With all this grad school, I forgot I was trying to be a beer writer.
I finally wrote another article for Indianabeer.com and I think it might be a little crazy.
I drop the F-bomb and say other strange things.
Click the picture to read it:
As with most Reno shootings, police believe suspect shot them just to see them die
From Fark.
I've decided to start posting my beer tasting notes at a whole 'nother blog.
Check it out here.
There's a decent article in the NY Times today about St. John's in the US Virgin islands. It's in their "36 hours in [insert destination]" series which I enjoy reading. Well, in this particular piece the author describes visiting the ruins of an 18th century sugar plantation thusly:
"Seeing what's left of the slave quarters, it's easy to see what led to the slave revolt against the plantation owners in 1733."
What?
If there had been better accomodations, then the slaves wouldn't have revolted? They weren't pissed about being slaves for other reasons?
Dr. Christopher L. Saunders sent me a nice set of college pictures yesterday. I really had an incredible time at Juniata College. Chris scanned these from actual-film-camera -pictures, hence the poor quality.
Actually, the first picture was after college, summer 2001, at Chris and Michelle's wedding. This is Ian, winner MIP2K5.
Me and THE Kathy Yeo signing at the wedding. Their wedding was really incredible. I've been spoiled with good weddings I think. 
All the Juniata people at the wedding. 
The proud graduates Chris and Ian with long haired Henri and short haired Matt Dunn.
The three philosophers: Mr. John Polloni, Dr. Robert Wagner and Dr. Chris Saunders. Wagner was a really good teacher. I only got to take one class with him, but it was really good. It was philosophy of art. It was hard but I learned a lot. 
Ok, this is a picture of the backyard at Chris, Ian and Adam's house near Williamsburg PA. It was out there. Along the Frankstown Branch of the Juniata River in Canoe Valley. Absolutely beautiful place. Chris and Michelle Lived there for more than two years I think. I loved it out there. I have a couple other pictures from there I'll post soon. CLICK IT FOR A BIGGER VERSION.
The cows roaming free on the road right in front of the house. Adam adopted a stray Australian Sheep Dog and it would herd the shit out of those cows. But then the farmer got made at them for letting the dog run in the field with cows. CLICK IT FOR A BIGGER VERSION.
This is a picture of "the cliffs". The cliffs were less than a mile away from the Juniata Campus and we hung out up there A LOT. I really miss it. CLICK IT FOR A BIGGER ONE. 
Some of this is cool. Some of it kind of sucks. But I think the good parts are worth watching the whole thing.
Check it out here.
My new favorite philosopher is Johannes Duns Scotus. 
He lived from about 1265-1308. I bet he drank a lot of dank medieval beer. He was a scholastic and most of his philosophy was actually theology. What a load of crap. But he also had some interesting things to say about logic and modality that apparently foreshadowed possible world semantics, something I thought about today because Dave asked me about it and then I talked with Brian about it. Also, I learned about Duns Scotus law in logic last semester; this sentence is a tautology, i.e., it can be derived from the empty set:
--- if not p, then (if p then q) ---
That Duns Scotus sure was smart.
Anyway, the reason I like Duns Scotus so much is because he has a great fucking name. And he's buried in Cologne Germany. I will someday visit his grave and drink a lot of Kolsch style beer. It will be good.
Well, I now have broken a bone in my body. I fractured my right radial head to be precise. I'm not really sure how it happened. I was riding my bike our of my driveway, like a do every day, and the next thing you know I'm flying over my handle bars. I was in the air a long time. I remember the feeling of flight. I put my right hand out of my head to arrest my travel. That's a really common way to break your radial head, apparently. At first I didn't think my arm that messed up. Sure, when I tried to use it to put my bike on bike rack to take it to the bike store to be repaired (the front wheel was bent like a pancake), it didn't work. I couldn't really exert much force with that arm. But I thought that would pass...just a little shook up. But on the way to the bike store I knew something was up. I couldn't shift gears and it really started to hurt and got really stiff. So I dropped off my bike anyway then went to the campus health center. They turned me away because they had closed 10 minutes before my arrival. Assholes. So I went to the Emergency room. They fixed me up real good. Except the x-rays were really painful. They had me bend my arm in all sorts of weird ways to get the right shots and it really fucking hurt. But now I'm on some Lortabs, which are like Vicadin, and they are really making me kind of sick. The first day or two they made me feel really good. Now they just make me nauseous and give me cotton mouth and I couldn't get another appointment until next Thursday. Oh well. I'm going to get my xrays soon too so I'll post them here. That will be cool.
Check out my discharge thing:
Prof. Myers has a post over at Pharyngula that comes down hard on Cheney not for shooting his buddy, but for shooting about a hundred birds on a "canned hunt". I almost posted the below as a comment, but then I thought twice about it because I'm not sure it makes much sense. Is it the sheer numbers of birds that were killed that makes the bird hunts unethical? Is it that you can catch and release fish? Or you're only allowed to keep 6 or whatever? What do you think?
Now I'm not trying to defend Cheney. At least not in general. But I think it's problematic to argue that canned hunts are unethical and "game hunting" is not. It just seems that using a high powered rifle to hunt deer is just barely a little more "part of the pattern of life." State game commisions manage deer populations for hunters. Sure they want to maintain "natural" or reasonable deer populations because they are part of the native fauna, but I'm pretty sure keeping hunters happy is part of their management practices.
What about fish stocking programs? Rainbow and Brown trout are stocked extensively, millions of fish a year, all over the range of the only native salmonid in eastern North America, the Brook trout. In fact, here in southern Indiana Rainbow trout have been introduced into some streams that haven't supported native trout populations since the last ice age (maybe?) and very rarely if ever manage to hold Rainbows over the summers. These fish are raised and stocked exclusively for sport fishing. Maybe in some places they are stocked for ecological reasons, to keep down populations of other invasives, but I doubt that's very common.
I guess the question is are fish on par with birds? Or do you disagree with fishing as well?
I agree that shooting a hundred birds just for shits and giggles is a bit whacko, but I think it's not as clear cut an ethical issue as you make it sound. But I'm no ethicist, so what the hell do I know?
Well, Darwin's birthday is tomorrow, but because that's a Sunday it was celebrated here on campus yesterday. There was a panel discussion about ID and evolution. The panel consisted of two education professors and a law professor. Bet that was awesome...shah...right. My first official Darwin Day celebration was in 2002 I think, at the source of Darwin Day celebrations, the University of Tennessee Knoxville. Massimo Pigliucci hosted it and Eliot Sober gave a talk on design arguments. It was pretty good.
Well, I missed the panel yesterday because our department had some talks at the same time. And they were pretty relevant to Darwin.
The first was Paul Griffiths. He talked about the Baldwin effect and genetic assimilation. It was pretty cool. He showed how according to Waddington, the Baldwin effect wasn't anything special, it was just an example of genetic assimilation in a sense. It's just how evolution goes. Anyway, this is relevant to Darwin because it was a really anti-Darwinian account of evolution in the sense that evolution isn't bean bag genetics and black bozed development. Billy Dembski would probably love it.
The second talk was by a job candidate Chris Smeenk. He gave a talk on early universe cosmology and fine tuning. The fine tuning thing is something ID folks pick on to. The fine tuning problem goes something like this: according to some of our current scientific theories, in order for our observations today to make sense, about the uniformity of the background radiation, the proportion of elements, etc., there had to have been a very specific set of initial conditions at the big bang. So the odds of getting our current universe are very very slim.
But Smeenk problematized this. He raised objections about probability (it's hard to make sense of probability in a system with only one event [the big bang] and that the probability of the initial condiditions being any one number AT ALL is actually zero), and problems stemming from the applicability of the theories we use to understand the universe now like relativity and quantum field theory seem to be inadequate to deal with the early universe and the fine tuning problem might be an artifact of these theories. I might have this wrong, but I think that's the gist of it.
Cool stuff.
Here is a catch all post from my doings over winter break this year. Some fun pictures here.
Adam Ziegler and I went on a picture taking expedition around West Chester at some point. It was pretty cool. We walked all over down town.
Here is Adam. CLICK FOR A BIGGER VERSION.
I was raised, until about 10 years old, Catholic. Here is the front of the church I attended, St.Agnes.
A really cool door of the West Chester fire house.
The rest of the fire house. CLICK FOR A BIGGER VIEW.
West Chester is a pretty old town and Chester County in general is one of the oldest counties in the Nation. 
The Iron Hill brewpub is now where the hospital was. 
This is a bit later history, but I think it's cool because Rothrock spent a lot of time in Central PA and I spent a lot of time in Rothrock State Forest when I was in college. A very cool place. 
A cool doorway of a 1848 house near the historical society in West Chester.
I went to a Quaker Friend's school for two years when I was a kid. West Chester was a huge Quaker town for a long time. It is a really old campus. This is part of it. 
More of the Friend's school. 
And now onto Ben and Leigh's New Year's Eve party. Ben has thrown a party every year for 8 years...and I've been at every one of them!
This is Pell's former roomate, Brian Hoffman:
BOBBY!
Joe Ready and R Kelly.
God damn hippies. CLICK FOR BIGGER VERSION.
Ben's neighbor lit off a bunch of M80s or some such thing. They were really fucking loud and you felt the concussive force of the explosion on your skin. It was a bit scary actually. 
A dance party broke out. Ben takes his dancing quite seriously. 
Greg and Melissa.
The hard-core from B. Reed Henderson High School. CLICK FOR BIGGER. 
A funny picture of Joe.
Around 6am. 
That is all.
The Times ran a good story about proposed legislation in Utah that would require the reading of a disclaimer about evolutionary theory, probably pointing the students to ID's infamous text book "On Pandas and People" or some such thing. About the same thing that was passed in PA until it was taken to court last year.
There was a lot of complaining about how the NY Times (and other media) handle the ID debate, and rightfully so. It seems journalists were convinced by the Discovery Institute et al. that there was really a plausible case for doubting "Darwinism"...so the media tended to present "both sides of the story".
Well, with this whatnot in Utah, at least the Times has changed it's tune a bit. In the above article, obviously false claims about evolutionary biology made by ID enthusiasts (and/or religious wing nuts) were corrected in the article:
"Evolutionary theory does not say that humans evolved from chimpanzees or from any existing species, but rather that common ancestors gave rise to multiple species and that natural selection — in which the creatures best adapted to an environment pass their genes to the next generation — was the means by which divergence occurred over time. All modern biology is based on the theory, and within the scientific community, at least, there is no controversy about it."
This quote is funny though because it seems to be endorsing a particularly controversial position about speciation (how one species becomes two or more species). Here they claim that natural selection caused the divergence of humans and chimps (and presumably bonobos) from our common ancestor.
It is a bit vague (or ambiguous [for the logicians] depending on your interepretation of "evolutionary forces") to say that natural selection caused the divergence, i.e. it's not clear if they mean to endorse reinforcement or a "traditional" Darwinian mechanism or the power of selection to produce reproductive barriers by chance in allopatry or sympatric speciation or simply to demonstrate their general dislike of drift-centered models.
I think it's great because I'm a big fan of disruptive selection as an important process in many speciation events and probably most biologists disagree. But I've got the NY Times on my side!
The upshot: this is the kind of thing that I think is funny.
Mine is a sad, strange world on Tuesdays.
No...time...for...breakfast...log...must...read...Linanthus parryae paper...very early morning...7am...lots of coffee...bananas approaching...ideal ripeness...one or two more days and they will...be...perfect...bananas...procured excellent new jam...all fruit...no sugar...added...blueberry...tasty........must read
I found another really good video blog/vid cast thinger. But this one really stretches the boundary of internet video. While Rocketboom isn't really about the production value (although they do have some really wonderful, creative and beautfully produced scenes), I like Rocketboom for the content. It tends to be interesting, commented upon in a witty fashion, and Amanda is charming. 
TikiBar TV, while the whole theme is a bit much for me, the production is absolutely top shelf for internet video. Very well done transitions and well managed tempo of the editing. In fact, I think the pace and rythym of the editing is really the most appealing aspect of the videos. But the production value in general is very high. The graphics look closer to professional than any others I'm seen on vidcast stuff. The camera work is very well done and the staging is really top notch. The cuts and pans are really great and the color and tone of the video is soft and pleasing. The set is also awesome. The writing is actually very clever and the humor is well done. The acting is very good, in my humble opinion. The out takes at the end are usually very funny.
Very well done. Very easy to watch.
Click the image above to visit their page.
I've been meaning to post something here about how my least favorite person in the whole entire world had moth balled his weblog. Yes. Billy Dembski announced on Dec. 26th, just 6 short days after the Dover ruling I might add, that he was done with his incredibly stupid blog, Uncommon Descent. I was really happy. But then, just a couple days later, he announced that some of his most prolific commentators on the blog were taking over as administrators. Fine I thought. They have to be even worse for ID than Dembski. And I was right. That DaveScot fellow is a real fucking loser. The shit really hit the fan a couple days ago when he decreed that nobody can criticize common descent anymore on the blog (note hilarious irony of blog title).
Well, that was a pretty huge mistake for ol' DaveScot. See this post here for a full story.
Anyway, Dembski has been back in the blog saddle now for some time (his hiatus very short lived, unfortunately). So yesterday he posted his official stance on common descent...and manages to get up to his old tricks again: misrepresenting good scientists. Also, I think it is absolutely fucking hilarious that the advert on that post's page is for the AAAS. HA!
While little Billy Dembski states that ID doesn't require any particular pattern of descent, he also writes that to ignore common descent altogether would also be to ignore the growing criticism of this entrenched Darwinian concept. He wants to do all he can to show that "Darwinism" is in general being challenged these days and that ID is just another challenge. However, as we know, this is not the case. Gould, Margulis and Woese would, I imagine, be quite upset by their appropriation by ID. While they may be challenging "Darwinian orthodoxy", firstly, it's unclear what Darwinian orthodoxy even is, and secondly, it is far from clear how their work is at all similar to Dembski's...aside from the fact that they disagree with some bit of orthodox Darwinism, whatever that may be.
So the latest misappropriation is this: "Likewise, Carl Woese, a leader in molecular phylogenetics, argues that the data support multiple, independent origins of organisms."
Indeed, that is what Woese proposes, in the most ambiguous and vague language ever. Woese proposes that towards the "roots" of the tree of life, things get a little messy. There was lots of horizantal gene transfer and probably multiple origins of different fundamental cellular mechanisms, but each of the three "foundational lineages" (Bacteria, Archaea and Eukarya) reached a "Darwinian threshold" where they became, in a sense, canalized, and unable to participate in the promiscuity of HGT. The lineages after these thresholds are the actual root of the universal tree of life and evolution after these thresholds proceeds in a fairly "regular" way. So, while there was a very complicated origin of the three fundamental lineages involving lots of HGT and the incorporation of many "genes" from now extinct other lineages that had evolved independently of the three major lineages, this "anti-Darwinism" is relegated to the very earliest stages of life.
I want to note three things:
(1) I'm not sure how much all of this is actually anti-Darwinian. Darwin claims in the last sentence or two of the Origin that there was one or a few original forms. And while he thought that the correct universal tree of life would someday be elucidated, it's not clear that a tree of life with a single root is necessary for Darwinism.
(2) I certainly don't buy into Woese's whole deal. He has some awfully strange ideas about processes: "Yet the forms in essence are the process." Problematic. But still, I certainly agree that there is a lot to be learned about the very earliest stages of life.
(3) I want to emphasize, if it wasn't already clear from the above, that this new understanding of the root of the tree of life doesn't really have much impact on the evolution of Eukarya in general, at least the Eukarya that ID cares about, namely , humans. Certainly all mammals share a common ancestor, as do all vertebrates and probably all animals. The question of whether or not all Eukarya have a common ancestor is probably less clear. The protists are a really fascinating (polyphyletic) group and need a lot more study before any claims are made. Also, this stuff may have interesting consequences for reconceptualizing what sexual reproduction actually is and what it actually does to lineages, i.e. how it can maintain lineages and how it breaks them apart in some sense.
That is all. I must now read Wright's really long 1930 paper for pop gen tomorrow. AWESOME.
Oh yeah, and here's a good overview of Woese's views. I took that quote above from this paper: PNAS 2002 99(13): 8742–8747
