Bill Egnor

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On-Line Gamers Map HIV Protein, Opening the way for New Drugs

By: Bill Egnor Tuesday September 20, 2011 5:01 am
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Screen shot of Foldit - Courtesy of University of Washington

My wife calls me “ulterior motive man” because I have this firm belief that a single reason is rarely if ever justification for any action. Thus taking out the garbage should be done when you can button hole that neighbor kid about mowing your lawn for you.

Today the L.A. Times has a story that gives ma a reason to play an on-line game, Foldit. This game allows users to work on determining the shape of molecules and more importantly viruses. In a mere three weeks this game has done something that more than a decade of traditional bio-molecular science has failed to do, it has map a protein that the HIV virus uses to replicate itself and become AIDS.

The protein is called M-MPV. It is the part of the replication mechanism of a simian AIDS variant. It has been remarkably resistant to the normal mapping technique of Molecular Replacement (MR). MR is in the field of X-ray crystallography and it can get a little deep, but bear with me and I’ll try to break it down to understandable bites.

X-ray crystallography allows us to map the position of electrons in the material embedded in the crystal. When we know where the electrons are we know where the atoms are and can determine the bonds between them. This technique has been in use since the 1920’s and moved into the field of bio-chemistry in the 1950’s.

MR is the process of taking a known structure map and then comparing it to a new sample and looking for the differences then trying to determine what the differing molecules are. It has been very useful but it uses a ton of computing power and has some notable failures, like M-MPV.

 

Water Cooler – Can Republicans Be any more Clueless how they Look?

By: Bill Egnor Monday September 19, 2011 5:59 pm

So much of politics is about perception. The fact that working class people keep voting Republicans into office even when they candid about not wanting to do anything for those voters shows just how perception can trump reality.

Which is why is beyond mystifying why rich Republicans keep doing everything they can to show they are in no way shape or form like the working class. Today’s Jethro is Rep. John Fleming.

This fellow is a multimillionaire and he went on MSNBC this morning and claimed that after he pays for the expenses of his 500 person company, that all he is left with is a mere $400,000 a year and that is hardly enough to feed his family.

Now I know there are readers here who have not been employed for a very long time and have made the best of their meager money to keep body and soul together who would love to have 400K to play with, just once, not every year.

This yahoo was complaining that “job creators” should not be taxed more than they are now because it is unfair to them. This same Jethro makes more than 8 times the median household income. And that is before is 174,000 a year Congressional salary.

It is no secret that most of the members of the House and Senate are wealthy. There are far more than the normal distribution of millionaires in their ranks. And I don’t even begrudge them that, they have a job we have decided as a nation to pay well for, so it is not surprising. But it is beyond unseemly for these people to say they are in any way underpaid or over taxed.

And this is not the only time this year that Republicans have done this. Rep. Steve Southerland complained that his Congressional salary was inadequate for the “hours” he works. How many people who work the night shift or have to put in long hours would love to get the kind 174, 000 annual salary of a Congressman? I sure would.

This is the thing that voters really need to get their heads around. Anyone that would complain about this kind of money is not one of the working class. They have priorities that are not even close to the normal citizen. They earn more than three times the median salary and many more times than that of poverty level, which 16% of the nation is now below.

But there is something you can do. Here is Reps. Southerland and Fleming’s office numbers, why don’t you give them a call and tell them exactly how much you feel for them that they only make 300 to 800% of what the average family makes in a year.

Rep. John Fleming – (202) 225-2777
Rep. Steve Southerland – (202) 225-5235

Be sure to be polite but also be sure to let them know that they are insulting tens of millions of American citizens by bitching about their good fortune.

What is on your minds tonight Firedogs? The floor is yours

AFL-CIO Outlines a Debt Reduction Plan that Would Actually Work

By: Bill Egnor Monday September 19, 2011 4:56 am
AFL-CIO Headquarters

AFL-CIO Headquarters by samirluther

Here we are in mid-September with 10 weeks of the “Super-committee” drama ahead of us. We’ll be waiting to see the posturing, the demands, the breath holding, the capitulations and, most likely, the intransigence of the Republicans forcing this whole exercise into failure.

The really sad part is that there is a plan out there which would actually reduce the debt by more than the 1.2 trillion this committee is charged with. That plan was laid out by the AFL-CIO and it does not require cuts to Medicare, Social Security or Medicaid.

The Hill is reporting that the venerable union has sent around a plan that outlines where trillions in deficit reduction savings could be found. If the real goal, as both Republicans and Democrats claim, is to reduce our national debt and get our people working then these are the ideas that should be discussed before we talk about cutting Social Security (which does nothing to add to our debt) or military retirement benefits.

The proposals run the gamut and they are pretty much what you would expect from a Labor Union; establish the public option as way to control costs for health care by competition with a plan that does not put profit first. Allow Medicaid to negotiate drug costs with pharmaceutical companies (why the hell we have not done this yet is a national shame) and allow the re-importation of prescription drugs from other countries. The AFL-CIO estimates that these three measures would save a total of $299 billion over the next ten years. As they say, that ain’t hay.

But that is not all the plan suggests. There are tax revenue ideas that make sense and are perfectly compatible with economic growth. The plan includes a changing the tax code so that capital gains are taxed at a rate just like income, a millionaires surtax, and the big Kahuna a small financial transaction tax on all trades on our stock markets. These measures are estimated by the union to provide, $168 billion, $400 billion and a $1 trillion dollars respectively over the next decade. That is more than the “Super-committee” is looking for in one fell swoop!

Water Cooler – A Laugh, the Death Star and Penne Arribbiata

By: Bill Egnor Sunday September 18, 2011 4:53 pm

So, it is Sunday night and I find myself in need of some laughs. My sister pointed me to this, it is a lego animation of an Eddie Izzard comedy ruetine about the canteen on the Death Star.

In case your are wondering Penne Ala Arrabbiata is a spicy red sauce made of garlic, tomatoes and red peppers served over penne pasta.

Now that you’ve had a smile or two, what is on your minds tonight Firedogs? The floor is yours!

Food Sunday – Maple Oatmeal Bread

By: Bill Egnor Sunday September 18, 2011 4:37 am

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Happy Sunday Bread Heads!

In a lot of places it is starting to fell like fall. The mornings are crisp, the days are not as hot and what we crave to start the day begins to change. Oatmeal and things drenched in maple syrup come back into the menu. Which brings us to this week’s bread.

Maple Oatmeal Bread is a wonderful loaf. It has the lovely hardiness of an oatmeal bread with a light sweetness. It smells and tastes of maple syrup with out being overpowering. And it is one of the best pieces of toast you will ever have for breakfast!

The downside, such as it is, is that you must use real maple syrup for this recipe. Using Aunt Jemima syrup will just not produce the results. Real maple syrup is rather expensive, but if you look around you can find it for less than $10 for an 8.5 oz bottle. A lot of that will depend on where you live, of course. The closer you are the North East United State, where most of the maple syrup comes from, the less expensive it will tend to be.

Now that I’ve teased you enough, let’s make some bread!

Water Cooler – Good News, The Webb Space Telescope Survives, for Now

By: Bill Egnor Saturday September 17, 2011 5:56 pm
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Web Telescope Orbit, Pic Courtesy of NASA

 

So there is some good news for the Space Cadet corps this week. The James Webb Space Telescope (JWST) has been fully funded in the Senate. This is big news because the House had fully defunded the project.

A lot of the press about JWST says that it is the replacement for the Hubble Space Telescope, but that really does not tell the whole story. You see, JWST is different in just about every particular from the Hubble.

The JWST is designed to “see” in infrared, as well as visible light. This is important because it will be able to further back into time (by way of distance) and give us new data about the early universe that can not be achieved with the Hubble.

It also features a huge and adjustable main mirror, that will be 21 feet in diameter when it deploys. That that the mirror can launch in a folded state and then deploy to the full size is a major difference between the Hubble and JWST. Hubble’s mirror was designed to sit inside the telescope by the new observatory will have it open to space.

With this design and infrared capability there are unique requirements for this telescope. It must be shielded from the heat radiated by the Sun and Earth and must be in a position that will be dark most of the time. The only one place where these conditions exist are at the L-2 point on the far side of the Moon. That is what the graphic above is of.

L-2 stands for Lagrange point 2. This is named after the mathematician who calculated places of orbital stability between orbiting objects. The most commonly known Lagrange points at L-4 and L-5 which are 60 degrees ahead and behind the orbit of the Earth. L-2 on the other hand is a lot closer, it is on the other side of the Moon.

If this project goes ahead, we will park the JWST about 1.5 million kilometers, or about 932,000 miles away. In this spot it will be able to maintain its position with very little use of its rocket fuel. And it will be protected (mostly) from the light and heat of the Earth and the Sun.

It is a very good thing that this project is going forward. Beyond the science which this telescope will be able to perform the experience of placing and operating an observatory this far from the Earth will be a major step forward in our deep space capability. The knowledge gained will help in many forms of manned exploration.

It remains to be seen if the money will stay in the budget for this project. Like everything this new and complex, it has run over budget by quite a bit. Then again so did the Hubble. Can any of you imagine what the world would be like without the pictures we have been treated to over the life of that telescope.

So tonight we can be happy that the JWST is still in progress for its 2018 launch. If there is even a little foresight in Congress it will make that launch date and we will take another huge step forward to learning about and understanding our Universe.

What is on your minds tonight Firedogs? The floor is yours.

Water Cooler -Rep. Peter King is an Embarassment, On Both Sides of the Atlantic

By: Bill Egnor Wednesday September 14, 2011 6:01 pm
Rep. Peter King (R-NY) Spinning For Rudy

Rep. Peter King (R-NY) Spinning For Rudy by DoubleSpeak Media

I come from an Irish family. When I say that I mean I have aunts and uncles born in Ireland, not that we’ve been here in the United States since the first potato famine. For all of that I am not one to engage in tribalism. I am proud of my Irish heritage, but it does nothing to blind me to the actions of those who would engage in terrorism in the name of liberty.

I have no truck with the I.R.A and not amount of family history about how this great-grand-father or that great cousin was hanged by the British is going to get me to say otherwise. But that is not always the case for everyone, especially a politician of no conscience like Rep. Steve King of New York.

Today Rep. King got a bit of comeuppance as he testified before the British Parliament about the radicalization of immigrants. Rep. King has been holding hearings (witch hunts) about the possible radicalization of American Muslims. This is the worst kind of fear mongering but he is the Chair of the House Homeland Security Committee and he can hold hearing about whatever he likes.

As far as any can find this is the very first time that a sitting United States Representative has ever testified to the British Parliament. Rep. King got to add his particular brand of anti-immigrant, anti-Muslim hysteria to the mix in England, but it did not come without a cost for the Republican.

You see Peter King has been a major apologist for the I.R.A. for a very long time. Today he was put on the hot seat by the committee about his vocal and hypocritical support for Irish terrorists, while treating every Muslim like a terrorist.

He was asked by Labor MP David Winnik about some of his more over the top quotes. In particular he was asked if he stood by his 1985 statement saying:

If civilians are killed in an attack on a military installation, it is certainly regrettable, but I will not morally blame the I.R.A. for it.

King replied:

“I stand by it in the context of when it was said

He then went on to blather about injustice and how as an Irish American he felt that those injustices gave some kind of moral justification for the acts. What he did not do was ever condemn the acts of the I.R.A. nor express any regrets for the deaths.

Water Cooler – Proud to be a Human Tonight

By: Bill Egnor Tuesday September 13, 2011 6:01 pm

We who deal with politics for a living have a pretty severe occupational hazard, namely cynicism. It is far too easy to see the failings of our fellow man in our political dealings and assume that there is just not that much honest goodness in the people of our nation. Then you see a story like this one.

The video at this link (the videographer asked that the embed be disabled but go take a look) is of a group of random people coming to the aid of an accident victim. They got together and lifted a burning (yeah, burning) car off of this man, and it was caught on film.

They did something startlingly human: they ran toward trouble and then helped out. When there were not enough people to get the car up, more came rushing. No one was standing back and talking about personal responsibility, they were just there doing their best for another person.

The video ends with the man being dragged out, as one of his boots is starting to catch fire. He looks well and truly dead, but this is a happy story. The L.A. Times is reporting that the young man, Brandon Wright, is going to live, though he does have broken bones and a long recovery ahead of him.

This kind of thing is something I wish that more of the “you’re on your own” set in our nation would see and learn its lesson. Humans are not solitary creatures; we have only been successful by being a collective bunch.

A single human is often hungry, dirty, lonely, and frankly a good meal for any other apex predator out there. A lone human is a nice meal for a tiger, but a group of humans is a flat disaster.

This is one of my central beliefs and I have written about it before, but the myth of total self-reliance is one of the most pernicious memes every released on this nation. It is there for one purpose only, to divide us so that those of us without wealth and power don’t realize our collective strength and take back that power from those who hold it.

For all that we have been told we are supposed to be only self-interested, scenes like this one belie it at the instinctive level. These people went towards trouble, towards fire to help someone they did not know, someone who would not be paying them for their help or was even in a position to ask for it.

Instead they saw a person in trouble and risked themselves, because that is what humans do. Tonight, and maybe only for tonight, I am proud of what we are at the core and what we can be.

What is on your minds tonight Firedogs? The floor is yours!