We're back from Hawaii, we got back on the red-eye last night. Since my last post, I managed to get my dissertation in acceptable shape and submitted it to the graduate school, 15 minutes before the end of the semester. (Close timing!). So on the day before I had to leave I fulfilled the requirements of the PhD. So I'm officially a doctor. (yea). It's wierd to be out of graduate school, i suppose it's alot like prison, what to do when released? Anyway i'll muse on that later I am sure.

I then took a long vacation to Hawaii with my wife and her sister. The most exciting thing that happened is our car got towed at a popular snorkling stop (along with dozens of others). Anyway, that was very upsetting, but just more money down the drain. Hawaii ended up being more expensive and draining (physically) than I thought, so lessons learned for the future. The most important lessons I think are no vacations longer than 7 days, it's too expensive and too draining, and to schedule at least two days post-vacation for recovery.

In Hawaii, we ended up doing lots of hikes and beach tours. I'll post some picts later. Nothing too exciting, we got to go to Hy's restaurant (my favorite) for my PhD celebration, and a xmas eve party that my step-mom throws every year, so I had my yearly turkey and potatoes meal. Other than that, it was just nice to sleep, do what we want, eat what we want...I'm now 185 lbs. Funny moment, I went into my father's office and his long-time technician (she knew me since i was a kid) said 'you've gained weight!'. Lots of people have been saying that...serious diet/exercise time for me.

Finally we just got home from getting the weasels. They seem very happy to be home. They were at a ferret shelter. Hopefully the downstairs neighbor's dog will shut up and we can get some sleep tonight.

Pretty good post on the recent happens of ID here
This is good blog of a surgical oncologist, worth reading in it's own right. I'll try to read it more often. I'm of two minds of the whole ID vs evolution debate. 1) Since i am a scientist and did have initial training in evolution (B.S.) I should weigh in on the matter. 2) I don't want to be one of the many 'me too' blogs dealing with evolution, that's not my niche. 3) All the blogs dealing with evolution inevitably deal with only the evolution vs ID debate, and there's much more to evolution than simply refuting ID or theological teachings.

ANyway i sent in a letter to the Houston Chronicle yesterday regarding this whole thing (it started as an editorial by two authors writing about the Scopes Monkey Trial, there is a story on it here, this is what I said.

Dear Chronicle,

Thank you for the editorial by Perry and Olasky, I
surely won't be buying their book on the Scopes Monkey
trial. As a scientist, and one trained in
evolutionary biology, I welcome discussion about
evolution amongst the public. However, at the very
least, people should frame the evolution vs
intelligent design (ID) debate in context. First, we
now believe that evolution is done at the molecular
level (DNA), and evolution is in response to
environmental change, and that it occurs by 'spurts',
great leaps of evolutionary change in a very short
period of time. Most of the time, evolution occurs
very slowly ('drifts') Second, evolution is not
"temporary, reversable" as the authors claim, if
species are to evolve, they aquire new mutations in
their DNA, which is more or less permanent. Usually
what happens is a gene or group of genes gets copied,
and the copy is free to mutate since the original gene
still maintains it's function. Evolution is no more
reversable than a baby's birth.

I think the real issue is that it's hard to debate
with religion (I.D.); remember how Galileo got
excommunicated from the Catholic Church by arguing
that the Earth revolves around the Sun? Also, I.D. is
not testable, nor does it draw upon facts, like
Darwinian evolution (there are a multitude of facts
that back up evolution). A test of I.D. would be:
When did God create Man? Does it agree with the
fossil record or DNA evidence? (We now think that
modern man arose 200,000 years ago, via DNA dating).
Another questions: Why did God allow such a cataclism
that ended the reign of dinosaurs?

Lastly, the author's arguement that evolution is like
assembling a bicycle by throwing parts over your
shoulder is not valid. Indeed it's hard to believe
that the complex beings we are were assembled
randomly, but at the molecular level things happen
extremely quickly. Even in bacteria, the laboratory
strain E Coli divides every 30-60 minutes; that's 24
generations per day, and each generation is different
from the last thanks to DNA mutations. That's not to
say there is no room for God or I.D. in evolution; the
big unanswered question in evolution is how did life
start in the first place? DNA requires RNA and
proteins for replication, yet we know that DNA
contains the hereditary information, and produces from
it RNA and protein (the "Central Dogma"). Some think
that RNA was the first molecule, and it's been shown
that RNA can self-replicate and evolve. But how did
RNA form? Some even believe that comets or meteors
seeded the planet with the first strands of
self-replicatable RNA. Regardless, this is an even
that happened likely 4 billion years ago. In that
timeframe, anything is possible.

Anyway back to work.

Update: Figured out why I can't find the editorial published yesterday; the chronicle only has todays editorials available, and the archives only cover 'news'. Sheesh. More crushing of decent. ANyway, back to work really.

UPDATE: Interesting comment on new theology of the origin of humans and my response (in the comments).

Well, for those (few) of you who have wondered, no, I do not have my degree yet. My defense was last thursday; at that time I received comments and correction requests by the committed. I went ahead and put all that into my dissertation, especially those comments from my advisor. I submitted this on Tuesday; my advisor still said it was inadquate (over the phone, for about 15'). It was apparently she read the table of contents and the first page of the introduction. So I had to change the whole thing. My advisor was then hurt in an auto accident on wed. On thursday I went to her house and sat down with her and finally was able to figure out what she had in mind (a week after the defense). So I stayed up all night and redid the thesis. On Friday she was in no shape to do anything, so I called a member of the committee who said he would take over the job of the corrections. So I submitted the dissertation to him and another member. I will hear back from them on monday; hopefully they will say nothing else is required and i can still graduate this semester. If not, i'll have to reenroll and get signatures all over again, and continue to kiss ass and get approvals. All this while the postdoc is held up, since I haven't offically graduated. All this without pay or benefits (ie health insurance). All this without being able to go talk to the grad school for advice, since I tried that previous and the committee found out and got pissed off (royally pissed off - I should have talked to them, my advisors friends, who are of course unbiased and have my best interests in mind). So...we'll see how it goes. If it doesn't happen, and I go through a few more weeks of this, then maybe I can go to the graduate school and ask for help. Anyway, i'll be glad to escape my advisor, although I won't truely escape until my paper is published. Until then, it's more kissing ass.

Science is the best journal there is, everyone reads it. So it's huge when the corresponding author retracts it. Pajama Media has more. And apparently the 'senior author', a US scientist, didn't have much to do w/ it. That's simply scandelous. Author order is such a huge thing. If you are first author of a science paper your career is almost assured. But when that paper tanks, so does your career.

So, I defended on Thursday, and usually students would be almost done, some minor revisions of the dissertation and paperwork filling out. No, not me. My advisor had a cow when she read my dissertation (the night before the defense), and grilled me on it during the defense. So, those are two ethics breachs, unspoken though. The advisor should help the student with the dissertation, and provide guidance. The advisor should not grill the student on things that she should have brought up beforehand.

ANyway, i survived, and have spent the last three days rewriting (cutting the dissertation in half), and working on the blessed paper. So today i plan to submit the dissertation to her and see what she says. I may have to get an override from the Dean, but I will try this first. If the committee approves the defense and dissertation, the dean can sign off on it w/o the advisor's approval. I feel that the dissertation I submitted to the commitee was solid, and no other committee member raised serious objections to the dissertation. Half actually read it, actually two out of five (not including the advisor).

I don't want to burn bridges, but my advisor is being unusually difficult for both me and my fellow student who is also graduating. Anyway, after three days of 8-10 hours in front of the computer I'm exhausted. I am still optimistic that this can be done, but it depends on the advisor; if she is super critical there is no way I can get her approval of the dissertation. I *so* look forward to leaving the lab. This whole experience has pretty much killed my enthusiasm for science, hopefully it will recover. The new lab sounds promising.

here

It's all stuff I read before, although this writer suggests paying off the mortgage asap. All the advice sounds reasonable if simplistic. 'Pay off debt because you don't want to be in debt' type things. And they make reference to the suggestion of saving 15-20% of your income for retirement. Some commenters take issue with that, and think they will deny their children of stuff (education, clothes, food, whatever) if that is true. Others pointed out that you can get educational loans but not retirement loans.

Actually that isn't true, you can now get reverse mortgages; if you own your home and are above a certain age, you can receive a steady income from the bank with the expectation that when you die, the home will be sold and it's equity given in part to the bank. It seems like a pretty good deal actually, although I am sure there is fine print. Banks are in business to make money, so there must be a catch.

Further, one commenter said that the inflation rate is 6% and the unofficial rate is twice that. The inflation rate for this year will actually be about 6%, but in the last 5 years it was between 1 and 3% (see here). So, anyway, take what you read on the net with a grain of salt (or a gallon).

So the marathon session of revisions begins. So far so good, I have a sense that my advisor wants to help. Maybe this will be the final round of revisions. God willing.

I guess the maelstrom of conflicting emotions is subsiding. I still feel lots of anger and depression; I think everyone (family included) expected that the defense would be the end of things. Intellectually I knew differently, but emotionally I did not. Anyway there is this black pit of dispair in my stomach, making eating and sleeping difficult. I just pray that if i can get this stuff done my advisor will sign off on the thesis. After that, finally, everything will fall into place. But it's really the uncertainty of dealing with an irrational person which makes life so vexing. I can't adapt to her world-view, its utterly alien to me. What is normal anyway? Normal is average, what the average joe expects a person to behave like. Anything outside the norm is abnormal (by definition), therefore all abnormal people are crazy. I feel for people who have to deal with multiple crazy people every day, i only have to deal with one. I never want to descend into her world, which is this nice, pure, happy place of logic, and utterly devoid of rational thought or reality, or really anything except her; that's what a narcicist does, really. I think most advisors, to their students, are utterly insane. Hopefully this next guy i'll be working with will be better, he's well grounded with a wife and kids. J's advisor is much much better behaved than mine, again he has a wife and kids. I see a connection.

Anyway here is a feel good story in Afghanistan.

So if Bush is doing the 'tax cuts for the rich' thing, why are tax revenues actually increasing? TaxProf has the numbers.

In other news...I sucessfully defended my dissertation yesterday. Success is relative, however. The committee members were mostly satisified with the dissertation, however my advisor, who read it the night before (insted of three weeks before, three months before), was not. She wants a rewrite of the entire thing, and major modifications which committee members didn't want. So basically now I have to rewrite it to make her happy, and get her to sign off, that's all that matters at this point, having her sign the paper. I don't know what that will take. It may take several more months of staying at home and writing, without any income, without a job or a postdoc, since i can't have those things until she signs the form. Yes, the advisor really does hold your career in her hands, until the last bloody moment. All i know is I have a week to get this in before the end of the semester, and 11 days before I go to Hawaii, so I just pray to god that i can get it done.

More damning evidence came to light today; the New England Journal of Medicine said that the authors of a vioxx trial deleted data showing that three additional patients had heart attacks. This is not a good development for Merck, it really calls into account their scientific credibility and why they decided to mislead the journal. The numbers don't really make a difference though. I think Merck made a collosal mistake when they released Vioxx; it's not that much better than naproxen (seemingly), and the risk of heart attacks is, according to this report, 7-fold higher. But it's one of those things that wouldn't be caught by clinical trials because of the huger numbers of people which are involved. Could we add another layer of clinical trials? Sure, but that would pretty much kill the drug market. One of ten drugs which enters clinical trials makes it. Another layer would decrease that probably two fold or higher, but more importantly it would make the drug cost so much that it wouldn't be worth it to market it. Why market a product that costs billions of dollars, when you only have a few years of patent life left to recoop? Sure, something needs to be done, but what I don't know. Anyway, Merck is looking to take a $50 billion dollar hit on this, plus the damage to their credibility. I wouldn't be surprised if they are bought out and 'disappear' in a few years.

Poll/story here

It says that things are much better off now than 4 years ago in Afghanistan (which isn't saying much, I suppose). I guess in a country with so many problems, even baby steps forward are a good thing; basically Afghanis and Iraqis are saying that anything is better than what they had before. Even if the reconstruction is 'screwed up', and I don't know that it is, both countries are still much better off after US invasion and occupation. How does that square with the leftists saying that we had no right to invade a foreign country? I think these polls give the invasion legitimacy; if the people think they are better off now than previously, regime change must have been a good thing. Too bad the leftists don't see it that way.

Okay, now i need to practice again.

2 hours before the end of grad school (somewhat, that doesn't happen until Dec 16th). So it will be nice to have the defense done, and maybe we can get the paper out next week, if my boss focuses on it somewhat. Anyway, going to go practice now.

Tomorrow is my dissertation defense; there many conflicting emotions raging within me; fear, anxiety, doubt, for sure, anger for being stuck in grad school for so long and the abuses received herein, elation that I am being released...these create a maelstrom within me that threatens to explode. Tomorrow these emotions will be released, but I know this is not the end. I still have to get this paper out before the 16th (that's next week Friday), and my boss is still making major revisions to it, so I really don't know if it will be submitted, this year or ever. Of course that leads to a huge anxiety over the future of my career, crippled from the lack of productivity in this lab; being stuck on a difficult project was not helpful, and being stuck with my current advisor wasn't helpful either. I can only hope that my next lab as a postdoc is successful; otherwise there is no point in continuing in science. With the environment this competitive, and me having little to show for almost a decade in the field (albeit all in grad school), it doesn't bode well. At least I have a presentation scheduled at a conference in February already, this will be helpful. If we can get the paper out I can apply for fellowships, which will be a boost to my CV, and will lead to further publications. Anyway, that is in the future, but tomorrow I have little reason to rejoice, except that my time in pergatory is reduced by that many days.

Up to 10 years, so they say, for fraud. But, what is interesting, is that my family (brother, mother, and I) met him in San Diego, about 15 years ago. He was a fighter ace in Vietnam; i remember him being pretty nice, but he had ulterior motives (trying to hit on my mom, and he was married at the time!) Oh well. It's funny who we call heros; I'm not sure if the label is inappropriate.

ANyway, one day left til defense.

Lots of cheery stuff coming from the Saddam trial. I think few people deserve the death penalty, but Saddam could die ten times and it wouldn't be enough justice for Iraq. And he has the audacity to complain about his treatment, when witnesses describe eating bread and water, regular torture and rape in prison? Audacity!

D minus two days and counting. D day H hour is Thursday at 1:30 pm. Currently I am preping the dissertation defense slides.

Anyway, so then i found this cute (not) review article on adrenal insufficiency. Long term asmtha patients may become adrenal insufficient due to long-term steriod use. Sounds familiar. Leads to immunoinsufficiency. I was also thinking of ferrets with hyperadrenalism and imagine the effects would be reversed; a boosted immune system, but cardiac issues due to the constant vasodilation, and probably other things...organ failure at the end. I imagine the effects would be systemic.

Every guy wants this: The Moller Skycar, capabile of vertical take off and landing (means it can park in a parking spot), cruising speed of 275 mph, and 20 mpg fuel economy (ethanol fuel). Alas, it's only a prototype.

Every guy wants this: The Moller Skycar, capabile of vertical take off and landing (means it can park in a parking spot), cruising speed of 275 mph, and 20 mpg fuel economy (ethanol fuel). Alas, it's only a prototype.

Here

It's not bad, i suppose, if you have $500 to drop on a guy. Otherwise it lacks originality... I mean if you are going to spend $500 on one person, you better know them pretty well. In that case, don't do gift guides. I'd like to see guides that don't assume you are Bill Gates.

If I were making a gift guide for random guys?

Games would be on the list, most guys my age play console or computer games.

Maybe something to do with poker, since that's a huge fad now.

Music, definately; but not the overblown Ipod. The Creative Labs MP3 players are pretty good but not as pretty.

Alcohol; you can't go wrong with a nice wine, but this is more of a couple gift.

Computer gear? Maybe an external hard drive? Everyone needs one of those, for all those Lost episodes that their wives make them download :)

Maybe a 1 gallon tank and a goldfish?

Or a bicycle to encourage fitness?

But, yeah, gift giving is hard. Either it's a specific request, or it's crap in my book. Hard to find something both non-crappy and surprising. Also for people my age, i think we buy whatever we want, so presents aren't that important to us.

Link here. Definately, definately not work safe (lots of foul language). But somewhat funny and truthful.

Arizona Wildcats lost to the Houston Cougars, 69-65. Don't let the score fool you, it was a blowout. After 10 minutes, Arizona only had one or two field goals (no 3 pointers); they scored mostly from foul shots. Their shooting was in the 20s, Houston shot everything. Houston's defense was unstopable. Arizona was in shambles. But it was still a fun game; the crowd was insane with glee; with chants of 'overrated' before the tip off. The Tucson Citizen has more. Seems like Lute has lost his touch.

Oh my, two Lost stars got busted on a DUI, in Honolulu. Driving on the Pali, none the less. For those who don't know, the Pali is a very dangerous highway cutting thruogh the koolau mountains. Lots of curves, high speed, etc. Sober and slow it's okay, drinking would certainly add to the challenge of surviving the Pali.

Maybe we'll see these people when we go there over xmas.

Knots landing was a 80s early 90s sitcom, they are doing a reunion. Who cares about that though.

However, did you know that the producer of KL is none other than the Fonzie from Happy Days (Henry Winkler). And that several of the 'Desparate Housewives' started in KL? That's interesting.

This is what I really want.