You'd think modern PCs would be able to play DVDs. Nope. In fact, to play a dvd, you have to download a special program called a MPEG2 decoder, and these all require license fees to the MPAA (or whoever setup this racket). I spent all night figuring out how to play a dvd in my PC. Essentially, they want you to buy an extra software for $20 or so, (there are zillions of programs, such as windvd and powerdvd that will do this). Or you can walk 5 feet, stick the dvd in your home dvd player, and press play. Hmm. Anyway, there is a free solution. Go to free codecs website, and download the XP codec pack; it includes Media Player classic, which is a very stripped down media player (but works fine). Most important, it's free.

Also note if you buy a DVD-ROM drive for your PC it will usually include a (usually bad) DVD playing program. How convenient.

Landis, I mean. The wiki has a great summary of his post-tour history, mostly his efforts to clear his name from doping charges. From what his lawyers say, there are pretty damning charges against the lab, ie the test result was at best inconclusive. I guess the thing is that if he were injecting testosterone, he'd be pretty stupid to do it at the end of the tour (when it's least likely to benefit him). Previous T/E tests were normal, so it's suprising that all of a sudden this one is high. ANyway, i hope he's cleared. IT's a shame this distracts from what is an amazing tour win.

As Cathy Seipp laid dying...

Moral: Be kind to all creatures big and small. Do unto others as you'd have done unto you.

That's why men's health wants you to believe. Anyway, this exercise is tough! I did 7 full single-leg squats. Seems like a good exercise for cyclists.

In mammals like us, IR causes DNA breakage which is either repaired or the cells undergo a programmed cell death (if able to). This becomes a standard treatment for cancer (and other diseases). However, a new study shows in a particular strain of bacteria (Deinococcus radiodurans) which can handle much higher doses of radiation, the secret is not the DNA damage, but is due to protein damage due to reactive oxygen species. This may have implications for radiation treatment; traditionally, it is thought that the only effect of IR is DNA damage, now we know protein damage also plays a role, and in radiation resistant cancers, the secret may be due to enhanced dna repair proteins.

Woohoo. ALso, two movies are in the process of being filmed and will finish in June! Movie 1Movie 2

This one is about the relationship between the media and the military. Excellent piece!

Restoring vision of the three (color-blind) mice.

Actually this seems like a really cool study, and shows that 'instant upgrades' to vision are doable. But do more receptors in the eye translate to vision? Likely yes, in these behavioral experiments, which form the linchpin of the study (my opin).

Jacobs’ group at UCSB developed behavioral tests to determine whether the female mice could discriminate among colored lights by comparing the relative activation of the M and L cone cells. The researchers conducted tens of thousands of tests in which two different wavelengths or intensities of light were displayed on three test panels. Mice received a drop of soymilk as a reward when they correctly identified which panel differed from the other two. The genetically altered mice demonstrated their new visual ability by choosing the correct panel in 80 percent of the trials. By contrast, normal mice only chose correctly one third of the time, the score that one would obtain by guessing randomly among the three panels.

So, translationally, other adaptations are possible for humans; better sense of smell (most mammals have much better sense of smell), better hearing, better vision...by studying animals with hightened senses, ie eagles for better vision, we can determine what creates that hightened sense at a biochemical level. Further, senses research can ultimately restore a sense to a deprived (ie blind) person.

Finally, release from Adobe Acrobat bloatware.

PrimoPDF. It even has a 64-bit version.

Cool! I've seen a handful of these. (the species, not the specific trees themselves)

Peter Wehner, of the Bush administration, says this about the new effort for the dems to insist on a timetable of retreat from iraq: "There is no precedent in American history for succeeding in a war when the commanders were taking battlefield direction from Members of the House and Senate. In the words of the Los Angeles Times (in an editorial titled, "Do We Really Need A Gen. Pelosi?")"

This is no change of the Bush admin. stance; no timetable, no outside (read Congressional) interference in Iraq; they've been saying it for years. The issue of when will the war be over is a vexing one, nobody knows. When will it be safe for our troops to come home? Heck, when will they come home? Everyone wants them home. But the new tactics by Congress to insist via legistlation that the troops withdraw at a certain date is not useful in fighting this war. The enemy is sitting us out, slowly ratcheting up the pressure. It's been four years of struggle, and no end is in sight. It's just like Vietnam, right?

No, here's how it's different. History has shown that a change in government in Vietnam didn't do shit. Vietnam had no strategic importance, no valuable commodity that we need. (more here on Vietnam-Iraq comparisons, esp. note the suicide attacks against civilians favored by Al Qaeda which were absent in Vietnam) Iraq does have huge stategic importance (its in the middle of the Arab world), and of course there's all that black gold, and now that Saudi Arabia is showing peak oil, we need other new sources of oil, desparately.

Then there's this: "If we retreat from Iraq, Islamic jihadists will not go gently into the good night." (from the above article). The Vietcong will not hope on a airline and be in New York in a day, to blow up...whatever. Al Qaeda has already shown that it's willing and able to attack U.S. soil with huge casualties. Now they are using chemical weapons in Iraq.

It's not scaremongering to say that either we hold them in their places, or they will be free to organize and plan and fly planes into buildings. Why aren't they doing it now, why have there not been further attacks on U.S. soil. Partially because all such attempts have been blocked. Further, Al Qaeda is very busy in Iraq. Additionally, its quite hard to find the great source of destruction that is plentiful in Iraq: artillery munitions.

How the RIAA will kill internet radio (and, incidently, NPR).

A nice, safe place to visit.

Hmm, this is interesting. It's not fresh news that Hillary wants our troops to stay in Iraq (great for her, allows possibility of moderate/conservative votes), but it's surprising to me that Dick Morris (the Karl Rove of the Clinton administration) agrees with her.

Nothing worse than flying with a corpse. For a 9 hour flight. And paying $5000 for the experience.

...for now...i finally got my experiments to work again after 2 months of failure.

Magnetic spin? New types of matter? Strings? Argh. Hopefully the physicists would appreciate it.

Well, I *finally* got my plasmid constructs created, i've only been working on it for, oh, 6 months now. DNA cloning is like that, it may work very easily or not at all. ANyway i thought i'd write down my thoughts that i've gleaned over the last few months regarding this system.

The Gateway system can be potentially quite useful if you have multiple uses for the clone, for example production of bacterial protein, immuno-flurescence, expression in mammallian systems. Also, the absolute cost of creating a construct can be quite cheap; the entry cloning kit will run about $30 list price per reaction, then the clonase reaction is $8 list/reaction. The destination vectors are originally costly, but you can get it from others or order it once and make midipreps of it; essentially it's a one-time purchase. Further, for all enzymatic reactions with invitrogen stuff (at least the Gateway system), you can half the reaction and it will work fine. For example, for the Entry cloning, use 0.5ul of TOPO vector. For the clonase reaction, use 1 ul.

ENTRY TROUBLESHOOTING
=====================

There are two main tricks I found. (okay, more than two)

1) You will always get some background with the entry cloning; ie if you do not put any insert in the reaction, you will get, say, 20 colonies. This number is useful to know , but obviously you'll waste a reaction finding out this info. However, if you know this, you don't have to waste time screening if your insert reaction doesn't contain more colonies.

2) The size and amount of insert used is rate-limiting. What i mean is that small sized inserts will work a heck of a lot better than large inserts (this was my issue). For a 0.5 kb insert, the cloning success was almost 100% (all clones contained insert). For a 1kb insert, it was about 50%. For my 2.8 kb insert, it was only 5-10%. This isn't covered by invitrogen in product literature, also the tech support was useless (they are morons, i swear).

The amount of DNA is also critical. I used 10 ng of a 2.8 kb insert, and 5 ng of a 1 kb or less insert. This is for 0.5 ul of TOPO vector. This is convered in the invitrogen book.

3) For larger inserts, you'll get alot of colonies, but 90% of them will be wrong. For all reactions, you should get several hundred colonies if you use 0.5 ul of TOPO vector. If you only get a handful, then the reaction didn't work. If this happens, ask your self some questions.

1) Do you really like science?
2) Are you tired of dealing with bullshit kits that make huge claims?
3) Okay, the first two questions are rhetorical. Really, the issues are:
a) Did you get a good PCR product, or was a smear? If a smear, optimize the reaction. PCR of plasmid should give a good, solid band. If you get a predominant product and some minor bands, gel purify it. What will happen is that the smaller bands, which potentially have the critical CACC 5' overhang, will preferentially ligand, and give you background. (For my 2.8 kb cloning, i gel purified, and still got a bunch of crap for 90% of clones)
b) Did your purification strategy work? I used the qiagen kit for pcr cleanup and gel purification. Oh, the new pcr cleanup kit says it's first buffer is not to be used for gel purification,I think the buffer is QB1 or something. ANyway, i accidentally used it, and it worked fine.).
c) If your PCR and purification was fine, you may just want to try a smaller fragment to ensure that you are not retarded and doing something stupid (it's probably not you, its probably the kit). Start with a 0.5 kb insert at first.


SCREENING
=========

Last but not least, when you do screening there are a few things you can do. 1) Run the plasmids out on a gel. 2) Digest with NotI or something and run it on a gel. 3) PCR using M13F&R. 4) PCR using insert-specific primers.

Ideally, your positive clone will be positive for all of the above (also sequencing is a good idea). My experience is that: The best thing is actually the simplist, just run the plasmids on a gel, pick the largest one. 2) NotI tends not to work (perhaps our Wizard preps are of low quality?), you'll get a mix of cut and uncut DNA, making it tough to figure out which is which (you should also run uncut plasmid to avoid this). 3 & 4) PCR inevitably gives high background. My thoughts for why this is so is that the during the insert reaction, the insert will actually loop out, and topo will catalyze the excision, thus giving you a plasmid clone with 5' and 3' ends of your insert but none of the middle. This is just a guess, really, I don't know for sure.

DESTINATION CLONING
===================

Fortunately, if you have a good entry clone, this will almost always work. Use the gus positive control if in doubt. Be warned that you can not grow the insert-less destination vectors in normal bacteria, you need the DB3 strain. Also be warned if you have a bad entry clone but it still has a insert (maybe it's not an insert than you want, but an insert none-the-less, you'll still get 'positive' results, ie bacterial colonies (garbage in = garbage out). So be sure of your entry clone before proceeding. (Sequencing is a great idea). I think you can also do NotI digest to confirm the destination clone (i don't remember exactly). The trick is that the vector alone will pop out the ccdB gene, thus its possible that the insertless vector is the same size as the insert-containing vector. PCR may help, or a restriction enzyme digest. Whenever I've done this, 100% of clones are correct (but see garbage in garbage out above).



Anyway hopefully this is helpful to someone, if it is, shoot me an email (gibbie99 at yahoo dot com)

Interesting short article on CNN/Money. Europe looks bad, Mexico & Carribean looks good; best time to buy is on Tuesday.

(here) Hey, i got 6 of 8. Not bad for not remembering much math. This kid got 8 out of 8. But he's a genius.

Some great jokes in there. Fred Thompson is a former U.S. Senator from TN who did a stint on Law and Order, one of the best shows ever made (17 years proves it).

Damn interesting, indeed. Niihau is a sparsly populated Hawaiian isle with a unique history during World War 2.

Drs. William Brinkley and Richard Tapia (VP and Dean of Baylor GSBS and Professor at Rice, respectively), had a great op/ed in today chronicle.

I'll post below, but its here (for now).

Texas must attract more students to science, math
State's prosperity clouded without skilled workers

By WILLIAM R. BRINKLEY and RICHARD A. TAPIA

The landmark 2005 report for Congress, "Rising Above the Gathering Storm," warns that the United States stands to lose its scientific and technological superiority in the coming century unless we can persuade a greater proportion of young Americans to choose science, engineering or mathematics as careers.

In a world where the link between scientific progress and a rising standard of living is becoming increasingly undeniable, the next generation of Americans is shrinking away from these fields that are so important for our economic future.

For example, the report notes that only 6 percent of U.S. college undergraduates major in engineering — the second-lowest proportion in the developed world. By contrast, 12 percent of European and 40 percent of Chinese undergraduates major in engineering. In the past, the United States has met its shortfalls by importing scientists and other experts from abroad, but that's become much more difficult as visa requirements have become more onerous in a post-9/11 world. Many other experts are choosing to stay home as well, seeking to participate in their own nations' burgeoning science and technology enterprise.

This problem is especially acute in Texas. According to the nonprofit Intercultural Development Research Association, more than one in three Texas students who entered the state's high schools as freshman in 2002-2003 were lost from public school enrollment by the time they should have been seniors.

The cost of these dropouts isn't cheap, and the price is paid for by all of us. A report by the Friedman Foundation estimates that each of these young dropouts will cost state taxpayers $3,168 annually in increased Medicaid and prison expenses as well as lost taxes and revenue.

Members of racial and ethnic groups that are underrepresented in science and medicine are at special risk. The IDRA report found that 47 percent of Hispanic students and 40 percent of African-American students were dropouts. Since Hispanic-Americans make up 43 percent and African-Americans, 12 percent of the population of Texas for a combined total of 55 percent, these youngsters are an important part of the state's future. They must be brought into the mainstream.

The high-tech world in which they will live requires more education, particularly in science and mathematics. Even if they are not scientists, mathematicians or engineers, they must understand the language of these disciplines to be part of 21st century society.

What is the problem in the United States and in Texas? How can we reverse this trend?

For one thing, our children are unfamiliar with science and mathematics. They need excellent preparation in these subjects but right now, they're not getting enough exposure to them. In fact, some children are even studying science with teachers who do not have adequate preparation to teach the subject they are assigned.

The authors of "Rising Above the Gathering Storm" recommend that educating teachers new and old is an important start for closing this gap in science and mathematics education. Specifically, they charge that improving science and math education will require 10,000 new teachers to reach 10 million young minds, along with renewed and advanced educational opportunities for 250,000 teachers already in the classroom.

How can we encourage our youngsters to become scientists, mathematicians and engineers?

"Rising Above the Gathering Storm" calls for a fresh look at teaching methods that take advantage of new technology, especially the Internet, to share and utilize information, and generate excitement in science and math among students. This adoption of new technology must start with the youngest students and continue until they graduate from high school, and beyond.

The Academy of Medicine, Engineering and Science of Texas (TAMEST) — an organization of leading Texas scientists who have been elected to membership in one or more of the national academies) has been charged by its founder, Sen. Kay Bailey Hutchison, to address the state's educational deficiencies, and to lead debate and decision-making about how not only to keep our children in school, but also to encourage them to become literate in science and math in a world increasingly driven by technological progress.

We, as members of the TAMEST education committee, are convinced that despite the obvious challenges, our state can chart a new course that will extend the American Dream to the next generation of Texans, and ensure Texas' place as an innovative leader in the global economy.

Brinkley is vice president and dean of the Graduate School of Biomedical Sciences and Distinguished Service Professor of Cell and Molecular Biology at Baylor College of Medicine. Tapia is University Professor and Maxfield and Oshman Professor in Engineering in the Department of Computational and Applied Mathematics at Rice University.

============

To which I wrote a letter in response.

The recent op/ed from Dr.s Brinkley and Tapia was informative, and I support their conclusions wholeheartedly. However, as a recent graduate with a doctoral degree in biomedical science from a Texas institution, I am somewhat concerned over the value of said degree in Texas. Typically, after receiving a PhD, a young scientist will spend at least 5 years in postdoctoral training, looking for a professorship. Just a few decades ago, it was common to get such a position immediately or soon after graduation. This nation graduates many more scientists, particularly biomedical scientists, that it can support. That plus the flood of foreign scientists, attracted to the US because of our preeminent science, means the likelihood of a new graduate getting a good job any time soon is very small. I agree that the nation needs more math and science education, but the fact is that the nation has more scientists than we can support; there has been little increase in the number of new professorships, and substantial decrease in NIH funding during the Bush administration. This, and other factors (specifically the doubling of the NIH budget in the 90s) has lead to a glut of the market, which will not be soon corrected. Significantly increased research and educational funding, however, would alleviate this.

==================

I'll add here what i wouldn't dare send to the chronicle. The fact remains that there are plenty of people just like me looking for the same jobs that I am. This a hard time for our profession; not only are there fewer grants in which to support ourselves, there are few mechanisms in place to allow an easy transition between postdoc and PI. The NIH K01 award is one mechanism, but its highly sought after, as is almost every other type of award (ie, only the best 5% will make the cut). So, just to move ahead in this profession, you must be better than 9 out of 10 of your peers. That's a pretty harsh statistic.

But that's not the public's problem, that's my problem. The public's problem is that, increasing science and math education is good, but it must be done at all levels of the ladder, ie grade school, high school, college, etc. Imagine what would happen if we turn kids on to science, but don't have enough resources at a higher level; thus they are dropped from the pool. Then, say that everything works and we increase the number of scientists and engineers. Well, for engineers, it's probably fine, the nation can always use more engineers. But for science, not so much. We are at capacity, and will likely to remain so for quite a while, until there are mechanisms in place to promote science job creation (and I don't see that happening any time soon). Such mechanisms: increase the NIH budget (will take an end to the Iraq war, and a Democrat in the white house); national science directives akin to the manhatten project or the apollo project, etc. It's not enough to have more teachers; its a vicious cycle (teachers train kids to be teachers/professors). We have to have meaningful and needed alternatives to educators for people with science degrees.
How does the rest of the world deal with this? Simple, they allow their best scientists to come over here, (take our jobs), and either stay here, or go back home and do great science at home. I don't discourage this, but when this occurs on a huge scale, there is no place for American scientists. For example, I may be the only person on my floor with a PhD who is a native American (okay, there is one other person). And the floor has probably 50 PhDs, i guess (dozens, at least). That is shocking, folks; that at our best institution, the number of american scientists is measured in the single digits percentage-wise. How can this not be a problem? Yet, I can't get grants, I can't get fellowships, because I am still not in the top 10% of Americans. I accept that, but if the nation is to retain people like me, we need to increase these funding mechanisms. What other industry routinely denies advancement to 9 out of 10 of its workers? And our industry is either advance or get kicked out; i only can be a postdoc for 5 years. Granted, we reward the best and brightest, and that's great, but what about the rest? Some people should not be in science, but, regardless, we should, as a nation, encourage most of PhD graduates to remain in science. (Think if 9 of 10 MDs never are allowed to practice, or 9 of 10 engineers are never certified)

Funny, apparently IV administration of potassium phosphate is a good way to kill a person. Apparently whoever killed this patient didn't know that. The family of the deceased is seeking a corner's ruling of homicide; i think this is pursuant to claims of negligent homicide. I think they have a strong case, not being a lawyer of course. You'd think they have training of ways to kill patients that should be avoided, or something like that.

Dying is a strong contender.

Bonus link: How to get in touch with live humans at major call centers


Who says the NYT is useless?

In Zimbobwae, it's 12 cents ($.12). Here at MD Anderson, the cost of each mouse is estimated (somehow) at $5000. To make our special mice for my project i think it was $10,000 to $20,000 up front cost, plus all my labor, plus housing and materials. We ended up with 8 mice for the first generation. We have 2 or 3 generations to go. I guess the first useful mice (if it gets to that point) will end up costing us at least $5,000 each. Anyway, its the price of research. Mouse research is very expensive (not as bad as large mammal research, though). If we are able to create this mouse it will be a very useful tool; but i think it will take a year more to get to that point (sigh).

Story here; from Instapundit

Reports that France surrendered in response to this story, however, are false. Arguably, the french get beat up too much by american press. However, they have not distinguished themselves in the last 50 years, particularly in the second world war. I guess they didn't expect Hitler to be a genocidal maniac bent on global domination...

The Economist decries all medical research as bunk, since some don't know how to use statistics properly. This is unfortunate, but perhaps most relevant to the consumer since they hear wacky things like your zodiac sign is a predisposing factor in disease.

However, the vast majority of medical research is far more basic and involves very simple things; ie does this protein have a role in cancer, is this pathway activated in this disease, etc. Very basic stuff, and we don't use stats on that type of data (generally we look for order of magnitude differences, since our tests are not that accurate; when you deal with very small scales it's hard to be very precise.) Anyway, my point is to be sceptical of statistics, but support the research that saves lives and leads to cures.

HDR = High Dynamic Range. Tutorial here.

A roundup of HDR tutorials is here

There is a recent theory suggesting solar activity is responsible for earth global warming, as the same thing is happening to Mars. Its here.

hat tip: instapundit

I believe there is a strong correlation between fossil fuel use and increased surface mean temperature, suggesting that man is responsible for global warming. But in all the debate i hear, there are critical questions missing.

1) If fossil fuel use is responsible for global warming, then the solution becomes obvious (reduce use).

2) If the earth is warming for other reasons, we need to figure that out en route to finding a solution to warming.

Its not enough to assign blame, the key issue is what we will do about warming. We can either accept warming and the consequences, or find solutions to reduce warming. The former doesn't require any investigation as to the cause of warming. The later, in contrast, essentially requires a cause such that the process can be reversed.

Also known as the Infant Savings Plan Act, wherein each kid born in CA gets $500 in a saving account. If CA banks savings plans are like here, the interest rate is a mind-blowing 0.7% for a $500 deposit. That works out to be about $60 in savings when the kid hits 18. At that point the govt wants its initial $500 investment back. Who does all this benefit? The banks, who use the investment as collatoral for loans and what not. Loanees will also benefit, since the banks have more money to loan. Sure, this might encourage savings, but starting at a savings account is a ridiculous place to start. Ditto for money market. Why not invest it in a CD or something, or a savings bond. $500 in 30 years will be $1000. Whereas that money invested in the savings account will be $600. Anyway, nice idea, but let us worry about our kid's future instead of govt doing everything badly.