Wu-Zhang, Schramm, Nabavi, Malinow, Newton (2012). Cellular Pharmacology of Protein Kinase Mzeta (PKMzeta) Contrasts with its In Vitro Profile. The Journal of Biological Chemistry.

At first I skimmed through and saw they used FRET and thought it would be easy one to argue against. Then I read it. ZIP doesn’t affect the phosphorylation rate of PKMzeta (on any substrate empirically shown to be phosphorylated by PKMz). They showed this effect using simple immunoblotting methods, not just FRET. I can’t believe this hasn’t been done already. Do you have any arguments against the findings?

Summary of Experiment Here

**UPDATE**
SPECIAL THANKS FOR THE CONSTRUCTIVE COMMENTARY FROM
Dr. Alexandra Newton (the article author) who’s research focuses on the functional mechanisms of phospholipase and kinase (PLC & PI3K) signaling pathways; and Dr. Todd Sacktor, who’s a long-standing pioneer of research on protein kinase C (PKC) isozymes in learning and memory.

The effects of perinatal choline supplementation on hippocampal cholinergic development in rats exposed to alcohol during the brain growth spurt

You don’t agree? Well think about this – We are probably the most intelligent living organism in the universe. Maybe that is a bold statement, but from the info we’ve gathered about life on other planets, we know that we are the most intelligent in our solar system. Astronomers have reported info on only several planets that might be earth-like; but they are in far away solar systems, such as the one orbiting a star in the constellation Libra. We know that much. The Earth is 1.00 AU from the Sun (~150 million kilometres). Good for life. Neptune on the other hand, is ~30 AU from the sun and with a mean temperature of 72 degrees above absolute zero, it’s a giant ball of ice. Not so good for life, but then again, Neptune is like 5 planets away from us. What about Venus and Mars, the next closest planets to Earth. Venus is 0.7 AU from the sun (not bad), and it is sometimes called Earth’s “sister planet” because they are similar in size, gravity, and bulk composition. Venus is also covered with opaque clouds of sulfuric acid, preventing visible light from reaching the surface. The water has most likely dissociated, and, because of the lack of a planetary magnetic field, the hydrogen has been swept into interplanetary space by solar wind. Shucks. At 1.6 AU, Mars is cool. Literally, the hottest Mars gets is -5 C which is probably the result of having almost no atmosphere and 10,000 km wide meteors hitting the surface.

So maybe those Earth-like planets in other solar systems are between 0.9-1.5 AU (we can’t tell precisely), which might result in that key temp for liquid water, a vital element for the spontaneous generation of life. This doesn’t come close to implying that there are creatures as intelligent as we are. There are still other obstacles; one being – the spontaneous generation of life. It took Earth about 4.53 billion years to produce humans. Also, evolution is not very good at yielding animals with “human-like intelligence.” I was reminded a few days ago that bacteria is as evolved as we are. Bacteria has also been able to reproduce and sustain itself longer than humans. The species with the next closest intelligence to humans lives right here on our own planet – Apes. These guys are locked into the alpha-male system of reproduction, meaning the biggest most baddass ape gets to spread the most seeds. Every once in a while there might be two equally baddass ape, and the smarter one may win, but that doesn’t happen very often, and it also doesn’t necessarily mean it will have ofspring any more intelligent than the other ape. So basically what I’m saying is, a human-level intelligence is an unusually high level under the laws of nature. We’re lucky.

That’s not all though. If there were creatures out there just a little further along in evolution, they would have contacted us by now. We obviously want to be contacted. We are obviously of no threat to them. Maybe they aren’t interested in us, because we’re too primitive, but still, we want to be contacted damnit!

But, that’s not my main point anyway. My point is, I am me; one of the few humans that have existed in the infinite history of time and space. Somehow a me was woven into my mental capacity, and every day I’ve woken up since I was a child, this me-ness has been the facilitator of my own actions. I am not a passive observer, and although I know more about the world, I am no different from the person I was a decade ago. Somehow, in all incalculable fate, I exist as a human in this universe, but if only for a fleeting moment.

I say you this — what the hell? If I was in charge of recruitment and acceptance for a graduate program, let’s say a neuroscience PhD program, I’d want the incoming students to have an exceptional understanding of …(get this)… neuroscience. Call me crazy. I would poll my faculty, and ask each of them to produce a list of 10 questions they’d want an incoming student to know. Then I would test potential students based on this pool of questions.

That’s just not how we roll here in the US. Esoteric vocabulary and impeccable grammar, that’s what separates grad students from undergraduates. Though, I’ve never quite understood the point of knowing a word that only 10 percent of aspiring graduate students know. Which means it is a word that nobody fuckin knows. But that’s how the GRE works. If everybody knew the word, then how can we tell if you’re smart!

Here’s the thing, devotees of grammatical studies have not been distinguished for any very remarkable felicities of expression. Correct English is the slang of prigs who wrote history and essays. A man would be a fool if he couldn’t produce and understand words spelled more than one way. It’s a uniquely human phenomenon, the capacity to deduce meaning from cmopeltyl scarbmeled wrods as if spelling is a footnote to an afterthought. But as long as you can looks smart by stealing quotes, substitute big words, and watch those split infinitives, you will do alright my friend. All others will die.

list of programming languages

First, no matter which language is chosen, master it! All programming languages share a set of core attributes. If you have a solid understanding these core features and how to use them — a mastery of the programming language — you’ll probably find a way to code 95% of your needs in any language. Also, I’ve gleaned that once you master one language, any other language is infinitely easier to understand. You’ll find that all languages have logical operators (true, false decision makers), loops (if-then-else), advanced mathematical and computational libraries, text manipulation (search and scrape, rearrange), arrays (data in the form of matrices), and methods (a way to call up prefabricated scripts, send a piece of data through the script to manipulate it in some way, and return a new value).

That said, there is still the task of choosing the language best suited for your needs. Even though most languages are cut from the same stone, it will prove to be incalculably beneficial to master a language that makes it easy to do the things you don’t want to do by hand. At the end of the day you don’t want to be a programmer, you want to be a scientist that knows how to program. Writing the code is just a means to deploy your innovative earth-shattering algorithm.

So the first thing I asked myself was “What do I want to be able to do with with the programming language?” These are the things I came up with off hand:

+ Write applications.
+ Write small scripts that can interact with other tools (matlab or excel).
+ The ability to scrape web content and turn the information into data.
+ The ability to launch programs from a web browser.
+ The ability to have other people interact with the programs from a web browser.
+ The ability to interact with a dynamic data set, and choose my database.
+ Developer tools for Unix/Linux which makes for easy development on Mac OS X
+ Open source programming language!

Each point above will be addressed in some fashion in the next few paragraphs.

When I first set out to find a language that could do all of those things, I was skeptical that one language suffice. However, with so many languages to choose from, I had a good chance to find one that meets most of my criteria. But there are so many! It was time to initiate operation — process of elimination.

I knew a good chunk of languages were developed prior to the internet explosion. And if they can’t run in a web browser, it’s out! A web-deployable language is important because I want the option (when relevant) to allow other people to utilize the final product without having to install the language environment onto their own personal computer. Furthermore, I don’t want to worry about cross-operating system compatibility (mac OSX darwin vs unix vs linux vs windows). Certainly none of the pre-compiled languages were going to cut it (C++, PASCAL, cLISP) because they are nearly impossible to deploy in a web environment. Thus, it would have to be a scripting language with a just in time (JIT) compiler. With this in mind, and a little research I narrowed it down to the 5 most popular scripting languages: PHP, Perl, Ruby, Java, and Python. All of these are full-blown programming languages, but also have a ways to be deployed by a web browser.

Java was the first language I considered. I took a few courses at SDSU in Java, so I was already somewhat familiar with the language. Java is user friendly, and is becoming the de facto language for teaching introductory computer programming courses. Sun (now owned by Oracle) relicensed most of its Java technologies under the GNU General Public License, so it’s free to use and deploy. Java applications are typically compiled to bytecode that can run on any Java Virtual Machine regardless of the users operating system. Java was built to give programmers the ability code some pretty gnarly dynamic web applications. Overall it’s a great language with lots of financial support for future development. For me, the only flaw with Java is that it doesn’t have strong integration with databases. This is a deal-breaker.

You may be asking, what is a database and why is it important? Essentially a database is exactly what it sounds like — a place to store data. This data can be the entire content of a webpage (like it is on Wikipedia), it could store user-unique content (like the Facebook and WordPress web blog databases), it could hold user preferences (like on Amazon or Pandora), or any other type of dataset you want to manage and manipulate. As a researcher, I have little use for a programming language that cannot interact with a large dataset. That is why Java is out of the race. I’ve discovered that Perl and Python are both extremely robust scripting languages in their own right, and meet most of my criteria listed above, the two languages with the best database integration seem to be PHP and Ruby.

PHP probably has the best database integration of the two. In fact, you would be hard pressed to find anyone developing PHP code not intended for use with a database (specifically mySQL or PostGreSQL databases). PHP is a general-purpose server-side scripting language designed for web development to produce dynamic web pages. As a little nugget for you, PHP was created by a developer to tally the number of visits or ‘hits’ to his webpage, and display this content as a little counter at the bottom of the page. (if you never seen a ‘hit counter’ you are too young to be reading this). The down side to PHP is that the language was originally implemented as an interpreter; and while several compilers have been developed to decouple the PHP language from the interpreter, its still very lacking in the stand-alone application development department. While PHP has great database integration, it’s not really intended for programming non-web content (thus it’s pros and cons are essentially the opposite of Perl and Python).

Ruby on Rails

So through the process of elimination, we have but one programming language left — Ruby. Does Ruby have what it takes to be my language of choice? Yes! Ruby is a fully supported, dynamic, reflective, general-purpose object-oriented programming language that combines syntax inspired by Perl and has JIT compilation abilities. Ruby is available on many operating systems such as Linux, Mac OS X, Microsoft Windows and most flavors of Unix. Ruby on Rails is specifically designed to let Ruby interact with multiple types of databases including SQLite and mySQL. And last but not least, I’ve read a lot of articles where the programmers say it is “fun to program in Ruby”! Needless to say, I’ll be mastering Ruby over the next year. I hope you do too!

On May 1, 2011, U.S. President Barack Obama authorized a raid on bin Laden’s suspected location in Abbottabad, Pakistan. The operation was successfully carried out by United States Navy SEALs, with intelligence support from the Central Intelligence Agency (CIA). During the 40-minute raid, bin Laden was fatally shot in the head. After intelligence searches of the compound were conducted, his body was taken into custody at which point genetic and facial recognition tests were performed. After positive identification, and within 24 hours of his death, bin Laden’s body was taken out to sea for burial.

Two questions. Why was he killed and not captured? Why was he immediately buried at sea?

A truly open market = might actually lead to a situation where consumers decide if they want to shop from a huge super corporation that outsources all their work to other countries or if they want to buy from companies that invest in their more localized economies with jobs and such. It seems almost impossible, at this point, to make the needed changes from the top down. the system needs to implode on itself and force people to reconcile with reality. that seems to be happening

The political-media side-show is manipulating people’s minds and distracting people from the seriously f$3*ed shit that is going on

Bradley Monk:
Hi there Jeff, I agree with you that in a smaller government there would be less federal employees to pay. For instance if we were to do away with the Federal Board of Education, which has 5000 employees that make a mean annual salary of 60k, we could add $300 million dollars to the fedral budget. That would make the budget go from $3.8 trillion dollars to $3.8003 trillion dollars, or simply $3.8 trillion dollars. Should we decided to just keep that tax money in our own pockets, every American would have an extra 95 cents a year! Personally I’ll pay 95 cents to have a Department of Education. You suggest that a smaller government would mean that corporations would have NO interest in influencing public policy. Riiiight. Sarcsim aside, we both want the same thing – for corporations and the extremely wealthy to be kept in check when trying to manipulate policy. If there is no Department of Education or Department of Pubic Health in Washington protecting those interests there would be a corporate shit storm, I assure you. I can think of a million situations of how this could be terrible (e.g. imagine if corporations like Pfizer no longer had to answer to the FDA). What needs to happen is less military spending. Currently around one fourth of that $3.8 trillion dollars ($900 billion) is to combat terrorism. Is that what it takes, really! Almost a trillion dollars to be safe from terrorism? Canada has a 20 billion dollar annual defense budget. Ask Canada how many terrorists attacks they’ve had lately. Bro, Canada spends 880 billion dollars less than us on Defense. They also don’t have a co-pay for a doctors visit, and don’t have to pay for private health insurance.

Jeff Smitt:
If i got to pick which branch or department to drop first, it would be military. I am with you all the way.

Prenatal Alcohol Choline Publication Monk

Prenatal alcohol exposure can alter physical and behavioral development, leading to a range of fetal alcohol spectrum disorders. Despite warning labels, pregnant women continue to drink alcohol, creating a need to identify effective interventions to reduce the severity of alcohol’s teratogenic effects. Choline is an essential nutrient that influences brain and behavioral development. Recent studies indicate that choline supplementation can reduce the teratogenic effects of developmental alcohol exposure. The present study examined whether choline supplementation during prenatal ethanol treatment could mitigate the adverse effects of ethanol on behavioral development.