A Day in the Life of...

Leroy Hood wants to revolutionize medicine though genetic screening. I have three problems with this.

1. Leory Hood is the cocreator of automated DNA sequencing. I'm not sure if Caltech pays him part of the royalties or not, but I'm guessing the answer is yes. So there's a conflict of interest.

2. There is a phenomenon called genetic buffering whereby one gene's product masks genetic variations from other mutant genes. An example of this is HSP90, a heat shock protein, that helps other proteins fold properly.

"Rutherford and Lindquist conclude that under normal conditions, HSP90 compensates for the small genetic glitches that would otherwise alter the stability and function of the fly's proteins."

Science 4 December 1998:
Vol. 282. no. 5395, p. 1796
DOI: 10.1126/science.282.5395.1796a

Genetic buffering has been seen in plants as well.

Science 28 June 2002:
Vol. 296. no. 5577, pp. 2348 - 2349
DOI: 10.1126/science.1073846

3. Environmental buffering affects phenotype as well. It has been shown that vitamins can promote correct protein folding in mutant proteins. The vitamin acts as a scaffold to help the protein fold properly. I wrote about this earlier. It turns out that drinking alcohol increases the amount of aldehyde dehydrogenase 2 in heart tissue and this enzyme prevents cellular damage and death during a heart attack. The researchers already have found a drug to produce the same protective effect as alcohol. So, it's not just the polyphenols in wine and beer that protect drinkers from heart attacks, but the production of aldehye dehydrogenase 2 as the cells metabolize the ethanol.

Science 12 September 2008:
Vol. 321. no. 5895, pp. 1493 - 1495
DOI: 10.1126/science.1158554

Genetic screening is a tool. It is also in its infancy and requires context. If done properly it will save lives and resources. If done poorly, it will waste resources and lead doctors down the wrong path resulting in lost time and effort. There is also the issue of genetic discrimination. If you have a mutant allele known to increase the risk of having a particular cancer, an insurance company might label that as a pre-existing condition. I'm not up on the law. Congress might have addressed that issue by now, but it is still a concern.

Labels: genetic screening genetic buffering epigenetics

Dallas PD helicopter circling my apartment at 4:46 AM this morning.




















Same @4:47AM














All you can see is the red navigation beacon and the klieg light.

Labels: Police helicopter

Bashful (Sept.14,2008)

Labels: one of a pair

Fingers will be pointed for some time and debates will rage about the causes of this "crisis". If one looks deeper though, the cause is obvious. The cause is the Cold War. America didn't win the Cold War, the Russians just went broke before we did. This was what my high school mentor, Jerry Workman, told me over ten years ago. He was quite prescient. Americans were living on borrowed time and credit. Well, there is no credit any more and we went broke. Both the United States of America and the U.S.S.R. drove themselves into economic ruin fighting the Cold War. Neither unfettered capitalism or communism are the answer. Both nations were the victims of their own ideologies. The question is now, " Will America suffer the same fate as Russia?" Will an oligarchy form and take over the government and economy? Clearly, capitalism on a local or regional scale is a good and resilent system. On a national or global scale, "too big to fail" is a recipe for disaster be it a capitalist or communist institution.

Labels: Systemic causes

Obviously, "Free" Market is an oxymoron. The only free market is war and war is win at all costs, no holds barred, winner take all contests. Markets regulating themselves is almost as disingenuous a phrase, since in retrospect, they didn't. American automakers just received a bailout from Washington while their Japanese counterparts who took the risk, retooled, and are now producing fuel efficient cars didn't get anything. In other words, Congress just rewarded American businessmen for their failures and socialized the losses.(If they don't retool to produce carbon fiber cars, then the money will be wasted. We'll just be getting ripped off. Would you buy a $40,000 Chevy Volt when Honda and Toyota sell better cars for less? Expect the Japanese to be angry as hell.) Expect Wall Street to receive a gift in exchange for nothing if we don't keep Congress accountable for their legislation. The lenders get bailed out and the borrowers get - nothing. We've been warned.

We need to correct the systems in place so that the incentives are in line with the behavior we desire. This is why we have rules and laws, though the way many of our laws are written, there's no incentive to do the "right" thing - right being the greater good.

Labels: rewarding failure

When worlds really do end, and not, in the metaphorical sense. A bigger picture and press release here.

Labels: planetary catastrophes

Ben and Hank are saying that we taxpayers have to buy Wall Street's trash at their asking prices to give Wall Street firms incentives to participate and not dither deciding whether or not to join the Treasury bailout plan. Strange, I thought going to the taxpayers for a bailout was supposed to be the last resort because you couldn't find any one else to deal with. Not only should taxpayers get equity in those companies availing themselves of our money, but their executives should be compensated in the same toxic paper they are selling to us instead of stock options. At least then we'll get a fair price for those assets rather than an inflated price. The plan as it stands is just another fleecing of taxpayers. It will be the last gift of this administration to its friends and benefactors before it leaves office. I don't know whether the white light Congressmen and Senators are seeing is a near death experience of their political careers being over, or the white light of clarity that something is seriously wrong, and panic from the Fed and the Treasury isn't helping the situation. We are finally seeing Congress acting as the legislative body with the purse strings, and the authority that goes with that purse, as the Framers of the Constitution intended.

It's sad that it had to come to this to get them to do their jobs.

Labels: About time

Does any one find it ironic that the Bush Administration and Wall Street finished what Bin Laden started? Or that the Fed and Treasury are just throwing money at problems without explaining their actions. It looks as if they haven't a clue as to whether their actions will have the desired effects, but like mad men, they keep doing what they know which is throw money at the problem until it goes away, or gets better, rather than step back and rethink their strategy. And, we are supposed to trust them and their opaque dealings which is how this whole financial mess started - too much trust and not enough transparency. Now there's no trust and little transparency, and credit and lending is frozen.

Some thoughtful alternatives instead of the "Cash for Trash" Treasury Plan are here and here.

Labels: Irony

MOAB used to mean "Mother of All Bombs". Now we have Washington debating on the "Mother of All Bailouts". How do the taxpayers know MOAB will not be the former instead of the latter? How does any one know? Calculated Risk basically gave the analogy of a drunk slot machine gambler playing the slots as an illustration of how the Treasury will spend the $700 billion dollars Congress will give it. (That money would buy 3.5 million $200,000 homes, but it's likely that the banks are overcommitted for much, much more than $700 billion, because of speculation in the housing market and other shady deals.) Can the US and the World afford the Republican Party and their policies (or the lack of them) after this "drunken" binge? Will the Democrats do any better, or will the job descriptions of politicians have to be rewritten along with those of the financial wizards who made this mess? I would hope that lobbyists aren't welcome on Capitol Hill this weekend, but that's likely in vain. We will likely see the Middle Class save the Wealthy from economic loss, but who will save the Middle Class (and their children) from foreclosure, unemployment, and higher taxes? If taxes double, then the tax rates on the extremely Wealthy (greater than $5 million/year income) should double or triple, capital gains be damned. As a percentage of their overall income, it's likely to be less than what the Middle Class pays. We will likely have to leave Iraq and move some of those troops to Afghanistan while disbanding other units to save money, as well as kill some expensive weapons systems. If the government goes broke, then we all go broke because our money will be worthless pieces of paper, and all of this nonsense was for naught. Maybe then we'll find out people's true worth and wealth, not just their wealth by how many pieces of paper they own.

Does any one feel like our leaders are just throwing money at a problem and hoping that it fixes it without exploring other options? They certainly don't seem to know if this idea will actually work. All of these measures thus far will likely cost the taxpayer $2-3 trillion dollars after all is said and done. It seems the financial industry is stuck in what scientists and engineers call a negative feedback loop or futile loop in biochemical terms (see Krugman). As Reich and Krugman point out, there needs to be an upside to this deal for the taxpayer, or it's not only a bailout, but a gift from the taxpayer to any one who applies and the Treasury deems eligible including foreign banks.

Labels: Mother of All Bailouts

The F-117s are not to be retired, but likely scrapped. As the article points out, the signs were there if one looked for them. Why don't we trade them for the worthless pieces of paper Wall Street wants to sell to the government? People would actually BUY the F-117s even if they are too expensive for the government to maintain. (Isn't Wall Street too expensive for the government to maintain as is as well?) Seems like a win-win to me.

Labels: Demise of the F-117

Tropical Storm Ike as it passed DFW on September 13, 2008.
























It rained quite a bit, but there was surprisingly very little wind. Chicago caught a lot of rain from Ike as well that they didn't need. Stormpulse is a slick weather site. Ten points for cool.

Labels: Hurricane Ivan

The Parable of the Rich Fool
13Someone in the crowd said to him, "Teacher, tell my brother to divide the inheritance with me."

14Jesus replied, "Man, who appointed me a judge or an arbiter between you?" 15Then he said to them, "Watch out! Be on your guard against all kinds of greed; a man's life does not consist in the abundance of his possessions."

16And he told them this parable: "The ground of a certain rich man produced a good crop. 17He thought to himself, 'What shall I do? I have no place to store my crops.'

18"Then he said, 'This is what I'll do. I will tear down my barns and build bigger ones, and there I will store all my grain and my goods. 19And I'll say to myself, "You have plenty of good things laid up for many years. Take life easy; eat, drink and be merry." '

20"But God said to him, 'You fool! This very night your life will be demanded from you. Then who will get what you have prepared for yourself?'

21"This is how it will be with anyone who stores up things for himself but is not rich toward God."
Do Not Worry
22Then Jesus said to his disciples: "Therefore I tell you, do not worry about your life, what you will eat; or about your body, what you will wear. 23Life is more than food, and the body more than clothes. 24Consider the ravens: They do not sow or reap, they have no storeroom or barn; yet God feeds them. And how much more valuable you are than birds! 25Who of you by worrying can add a single hour to his life[b]? 26Since you cannot do this very little thing, why do you worry about the rest?

27"Consider how the lilies grow. They do not labor or spin. Yet I tell you, not even Solomon in all his splendor was dressed like one of these. 28If that is how God clothes the grass of the field, which is here today, and tomorrow is thrown into the fire, how much more will he clothe you, O you of little faith! 29And do not set your heart on what you will eat or drink; do not worry about it. 30For the pagan world runs after all such things, and your Father knows that you need them. 31But seek his kingdom, and these things will be given to you as well.

32"Do not be afraid, little flock, for your Father has been pleased to give you the kingdom. 33Sell your possessions and give to the poor. Provide purses for yourselves that will not wear out, a treasure in heaven that will not be exhausted, where no thief comes near and no moth destroys. 34For where your treasure is, there your heart will be also.

Labels: The Bible

The destruction of a nation of The People has likely begun. The Bush Administration has begun the Bailout of all Bailouts, as Robert Reich has commented on. What is surprising is the lack of deliberation or even debate. People seem to want the government to "do something NOW". This is a bad idea to give into the panic. This crisis started back in the late 1990s when Clinton and Congress repealed the Glass-Steagall Act. The four speculative bubbles in the last 30 years, 1987 Savings and Loan Crisis, the 1990-92 Biotech Bubble, the Dot.com bubble of 1992-2001, and now the Housing Bubble of 2003-2008 are due to the gaming of the financial system by S&Ls, banks and wealthy investors, a lack of investor research, and a complete lack of regulatory oversight by the Fed, the SEC, and other federal and state agencies. It took over five years to destroy one hundred year old institutions. The survivors are looking to the government to bail them out of this mess. The "government" needs to think this through and see if it's such a good idea for taxpayers to assume all of this risk. That debt is going nowhere fast and why should the taxpayer pay for all of those bad pieces of paper? In the end, we are likely to be throwing all of that money away any way and those firms will fail regardless due to lack of investor trust and confidence, so why go down this path?

There may be no "good" solution here. We may have to choose the least painful remedy. I was looking at my retirement funds. All of them have lost 13-15% this year. The ten year yield will likely be around 2-3%, which means that I'll have lost money when inflation has been taken into account. I'd have done better to put the money in a CD or money market account the last ten years rather than mutual funds indexed to the stock market. But if I go broke, the government will not buy my bad debt or bail me out, so why bail out Wall Street? I think Reich has an interesting idea that should be pursued. Stiglitz has other ideas, but both come down on more regulation. Almost all economists are beginning to agree that the investment banking community will have to be regulated and their dealings made more transparent. Too little, too late, I'd say. We'll be repairing the last disaster, waiting for the next one to strike as time passes and people forget the bad days and believe them past, so they weaken regulations and oversight leading to the next speculative bubble and financial market failure. It's also quite possible that we will no longer be a superpower after this mess is over. The geopolitical ramifications of that are yet to be known or felt.

Labels: financial meltdown Stock Market Crash

I ran out and bought a copy of SPORE last Sunday. After work, I installed it and played it a bit. It was a general disappointment. Last night, their commercials started saying something along the lines of "Buy SPORE, create your own universe!"...etc. I was hoping for a game along the lines of real evolution. Something like design your creature and then let evolution take its course, but the game never works along those lines. The creator not only creates the creature, but adds traits the creator picks and chooses that the creature earns to it. The creator/ gamer is doing all of the work. There is no fitness test per say. One's creature can't live and die on its merits. The evolution is Lamarckian at best, not Darwinian. Animals don't obtain traits via evolution from structures and functions they already have, but the new traits are chosen from a parts list. There's a design bias as well. The creature has to be an animal, and it can't switch it's diet as far as I can tell. So, you can't start out as a herbivore and become an omnivore like humans did. You also can't have sentient plant life. Intelligent designers and creationists will love this game, but I can only see biologists cringing unless the game piques people's interest in learning about living things and evolution. Given that people fear genetically modified foods and the LHC being turned on, or at least that is the perception of the media, I am not hopeful.

The Register has an article accusing Oxfam, a charity, of hypocrisy. Basically, preventing poor people from using GM crops modified to survive harsh conditions and provide better nutrition, as well as other modern agricultural technology to improve people's lives because of irrational concerns will keep them poor and voiceless. Oxfam being the voice of the voiceless supposedly knows what's best for the poor by preventing them from having what the developed countries already have - plentiful and cheap supplies of food. The current policies also cause more harm to the environment. If you don't need fertilizer or pesticide to protect your crops, you won't pollute the water or poison the wildlife as much.

Labels: Signs of trouble

I discovered Phillip K. Dick's Black Iron Prison while looking up VALIS which I haven't read. How can one come so close and see something so beautiful as a prison? Didn't the famous Earthrise photo prove that Earth is an oasis of Life in the emptiness of space? Every human being individually makes this world a Heaven or a Hell through one's actions as illustrated in this story, The Gates of Paradise. Collectively, Humanity is doing the same as well.

For this world to be a psychological paradise, all we have to do is be kinder and gentler to one another on a daily basis, treat this World and its lifeforms as a sacred gift and a privilege rather than something to be exploited economically, and listen intently to the silence within oneself. The physical planet always was and will be a Paradise for at least a billion years, or longer, if we can move the planet out into a slightly higher orbit.

Labels: correct data, flawed analysis and conclusion