Interoperability, standards, and the evolution of the codon

Standards are a big deal in healthcare IT (my industry). Standards for the building blocks of knowledge, standards for the way knowledge is assembled, standards so that software can act on knowledge and exchange knowledge between systems.

It is surprisingly hard to make the case for these standards. They have an up front cost, particularly early on. If you've got something that works, why change? The strongest argument is from economics -- even if it's tough to adopt a standard, eventually network effects will mandate its use and time will address the defects. (The hard part, of course, is knowing what the real standard will be ...) The future cost may be much higher than near term adaptation ...

Now we have a possible supporting argument from the history of life on earth. Standards adoption by proto-life was important to intra-organismal interoperability ...

The Loom : In the Beginning Was Linux?:

... Scientists have long debated how the same genetic code wound up in all living things. Why twenty amino acids? Why three nucleotides? One possibility was that it was just a "frozen accident." Another has been that it evolved in an ancient lineage and provided an evolutionary edge against others with different codes. ...

...Evolution gradually produced more precise genetic codes, Woese and his colleagues argue, but different communities of microbes evolved different codes. In each community, a shared code made it easier for microbes to share genes. If you plug a gene into an organism with a radically different code, it will produce a radically different protein--mostly likely one that is useless as well. It's like grabbing a piece of software and trying to run it on the wrong operating system.

The more microbes used the same genetic code, the bigger the pool of genes they could all take advantage of. Those shared innovations benefited the entire community as it competed with communities with other genetic codes. Imagine microbes colonizing some bizarre new ecological niche--a seep of petroleum, for example, or undersea volcanic chambers. The microbes that can take advantage of more innovations will outcompete the ones that belong to the smaller community. This advantage would also drive the evolution of different genetic codes to be more like one another, because communities of microbes would get access to even more innovations.

Over time, the benefits of a big innovation pool wiped out the original diversity of rare codes, replacing it with one universal language. Only later did life begin to lose its communal nature and begin to evolve into separate lineages that we see now as the tree of life. While those lineages produced things as different as humans and bacteria, they all share the same genetic code that evolved during that communal age.

Great analysis, but a better analogy would have been file formats and software, not operating systems and software (ok, so the distinction is blurry). Government lawyers made the same mistake in the Microsoft monopoly trial and the judge made the same mistake during the penalty phase. Data formats are far more important than software. Our software/os/interpreters are quite different from those of viruses and bacteria, but the data formats persist. Microsoft should have been forced to surrender control over their data formats -- and forget about their software.

In that regard evolution has something to teach open source movements, which historically have paid far too much attention to software and not enough attention to data. Health informatics understood this twenty years ago, and now fights over file formats with state governments indicates others are catching on ...

ID - nucleosomes and DNA control

Another example of icomprehensibly baroque and bizarre "design":

Scientists Say They’ve Found a Code Beyond Genetics in DNA - New York Times

... Having the sequence of units in DNA determine the placement of nucleosomes would explain a puzzling feature of transcription factors, the proteins that activate genes. The transcription factors recognize short sequences of DNA, about six to eight units in length, which lie just in front of the gene to be transcribed.

But these short sequences occur so often in the DNA that the transcription factors, it seemed, must often bind to the wrong ones. Dr. Segal, a computational biologist, believes that the wrong sites are in fact inaccessible because they lie in the part of the DNA wrapped around a nucleosome. The transcription factors can only see sites in the naked DNA that lies between two nucleosomes.

It's described a kind of statistical code, not directly deterministic, but on average the right places get bound. I suspect it's another variant of meaning being embedded in topology as well as sequence. Only a madman would design such a bizarre system of encoding information, yet it is incomprehensibly robust ...

Fritos flavor twists: exhibit A in the American Obesity epidemic

My wife showed me a small bag of FRITOS FLAVOR TWISTS™ Honey BBQ Flavored Corn Chips. These are the sort of thing horrible parents like us sometimes allow their poorly served children to have. This itty bitty snack sized bag contains "4 servings".

Four. 4.

Why did FritoLay corporation decide to call this a "four serving bag"? Maybe it's because one serving has 160 calories and 15% of the fat RDA. So the typical snack sized bag priced at 99 cents, has 640 calories and 60% of the fat RDA.

In other words, one bag has about half the calories the average adult needs in a day.

I used to think the tobacco companies were all alone in the pit of corporate damnation. Philip Morris, meet FritoLay.

Domesticating rats, domesticating humans

Soviet-era geneticists showed they could domesticate foxes and rats in a human lifetime. The tame animals show white spots in their fur, smaller skulls and floppy rounded ears. Now researchers are trying to figure out which genes were selected for. The same genes might have been responsible for the domestication of humans ...

Nice Rats, Nasty Rats: Maybe It’s All in the Genes - New York Times

...Richard Wrangham, a primatologist at Harvard, has proposed that people are a domesticated form of ape, the domestication having been self-administered as human societies penalized or ostracized individuals who were too aggressive.

Dr. Paabo said that if Mr. Albert identified the genes responsible for domestication in rats, “we would also look at those genes in humans and apes to see if they might be involved in human evolution.”

Human self-domestication, if it occurred, would probably not have exactly the same genetic basis as tameness in animals. But Mr. Albert said that if he could pinpoint the genetic difference between the tame and ferocious rats, he would compare the chimp genome and the human genome to see if they showed a similar difference.

One possibility is that a handful of genes — perhaps even just one — underlie all the changes seen in domestication. A structure in the embryo of all vertebrates, known as the neural crest, is the source of cells that constitute much of the face, skull and pigment cells, and many parts of the peripheral nervous system and endocrine system. If the genes in the neural crest cells were delayed just a little in coming into action, a whole range of tissues could be affected, including the maturation of the adrenal glands that underlies the first fear response of young animals, Dr. Fitch has written.

Could a single gene that affects the timing of neural crest cell development underlie the whole phenomenon of animal and human domestication? “There would be one happy science Ph.D. student if that were true,” Mr. Albert said.

Of course the domestication of humans might have occurred long before homo sapiens, perhaps in homo erectus. Or maybe it's just ongoing. There may be a tension between domestication and sexual selection behaviors; it would be easy to imagine domestication varying over the course of human history ...

Update 7/26: I didn't give enough thought to the key concept here -- how quickly this transition occurs. Eight generations for the foxes. That's not an eyeblink, it's an instantaneous flip/flop on evolutionary time scales. This wild/tame behavior smells like some kind of evolved "switch mechanism" -- the organism can range from 'viscious' to 'tame' very quickly depending on environmental changes. I think there may even be evidence of this in baboon troupes that have been isolated by rivers and the like. I wonder if this is unique to mammals or if it's seen in birds and other social animals. (Ants, perhaps?)

With this kind of responsiveness isolated groups of humans and pre-humans might have gone back and forth many times over the past million years or so, depending on the local environment. We know the level of violence in medieval times was shocking by today's standards, and we know from gene frequency studies that human evolution can act on surprisingly short time scales. Wouldn't it be interesting if anglo-saxon of 2006 were genetically more domesticated than the anglo-saxon of 1000 ACE?

Using the futures market to predict the efficacy of clinical claims to cure Alzheimer's

The BBC today headlined a claim that  Daily pill to 'cure Alzheimer's'. In mice, of course.

Now there is some justification for the interest in PBT2. It's similar to a medication that's been approved in humans, and they've done some preliminary testing for toxicity in humans. On the other hand, we can cure tons of stuff in mice, and we don't really know the relationship between amyloid and dementia.

In some amounts amyloid seems to help protect the brain from injury, so if you reduce the amyloid you might be enabling another injurious process. (Of course we know of many human disorders where the body overreacts to injury, such that the response is 'worse than the disease'. Amyloid deposition could fall into that category.)

There are a zillion reasons this might not go anywhere. On the other hand, the economic impact of slowing dementia onset is enormous. Many more people would work into their 60s and 70s. (A large number of Americans stop work in their 50s, and numbers are even higher elsewhere.) The social security problems would diminish greatly as would medicare costs (dementia is a slow and costly killer).

So one way to judge how real this is would be to look for movement in the 30 year bond rates and related markets … If one really thought this would work, there would be some interesting speculative opportunities …

Ten decluttering tips

From a web site devoted to ... decluttering. Lord, talk about narrowcasting. Great Tips however. I think my wife might go for this one.

Smoking is good for the earth, bicycling is bad

Before I tell you the story, think about the title. Why would that be true?
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It's the longevity, of course (NYT).Incredibly, a witty fellow has earned great fame by pointing out that since bicycling is associated with longevity, bicycles are bad for the environment. Hmm. Sounds obvious, and conversely, smoking is good.

I suspect the tricky part of the paper was showing that whatever one saves on the bicycle, is more than made up in more years of using electricity and consuming stuff. The caveat is that if bicycling is somewhat dangerous, and I wonder if he took the increased trauma risk into full account.

It's a funny story, but the bicyclist author has a serious point to make. Whatever lifestyle changes we make, they can be swamped by increasing lifespan. If gas prices rise we drive less and walk more, using less gas but living longer and thus using more energy ...

Landis on the Tour: The greatest victory in the history of sport?

Floyd Landis is expected to win the Tour de France. If this happens, it will likely be his only win, as he's scheduled to have his osteonecrotic hip replaced after the tour. He will then be able to walk up stairs, but it is unlikely that he'll compete again.

He was profiled in the NYT Magazine a week ago. His physicians thought he was insane to compete, but realized he was beyond mere reason. Landis believed that relentless bicycling would wear a groove in his shriveled femoral head that would enable him to ride competitively. Maybe it did. I would like to see the post-op pictures, I hope Landis will publish them.

A few days ago he was in 11th place. Yesterday, against all reason, he fought his way back to 30 seconds behind the leader. Now he is 59 seconds ahead.

Even if he wins, there may have been greater victories in the history of sport. Maybe. Maybe not.

Update 7/27: Damn.

The Cult of Reason and Rand

Yesterday I mentioned Ayn Rand's connection to the oxymoronic phrase 'Kantian Nihilism'. Rand must be particularly memic today, because Brin quotes Stacey quoting Shermer on Randism (Objectivism):

Contrary Brin: An Interesting Guest Posting...

Blake Stacey: "One quick note before I forget: on the subject of Ayn Rand, you should check out (if you haven't already) Michael Shermer's essay 'The Unlikeliest Cult', which was published in **Skeptic** magazine and reprinted as a chapter of his book **Why People Believe Weird Things**. I was able to dredge a copy out of a Google hit parade:

Here's the money quote:

'The cultic flaw in Ayn Rand's philosophy of Objectivism is not in the use of reason, or in the emphasis on individuality, or in the belief that humans are self motivated, or in the conviction that capitalism is the ideal system. The fallacy in Objectivism is the belief that absolute knowledge and final Truths are attainable through reason, and therefore there can be absolute right and wrong knowledge, and absolute moral and immoral thought and action. For Objectivists, once a principle has been discovered through reason to be True, that is the end of the discussion.

If you disagree with the principle, then your reasoning is flawed. If your reasoning is flawed it can be corrected, but if it is not, you remain flawed and do not belong in the group. Excommunication is the final step for such unreformed heretics.'

I don't know if I'd have phrased it the way Shirmer did, though I agree in part. I don't like the implication that "Truth" cannot be obtained by reason. Yes, Goedel proved that any self-consistent non-trivial system of expression has true statements that cannot be proven, but the phrasing suggests another path to "Truth". We don't know of any.

I would say that Rand's flaw is more that values can be intellectually derived. Most modern geeks try that in their youth and give up [1], but Rand persisted [2]. Human values are a byproduct of natural selection, early environment, and memetic flux. They are emergent, not deduced -- though there is a trend over time and wealth towards values of compassion and tolerance. Rand started with 'freedom' and tried to deduce all else, other's start with 'duty' (she hated that). Both are arbitrary starting points. Most of us ride both horses. Her problem wasn't that she chose a horse to ride, it's that she thought her choice was rational. It wasn't and it can't be.

That's why she's the queen of the Cult of Reason.

PS. Ever notice Rand's stories don't have disabled persons or children in them?

[1] I tried to derive a system that wasn't human centric. Not a pretty result.
[2] Oddly enough, I just remembered I once won some sort of prize for an essay on the emergent nature of human ethics. Forgot about that. It was a long time ago ...

Update 7/23/06: Crooked Timber gives us some more background on why Kant was accused of Nihilism. This was the money line for me:

[Andrew Bowie] ... Kant, who himself avowedly believed in God, was regarded as a threat in his own time because he rejected the idea that philosophy can have access to the (theologically) inbuilt structure of reality. However this aspect of Kant’s thought is understood, it evidently puts into question the idea that the ultimate truth of the world is accessible and therefore constitutes the knowable goal of philosophy or natural science.

So now we understand why the Queen of the Cult of Reason (Rand) would coin the phrase 'Kantian Nihilism'. Kant was an (old) threat to the magical belief of Rand and others that Truth (moral virtue) could be deduced by Reason from First Causes. Doesn't work guys. We've been at it for thousands of years. Ethics is a post-hoc justification for the things humans want to do, and the wants (like everything else about humans) are the result of natural selection, happenstance, and social environment ...

Do plaque causing bacteria secrete a local anesthetic?

If you were a bacteria munching on oral stuff, wouldn't you secrete a local anesthetic? After all, mosquitoes are far less evolved than bacteria, and they've mastered that trick.

I couldn't find anything written about it. Seems like a fun, albeit risky (might turn up nothing), research topic for a dentist somewhere.

Kantian Nihilism and Caligulan Propriety

People who get their intellectual history from blogs like this sometimes use the phrase "Kantian Nihilism" as a shorthand for leftie commie pinko traitor sex drugs and rock and roll ideology. Ayn Rand liked it (apparently she was even dimmer than I'd thought).

The term triggers a full scale rant from Obsidian Wing's Hilzoy -- with this memorable sentence ...

Obsidian Wings: My Head, She Explodes!

... Since truth is one but error is infinite, there's no shortage of further subjects for Chris Muir's strips: Leninist anarchism, Kierkegaardian rationalism, Thomist atheism, Nazi Judaism, cautious and sober Maoism, Britney Spearsian profundity, Caligulan propriety and decency, Robespierrian restraint, Mozartian lugubriousness, and of course Muirian thoughtful, well-informed commentary.

Update 7/23: There's more later ...

Kauzlarich campaigns for assertive atheism

I'm of the older, quieter, traditional brand of agnostic/atheistic secular humanist pinko commie geek intellectual.

I have a great deal of sympathy and affection for religious belief and religious people -- despite some knowledge of the dark (very dark) aspects of religious history. I've read and studied more about religion(s) than most believers. People like me find the assertive atheism of the young-uns harsh and unkind.

On the other hand, people like Lt. Col. Ralph Kauzlarich make a more aggressive stance understandable ...

Pharyngula: IOKIYAC

... Kauzlarich, now a battalion commanding officer at Fort Riley in Kansas, further suggested the Tillman family's unhappiness with the findings of past investigations might be because of the absence of a Christian faith in their lives.

In an interview with ESPN.com, Kauzlarich said: 'When you die, I mean, there is supposedly a better life, right? Well, if you are an atheist and you don't believe in anything, if you die, what is there to go to? Nothing. You are worm dirt. So for their son to die for nothing, and now he is no more — that is pretty hard to get your head around that. So I don't know how an atheist thinks. I can only imagine that that would be pretty tough.'...

Why can't scientists come to agreement about global warming?

So asks Peggy Noonan.

The words 'moron' and 'idiot' are tainted by their original use to describe persons with cognitive disability. We need an entirely new term to describe people with fully functional nervous systems whose deep personality flaws cause them to think like a pithed frog.

I suggest Noonatic.

Cringely 1997 - WinTrust, IE and the death of Netscape

In a recent column Cringely mentioned that his archives go back to 1997. Net eons ago. And so they do. Here he writes about something called WinTrust, which sounds like Google Checkout. (Anyone remember Microsoft Wallet? No, I didn't think so.) He also claims that the future of the net is in Cybercash (no, didn't happen), online transactions (duh) and advertising (oh, yes).

I, Cringely . November 17, 1997 - Take a billionaire to lunch | PBS

... And then there's WinTrust: Microsoft is laying the groundwork so that all electronic transactions will go through Redmond. This may be the real reason Microsoft is pushing IE4 onto the OEMs so hard.

Cybercash, online transactions, Internet advertising. The browser is simply the front door to these innovative services/profit centers. The only way to make sure everyone will see those centers is to make sure everyone uses Microsoft's browser. Netscape has no interest in enabling WinTrust, so Netscape must die. Microsoft will gladly give away the browser for free regardless of the presence of Netscape just to be sure they can control the online gateway. From a business standpoint, this is sheer brilliance. But to some folks it's Big Brother coming from Washington state instead of DC.

Cringely was claiming Microsoft's original agenda was not a defensive move against Netscape, but rather an offensive move to direct all transactions through Microsoft. In retrospect, I don't think they were so clever.

Israel and Lebanon: why I can't condemn Bush (for once)

I've never been in a war. I would prefer not to be. Those who've read me will not mistake me for a Bushie, a neo-con, or a chicken-hawk.

But.

Hezbollah is a terrorist organization embedded in Lebanon deep among the civillian population. They claimed to have 10,000 missiles and they were lobbing them into Israel. How wrong is Israel to invade Lebanon? Certainly they seem to have as strong a claim as the US had to invade Afghanistan (heck, Jimmy Carter supported that!), and a far stronger claim than the US had to invade Iraq.

Early Warning by William M. Arkin - washingtonpost.com

... When the U.N. high commissioner for human rights and former war crimes prosecutor Louise Arbour raises war crimes and argues that there is 'indiscriminate shelling of cities,' I guess she is referring to Hezbollah's indiscriminate attacks upon Israel. I might not like what Israel is doing, and my personal tendency might be anti-war, but I just don't see war crimes or indiscriminate anything in Israel's conduct.

I remember when Isreal was internationally attacked for going into Gaza City in pursuit of embedded terrorists. They were intensely criticized, and I joined in as well. I read the follow-up, however. In retrospect Israel's conduct during that assault was at least as "cautious" as the US seems capable of executing, and maybe even a cut above what we can do - even when we're trying.

I believe Bush will move with deliberate slowness, barely cooperating with international diplomatic efforts, aiming to give Israel a window in which to attack Hezbollah. This is one of the rare times I'm not absolutely certain Bush is being incompetent or wrong.

PS. Even more oddly, I sort-of-barely-sympathize with Bush's stem cell research veto. I think the nation is very much in denial about the "slippery slopes" in biotech and we do need more public engagement than we've had.