Pooping prions - this is more than interesting

Stanley Prusiner won his Nobel prize in 1997 at age 55 for discovering that protein malformation could be contagious. He called the twisted proteins that could catalyze like malformations prions.

Turns out he's still at work ...

Study Gives Insight Into Spread of Chronic Wasting Disease - NYTimes.com

... Researchers are reporting that they have solved a longstanding mystery about the rapid spread of a fatal brain infection in deer, elk and moose in the Midwest and West.

The infectious agent, which leads to chronic wasting disease, is spread in the feces of infected animals long before they become ill, according to a study published online Wednesday by the journal Nature. The agent is retained in the soil, where it, along with plants, is eaten by other animals, which then become infected.

The finding explains the extremely high rates of transmission among deer, said the study’s lead author, Dr. Stanley B. Prusiner, director of the Institute for Neurodegenerative Diseases at the University of California, San Francisco.

First identified in deer in Colorado in 1967, the disease is now found throughout 14 states and 2 Canadian provinces. It leads to emaciation, staggering and death.

Unlike other animals, Dr. Prusiner said, deer give off the infectious agent, a form of protein called a prion, from lymph tissue in their intestinal linings up to a year before they develop the disease. By contrast, cattle that develop a related disease, mad cow, do not easily shed prions into the environment but accumulate them in their brains and spinal tissues.

There is no evidence to date that humans who hunt, kill and eat deer have developed chronic wasting disease. Nor does the prion that causes it pass naturally to other animal species in the wild....

... In captive herds, up to 90 percent of animals develop the disease, Dr. Prusiner said. In wild herds, a third of animals can be infected...

... prions tended to bind to clay in soil and to persist indefinitely. When deer graze on infected dirt, prions that are tightly bound to clay will persist for long periods in their intestinal regions. So there is no chance chronic wasting disease will be eradicated, he said. Outside the laboratory, nothing can inactivate prions bound to soil. They are also impervious to radiation.

So what's the chance that this is the only instance of fecal-oral Prion disease in all of history?

Right. This is probably as common as dirt.

We're going to be learning a lot more about fecal-oral prion disorders in all animals, including humans. We'll also learn how organisms adapt to an indestructible infectious "agent".

This is a big discovery.

Global finance and parasites

A year after the crash, Wall Street banks are little changed - but bigger. Reform has failed, and though Obama is trying few expect him to succeed.

Kudos to those veterans who predicted nothing would be fixed.

I don't blame Obama. Between the Great Recession, Health insurance reform, North Korea, Peak Oil, global warming, Pakistan, the Bush legacy of torture, corruption and the dismantling of government, Africa and Klan 2.0, the man has a few things on his mind.

In the absence of Presidential authority bank reform is a long shot. This gang can buy a Senator for pin money and a Congressman for loose change [1].

As they say in DC, "If you want a friend, get a dog. If you want justice, give up."

This time the US government can't help us. What's a small investor to do?

Personally, I want to read a book called "Investing in a Crooked Market", but I haven't found it yet. So, what the heck, I'll speculate that ...

1. Without real reform we can expect that banks will continue to pick investor's pockets -- including the pockets of their own shareholders.
2. There'll be a mega-Recession every 7 to 10 years and we'll read more about 19th century "cycles".
3. Traditional "value investing" will become a chump's game.
4. Investors will look to well regulated markets in Europe and Canada, forsaking London and the United States.

There's probably some way to make money playing this crooked game but it has nothing to do with creating value. It's about cold blooded application of the Greater Fool principle in a bubble economy.

In the longer run, I wonder if we can think of these corrupt banks as a form of overly successful parasite on the current model of corporate finance. Biological parasites weaken their hosts, and these Finance parasites will have the same effect. They'll reduce the competitive advantage of stocks over other forms of corporate finance.

In time a new way to fund corporations will emerge as an alternative to the traditional publicly traded company. The old stock market will die off, and new parasites will emerge to start the cycle all over again ...

Update: When I wrote this post I created a new tag to group my Great Recession posts. Along the way I came across a 2004 speech by Morgan Stanley's Stephen Roach. I'd say he came out of this looking rather clever.

Update 9/15/09: Consider regulatory oversight. Regulatory agencies breed lobbyists. Lobbyists breed campaign donations and post-political wealth. Therefore Senators want regulatory agencies. The more agencies, the more "regulatory arbitrage"-- opportunities to game the agencies. So banks and other regulated for profit corporations also want more regulatory agencies.

Since both politicians and finance corporations want more regulatory agencies we get more of them every year. Reform seems impossible. (NPR 9/15/09)

Update 9/15/09b: Chris Mealy, in comments, points to a reference (pdf) on using a Proxy Exchange to mitigate some of the problems of corporate non-governance.

Surprise - physicians are big Obama supporters

Physicians are big "ObamaCare" supporters.

Surprise. Not.

Poll Finds Most Doctors Support Public Option : NPR

... a new survey finds some surprising results: A large majority of doctors say there should be a public option.

When polled, "nearly three-quarters of physicians supported some form of a public option, either alone or in combination with private insurance options," says Dr. Salomeh Keyhani. She and Dr. Alex Federman, both internists and researchers at Mount Sinai School of Medicine in New York, conducted a random survey, by mail and by phone, of 2,130 doctors. They surveyed them from June right up to early September.

Most doctors — 63 percent — say they favor giving patients a choice that would include both public and private insurance. That's the position of President Obama and of many congressional Democrats. In addition, another 10 percent of doctors say they favor a public option only; they'd like to see a single-payer health care system. Together, the two groups add up to 73 percent...

This is only "surprising" if you think the AMA, which more or less supports insurance reform, represents physicians.

In reality the AMA represents surgeons and proceduralists. These specialists may well lose income with health insurance reform, so it's impressive that the AMA is not marching with the 9/12 neo-Klan. Even many physicians who've most benefitted from the crazed economics of American healthcare know it's broken.

On the other hand, most physicians are not surgeons, and most don't belong to the AMA. Support in this group is probably in the 85% range since reform may be relatively beneficial -- and it will help their patients.

Physicians are just one of Obama's secret weapons. He's keeping them in reserve on the left flank. On the right flank are the nurses ...

Montreal style rent-a-bike coming to Minneapolis?

Looks like Minneapolis is going to introduce the public bikes we saw in Montreal ...

" ... Nonprofit Nice Ride Minnesota plans to inaugurate a $3.7 million system of 1,000 heavy-duty bikes and 80 locking kiosks in and around downtown Minneapolis next May. For an annual fee of $60 or a daily charge of $5, you'll be able to take unlimited free rides of up to half an hour between the computerized locking stations..."

We saw quite a few riders on these Bixi ultra-rugged bikes. In Montreal if you exceed the 30 min ride, the cost is another $5 or so. Beyond that the price rises exponentially; the pricing ensures that riders bike between the locking kiosks and that bikes are moved into circulation when not in use. The sheer mass of these low performance/high reliability bikes makes long trips unfeasible anyway.

I don't know if they'll play as well in Minneapolis. As much as I love the Twins, they're not in Montreal's league for tourist attractions. On the other hand, we do have a marvelous network of bicycle paths.

It's a cool experiment. I'll probably buy a one year pass just to help encourage them.

Update 10/30/09: The NYT has some background. The bikes are "Velib", they cost about $3,500 each, and they originated in Paris. Unfortunately, they've become the target of Parisian sociopathies and have been heavily vandalized. I think they'll do a lot better in the Twin Cities.

Update 6/4/10: Visiting Montreal, I noticed a significant problem with the scheme. They now allow no more than two bikes to be charged on one credit card. So if you have one parent and two children, or two parents and three children, you're out of luck.

Birthers, Deathers and Truthers - the reason behind the madness

Birthers believe Barack Obama's birth certificate was faked. Deathers believe Obama's health care reform bill is Soylent Green in disguise. Truthers believe the 9/11 attack was an inside job, that mines detonated prior to airplane impact.

Millions believe these things. I've been astonished to find that even learned people fall for one or the other -- particularly people raised in cultures where the media makes our flacks look good.

Millions believe in these stories, but they can't for the life of them spin an evidence-based or even rationally empiric argument for their positions.

So should we mock the weak, or, with greater wisdom, accept that Reason is a hard road that few follow?

I would say neither.

I have had the opportunity to observe someone with a quite low IQ be right when I am wrong. True, he cannot usually explain his reasoning - perhaps because he cannot translate the workings of his mind into words. Nonetheless, he's right more often than chance would allow. Sometimes the weak are wrong, but sometimes there's a rightness they cannot express.

So instead of mocking them, I will try to articulate the unexpressed reasoning of the Birthers, Deathers and and Truthers.

The Birther claims are utterly implausible. Yet, how plausible is that the same America that reelected George Bush and Dick Cheney would elect a brilliant champion of Reason with a Black wife, Black children, a Black father and the middle name of Hussein?

Really. Think about it. America?! It's absolutely implausible.

The Birthers are delusional, but perhaps they are reacting to the sheer implausibility of Barack Obama. Myself I tend to suspect the benign intervention of extra-terrestrials.

The Deathers are likewise perversely wrong about the health care reform mission. They are not wrong to worry however. If Obama succeeds, as I think he will, the world of health care will be recast. Nobody knows what all the side-effects and unanticipated consequences will be. The Deathers' are right to be fearful, though they should fear the status quo more.

Lastly, the Truthers. To defend their irrational beliefs, consider my own story.

When the towers fell I was sure that we'd face a long struggle against a brilliant and implacable foe. I forecast mass casualties in America. The falling cost of havoc meant we'd soon face detonation of a truck born black market nuke in an American city. There were so many, many ways for smart people to wreak havoc on a modern industrial nation - a terrible struggle lay ahead.

Except, like a lot of other people, I was wrong. When poor, pitiful, Richard Reid tried to ignite his shoes I began to doubt, and the more we saw, the more al Qaeda seemed to be a conspiracy of the dullard -- especially compared to, say, Hamas.

So how could these medieval drudges have ever been so horribly, terribly successful? It defies Reason that such a convoluted plot should have worked. Nobody has a confident answer -- save the Truthers.

Birthers, Deathers, Truthers -- all of them wrong in what they say and write. Yet, despite the wrongness of their words, their feelings are easy to understand. We live in a profoundly strange and unpredictable world.

Pawlenty's humorous political move - opting out of health care

Minnesota has term limits. So my GOP governor, Tim Pawlenty, is not running for reelection.

If he were, this bit of inside humor would finish him ...

Pawlenty: It's "A Viable Option" To Invoke State Sovereignty, Keep Minnesota Out of Health Care Reform | TPMDC

Gov. Tim Pawlenty (R-MN), a possible presidential candidate in 2012, is now indicating that he could invoke state sovereignty and prevent his home state of Minnesota from participating in a federal health care reform effort if one passes, Minnesota Public Radio reports.

"Depending on what the federal government comes out with here, asserting the 10th Amendment may be a viable option," Pawlenty said, when asked about it by a caller on a Republican Governors Association conference call. "But we don't know the details. As one of the other callers said, we can't get the President to outline what he does or doesn't support in any detail. So we'll have to see, I would have to say that it's a possibility."

Pawlenty made it clear that he and other Republican governors will be more assertive about the 10th Amendment: "I think we can see hopefully see a resurgence in claims and maybe even bring up lawsuits if need be."

The same view -- properly called nullification, a doctrine dating back to the pre-Civil War days in the South -- had previously been expressed by Sen. Jim DeMint (R-SC) and Rep. Michele Bachmann (R-MN).

Pawlenty would be commuting by helicopter if he ever did anything so stupid, but it's not going to happen.

Pawlenty is an ambitious egomaniac, but he's not stupid. Problem is, his presidential ambition means he needs the support of the GOP base. That base is now largely frightened white men fearing the end of privilege, so Pawlenty has to say a lot of stupid things.

He can't leave Minnesota soon enough.

9/13/09: He chickens out.

The Speech

I read The Speech.

Shorter version:

Dear Democratic Senators:

I'm going to do this. Oppose me and I'll take you with me to the grave. Stick with me and you might live.

Why do I think he'll win?

Because two days ago he sucker punched the birthers and the deathers, and their media and GOP exploiters. He had them all frothing mad about his socialist education speech, and then told students to work hard and listen to their parents. Played 'em all for fools, so they're off balance when he delivers The Speech.

That was just a love tap. Obama, Emanuel, and the rest of the team have not yet begun to fight.

My money is on Obama to win.

The good side of the Wiki - search

Will we have Wikis in ten years? I don't know. Maybe something else will turn the Wiki into the Gopher of 2010.

Whatever comes along, I hope it preserves some of things that make Wikis work. Not all of these features are obvious, so I'll provide some personal background.

I use a Sharepoint* Wiki to manage all the information surrounding some new software we're developing. Not everything goes into the Wiki, but everything I work with has a Wiki pointer. It's where I go to find things.

I use the Wiki because Search Works for Wikis. It works for the same reason that full-text search works so well for email. The units of information are small (1-2 screens instead of 100 pages), titles can be descriptive, and author and date metadata are available. Wikis have the added advantage of the hyperlink enabling link weighted search results.

I can find things in the Wiki very quickly.

Whatever replaces the Wiki in the next generation of tech churn, I'm hoping it will be as Search friendly as the Wiki of 2009.

* How do I know humanity is doomed? Sharepoint 2007 is a fantastic commercial success -- and it's bloody awful. That's another story though.

Death of email part XI: forwarded emails with big red phishing warnings

I own a few domains, including a Google Apps domain we use for our family [1]. My immediate family members, excluding Kateva (canid), have calendars and emails in the family domain. Overall, it works pretty well. It pounds Apple's warped MobileMe into the sand. Savagely.

For reasons that aren't worth trying to describe, I've used an email redirector for some of these accounts. This is forwarding at the domain level, not forwarding from an email account.

This used to work pretty well, but when I tested it on a new account two problems appeared:

1. It was filtered to Google spam.
2. A BIG RED PHISHING warning appeared when I opened the email.
   

I was able to correct this by marking it as 'not spam' and 'not phishing' (the UI for the latter is a bit non-obvious, I had to follow the help link in the phishing notice).

This is a great example of the tech churn meme I wrote of yesterday. Email is in a troubled state as it painfully moves from the old world of the naive net to the new world of authenticated messaging [2].

This redirect mechanism is clearly not going to work, perhaps because the redirecting domain has been used by spammers in forged email headers [3].

Ouch. This is definitely a problem. I have some workaround ideas, but this will be a bugger to test since Google doesn't talk much about what it's doing.

--

[1] Free edition. If google drops the price on their small business product I'd upgrade to get some customer support options.
[2] One reason people like facebook messaging is that it's deeply authenticated.
[3] The curse of old, private, domains. Mine is very old. There's no defense against such forgery. See also two 2006 posts about a related problem (this isn't new)

• Gmail spam filtering threatens services
• Spam - blacklists are back

Google storage isn't so free any more ...

Remember when Gmail storage was supposed to be "infinite"? That didn't last long, but at least the storage seemed to grow all the time.

Not so now. My Gmail storage is pretty static. When I started using Picasa I had to pay $20 a year to store my images with a 10GB limit.

I'm nearing the limit, and the next step is "40 GB ($75.00 USD per year)".

Ouch!! That's comparable to the cost of MobileMe, and it's just storage.

Google is getting to be expensive.

Update 9/6/09: I looked over a few of the usual suspects. I have a five year old SmugMug account, but their iPhoto uploader is awful. (PictureSync, which I used to use with them, has been abandoned.) I considered Flickr, but I don't want yet another service. MobileMe is about $70 for 20GB, so it's about the same cost as Google's services once you factor in its other features.

Through DreamHost (KATEVA is my promo code) I have unlimited storage that I'm already paying for, and automated installation of ZenPhoto. I have to export my images from iPhoto and upload them via FTP or sFTP to DreamHost. The downside is there's no provision to pass on any iPhoto metadata, but then that barely works with any of the alternatives. (Maybe MobileMe is better, but Apple routinely screws up anything to do with the intertubes.)

I'm still turning this over. For the meantime I'll use Facebook more (low res images) and use Picasa selectively to reduce my storage drain. Maybe Google will come up with a better approach in the near term

Whatever I do the good news is that I've long used a private blogger blog to track where photos go. So even if I change providers there's a single index to all of our albums.

Update 11/11/09: Google gave us a 75% drop in storage costs. About six months late, but very welcome. So I'm cool with Picasa now.

Baseball parent communication: is it getting easier?

Naively, one would think it's getting easier to communicate with the parents of a 10 yo baseball player. After all, we have so many more ways to communicate than we did in the dark ages. Let's count them ...

1910 (2)

• Letter
• Handout (person present)

1950 - all of the above plus (4)

• Home phone (both parents)
• Work phone (father)

1990 - all of the above plus (11)

• Home phone (father) + answering machine
• Home phone (mother) + answering machine
• Work phone (mother) + answering machine
• Home email (father)
• Home email (mother)
• Work email (father)
• Work email (mother)

2009 - all of the above plus (now using m/f to represent mother/father) (20+)

• Mobile phone (m/f) + answering machine
• Web page
• Blog with feed
• Twitter
• Facebook page
• Google group or similar
• Google Voice
• SMS
• MMS
• Instant Messaging (multiple variants)
• Other email (m/f)
• and many more ...

So in about 100 years we've gone from 2 communication options to at least 20. So communicating about practice times, rain-outs, schedules, playoff and so on must be at least 10 times easier ...

Yeah, right.

Writing as a kid baseball coach, I'm guessing 1950 was probably the heyday of parental communication. Back then phone trees more or less worked and families were forced to more or less live in the same space. This year it was damned near impossible -- perhaps due to the profusion of communication channels, the increasingly failure of email (spam, message loss, account turnover) the disruption of employment changes (phone changes, lost mobile phone, etc), the failure of the feed reader, and the virus infestations that have disabled many XP-based home computers.

We tried to use a blog (so web access + feed) supplemented with email and, when pressed, a phone call (inevitably to a voice mail that seemed to be rarely checked). It didn't really work, but I"m not sure what would.

When it comes to communication, we're in full throttle tech churn. There's no common, standard communication channel that reaches a diverse group of people. We had one parent on Twitter, a few that checked their email somewhat reliably, perhaps 1-2 who would visit the web page, and several that were fairly unreachable.

I'm betting that we've reached an apotheosis of communication of communication dysfunction. Communication is important, and, sooner or later, people are going to figure out that we need fewer, better, options.

Alas, I suspect we won't get back to the highpoint of the 1950s for decades to come ...

Armstrong admits moon landing faked!!

OMIGOD!!!

Conspiracy Theorist Convinces Neil Armstrong Moon Landing Was Faked | Aug 31, 2009

Apollo 11 mission commander and famed astronaut Neil Armstrong shocked reporters at a press conference Monday, announcing he had been convinced that his historic first step on the moon was part of an elaborate hoax orchestrated by the United States government...

The best part is that apparently some people read this Onion spoof as fact. A delicious hit. (Sorry for the late post on this, I was on holiday when it was published. Just glad I got to read it.)

Update: more coverage from the BBC.

Obamacare. Wait. It's not over.

Birthers. Tea baggers. Deathers. Glen Beck inspired assassin wannabes. The weak dancing to their amoral master's tunes. Elders at town meetings demonstrating the pernicious effects of early dementia. Ratings starved media playing destructive games. Rupert Murdoch's Fox News and Wall Street Journal. Obama below 50%, vilified by the raving right and attacked by the fearful left. Kennedy dead and Robert Byrd 91 and ailing. Congressional democrats retreating on health care. And then there's the "bipartisan" "gang of six".

It's been a bad August for anyone worried about civilization. Despair is easy.

Don't despair.

This isn't new, and Obama is both lucky and good. It's not just him, look at his team. They're extremely formidable, and they've been in this game a while. They know the nation they're dealing with.

It's easy to underestimate Obama. He's identified with a tribe (black America) culturally associated with defeat. Unlike both Bill Clinton, GWB and most every GOP politician he doesn't rant and rave.

And yet, he tends to win.

For those who fear the worst, I suggest John Harwood's NYT article and John Scalzi's recent summary post.

Remember, any remotely sane American has to think that reform with enemies like Beck and the Birthers must be good.

Obama has been falling back, and the enemy has been charging forward. They think they see a soft center -- but they've forgotten about the hills on both sides ...

Update 9/9/09: I was early on this train, but now the NYT is catching up. President Barack Hussein Obama has not yet begun to fight.

PS. In case my use of the term "Obamacare" is confusing readers, I should mention that we have an inaugural postcard of President Obama prominently featured on our kitchen corridor wall at the children's eye level. I give it a nod every so often.

Update 10/1/09: As predicted, the forces on the western hill are now swooping down on the battle crazed spittle-flecked GOP berserkers. The eastern hill is standing by. Reminds me of the scene in "The Two Towers' when Gandalf leads the Horsemen of Rohan down upon the Orcs.

The evolution of comment spam - from parasite to symbiote?

Lately I've been getting blog comments that blur the spam/non-spam species boundary.

Comment spam used to be pretty clear. It would be unrelated to the post topic, and contained a link to a splog or other more or less fraudulent web page. These were easy to automatically block, so spammers dropped the links. Second generation comment spam aimed for search engine "optimization" through reputation enhancing back links to the author URL. Second generation comment spam was made of strings like "thanks for the the great post"

These were harder to machine reject, but easy for human reviewers to spot.

Now I'm seeing third generation comment spam. These have no links, and they're actually related to the original post. Sometimes they're almost non-sequiturs, but mostly they read like a fourth grade student answering a homework assignment. The grammar suggests either a very young or non-english writer. They do link back to splogs.

So how's the new species of comment spam being authored? It could be AI based -- maybe calling Wolfram Alpha or Wikipedia to retrieve relevant strings. It's probably human though -- outsourced work being done by low paid labor churning out comments at high speed.

This third generation spam isn't trivial to reject. Sometimes I have to think about it.

We know where this is going. Fourth generation spam comments will actually make sense. They'll be legitimate comments.

Fifth Generation spam comments will be very high quality. Skynet will appreciate them.

Update 9/4/09: Another (funny) take on the theme. Also, see the comment by one of my favorite writers.

Update 1/1/10: Cory Doctorow's excellent 2006 novella I, Row-boat (read it, it's online) tells us how Robbie the row-boat's ancestors became sentient ...

“Back in the net’s prehistory it was mostly universities online, and every September a new cohort of students would come online and make all those noob mistakes. Then this commercial service full of noobs called AOL interconnected with the net and all its users came online at once, faster than the net could absorb them, and they called it Perpetual September.”...

... “AOL is the origin of intelligence?” She laughed, and he couldn’t tell if she thought he was funny or stupid. He wished she would act more like he remembered people acting. Her body-language was no more readable than her facial expressions.

“Spam-filters, actually. Once they became self-modifying, spam-filters and spam-bots got into a war to see which could act more human, and since their failures invoked a human judgement about whether their material were convincingly human, it was like a trillion Turing-tests from which they could learn. From there came the first machine-intelligence algorithms, and then my kind...

OS X 10.6 - do you feel lucky punk? Do you?

I need to use my machines. So I'm the kind of geek who likes to, barring the addition of a new non-critical machine, wait 6-18 months before switching major releases of OS X.

As it happens I am going to buy an iMac in the next few months, but for now I've no hands on experience with 10.6. Still, if you review the late Aug 2009 late Aug 2009 OS X related reads the dog whistles are loud and clear.

Snow Leopard breaks stuff. Lots of stuff. It's also slower or only minimally faster than 10.5 on most machines, and Apple blew their major security feature (memory randomization) -- they obviously couldn't get it to work. So Windows 7 has better fundamental security -- as does Vista for that matter. Resolution independence? Oh, you remember that from 10.4 days? Of course not.

The only good news is that you can (illegally) install the $30 of 10.6 over 10.4. Considering Apple's long tradition of abusing early adopters I give everyone my ethical permission to do so. It's only fair.

There's good stuff in 10.6, and there's bad stuff. (For example, it looks like Apple continues to wreak havoc on pioneering concepts in the old Mac Classic file system.) There's enough good stuff that I'm looking forward to running 10.6.1 on a non-essential new iMac. Otherwise I strongly advise waiting 6 months before updating -- and even then you should confirm that your current printers and scanners and so on will work with 10.6.

Unless, that is, you're feeling lucky.

Update: This is the best review so far.

Update 9/6/09: I played with Snow Leopard in the Apple store today. As others have noted, it's hard to find any differences from 10.5. From what I read at least as many things have been broken as have been fixed. Unless you have to upgrade from 10.4, or you're buying a new machine, you shouldn't consider Snow Leopard before March of 2010.

Update 3/13/2010: I was too optimistic. My 10.6.2 machine crashes hard frequently. Among other issues, Apple screwed permissions and firewire. As usual.