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Jim Manzi on epistasis

Jim Manzi has a long post up on epistasis, that is, gene-gene interactions: We could call this process of competing algorithms struggling to find the best solution as fast as possible "meta-evolution". That is, each potential search method must compete for survival. The fact that the algorithm that has won this (idealized) competition in the real world has the form of a GA seems to indicate that there is some structure to the relationship between gene vectors and physical outcomes, but that it is much more complex that simple linear combinations without interaction terms, otherwise nature…

Correlation and causation, science and religion

Sometimes someone tricks me into reading Jerry Coyne's blog.  He tends to trot out the same bad arguments, sometimes it's worth pushing back.  For instance, he recently set out to demonstrate that science and religion are incompatible, in part because of: the well known data on the greater prevalence of nonbelief among scientists than among the general public. In the elite U.S. National Academy of Sciences, for example, only 7% of members accept a personal God, with 93% being agnostics and atheists. In the U.S. general population, these figures are almost exactly reversed. And, of course, in…

The deal on taxes

Lotsa people are pretty pissed right now. The President and Republicans in Congress cut a deal that will extend Bush-era tax cuts â taxes opposed vigorously by Democrats and fiscally sane Republicans at the time. In exchange for giving in to Republican demands on the tax cuts, the President got a payroll tax holiday (which benefits lower income workers), an extension of unemployment benefits, and tax credits to encourage business investment. Nothing huge, but those are policies which will be at least modestly stimulative, moreso than tax cuts for the super-rich. So the President got a…

A Prak-tical guide to confrontationalism and accommodationism

Hemant Mehta, the Friendly Atheist, considers the confrontationalist/accommodationalist disagreement: Hereâs the difference between the two sides: You know that courtroom phrase, âtell the truth, the whole truth, and nothing but the truthâ? Both Mooney and PZ want to tell the truth about science and evolution. Only PZ is willing to tell the whole truth â that the logical conclusion of accepting science fully is that you must dismiss any notion of gods, miracles, and the supernatural. Mooney thinks itâs bad PR for us to admit that â and he may be right â but itâs wrong to let Christians keep…

Proposition update

As an addendum to last week's post about the California budget propositions, let me say that I voted for 1B (raising school funds if 1A passes) and against the rest. I am apparently not alone, as it appears all but 1F (legislator pay caps) failed. The chair of the Assembly Budget Committee told the AP, "I think the voters are sending a message that they believe the budget is the job of the governor and the Legislature. We probably need to go back and do our job." Um… yeah. As a reminder to the politicians and opinionmakers, I want to return to a theme in that previous post. I wrote:…

Evolutionary Medicine: Does reindeer have a circadian stop-watch instead of a clock?

Whenever I read a paper from Karl-Arne Stokkan's lab, and I have read every one of them, no matter how dense the scientese language I always start imagining them running around the cold, dark Arctic, wielding enormous butterfly nets, looking for and catching reindeer (or ptarmigans, whichever animal the paper is about) to do their research. If I was not so averse to cold, I'd think this would be the best career in science ever! It is no surprise that their latest paper - A Circadian Clock Is Not Required in an Arctic Mammal (press release) - was widely covered by the media, both…

Hurricane Arthur May Be Category Two On Contact With North Carolina Tonight.

The Hurricane may (or may not) directly strike the Outer Banks.) I've updated the title of the post to update concern that Hurricane Arthur has a much increased chance of directly striking coastal regions in North Carolina. Scroll down to the most recent update below to find out more. I'm adding updates to a single post rather than writing new posts because I'm almost out of paper for blog posts. No, not really, it does not work that way. I'm doing this as an experiment in keeping things organized, especially handy-dandy images of the process unfolding. The previously mentioned tropical…

Muslims in the ACLU

Just when you think STACLU can't get any more ridiculous you come across this post by davef, announcing breathlessly that a - gasp! - Muslim has joined the national board of the ACLU. Laila Al-Qatami of the Arab-American Anti-Discrimination Committee is joining the ACLU board and, apparently, davef thinks that the mere fact that she's Muslim makes her a terrorist. He tries mightily to make this sound like a bad thing, and fails miserably. He begins: Laila Al-Qatami has long been the spokes person for the Arab-American Anti-Discrimination Committee, an organization with previous ties to the…

David Freedman responds to criticism of his CAM apologia

The other day, I expressed my displeasure at an article published in The Atlantic that, boiled down to its essence, was one long apologia for unscientific "complementary and alternative medicine" (CAM) and "integrative medicine" (IM). Yes, I was quite critical, but, I believe, not unfairly so. Not surprisingly, however, the author of the article, David H. Freedman, was quite displeased, so much so that he actually showed up in my comments to take me to task. He didn't just take me to task, though. He took all of you to task, as well, at least those of you who piled on. Unfortunately, his…

Fear of the frame

After all the chatter that's been going on throughout ScienceBlogs about Matt Nisbet and Chris Mooney's editorial, Framing Science, published in Science on Friday, I almost thought that there was nothing really left for me to say. Of course, regular readers of this blog know that there's rarely an issue that's been so thoroughly picked over by my fellow science bloggers (ScienceBloggers and otherwise) that I can't find something else to say about it. And I'll do it by, in effect, "framing" the issue in perhaps a slightly different way than Mooney and Nisbet did. But first, let's examine a bit…

Being a console geek in Linux

This is the first in a series about using the "command line" in Linux. It is also about knowing when to use a gui instead. But before going into any of that we need to understand what is meant by a "command line" application. You'll find that as we explore that idea, a lot of things that are not really true 'cli' (command line interface) apps arguably count as cli, including menu driven console based apps and even gui apps. This will be controversial. Let's start with some basic definitions. If anyone has any problems with any of the following just let me know. Consider this a first…

No! Not the list of stumpers again!

There's a common tactic used by creationists, and I've encountered it over and over again. It's a form of the Gish Gallop: present the wicked evolutionist with a long list of assertions, questions, and non sequiturs, and if they answer with "I don't know" to any of them, declare victory. It's easy. We say "I don't know" a lot. Jack Chick's Big Daddy tract is a version of the creationist list, and contains a fair amount of fantasy as well. You know what they believe will happen: they'll ask that one question that the scientist can't answer, and then they'll have an epiphany, a revelation, and…

Vaccine injury and compensation

The comment thread for my post last week about how philosophical vaccine exemptions in California are endangering herd immunity is rapidly approaching 500 comments as I write this and may well surpass that number by the time this post "goes live" in the morning. I mention this because buried in the comment thread are a number of comments by our old "friend," that anti-vaccine-sympathetic pediatrician to the stars, Dr. Jay Gordon doing what Dr. Jay does best and basically making a fool of himself on matters of vaccine science through his preference for anecdote over sound epidemiology and…

The Faith Equation: Part Two of the Review

The bulk of this part of the review is looking at the total train-wreck that is chapter 4, which contains Bittinger's version of dreadful probabilistic arguments for why Christianity must be true. But before I do that, I need to take care of one loose end from part 1. I should have included chapter three in part one of the review, since it's really just a continuation of the paradox rubbish, but I didn't. The basic idea behind chapter three is that Jesus is the most fundamental resolution of paradox. All of the most important of the (Bittinger) paradoxes that we encounter in our lives are…

Around the Web: Some readings on Climate Change, Canada and COP21

I think this post might signal the birth of a new all-consuming blogging obsession -- climate change in general and specifically how the realities of climate change play out in the Canadian context, especially as it relates to public policy. With the COP21 climate talks coming up in Paris, this seems like as good a time as any to focus more carefully and closely on what is probably the most defining issue of our times. Not that this is the first time I've blogged about climate change. I've kept track of the issues fairly closely over the years and that has spilled into the blog, mostly in the…

It's a quorum. Bonnie Bassler awarded 2012 L'ORÃAL-UNESCO Award in Life Sciences

Bacteria can talk. Yes. Talk. These unicellular, primitive creatures have their own language. They secret chemical words to their environment, where their neighbors can listen, comprehend and react to those messages. This bacterial communication is called quorum sensing (QS). Although the first discoveries in the field of bacterial communication where made more than 40 years ago in the marine bacterium Vibrio fisheri (1), they simply did not have the quorum to be heard. Until Bonnie Bassler came along. Thanks to Bonnie and her colleagues, today, microbiology courses throughout the world…

Great Men and Science Education

. This is a post intwo parts - the second being a reaction to the responses that the first one engendered. They may be a little rambling, especially the first one, but I still think that there is quite a lot there to comment on. Great Men and Science Education - Part 1 There is an interesting thread here about "faith" in science and the way science is taught. Why no science textbook is a "Bible" of a field. Here are some of my musings.... So much science teaching, not just in high school but also in college, is rote learning. Memorize Latin names for body parts, Krebs cycle, taxonomy of…

Doing the math on Walmart: Average take-home barely covers the basics

On the shopping day known as “Black Friday,” activists held protests at Walmart stores across the country to protest the company’s low wages. In one of the eight press releases the company issued in the 24 hours between Thanksgiving Day and the close of the November 29 “Black Friday,” shopping day, Walmart corporate communications vice president David Tovar stated: “For our part, we want to be absolutely clear about our jobs, the pay and benefits we offer our associates, and the role retail jobs play in the U.S. economy. Walmart provides wages on the higher end of the retail average with full…

New European Chemicals Policy Overhaul Begins to Take the Handle Off the Toxics Pump

By Joel Tickner  The European Union (EU) recently issued new regulations requiring chemical firms to develop health and environmental data on chemicals used to make everyday products and provide reasonable assurances of safety. What a novel concept. The sad truth is that it is.  Despite the fact that most public surveys find that people believe (and expect) industrial chemicals are regulated like drugs (governments would never allow companies to place a dangerous, untested chemical into their products, would they?), most government toxics policies, do not follow this expectation.  Until…

Clock Classics: It all started with the plants

This is a repost of a May 29, 2008 post: I was wondering what to do about the Classic Papers Chellenge. The deadline is May 31st, and I am so busy (not to mention visiting my dentist twice week which incapacitates me for the day, pretty much), so I decided to go back to the very beginning because I already wrote about it before and could just cannibalize my old posts: this one about the history of chronobiology with an emphasis on Darwin's work, and this one about Linnaeus' floral clock and the science that came before and immediately after it. In the old days, when people communed with…

White House transparency doesn't apply to industry meetings on worker safety rules

The practice of posting a notice about meetings between regulated parties and OMB staff began during the GW Bush Administration, not a group known for transparency. Even that very secretive Administration saw the value in informing the public promptly of such meetings. The Obama Administration's OIRA is now 0-2 when it comes to disclosure of meetings about OSHA rules. (Their performance may actually be even worse. For all I know they've had other meetings. We just don't know to look for them on OIRA's website.) Serious health effects related to overexposure to respirable crystalline…

How to use Ubuntu Unity

This is one of four related posts: Should You Install Ubuntu Linux? Installing Ubuntu 16.04 LTS How to use Ubuntu Unity Things To Do After Installing Ubuntu 16.04 LTS Some Linux/Ubuntu related books: Ubuntu Unleashed 2016 Edition: Covering 15.10 and 16.04 (11th Edition) Ubuntu 16.04 LTS Desktop: Applications and Administration The Linux Command Line: A Complete Introduction If you have installed Ubuntu with the Unity desktop, you'll learn how to use it mainly by playing around with it. Discoverability of its various functions is more or less built into the design. But there are a few things…

How much can the sea level go up with global warming and how fast will it happen?

According to some estimates, if sea levels rose one meter, Boston would lose 3% of it’s land surface, Washington DC a mere 1%. Tampa and Miami would lose 18% and 15% respectively. New Orleans would lose 91%. A six meter rise would result in much larger losses. Norfolk, Virginia and Miami Florida would be essentially gone. These estimates use the assumption that the sea level rises in those areas vertically, and the corresponding topographical level in the coastal city becomes the shoreline. They don’t account for the fact that the ocean does not work that way. (see Sea Level Rise…Extreme…

The Cherry Blossom Classic, Part One

No Sunday Chess Problem this week, but I do have a good excuse. It's because I just spent the past few days participating in the Cherry Blossom Classic chess tournament. Enough with made-up chess positions! Sometimes it's good to experience the real thing. For about ten years now I've been mostly retired from serious chess competition. I've never given it up--I read chess magazines and follow the big events--but I haven't been studying or trying to improve my rating or anything like that. Sure, I would play in the big amateur team event every year, but that's really a social event where…

In which the obnoxious atheist addresses his critics, and makes a polite suggestion to his fellow bloggers

This week, I tossed off a casual, flippant comment that launched a thousand ineffectual bastinados. I described a map that purported to show the frequency of religious adherents in the US this way: It shows the concentration of ignorant, deluded, wicked, foolish, or oppressed victims of obsolete mythologies in the United States, with the lighter colors being the most enlightened and the dark reds being the most repressed and misinformed Fury, outrage, and massive snits ensued. Blogs were riven to their very foundations by anger — "How dare Myers insult me…I am offended!" — and the sun was…

A Guide to Linux Graphics Software 01: bitmap vs vector

Graphics software for Linux is superior to most other software for several reasons. Since the Linux system is inherently more efficient than other systems, memory-hungry graphics operations will always run faster, better, and more reliably on a Linux box than on, say, a Windows box, all else being equal. Day to day graphic needs can be met with a wider range of software on Linux than on other systems. Most of the available applications are OpenSource, so not only are they free and easier to install, but no puppies were mutilated during the production of the software. The purpose of this…

Why are you an atheist?

Once again, I have proven my ability to drive people into a frothing rage against me. Only this time it isn't a mob of religious fanatics and anti-choicers who have called me pond scum who will go to hell, an insect souled vile man, a black-souled amoral monster, pure evil, morally depraved, with a depraved mind, descend[ing] down the various stages into madness, and so forth…but I have this time managed to antagonize a bunch of atheists. Feel my pain. All right, to be honest, it really doesn't sting that much. The godless raged at me on youtube and twitter, thanks to the recent broadcast of…

How not to think

Thankfully, I don't receive all that much blog-related mail. But this weekend I received several communications about a piece in popular liberal blog. The piece is (ostensibly) about Lyme disease, which coincidentally happens to be one of the topics of my first post here at SBM. In fact, I've written about Lyme disease a number of times, and Dr. Novella has a very good summary of the controversy at one of his other blogs. Since we've discussed this so many times, I won't be reviewing the entire controversy, but looking at this particular blog post to examine how our personal experiences…

Pharmacists, emergency contraception, and the responsibilities of a profession

As someone who has been associated with colleges of pharmacy as student or professor for 25 years, I feel compelled to weigh in on the debate raging in the US between a pharmacist's right of conscientious objection to filling certain prescriptions and their responsibilities as a licensed health professional of the state. I originally intended this discussion to target the emergency contraceptive, Plan B. However, today's post by Tara about a pharmacist refusing to fill a Vicodin prescription for a relative after breast surgery reminds me of the slippery slope we face in permitting health…

What philosophy of science and "postmodernism" have in common

Lately there has been a rediscovery on the blogia of C. P. Snow's Two Cultures - which initially was the divide between those who understood the Second Law of Thermodynamics and those who don't, but is now, it appears, between those who know math and those who don't, and the respective attitudes. In Chad's initial post, the discussion turned to the Sokal hoax and what it is supposed to prove. So what I want to do here is a little "compare and contrast" between what is usually thought to be the main themes of postmodern philosophy (not being an expert, I may be... no I certainly am…

Two Types of Patriotism

It's not uncommon these days to hear someone on the right side of the political spectrum refer to people on the left side as "America haters." It's a nice way to dismiss any criticism of the United States' policies or behaviors, and current administration in particular, because instead of addressing the criticism, one simply has to say, "They're just saying that because the hate America." Still, I think some people have come to genuinely believe that people on the left hate America, and aren't using the label as a rhetorical device designed to disarm one's opponent. To these people, the…

Does Ceiling Height Affect the Way You Think?

File this one in the annals of "huh?" There's been a lot of research over the last decade or so on what only be described as the bizarre implicit priming of social concepts. In a typical experiment, participants are given lists or scrambled sentences that contain words associated with a particular stereotype or attitude and people will subsequently behave in a way that's consistent with that stereotype/attitude. For example, Bargh et al.1 gave participants scrambled sentences with words associated with the elderly (e.g., worried, old, lonely, and Florida... no seriously, Florida), told them…

Integrative medicine does not "bring deeper meaning to personalized health care"

I've discussed the evolution of "integrative" medicine on many occasions. To make the long story discussed over many posts short, medicine based on prescientific and/or unscientific ideas was once, appropriately, referred to as quackery, and those practicing it, appropriately, as quacks or charlatans—or other derogatory terms. Then, beginning sometime around the 1960s and 1970s, such quackery became known as "alternative" medicine. This was a less derogatory term than what used to be used, but still unsavory. As I put it, alternative medicine was (and is) medicine that does not fit into the…

An acupuncture bait and switch on hypertension

Acupuncture is a theatrical placebo, but it's hard not to grudgingly admire just how—shall we say?—malleable or adaptable a placebo it is. What I mean by this is that, if you believe its practitioners and adherents, acupuncture can treat almost literally any disease or health problem. Any! Pain? Acupuncture. Allergies? Acupuncture. Biliary colic? Acupuncture. Infertility? Acupuncture. Menstrual problems? Acupuncture. Prostate problems? Acupuncture. Asthma? Acupuncture. Well, maybe not asthma, but that doesn't stop acupuncturists from claiming that acupuncture can treat it. Oh, and if you're a…

The annals of “I’m not antivaccine,” part 18: Dr. Bob goes full Godwin over SB 277

Antivaccinationists like Holocaust analogies. I've described this particularly loathsome phenomenon more times than I can remember, most recently when Robert F. Kennedy, Jr. compared the "vaccine-induced autism epidemic" (vaccine-induced only in RFK, Jr.'s imagination and that of antivaccinationists) to the Holocaust. True, even he was forced to apologize, although it was a classic "notpology": "I want to apologize to all whom I offended by my use of the word holocaust to describe the autism epidemic," Kennedy said in a statement. "I employed the term during an impromptu speech as I struggled…

Does a positive attitude prolong cancer survival?

I've always wondered, as I'm sure many of my readers have, whether human beings have it in them to delay their own death, even briefly. Very early in the history of this blog, a mere 11 days after I started it, I discussed a study that strongly suggested that we cannot. In brief, it looked at the common belief that people dying from cancer can somehow, through sheer force of will, hold death at bay for brief periods of time, usually until some milestone that they wanted to see one more time is reached, be it a birthday, anniversary, holiday, or whatever. After they reach that milestone, the…

Framing vaccines, revisited: The "empathy" gambit

NOTE: This post, which is related to a discussion of Dr. Paul Offit's Book Autism's False Prophets, originally appeared over at The ScienceBlogs Book Club. However, now that the book club for this particular book has concluded, I am free to repost it here for those who may not have seen it and to archive it as one of my own posts. Besides, I know the antivaxers are more likely to see it here... On Friday, while discussing what is perhaps the aspect of Autism's False Prophets that is at the same time the most important set of observations (namely, how the media and government miscommunicate…

The life cycle of translational research

You can tell I'm really busy when I fall behind my reading of the scientific literature to the point where I miss an article highly relevant to topics I'm interested in, be they my laboratory research, clinical interests, or just general interests, such as translational research. As you know, I like to think of myself as a translational researcher. Translational research is research that (or so we try to do) spans both basic science and clinical science; i.e., bridges the gap between basic and clinical science. Now don't get me wrong; I don't devalue basic science, and I've said so many times…

The Z2K9 Problem

I've been getting a lot of emails asking about the so-called "Z2K9" problem. For those who haven't heard, the software on a particular model of Microsoft's Zune music player froze up on New Year's eve, because of a bug. Apparently, they didn't handle the fact that a leap year has 366 days - so on the 366th day of 2008, they froze up for the day, and couldn't even finish booting. Lots of people want to know why on earth the player would freeze up over something like this. There was no problem with the date February 29th. There was nothing wrong with the date December 31st 2009. Why would…

Framing Social Security

Hopefully, talking about Social Security will be marginally less inflamatory than evolution or global warming, and it illustrates many of the points made in various discussions. First, though, I want to clear the deck about some misconceptions about Social Security (I have a lot of the links here and here, so I won't repeat them below): 1) Social Security will most likely be solvent in perpetuity without any need for tax increases or benefit cuts. No, really. For even marginal tax or benefit alterations, the economy has to grow at a rate about 20% lower than the average U.S. historical…

Goverment Jobs Are Bad, But Government-Subsidized Jobs Are Normal?

One of the ludicrous notions that has infected our political discourse is that government jobs aren't 'real' jobs (tell that to fireman when your house is burning down...). But a lot of private sector jobs are heavily subsidized by the government. I'm not referring to private contractors hired by the government, but jobs that are supposedly private sector. Low wage private sector jobs. How are these jobs subsidized? Food stamps (now known as SNAP; italics mine): Saucedo, who earns $9.70 an hour for about 26 hours a week and lives with her mother, is one of the many Americans who survive…

It's a big weekend for the creationists in Minnesota

We have a couple of unfortunate events happening. One is the Creation Science Fair. I've been thinking for years that I ought to drop in on this event, and every year it rolls around and I find myself completely unable to do it. I can cope with adults who do stupid things — they are independent and presumably responsible, after all — but these are kids who are being lied to and led deeper into ignorance. It would be like going to a puppy-kicking party, and I'd just want to gather up all the victims and take them home with me. The other event this weekend is a debate…a debate between a…

What I Learned About Clostridium difficile Infection Control

So I was at the ASM meeting last week, and one of the talks I heard was by Kim Ware about Clostridium difficile infection control: how one hospital learned to contain and prevent outbreaks (Note: these are from my notes; I haven't downloaded the presentation yet). C. difficile is a bacterium that causes diarrhea and more serious intestinal conditions such as colitis. It is often associated with antibiotic therapy and stays in healthcare environments: this is primarily a 'hospital disease.' While most cases result in diarrhea (which isn't trivial if you're already very sick), eleven…

This Is Not the Social Media Revolution I'm Waiting For

I came across this post, "10 Ways Social Media Will Transform Events in 2010", and, after reading it, I was reminded of Ray Bradbury's quote, "I don't try to predict the future, I try to prevent it." Anyway, the post is about how social media and other technologies will change meetings. First, some fisking. Consider this: Attendees will not wait for microphones to ask questions. They will text or tweet those questions as they think of them. Attendees will not wait until the end of a session to ask questions that came up in the first five minutes of the presentation. This does not mean…

A Science News Story About Funding! (And It's Pretty Good, Too)

A while ago, I wrote, "Someday, a science reporter is going to hybridize with an economics reporter and then the topic of how science is funded will actually be covered accurately. Until then, you're stuck with the Mad Biologist." Well, I don't know if the hybridization experiment has been successful, but a Nature news article by Kendall Powell describes the grant selection process very accurately. Before I get to the article, it's not anything shocking or especially revealing to most scientists, but my hope is that journalists (and members of the chattering class) will read it and realize…

Inconvenient Truths, The Disappeared Party, and Wikileaks

"Information Wants To Be Free. Information also wants to be expensive. Information wants to be free because it has become so cheap to distribute, copy, and recombine---too cheap to meter. It wants to be expensive because it can be immeasurably valuable to the recipient. That tension will not go away. It leads to endless wrenching debate about price, copyright, 'intellectual property', the moral rightness of casual distribution, because each round of new devices makes the tension worse, not better." -Stewart Brand Many pundits have been discussing what Wikileaks means for either…

Birdbooker Report 58

tags: Birdbooker Report, bird books, animal books, natural history books, ecology books "One cannot have too many good bird books" --Ralph Hoffmann, Birds of the Pacific States (1927). The Birdbooker Report is a special weekly report of a wide variety of science, nature and behavior books that currently are, or soon will be available for purchase. This report is written by one of my Seattle birding pals and book collector, Ian "Birdbooker" Paulsen, and is edited by me and published here for your information and enjoyment. Below the fold is this week's issue of The Birdbooker Report which…

Building a new scholarly communications ecosystem from first principles

Like the old saying goes, information wants to be free. In particular, the consumers of information would prefer for the most part not to have to directly pay for the information they are consuming. The information itself, if I may anthropomorphize for a moment, also wants to circulate as freely as possible, to be as consumed as widely as possible, to be as highly regarded as possible. That way it gets to be the information that "wins" the best-used-most-used information sweepstakes. This seems to me to be a first principle for scholarly communications. Both the users of the information and…

How to feed a hungry world

This week, the G20 Agriculture Ministers gathered for their first-ever meeting to discuss potential measures to address price volatility and record high food prices. The key to any long-term solution is acknowledging that we need to empower the very people whose lives are most affected by food shortages. Three-quarters of the world's poorest people get their food and income by farming small plots of land. The potential of small farmers for getting us out of this and future food crises cannot be overstated. Today, we find that millions of lives depend upon the extent to which agricultural…

Commensal E. coli and other matters

My SciBling Mike the Mad Biologist, who is an expert on antibiotic resistance, has an interesting post about an "epidemic" of commensal E. coli. It seems (if I understand his post correctly) that there is not the genetic range of E. coli lineages in humans as in animals. About 20% of our gut E. coli comes from one of three clones. There is no apparent reason for this as the E. coli don't seem to have any features that make one better off than another. I have nothing to add to the basic observation, but I thought I'd use it to review some elementary microbiology, since we talk a lot about…