DNA expression continues to get even more complex

Eight-legged evolution exploits editing
RNA tweaks adapt octopuses to water temperature
http://www.sciencenews.org/view/generic/id/337413/title/Eight-legged_evolution_exploits_editing

This is quite interesting because, as the author states:

Researchers used to think that dialing down or amping up the activity of genes through DNA mutation was evolution’s main trick for fine-tuning the body’s machinery. But there’s a downside: Change the DNA and you can’t easily go back.

Already there is the area of research termed ‘epigenetics‘ that looks specifically at how non-mutation events (primarily being DNA methylation and in principle being reversible) can have dramatic influence (sometimes starting even in the womb!) on the actual patterns of gene expression of an organism, often for life (this helps explain the differences between identical twins, doanchano).

It is sometimes quite amazing to me how much our knowledge of genes and gene expression has evolved since I studied it in school 20-ish years ago. I remember interviewing at the National Center for Biotechnology Information (NCBI, something I thought would be the perfect job, sadly that was far from the case, though I did wind up putting in 7 years there) and being staggered to learn that the one-gene-per-stretch-of-DNA paradigm I had learned was totally obsolete as genes could go both directions on the DNA strand, they could overlap and they could result in different combinations of introns and exons. All barely conceivable when I studied it (this activity was only known (when I went to school) in mitochondria DNA and a few species of highly evolved microbes (like the one behind tuberculosis)).

This what I love so much about science! Every time you find out you have been wrong about something your understanding has to evolve (sometimes dramatically) to cope with the new information (unlike, say, the GOP where they simply ignore any new information if it is inconvenient to their chosen world view).

Chinese scientists make rain

Thanks to Erik for pointing this out…

Chinese Government Plans to Cause Ten Percent More Rain By 2015
http://www.popsci.com/science/article/2011-12/china-aims-modify-weather-producing-more-rain-produce-more-crops

Actually, if they are successful in increasing rain by 10% for a measly $157 million, they might be on to something. I am quite sure that during Texas’ drought over the summer a wee bit more rain would have made a huge difference (of course, the idea of using science to try to increase rain goes against the governor and his ‘pray for rain’ crusade (how did that go anyway?)). Also, I suspect that with some careful thought, seeding rain could help diffuse or minimize storms and spreading the rain out over a longer time period tends to be better for crops (and erosion control) as well.

It is very hard to do controlled studies of these sorts and as such it is hard to get main stream science to take the work seriously, but there is an industry devoted to seeding rain clouds and I find it hard to believe there would be an industry at all if there were no positive effect at all.

The real agenda, it seems

The GOP’s bizarre war on sex
Polls show we’re pro-choice, pro-gay marriage and ever kinkier. So why are the Republican candidates such prudes?
http://www.salon.com/2012/01/07/its_the_sex_stupid/singleton/

Yet another reason (as if it were needed) why I can no longer fit in with the GOP. There are already way too many damn humans, the idea of doing anything to increase our numbers is nonsensical at best.

As the article alludes, it seems to me that much of this boils down to the strong urge to repress women as nothing appears to be more liberating to women than being able to make their own decisions about reproduction (women having to invest such huge resources in comparison to men). So, to me, this ultraconservative right-wing blather about every sperm is sacred is a smoke screen for their real goal: minimize women and their impact on society. As long as women are barefoot and pregnant then they are serving their only ‘real’ purpose and while it might be charming to have an intellectual conversation with one of ‘them’, education beyond what their own mothers taught them about baby rearing is totally wasted. Seen in this light, the anti- contraceptive blather coming out of Santorum’s mouth makes a lot more sense. I bet if the media (as if!) were to play up this angle that Santorum’s poll numbers would crater overnight and he would never be seen or heard of again.

The solution is clear, the implementation is not

The political power of being naïve
Cynicism makes us complacent. 2011’s successful protests show how hope can change the system
http://www.salon.com/2012/01/05/the_political_power_of_being_naive/singleton/

The core of the problem is money. Remove the money and turning things around gets orders of magnitude easier (but not ‘easy’!). As long as the money remains, change is impossible. The author blithely talks about a Constitutional amendment, but I see that as virtually impossible also. I find it very hard to avoid cynicism, I am not sure there is a viable path forward. I would like there to be, but I am of the opinion that our oligarchy is firmly entrenched and the best we could possibly hope for would be for the oligarchy to decide to increase the illusion that the 99% matter (the worst case, in my mind, is the 99% continues in it’s anti-science, anti-elite backlash like Mao fermented in China where people like me are driven out of the country (believe me, I am thinking about it on a weekly basis already!)).

Wimpy processors and Compute RAM

Prof Aims to Rebuild Google With Stuff In Desk Drawer
http://www.wired.com/wiredenterprise/2012/01/wimpy_nodes/

I have studied process optimization for many years, almost exclusively as a hobby because there is so little need for that skill that I can’t find any jobs (at least jobs that pay well; why is it that interesting work pays least and boring work pays most?). I have felt for years that the blazing fast CPUs that are churned out today are counter productive except in some narrow situations (highly tuned optimum programs are still in a wait state some 70% of the time; routine programs might only utilize 10% of the cycles available) and it would be way better to have the CPU slowed down to the point where it can access RAM at the same speed as registers. Not only would that lead to vastly simpler chips (no need for all these levels of cache everywhere and why bother with pipe-lining or out-of-order instruction execution), but probably faster throughput for most routine programs. The logical extension of that is ‘compute RAM’ where vastly simpler CPUs are interspersed within in RAM modules so there is no latency in access. To my knowledge (sadly several years out of date), no one has tried to commercialize compute-RAM, but it would be an interesting thing to study (if, of course, I could get paid well to study it, instead of being paid buckets to do crap work). I actually started down that path of reading because for a couple of years at the turn of the millennium I was marketing a business plan to produce molecular scale computing devices (I was going to start with the equivalent of a solid-state disk). I was really interested in the idea of building a molecular scale computer and due to the complexity was studying minimal instruction sets, the RISC paradigm, etc. I felt at the time (and still feel, though as I say, my knowledge has got stale) that having reduced latency between the CPU entity and the storage (RAM) entity would be the key to vastly accelerated throughput. I remember many enjoyable hours learning and thinking about CPU design and how it could be manifest in the world of biological molecules. Sadly (as is so common in my life), no one was interested in backing my plan (I stupidly chose the height of the dot.com hysteria to market it), so I have moved on to research and prepare other proposals to be ignored by investors.

If I were taught this way I would be a ‘genius’

Physicists Seek To Lose The Lecture As Teaching Tool
http://www.npr.org/2012/01/01/144550920/physicists-seek-to-lose-the-lecture-as-teaching-tool

I was thinking to myself as I read this article that if I had exams that tested comprehension of the concepts (as opposed to rote memorization of formulas and facts) I would have got straight A’s in all my classes and would probably have had a dramatically different life. Instead of always being a mediocre (at best) student always struggling to pass exams (one example I like to give: for a physical chemistry exam we needed to memorize about 14 formulas. I copied them over and over again as well as studying them intently, then when I got the exam, I put my sheet away and copied from memory onto the back of the exam all the formulas. I got about half of the formulas wrong, thus failed the test.) I would have been one of the stellar students and top in my class at high school. That, naturally, would have totally changed my educational trajectory and given my native interest in research I probably would have easily gone on to get a couple of PhDs and been taken seriously when I suggested lines of novel research, some of which very likely (at least given the success other people who have had the resources to act on the exact same ideas I have had) would have been successful. Man it sucks to be me!

I really like this quote regarding lectures… Why the heck should anyone need to actually attend class to get the lecture and why shouldn’t we all be watching the same lecture on video? No rational person can possibly believe that each and every lecturer in the country is equally superior and capable!

“With modern technology, if all there is is lectures, we don’t need faculty to do it,” Redish says. “Get ’em to do it once, put it on the Web, and fire the faculty.”

Some faculty are threatened by this, but Mazur says they don’t have to be. Instead, they need to realize that their role has changed.

“It used to be just be the ‘sage on the stage,’ the source of knowledge and information,” he says. “We now know that it’s not good enough to have a source of information.”

Mazur sees himself now as the “guide on the side” – a kind of coach, working to help students understand all the knowledge and information that they have at their fingertips. Mazur says this new role is a more important one.

This comes way too late to help me, but given the massive inertia in our educational industrial complex I suspect it is also too late to help my boy, since he is already in second grade.

This is a serious issue that no one takes seriously

Patients at risk after scientists withhold test results from clinical trials of new medicines
http://www.dailymail.co.uk/health/article-2082116/Patients-risk-scientists-withhold-test-results-clinical-trials-new-medicines.html?ito=feeds-newsxml

There is already a huge bias in science where (almost) only positive results are ever reported, but, at least in most cases, there are not dollars riding on the publication either way. However, in the world of clinical research, there is almost always huge dollars riding on the outcome of research and negative trials (i.e., those that failed to match the expectations of the authors) rarely, if ever, make it to peer reviewed journals, thus the information is lost forever. Since it is well know that data is subject to statistical manipulation, by hiding negative results it is quite trivial to amplify random results into statistical significance or, using the same techniques, minimize side effects. The reason why everyone should care is that this results in unsafe and/or unproven drugs getting approval for sale to an already credulous and ignorant population (and I am not just talking about doctors!). I believe (and I thought NIH was putting this policy into place, but perhaps there are too many loop holes) that all clinical results should be entered into a common, _public_, database regardless of the outcome of the trials. That this isn’t the case, to my mind, calls for an examination searching for a government conspiracy at the highest levels (and I am not being cute here, I am serious). Since our country is run by an oligarchy and since pharmaceutical companies are clearly a large part of that ruling coalition, it seems clear that the system is being manipulated to produce the illusion that the FDA is riding oversight on the testing of new drugs. The reality is far from that, however, and positive clinical trials are routinely ‘purchased’ and used as justification for a marketing campaign. And if that doesn’t work, then the companies ‘leak’ the positive results (with, of course, all negative results or side effects removed) to the target clinical population and then complain that the FDA refuses to allow them to market this supposed life saving drug to those in need.

Man does our system stink!

I’m jealous

Software Scientist
With a little data, Eureqa generates fundamental laws of nature
http://www.sciencenews.org/view/feature/id/337207/title/Software_Scientist

Hopefully this content will remain available.

This is something I would really have liked to be part of (see Eureqa). Conceptually it is the same as the core of my idea for a genetic programming / machine learning idea for video compression / meta data extraction or stock market prediction algorithms, which means that yet again my dilly dallying (I initially thought of this algorithm idea over a decade ago) has me scooped on yet another great idea. As I get older without having done anything I had originally planned (I was supposed to be running my giga corporation from my orbital headquarters by this point in my life) I find myself increasingly depressed when I see other people commercialize ideas I had long ago. Too bad, so sad; woe is me.

Are humans incapable of learning from their mistakes?

Bt: The lesson not learned
Science News reported 60-plus years ago how indiscriminate use of DDT ruined that chemical’s value: Now history seems to be repeating itself with Bt
http://www.sciencenews.org/view/generic/id/337240/title/Bt_The_lesson_not_learned

I am not sure if this content remains free, so my apologies if you can’t access it.

As could be (was) predicted, resistance is springing up against the ‘miracle’ Bt genetically engineered biological pesticide. Like antibiotics (and the DDT mentioned in the article), human’s profligate use of the product has begun to render it useless. It seems ironic to me, though, that because of the way patents are granted, the holders of the intellectual rights are incentivised against trying to restrict any usage of the product as once it goes off patent their profits will crater, so they want to sell as much as they can before the patent expires.

Equal opportunity is the key

What Americans Keep Ignoring About Finland’s School Success
The Scandinavian country is an education superpower because it values equality more than excellence.
http://www.theatlantic.com/national/archive/2011/12/what-americans-keep-ignoring-about-finlands-school-success/250564/

A very interesting article on education. It seems the Fins (as I believe the Finnish people are called; if it is rude, please pardon me) decided that what was missing was equal opportunity to education to everyone AND that teaching should be a sought-after profession that is highly competitive and challenging to enter. As I have mentioned here before, in our country there is a very wide disparity between opportunity based on location and if you are in a poor part of the country then your educational opportunities (for the most part) suck and there is little to nothing you can do about it.

My primary objection to the common European format where children have to test into each area of academics is that some people (I consider myself an excellent example of this) are slow to get started (though how much of that was because I was in a crappy educational system is hard to sort out) and in the European method that would mean I would be relegated to menial, blue-collar type of work because I would never have been allowed into higher education. It is not clear from the article, but perhaps that is not the case for the Fins, perhaps they are allowed to take their education at the rate at which it suits them. Anyway, given the enduring unsuccess of our approach and the prospects of solidifying the educational industrial complex I think a breath of fresh air might be warranted.