovakia tonight, and Vicken admitted to me that he used my ex in a lecture. I'm like "really?! what was it about?" And he smiled and said "maladaptive behavior."
The idea is that environmental variability makes it adaptive for humans to use social learning. Individual learning is costly, so social learning is more adaptive (because of a lower cost). Why pay the cost of individual R and D when some jackass has already done it for you?
There are different mechanisms for how social learning works. For example you could copy from prestigious, successful individuals, which might make sense, or it might make you do stupid shit (evolutionarily-speaking, of course) like rock climb without a rope, because climbers who do crazy shit without a rope get prestige, and become successful (such as Bachar and Croft).
So the capacity for social learning is adaptive, but it opens you up to adopting specific behaviors that are not adaptive...["and then you die" - Vicken].
There are a ton of other examples, like delaying reproduction (which I'm guilty of...). Of course to get around this fitness cost of free soloing (and dying, should that happen), you could have a bunch of kids and make sure they are taken care of, and then go off and climb wtihout a rope. Of course, if gaining prestige through doing anything at all gets you lots of sex and you spawn offspring all over the world, then I guess it's not so maladaptive.
Vicken has some recommended reading on the subject:
by Pete Richerson
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