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Junk DNA and really bad timing

The NYTimes has an article about a “flotilla of papers” that are coming out on Junk DNA.  Junk DNA was, up until recently, thought to be just irrelevant pieces of DNA that hitched a ride with the real genes in your body.  As it turns out, they’re much more important than that:

As scientists delved into the “junk” — parts of the DNA that are not actual genes containing instructions for proteins — they discovered a complex system that controls genes. At least 80 percent of this DNA is active and needed. The result of the work is an annotated road map of much of this DNA, noting what it is doing and how. It includes the system of switches that, acting like dimmer switches for lights, control which genes are used in a cell and when they are used, and determine, for instance, whether a cell becomes a liver cell or a neuron.

In one of the Nature papers, researchers link the gene switches to a range of human diseases — multiple sclerosislupusrheumatoid arthritisCrohn’s diseaseceliac disease — and even to traits like height. In large studies over the past decade, scientists found that minor changes in human DNA sequences increase the risk that a person will get those diseases. But those changes were in the junk, now often referred to as the dark matter — they were not changes in genes — and their significance was not clear. The new analysis reveals that a great many of those changes alter gene switches and are highly significant.

“Most of the changes that affect disease don’t lie in the genes themselves; they lie in the switches,” said Michael Snyder, a Stanford University researcher for the project, calledEncode, for Encyclopedia of DNA Elements.

So, you might ask how we missed the importance of junk DNA while we were doing all that sequencing and stuff.  To understand how junk DNA functions, we have to stop thinking about DNA as a 1 dimensional string of letters (A, T, G, C) and start thinking about it as a three dimensional object.  Picture a spiral telephone cord, if you’re old enough.  Remember what happened to that sucker when it got twisted?  It kind of bunched up?  Imagine that cord wrapped around an octet of soccer balls called a histone.  And then those octets are twisted and assembled into a chromosome and we all have 23 pairs of chromosomes.  Here’s a pic from the EMBL (European Molecular Biology Laboratory) blurb on the ENCODE papers:

When a cell has to transcribe or duplicate a gene, it has to unwind parts of that structure to locate the string of nucleotides to work on.  That part everyone knew.  But there were long strands of material that didn’t seem to perform any function in the gene sense- until they were twisted.  Then, the location of the junk DNA to the gene that was actually transcribed made sense.  The Junk DNA can affect the transcription of the gene because it is functional when the DNA strand is twisted and puts it proximal to the gene of interest.  Proteins work in a similar way.  In a 1 dimensional sense, the sequence of amino acids is meaningless.  It’s only when a sequence is twisted into its 3 dimensional shape that the right amino acids come in contact with or form functional relationships with each other.  When the amino acids are stretched out, the important amino acids may be far apart from each other on the string and do not look like they relate to one another.  It’s only when you compare sequences of related proteins that you see the patterns that indicate the active site of the protein.

Anyway, this is kind of a big deal and I will probably scoot on down to Princeton’s library to read some papers on the whole thing.  There will be reams and reams of data.  This could be very important to cancer research because recently, we have been looking for biomarkers, genes that are common for a particular cancer, and the results have been ambiguous.  But if junk DNA can explain why some genes get switched on inadvertently and others don’t, that might open up a whole new area of drug research.  It’s the kind of thing that people like me and my former colleagues could probably be retrained to do pretty easily.

Unfortunately, industrial R&D has been laying us off left and right and upside down and academia does not have the funds to absorb us.  So, here we are, all kinds of data and no place to go.

I suppose we *could* just work without pay and be selfless and shit.  But there are already people doing that and besides, at some point, our kids need caloric intake as much as any banker’s brats.

Anyway, this discovery comes at a really bad time for the life sciences professional.  It’s not like we’re not out here.  Structural unemployment is NOT the problem.  And this kind of research can be done from the home office so no one even has to move.  It’s just that no one wants to pay for it.

I love this bit of the article:

The new result “is a stunning resource,” said Dr. Lander, who was not involved in the research that produced it but was a leader in the Human Genome Project. “My head explodes at the amount of data.”

Yes, I’m sure all of our heads will explode.  There are more than enough projects to keep every scientist I know over their heads in work for generations to come.  It’s such a shame that hundreds of thousands of us aren’t doing it because some rich assholes in the finance industry see research only as a money pit.

It’s an even worse shame when the political parties either don’t want to acknowledge or don’t care that our scientific industry is dying in this country.  If there was ever a reason for the government to invest in a jobs program that would put thousands of people back to work, this would be it.

By the way, this article in Slate about how wonderful the job market is for the STEM PhD is total bullshit.  I’m living in ground zero where PhDs are getting laid off all around me on a daily basis and most of them regret they ever chose science as a career.  They love science but they sure don’t like being the new precariats, overworked, overeducated and expected to suck it up when they get laid off.  It tends to cool one’s enthusiasm for the lab pretty quickly.  Many are getting out of science altogether and are training to become teachers (probably expected to work without pay) and lawyers.  That’s in addition to their PhD.  This stupid article is how the structural unemployment crap gets spread and it’s pretty unbelievable to those of us who are living through the nuclear winter of the R&D industry.

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Friday Science Horror Stories

So, what does that make this, the third or fourth week of rainy weekdays?  I can’t remember.  The grays just blur into one another with teasers of blue sky.  Yes, we had a very nice weekend last week but it’s happened so rarely lately.  Mostly, it’s drizzling when I wake up, I have all kinds of plans to sand my deck and replant the bed out front where the creeping juniper used to be and I just have to sit on all of those things until the sun comes out.  No use in renting a sander unless I have a good four hours of no rain and I just can’t count on that these days.  The forecast is for more unpredictable precipitation until next Tuesday, although I might catch a break in the cloud cover tomorrow.  So, there’s hope that I can finish the f^(*ing deck.

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Update for my pharma friends:

Chemjobber has a post about visitors to the White House and how many of them have been from the science industry. Very interesting. Jeffrey Kindler, the ketchup king and now deposed head of Pfizer, was there many, many times.  Hey, did I mention that Pfizer decided recently to stop offering employees pensions so that they could risk all of their retirement money in 401Ks?  And Chris Viehbacher, he of the “good scientists don’t want to work for big pharmas” fame, (which indicates that he’s never actually gotten down from his lofty perch and spoken to any of the good scientists in his own labs), was there on March 11, 2011, about four months after his company bought Genzyme and proceeded to lay off most of his new acquisition’s chemists.

Well, they probably didn’t want to work for a big company anyway so, you know, conscience clear, and all that.

If you’re in the pharma industry,check it out and see if a CEO has been to visit the president or his advisors and viciously lied to them or collaborated with them or whatever those guys do in the White House.

*******************************

I’m almost done harping on Pharmageddon.  Yesterday, I had a conversation with a reporter from the Washington Post who says he is looking into the high number of layoffs among STEM professionals. (Many thanks to everyone who helped get the word out.  We appreciate it.)  Let’s hope there’s a crack in the cloud cover on this issue.  Either I’m paranoid that the present elected officials don’t want anyone to know how our scientific infrastructure has been decimated, or those same elected officials are dumber than a box of rocks and will believe anything the bonus class is telling them about structural unemployment, or there are too many scientific morons on the Republican side of the aisle in Congress, or they’re all being mislead by the out-of-date numbers of the Bureau of Labor Statistics. None of those possibilities give me peace of mind.  On the other hand, since there are so many of us out of work right now, we should look into replacing the clueless in Congress with our own geekier representatives.  At least there are two good years of employment and health bennies to look forward to.

Derek Lowe at In the Pipeline has a question for the ex-pharma crowd: What’s the craziest misinformation you’ve heard about the pharma industry or science in general?  He’s listed a couple that I’ve heard over and over again.  The first is that industry has found the cure for cancer and it’s sitting on it.  Friends, I know that anyone who reads this blog is smarter than the average smartass lefty blogger so I shouldn’t have to tell you this but that idea makes no f^&*ing sense.  If industry had the cures for cancer, they’d be marketing the hell out of them and charging whatever the market would bear, which would be plenty.  If you’ve ever had a family member who is terminally ill with cancer, you know that you would mortgage your house to buy him a cure and the guys in the marketing department of Trustus Pharmaceuticals know it too.  So, this is a ridiculous idea.  The truth is both good and bad.  We’re getting closer to understanding the mechanisms of cancers but we’re still a long way off from beating it.  What we need is more money and more commitment from our governments.

The second idea is that all of the science comes from government funded grants.  While it’s true that grants fund a lot of basic research, it is NOT true that industry takes that already discovered and perfect drug and markets it for a profit.  No, no, no, no, noooooooo.  At best, industry gets a clue from academia, maybe some insight, a mechanism, and occasionally a germ of a drug in its earliest form.  What industry does is accumulate all of the information about the proposed target as it can, sifts through it, determines if there is something it can work with, and then sets about doing the years and years of research it takes to develop those ideas into a therapy.  It’s a long hard slog that involves many steps of biology, chemistry, pharmacology and animal models to get to the point where *maybe* there’s a drug in there somewhere.

That doesn’t diminish the government’s role in funding research.  This research is vital to what comes after.  But it’s like Edison’s 1% inspiration followed by industry’s 99% perspiration.  And along the way, industry is able to add insights to the original problem.  We’re not just applied science monkeys.  We make our own discoveries along the way and add to the body of knowledge on a subject through our own papers and presentations.  That, in turn, helps feed science in general.  The more knowledge that’s out there, the more chances that academia and industry will find places to collaborate.  We are now seeing a lot more collaboration between academia and research.  And while that’s a good thing, academia needs to be funded more generously for new collaborations to work optimally and to boost academia’s contribution past that 1% inspiration.  Biology is undergoing a modern, “paradigm shifting” revolution right now.  We can’t afford for any government lab to be underfunded or our nation will be left behind.

What our elected officials need to do is make sure that the people who fund the collaborations benefit as well as the industries that develop the ideas.  Can we do it?  Sure we can.  We just need to think of the American people as stakeholders.

And here’s what will happen if we do not take this challenge seriously.  A recent article in the NYTimes says that American Physicists fear that we are losing our edge:

When three American astronomers won the Nobel Prize in Physics last year, for discovering that the expansion of the universe was speeding up in defiance of cosmic gravity — as if change fell out of your pockets onto the ceiling — it reaffirmed dark energy, the glibly named culprit behind this behavior, as the great cosmic surprise and mystery of our time.

And it underscored the case, long urged by American astronomers, for aNASA mission to measure dark energy— to determine, for example, whether the cosmos would expand forever or whether, perhaps, there might be something wrong with our understanding of gravity.

In 2019, a spacecraft known as Euclid will begin such a mission to study dark energy. But it is being launched by the European Space Agency, not NASA, with American astronomers serving only as very junior partners, contributing $20 million and some infrared sensors.

For some scientists, this represents an ingenious solution, allowing American astronomers access to the kind of data they will not be able to obtain on their own until NASA can mount its own, more ambitious mission in 2024.

But for others, it is a setback. It means that for at least the next decade, Americans will be relegated to a minor role in following up on their own discovery.

American scientists are facing a real dilema.  If our government is not going to invest in basic research, we will be putting ourselves decades behind.  As science accelerates in the rest of the world, we will fall back even faster.  Pretty soon, America will start to resemble one of those 2nd world countries where corruption is pervasive and where government is permanently underfunded and the number of Nobel prizes going to that country’s scientific infrastructure is vanishingly small.

We are at Robert Frost’s “two roads diverged in a yellow woods”.  The decisions we make now will affect the way our country develops.  Are we going to continue to cater to the conservatives who insist on allowing ignorance on evolution, climate science and private sector funding take us down the road to scientific obscurity or are we going to recommit to taking the lead in science and technology and demand that the wealthy step up, pay their taxes and help us refund our efforts so that American citizens, the stakeholders, benefit?  Can we afford for so many Americans to feel entitled to their ignorance?

Anyone?  Anyone?  Barack?

Thursday: Fantasies of a Lab Rat

What happens at the lab when the managers and the MBAs go to an international meeting and leave the labrats in charge of themselves:

Can we get an Amen?

*****************

True Story:  Last week, I was standing in front of a halal grease wagon in Philadelphia waiting for my baba ganouj, when some African American dude selling a book started chatting me up.  Much eye rolling ensued but he was actually kinda of interesting and I had some time to kill.  I wasn’t interested in buying his book because I told him I was out of work and trying to save money (yeah, yeah, I should have brought my lunch but I had a yen for roasted eggplant.  So sue me.)  He asked me what I did and I told him I was a drug designer of oncology drugs.  Oooo, he said, does that mean your companies have figured out the cures for cancer and are just sitting on them?  I hear this kind of uninformed opinion all of the time, that the pharmas are sitting on some big cancer cure and they’re holding out in order to, um, to, well, hell, I don’t know.  This accusation never did make any damn sense to me.  If the pharmas had THE definitive cures for cancer, they’d be screaming and jumping up and down at the FDA to approve them right away.  Cancer is big business and there’s a lot of potential extortion money to be made.  People who are frantic to survive to see their kids grow up will pay just about anything for a cure.

Sadly, there is no cure for cancer yet, mostly because cancer is not just one disease but many diseases.  You would think that with all of the work that is left to do to cure cancer and all of the discoveries that we are making in cell biology in the past decade that every scientist in the world would be overwhelmed with work instead of getting laid off and scraping together a meager existence.  But the truth is that those of us who should be working round the clock to do protein expression, structural biology, genomics and medicinal chemistry are falling out of the middle class and into the realm of a precariat existence while cancer goes uncured and the amount of resources thrown at is is parsed into “need to know” CRO operations in foreign countries.

So, when I saw Derek Lowe’s morning post on the hope of curing cancer, I got a little wistful.  Derek ends his post:

But I’m operating on a different time scale from Eschenbach. Here he is in 2006, in The Lancet:

 

“Think of it”, von Eschenbach says, “for thousands of years we have dealt with cancer working only with what we could see with our eyes and feel with our fingers, then for a 100 years we’ve dealt with cancer with what we could see under a microscope. Now, we have gone in 10 years to a completely different level.” This new science “is going to change how we think, it’s going to change how we approach things; it’s going to change everything.” 

. . .He points to the example of testicular cancer. The development of treatments for this cancer was a great success, von Eschenbach says, but one that “took decades of trial and error, one trial after another, after another, after another”. That hit-and-miss approach is no longer necessary, von Eschenbach says. Now, if 10% of patients responded to a treatment, he says, “you take the tools of genomics and go back, reverse engineer it, and ask: what was different about that 10%? Well, they had an EGF [epidermal growth factor] receptor mutation, ah ha!”

 

Ah ha, indeed. Here’s more in a similar vein. The thing is, I don’t disagree with this in principle. I disagree on the scale. No one, I think, knows how to eliminate deaths from cancer other than the way we’re doing it now: detailed investigation of all sorts of cancers, all sorts of cellular pathways, and all sorts of therapies directed at them. Which is all a lot of work, and takes a lot of time (and a lot of money, too, of course). It also leads to a huge array of dead ends, disappointments, and a seemingly endless supply of “Hmm, that was more complicated than we thought” moments. I don’t see that changing any time soon. I’m optimistic enough to think that there is a bottom to this ocean, that it’s of finite size and everything in it is, in principle, comprehensible. But it’s big. It’s really, really big.

There are people who defend goal statements like Eschenbach’s. Such things force us to aim high, they say, they focus attention on the problem and give us a sense of urgency. Taken too far, though, this point of view leads to the fallacy that what’s important is to care a lot – or perhaps to be seen to care a lot. But the physical world doesn’t care if we care. It yields up its secrets to those who are smart and persistent, not to the people with the best slogans.

Or the best MBAs that money can buy.  I guess the pharmas really are sitting on a cure.

*****************

Speaking of Amens, our poll shows that an awful lot of us (about 76%) are heathens with a naturalistic worldview.

Alright!  {{high fives}}

Oh, sorry about that, believers.  We’ll try to be nice.

If you haven’t had a chance to declare your godlessness or semi-godlessness, as it turns out, check it out here.

****************

Sounds like it was “Rick Santorum has cooties” night at the Republican playground debate last night.  I didn’t know that Romney supported Arlen Specter over Pat Toomey. I like the end of this article for its “I know you are but what am I?” flavor:

Mr. Romney, who has struggled to win the trust of party activists, is under intense pressure to prove his conservative bona fides. He was asked about a recent statement that he was “severely conservative” when he was governor. He defined his meaning as “strict,” saying he empowered state police to enforce immigration laws, pushed English language immersion programs and “stood up and said I would stand on the side of life.”

Mr. Paul, in response to a question about the biggest misconception about him, complained about the perception that he could not win against Mr. Obama in the general election, pointing to a recent poll that showed him closer to the president than the other candidates.

When Mr. Romney was asked to describe a misconception about him, he demurred, borrowing from Mr. Gingrich’s debate-the-moderator playbook and saying sharply, “You know, you get to ask the questions you want; I get to give the answers I want.”

But the discussion kept returning to Mr. Santorum.

When the moderator asked Mr. Paul why he was running a new television advertisement calling Mr. Santorum “a fake” conservative, Mr. Paul answered simply, “Because he’s a fake.”

“I’m real, I’m real, I’m real,” Mr. Santorum said, shaking his head.

Oooo, I think the debate game has run its course (about 15 debates ago) and everyone is getting a little testy.  For Pete’s sake, can we just have Romney appoint Santorum as his VP running mate and get on with it already?

*****************

Speaking of Santorum, I LOVE his condescension of other religions, even other Christians, as being inferior to Catholicism.  Whoo-hee!, too funny!  Evangelical Fundamentalists do that to more liberal brands of Christianity all the time.  Presbyterians are just posers to them.  It’s kind of amusing for some Pennsylvanians who are Santorum admirers to get a taste of their own medicine.  You’re nothing to Rick if you’re not a Pope toady.  Papists rule, Protestants!

Pass the popcorn.

Psych! Prions and Ice Nine

3D structure of amyloid fibrils

I saw this post about the possibility that Alzheimer’s is an infectious disease at Derek Lowe’s blog, In the Pipeline.  There’s a new paper out that reports that animals whose brains were exposed to misfolded amyloid-β protein extracted from patients with Alzheimer’s disease will go on to also develop amyloid plaques while control animals do not.  While there is a reputed genetic component to the development of Alzheimer’s disease, this study suggests that it can be induced by the transmission of a prion from one animal to another.  Prions are infectious bits of protein.  They’re teensier than viruses even.  In the case of amyloid disease, the protein under investigation is about 42 amino acids long, which is tiny.

The principle is this: in order to function properly, proteins need to fold into distinct secondary patterns and then a specific 3D shape.  If the protein is misfolded, it doesn’t work properly or it can aggregate, ie form clumps.  The sneaky think about prions is that they can induce other proteins to misfold.  The misfolded protein is in a lower energy state than the properly folded state so the protein can’t unfold itself and refold properly.  It’s stuck.

If any of you have read Kurt Vonnegut’s novel, Cat’s Cradle, and can remember anything beyond spritual footrubs and Bokononism, you may recall that one of the characters created a substance called Ice-9.  A single crystal of Ice-9 had the potential to freeze all contiguous bodies of water.  Throw it into a bathtub, the bath water freezes.  Throw it into an ocean, the ocean freezes.  I can’t recall if it stayed that way permanently but after Ice-9 was released, the world started to die of thirst.

The introduction of amyloid-β prions into a healthy brain may be doing an analogous thing by inducing newly formed amyloid protein to misfold.  And an excess of misfolded protein tends to aggregate, triggering inflammation and, down the road, dementia.  Mad cow disease is also a prion disease that in sheep manifests itself as scrapies.

Er, no one knows how to fix it yet.  One of the problems with developing a drug for Alzheimer’s disease is that the enzyme that normally would be targeted for inhibition, γ-secretase, is also used to cleave a protein called Notch, which the cell can’t really do without.  So, there’s that.  Drug discovery is much harder than it sounds, as Derek says in this recent podcast that he did with Paul Howard from the Manhattan Institute.

The frustrations of the drug discovery process that Derek describes reminds me of the central tenet of Bokononism:

Beware of the man who works hard to learn something, learns it, and finds himself no wiser than before. He is full of murderous resentment of people who are ignorant without having come by their ignorance the hard way.

Well, we *are* learning but the truth comes slowly and the answers to the questions are frequently accompanied by a whole new set of questions that must be answered.  This is in part why the pressures of the financial industry have been particularly harmful to the pharmaceutical industry and may have contributed to the high price of drugs.  Drug discovery is a long term process.  It can’t be sped up just to meet the numbers on a spreadsheet for the bean counters.  Cost controls that are intended to whip researchers to pick up the pace are bloody useless and counterproductive when applied to the complexity of the cell, something that the guys with executive hair may just now be realizing.  There’s not a whole lot more of mergering, cutting and restructuring that can be done at this point.  And the patent cliff still looms.  It’s going to be a rough ride for the drug industry for the next couple of years.

Derek also points out that the drugs that are now being approved were probably first discovered or synthesized in the mid 1990’s.  That means the patent clock has been running down for some of them and if there’s not a lot of time left to recoup the costs of discovery, it gets passed on to the consumer as higher prices.  There are other contributing factors to the cost of drugs but the length of the process is a significant one.

I encourage readers to check out the podcast.  Derek also discusses a new therapy for cancer that involves harnessing the immune system.  Fascinating and promising.

Saturday: Lessons Learned

I want to thank all of you who have helped me through this difficult period of time.  Special thanks to Katiebird, DandyTiger, my own BFF who was exceptionally sensitive and kind to me and my ex who suspended hostilities.

I tried to go out on a high note at work.  This wasn’t easy and I’m not sure I was entirely successful.  I worked on my projects literally to the very last hours, depositing my final thoughts on a structure I had been working on just before I shut off my computer for the last time.  Some people may think this is crazy.  I didn’t owe anything to the bastards who laid me off.  I see it differently and am starting to realize what must have been going on in Hillary Clinton’s head during the Democratic Convention of 2008.  In fact, she was on my mind a lot in the past couple of months.  What would Hillary do in this situation?  I decided to give it my all on my projects.  A couple of weeks ago, I found out that the project I had spent the last five years on was going to be used to fight the same cancer that killed my father.  I cried like a baby after that project team meeting.  Did I do enough?

Getting laid off has been a learning experience.  Here are some of the things I have learned:

1.) There is nothing more valuable in life than having a job you love, no matter how much it pays.  The hardest thing about leaving work was realizing what my passion was in my last year of employment and having it gone in a blink of an eye by the penny pinching decisions of a company bureaucrat.

2.) You never know what the right kind of nurturing and opportunities will bring out in people.   I will be forever indebted to the two supervisors who gave me high profile projects and pushed me (sometimes very hard) to learn new things as quickly as I could.  The last year was very challenging but very rewarding and even though I was sometimes stung by the constant revisions requested of my work, I appreciated the demands for rigor.  I think it made me a better scientist.

3.) Lay-offs do not bring out the best in anyone.  Very few people can resist the urge to undermine, take credit or speak ill of other people when they’re under this much stress.  There are no exceptions, not even me.  We all have our faults and layoffs tend to exaggerate them.  It is very hard to focus on our work when we are in desperate competition with each other to save our livelihoods.  Favoritism and kissing ass take the place of diligence and merit.  And those of us who refuse to kiss ass, because, really, it doesn’t serve management well at all, no matter how flattering it is, end up the losers.

4.) Managers who like their work, like to be productive and would prefer to concentrate on science, are frequently overlooked by the powers that be.  They are the best people to work for and their staff loves them.  But they can’t protect their people or even their own positions from the ax as well because they’re not into political games.  That has a bad effect on research in general.  There are a lot of excellent scientists left in the labs.  But they know they have to watch their backs and learn whose ass to kiss.  What a waste.

5.) Never look back.  I haven’t always done my best but in the past two years, I believe I have.  But now it’s time to put it aside and move on. I have no regrets.

I love my colleagues.  Yes, even the ones who were the biggest pains in the ass, snobs and ruthless, aggressive, ambitious bastards I have ever seen who leave a trail of destruction, resentment and dead bodies in their wakes.  They are all without exception  highly intelligent and genuinely interesting people.  If I were stranded on a desert island with any of them, I’d be in good company and wouldn’t be stuck for long.  I wish them good luck.

I love the company I worked for.  I’m not too crazy about the management at the upper end because even though they are getting pressure from Wall Street, they have not thought through this problem well.  They are taking the easy, expedient route.  It is going to result in some painful lessons for all parties involved, sooner rather than later, if what I’m seeing is any indication of the future.  But they’re not the only company making bad decisions right now due to the very same pressures.  I still love the corporation and want it to succeed, not just because it will keep my former colleagues employed (I hope), but because it is the right thing to do for the customers of the products.  I was well compensated, my severance package is good and I enjoyed working there.

So, now my job is to find a job.  This should be interesting.  I don’t think I have to give up trying to cure cancer though.  I’ll just be doing it from the privacy of my own home for awhile.  There are plenty of free resources for me to use.  And now, I know how to do it.

😉

Monday: Promises, Promises or Why Does Robert Samuelson Hate America?

From Global-Greenhouse-warming.com: the ecology of snow.

There is snow in my driveway.  I thought this stuff was supposed to turn to rain.  Already, the rhythmic scraping snow shovel on asphalt is coming from my neighbors’ driveways.  I have to get out there and shovel before I’m the only one with snow in my driveway and the cul de sac shuns me for non-compliance.

Let’s get on with the news.

First up, Robert Samuelson tries to justify the stingy, selfish, hard-hearted, cheatin’ ways of the Villager class when it comes to Social Security in On Medicare and Social Security, be unfair to the boomers.  See, it’s not the wealthy’s fault.  It’s YOURS for being so demanding of your money.  But Samuelson is trying to make a case for cutting boomer benefits because to not do so would be unfair to future generations.  So, let’s be pre-emptively unfair to boomers:

If we don’t, we will be condemned to some combination of inferior policies. We can raise taxes sharply over the next 15 or 20 years, roughly 50 percent from recent levels, to cover expanding old-age subsidies and existing government programs. Or we can accept permanently huge budget deficits. Even if that doesn’t trigger a financial crisis, it would probably stunt economic growth and living standards. So would dramatically higher taxes. There’s a final choice: deep cuts in other programs, from defense to roads to higher education.

Yet, neither political party seems interested in reducing benefits for baby boomers. Doing so, it’s argued, would be “unfair” to people who had planned retirements based on existing programs. Well, yes, it would be unfair. Indeed, it’s hard to imagine a worse time for cuts. Unemployment is horrendous; eroding home values and retirement accounts have depleted the elderly’s wealth. Only 19 percent of present retirees are “very confident” of having enough money to live “comfortably,” down from 41 percent in 2007, reports the Employee Benefit Research Institute.

But not making cuts would also be unfair to younger generations and the nation’s future. We have a fairness dilemma: Having avoided these problems for decades, we must now be unfair to someone. To admit this is to demolish the moral case for leaving baby boomers alone. Baby boomers – I’m on the leading edge – and their promised benefits are the problem. If they’re off-limits, the problem is being evaded. Together, Social Security, Medicare and Medicaid represent two-fifths of federal spending, double defense’s share.

{{rolling eyes}}

There’s more garbage where that came from.  Samuelson does acknowledge that outside his mighty fortress of wealth and privilege, there are little people who are being crushed by this Recession and can’t put money in their tax deferred 401Ks.  But I don’t think he is getting the full picture like I am where I am literally *surrounded* by the walking dead former employed high salaried baby boomers who no longer have access to a tax shelter.

Let me count the ways that Robert and his ilk are wrong and should be strenuously resisted:

1.) In the 1980’s, the tail end of the baby boom generation, that would be people like *me*, were assured by the Reagan Administration that if we accepted higher payroll taxes on our minute, nascent post college salaries, we would be paying for our future social security benefits that required a surplus fund “because we are too menny”.  Is this not true, Robert?  We’ve already made our sacrifice.   We were promised that if we deferred our compensation, it would be there when it was time to retire.  If it is not there and we are asked to take a cut in future benefits, that would be equivalent to imposing a significant extra tax over the past 30 years on those of us in the younger cohort of the babyboom generation because people like Robert and David Broder and Sally Quinn liked their Bush era tax cuts.  Robert has a lot of nerve lecturing us about unfairness.

2.) The problem is not social security, or at least, it wasn’t until the latest boneheaded tax deal.  The problem is everything else that needs to be paid for.  It’s funny how social security recipients are always being asked to foot the bill though.  How about we end the costly wars before we ask future old people to retire in poverty?  Or why don’t we end the Bush deficit increase plan early?  I know!  Robert and his friends can volunteer to pay the taxes they’ve gotten away with not paying in the past 10 years!  That would be the unselfish thing to do.  No?  Then, shut the fuck up, Robert.

3.) In all the turmoil over stimulating the economy, I find it odd that the one thing I did not hear was giving anyone who is forced to tap into their 401ks a tax break.  There are a lot of people who have been out of work for so long that they have to use their 401Ks to pay for calories and shelter.  But they are taking a huge hit in taxes in order to do so.  How come a tax holiday on the 401K was never offered to the long term unemployed?  Wouldn’t that have had a more stimulative effect on the economy than the measly 2% break on social security, which is too small to do anything with and too large to make up for with money from the general fund?  But curiously, the 401K tax penalty was never put on the table.  Does it have anything to do with the idea that the stock market would take a hit if the long term unemployed siphoned money from the casino?  Whoa!  We can’t have that.  That would be unfair to the bonus class, not to mention the giant 401K Ponzi scheme that Robert’s business buddies forced those younger boomers into in lieu of pensions so that Robert could retire on his investments.

4.) When you issue a promissory note to people you borrowed money from, that means you are promising to pay it back at some future date.  If the rich of this country took money from future social security beneficiaries, in order to pay for the tax breaks they got so they wouldn’t have to pay for infrastructure and dirty stuff like that, they need to realize that there is a time that they will have to pay it back.  And when they do, they will have to pay for it with taxes on the wealth that they accumulated in the past 30 years while they imposed an additional tax on the 2o somethings they burdened with an additional payroll tax.  You know, like the way you stuck us younger generation boomers with this burden and now you want to stick us again so we don’t pass it on to our children?  Do we look like we fell off the turnip truck, Robert?   We’re not stupid.  You gave us IOUs, now we want our money back.

Don’t try to sell us on the idea that we can retire at a later age.  I won’t be able to use a microscope and fish crystals out of a 1 uL drop with a tiny nylon loop when I’m 70.  I’m sorry, we’re not all janitors.  Some of us will still need fine hand-eye coordination if we’re lucky enough to still have the highly technical jobs we already have.

And don’t try to make it sound like those of us with higher salaries can afford to take this hit.  As I’ve mentioned before, a high salary in Kansas means nothing in NJ.  On 100K around here, you’re barely middle class and there is not a lot of disposable income to sock away for a rainy day.  But more than that, I’ve seen people with salaries much higher than mine who a few years ago thought social security was beneath them who have now been brought low by this Recession and for whom social security is their life saver.  For them, social security is serving the purpose for which it was originally intended.  If people of Robert’s class are having an “Oh, shit! Now we have to pay back the surplus fund with higher taxes” moment, too fucking bad.  Pay up, Robert.

What we do with the money we get from social security is nobody’s damn business.  I won’t have someone asking me to account for buying a nice steak someday.  I won’t have a bench of tut-tutters asking me what I intend to do with the money.  Social security is not a welfare program.  It’s my retirement money, I paid for it and damn it, I want it back without strings attached.  I don’t ask Robert how many summer houses he owns at the shore using money he’s been stealing from the surplus fund over the last 30 years.  If he and his class pay it back by taking a modest hit in taxes, I won’t press him on the matter.  Just return the money and no questions will be asked.

Here’s the thing, Robert.  A promise is a promise.  This country made a promise to the future elderly that they would not retire in poverty.  And they took our money promising to pay for those future benefits.  And the rest of us relied on that promise so that we could plan our lives, family size, mortgages, savings accordingly.   And now that the country has fallen on hard times, through no fault of the hard working people who believed in those promises, the wealthy and well connected want to reneg on those promises in a manner that is no different than some corrupt third world country run by some petty dictator and his greedy retainers.  That’s where you’re taking us, Robert.  Why do you hate America?

We’re not just going to hang ourselves to relieve you of the burden of caring for us, Robert.  We  have every right to expect to get our money back.  So, take the austerity plan that you and your friends have cooked up for us and stick it where the sun don’t shine.  Pay up or shut up.

In other news:

Cancer is complicated.  Multiple genes and proteins are involved and then there are feedback mechanisms and the intricate machinery of a cell that, once unbalanced, is difficult to set straight.  To make it even more maddening, the cell adapts by developing resistance to chemotherapy drugs over time.  Now, researchers are asking the dying to help them figure out which mechanisms are causing drug resistance so that the next patient on therapy benefits.  In Enlisting the Dying for Clues to Save Others, the NYTimes illuminates the research process:

Lacking tumor samples from patients in the Roche trial, Dr. Lo instead sought to replicate the cancer’s resistance to the drug by feeding a steady diet of the drug to melanoma cells taken from three previous patients who had never received it. When the few cancer cells that survived the onslaught began to grow in their petri dishes, he used those, now resistant to the drug, to begin his search.

It could have been straightforward. Many researchers believed the answer would be that the gene whose mutation initially made the protein that drove the cancer’s uncontrolled growth had mutated again, as had happened in other cancers. In a few cases, a new drug tailored to the new mutations had lengthened remissions.

But Dr. Lo found no evidence of this. Nor did he find the smoking gun in several other genes linked to the growth of other cancers.

Instead, he began the painstaking process of measuring the activity of hundreds of proteins that might have driven the cancer’s uncontrolled growth. The experiments required modifying the levels of each protein in the drug-resistant cells, dosing them with the drug and checking every few hours to see how fast they were growing. With only two junior scientists and a technician in his laboratory, Dr. Lo performed much of the work himself.

Even so, he knew, nothing he found in the cells whose resistance he had artificially bred in the lab would matter unless he also found it in the patients who had relapsed.

It’s a painstaking process of trial and error and careful observation.

Last but not least, the vaginal steam bath:

Pungent steam rises from a boiling pot of a mugwort tea blended with wormwood and a variety of other herbs. Above it sits a nude woman on an open-seated stool, partaking in a centuries-old Korean remedy that is gaining a toehold in the West.

Vaginal steam baths, called chai-yok, are said to reduce stress, fight infections, clear hemorrhoids, regulate menstrual cycles and aid infertility, among many other health benefits. In Korea, many women steam regularly after their monthly periods.

There is folk wisdom — and even some logic — to support the idea that the carefully targeted steam may provide some physiological benefits for women. But there are no studies to document its effectiveness, and few American doctors have even heard of it.

“It sounds like voodoo medicine that sometimes works,” said Dr. Vicken Sahakian, medical director of Pacific Fertility Center in Los Angeles.

Niki Han Schwarz believes it worked for her. After five steams, she found she had fewer body aches and more energy. She also became pregnant eight months ago at the age of 45 after attempting to conceive for three years.

So, there you go!  Sit over a vaginal steam bath, get pregnant!  And my health teachers used to say such things weren’t possible.

Oh, those crazy Koreans.

What are you finding around the web?

Farrah Fawcett Living Downstream

Dividing Breast Cell

Dividing Breast Cell

Farrah Fawcett’s death is both poignant and embarrassingly mundane. It is poignant because she gathered the energies she gained from being an “it” girl and used them to bring to light some common, and less common, plights of women in general. Farrah’s touch of America, brought America in touch with some of its hidden aspects.

Her death is embarrassingly mundane in the way that “The Burning Bed” examined the embarrassing mundane phenomenon of domestic violence. When we should be embarrassed by the commonality of a social practise, it is embarrassingly mundane.

Farrah’s death by cancer is merely one death in many that is the result of the societal choice to poison or chemically-load the places that provide our sustenance and give us shelter. In death, her personal struggle with cancer highlights our society’s embarrassingly mundane choice to slowly poison, or biochemically alter, ourselves, our children, and our children’s children, so that some of us can pay less for things.

Whom among us can claim a family that is untouched by cancer? How have we also been touched?

“According to the American Cancer Society, [cancer]… is the second leading cause of death in the U.S. with half of all men and one-third of all women developing some form of cancer during their lifetimes.” (The good news is that cancer rates have stabilized and even declined, since 1992, after steadily rising for many years.)

In terms of other touches, the growth in childhood asthma has reached epidemic status; the early onset of puberty in girls (precocious puberty) has become normal; and sperm counts in males, and the volume of healthy sperm produced, continues to steadily decline (due to environmental endocrine disrupters), to name a few.

Sandra Steingraber, a biologist and cancer survivor, coined the phrase “living downstream” to describe the phenomenon of societies following development trajectories that lead to adverse health outcomes. The parable below is borrowed from a website tied to a documentary that is derived from her research:

There once was a village overlooking a beautiful river.
The residents who lived here began noticing increasing numbers of drowning people caught in the river’s swift current and so went to work inventing ever more elaborate technologies to resuscitate them.
So preoccupied were these heroic villagers with rescue and treatment that they never thought to look upstream to see who was pushing the victims in.
Living Downstream is a walk up that river.

One does not have to look far upstream to find Sarah Palin, Barack Obama, George Bush Jr. and the United States Supreme Court pushing their fellow citizens into the river. They’ve made, and continue to make, choices that chemically-load or poison the citizens they represent.

A mining company was given the go-ahead by the Supreme Court on Monday to dump waste from an Alaskan gold mine into a nearby 23-acre lake, although the material will kill all of the lake’s fish.
By a 6-3 vote, the Supreme Court said a federal appeals court wrongly blocked on environmental grounds the Army Corps of Engineers’ waste disposal permit for the mine project. The Alaska mine, which had been closed since 1928, now plans to resume operation and will dump about 4.5 million tons of mine tailings — waste left after metals are extracted from the ore — into the lake located three miles away in the Tongass National Forest.
The court said that the federal government acted legally in declaring the waste left after metals are extracted from the ore as “fill material” allowing a federal permit without meeting more stringent requirements from the U.S. Environmental Protection Agency under the Clean Water Act.

The ruling was rejected by 3 moral voices in Ginsburg, Stevens, and Souter.

In a dissenting opinion, Justice Ruth Bader Ginsburg said it is “neither necessary or proper” to interpret the waterway protection law “as allowing mines to bypass EPA’s zero-discharge standard by classifying slurry as fill material.” She argued the lower court had been correct in concluding that the use of waters as “settling ponds for harmful mining waste” was contrary to the federal Clean Water Act.

Sarah Palin confirmed her status as a “pro-life without the chance of parole” candidate.

Alaska Gov. Sarah Palin called the decision “great news for Alaska” and said it “is a green light for responsible resource development.” The Kensington Goal Mine 45 miles north of Juneau will produce as many as 370 jobs when it begins operation.

In this regard, Governor Palin pales in comparison to President Obama, who continues to provide evidence that he is merely a better looking, more articulate version of George W. Bush. Following their standard modus operendi, the Obama Whitehouse, in the form of Ken Salazar, the Secretary of the Interior, stated that Bush’s policy on mountaintop removal mining did not pass the smell test and then proceeded to hold their noses and put Bush’s policy into practice. Thankfully, the Senate may yet have something different to say.

Farrah Fawcett, like the rest of us, lived downstream from the choices of others. She touched America and America touched back. Unfortunately, some of those touches gave her cancer, like they’ve done to too many others, and like they continue to do today in many different and harmful ways. This is unlikely to change anytime soon because, as related in Steingraber’s parable, the most prominent politicians in the United States today continue to push their fellow citizens into the river.

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