Starting my PhD was hard, apparently finishing it won’t be any easier.  I’m basically one figure away from publication (and hence graduating)…….but I don’t know what that figure/experiment is.

I thought I had it last week (see my very happy post), but further experimenting showed I was on the wrong track.  FUCK!  Sorry, sometimes the frustration just slips out.

I love research, really.  I just want to finish my PhD, and sometimes it is quite difficult.  This sounds really corny, but right now the only way I am getting through this is my new wife.  She’s my rock, who works hard, makes all of our money, and takes care of me when I come home from a day of disappointing results.  I don’t know how I was able to start down this path without her, and I know that if she hadn’t come along, there is a good chance I wouldn’t have been able to finish.

I just finished Cory Doctorow’s newest book, Little Brother. Um….wow, it was really, really good. You’d think I’d be a bit more eloquent after reading some absorbing fiction, eh?

This book is about a government crackdown on San Fransisco after a big attack and follows a teenager whom is caught in the government’s clutches in the aftermath. However, this book isn’t about the plot. It is about the idea of freedom.

In a society where there is information about us everywhere (take a second and think about how much of your information is in computers) and the government reads our email (remember Carnivore?), this book does an excellent job of talking about the ideas of privacy, freedom, disobedience to authority, cryptography and cool technical hacks through an interesting story.

Basically, it was a kick-ass book that was well worth the time it took to read. I even learned a bit more about cryptography :).

Because Doctorow has an excellent philosophy about copyright, his book is published under a creative commons license. If you want to read it online go here. Otherwise, it is available at brick and mortar stores in physical form. But seriously, who actually goes to the book store anymore ;). At any rate, put this book at the top of your pile, physical or virtual, and read it.

Did I mention I still love my kindle?  Now off to install linux on a USB hard drive so I can fiddle on something else for awhile.  The coolest tidbit in this book is a hypothetical linux distribution called “paranoid linux.”  I wish it was real….I’d download it.  So…..sick…..of…..windows.

I was at lab until 9pm last night…not for some cool experiment, not to slog through more of my paper and review that need to get finished, but to help get the new computer set up for our confocal microscope.

I’m the resident computer expert in my lab, not really sure how that happened, but every time there is a new system upgrade I get enlisted to help.  I don’t mind……too much at least.  However, as the finish line for my PhD approaches, I am less and less charitable with my time in lab.  Things like tinkering around with the user management software on the old machine, which was written in the dark ages (2001) is annoying.

What is most amazing is how everyone feels the need to constantly upgrade their computers for fixed tasks.  The confocal software doesn’t really require anymore processing power now than it did 6 years ago.  It is still the same microscope, and the data being dealt with is still of the same magnitude.  However, computer software and operating systems really aren’t backwards compatible.  Unless you are on an upgrade cycle of 4 years or less(give or take), getting a system on Windows XP setup to resemble a system that was set up on Windows server 2000 is a major pain in the ass.  Part of this is incompetence on Microsoft’s part, I’ve always had backwards compatibility issues with them, thus I won’t switch my personal systems from XP (which runs on all of my systems and is tweaked *just right*) to Vista.  The biggest reason is that nothing I have painstakingly setup will work!  (Plus Vista really sucks).

I don’t understand why Operating systems need to be changed all the time.  How much basic functionality does a computer need out of the box anyway.  I don’t see why a good operating system can’t be written that will have a product “lifecycle” of significantly more than 4 years.  I don’t understand why anyone needs Vista instead of XP.  I still haven’t heard of a killer app for Vista that would make me even consider leaving XP.   The most likely reason in my mind is profit.  If everyone keeps their software for 10 years at a shot, you won’t make money.

Don’t get me wrong.  I love that computers get more powerful and cheaper constantly.  I just don’t think that performance improvement should be devoted to running newer, bloated, resource-hungry operating systems.  Crap - sounds like I should just switch to linux.  Of course then I’d have to set up everything again anyway….

I was out for a run earlier, in my current battle to keep my naturally expanding waistline under control. Of course, it was really hot out, and this was a fairly miserable run. This combination made me wish for an easier way to lose weight.

Nearly every American wishes this at some point or other, which is why there is weight watchers, the south beach diet, the Atkin’s diet and so on. However, all of these diets miss a fundamental point: (Calories in - calories out)/3500 = pounds gained or lost. To translate from math into English, if you consume 3500 calories more than you burn, you gain 1 pound. Conversely, if you burn 3500 more calories than you consume, you lose a pound. Simple, right?

So, it follows that there are two ways to lose weight:

1) Eat fewer calories. OR 2) Burn more calories.

Step 1 is where so many diets come in. If you eat less, and can stand feeling like you are starving all the time, you will lose weight. Your body doesn’t like this so much, because it thinks you are literally “starving.” So, as soon as you go off the diet, your weight goes back up because your body wants more food to get back to its “set weight.”

I think step 2 is easier, but I usually like to exercise. If you exercise, you burn calories. If you are careful and don’t consume too many extra calories, you will lose weight this way too. However, as soon as you stop exercising, your weight will start trending back up again.

The only way to permanently lose weight is to make permanent changes. You need to permanently eat fewer calories per day (for me this means 1 pop/day) and permanently exercise 3-5 times a week. This will cause permanent weight change every time as your body’s weight comes to a new equilibrium with the calories you are consuming compared to the calories you are burning. It is just so damn difficult! No wonder nearly everyone goes for diet of the week.

I was talking with a friend about politics yesterday, and it turns out he is going to vote for McCain in the fall.  Which I found mildly surprising.  Granted, my friend is rapidly moving to upper-class status (in income) and taxes are an important issue for him and his wife.  However, I’m still surprised.

When I asked him what issues he really cared about that influenced his decision, he said 1) He wants lower taxes, and 2) Barack and Hillary both seem crazy in their current campaign.

This scares me.  A lot.  If he is going to vote republican because of the fate of the bush tax cuts and because Hillary is tearing into Obama (and vice versa), the general election won’t be a landslide for the eventual Democratic nominee (or even necessary winnable).  Mostly, I know lots of very intelligent people who are sick of the democrat bickering, think they’ll pay less taxes under a republican and thus have made up their minds.

Granted, everyone has a right to whom they wish to vote for.  It just makes me sad that their reasons are short-term tax gains (taxes have to go up eventually, we are running a HUGE deficit, have commitments to social security and medicare, and have millions of people that can’t afford health care) and because the dem primary process has been so divisive.

I’m a die-hard idealist, and I wish people would vote on the issues and their long-term best interests…..but I guess that doesn’t happen (or my world view is skewed…).

Human Immunodeficiency Virus (HIV), is of course the virus that leads to AIDS. Up until 1996, this virus was a relatively swift death sentence. Then antiretrovirals were developed and released to the public.

Antiretrovirals are a particularly cool set of therapeutics that target different aspects of HIV replication. For example, AZT, one of the most common antiretrovirals, mimics a DNA base (Thymidine). HIV’s has an error prone reverse transcription (RT) step where it makes DNA out of its RNA backbone. The RT enzyme can’t tell the difference between Thymidine and AZT. This and other similar drugs (some have different mechanisms) led the community at large to believe that HIV was ‘cured.’ However, this was not the case. As with many infections agents (with the exception of syphillis for some reason) HIV can mutate and survive in spite of various compounds that are thrown at it. Taking anti-retrovirals can completely remove active HIV from a person, to the point where it can no longer be detected in the blood. This is an impressive feat on the part of the scientific community.

However, this comes with a catch. Over time(as the virus gains resistance), or if a person stops taking anti-retrovirals, the virus comes back. HIV evolves and HIV can hide. In certain immune cells, HIV will incorporate itself into a person’s DNA. Essentially in ‘hibernation’ the virus is safe from medication that targets actively dividing cells.

So, how to force HIV come out of hiding so it can be hunted down? There have been a number of attempts in recent years, however, one of the most promising sets of compounds is related to prostratin. Until recently, prostratin has only been available as an exract from the Mamala plant in the Samoan rainforest. This meant that there was a very limited supply. However, in a recent article, a group of chemists have figured out how to make prostratin from Croton tiglium, a common plant that makes oil in Asia. The science daily story on this process is here.

Of course, this isn’t the cure for HIV, and may never lead to one. In earlier trials, prostratin+interleukin-8 (an immune signaling compound) led to flushing out 80% of the virus that was in hiding. While this is a promising result, leaving any virus left is short of a ‘cure.’ However, from here, synthetic chemists can use the chemical steps discovered to make and then modify prostratin and try and improve on these results.

The reason I find this particular story (and many others like it) so interesting is that it demonstrates the power of combining natural compounds and synthetic chemistry. Nature has found many ways to make many compounds with particular purposes. If we can find these compounds (often from rare plants), we can learn to make them. Some of these compounds will likely be the “magic bullets” of the future. There is one slight catch: the rain forest, marine environments, etc. still have to be there for natural compounds to be found.

Just one more reason to try and save the rain forest.

Hey, look at the pretty graph!

This unassuming piece of data means that my last assay works (IT ONLY TOOK 2 MONTHS OF MY LIFE), and I’ll be able to finish my paper this month!!!!!!

Which means…..I get to graduate soon!!!!!!!!!!!!!

After I finish up the follow-up experiments……

And write the paper…..

And write a review…..

And write my thesis….

But it is getting close!

Lately the word elite has been used a lot by the media and in particular the Clinton campaign. Let’s take a look at the definition from dictionary.com:

1. the best of anything considered collectively, as of a group or class of persons.
2. persons of the highest class: Only the elite were there.
3. a group of persons exercising the major share of authority or influence within a larger group
4. representing the most choice or select; best: an elite group of authors.
5. a group or class of persons enjoying superior intellectual or social or economic status

This seems to be Hiliary’s favorite new word to attack people with. Apparently being the best is a bad thing. Okay, I’m mischaracterizing her usage of the word. By claiming he is an “elitist,” Hiliary is saying that Obama believes he is one of the “persons of the highest class” in definition #2. This is the only option as she surely isn’t referring to her opponent as having superior intellectual status or having the most influence.

This seems disingenuous to me, as he comes from a single parent-family and his family didn’t have a lot of money prior to his emergence on the political scene, while she is the wife of a former president and they have over $100 million dollars according to tax returns. As political posturing, this is ridiculous, but I think I see where see is going with this.

Hilary is pandering to working, blue collar voters who distrust those “elite” academics, who don’t understand what it is like on a tight budget. And now, with its apparent effectiveness against Obama, Hilary is using the “Elite” title on economists. Hilary’s ridiculous gas-tax idea, which I blogged about earlier, was lambasted by economists. So now, they are “elitists” who don’t understand the needs of working class Americans.

This is a worrying trend. I distrust a candidate who would lambaste an entire fiscal discipline (one that helps run our economy by the way) for policy points, and try to widen the already deep divide between working-class democrats (part of her base) and affluent, educated democrats (part of Obama’s base) using disingenuous labels. I suppose that Hillary doesn’t know the average salary of an academic economist. It isn’t tiny, but if you work in academia, it certainly doesn’t put you our of the “hard-working middle class.” (There are those who work on wall street and are compensated greatlly, but that isn’t all of the economists. Who taught your Econ 101 class in college?) As a graduate student I make well under $30,000/year. This whole episode reminds me uncomfortably of the “unpatriotic” that was used to quell dissent and pass the patriot act after 9/11.

If Obama is an Elitist, and Economists are Elitists, then as a scientist, I must be an elitist too. Maybe we should all strive to be Elite….America might be a better place if we all strive to be our best.

This post is inspired by my reading of a blog post here, about how horrible the idea for a summer gas tax holiday is (coming from both McCain and Clinton).  However, the problem is much larger than the price of gas alone indicates and I thought it warranted some further discussion.

Why is gas so expensive right now?  And why are the high prices persisting for so long?  Ask anyone and you’ll probably get a different answer.  I think the explanation is very simple.  Think back to your high school economics course (I know it was a long time ago, and if you were like me you were probably asleep, but think hard).  Remember supply and demand?  Yep, that is why the price of gas is so high.  There is huge world demand for “black gold” right now. This is due in part to our country, which loves our SUVs and fertilizers (20% of the fossil fuel we use is to grow food).  However, part of this demand is the rising economic status of other countries, such as China and India (to name a few examples with a few billion people).  As they have more money (mostly coming from us, incidentally) they consume more resources.  For example, more and more people on the planet have cars, which consume gasoline.  And, as they move up the economic ladder people like other luxuries such as meat.  Meat takes 10x as much energy (from petroleum) to make as calories in corn or rice.  (For a good discussion of this read Micheal Pollan’s Book the Omnivore’s Dilemma, especially part II).

Barring a major world economic recession (which could always happen), demand for gasoline is going to continue to rise and certainly isn’t going to go down on its own.  This is one specific reason why the Clinton/McCain gas tax holiday proposal is so ridiculous.  There is so much demad for gasoline, that if the taxes are removed, the price will just go up to the level it was before the tax break.

It is supply and demand, so one fix to reduce the cost of gas is to increase the supply.  There is one reason that this isn’t happening.  IT ISN’T POSSIBLE.  Gas is a fixed quantity, and at current prices everyone everywhere is extracting as much of it as they can.  OPEC tries to keep prices lower than this to keep us addicted to gasoline.  If better alternatives are developed, their precious resource is worthless.  However, their spigot is all the way open right now.  In the past expansion has been provided by drilling more wells and opening new oil fields.  I believe that era is at an end.

In the early 50’s I believe (I could be off by a few years) a geologist working for Shell named Hubbert forcast that gas production fell on a bell curve.  As new fields are found, production goes up.  As resources are tapped, production plateaus and then decreases.  He correctly projected America’s oil production peak in the 1970’s and the subsequent decline(Hubbert’s Peak).  Hence our current dependence upon foreign gasoline for power, food and transportation.  The scary thing is that eventually this will happen with the world’s supply of oil.  As a finite supply (or only renewable over millions of years, to be technically accurate) we will eventually (or sooner) plateau and then decline in the world production of oil.  As demand is growing and supply is slowing starting to plateau, prices are only going to get higher.

So, gas costs a lot?  Why?  Lots of people want it and can now afford it.  Can we make more?  No.  Will a gas tax holiday help?  No.  Expensive gas is here to stay.  At least until we get our collective act together and move on to better (i.e. cleaner and renewable/perpetual) energy sources.  Sorry for anyone who drives a big car.  The days of $1/gal gasoline are gone for good.

I follow politics pretty closely, even though I haven’t blogged about it before.  This particular obsession has only gotten worse with each election cycle and as I feel a more vested interest in how our (The US) government behaves, both in terms of domestic programs/funding and as the currently most powerful single presence internationally.  However, the coverage of this year’s presidential election by the mainstream media has been, in my eyes, particularly heinous.

There are a huge number of issues to be tackled by the next president.  To name a short list:  how to deal with Iraq, how to deal with the end of cheap energy (by this I mean cheap oil), how to educate people in our socitely (of all ages), how to provide realistic health and dental care to the public at large, how to fund science, how to explore space (or should we), and how to pay for anything we decide to do.  Not to mention regulating (sub-prime loans anyone?) and promoting economic growth.  Disclaimer:  These are just the issues off the top of my head, and they are all important in my mind which may give a slight indication of my priorities.

These issues make a rich tapestry for discussion and debate amongst candidates, with the public, and with the media as a whole.  How the next president handles these issues (or understands them) will have a huge effect on how our country proceeds forward into this century and what the average American’s life will be like for the next four years and beyond.

Thus, my current outrage at the mainstream media.  The mainstream media is owned by large corporations and is used for one purpose.  Any guesses from the crowd?  To inform the public?  Sorry, nice guess.  Profits?  News divisions are now used to generate profits for large businesses.  I’m not saying that this in and of itself is a bad thing.  We live in a capitalist society and money is how I pay for my food, housing and all of my needs.  What is disturbing is what the pursuit of profit in the mainstream media leads to.

The current election cycle has been about a few key topics.  Iraq and the economy have gotten some attention.  However, I have yet to see a good newscast that explains to me what the current economic news means.  How many of you know the technical definition of a recession?  Our current president doesn’t.  To quote:  “We are in a slowdown, but not a recession.”  A recession is an economic slowdown that lasts for 2 quarters (six months).  The only show I saw that commented on this was the Daily show with Jon Stewart.  Why can’t we have in depth news pieces that gives the news and also makes an attempt to explain it?  Such as a report on whether or not we are in a recession and one that lets us know what a recession means.  Real news should inform.

This leads me to the media’s current obsession:  Jeremiah Wright.  Why is this guy even news?  To me most preachers saw things that are stupid and obscene.  I’ve heard my parents’ pastor make absurd statements in the past.  Should they be held accountable for his statements?  There are priests that have molested children, is this the fault of the congregants?  What makes this even worse is that Wright was a spiritual adviser to Bill Clinton during Monicagate and strange pastors (Billy Graham) that say strange things have been at the right hand of presidents for years.  How does 8 news cycles of Jeremiah Wright make me an informed voter or citizen?

But why does the media do this?  To make money obviously.  Why does this make money?  Because we fall for it.  We pay attention to sensationalist stories about crap that doesn’t matter and ignore in depth stories about the issues.  Until we the people change our viewing/reading/whatever habits to looking for news that actually contains information, explanations and examines the world for what it is, this tripe is all we really deserve.