NIGMS Director Search - It looks rigged

I got an email message today with a listing of those who will be on a committee to search for a new Director of NIGMS. As many are painfully aware, Jeremy Berg is leaving NIH...

Here is the list of folks on the committee:

• Harold Varmus, Director, National Cancer Institute (co-chair)
• Story Landis, Director, National Institute of Neurological Disorders and Stroke (co-chair)
• Anthony Fauci, Director, National Institute of Allergy and Infectious Diseases
• Eric Green, Director, National Human Genome Research Institute
• Roderic Pettigrew, Director, National Institute of Biomedical Imaging and Bioengineering
• Carol Greider, Professor, Johns Hopkins University
• Stan Fields, Professor, University of Washington
• Steven McKnight, Professor, University of Texas Southwestern Medical Center
• Joan Steitz, Professor, Yale University

Here is the problem with that list, it includes a bunch of people who are deeply political and have a vested interest in ensuring that the NIGMS director is ineffective. I'm talking mosly about other center directors. One may make the argument that these centers interact the most with NIGMS and need to play well in the sandbox together.

However, more realistically, this is where Varmus and Fauci fight with one another to try and figure out who can get someone they personally want and to ensure the NIGMS director can't outfight them for a better budget for basic science.

I look at this committee and think to myself one thing: it's likely that the community will get a director that is not necessarily to their liking, but someone who is to the liking of Varmus, Fauci and a few others with an axe to grind.

Japanese Nuclear Plants: Good Engineering Wasn't Enough

Reactor failures, meltdowns, exposed fuel rods... It's happening in Japan.

First things first, this was not an accident. Any media outlet calling it one is proving they do not have anything resembling a mastering of english. The modern marvel of Japanese construction, urban planning, and building codes was designed to withstand a roughly 7.0 magnitude earthquake. The Tsunami walls protecting their nuclear facilities were 25 feet high.

Simply stated, the engineered the living daylights out of their facilities. The deeply sad part of what is happening over there is that mother nature always bats last in this game. A magnitude 8.9 earthquake - the biggest ever actually recorded on the Richter scale and not by historical analysis - was just too close to where people live.

What does this mean for our understanding of nuclear safety?

Well, we now know that something that was built for a 7.0 earthquake doesn't really hold up for 8.9. That's not news. It's sad, it's frightening; but it's not news.

As unlikely as it was in the minds of the brave workers who are still on site trying to cool reactor cores, keep fuel rods from being exposed to the atmosphere, and generally attempt to hold together a crumbling infrastructure ravaged by a home run by mother nature; these folks understand that they are extinguishing their lives for the larger good. Let us all hope that this can be contained in a swift manner and that exposure and risk to human life is as limited as possible.

What went right?

The Japanese people did everything correct they could have done. They were prepared. They do drills to prepare for Tsunamis, and are in an earthquake zone. It is in their culture to expect disasters. It's still terrible that so many have died and such destruction has befallen them. But, all told, they were more ready for it than almost any other society on earth.

Further, the building codes were such that many fewer structures were close to the water than any other comparable place on the coast of the United States or other countries. Their towers were built with much stricter building codes than almost anything we have in the United States or the European Union. The containment facilities and engineering of their nuclear plants far exceed US and EU standards.

What can the rest of us learn?

The people of Japan have incorporated into their culture how to be prepared and how to respond. We all could take a good dose of that to heart. The infrastructure was braced and ready for a large event. Unfortunately, that infrastructure was tested by something with record force.

We should look at our building codes and compare them to those of the Japanese. We can learn a lot from them about how to do good urban planning. HUD, take note.

Did the United States get swindled by Dennis Montgomery?

On a rather lazy Sunday morning, I pick up The New York Times and stick a sliced bagel in the toaster oven. My morning ritual has begun.

There, staring back at me on the front page is an article entitled "Hiding Details of a Dubious Deal, US Invokes National Security." I scan the rest of the headlines and read something else first. Namely, that article about how we won't be able to fund the government in another month. Granted, I knew in November that we will probably not pass a Federal budget for another two years, but somehow I'm still reading about this process as if something useful wil come of it.

After being disappointed by the budget article, as I often am, I returned to that first one. This is when I discovered there is something more interesting in the details here than the usual Military-Industrial-Complex story we hear time and again involving companies getting big contracts from the government in backdoor deals and shady people making oodles of money living off of fear of Americans. No, this one has an interesting technical bent to it.

Dennis Montgomery, formerly a biomedical technician, managed to get roughly $20 million in contracts to develop and deliver computer technology supposedly useful to the government for national security purposes. Now, Mr. Montgomery is also on trial in Las Vegas for over $1 million in bad checks to casinos. Let's not pretend that anything the government will do to him is anywhere near as bad at what the angry people in Vegas do to a guy bouncing that many bad checks. He'll get his just reward.

What I think is worth focusing on is how on earth the fanciful claims this guy made were ever acceptable to the government. Patenting algorithms and making claims that he could predict terrorist plots by analyzing the Arab media is absurd. The absurdity of this is at least two-fold.

First, it was using Al-Jazeera. Someone watching Al-Jazeera is not going to find hidden terrorist plots. If they find them there, they'll also likely find them on Fox News as well. I've been reading and watching Al-Jazeera for a while. It happens to have a lot of useful and interesting reporting in the Middle East that I can't find anywhere else. It also has been all over the Egyptian, Tunisian, Bahrain, etc. uprisings and has done an amazingly good job.

The second reason this is absurd is the underlying assumption; that there is a conspiracy of such a global scale as to be audacious enough and crafty enough to co-opt the media and broadcast coded signals via the media. The ideas and 'algorithms' are predicated on an utterly extreme conspiracy theory.

In a mix up of intergovernmental proportions, the CIA had rightly determined that the software was fake by 2003, but somehow this analysis never made it to the DoD Special Operations Command who had contracted Montgomery. In 2006, the FBI (as the NYT story relates) also had information indicating the software was bogus. All that said, in 2009, the Air Force still inked a $3 million dollar deal with them, despite warnings from a contract officer.

Much of the rest of the story is a sordid and complicated series of anecdotes and bad outcomes related to the technology. A particularly unsettling tale includes the grounding of planes coming from France and Britain. This led to the French initiating a study, where they concluded the technology was bogus.

As a scientist, this story and the farce technological claims troubles me. Where did things break down?

1. For starters, the communications between government agencies here was atrocious. The CIA, FBI, Dod (Special Ops), Air Force, and White House spent 7-9 years not being on the same page. Also, with something this technical, where was the White House Office of Science and Technology Policy? Right, under Bush and the absentee Science Advisor Marburger, anything went. What we can learn here is that some coordination for technologies that multiple agencies might want to use ought to be done centrally to collect both short-term and long-term information on the relative merits and concerns related to the technology. That was not done here.

2. Where were the science advisors and analysts? Why is a contracting officer, who has no technical background, presenting analysis on something well outside of his professional training? When the article in the NYT described an Air Force contracting officer saying he 'believed' in this and didn't care of he lost his job supporting it, one has to wonder. When it comes to something technical or scientific, beliefs have nothing to do with it, thinking is what matters.

3. The frame of all actors involved, including The New York Times. Nobody has questioned the underlying assumption I previously mentioned. To assume without questioning that a media organization could be so corrupted and brazen as to be entirely co-opted and part of a large conspiracy so as to justify the basic assumption for the fraudulent technology Mr. Montgomery sold for millions to the government is a disturbing sign of the frame of mind our government and military has.

One last point. I think this can and will happen again. There is next to nothing standing in the way of something this horrifically stupid from occurring. The White House Office of Science and Technology Policy doesn't track this (and neither does their back-end analytical support at the Institute for Defense Analyses). The CIA, DoD, Air Force, and other stakeholders including DHS still don't speak to one another and have no means for coordination. And lastly, if you look at the requests for proposals from these agencies, they still predicate themselves on the flawed assumptions and are requesting technologies that are not only useless, but people are likely to make things up and lie to the government claiming they can make them, especially since the non-scientists are the ones hearing the presentations and handing out the money without asking technical experts to advise them.

Anonymous- How the Media doesn't get it

What is Anonymous?

First, they are not your personal army.

What is Anonymous?

It's a loose association of individuals who collectively protest via cyberspace, broadly defined.

What is Anonymous?

Is often seen at the /b/ board. Go find it yourself, I won't link it here. Caution, it contains material not safe to look at while at work, and in many cases the material could be borderline illegal. In short, unsafe for human consumption.

What is Anonymous?

If it can be said to have a cause, it would be internet freedom for all. Even that is a stretch.

What Anonymous is NOT?

Again, not your personal army.

What Anonymous is NOT?

A terrorist organization, no less an organization at all.

What Anonymous is NOT?

A group of either all good, or all bad individuals. There are extremes of both.

What Anonymous is NOT?

It is not motivated by political or monetary gain.


What will Anonymous do?

Usually back up other fellow Anons. But, then again, don't count on it.

What will Anonymous do?

It can be a force for good. If you plan to do something bad, like blow up a school or shoot up a mall, they have been known to work with authorities to prevent that. Example 1: http://www.thelocal.se/17354/20090204/ Example 2: http://www.heraldsun.com.au/news/students-massacre-threat/story-e6frf7jo-1111115067368 Example 3: http://www.switched.com/2011/02/08/4chan-turns-ali-saad-in-school-massacre/?c

What will Anonymous do?

Point out that people attacking Anons may suddenly discover unsettling, possibly illegal, material on their personal computer.

Most Processed Foods - A Lunch Topic

Today, I went out to lunch with some friends from the laboratory where I got my PhD. Being biochemists, naturally our lunch topic meandered to that of the amount of synthetic stuff in various foods. This turned into trying to name some of the most processed or chemical-laden foods that are incredibly popular here in the United States.

This is the preliminary list of things we came up with:

Twinkies: Perhaps most well known for the discussions of their shelf life, jokingly estimated to be sometime after the apocalypse and capable of withstanding nuclear holocaust. Recently, a photographer did a nice set of images of the 37 ingredients in twinkies

http://www.fooducate.com/blog/2010/06/11/a-visual-of-twinkies-37-ingredients/

Ingredients: Enriched Bleached Wheat Flour [Flour, Reduced Iron, B Vitamins (Niacin, Thiamine Mononitrate (B1), Riboflavin (B2), Folic Acid)], Corn Syrup, Sugar, High Fructose Corn Syrup, Water, Partially Hydrogenated Vegetable and/or Animal Shortening (Soybean, Cottonseed and/or Canola Oil, Beef Fat), Whole Eggs, Dextrose. Contains 2% or Less of: Modified Corn Starch, Glucose, Leavenings (Sodium Acid Pyrophosphate, Baking Soda, Monocalcium Phosphate), Sweet Dairy Whey, Soy Protein Isolate, Calcium and Sodium Caseinate, Salt, Mono and Diglycerides, Polysorbate 60, Soy Lecithin, Soy Flour, Cornstarch, Cellulose Gum, Sodium Stearoyl Lactylate, Natural and Artificial Flavors, Sorbic Acid (to Retain Freshness), Yellow 5, Red 40.

Spam: This tasty meat product was originally invented in 1937 by Hormel Foods. It was reportedly going to be called 'spiced ham,' hence the name. It was a popular commodity purchased by the US military during WWII, some 20 thousands tons of it were given to our troops.

Ingredients: from this website... http://www.madehow.com/Volume-6/Spam.html

"The primary ingredient in Spam is chopped pork shoulder meat mixed with ham. About 90% of Spam is pork from a pig's shoulders. The remaining 10% (or so) comes from the pig's buttock and thigh, better known as ham. This ratio varies according to ham and pork prices. The U.S. Department of Agriculture does not permit any nonmeat fillers in lunchmeat, nor does it allow pig snouts, lips, or ears. The second ingredient is salt, added for flavor and for use as a preservative. Also, a small amount of water is used to bind all ingredients together. Sugar is also included for flavor. Finally, sodium nitrate is added to prevent botulism and acts as a preservative as well. It is the sodium nitrite that gives Spam its bright pink color—without it, Spam would discolor and become brown."

Starburst: Who doesn't like all the flavors in Starburst? I remember getting tons of them on halloween, and boy are the newer Starburst jelly beans really excellent. However, we tend to think that there's not much natural or unprocessed ingredients in a Starburst. In fact, we weren't really sure what, besides sugar, is in one.

Ingredients: According to Answers.com, this is the list. Corn syrup, sugar, hydrogenated palm kernel oil, fruit juice from concentrate (apple, strawberry, lemon, orange, cherry), citric acid, dextrin, gelatin, food starch-modified, natural and artificial flavors, ascorbic acid (vitamin c), coloring (red 40, yellow 5, yellow 6, blue 1).

Mountain Dew (and many other sodas): Our favorite for a soda to list was Mountain Dew. We were fairly certain that many sodas could substitute, but none are more popular for being full of chemicals than the Dew. Also, there was that whole myth about the properties of Yellow 5 that made this a winner for our list of processed foods.

Ingredients: Again, answers.com was useful here listing the ingredients as...

• Carbonated water, High fructose corn syrup (HFCS), Concentrated orange juice and other natural flavors, Citric acid, Sodium benzoate (preserves freshness), Caffeine (55.2 mg per 12 oz.), Sodium citrate, Gum arabic, Erythorbic acid (preserves freshness), Calcium disodium, EDTA (to protect flavor), Brominated vegetable oil, Yellow 5
• 
  

Cheese Whiz: Anytime something is called a "processed cheese food," rather than cheese, it must be processed heavily. Especially telling is that it comes in a can that sprays it. Lovely.

This gem of processed food is pretty old, originally released in 1953 by Kraft foods. What you'll notice in the ingredients list below is that cheese culture is surprising late in the list.

Ingredients: Whey, canola oil, milk protein concentrate, maltodextrin, sodium phosphate, contains less than 2% of whey protein concentrate, salt, lactic acid, sodium alginate, mustard flour, worchestershire sauce, (vinegar, molasses, corn syrup, water, salt, caramel color, garlic powder, sugar, spices, tamarind, natural flavor), sorbic acid as a preservative, milkfat, cheese

culture, oleoresin paprika (color), annatto (color), natural flavor, enzymes.

Movie Theater Popcorn butter: One of the most common ones is made by Paragon and is actually called 'Movie Theater Popcorn Butter Topping.' We've all seen this goo in what looks like a saline bag at the theatre. It's warmed and then oozed out of a very noisy squirting device all over your $5 bag of popcorn. We all were convinced that there had to be very little real butter in there.

Ingredients: Partially hydrogenated soybean oil, Beta carotene, Buttery flavoring, TBHQ, Polydimethylsiloxane.

Jello: Almost everyone has had Jello. It's gelatin, sure we know that. But, what else is in there that makes this oddly textured and vibrantly colored food stuff?

Ingredients: Yet again, answers.com was useful here...

• Gelatin, Maltodextrin, Adipic Acid / Fumaric Acid, Disodium Phosphate, Butylated Hydroxyanisole (BHA), Sugar, Artificial flavors,, Food Colors.

Sunny Delight: Yes, that wonderful fruit inspired drink. I like to think of it as a citrusy version of terpentine.

Ingredients: Water, High Fructose, Corn Syrup and 2% or Less of Each of the Following: Concentrated Juices (Orange, Tangerine, Apple, Lime, Grapefruit). Citric Acid, Ascorbic Acid (Vitamin C), Beta-Carotene, Thiamin Hydrochloride (Vitamin B1), Natural Flavors, Food Starch-Modified, Canola Oil, Cellulose Gum, Xanthan Gum, Sodium Hexametaphosphate, Sodium Benzoate To Protect Flavor, Yellow #5, Yellow #6

Quiet Super Bowl Victory - Chevy Volt!

I sat in front of the big screen TV at my parents house in Raleigh, NC watching the game. I reveled at the commercials, ranging from Doritos dust performing a resurrection to a Best Buy commercial asking the important question "What's a Bieber?" to which the response was "I don't know... kind of looks like a girl."

However, it was the automobiles that stole the commercials. The most moving of them was the Chrysler commercial with Eminem rolling through the streets narrating an American dream and touching the grit of our national souls, revealing the new American car slogan - Imported from Detroit. While this may have been the most moving commercial I saw, it was not backed up by the best product.

The product that won the super bowl is the Chevy Volt. If you aren't familiar with this modern marvel, then the Washington Post article reviewing it recently is worth a read. Especially, since the former director of the CIA makes an appearance in the review. ( http://www.washingtonpost.com/wp-dyn/content/article/2011/01/21/AR2011012105347.html )

The most impressive thing I've read about the Chevy Volt is how the petroleum engine in it works. It runs at a constant rate and produces electricity to run the motor. It's so elegant and smart. An engine running at a constant rate, producing the electricity for an electric engine will have less wear and tear from revving up and down. It can be tuned to maximally produce electrical output. Obviously, this is what they did, as the engine can get around 37mpg when it's running off of the gas-producing-electric-configuration.

Functionally, the consumer gets an electric car for the short daily commutes (40 mile range). Then, if it is the weekend and you're running a ton of errands or go for a road trip, you are riding around in a car that gets 37mpg. This is a win-win.

If I had the money to invest, I'd go Chevrolet for stock right now. Then again, it's only a matter of time before Toyota takes the Camry, or Honda takes the Accord and tunes it to get 60mpg with it's own gas-producing-electric-configuration.

Collins should go, not NCRR

Out of all the misguided things an NIH director could propose doing, getting rid of NCRR nears the top of the list, of, well, misguided things.

This may not be an affront that is political in nature, though maybe that is how it was devised. It is a direct affront on basic science. The simple truth is that NCRR and NIGMS are the last places in the NIH who do not have either a disease focus, or an area of the body focus. Put in a much stronger way, they are the only two centers that do not primarily fund what I would call 'contract science.'

What is contract science? It's when NIH gives grants for research that looks like a foregone conclusion. This model, widespread among all NIH centers, works against basic science. The extreme logic flaw of contract science is that it destroys the creativity and capability for scientists to make groundbreaking discoveries. Instead, it harnesses the university research enterprise and turns it into large collections of technicians doing boring experiments, and generating grant proposals tailored to the study sections, not tailored towards new discovery.

That Dr. Collins would put NCRR on the chopping block is no surprise. This is a man who helped create a center (NHGRI). The work and model of NHGRI is entirely contract. It was initially a large contract to sequence the human genome. A technological marvel for sure, but more of an engineering question than a basic science question (and don't get me wrong, a worthwhile and difficult engineering question at that). What this does is create a feeding frenzy amongst the other NIH center directors. Everyone will want a piece of what NCRR has.

What stinks is that the capabilities and the protection for the most basic infrastructure for basic scientists and the support system for all the other centers will be destroyed if NCRR goes. Instead, the big clouted political figures like Harold Varmus (former NIH director and currently the head of the extremely bloated NCI) will merely snatch up large swaths of NCRR and put them into use in their center, forsaking all others.

Ok, I've gone on enough with this. Here's some points for the discussion. Hopefully someone will raise these to Dr. Collins. However, I doubt he'll listen. He's clearly already made up his mind.

1. NCRR is one of two centers out of the thirty plus centers at NIH whose sole focus is on basic science. Taking that away is an affront on basic science

2. NCRR has an infrastructure component that supports not only all other centers at NIH, but funds necessary infrastructure for basic and applied sciences across the United States.

3. Dismantling NCRR and giving pieces of it to others will result in an increased inter-center bureaucracy.

4. Dismantling NCRR and giving pieces of it to others will result in budget hogging and a political battle over the remains of the center.

5. Nearly 1100 letters and comments, many of which oppose this move, are being flatly ignored by Collins. This includes misrepresenting the level of support for this move in the NY TImes article.

There is one simple question that needs to be asked of Dr. Collins, and I anxiously await an answer....

What factual evidence and arguments does Dr. Collins have that supports getting rid of NCRR?

That query needs to be answered, and to the satisfaction of the scientific community before any other movements or agreements to set this in motion occur.

I will tell you this, I'm calling my Congressman and telling him about this.

Additional Links to more on this story...

An excellent blog post about Collins from a friend of mine

http://networkedblogs.com/dovqZ

Interview with Science (the one where he looks like a jerk)

http://news.sciencemag.org/scienceinsider/2011/01/nihs-collins-explains-why-ncrr.html

Original article from Science on breaking up a center

http://news.sciencemag.org/scienceinsider/2011/01/nihs-plan-to-break-up-a-center.html

The New York Times article that serves as a PR campaign for Collins

http://www.nytimes.com/2011/01/23/health/policy/23drug.html?src=me