Britannica finally goes social

I've been a Britannica Online subscriber since they launched -- mostly out of sentiment. I really don't use them very often -- even though I set Google up so Britannica is searched with every Google query.

Years ago I hoped they might find common cause with the New York Times and build a joint community. Heck, I'd have been happy if they simply built their own community.

They never did, and eventually I figured they'd lost their way for good. I mostly forgot about the EB, even though I still subscribed. Recently, though, I began reading the Britannica blog. It's pretty good. A sign of life!

Today there were two blogs on Britannica's long delayed social reinvention. It sounds like they'll try to merge a Wikipedia like community with the core formal encyclopedia

• Britannica's New Site: More Participation, Collaboration from Experts and Readers
• Collaboration and the voice of experts

I hope it works, I'm just glad to see there's some energy left in the place.

Evolution in action - captured and dissected

A 20 year longitudinal study of bacterial evolution is further constraint on the argument facades creationists use to conceal their faith-based opinions. Emphasis mine, arguably this research evolved a new species of bacteria ...

The Loom : A New Step In Evolution (yes, Carl Zimmer again)

... After 33,127 generations Lenski and his students noticed something strange in one of the colonies. The flask started to turn cloudy. This happens sometimes when contaminating bacteria slip into a flask and start feeding on a compound in the broth known as citrate...

...Many species of bacteria can eat citrate, but in an oxygen-rich environment like Lenski's lab, E. coli can't. The problem is that the bacteria can't pull the molecule in through their membranes. In fact, their failure has long been one of the defining hallmarks of E. coli as a species.

...In nature, there have been a few reports of E. coli that can feed on citrate. But these oddballs all acquired a ring of DNA called a plasmid from some other species of bacteria. Lenski selected a strain of E. coli for his experiments that doesn't have any plasmids, there were no other bacteria in the experiment, and the evolved bacteria remain plasmid-free. So the only explanation was that this one line of E. coli had evolved the ability to eat citrate on its own.

Blount ...went back through the ancestral stocks to see if they included any citrate-eaters.... in generation 31,500, they made up 0.5% of the population. Their population rose to 19% in the next 1000 generations, but then they nearly vanished at generation 33,000. But in the next 120 generations or so, the citrate-eaters went berserk, coming to dominate the population.

This rise and fall and rise suggests that the evolution of citrate-eating was not a one-mutation affair. The first mutation (or mutations) allowed the bacteria to eat citrate, but they were outcompeted by some glucose-eating mutants that still had the upper hand. Only after they mutated further did their citrate-eating become a recipe for success.

... Lenski's research has shown that in many ways, evolution is repeatable. The 12 lines tend to evolve in the same direction... Often these parallel changes are the result of changes to the same genes. And yet when it comes to citrate-eating, evolution seems to have produced a fluke.

To gauge the flukiness of the citrate-eaters, Blount and Lenski replayed evolution. They grew new populations from 12 time points in the 33,000-generations of pre-citrate-eating bacteria. They let the bacteria evolve for thousands of generations, monitoring them for any signs of citrate-eating. They then transferred the bacteria to Petri dishes with nothing but citrate to eat. All told, they tested 40 trillion cells...

... Out of that staggering hoard of bacteria, only a handful of citrate-eating mutants arose. None of the original ancestors or early predecessors gave rise to citrate-eaters; only later stages in the line could--mostly from 27,000 generations or beyond. Still, even among these later E. coli, the odds of evolving into a citrate-eater was staggeringly low, on the order of one-in-a-trillion...

If E. coli is defined as a species that can't eat citrate, does that mean that Lenski's team has witnessed the origin of a new species? The question is actually murkier than it seems, because the traditional concept of species doesn't fit bacteria very comfortably. (For the details, check out my new article on Scientific American, "What is a Species?")...

There's a tangent here Zimmer didn't call out.

The researchers were able to replicate the speciation-vent, but it took trillions of tries from the relatively late stage precursors of the citrate eaters. It might take hundreds or thousands of trillions of "tries" to get the same outcome from wild E. Coli. Of course that's only a few hundred years of bacterial evolution.

If they repeated the same experiments fifty times, they'd probably get other one-in-a-hundred-trillion flukes over a 20 year trial, but they'd likely be different flukes.

Flip a coin a thousand times and there's a 100% probability you'll get a sequence made up of Heads and Tails. The chance that the next thousand flips will get the same sequence is very, very low.

Naive old-style creationists got hung up on the impossibly small probability that evolution, replayed from the start, would produce us.

Well, ummn, no, it wouldn't.

The more interesting question is, if you replayed evolution on earth 1000 times, how many times would you produce something that would do experiments about evolution on earth?

That's a Drake equation question. The "expert" wild guesses are in the 20% to 0.33% range, but we could do with a few data points ...

Aging is a very old strategy -- proteins in the cap

I almost missed this astounding Boston Globe article. Mercifully I track Zimmer's blog, so I'm only 48 hours behind.

Note the explanation of why evolution has not produced immortal species (it sucks resources from adaptive capacity), and the analogy between bacterial "caps" and human eggs (emphases mine) ...

Aging is older than you think - The Boston Globe Carl Zimmer

... why hasn't evolution favored perfect repair - in other words, immortality?

"Immortality is not cost-effective," says Stewart.

To never get old, organisms would have to invest a huge amount of energy in repair. They'd be left with little energy to reproduce. Natural selection would instead favor other organisms that put less energy into repair and produced more offspring.

A common solution to this trade-off is to set aside a special population of cells that will reproduce. Our bodies put a great deal of energy into keeping eggs and sperm from becoming damaged. They put much less care into repairing the rest of our cells.

"My children are born young and rejuvenated. So the damage of my aging is kept just to me," says Stewart.

Many scientists assumed that symmetrically dividing microbes could not take advantage of the aging strategy we use. "Every problem that would arise, the cell would have to fix," says Stewart...

... Stewart and his colleagues have revealed that even symmetrically dividing bacteria get old.

They put a single E. coli on a slide and allowed it to reproduce. They engineered it to produce a glow, which made it and its descendants easier to film. Using sophisticated image-processing software, they were able to track 35,000 cells, observing how long each one took to divide.

In 2005, Stewart and his colleagues reported that some bacteria began to reproduce more slowly than their cousins, and over the generations their descendants slowed down even more.

There was one crucial difference between the old and young microbes: the caps at each end of their rod-shaped bodies. Each time E. coli divides, the two new microbes each inherit one of its caps, and the microbe must manufacture a new cap for each one. When these two microbes divide again, they each make two new caps. Over the generations, there will be some bacteria that inherit the original caps from the common ancestor of the entire colony, while others have younger caps. After a cap ages for 100 generations, the scientists estimate, the cell can no longer reproduce.

The scientists then took a closer look at what was happening inside the bacteria. Earlier this year, they reported that clumps of tangled proteins grow in E. coli. As the bacteria divide, these clumps end up in the old caps. Somehow, the defective proteins help slow down the growth of old bacteria.

Stewart sees these results as evidence that single-celled bacteria use the same strategy multicellular animals do to cope with cell damage.

"It's probably cheaper to throw away your garbage in one cell while the rest of your population grows."

Daniel Promislow, an expert on the genetics of aging at the University of Georgia, finds the research exciting. For one thing, it suggests that the common ancestor of bacteria and animals was already aging 3 billion years ago.

"Aging would be a really old phenomenon," he says.

Studying aging in quick-breeding E. coli could allow scientists to get answers about the process faster than with other lab animals, like flies or mice, Promislow says. "There's a lot you can do in a short amount of time."

It might even be possible to translate some of those lessons to medical applications. Alzheimer's disease, for example, is associated with clumps of proteins called plaques that form in neurons.

"It may be possible to find a way to alleviate protein damage in E. coli that would have a use in higher organisms," says Stewart. "I'm not saying it's going to be easy to find, though.

To the non-expert this certainly has the smell of "breakthrough". Changing the evolutionary address of aging is a big deal, and developing a new "instrument" to study aging is an equally big advance.

It feels astounding to me, but I'm easily excitable.

PS. While Death sacrifices the individual to power adaptation, Sex sacrifices offspring to power adapatation. Sex is an even more radical gambit than Death, so it's not surprising that while Death is universal, Sex can be sacrificed even in multicellular organisms.

Buying Obama bumper stickers

Oddly, there's nothing on the front page of the official site about buying campaign paraphernalia. I had to go to the answers database and search ...

Answer Center Barack Obama

You can buy buttons, t-shirts, bumper stickers, lapel pins, and party packs here.

...yard signs will be available at the store.barackobama.com this summer...

Someone needs to put this stuff on page one.

The melamine is still coming from China ...

The report of this successful intercept was published on Dec 26, 2007:

FDA Says It Halted Melamine-Tainted Pet Treats

...Sampling by the FDA’s Los Angeles District showed that pet treats imported from China, including treat seed sticks for cockatiels and honey cakes for hamsters tested positive for melamine, according to a government report...

You gotta love those Google alerts -- a small release in a bird focused pet site shows up on my news page as though it were on the front page of the NYT.

This is not good news. Yes, it's nice to know the FDA is catching some melamine contaminated imports, but that's a bit like reading about the DEA making a big cocaine haul.

It just tells us that the supply lines are still running.

The one bright spot is that if the Dems hold the Senate and Obama takes the Presidency, then there's hope for a resurrected FDA and policies that hold importers liable for product defects. The FDA only has to hold on until then ...

Of course if McCain wins ...

Anti-science and global warming - the GOP's corporate rule

The Bushies understood six years ago that the best available science predicted rising CO2 emissions would lead to global warming and disruptive local climate transformations

They must have understood this, or they wouldn't have made strenuous efforts to hide the science ..

Editorial - The Science of Denial on Global Warming - Editorial - NYTimes.com:

... An internal investigation by NASA’s inspector general concluded that political appointees in the agency’s public affairs office had tried to restrict reporters’ access to its leading climate scientist, Dr. James Hansen. He has warned about climate change for 20 years and has openly criticized the administration’s refusal to tackle the issue head-on.

More broadly, the investigation said that politics played a heavy role in the office and that it had presented information about global warming “in a manner that reduced, marginalized or mischaracterized climate-change science made available to the general public.”...

... What was most noteworthy about the latter report was that it made it to the light of day. A 1990 law requires the president to give Congress every four years its best assessment of the likely effects of climate change. The last such assessment was undertaken by President Clinton and published in 2000. Mr. Bush not only missed the 2004 deadline but allowed the entire information-gathering process to wither. Only a court order handed down last August in response to a lawsuit by public interest groups forced him to deliver this month.

I do find it hard to write about this stuff. If we don't read, and write, however, we're surrendering. We don't deserve the option of surrender.

It's always the same story with the Bush GOP. They aren't rationalists. They believe what they want to believe. They silence opposing voices. They ignore laws they don't like. They know they'll get away.

If the Dems didn't hold the Senate by one vote (Senator Leiberman, basically) the Bush GOP would have gotten away with everything.

One lousy vote.

So where is this type of behavior normal? In corporations. Corporations are not democracies (shock!), they are more like feudal nations. Corporations have an obligation to obey the laws (ok, unlike the GOP), but they don't have an obligation to objective truth. If you work for Exxon, you have no right to complain if Exxon refuses to publish your Exxon-funded research on global warming. There's nothing wrong with that -- that's the nature of a business.

Governments are supposed to obey the law (unlike the Bush administration), but governments in a democracy have an obligation to give citizens the knowledge needed to make informed voting decisions.

The GOP doesn't believe this. Really, it's not in their DNA. They believe they know best, and the truth only confuses the masses. Government should be run like a corporation, and the masses should be told what they need to know.

Rule by the elite, knowledge for the elite, propaganda for the masses.

Give thanks to the public interest groups who sued to get the Bush GOP to obey the law. When I find out who they are, I'll look for a way to donate money to them. I'll post that here.

Vote Obama.

Bush III

Since the current Bush is Bush II, that makes McCain Bush III ..

McCain: I'd Spy on Americans Secretly, Too | Threat Level from Wired.com

If elected president, Senator John McCain would reserve the right to run his own warrantless wiretapping program against Americans, based on the theory that the president's wartime powers trump federal criminal statutes and court oversight, according to a statement released by his campaign Monday...

...McCain's new position plainly contradicts statements he made in a December 20, 2007 interview with the Boston Globe where he implicitly criticized Bush's five-year secret  end-run around the Foreign Intelligence Surveillance Act...

One the one hand, Barack Obama.

On the other hand, Bush III.

I think America is perfectly capable of electing another George W Bush.

Yep, I'm afraid.

Lessons from great software - FrameMaker

New, even in software, does not mean better …(via Gruber)

…DF reader Cory Johnson emailed to point out that Apple’s new Leopard Security Configuration book, released yesterday, was produced in Framemaker 6.0, too. As Tsai wrote last year:

Michael Tsai - Blog - Old Meets New (2007)

… The iPhone User’s Guide contains lots of interesting information about the iPhone. But the most interesting thing, to me, is that the document was created on a Mac using Adobe FrameMaker 6. This version of FrameMaker was released in 2000 and ran under Mac OS 8 and 9. FrameMaker 7.0, the last version that ran on Macs, was released in 2002. Old Mac OS software can run under Mac OS X in Classic, but only on PowerPC-based Macs, the last of which was discontinued almost a year ago. Apple is apparently using some old software and hardware to document its newest product. I totally understand; FrameMaker 6 is a great piece of software, and there’s nothing like it for Mac OS X…

FrameMaker is widely regarded as a work of genius. MORE 3.1 was a work of genius.

Neither of them will run on any computer hardware sold today -- and there are no truly equivalent products from any vendor (OmniOutliner comes closest to MORE).

Creating a product as massive and complex as these software solutions, and then sustaining an original design through many iterations – that’s a rare feat. We don’t know how it’s done. It’s a lot easier to see why similar projects fail.

My guess is that you need continuity of a few very good people over at least ten years, with superb recruitment and training of replacements. That means those people have to be incented and rewarded. I think Apple knows how to do that, I have trouble naming any other large publicly traded company who has the recipe. Maybe Google?

PS. Maybe I can sell my PPC iMac (runs classic!) to a Minnesotan running FrameMaker …

Why talk about The Singularity?

Well, for me it has the hypnotic ghastliness of a train wreck seen from a moderate distance, or the horror and wonder of a supernova seen from a very great distance*. Hard not to talk about those things.

On the other hand, I don't think that humanity can do anything about the Singularity one way or the other, so I wrote of the IEEE Singularity issue

..I'll read the articles and make note of anything novel, but I'd be surprised to find any new insights. This topic has been well discussed in geek circles. Now all we can do is wait and see what happens...

In his IEEE epilogue, Vinge replies to similar comments, making the case that under some circumstances there might be a role that an informed public could play ...

IEEE Spectrum: Signs of the Singularity

...Both Horgan and Nordmann express indignation that singularity speculation distracts from the many serious, real problems facing society. This is a reasonable position for anyone who considers the singularity to be bogus, but some form of the point should also be considered by less skeptical persons: if the singularity happens, the world passes beyond human ken. So isn't all our singularity chatter a waste of breath? There are reasons, some minor, some perhaps very important, for interest in the singularity. The topic has the same appeal as other great events in natural history (though I am more comfortable with such changes when they are at a paleontological remove). More practically, the notion of the singularity is simply a view of progress that we can use—along with other, competing, views—to interpret ongoing events and revise our local planning. And finally: if we are in a soft takeoff, then powerful components of superintelligence will be available well before any complete entity. Human planning and guidance could help avoid ghastliness, or even help create a world that is too good for us naturals to comprehend...

So if we have a 10-20 years notice that we're going to build artificial minds far more capable than the crude models in our heads, then maybe we could try to design the 1st generation to be both kindly (to us) and sentimental.  Doing that would require a lot of worldwide trust and cooperation, so it might help to think about the problem for a decade or two first.

Heck, it's worth a try.

I did laugh though at the thought that Singularity speculation is going to impede progress on, say, global warming. I suspect on the list of significant distractions this one is pretty far down  -- more's the pity.

* It's rarely mentioned that when those suckers go off they probably sterilize a zone 25-200 light years across. If life is as common as we think it is, the light of a mature galaxy supernova carries very grim news. (Immature galaxies need Supernovae to produce the elements that allow planets like ours to form. Supernovae giveth and taketh.)

IEEE - The Singularity Issue

Via Nick Carr I discover the professional journal of electrical engineers has devoted an entire issue to the Technological Singularity (aka The Singularity) beginning with a Vinge essay:

IEEE Spectrum: Special Report: The Singularity

... The writer who first postulated the singularity answers skeptics and tells us what to look for as the world slips closer to the edge...

Well blow me down.

I was so surprised by the six article special issue I did a quick test to see if they'd referenced the "unavoidable Singularity" answer to the Fermi Paradox but they didn't.

As a card-carrying geek I am well versed in the Gospel of the Geeks, the Rapture of the Nerds and Ascension unto Silicon. I call that threat skynet, in honor of the governor of California.

Alas, as a confirmed unbeliever in the kindness of deities I would not expect much of us to survive even 8/10s of a Singularity, save perhaps as an arcane footnote.

I give much credit to IEEE for tackling the most unnerving of topics, and publishing an issue that, if we're still around in 100 years, will be endlessly mocked*. For more on the topic see my skynet thread, or the footnotes to my old Fermi Paradox page.

I'll read the articles and make note of anything novel, but I'd be surprised to find any new insights. This topic has been well discussed in geek circles. Now all we can do is wait and see what happens.

PS. My quote from the issue credits Vernor Vinge with the invention of the Singularity concept, but I see him more as the person who reified the Singularity in the popular mind. He brought it from a fuzzy concept in science fiction dating back to at least 1982 into the wider geek consciousness.

I have, by the way, an original copy of the issue of Whole Earth magazine where Vinge's first popular Singularity essay was published.

* Vis: Bill Joy. I think it's possible we won't see a Singularity by 2108, but if I'm sentient in 2040 and there's no sign of one beginning, I'll be inclined towards an even more peculiar, but very popular, explanation of the Fermi Paradox.

Auctorial

It's been a while since I came across an english word that was completely new to me:

Making Light: Just a lotta animals

...blatant auctorial favoritism...

Auctorial means by the design of the author.

The paradoxical security of Windows 2000

I've been using Windows 2000 SP4 in my Parallels and (now) Fusion VMs:

Gordon's Tech: Parallels to VMware - my experience

As part of my move from 10.4.11 to 10.5.3 I switched from Parallels (Windows 2000 VM running Office 2003 and MindManager to VMWare Fusion (updated 5/30 for 10.5.3). Here's how it went...

Windows 2000 SP4 runs Office 2003 and most business apps without any problems -- that's all I need. I have two unused Win2K licenses, so it costs me nothing. It's much more compact than XP, it demands fewer CPU resources, and it runs happily in only 256MB of memory.

It's a perfect match to my needs.

There's only one catch. Microsoft isn't updating Windows 2000 security any more, and I don't use antiviral software on any platform* (except at work, where it's mandated). Well, I don't expose the Windows VM to the net, so that's probably not an issue.

But is Windows 2000 really all that insecure nowadays? It must be an exotic environment on the modern net, I can't believe it would be a profitable target. I suspect it's actually becoming more secure with every passing day.

I wouldn't bet on that of course. I really don't have a need to take the Win2K environment for a walk in the wild side. Still, I suspect it's true ...

* Modern antiviral software behaves like a virus infestation (performance and reliability suffer greatly), antiviral vendors blew it by choosing not to block SONY's spyware 1-2 years ago, it often fails against modern attacks, and it's been years since I've received email with an attached virus (Gmail filters them).

Gmail's biggest missing feature - and it's a whopper.

Outlook is the only email application I know of with the absolutely critical feature that Gmail most urgently needs.

In Outlook I can edit the subject line of messages I've received*. (You can edit the body and attachments of received email as well; that's very nice but not essential.)

Gmail can't.

Neither can other email packages, but the problem is more severe in Gmail because it threads conversations by subject line. Since most humans are still living in the 20th century they don't use intelligent subject lines; important messages get lost in the same-subject-line thread. To add insult to injury, Google's threading model discourages intelligent subject lines.

21st century people know subject lines are critically important. We don't do folders, we do search. The initial presentation for a search result always includes the subject line -- it tells us what's important.

(Digression. I do find it a bit odd that Googlers evidently don't do search.)

If all my correspondents were 21st century I wouldn't have as dire a need to edit the subject lines of their messages, but even so what I consider important may differ from their opinion. I'd still like to be able to edit their subject line on occasion. (Note: Emily, you do fabulous subject lines. I'd say that even if you weren't my wife.)

Sure, this breaks the evidence chain of email. I don't give a damn. I have zero interest in preserving the email I receive in some kind of pristine state. When I archive it I'm doing it for my own benefit, not for anyone else's benefit.

Google, you can fix this. It will help break your compulsion to thread conversations by string matching the subject line (which also breaks Google Groups, but that's another story).

* It's amazing how many people don't know this. Just click on the subject line of an email you're received and type. Shocked?

Google's infinite storage solution

A year or two ago I paid a modest fee for extra Picasa web album storage. The storage pool is shared with my Gmail account.

I realized today that even though I add images and my email volume grows, I don't seem to be running out of space.

Basically, Google is adding to my allotment at roughly the rate I'm consuming it. The current number is:

6.5 GB (39%) of 16.6 GB

It's been about 35-40% for at least a year. For my current usage rates Google's storage allotment is essentially unlimited.

The odd thing is that we've come to take this for granted, so much that nobody comments about it any more.

I am fascinated by the big changes that, for the most part, we don't recognize ...

My iPod has run out of room, so the iPhone is more appealing

Since I don't have much video on my iPod, I though 30 GB would be plenty of room. Our family music library used about 14GB, and a few videos used 3-4 GB.

I didn't reckon with Podcasts. I'm out of room now.

Ironically, this actually negates one of the relative disadvantages of my iPhone-to-be. I'm going to have be selective about what I carry, whether I use an iPod or a 16 GB iPhone.

If 30GB isn't enough, then 60 won't be either, so there's no point in trying to outpace this stuff. I just need to get used to managing the playlist sync.