Aminopterin, melanine and what else?

We don't know much about what's likely killed hundreds, or thousands, of us pets. Aminopterin could not be isolated from pets,
Melanine is in the Chinese gluten, but it's not supposed to be nephrotoxic. The focus is still on the Chinese gluten (which apparently has lots of fun ingredients), but maybe it's not the gluten after all. A dry cat food has also been recalled.

I hope Homeland Security is paying attention.

In the meantime, my personal conclusion that our family needs to switch to human-regulated foods for our dog stands.

A clear flaw with closed source: longevity

For longevity, one needs unencumbered (no patent issues) file formats at a minimum, and probably open source code ...

MacInTouch 3/07: Archival Issues (reader contribution)

... One of my fondest treasures is a 32 disk CD-ROM set in a mahogany box, "The Complete National Geographic" magazine. It was a searchable collection of every page of every issue of National Geographic for 109 years. I bought it in system 7.5 days and used it up thru OS 9. But support for this collection met a tragic death

National Geo had farmed out the development to a chain of third party developers...Mindscape, The Leaning Center, and Broderbund (of PrintShop fame) whom for whatever reasons had "difficulties" in sustaining the project regardless of its merits. Each company's edition under the National Geo brand came with a proprietary Reader/Searcher. The various versions were not compatible, not even in consecutive years... The series died about 1999 and support for it didn't last much longer. Some of those companies still exist but avoid all talk of the Complete National Geo debacle. I've tried. Even National Geographic customer service is curiously mute.

It's exasperating to think that all that historical data, all those articles, all those photographs, are sitting on my shelf and cannot be viewed with today's operating system. ( The Reader/Searcher looked to my naive eye like a kissing cousin to Acrobat.)

If only the source code for the Complete National Geographic CD-ROM set were available and could be updated to run natively on OS-X and other contemporary platform...

Let's learn from this. Don't invest in products dependent on closed source solutions. Speaking of FairPlay and every other DRM solution ... What do you think the chances are you'll be able to read a FairPlay DRMd file in 10 years?

Shame on National Geographic, btw. The best explanation is they didn't negotiate their contracts properly ...

Apple TV ships, iTunes Store a smoldering crater

Is it coincidence that within a few days of Apple TV reaching consumers the iTunes Store is unusable? It's not quite dead, but it's too slow to buy from.

An ominous hint of what consumer video distribution will mean to the net? Not all bad news for Apple though ...

Kristof on how to turn lunch money into hope

Kristof, who never gives up, has an article on how micro-finance has become personal. He visits his business partners in Afghanistan...

The New York Times
March 27, 2007
You, Too, Can Be a Banker to the Poor
By NICHOLAS D. KRISTOF

...From my laptop in New York, I lent $25 each to the owner of a TV repair shop in Afghanistan, a baker in Afghanistan, and a single mother running a clothing shop in the Dominican Republic. I did this through www.kiva.org, a Web site that provides information about entrepreneurs in poor countries — their photos, loan proposals and credit history — and allows people to make direct loans to them...

... Mr. Abdul Satar said he didn’t know what the Internet was, and he had certainly never been online. But Kiva works with a local lender affiliated with Mercy Corps, and that group finds borrowers and vets them.

The local group, Ariana Financial Services, has only Afghan employees and is run by Storai Sadat, a dynamic young woman who was in her second year of medical school when the Taliban came to power and ended education for women...

...Web sites like Kiva are useful partly because they connect the donor directly to the beneficiary, without going through a bureaucratic and expensive layer of aid groups in between....

...A young American couple, Matthew and Jessica Flannery, founded Kiva after they worked in Africa and realized that a major impediment to economic development was the unavailability of credit at any reasonable cost....

Yes, it's a bit gimmicky, it would presumably be more efficient to give the money to CARE.ORG and let them donate to a microfinance organization. Still, the human angle might help draw in some extra funds. Going forward, the interesting possibility is going the next step, and becoming an active business partner. So make the loan, but also become involved in the enterprise. A bit like being an armchair peace corp person.

I'll give it a try.

Aminopterin update: likely thousands harmed

There's not much coverage now, but Google picks up this update. I will wager, based on the VIN reporting, that the number of animals harmed is in the mid to upper thousands.

ABC News: Group Says Pet Food Deaths Underreported

ALBANY, N.Y. - At least 471 cases of pet kidney failure have been reported in the 10 days since a nationwide recall of dog and cat food and about a fifth of those pets have died, a veterinarians' information service said Tuesday...

... Paul Pion, founder of the Veterinary Information Network, which counts 30,000 veterinarians and veterinary students as members, said Tuesday the number of reported kidney failure cases had already grown higher than the 471, but he said he wouldn't have an updated tally for a few days.

Of the reported cases, he said, 104 animals have died. The network's survey results were earlier reported by the Los Angeles Times.

Pion, a California veterinarian, said only 10 percent to 20 percent of the people who belong to his Web site had responded to a request for information.

... Researchers at the New York food lab, Cornell University and other labs were still working Tuesday to pinpoint which individual ingredients were tainted with the poison, officials said. They also said there could still be undetected hazards in the food...

The labs are having trouble working with the gluten, so it will be some days before they can determine if gluten was really the source, and if the contaminated gluten is entirely Chinese. They are careful to note they cannot exclude other toxins. If we ever understand how the Aminopterin contamination occurred, we will have a better idea of the likelihood of secondary toxins.

A conservative extrapolation of Pion's numbers suggests a renal failure toll to date of about 4,000 pets, with a death rate still running at around 20%. It is likely the majority of the sick had more vulnerable kidneys, probably older cats. A larger number of animals will suffer significant kidney damage without symptoms. Their lives may be shortened. It is likely that significantly more than 4,000 animals will have been harmed.

When we learn how this happened, we will also be able to draw inferences about how often lesser problems may have occurred with pet food manufacturing and distribution over the past few years. It would be surprising if all the problems are being detected; error analysis in other domains always finds that these "sentinel events" represent the "tip of the iceberg".

We will continue to investigate if we can substitute human-regulated food for a significant portion of our dog's diet going forward.

Fear in the blogosphere: Microsoft hunts again

I suspect there are a few young techies who do not fear Microsoft. They don't remember when Gates et al pillaged the landscape, sowing salt on the burning embers of resistant villages, conquering with ruthless power and endless treachery. I confess, I have contributed to a false sense of security by pointing out how incompetent Microsoft has been in the past few years.

It is time for me to right my wrong. Microsoft hunts again.

There is only one good tool on any platform for efficient blogging in both Google's Blogger and the open source Community Server (metaweblog API) environment, and it's Microsoft product - Windows Live Writer. I've tried all the rest, they don't compare. [See Update!]

Live Writer only works with IE. It only works with Windows. Yes, there's a Firefox plug-in for Live Writer. It broke long ago, and, oddly enough, it's never been updated.

BlogJet was very good in version 2.x, but version 3.x is a mess. Scribefire is very minimalist and just broke with Firefox 2.03. One the Mac side Mars Edit and Ecto aren't even in the race -- they assume that all writing is done from a single machine. They can't properly handle fetching and editing past posts. They are also updated slowly if at all -- I could go on. They are goners.

Google's integrated "BlogThis!" bookmarklet hasn't been updated to support Blogger 2.0's tags and it's slow, quirky, and underfeatured (Blogger 2.0, btw, is a vast improvement over Blogger 1.0).

So Microsoft has a free tool that is vastly better than anything else, it only works with IE/Windows, and it's smack in the middle of a strategic market. Wow, doesn't this feel familiar?

Is anyone awake out there? Have all the geeks been lulled to sleep by Microsoft's seeming incompetence over the past few years? Where's Google anyway? What happened to all those Firefox development efforts? Is Apple trying to ignore the blogging world? (Anyone remember the transient blogging tool once bundled with new Macs?)

All is not lost. Sharepoint 2007's blogging support is miserable, and Microsoft has invested a lot in Sharepoint. Maybe the Sharepoint team will end up destroying Live Writer. I know I'm rooting for them, because as much as I like Live Writer, I've seen this movie before ...

[1] Update 1/5/09: Thanks to very helpful comments on this post I have learned that Adobe Contribute for OS X and Windows (list $170) will work with Blogger and other standards compliant platforms. It's very expensive and suffers from being an Adobe product (they don't seem to understand how to install OS X software) but I'll try to get a look at it.

Aminopterin update: isolating the source and it's not the FBI's job ...

Aminopterin poisoning of the feline and canine foodstream has fallen off the mainstream news radar, but Google has an answer to that. Here's today's update:

Helena Independent Record

... The laboratory that identified the poison believed to be responsible for the death of pets around the country has started testing individual components of the tainted pet food to determine which ingredient was contaminated, officials said Monday.

Scientists at the New York State Food Laboratory on Friday identified aminopterin as the likely culprit in a poisoning scare that prompted the recall of 95 brands of "cuts and gravy" style dog and cat food.

Department of Agriculture and Markets spokeswoman Jessica Chittenden did not know when the lab would have results from the new tests.

The federal Food and Drug Administration has said the investigation into the pet deaths was focused on wheat gluten. Stephen Sundlof, the federal agency's top veterinarian, said Friday it remains the suspected source of the contamination...

... Cornell University's veterinary school also is testing the food. Dr. Donald Smith, dean of the school, said the tests of the individual food components would likely take days.

"It's a very challenging set of procedures," he said. "We have to keep in mind there are other things out there that could potentially be hazardous. We are working very hard to confirm it was aminopterin."

... FBI spokesman Stephen Kodak said the agency is "not involved in any way, shape, or form." He said the FBI would likely only get involved if evidence pointed to the products being tampered with while on store shelves.

Chittenden said any criminal investigation would have to be initiated by the FDA...

Interesting that the FBI's responsibilities do not extend to products tampered with outside of store shelves. I wonder who handles those? Homeland security to be sure, but they don't launch criminal prosecutions ...

British government concedes the 650,000 death toll for Iraq is credible

The British government is not saying that Blair believes 650,000 Iraqis have died because of invasion that would otherwise have lived. The government is admitting that it's as good a number as any, and probably more reliable than most:

BBC NEWS | UK | UK Politics | Iraqi deaths survey 'was robust'

... The British government was advised against publicly criticising a report estimating that 655,000 Iraqis had died due to the war, the BBC has learnt.

Iraqi Health Ministry figures put the toll at less than 10% of the total in the survey, published in the Lancet.

But the Ministry of Defence's chief scientific adviser said the survey's methods were "close to best practice" and the study design was "robust".

Another expert agreed the method was "tried and tested"....

I wrote this when the estimate was 100,000 and this about the 600,000+ estimate:

... If we adjusted the Iraqi toll to our population of 300 million, the conflict would claim 6 million Americans lives. Would we call that a civil war? The "conflict" in Iraq is now up to about 60% of the death total of a war that most of would consider "civil"...

In the US we consider our civil war to have had horrific casualty figures, though ours were concentrated among combatants (young men). Whether the "true" number is 200,000 or 650,000, the conflict in Iraq is within range of the carnage of the American civil war.

Phil Carter on the six year free fall of America

Phil (Intel Dump) Carter is my most trusted perspective on the American conquest/occupation/entrapment of/in Iraq. After Phil, things trail off rather sharply, due to my inverted trust in Cheney Bush (if they say it's sunny I pack my umbrella) and the extreme danger of in-country journalism.

Phil comments on a Zbignew Brzezinski editorial in WaPo: INTEL DUMP - The only thing we have to fear is . . . us. In brief, the choices of Cheney/Bush have been a disaster for the US and the world.

And yet ... I still think that we're extremely vulnerable as a society to attacks that would dwarf the destruction of the twin towers. Much of the reaction to 9/11 has been driven not only by what happened, but also by what imaginative people thought could and would happen next. Brzezinski wrote:

... The terror entrepreneurs, usually described as experts on terrorism, are necessarily engaged in competition to justify their existence. Hence their task is to convince the public that it faces new threats. That puts a premium on the presentation of credible scenarios of ever-more-horrifying acts of violence, sometimes even with blueprints for their implementation...

So is he saying the scenarios were and are not credible? Scanning the rest of the editorial he seems to be saying the threats are indeed credible, but that our responses to date are a panicked, ineffective and dangerous distraction for what we should be doing.

My position is that while Cheney/Bush are the most incompetent American leadership since the end of the 19th century, that the danger is real. That makes their failures all the worse. We have been digging holes instead of building dikes. [1]

[1] Note, invading Afghanistan is not an exception to the Cheney/Bush disaster. That was an automatic and valuable response -- not even Cheney/Bush can completely mess up everything.

Aminopterin update: more details from blogs

Obviously I'm interested in the aminopterin story, but mainstream media coverage has been slight. I decided to try search blogs, which is how I came to link to a conservative humor site. I think that's the first time I've linked to a conservative anything, except perhaps for conservapedia:

Conservative Cat: Menu Foods Recall and the 40 Parts Per Million

...We now have more information about the contamination in the Menu Foods products. The New York State Animal Health Diagnostic Center at Cornell University and the New York State Food Laboratory tested three samples of the contaminated products. One sample was clean, but the others contained aminopterin at a level of 40 parts per million. According to Cornell lab director Bruce Akey, this is a sufficient concentration to cause kidney failure in dogs and cats.

The operating hypothesis at this point is that the aminopterin was sprayed on the wheat during shipping or storage in order to prevent rats from eating the crop. Because the normal method of creating gluten from wheat is by washing it, this had to have happened after the wheat had been converted.

Wheat gluten is high in protein and has a chewy texture. The so-called cuts and gravy pet foods use the gluten to to make the food bits feel meatier when they're being chewed. This is not necessary in your standard canned or dry pet foods. The safest protocol for buying pet food right now is to look at the ingredients, and if it does not say wheat gluten, you're safe no matter who makes the product. You'll end up passing over some good stuff that's not contaminated, but it's much easier than memorizing the long list of brand names. This is just until the crisis passes, by the way. There's nothing wrong with wheat gluten when it hasn't been poisoned.

Before the government does something drastic and saddles them with a lot of expensive testing procedure, Menu Foods and other manufacturers should consider getting their wheat locally and plastering 100% American Made on the can and pouch labels. It will mean a price increase, but it's nothing compared to the cost of a new Federal agency for pet food regulation...

The proposal is the appropriate Libertarian solution -- let the market decide. I'm not sure, but this might have worked for tuna and dolphin kills. It requires a credible threat of a consumer boycott to motivate manufacturers to take these measures. This will increase product costs, a manufacturer can't take this step unless the entire market moves at once. That requires either regulatory action or a very committed consumer based. Consumers can muster that focus for a few products, but not for all of them all the time. It's an unwinnable battle in the real world. Regulation is cost inefficient, but the alternative very, very, rarely works. It just doesn't scale across the range of an economy.

Update on the unfinished count of the human genome

I'm a big fan of Bill Clinton, but he did have a talent for useful hokum. It often served a greater cause, but it did have the disadvantage of being a bit ummm untrue. The Y2K "human genome sequenced" story was a bit like that. The real timeline of the project seems suspiciously close to how long the grumpy old skeptics thought it would take. We're still slogging away. Carl Zimmer brings us up to date. The original article has a fascinating link to "PANTHER", an academic project for assigning genes to functional categories. Don't miss Zimmer's ending sentence ...

The Loom : You Don't Miss Those 8,000 Genes, Do You?

... When Craig Venter and his colleagues published their rough draft of the human genome in 2001 they identified 26,588 human genes. They then broke those genes down by their functions. Some were involved in building DNA, some in relaying signals, and so on. Remarkably, though, they classified 12809 genes--almost half--as "molecular function unknown."

... There are web sites where you can observe works in progress, such as the human genome. One of those sites is called PANTHER. I contacted the top scientist behind it, Paul D. Thomas, with my question, and he sent me a link. When I clicked on the link, I got the pie chart I've posted here (click on the image to go to the original page if it's hard to read).

The pie shows that we're now down to just 18,308 genes. That's over 8,000 genes fewer than six years ago. Many sequences that once looked like full-fledged genes, capable of generating a protein, now don't make the grade. Some genes turned out to be pseudogenes--vestiges of genes that once worked but have been since wrecked by mutations. In other cases, DNA segments that appeared to be parts of separate genes have turned out to be part of the same gene.

Today scientists still don't know the function of 5898 genes in the human genome...For all the work that has poured into the genome, for all the grand announcements, we still don't know have the faintest idea of what about a third of our genes are for.

... few human genes have experimental evidence for their function in humans. In one study of 35329 proteins, scientists estimated that only 2784 met this gold standard.

... And then there's the whole matter of all the other DNA that doesn't encode proteins (98.5% of the genome all told). A lot of it is most likely a mishmash of broken genes and viral DNA. It's possible to cut huge swaths of it out of a mouse's genome with no apparent ill effect. But there are also a lot of important players hiding in that wilderness--switches that proteins can use to turn genes on and off, sequences that do not give rise to proteins but rather RNA molecules that create their own control system for a cell. In all of these complications, scientists will probably find the answer to the question, "How do roughly the same number of genes encode such different kinds of animals?" Complexity isn't purely a matter of the number of genes you have. It's also how you use them.

...few human genes have experimental evidence for their function in humans. In one study of 35329 proteins, scientists estimated that only 2784 met this gold standard...

... I would not have been able to have created this pie chart without Thomas's help. Perhaps some science writers will become more like investigative political reporters who know how to sift through Federal election databases for the real news...

I recall from Dickson's 1970s "Dorsai" cycle that much research in that "space opera" consisted of mining "the encyclopedia" (re: the web) for knowledge. Zimmer is quietly predicting "knowledge mining" will become a bit part of science description -- not just writing, but also doing science. In fact, I'm not sure there's a clear difference between knowledge mining and classic science, though I confess knowledge mining seems to have some resemblance to the medieval scholasticism.

We're now in the story of the 'incredibly shrinking genome'. Meanwhile we learn elsewhere in Zimmer (I think it was there) that humans and chimpanzees are much less alike than we'd thought. There are many ways to encode complexity, and evolved organisms have a rather baroque approach to solving such problems.

Update: If we extrapolate a bit, it would not be surprising to discover that we have about 16,000 genes that code for 35,000 proteins. So there's a 2:1 compression ratio from gene to expression, which is comparable to best lossless compression algorithms run against highly complex data. The 2:1 ratio presumably must have some implications for how natural selection can proceed. It's easy to imagine that a mutation in a gene that "improves" the function of one protein product might disable another protein coded by the same gene. So evolution would typically proceed "two steps forward and one step backwards", or at best with peculiar side-effects on a secondary protein arising from changes to the primary protein.

Elizabeth and John Edwards

The NYT interviewed the Edwards about their decision to continue John's presidential campaign despite Elizabeth's metastatic breast cancer:

Facing a New Battle, Mrs. Edwards Set Campaign’s Fate - New York Times:

...Mrs. Edwards — whose decision to push her husband to run for president in spite of her life-threatening illness provoked an intense discussion across the country about illness, ambition, child-rearing and death — said her husband’s candidacy was not only about his needs and desires, but also her own life and her wish to be something other than a woman best known for her life-threatening illness.

“I expect to live a long time,” Mrs. Edwards said. “I expect us to have lots and lots of years together. I do believe that. But if that’s not the case, I don’t want my legacy to be that I pulled somebody who ought to be president out of the race. It’s not fair to me, in a sense.”

Saying she hoped to be “heavily involved” in her husband’s campaign, she said: “My feeling is, if we gave up what we have committed to as our life’s work, wouldn’t I be getting ready to die? That’s what I’d be doing. This cause is not just John’s cause, it’s my cause.”...

The Edwards' know a bit about hard times. What I think is irrelevant, but in fact I'd have "approved" (like that matters!) whatever they decided. Bad things happen to even the luckiest of us mortals, we can't fall over every time tragedy whacks us -- though some tragedies will put most anyone down for a while. An early death of a parent and partner is a bad thing, but they've lived through worse.

Anyway, the odds are decent that Elizabeth will live a through at least part of a second term, and she knows how badly we need the leadership John and his team can deliver. This is her legacy. I hope we are wise enough to justify her gift.

In the absence of Al, I've been leaning towards John. I'm glad I'll have the opportunity to learn more about him.

A review of the pet food industry

Aside from globalization, factory food, homeland security, and personal tragedies, the aminopterin poisoning of 2007 has shed some light on the pet food industry. Emphases mine. I admit, I was surprised to learn that pet food is less rigorously regulated than cow feed -- because we don't eat pets ...

Pet Food - Pets - Menu Foods - Poisonings - Dogs - Cats - New York Times

.... Q. What’s in pet food then? Is it regulated?

A. Pet food is regulated by the F.D.A. through the same state agencies that regulate food for farm animals. But product excluded from animal feed can go into pet food — meat and bone meal, nervous system tissue — parts of animals not allowed for anything else. There were cases of mad-cow disease in cats in England. The opportunity for cheap byproducts is much greater in pet foods. The assumption is that better brands don’t do that, but it’s not verified.

Q. If a few companies are making many of the brands, are pet foods all the same then?

A. Nutritionally, they have to meet the same industry standards, though they’re priced very differently. You read the labels and they all look alike — corn is the first ingredient in a lot of dry food.

Q. Why are some brands more expensive?

A. The quality of the ingredients. Are you using human-grade food or food that humans wouldn’t care to eat? It doesn’t matter to animals but it matters to the people who own them.

Q. What about health claims?

A. When you see food claims on breakfast cereal — for instance, that it lowers cholesterol — there has to be some scientific substantiation behind them. Pet foods have claims on them, that they support a healthy immune system, reduce risk of whatever, but they don’t have to be supported by large amounts of science. They’re worded in such a way that doesn’t violate the F.D.A.’s labeling rules. I think the F.D.A. will have to take a much closer look at pet foods — this is the second recall in a short time.

Q. What do cats and dogs enjoy eating?

A. Cats don’t have a taste for sugar; they don’t taste sweet things. They have a particular taste for what is referred to in the industry as “animal extract” — God knows what’s in it. Dogs can taste sweet, but, dogs will eat anything. Cats are very fussy, as any cat owner will tell you. The one thing that’s never been studied is to find out how long it would take for a cat to eat something it doesn’t like — owners never wait it out. People are very attached to their pets, and it’s painful to watch a cat not eat.

Q. Should owners prepare their own food for pets or feed them table scraps?

A. There’s evidence that dogs can be fed table scraps and do quite well, provided they’re healthy table scraps — meat, dairy, vegetables, fruit. The problem is a lot of humans don’t eat that way.

A mixture of expensive "organic" pet food and healthy table scraps sounds good and perhaps relatively cost-effective. It's impressive how little we know about whether our "premium" pet food is really very premium at all.

Six "top 10" lists for software people

Coding Horror: Top 6 List of Programming Top 10 Lists is excellent. Read and study them all. I've copied the entire post to a "note" in my Palm [1] so I can periodically refer to them. So far they all feel familiar, but I love this kind of review. Nice job assembling them CH!

[1] The Palm OS Note or Memo is the simplest possible application. The Microsoft Outlook Note is barely more sophisticated (it has categories, but no scroll bar, so maybe they're even). The two sync almost perfectly (category problem). Thanks to full text search (Lookout for Outlook, native to the Palm) they are very powerful tools. Nobody uses them. Rock solid. Simple. Useful. Puzzling ....

Are you an engineer? (and a joke)

CH quotes from The Inmates Are Running the Aslum who quotes an old joke. Here's the joke:

Coding Horror: The Rise and Fall of Homo Logicus:

Three people are scheduled for execution: a priest, an attorney, and an engineer. First, the priest steps up to the gallows. The executioner pulls the lever to drop the hatch, but nothing happens. The priest claims divine intervention and demands his release, so he is set free. Next, the attorney takes a stand at the gallows. The executioner pulls the lever, but again nothing happens. The attorney claims another attempt would be double jeopardy and demands release, so he is set free. Finally, the engineer steps up to the gallows, and begins a careful examination of the scaffold. Before the executioner can pull the lever, he looks up and declares, 'Aha, here's your problem.

Yeah, I might do something like that. It's a good test to see if you're an engineer-type. The rest of the post is worth reading too, it's really a rant that "engineers" need to realize that their customers are usually not like them. That's very true, but it's not just engineers who fall into this trap. The single most important thing I was taught about product management was never to assume that I resembled the customer in any significant way. I had to be taught this, I didn't figure it out on my own -- but once I heard it I knew it was true.

My (few) readers may think that it's obvious that I don't resemble many people, but, to be honest, at some unconscious level, I thought I was pretty typical. I think this is a common misapprehension among engineering types -- it's probably related to having a touch of autism. My guess is that there are some neural configurations that are prone to this self/other error, and some aren't.