The evolutionary biology of Giardia - no mitochondria

Giardiasis is an annoying and fairly common infection, but we don't think it's not a big deal for a healthy adult. Turns out that the Giardiasis bug, Giardia, has some very interesting biology ....

The Loom : Carrying Ancient History In The Gut

... Giardia, many researchers suspected, was one of those early-branching eukaryotes. This suspicion was generated at first by simply eyeballing the creatures. They are quite weird. Their teardrop-shaped bodies have eight tails for swimming and a suction pad to clamp onto the wall of the intestines. They also carry two nuclei, each with its own DNA. How Giardia manages to keep all those genes coordinated--and why it even has two nuclei--remain mysteries. Bizarre single-celled eukaryotes are pretty easy to find. What set Giardia apart from most other eukaryotes was what it lacked. Scientists could not find a lot of those compartments in which the business of most eukaryote cells takes place.

Most significantly, it was missing mitochondria. Lots of things take place inside these sausage-shaped structures, most importantly the generation of ATP, the energy-bearing molecule found in all living things. Mitochondria started out as free-living bacteria and later evolved into permanent symbionts inside the eukaryote cell. (Mitochondria still carry some DNA of their own, which bears a strong resemblance to one group of free-living bacteria.) The fact that Giardia seemed to be missing mitochondria hinted that it was a transitional eukaryote...

Alas, the story is more complex than this, so you do need to and read Carl Zimmer's essay. Fascinating stuff.

I probably invited this bug onboard during a particularly rough college train trip through Mexico. I didn't realize I was carrying a possible echo of biology's "big bang".

Incidentally, speaking of parallels to cosmology, there's apparently a suspicion among some biologists that there's a kind of "dark matter" component to biology. They're looking for terrestrial life forms so bizarre that we don't even recognize them as "living" ...

Apple is at war with its own uber geeks

When Apple last returned from the grave, for the second or third time, geeks were important. OS X is a respectable piece of software, and geeks made it work. In several domains, particularly in communications and knowledge management, OS X now has a better range of solutions than XP.

Today, however, Apple is at war with its uber-geeks -- because of the iPhone. Saul Hansell describes the mood in the NYT, though he's confusing the unlockers with those who want the best possible iPhone on AT&T...

Steve Jobs Girds for the Long iPhone War - Bits - Technology - New York Times Blog

... This afternoon, Apple did release the update. And the gadget blogs confirm that it does indeed wreak havoc on modified iPhones. Some phones have indeed been “bricked.” In others, unofficial applications have been disabled. And there are worries that hacking the updated phone will be harder.

The result: Serious hackers will keep find new ways to break in. Less technically inclined may well find themselves chastened into technological submission, assuming they can get their pricey toys to work at all. Will Apple really refuse to help people with iBricks?

Speaking in London last week, Steve Jobs, Apple’s chief executive, said the company is in a “cat and mouse” game with hackers.

“People will try to break in, and it’s our job to stop them breaking in,” he said.

There is something futile about the way Apple appears to be fighting some of its most ardent fans, those who want to use the full capabilities of the iPhone...

... Since the iPhone is a very sleek, capable handheld computer, people are going to want to run programs on it. They are going to want to hack and see what they can build. It’s a law of nature. And Apple might as well be fighting gravity.

Many other cell phones are locked down, of course. But few other phones capture the imagination of programmers the way the iPhone does.

There are two loosely allied groups of Apple geeks now at war with Apple. The unlockers want to use the phone with other providers; but most of Apple's geeks are willing to respect Apple's deal with Satan -- especially if the iTouch is improved. Everyone, however, is now united for at least a partly open iPhone and iTouch native development platform.

Geeks don't trust Apple to put the solutions we need on the iPhone. Apple's aiming at the mass market, and we're not mass market. We understand Apple can't justify investing in the solutions we need, but that's ok. There are lots of small, low overhead, high quality OS X development shops that will be able to make a very good living off the markets Apple doesn't want. Would it really kill Apple to have a 3rd party bluetooth keyboard added to the iPhone? How about the PIM/Outlook solutions Apple won't build? FileMaker Mobile? The list is long.

If Apple keeps the iPhone closed they'll alienate their uber geeks -- not just from the iPhone, but from the entire OS X platform. Maybe they're ready to run that risk, but I don't think the gain outweighs the likely costs. Keeping the iPhone virus free is a good reason to have a software certification program and a signed secure installation package, but it's not sufficient justification to close the platform.

Apple doesn't need to open the iPhone today, but they need to provide a roadmap in the weeks to come. Otherwise the Apple blogs are going to turn mean ...

Update 9/28/07: Wired has a brilliant summary of what Apple is failing to do -- the iPhone pre and post bricking. Some Apple employee ought to paste the Wired graphic to Steve Jobs door.

My double rainbow

Wikipedia's picture of a double rainbox (left, credit) is lovely, but mine was even better. The secondary rainbow was better defined, and I think I counted nine distinct bands in the primary. It arced, like this picture, from ground to ground.

I wasn't in a beautiful Alaskan national park, I was leaving my office in Roseville, Minnesota. There'd been a downpour, but the rain was now steady but widely spaced, an odd pattern I don't see much. The sun was at about 25 degrees above the horizon, and the western sky had cleared, so the light was completely unobstructed.

I stood and watched in amazement. It lasted only about four to five minutes, then the secondary began to fade. I phoned home when I saw it, but it couldn't be seen even 15 miles south of me. It was a private show.

I don't think I've ever seen a rainbow like that, and perhaps I never will again. It was just one of those odd, unexpected gifts, like a letter from an old friend.

Cringely runs the shark over

My favorite tech commentator has not merely jumped the proverbial shark, he's run it over. Cringely is going to launch a rocket to the moon and drive a rover around. The man needs a vacation.

I'll have to donate some money of course. Lunacy of this sort must be encouraged.

BBC IOT - Theories of Everything With Brian Greene

Even In Our Time has its limits. I wrote last April that Lord Bragg was struggling with the Poincare Conjecture, and compared it to my physics reading then ...

... Which brings me to my recent readings in physics. I'm reading Gribbins on Quantum Mechanics (1994) and Brian Greene with another cosmology/string theory overview, the Gribbins book is my personal favorite, but it's a bit dated now. Together though, they make it hard to overlook that physics seems to be getting harder and harder. We have more physicists than ever, and I'd wager there's a Feynman or two in the bunch, but we've been stuck for decades now...

I've been savoring Greene's The Fabric of the Cosmos ever since, reading a few pages every day. It's rich stuff! I'll have a post on the book soon, but I confess I'd underestimated the progress of the 90s; quantum speckles on the microwave echoes of Higgs driven inflation is darned impressive.

Which brings me to the podcast I'm listening to now -- Theories of Everything, feature none other than ...

Brian Greene, Professor of Physics and Mathematics at Columbia University and author of The Fabric of the Cosmos (Allen Lane, 2004)

John Barrow, Professor of Mathematical Sciences at the University of Cambridge and author of The Constants of Nature (Vintage, 2003)

Dr Val Gibson, particle physicist from the Cavendish Laboratory and Fellow of Trinity College, Cambridge

Further reading
The Elegant Universe by Brian Greene (Vintage, 2000)
[jf: odd choice, they should have recommended The Fabric of the Cosmos, his current book]
Theories of Everything by John Barrow (Vintage, 1992)

Now that's ambitious. Alas, Bragg is weakest when he ventures into math and physics, and his guests seemed to be struggling as well. At one point Gibson and Green talk about the relationship of extra dimensions to string theory, but they just miss making the key point -- that while finding extra dimensions won't prove string theory, not finding them will severely weaken string theory.

I was also left with the impression that the "string" metaphor is overdone. Maybe it would work better if Green were to say something like "we've developed very fancy maths that allow us to model both the jittery quantum world and the continuous world of cosmology", and one way to imagine the mathematics is to think that it's describing wee little bits of strings ...

Full points to IOT for courage, but Lord Bragg was traveling in alien territory ...

Update 9/30/07: I wrote this post pretty quickly -- like all my posts. Melvynn stayed lost, but his guests warmed up around the half way mark, so it did turn into a strong episode.

Amazon MP3 Store: great news for Apple customers

Amazon's MP3 store is a smash hit among OS X gurus like Gruber:

Daring Fireball: The Amazon MP3 Store and Amazon MP3 Downloader

...The songs sound great and come with high-resolution album art. Singles cost $.89 or $.99, and album prices start as low as $4.99 — i.e. they’ve introduced variable pricing to sell music for less, not more, than the iTunes Store. When you search for songs from an artist whose entire catalog is not available through their MP3 store, Amazon provides a direct link to the artist’s catalog in their CD store. Two million total songs is far less than the six million Apple offers at the iTunes Store, but it’s a pretty good start, and all of Amazon MP3’s songs are DRM-free. I’m not sure how many DRM-free iTunes Plus tracks Apple offers, but it certainly seems like far fewer than one-in-three, and thus far fewer than two million. So while Amazon can’t claim to offer the most songs, they might be able to claim the most DRM-free songs. In just a few minutes of shopping, I found plenty of songs at Amazon that are only available from the iTunes Store with DRM. Given the Amazon MP3 Store’s audio quality, prices, and user experience, I can’t see why anyone would buy DRM-restricted music from iTunes that’s available from Amazon. And given that Amazon is quite a bit cheaper than iTunes Plus, you might as well check Amazon first. I plan to...

Hallelujah. Amazon's not messing about, they launched this for OS X and Windows simultaneously. At last, Apple has very serious competition.

Of course since Amazon's tunes work perfectly with iPods, it's not going to hurt Apple's revenue stream all that much. I wouldn't be surprised to see Apple's share price fall a bit then recover as investors realize Amazon's play is poison for Microsoft's strategy.

The joy of it is that it will make Apple work harder to keep its customers happy, and it will strengthen the anti-DRM solution.

Now, just wait until Gruber realizes that Amazon has embedded a unique identifier in each song that they can connect back to his credit card* ....

* How do I know this? I don't. I'd bet on it though. I'm sure Apple does the same sort of thing with their non-DRMd tunes, I even expect that an AAC you burn from a CD using iTunes contains some sort of embedded identifier.

Update 9/26/07: I'm 99% sure John Gruber doesn't read this obscure blog, but shortly after I worte of the "Amazon unique identifier" he told us that while Apple embeds an identifier (which happens to resemble an email address but is tied to credit card identification) in their DRM-free downloads Amazon, in the NYT, says they don't (!). Well, gee, I was wrong. That's never happened before :-). Gruber has an essay on the broader implications too.

Error types in software and fort construction

CH pointed me to this one. A programming guru classifies errors in a family constsruction project, and relates them to software development. Emphases mine, number 4 is my fave.

Building a Fort: Lessons in Software Estimation - 10x Software Development

1. Numerous unplanned problems collectively added up...

2. Underestimation of unfamiliar tasks. My estimates weren't too far off for a lot of the work that I'd done before. But some things, like mapping out the site for the footing holes, I assumed would be 15-30 minute task ended up taking several hours.

3. Not decomposing big tasks into smaller subtasks. I'd planned out my project in whole days. At a birds eye view nothing seems obviously wrong with planning "frame the fort in one day." But when you break it down ... you start thinking, can I really do a whole wall in 2 hours? If the answer's even close to "no," then you start to realize that the whole estimate for that big task is probably wrong.

3. Using overly round time units. Using round units like "1 day" contributes to not thinking hard enough about decomposing large tasks into smaller tasks.

4. Substituting a target for an estimate. I had 7 days to do the project, and my estimate turned out to be 7 days. That's a little suspicious, and I should have known better than to make that particular mistake!

5. Sweeping numerous little tasks under the estimation rug....

6. Never creating a real estimate. The fact of the matter is that I carried around a rough plan in my head for weeks, but I never actually committed a schedule to paper...

7. All's Well That Ends Well. My kids love their fort, and I had a great time building it. "All's well that ends well" is one reason that companies don't improve their software practices more often than they do. If people like the software that the team produced, and the software is successful, then that reduces the incentive to try to do better next time.

Broadband speed trickery: couldn't happen here

In the UK broadband firms advertise speeds using the words "up to". Shockingly, the reality is typically less than 50% of the "up to" number...

BBC NEWS | Technology | Broadband speeds under scrutiny

Broadband speeds in the UK are much slower than advertised by internet service providers, a study by Computeractive magazine has found. Some 3,000 readers took part in speed tests and 62% found they routinely got less than half of the top speed advertised by their provider. It is the latest in a series of questions over the way net firms advertise broadband services...

Scandalous. It would never happen here of course.

Seriously, the interesting bit here is that a trade magazine actually did something useful. There was never much life in the trade journals (except for BYTE) to begin with, and I'd thought the web had completely killed them.

The market answer to dementia: Soylent Green

Markets are good at solving problems. Shut out all the reasonable options, and markets will come up up with unreasonable solutions. That's what's happening with our dementia problem.

The traditional approach to the care of the demented is very expensive. Americans don't want to pay for full-service nursing home care, but they refuse to consider the alternatives. That means market is going to invent an alternative, which it has.

The answer is - kill the demented elders faster, but setup ownership to avoid prosecution...

More Profit and Less Nursing at Many Homes - New York Times

Habana Health Care Center, a 150-bed nursing home in Tampa, Fla., was struggling when a group of large private investment firms purchased it and 48 other nursing homes in 2002.

The facility’s managers quickly cut costs. Within months, the number of clinical registered nurses at the home was half what it had been a year earlier, records collected by the Centers for Medicare and Medicaid Services indicate. Budgets for nursing supplies, resident activities and other services also fell, according to Florida’s Agency for Health Care Administration.

The investors and operators were soon earning millions of dollars a year from their 49 homes.

Residents fared less well. Over three years, 15 at Habana died from what their families contend was negligent care in lawsuits filed in state court. Regulators repeatedly warned the home that staff levels were below mandatory minimums. When regulators visited, they found malfunctioning fire doors, unhygienic kitchens and a resident using a leg brace that was broken.

“They’ve created a hellhole,” said Vivian Hewitt, who sued Habana in 2004 when her mother died after a large bedsore became infected by feces.

Habana is one of thousands of nursing homes across the nation that large Wall Street investment companies have bought or agreed to acquire in recent years.

Those investors include prominent private equity firms like Warburg Pincus and the Carlyle Group, better known for buying companies like Dunkin’ Donuts.

As such investors have acquired nursing homes, they have often reduced costs, increased profits and quickly resold facilities for significant gains.

But by many regulatory benchmarks, residents at those nursing homes are worse off, on average, than they were under previous owners, according to an analysis by The New York Times of data collected by government agencies from 2000 to 2006.

The Times analysis shows that, as at Habana, managers at many other nursing homes acquired by large private investors have cut expenses and staff, sometimes below minimum legal requirements...

It's a "soylent green" class solution. Anyone could come up with the solution of "make them die sooner", but it took genius to figure out a way to do this and avoid prosecution.

Markets always answer "problem of the weak" questions this way. That's why we need government ...

The human eye vs. a camera: how do they compare?

Humans are a visual species, so it's not surprising that our eyes work pretty well - though we don't compare to avians. ClarkVision compares the eye to a digital camera, and claims a resolution equivalence of about 580 megapixels, a relatively mediocre ISO 800 sensitivity (and only grayscale for that), roughly f3.5 and @ 20mm focal length, and an awesome (albeit complex) visual range. (link via Kotke)

It's a great set of references from a photographer and professional astronomer*. I'm not sure how this translates into realtime perception however, and that's the bit that matters. I recall reading that the pathways beween the retina and the visual cortex have pretty limited bandwidth, and the visual connections to the prefrontal cortex are astoundingly weak. It's as though the world's best camera were connected to your computer by an RS-232 serial cable. There has to be an incredible amount of pre-processing and lossy compression to get any useful realtime work, and for us only realtime counts. On the other end of the circuit, the brain is doing a lot of informed guessing to create it's simulacra of "reality".

This is why a human studying a photograph will get much more from the image than they can ever perceive from a realtime glance. The eye is a marvelous camera, but evolution hasn't had harder time optimizing the neural interfaces.

By the way, how good might the eye/brain be at lossy compression and re-representation of image input? One clue is how successful living organisms are at storing their "construction specifications" and startup machinery in a single cell (egg, the sperm could be eliminated). That's a level of data compression/packing (relatively lossless) orders of magnitude greater than we can achieve with current technologies.

* I've noticed less repetition lately of the absurd "bloggers are ignorant fools" meme.

UPS delivery record fraud - how to respond

I've experienced this twice in the past year. UPS claims they attempted a delivery at my home, but I've reason to believe they didn't. Kotke reported the same thing a few months ago ..

Harry Potter and the Phantom Delivery (kottke.org)

... At some point after 7pm, the UPS status page updated to say that a notice was left at 3:36 pm, implying that a delivery attempt was made and no one was home to receive it. (Amazon's tracking page says that UPS told them "Delivery attempted - recipient not home".) No such notice was left. My door buzzer did not ring at 3:36 pm (I was home all day on Saturday) and the doorman of the building next door who takes the deliveries for our building when people aren't home reported no notice or delivery attempt...

Recently I wrote of UPS' package-crushing habits.

UPS is following the airlines down the tubes, perhaps for similar reasons. Today I'd recommend the USPS over UPS. If you run into UPS problems with an Amazon order, use the Amazon feedback option linked to your order to complain. Don't bother contacting UPS, they're too far gone. We need Amazon to shift them, or to find another solution.

That Jena business: it's time to stop watching television news

Since I don't watch TV, news of the "Jena Six" passed me by. I kept seeing references to the topic though, so when Google News suggested an AP article by Todd Lewan I read Black and White Becomes Gray in La. Town. It's a persuasive summary; from it I concluded that Jena's racism level is at least American average, but probably not above the 80th percentile. I suspect a jury of enlightened rationalists would have punished at least some of the Jena Six, though with more creative and useful sentencing.

The story is thus mostly interesting as an example of how narratives are created in America's divided communities, and I suspect the real criminal here is American television news (CBC, NCB, ABC and Fox in particular*) and the people who persist in watching it.

Now, you might question how I can say this, since I told you I don't watch TV. Well, I do sometimes catch network TV news when walking through airports or sitting at restaurants. In the seconds before I can avert my gaze the shocking stupidity of it shines through. On the other hand, I read a lot of print media, and it's not so bad.

America, stop watching television news. It's a drowning beast that will grab onto anything above the water line. Just turn it off. Now.

* What about radio talk shows? Good question. I can't comment there, because it's been years since one of those accidentally crossed my radio. I mostly listen to podcasts these days ...

Today, would Gerald Ford be to the left of Hillary Clinton?

In a NYT Magazine article John Paul Stevens, the 87 yo "liberal" justice, reminds us he was appointed by Ford and is a "moderate republican"...

Justice John Paul Stevens - Supreme Court - Law - Washington - New York Times

Stevens, however, is an improbable liberal icon. “I don’t think of myself as a liberal at all,” he told me during a recent interview in his chambers, laughing and shaking his head. “I think as part of my general politics, I’m pretty darn conservative.” Stevens said that his views haven’t changed since 1975, when as a moderate Republican he was appointed by President Gerald Ford to the Supreme Court. Stevens’s judicial hero is Potter Stewart, the Republican centrist, whom Stevens has said he admires more than all of the other justices with whom he has served. He considers himself a “judicial conservative,” he said, and only appears liberal today because he has been surrounded by increasingly conservative colleagues. “Including myself,” he said, “every judge who’s been appointed to the court since Lewis Powell” — nominated by Richard Nixon in 1971 — “has been more conservative than his or her predecessor. Except maybe Justice Ginsburg. That’s bound to have an effect on the court.”

I usually think that the GOP has moved to an extreme position, so much so that a Ford Republican is a liberal today. On the other hand, is it correct to say that Gerald Ford would be to the left of Hillary?

It's a tricky question. These days even commies like me respect the power of markets, even as we fear the answers markets give the weak. Ford-era price controls aren't "liberal" today, they're dumb. On another paw, Ford @1970 would be far less tolerant of non-heterosexual gender relationships than most of today's GOP (ignoring their theater for a moment).

Bottom line, I don't think Gerald Ford @ 1970 would map onto any part of today's political spectrum. Probably not the Democrats, and certainly not today's GOP. Stevens and the few Republicans like him have been left adrift as the GOP has moved to some weird political dimension ...

kottke.org - Gordon's Notes on steroids, more art, less physics

I enjoy writing Gordon's Notes. It's my own little candle in the darkness. I have no pretensions to grandeur, but I do think it's a bit unusual in terms of the breadth of topics. Most blogs these days are more specialized, or represent multiple voices.

Except for one I came across today for the first time:

kottke.org :: home of fine hypertext products:

... kottke.org is a weblog about the liberal arts 2.0 edited by Jason Kottke since March 1998. You can read about me and kottke.org here. If you've got questions, concerns, or an interesting link for me, send them along. Follow kottke.org via RSS kottke.org RSS feed, see what I'm up to on Twitter, view my Flickr photostream, or check out some random entries from the archives. You may also be interested in my thoughts on books & movies or some photos I've taken. I also made a tiny bitmap font called Silkscreen several years ago...it's free and works on OS X, Windows, and Linux...

This blog has tends of thousands of readers on bloglines alone and includes gems like this review of the NYT archives. Compared to me Jason Kottke is a much better writer, and is more interested in the arts, movie and culture than exotic physics. He's also bawdier than me and lives in Manhattan rather than Saint Paul*, so be careful when reading at work.

His growing tags collection is a good topics guide:

Some recommended tags
photography economics lists bestof infoviz food nyc firstworldproblems cities restaurants video timelapse interviews language maps fashion nsfw remix

Recently popular tags (last 3 weeks)
indianajones multitouch harrisonford ratatouille movies firstworldproblems iphone facebook desktoptd aol jasonkottke nyc jenbekman mobiletelephones design pixar apple photography art mcsweeneys harrypotter geography books tv tennis

All-time popular tags
movies books photography nyc science food lists design business sports weblogs music art video bestof games tv funny apple language videogames google restaurants interviews maps

Random tags
bengibbard ajax sony pizza arthurclarke mattwebb kenjennings lordoftherings d70 soda textmate vogue anildash lifeaquatic china starbucks anaisnin barnabyfurnas stevenspielberg upperdeck election2008 meteorology uptonsinclair legendofzelda foodnetwork

I recommend a trip to the archives, including the very earliest posts. I enjoyed the "about" page as well. Great fun!

Update: *Kottke was born in the Twin Cities, where I now live. He left at an early age though.
Update 9/23/07: Browsing Kottke's archives, I see he was back in Minneapolis from 1996-2000. Ahh, that explains it. Nice post on the Mill City Museum too.

Do you know where your identities are?

Yes, this chap has more than most geezers, but you probably have more selves than you realize.

Gordon's Tech: Online identities: management and multiplication:

... I currently have manged 'major' identities at Amazon, faughnan.com, faughnanlagace.com, Google Gmail/Blogger, LinkedIn, and, yes, even Facebook -- and those are only the ones I can remember right now. I debated including my Yahoo! identity in the mix, but unless Yahoo does something remarkable with Zimbra that's just a front for spammers. I do have a Microsoft Passport (or whatever they call that now) identity as well, but I try to forget that one. I used to have a .Mac identity, but Apple's .Mac hasn't delivered much value for money so that one is in abeyance. There are a myriad of 'unmanaged' lesser identities, and of course all my emails have some form of identity associated with them ...

It's the gold rush of the 21st century, each identity a piece of reputation management. Which ring will bind them all?