Adina Levin's weblog. Mostly for conversation about books I've been reading. Other stuff too.
Friday, November 29, 2002
Travelling and offline for the weekend
Blog Prom Queens
New blog database shows who links to your blog and lets you watch your rank in the blog hierarchy; and provides a for-pay service to track your blog ranking.
What I like: lets you discover inbound links.
What I don't like: treats blogs like a high school popularity contest.
The single-peaked popularity ranking obscures "subcommunity" patterns -- there are knots of java bloggers and political bloggers and Austin bloggers; and plenty of bloggers who participate in multiple communities (like physical life).
When Blogdex started picking up a lot of Persian blogs in its top rankings, the designer considered reducing his coverage to english-language blogs only. That's exactly wrong. The right thing to do is to reveal blog blogcommunities, and identify leading voices in those subcommunities. Hmm... Valdis Krebs probably knows how to do this...
And raw popularity seems beside the point. Some of my favorite blogs are low-traffic blogs from people who don't do much self-promotion. This blog is a place to write about the various topics I'm interested in; not filtered by which topics are most popular.
Web Services We'd Like to See
From from Timothy Appnell at O'Reilly; Ebay, Yahoo Groups and Calendar, PayPal, more.
Contradictory NYT articles about China
The glowing numbers that support the first story do not include the provincial poverty shown in the other stories. This Economist article from earlier this year talks about Enron-sized flaws in the Chinese economic growth numbers.
Thursday, November 28, 2002
Links of Thanksgiving
What are they trying to tell us?
Scott Rosenberg asks a really good question about why the Pentagon's war plans keep showing up on newspaper front pages.
Tuesday, November 26, 2002
The O'Reilly editors talk about rich web clients. More of the editors seem to like Flash. The articulate comments favor non-proprietary approaches using XHTML, XUL, SVG. Some tasty links in there to follow up.
Monday, November 25, 2002
South Asian bluegrass...
Caught a fun show at the Clay Pit this weekend, with Ganesh, a percussionist visiting from Madras, India, who has played with Max Roach, Zakir Hussein, Glen Velez and is currently recording with both Bela Fleck and the Flecktones and the Violent Femmes.
The musicians on stage had varying levels of fluency in traditional Indian and Middle Eastern classical music, bluegrass, blues, jazz, rock, and country music. They improvised in various combinations of the musical genres; the audience and the musicians were all having fun.
Sunday, November 24, 2002
A Mediterranean Society
I recently read the one-volume synopsis of SD Goitein's five-volume masterwork summarizing Goitein's research in the Cairo Geniza. A geniza is a synagogue's repository of worn-out texts. In the Jewish tradition it is forbidden to dispose of texts that mention the name of God; and ordinary legal documents, business documents, and personal letters often mentioned the deity. The Cairo Geniza is a trove of documents holding evidence about the daily life in the Jewish community of medieval Cairo between the 10th and 13th centuries.
A Mediterranean Society, edited and abridged by Jacob Lassner, portrays the texture of life of that time for Jews, Muslims, and Christians, and the surrounding world which was linked by commercial and communal bonds.
Topics include the family, social life, education, business, community organization, and law. Christian and Jewish minorities were largely self-governing with respect to civil law, family law, and social services and well-integrated with respect to residential patterns and business dealings. In the 11th and 12th centuries, conditions were more stable; later on, as the surrounding society declined, the Jews experienced economic hardship and persecution.
Following Peterme's train of thought, one of the things that stands out most about the Geniza world is the efforts of the Jewish community to take care of people in need. The community ran a multi-layered charitable system, providing food and clothing on a daily and weekly basis, and making longer-term provisions to house refugees, to educate orphan children, to support the marriage of orphan girls and to ransom of captives at a time when piracy and war-related kidnapping was endemic.
Maimonides, the great Jewish scholar and leader of the Egyptian community in the late 12th century wrote that the best way to bring someone out of poverty was to give them the tools to be self-sufficient. But that perspective did not get in the way of ongoing, systematic efforts to feed the hungry and house the homeless.
Another notable thing is the vibrancy of economic life. Janet Abu Lughod wrote an birds-eye view of the world economic system between 1250 and 1350, describing a trade system that tied together Europe, the Muslim world, and the East. Goitein portrays the day-to-day reality of that system for the people who lived it; weddings scheduled for early Spring so merchants can leave in time to catch the favorable winds to India; marital troubles and divorces among couples who were separated by travel most of the time.
Goitein counted 450 occupations mentioned in the Geniza, which is the largest number of job categories in any pre-modern city. Jews participated in an array of activities including manufacturing: textiles, metals, glass, pottery, paper; construction; agriculture (flax, wheat, olives); trade; civil service, medicine, education. Jews in Medieval Egypt participated in most sectors of the economy; often in business partnerships with Muslims and Christians. The situation was quite unlike medieval Europe, where Jews were forbidden from owning land and participating in trade guilds, leaving finance among the few ways to make a living. Unfortunately, Lassner condensed Goitein's sections on economic life more than the other sections of the book, assuming that readers would find it dull. Not this reader. I may eventually have to find and read that volume of the Goitein series.
The Geniza provides a tantalizing window on the social life of the time. Pilgrimages were quite popular, although less reverant than the purist clergy wished. A ruling was issued regarding one of the more popular pilgrimage sites,
Clearly, people were having a lot of fun doing all of the things the clergy didn't approve of!
The divorce rate was quite high; as evidenced by the number of second and subsequent marriages found in Geniza documents. Goitein attributes the divorce rate to the custom to marry women off when very young to men they didn't know, and to the prevalence of travel that kept couples apart for months and years at a time.
The figure of Moses Maimonides occurs frequently in the book's pages. Maimonides is most famous as philosopher who incorporated the rationalism of Greek philosophy into the revelation-based monotheistic Jewish tradition. In the Jewish tradition, Maimonides reputation rests on his work as as a commentator and jurist; he was one of the leaders in the medieval project to organize the vast textual sprawl of the Talmud into a systematic legal code.
In Goitein, however, Maimonides makes frequent appearances as a communal leader; making judgements that are often fair and wise. For example, a judge in a town refused to allow a twice-widowed woman to remarry, because of a custom that considered a twice-widowed woman a "killer wife." Maimonides ruled that the couple should marry before two witnesses (legal according to Jewish law), and should then have this marriage ratified by the court. In another example, a cantor newly appointed to a town protested to Maimonides that his congregation enjoyed non-traditional poems inserted into the liturgy; Maimonides replied that the addition was improper, but keeping the poems was prefereable to the strife that would accompany an attempt to prohibit them.
However, Maimonides' judgements sometimes reflect the stricter social norms of Morocco, where his family lived before emigrating to Egypt. For example, Maimonides bans games of chance that were popular on the sabbath in Egypt, and favors wife-beating, which was apparently more socially acceptable in Morocco than in Egypt.
The book reads rather like a collection of encyclopedia entries, on the family, judicial system, communal structure, and other topics related to the life in the Geniza community. If you're interested in the subject of the book, you'll enjoy it. If you're lukewarm on the topic, the book doesn't have spine-tingling plot twists or insightful arguments; just rich portraits of a distant world.
Saturday, November 23, 2002
Successful cooking experiment
LENTILS WITH BUTTERNUT SQUASH AND WALNUTS, from Epicurious
I tripled the recipe to serve a larger group. The cookbook says the recipe can be prepared in 45 minutes or less; if you need to make more, leave more time for all of the chopping. Also, I microwaved the squash til it was easy to peel and slice, and then combined the first two cooking steps.
1 small butternut squash (about 1 pound)
1 large shallot
2 tablespoons olive oil
1 1/2 teaspoons curry powder
1/2 cup walnuts (substituted tamari almonds)
1/3 cup lentils
2 tablespoons chopped fresh cilantro sprigs
fresh lime juice to taste
Preheat oven to 425°F.
Halve, peel, and seed squash and cut into 1/2-inch pieces. Finely chop shallot and in a shallow baking pan toss with squash, oil, curry powder, and salt and pepper to taste until combined well. Bake squash mixture in middle of oven until almost tender, about 15 minutes.
Chop walnuts and sprinkle over squash. Bake squash mixture 10 minutes more, or until walnuts are lightly toasted and squash is tender.
While squash is baking, in a saucepan of boiling water cook lentils until just tender but not falling apart, about 20 minutes. Drain lentils in a sieve and transfer to a bowl.
To lentils add squash mixture, cilantro, lime juice, and salt and pepper to taste and toss until combined well.
Serves 2 as a side dish.
Thursday, November 21, 2002
Nifty blog referrer gizmo from Mark Pilgrim
It reads your blogroll and gives you recommended sites that you might like, using data from Phil Pearson’s Blogging Ecosystem.
Like Amazon's recommendations, you can tell it which recommendations you've read already or aren't interested in, and it will update the list of recommendations.
Mark does an insightful thing with the algorithm, which works by:
So the gizmo doesn't just refer you to Doc and Dave and Dave and Slash -- it finds less overwhelmingly popular sites that you might be interested in.
This overcomes a flaw in the arguments of Linked and Nexus, which both focus on the winner-take-most chacter of small-worlds networks, and ignore the interesting ecological roles played by sub-hubs.
How Will the New Homeland Security Bill Affect You
Christian Science monitor interview with the journalist who's been covering the bill. Good mid-level overview of the content and implications of the bill.
"Secrecy is also a chief concern among critics. The Homeland Security Department's actions will largely be exempt from Freedom of Information Act oversight by ordinary citizens and will be subject to a decreased level of congressional oversight, critics say."
The founding fathers created laws to forbid searches without warrants and secret trials because they knew from experience with European monarchies that these sorts of policies were subject to abuse. The laws and policies should protect citizens in case the government abuses our trust. That is part of what they meant when they talked about forming "a government of laws, not of men."
Don't other people remember this from civics class (and I wasn't paying that close attention, either)? Do the legislators remember?
Wednesday, November 20, 2002
Joel Spolsky's mailing list got spamblocked too.
p.s. The problem seems to have cleared up, presumably thanks to Earthlink.
Monday, November 18, 2002
Been using a wiki for business collaboration...
...on a project over the last few weeks, with a group of geographically dispersed colleagues. For the most part the experience has been quite pleasant. For folks who aren't familiar with wikis, they're collaborative web spaces that anyone can edit.
* The wiki is used to post meeting times, resources for the group, and for individuals to post what they're working on.
* We typically email to brainstorm ideas; then post the results of the brainstorming to the Wiki where it can be sculpted.
* The absurdly low overhead is delightful -- click "edit this page" to edit the page. Even easier than keeping an intranet and ftp-ing html pages (which I've done in a previous startup). Less likelihood of versionitis caused by ftp-ing an old file version onto a newer one.
* Easy to keep track of what's new by clicking on "recent changes"
* Keeps behind-the-scenes work out of email, freeing email for interactive conversation
The easygoing "anyone edit" system works well except when more than one person is editing the same document on a deadline. Upon which we needed to implement "social document management" by verbally "checking-in" and "checking-out" sections.
After the first dozen or so entries, you need to start gardening the home page to keep it from getting tangled and overgrown.
The hyperlink-tyranny of the Wiki interface makes multi-page structures rather dizzying to navigate. This method will top out above a certain level of complexity, without the ability to add more navigational cues.
Using a Wiki is much easier and more pleasant than the corporate Microsoft monoculture, which requires the use of rock-heavy tools like PowerPoint and Word to do simple things.
Using a Wiki requires collaboration and trust within the workgroup. Knowledge management isn't technological, it's social.
It will be interesting to see how and whether the use of Wiki will scale when and if the project matures. In the mean time, there's a set of rapid, low-overhead collaboration processes that the Wiki works really nicely for.
Congress passes bill saving small webcasters from destruction
from Kurt Hanson's blog, via SlashDot
"In a stunning victory for webcasting, both the Senate and the House of Representatives unanimously passed a revised version of H.R. 5469 late last night that clears the way for copyright owners to offer webcasters a percentage-of-revenues royalty rate, essentially allowing the parties to mutually agree to override the CARP decision of last spring."
Aggressive lobbying stopped previous versions of the legislation with fixed royalty fees that would have put small webcasters out of business, and helped pass a bill that allows small webcasters to pay fees on a percentage of revenues.
The story isn't over, according to a Washington Post article; rather than fixing the rates the bill delegates rate-setting to a negotiating process between SoundExchange, a recording industry organization, and the webcasters. But small webcasters support it, according to the coverage I've seen.
The Post article doesn't display correctly in Mozilla, but appears fine in IE.
Blogstreet searches a database of 28,000 blogs.
Blogstreet can show which blogs are related to other blogs. If you type in a Blog URL, Blogstreet will show you a list of related blogs derived from their blogroll, and the list of blogs that blogroll it. This would be even more helpful if the neighborhood was assembled using topics and other references. After all, it's easy enough to blogrollsurf already.
Sunday, November 17, 2002
So I was thinking about the latest worrisome developments, like John "Iran-Contra" Poindexter running a Defense Department program to set up a vast data mining operation, which will sift through credit card records, medical records, travel records, and email, along with government and legal records, on a vast and random fishing expedition for signs of potential crime.
No prior cause, no warrants, no permission necessary.
William Safire's tirade against the program, if you haven't read it yet. Posted by David Weinberger in full, here.
The ACLU's arguments against it.
And I thought that the one thing we were missing was a real, honest-to-goodness secret police.
Then I saw this. The President's national security advisors are recommending the creation of a brand new domestic spy agency.
I've been spam-blocked!
Late last week I got a return email with a distressing header:
> SPAM: -------------------- Start SpamAssassin results ----------------------
> SPAM: This mail is probably spam. The original message has been altered
> SPAM: so you can recognise or block similar unwanted mail in future.
> SPAM: See http://spamassassin.org/tag/ for more details.
SpamAssassin has been flagging my email as spam!
Perhaps the problem results from the time when my return address was forged by a spammer earlier this year -- I found this out when I got bounced emails, selling something dubious, with my name as the return address and the spammer's address buried deep in the full email header.
When I browsed the SpamAssassin site to see if I could solve the problem myself, they simply listed links to three or four keepers of blacklists; none of which seemed to have me listed.
The instructions on SpamAssassin and the various blacklist sites all assumed that senders who'd been flagged as spammers were obviously low-life spamming scum who wanted to squirm off the list in order to ply their loathsome trade once more. They were not trying to make things easy for an ordinary citizen plagued with return address identity theft!
I turned this over to the support folks at Earthlink (which is also what I did when I got the first signs of return address forgery.)
If you've ever run into this problem and solved it, advice would be most welcome.
Spamblocking seems like a worthwhile activity; but the cure feels worse than the disease today.
Update: Seems like the problem related to Earthlink in general -- SpamAssassin has identified it as the source of an open relay -- rather than me in particular. Still bad, but less Kafka-esque. Hopefully this will get fixed soon.
Friday, November 15, 2002
Delta relieves "gate stress" with new display for waiting passengers
John Udell writes about a new system that Delta has designed to give passengers waiting at the gate more information about the boarding process, like updates on how many people have checked in, and the state of the standby list.
Sounds really helpful for those times you're standing there anxiously waiting to see if you'll get on the flight.
Thursday, November 14, 2002
Web, code, and Talmud
Reflecting on David's puzzlement about the Jews and software meeting in Boston the other day, I recalled this Joel Spolsky essay on how reading code is like studying Talmud, in that it is best done in pairs, puzzling through and arguing about the meaning of the text.
When you think about it, the "link" form of the weblog has similarities to the classical Jewish form of text commentary. The blogger links to an article somewhere on the web, and then writes a commentary on the original text; then other commentators refer to the original commentator. In the traditional form, Jewish scholars wrote texts that commented on the bible or on the writings of earlier rabbis; and other rabbis wrote texts that commented on the earlier rabbis' writings.
Because they didn't have hypertext at the time, commentaries linked using chapter and sentence references; so when you study traditional texts, you wind up with a table full of books following the cross-references from book to book.
The form of the Talmud is similar to a recorded newsgroup or blog comments discussion. In the classical rabbinic academies, scholars discussed and debated a wide variety of topics, and those discussions were eventually edited into book form. The editors were concerned with representing the debate of ideas, not with historical accuracy -- often, there are arguments between rabbis who didn't live at the same time.
Its not that the Rabbis didn't know how to write neat, logical, linear exposition. The classic rabbinic period was contemporaneous with the Hellenized civilization of the ancient world; they had the models of Greek thinking all around them, and they borrowed when it suited them -- the Passover seder is modeled after the Platonic symposium. They looked at neat, logical, linear, hierarchical writing, decided that they didn't like it, and wanted to write in weblog form instead.
Tuesday, November 12, 2002
On Data as Narrative
Intriguing Advogato essay by GaryM, sparked by David Gelernter's NYT advertorial on the obsolescence of the file cabinet metaphor for organizing data.
"David Gelernter's thinly disguised advertising piece Forget the Files and the Folders: Let Your Screen Reflect Life, for all it's absurdities, is still something of a thread of a good idea in his "narrative file system" thesis: the idea of desktops, files and folders is a quaint retrieval from an office world very few of us remember and an organizational tool alien to the way people view their data.
The article describes the problem nicely, doesn't propose any useful solutions. Too bad.
The Airline of the Dalai Lama
Check out the list of titles in this British Airways registration form. It is too funny.
They serve people from many regions and cultures with different languages (Herr, Fraulein, Monsieur, Sheikh). There are special needs, such as serving Muslims on pilgrimage (Alhaji).
England is a class-conscious society, so they probably had customers wanting to register with their social and military titles. I can just see the secretary for some elderly Baron or Viscountess dressing down some poor BA functionary for not listing the correct title. I can see some web programmer throwing their hands up in despair, getting a book of titles, and including every last one.
Besides, the Pope and the Dalai Lama do fly fairly frequently with retinues. The field for "His Holiness" has probably been used.
At the bookstore....
... this afternoon, looking for a book on Perl, for some weekend entertainment that I'll tell you about if and when it's closer to working.
In the computer aisle, a retired gentleman approached me and asked me for advice. He did some hobbyist programming in BASIC 20 years ago, balancing his checkbook and doing calculations for a rather complicated-sounding home construction project (had to do with calculating the fluid volume in pipes).
He wanted to do some programming as mental exercise, and asked what I would recommend. I showed him the Microsoft VBasic.NET books, and Python, and PERL. Then I described the Computational Beauty of Nature, and his eyes lit up.
That was a good "neighbor moment."
Monday, November 11, 2002
User Interface Decay
When good interfaces go crufty has lots of well thought through examples of user interface traits that are artifacts of obsolete design constraints.
One such example: applications use awkward little filepickers to open or save files because when the Mac was first designed, it wasn't able to run the file manager and an application program at the same time.
Installed base dependencies and cultural habits can cause cruft to be highly persistent. Think about it -- the school year in the US begins in September and ends in May, to allow students time off to help with the family harvest.
One nit -- Internet Explorer's lack of an exit menu item is a bug, not a feature. If you've got more than one window open, you need to close them, tediously, one at a time.
The essay was slashdotted, so you may have read it already :-)
Sunday, November 10, 2002
We're looking for people who have almost everything
Please accept the most luxurious edition of Moby Dick ever published, for just $5.95! (Regularly $39.95)
Leather-bound and accented with pure 22-carat gold.
Imagine this Luxurious Volume on Your Library Shelves,
At a holiday party at the home of an executive, I once saw an astonishing library. Two full stories of shelves lined with books, with a rotating ladder to reach the upper shelves. The books were bound in leather, carefully arranged by color and height.
The lobby of an upscale apartment development in Austin was trying to achieve a similar effect, I noticed a couple of years ago. On the walls they had paintings of people in English hunting costume, accompanied by horses and dogs. They had shelves lined with books across from leather couches. I was waiting, so I picked a book from a shelf. It was a math text in Swedish.
Lawn mower wisdom
This past summer I purchased a lawn mower for the first time in my life.
Like other acts of homage to the spirits of hardware, the search for a lawn mower was a learning experience.
At first I considered a manual mower. I don't have that much grass, I don't have big hills -- it seemed like the simplest solution.
I hadn't realized that manual lawnmowers had evolved from utilitarian garden implements to totems of yuppie nostalgia and sentimental patriotism.
Lawn mower of the past
Then I read that manual lawnmowers tend get stuck on twigs; and they can't cut grass if it gets more than 5 inches high. So I looked further....
And found that advanced technology now can automate the lawnmowing process completely. You buy a little, round, red or yellow Pacman-like robot You install a wire around the edge of the lawn. The robot lawnmower then buzzes around the grass, munching away within the wire perimeter. They haven't worked out the bugs yet -- the algorithm doesn't cut evenly and hit has some trouble with bumps and sticks. And it costs a bit more than I wanted to spend. So I searched on.
Lawn mower of the future
And I discovered that cutting the grass was no simple yard chore. Mowing the lawn is an opportunity to transcend the life of this world, and commune with the world of the spirit.
Lawn mower of the world to come
While I steeped myself in lawnmower lore and learning, I borrowed a gasoline mower from some friends to mow the lawn before the yard turned into a jungle. It was loud. It was smelly. And it was too heavy for me to lift.
I finally settled on the prosaic, best-selling Black-and-Decker electric mower from Amazon.com. It's quiet. It won't explode. I can easily move it up and down stairs.
Lawn mower of the present
Thursday, November 07, 2002
Computers won't be reading Plato any time soon, Part 2
Thanks to Ed Nixon for a link to an interesting article by philosopher
John Searle, arguing against Ray Kurzweil's contention that computers
will soon be smarter than people.
The strong part of Searle's article is the argument that "syntax is not
semantics" -- a computer that can calculate chess moves based on
pre-defined algorithms does not actually understand chess. Searle argues
successfully that Deep Blue is unintelligent in the same way that a
pocket calculator is unintelligent; it is simply manipulating symbols,
just as a human who speaks Chinese phrases using a transliteration is
manipulating symbols but does not understand Chinese.
Searle is right that Deep Blue is very far from being conscious. The
fact that a computer can beat a human at chess means about as much as
the fact that an automobile can move faster than a runner. Humans
designed the automobile; and human programmers chose the heuristics that
drive Deep Blue's decisions.
Searle is less successful with the argument that a computer cannot have
intelligence, since a computer contains a mere model of intelligent
processes; and models are different from the physical things that they
Searle acknowledges that human intelligence is an emergent property of
neurons firing in the brain. This means, though, that intelligence is
based on circuitry, a pattern of information. Similarly, scientists are
gradually deciphering the informational patterns of genes and gene
expression. The lines between information and reality are not so clear
cut; it may be possible to develop living, even intelligent patterns in
some other medium.
Human intelligence probably has subtle dependencies on the biochemical
nature of the brain and the organism. Tom Ray makes this point
beautifully. But it does not follow that the only possible kind of
intelligence requires a body; it certainly does not follow that theonly
kind of intelligence requires this sort of body.
It may be theoretically possible for intelligence to develop in some
other medium. But despite Kurzweil's optimism, there is little evidence
that we have any idea how to do this. Searle is right that just because
we can program computers to play chess does not mean we are anywhere
near creating computers with conscious minds.
Wednesday, November 06, 2002
& & & ! !
Have run into several pseudo-debates today about the relative benefits of websites and e-mail. The answer is both.
Mitch Ratcliffe cites an argument between Mark Hurst, who argues that email is better than weblogs, and John Robb over at Userland who argues in favor of weblogs.
Meanwhile, John Robb cites Ray Ozzie, who argues in an Infoworld interview that people ignore collaboration tools and portals because they aren't as "natural" as phone, fax, and e-mail.
"Natural" has nothing to do with it. Right tool for the job has everything to do with it.
When you're trying to reach another human immediately, you phone, fax, email (or IM). Why waste time browsing a web site when you just want to talk to Ed?
But when you want to talk to a person whom you haven't spoken in a while, you probably look up their website first. You don't call Ed and ask, "Ed, are you still working as Director of the Do-Gooders Coalition?" You look up the Do-Gooders' coalition website first, and when you talk to Ed, you congratulate him on the success of their recent fundraiser.
Ratcliffe is respectful about Hurst's advocacy of push email vs. pull websites but with all due respect, I think the point is ridiculous. Email is wonderful AND you don't want all of the information in the universe piling up in your email box! Some things are important enough to deserve regular attention, and you want to receive them by email. Other things are interesting, but can wait till you go fetch them.
The tools work best together.
I'm politically pretty moderate, with some very strong opinions on specific issues that cross party lines.
The current administration is in favor of:
I'm pretty worried about the consequences of these policies. They could make this country and the world a lot worse for a long time.
(The Economist article might cost money to read; it's Jeffrey Sachs on proven-effective ways of reducing poverty and suffering around the world. If you want the article, I'm pretty sure I can email it in a way you can read it for free, so ask.)
Monday, November 04, 2002
The Origin of Animal Body Plans by Wallace Arthur
Unfortunately, the Amazon API does not seem to cover reviews; I would love to be able to cross-post reviews to Amazon and the weblog!
This book looks nontrivial but fascinating. Into the to-read queue it goes. So many books, so little time.
Sunday, November 03, 2002
Acquiring Genomes: A Theory of the Origins of Species
Acquiring Genomes: A Theory of the Origins of Species contains some fascinating biology surrounded by a muddled argument in a poorly organized book.
Authors Lynn Margulis and Dorion Sagan are advocates of a theory that compound cell structures evolved by means of symbiogenesis -- symbiosis which becomes permament.
The best-known example of symbiosis is lichen, in which a fungus lives together with an alga or cyanobacterium; the organisms propogate together in a joint life cycle. The book includes many other wonderful examples of symbiosis. A species of green slug never eats; it holds photosynthetic algae in its tissues, and it crawls along the shore in search of sunshine. A species of glow-in-the-dark squid has a organ which houses light-emitting bacteria. Some weevils contain bacteria that help them metabolize; others have bacteria that help them reproduce. Cows digest grass using microbial symbionts in the rumen; humans take B-vitamins from gut-dwelling bacteria.
The associations take numerous forms; a trade of motility for photosynethsis; nutrition for protection; one creature' waste becomes
another's food. The authors argue that the posession of different set of symbionts can leads to reproductive isolation and speciation. Much more than that, the authors argue that all species are the results of symbiosis that became permanent and inextricable. The bacteria that fix nitrogen for pea plants are no longer able to live independently. The biochemistry of the symbionts become intertwined; the symbionts together produce hemoglobin molecules to move oxygen away from the bacteria; the heme is manufactured by the bacteria, while the globin is produced by the plant.
The final symbiotic step is a fused organism. The authors contend that algae and plants developed photosynthesis by ingesting photosynthetic bacteria and failing to digest them. Based on research by several scientists, the authors believe that a cell structure called the karyomastigont, including the nucleus and its connector to a "tail' that enables the cell to move, was once a free-living spirochete which became enmeshed in another bacterium that was good at metabolizing the prevalent resource (sulfur?), but could not move well by itself. The bacteria merged their genomes, as bacteria are wont to do, and henceforth reproduced together.
At least at the cellular level, the symbiogenesis argument is fascinating and plausible for the origins of the first species. Species are conventionally defined as creatures that can interbreed. But bacteria of various sorts, whose cells lack nuclei, can and do regularly exchange genetic material. Their types change fluidly. Therefore, bacteria don't have species. According to the theory of symbiogenesis, eukaryotes, organisms whose cells have nuclei, were formed by the symbiosis of formerly independent bacteria. Eukaryotes, including fungi, protoctists, plants and animals are all composite creatures. Margulis and Sagan propose a new definition of species: creatures that have same sets of symbiotic genes.
According to Margulis and Sagan, therefore, the graph of evolution is not a tree with ever-diverging branches; it is a network with branches that often merge.
The symbiogenesis theory is a logical proposed solution to the puzzle of how nature can evolve living systems with multiple components. If you look at software as another kind of information-based system; it seems only reasonable that composition would turn out to be an effective means of creating larger, more complex units. None of the artificial life experiments that I know of have achieved this so far (although the Margulis/Sagan theory suggests a way to test this, by creating artificial metabolisms that can evolve codependency).
While Margulis and Sagan make a plausible argument that symbiogenesis is a plausible mechanism for evolution, they fail to persuade that it is the primary mechanism for all of evolution.
The authors contrast evolution by symbiogenesis with a "neodarwinist" view that evolution proceeds in gradual steps by means of random mutation. They observe that in ordinary life, mutations are almost always bad, and therefore cannot be a source for evolutionary change.
But this argument against change by means of gradual mutation is a straw man compared to contemporary theory. First of all, mutation may not be the prime source of fruitful genetic variation. The math behind genetic algorithms shows that where sexual reproduction or other genetic recombination is used in reproduction, these recombinations generate more variation and often more fruitful variation than random mutation. This may also be true in nature. Reproductive recombination may be a fruitful source of natural variation that is more important than mutation.
Second, evolutionary biologists including Stephen Jay Gould have moved away from the notion of slow, gradual change, toward a theory of "punctuated equilibrium", positing faster change driven by times of stress. The theory of stress-driven change also helps combat the argument about the uniformly deleterious effect of mutation. In a stable circumstance, most changes to the status quo are going to be bad. In a sulfurous atmosphere, bugs that breathe sulfur and are poisoned by oxygen live well; a sport that preferred oxygen to sulfur would soon die. But if the atmospheric balance changed to include more oxygen, an oxygen-breathing mutant would be at an advantage.
Margulis and Sagan bring up the old canard that gradual change can't create a complex structure such as a wing. However, Shapes of Time, a book about about the role of the development process in evolution, explains elegantly how substantial changes in form can be produced by small modifications in the algorithms coding an organism's development. Margulis and Sagan don't have any explanation for how symbiogenesis could possibly explain the evolution of four-legged creatures from fish, or humans from chimps; developmental theorists have plausible explanations for these transformations.
The symbiogenesis argument is seems strongest in dealing with single-celled organisms, where the fusion of genomes is not hard to imagine, and harder to explain in dealing with more complex life forms. The most dramatic argument from the symbiogenesis camp is that the larval stage found in many species is actually an example of symbiogensis. At some point, frogs, sea urchins, and butterflies aquired the genomes of larva-like animals. It would take a lot more explanation to make the case for this -- if different creatures acquired a larval form by means of symbiosis, why would larval form always be at beginning of life cycle; why doesn't a butterfly molt and become a caterpillar? If the animal contains two seperate genomes, what developmental process would govern the switchover from the first genome to the second. I will certainly look for other evidence and arguments to prove or disprove this one. Readers who are familiar with this topic, please let me knowif this argument has been discredited or if any more evidence has been generated to support it.
The summary of the book's argument here is more linear and direct than the book itself. Chapters 9 through 12 focus on the area of the authors' scientific expertise -- examples of bacteria, protoctists, and fungi in symbiotic relationships, and proposed mechanisms for the role of symbiosis in evolution. These chapters are the strongest and most interesting in the book. The rest of book contains vehement yet fitful arguments about various tangentially related topics
The authors have some seemingly legitimate complaints with the structure of biological research. The authors believe that symbionts are a primary biological unit of study; yet scientists who study plants and animals are organizationally distant from those who study fungi and bacteria, making it difficult to study symbiosis. Moreover, the study of small, slimy, obscure creatures generates less prestige and money than the study of animals, plants and microbes that relate directly to people; slowing progress in the field of symbiosis and rendering it less attractive to students.
The book has a section on the Gaia hypothesis -- the argument that the earth itself is a living being. The connection to the book's main thesis is not made clearly, and the section is rather incoherent. The authors have a written a whole book on the subject, which may be worth reading; or there may be some other treatment worth reading (recommendations welcome, as usual).
The book includes a section attacking the commonplace metaphors of evolutionary biology, such competition, cooperation, and selfish genes. But the authors don't seem to use metaphors any less than the people they attack -- they have a particular fondness for metaphors of corporate mergers and acquisitions, and human intimate relationships. The use of metaphor in science has its advantages and limitations; but this book doesn't add anything intelligent to that discussion.
In general, the authors are aggressively dismissive of other approaches to evolutionary biology. In a typically combative moment, the authors argue that "the language of evolutionary change is neither mathematics nor computer-generated morphology. Certainly it is not statistics." The authors clearly have a hammer in hand, and see a world full of nails. In posession of a strong and original idea, the authors lack the perspective to see their own idea as part of a larger synthesis incorporating other ideas.
In summary, I enjoyed the book because of the strange and wonderful stories of symbiosis and the description of the symbiogenesis theory. But the book as a whole is not coherent or well-argued. Read it only if you're interested in the topic strongly enough to get through a muddled book. And don't buy retail.
Friday, November 01, 2002
Clicks and Mortar
Execution happens at ebb tide, when the hype waves have receded offshore. I was looking for The Self-Made Tapestry and found that Barnes and Noble Online now lets you search inventory of its local stores, enables you to reserve the book online for pick-up at the store, and even tells you in what section of the store it can be found. I wish that the local bookstores had this capability, but they don't yet.
The last feature is particularly helpful for those who prefer books that aren't clearly in one subject area. Is The Computational Beauty of Nature in Biology, Math, or Computer Science? Is The Printing Press as an Agent of Change in History, Sociology, or someplace else? Much time has been spent wandering bookstore aisles in search of books without an obvious category; this is one reason that I buy a lot of books online (of course, they could always reshelve sections on Social History of Technology and Computational Biology...).
By the way, they didn't have Self-Made Tapestry, so I bought Acquiring Genomes instead, which is on the Lynn Margulis theory that cell organelles used to be free-swimming critters.