Keeping up with the metagenome

Biology has changed a bit since the day -- and yet not so much. In my 1970s biology classes ecosystems and emergent interactions were very fashionable ...

John Hawks Anthropology Weblog : 2006 12 0 The metagenome and obesity

...the introduction to the paper by Turnbaugh et al. (2006:1027) puts it well:

The human 'metagenome' is a composite of Homo sapiens genes and genes present in the genomes of the trillions of microbes that colonize our adult bodies. The latter genes are thought to outnumber the former by several orders of magnitude. 'Our' microbial genomes (the microbiome) encode metabolic capacities that we have not had to evolve wholly on our own but remain largely unexplored. These include degradation of otherwise indigestible components of our diet, and therefore may have an impact on our energy balance.

Hawks is highly recommended for anyone who wants to track the development of modern biology and, of course, anthropology.

Fertility and wealth: a paradox resolved?

The wealthier and more powerful women become, the fewer children they have.

I've heard dozens of explanations for this seemingly biologically insane behavior, but none of them made sense to me. It's been in the back of my mind for over twenty years.

Now the paradox may be heading towards resolution:

BBC NEWS | Health | Large families 'bad for parents' : "

...They add the findings also suggest why women now tend to have fewer children.

'If women have generally incurred greater fitness costs of reproduction, this could explain why they generally prefer fewer offspring than their husbands and reduce their fertility when they obtain more reproductive autonomy.'

The researchers assert a strong correlation between number of children and maternal mortality. If true this would help understand the apparent wealth paradox. A caveat however, I have little faith left in case control studies. The only reason this one has any persuasive power is that it fits with what we see in other animals.

It's probably not only the direct effect of bearing children -- the paternal mortality also rises ...

Racism is alive and public in Virginia's Republican representative

Of course racism never went away in American culture or politics, but for years it was at least disguised. Virgil Goode Jr, the GOP representative for Virginia, has done the nation a great service by ripping off the disguise. His racism, and perhaps that of his constituents, is now on international display. Emphases mine ...

Congressman Criticizes Election of Muslim - New York Times

In a letter sent to hundreds of voters this month, Representative Virgil H. Goode Jr., Republican of Virginia, warned that the recent election of the first Muslim to Congress posed a serious threat to the nation’s traditional values.

Mr. Goode was referring to Keith Ellison, the Minnesota Democrat and criminal defense lawyer who converted to Islam as a college student and was elected to the House in November. Mr. Ellison’s plan to use the Koran during his private swearing-in ceremony in January had outraged some Virginia voters, prompting Mr. Goode to issue a written response to them, a spokesman for Mr. Goode said.

In his letter, which was dated Dec. 5, Mr. Goode said that Americans needed to “wake up” or else there would “likely be many more Muslims elected to office and demanding the use of the Koran.”

“I fear that in the next century we will have many more Muslims in the United States if we do not adopt the strict immigration policies that I believe are necessary to preserve the values and beliefs traditional to the United States of America and to prevent our resources from being swamped,” said Mr. Goode, who vowed to use the Bible when taking his own oath of office.

... Mr. Ellison dismissed Mr. Goode’s comments, saying they seemed ill informed about his personal origins as well as about Constitutional protections of religious freedom. “I’m not an immigrant,” added Mr. Ellison, who traces his American ancestors back to 1742. “I’m an African-American.”...

... “I’m looking forward to making friends with Representative Goode, or at least getting to know him,” Mr. Ellison said, speaking by telephone from Minneapolis. “I want to let him know that there’s nothing to fear. The fact that there are many different faiths, many different colors and many different cultures in America is a great strength.”

... Dennis Prager, a conservative columnist and radio host, condemned the decision as one that would undermine American civilization.

“Ellison’s doing so will embolden Islamic extremists and make new ones, as Islamists, rightly or wrongly, see the first sign of the realization of their greatest goal — the Islamicization of America,” said Mr. Prager, who said the Bible was the only relevant religious text in the United States.

“If you are incapable of taking an oath on that book, don’t serve in Congress,” Mr. Prager said.

In his letter, Mr. Goode echoed that view, saying that he did not “subscribe to using the Koran in any way.” He also called for ending illegal immigration and reducing legal immigration.

Linwood Duncan, a spokesman for Mr. Goode, said the Virginia lawmaker had no intention of backing down, despite the furor.

“He stands by the letter,” Mr. Duncan said. “He has no intention of apologizing.”

Bravo Mr. Goode. Please don't retreat into some feigned mealy-mouthed faux apology. Your pretty blond face will give us a living symbol of the evil that lives at the heart of the GOP. I didn't get to vote for Mr. Ellison (neighboring district), but now I wish I could have. Mr. Ellison's reply, "making friends" is diabolical; guaranteed to drive Mr. Goode into a frothing rage that somebody will capture for YouTube.

I'm sure Mr. Goode and Mr. Prager would feel much the same way about, shudder, a Jew, Hindu, or ... horror of horrors ... no, I dare not mention it ... an atheist taking office.

John McCain -- this is your party ...

UK robotics report: why you should really read science fiction

As a proper geek-child, I was very fond of comic books and science fiction. I also took a typing class, which in my day was considered the province of secretaries. I never imagined both choices would prove to be so practical. A good lesson for our latest educational obsessions.

The value of my 1970s typing classes is, of course, now obvious. The value of my science fiction vice is having been long prepared for the latest news:

BBC NEWS | Technology | Robots could demand legal rights

.... Robots could one day demand the same citizen's rights as humans, according to a study by the British government.

If granted, countries would be obligated to provide social benefits including housing and even 'robo-healthcare', the report says.

The predictions are contained in nearly 250 papers that look ahead at developments over the next 50 years.

.... The research was commissioned by the UK Office of Science and Innovation's Horizon Scanning Centre.

The 246 summary papers, called the Sigma and Delta scans, were complied by futures researchers, Outsights-Ipsos Mori partnership and the US-based Institute for the Future (IFTF)....

Duh. Well, yes. If robots, or non-robots for that matter, become sentient they will acquire rights. The tricky part, which I wrote about in my Williams College ethics class in 1981, is how "rights" are afforded when one steps away from DNA. Does a severely retarded human child earn more "rights" than a genetically enhanced chimp? Does a super-sentient AI get more "rights" than the most brilliant, wise, handsome, rich, etc human? (My 1986 medical school ethics essay was about how those questions expose the degree to which morals and mores are a pragmatic compromise between ethical theory and the limits of human wisdom.)

Overall, I suspect the "Horizon Scanning Center" would have done as well to buy a copy of each the yearly "hard" SF anthologies printed since 1975, but it must have been great fun to work on the reports and I'd enjoy reading them. I hope they go online sometime.

I was struck, when I first heard this news on NPR, that the journalists were relatively sober. That's noteworthy. Ten years ago the chatter would have been flip, today there was only a hint of humor. These memes are infiltrating the human gestalt...

MS and sunlight

Twenty years ago I remember a medical school lecturer mentioning that MS had a peculiar latitudinal distribution based on where a person grew up. The further north one went, the more common it was. I'm sure I wasn't the first person hearing that to think that there was some connection to sunlight exposure in early life.

Maybe there is ...

Vitamin D may lower risk of multiple sclerosis, study finds - USATODAY.com:

Among whites, those with the highest blood levels of vitamin D had a 62% reduced risk of developing the disease. The protection was the strongest for people who were younger than 20 — a finding that suggests that to be effective, a protective agent might need to kick in very early in life, Ascherio says...

Laws that are universally disobeyed

How many people who bought two way radios for their children this Christmas have gotten their FCC licenses?

Motorola Talkabout FV200 AAA Radios - 2 Pack from REI.com

... FV200 radios operate on radio frequencies that are regulated by the Federal Communications Commission (FCC); license and fees required...."

I think someone should try to register just to see what the FCC does.

Note to Congress: a law that's never obeyed and never enforced is simply silly.

AOL and Yahoo: email down the tubes

AOL has been on a long slow death spiral for about 10 years, but I didn't realize Yahoo was in dire straits until I read this announcement from my ISP:

VISI | Announcements | Difficulty sending mail to yahoo.com or aol.com?

Over the past weeks, it appears that Yahoo has begun grey-listing all (or most) incoming mail. This means that they are rejecting the first mail delivery attempts and telling sending servers to try again later. Yahoo also appears to be grey-listing with content filters. In this case, customers may see the error message: message text rejected by mx1.mail.yahoo.com: 451 This message indicates that suspicious content was detected, but that the sending server may try again.

For mail grey-listed automatically or by IP, users may see: : connect to x.mx.mail.yahoo.com[209.191.aaa.xxx]: server refused mail service You may also see error code 421 in the error response.

Generally, this email is also being retried, however, if retried too soon, it will be rejected again. It may even be rejected permanently by Yahoo with no change in error message that we have found. Yahoo's documentation claims that they are not grey-listing, but instead are filtering mail based upon the sending server's compliance with standard mail practices. Our servers, however, are compliant, but we are still seeing significant deferrals. Yahoo is also testing DomainKeys verification, which we are reviewing to potentially mitigate the problem. There appears to be no way to contact Yahoo about this except via web forms that do not generate any response except confirmation of receipt. We recommend that any users forwarding email to yahoo.com addresses cease forwarding or redirect to another location.

Of course, this affects not only customers forwarding mail to Yahoo, but ANYONE attempting to send mail to Yahoo addresses.

AOL AOL uses an automated system to block mail from potential spam sources. When mail is reported as spam by users, the IP addresses for servers used to transmit the mail are recorded, and, once their limit has been reached, IP addresses are blocked from sending mail to AOL for 24 to 48 hours. This can be exacerbated by VISI customers forwarding email to their own AOL accounts and then reporting any forwarded spam, which can result in temporary blocks of VISI mail server IP addresses. The automated system is COMPLETELY automatic, and no intervention is possible in expediting removal of IP addresses. Unfortunately, this will affect ANY customer attempting to send to AOL addresses, not just forwards to AOL accounts. As with Yahoo, above, we recommend that any users forwarding email to aol.com addresses cease forwarding or redirect to another location.

I ran into a variant of this problem with Gmail. I was redirecting an unfiltered email stream to Gmail, and when I read the mail in Gmail I "marked" the spam. Alas, Gmail looks at the redirect as the source of the email, so the more I marked as spam the lower the reputation of the redirector fell. Over time Gmail marked more and more valid emails as spam, and missed more and more spam. I fixed it by filtering the mail stream, and never marking anything that was redirected as spam (I just delete it).

The Yahoo and AOL bizarre responses to the spam deluge tells us how dire their financial situations are, but I must also say that Visi should have figured out DomainKeys a year ago. Maybe Yahoo is doing this in part to force adoption of DomainKeys; too bad their execution is incompetent.

In the meantime, encourage anyone you know who's still using Yahoo or AOL to get out fast and switch to Gmail.

Update 12/21/06: There's a good defensive strategy for those of us still using SMTP services (non-webmail) btw. Get a Gmail account and configure your dedicated email client to use Gmail's smtp service. If Google is your sending service, I suspect Yahoo and AOL won't be blacklisting the sending domain.

Google is NOT slowing down

Google folk were rumored to be catching their breath. No. Rather than doing new products, they're extending existing products in innovative ways and discovering innovative, micro-NLP based, ways to do ad-hoc interoperability across Google and with non-Google products.

I have an embedded link one one of my blogs to a Custom Search Engine. Today when I used it, a dialog box appeared asking if I'd like to add this custom search to the button list that appears next to the search box in my Google Firefox 3.0 beta toolbar.

I said yes, and now it's there. When I get home and login to Google/Firefox, I would not be astonished to see the button migrate.

Today I noticed the addition of the 'call' link to Google local search, as well as a few other clever tweaks (though they need to do better about exposing links so one can send a link to recreate a local search context).

Google is not slowing down. If anything, they're ramping up. Scary and exciting.

Mankiw plays tricks, but is saved by a Dave Barry column

Greg Mankiw, a respectable Republican, claims that the study of economics makes students more "conservative". Of course he's playing semantic games; he knows his more naive readership will equate "conservative" with Republican. It's only at the end of his post that his conscience forces him to confess that he really means "classically liberal"; in other words the very antithesis of modern Rovian Republicanism. Classic liberalism (championed by The Economist in the 1980s and early 1990s, and parodied by The Economist ever since) is a respectable doctrine, albeit one that struggles with "the problem of the weak".

Despite this bit of weaselly trickery, the column is redeemed by a link to a classic Dave Barry column. I do miss Dave Barry's writing, but he seems to have decided to semi-retire. Dave Barry in his heyday was a rare public and populist intellectual, of a sort we most desperately need.

Car rental: enter gold number, price jumps $200

The 'arms race' of modern pricing continues apace. I priced a personal 5 day van rental twice on Travelocity - once with no loyalty number added and again with the loyalty number.

The price of loyalty, was a $200 increase. Yes, I would pay Avis for the joy of being a loyal customer.

To their credit Travelocity listed Avis twice after I entered my registration number, once at the disloyal price and again at the inflated loyal price.

These days it is increasingly foolish to do any price negotiation directly with a travel related vendor.

Against Stupidity: Citibank Visa security

I was a huge Asimov fan as a kid. He died young of AIDS (blood transfusion); one of his last books was probably his very best. The title was a winner - 'The Gods Themselves'. It was taken from a quote by Schiller 'Against stupidity, the gods themselves, contend in vain.

I thought of that quote when Citibank Visa asked me to provide answers to not one, not two, but three! (or four?) "security questions". Information only I am supposed to know. Top secret information, that will be firmly protected with all the customary security employed by banks and credit card companies to secure customer data.

Meaning I might as well publish the answers in my blog. Imagine how much easier these security questions are making identity theft. Add them all up, and there's no "thing only I know" that won't be known to a potential thief.

I did manage to keep my responses printable, though they're not at all memorable or useful. If Citibank ever requires me to answer them I'll switch to another Visa franchise.

Dumb.

Avian Influenza: A guide for the interested layperson

American Family Physician is a review journal for FPs. Unusually, all of the journal is freely available on the web. The quality is usually good; the best articles are written by family physicians. The very best are so clearly written that anyone with a basic interest in science can follow them.

Gregory Juckett's review of avian influenza (H5N1) is top notch, and is only a bit more technical than the Scientific American. Highly recommended for the curious. A few tidbits that I took away:

• Like the 1919 (H1N1) pandemic death is most often from acute respiratory distress syndrome and is probably due to a hyperactive immune response. That's why mortality is high among young adults -- they have the most aggressive and twitchy immune responses. The most promising therapy involves 'statins' (drugs like Lipitor) that [surprise!] suppress the cytokine component of the immune response. [jf: Cytokine suppression is not always a 'feature'; one must wonder how many times statin-induced immune suppression is harmful or lethal. I'm sure we'll here more about this over the next year.]
• The early returns suggest the lethality of the current H5N1 strain of Avian influenza is more comparable to the 1957 H2N2 or 1968 H3N2 lethalities, so not in the same league as the 'Spanish' flu.
• The Swine flu of 1976 was an H1N1 strain. We still don't know why it didn't wipe the floor with us. President Ford ought to have earned accolades, not scorn, for the emergency vaccinaton proram later associated with an inflammatory polyneuropathy.
• Ventilator availability is a major problem for Avian flu response. We can't make Tamiflu faster (Star Anise supplies have some production limit.), but we could make a lot more portable vents. If we don't need them, we could donate them to other nations.

The AAFP has launched a practice-oriented support web site. (Sadly, the URL was botched in the 9/1/06 editorial. You think that by now they'd have setup a redirect! I'll send them a note.)

A plea for Google: meta tags for dates

A plea to Google, inspired by the ancient pages on my legacy hobby site.

Google Groups: Crawling, indexing, and ranking

I still get emails of gratitude from visitors to my legacy personal web site, even for pages that haven't been updated in five or six years. Much of the material is of historic or special interest -- some of it goes back about 10 years -- but there's a place for such content.

Alas, it's noise for most searchers, especially since Google can't handle date constrained searches very well. Which leads to a plea for Google to support date range meta tags.

If Google supported a 'creation date', 'last revised date', and 'archival date' users could create searches that would either filter out, or focus on, old pages. Sure crooks and scammers would produce invalid dates, but the bias would probably be to create invalid new dates. The value of false archival dates would be much less, so Google's algorithms could make inferences about the utility of the date information and act on it. (Archival dates are more likely to be true, date information from unchanging pages more likely to be true, date information from higher ranked pages more likely to be true, etc, etc.)

Thus my plea.

Retail organs: not a slippery slope

The transfer of organs from the weak to the strong, from the poor to the richer, is not a slippery slope. No, not at all.

Slippery implies some possibility of friction. Slope implies the possibility of balance. We need a better metaphor. How about 'obvious cliff'?

Alas, the trade continues to expand exponentially, despite my screed of last April. The Economist is the latest champion.

Gee, you'd think nobody reads this thing. The egg-donation and kidney transfer trade is big these days, much bigger than the involuntary donations of Chinese "criminals". It's a true 21st century growth industry. Niven, alas, was spot on thirty years ago. If we come up with really good anti-rejection treaments the exponential growth curve will go vertical. Eye transplants anyone? After all, one can live well with one eye.

Sigh.

There is a darkly millenial bright side. Sooner or later, maybe after the eye donations and the hemi-hepatectomies are booming, this trade will tip us into reexamining the duties of the strong to the weak, the rich to the poor, and the limited adaptability of the human to a logically utilitarian ethos.

I'm sure I'll have similar comments in another 6-12 months.

Common Good Books: A place to visit in Saint Paul

Garrison Keillor, a wealthy celebrity and twin cities fixture, has decided to blow some cash on an independent bookstore called
Common Good Books. As best I can tell it doesn't have a web site or a marketing budget. It's downstairs from Nina's Coffee Shop, an upscale bohemian hangout in what was once a chancy neighborhood. Purely by coincidence, it's across from Representative Betty McCollum's office. (Keillor is a hard core democrat.)

Emily and I wandered in, and fell in love with both the bookstore and Nina's upstairs (there's a staircase from inside Nina's to the bookstore, Nina's has wifi). It's not a big place, but every book is remarkable. The reading nooks with the overhead skylight are irresistible. It reminds me of the much grander bookstores west of the University of Chicago, and of a much mourned East Lansing fixture that died after an ill-fated move. Odegard's of Saint Paul was like that, but perhaps a bit more commercial.

Keillor is wealthy enough to fund bookstore for decades -- if he wants to. There are worse ways to lose money. Oddly enough, the bookstore and the location are sufficiently appealing and unusual that, despite the negligible marketing budget, he might one day break even ...