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Corante Blogs examine, through the eyes of leading observers, analysts, thinkers, and doers, critical themes and memes in technology, business, law, science, and culture.

The Press Will Be Outsourced Before Stopped

Vin Crosbie, on the challenges, financial and otherwise, that newspaper publishers are facing: "The real problem, Mr. Newspaperman, isn't that your content isn't online or isn't online with multimedia. It's your content. Specifically, it's what you report, which stories you publish, and how you publish them to people, who, by the way, have very different individual interests. The problem is the content you're giving them, stupid; not the platform its on."
by Vin Crosbie in Rebuilding Media

Travels In Numerica Deserta

There's a problem in the drug industry that people have recognized for some years, but we're not that much closer to dealing with it than we were then. We keep coming up with these technologies and techniques which seem as if they might be able to help us with some of our nastiest problems - I'm talking about genomics in all its guises, and metabolic profiling, and naturally the various high-throughput screening platforms, and others. But whether these are helping or not (and opinions sure do vary), one thing that they all have in common is that they generate enormous heaps of data.
by Derek Lowe in In the Pipeline

Disrobing the Emperor: The online “user experience” isn't much of one

Now that the Web labor market is saturated and Web design a static profession, it's not surprising that 'user experience' designers and researchers who've spent their careers online are looking for new worlds to conquer. Some are returning to the “old media” as directors and producers. More are now doing offline consulting (service experience design, social policy design, exhibition design, and so on) under the 'user experience' aegis. They argue that the lessons they've learned on the Web can be applied to phenomena in the physical and social worlds. But there are enormous differences...
by Bob Jacobson in Total Experience

Second Life: What are the real numbers?

Clay Shirky, in deconstructing Second Life hype: "Second Life is heading towards two million users. Except it isn’t, really... I suspect Second Life is largely a 'Try Me' virus, where reports of a strange and wonderful new thing draw the masses to log in and try it, but whose ability to retain anything but a fraction of those users is limited. The pattern of a Try Me virus is a rapid spread of first time users, most of whom drop out quickly, with most of the dropouts becoming immune to later use."
by Clay Shirky in Many-to-Many

The democratisation of everything

Over the last few years we've seen old barriers to creativity coming down, one after the other. New technologies and services makes it trivial to publish text, whether by blog or by print-on-demand. Digital photography has democratised a previously expensive hobby. And we're seeing the barriers to movie-making crumble, with affordable high-quality cameras and video hosting provided by YouTube or Google Video and their ilk... Music making has long been easy for anyone to engage in, but technology has made high-quality recording possible without specialised equipment, and the internet has revolutionised distribution, drastically disintermediating the music industry... What's left? Software maybe? Or maybe not."
by Suw Charman in Strange Attractor

RNA Interference: Film at Eleven

Derek Lowe on the news that the Nobel Prize for medicine has gone to Craig Mello and Andrew Fire for their breakthrough work: "RNA interference is probably going to have a long climb before it starts curing many diseases, because many of those problems are even tougher than usual in its case. That doesn't take away from the discovery, though, any more than the complications of off-target effects take away from it when you talk about RNAi's research uses in cell culture. The fact that RNA interference is trickier than it first looked, in vivo or in vitro, is only to be expected. What breakthrough isn't?"
by Derek Lowe in In the Pipeline

PVP and the Honorable Enemy

Andrew Phelps: "Recently my WoW guild has been having a bit of a debate on the merits of Player-vs.-Player (PvP) within Azeroth. My personal opinion on this is that PvP has its merits, and can be incredible fun, but the system within WoW is horridly, horribly broken. It takes into account the concept of the battle, but battle without consequence, without emotive context, and most importantly, without honor..."

From later in the piece: "When I talk about this with people (thus far anyway) I typically get one of two responses, either 'yeah, right on!' or 'hey, it’s war, and war isn’t honorable – grow the hell up'. There is a lot to be said for that argument – but the problem is that war in the real historical world has very different constraints that are utterly absent from fantasized worlds..."
by Andrew Phelps in Got Game

Rats Rule, Right?

Derek Lowe: "So, you're developing a drug candidate. You've settled on what looks like a good compound - it has the activity you want in your mouse model of the disease, it's not too hard to make, and it's not toxic. Everything looks fine. Except. . .one slight problem. Although the compound has good blood levels in the mouse and in the dog, in rats it's terrible. For some reason, it just doesn't get up there. Probably some foul metabolic pathway peculiar to rats (whose innards are adapted, after all, for dealing with every kind of garbage that comes along). So, is this a problem?.."
by Derek Lowe in In the Pipeline

Really BAD customer experience at Albertsons Market

Bob Jacobson, on shopping at his local Albertsons supermarket where he had "one of the worst customer experiences" of his life: "Say what you will about the Safeway chain or the Birkenstock billionaires who charge through the roof for Whole Foods' organic fare, they know how to create shopping environments that create a more pleasurable experience, at its best (as at Whole Foods) quite enjoyable. Even the warehouses like Costco and its smaller counterpart, Smart & Final, do just fine: they have no pretentions, but neither do they dump virtual garbage on the consumer merely to create another trivial revenue stream, all for the sake of promotions in the marketing department..."
by Strange Attractor in Total Experience

The Guardian's "Comment is Free"

Kevin Anderson: "First off, I want to say that I really admire the ambition of the Guardian Unlimited’s Comment is Free. It is one of the boldest statements made by any media company that participation needs to be central to a radical revamp of traditional content strategies... It is, therfore, not hugely surprising to find that Comment is Free is having a few teething troubles..."
by Kevin Anderson in strange
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

The Loom

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October 03, 2005

A Prize Bug

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Posted by Carl Zimmer

Pylori.jpg

This year's Nobel Prize in medicine or physiology was announced this morning. Barry Marshall and J. Robin Warren won for discovering that ulcers can be caused not by stress or genes but by a bacterium called Helicobacter pylori (shown here). As my fellow Corantean, Derek Lowe, observes, this story follows the classic arc from, "You're completely bonkers" to "You're going to Stockholm." But it also illustrates a point that I made when last year's Nobelists were announced: it demonstrates how intimately woven evolutionary biology is becoming with medicine.

It turns out that Helicobacter infects half of all people on Earth. Once Marshall and Warren showed that this bug caused ulcers (as well as certain cancers and other diseases), scientists began studying the DNA of strains around the world. They wanted to find genetic variations in the bacteria--as well as variations in how sick it made people. While three billion people may carry Helicobacter pylori, only one in ten get sick from it.

The scientists documented a surprising variety of genes in the bacteria. Each ethnic group they looked at carried a distinctive strain. The differences between the bugs arose partly from the familiar sort of inherited mutations, in which a single letter in the DNA might change or in which some chunk of the genome got rearranged. Even within a single host, Helicobacter can undergo significant adaptation, evolving into a "quasi-species" of its own.

But Helicobacter also has a penchant for trading genes--both with other Helicobacter and even with other species. When scientists sampled the bugs in the stomachs of two European subjects, they found 52 genes in one strain not found in the other, while the other strain had 110 unique genes. Giant clusters of genes have been traded as well, which have then been fined tuned through evolution for thriving in the hostile environment of our stomachs. (Here's the free full text of a review from earlier this year in Annals of Clinical Microbiology and Antimicrobials that covers this research,)

As scientists got to know the global variation of Helicobacter better, they began to discover a remarkable pattern. They mapped out an evolutionary tree of the strains of the bacteria and found that it lined up very well with the migrations of humans over the past 50,000 years. One study looked at the Ladakh province of northern India. Muslims and Buddhists have coexisted there for 1000 but remain isolated from one another. It turns out that Muslim Ladakhs only carry a European strain of Helicobacter, while Buddhists carry a mix of European and East Asian bugs. In Peru, Indians who have lived in relative isolation from European colonists carry Helicobacter that is akin to the bugs in East Asia, a major source of migration into the New World. Peruvians from the cities, on the other hand, carried European Helicobacter. It appears that Helicobacter existed in our species before humans began to move beyond Africa, and was then carried around the world as our ancestors traveled the globe. But exactly how long ago this parasite first made its home in us remains to be discovered. (Here's a free pdf of a review in the October 2005 issue of Molecular Ecology.)

Scientists have a long way to go in order to understand the full evolutionary story of Helicobacter. Many ethnic groups have yet to be sampled, and the evolutionary contortions of their bacteria have yet to be documented. This work promises to offer some guidance about what we should do about this remarkable bug. Antibiotics can wipe it out, but that doesn't necessarily mean we should eradicate it from our species. It produces some proteins that kill other microbes, and one study suggested that it reduces the chances of children getting diarrhoea. Other studies have suggested that while Helicobacter causes some kinds of cancer, not having it increases the chances of other kinds. It's possible that a long coevolution has made Helicobacter part parasite, part mutualist--much the same as intestinal worms may have prevented our ancestors from getting allergies. It's even possible that Helicobacter's high-speed evolution allowed it to become more parasitic in some parts of the world and more mutualistic in others. Before we decide on its future, it will serve us well to understand Helicobacter's past.

Comments (4) + TrackBacks (0) | Category: Evolution | The Parasite Files


COMMENTS

1. Steviepinhead on October 4, 2005 04:51 PM writes...

Another fascincating post, Carl, that goes well beyond the Nobel hoopla in the papers.

What struck me in reading about the initial skepticism that these researchers overcame was how *superficially* it sounded similar to the usual litany of creationist-designerist complaints: we're being shunned and ostracized and ridiculed and boo-hoo, boo-hoo.

In reality, of course, THESE guys just rolled their sleeves up and went to work. They rounded up and sampled more patients, they cultivated the suspected pathogen, they tested its effects, they persevered, and they eventually nabbed a Nobel. They didn't just whine about being excluded and mistreated, they made observations, formulated a novel hypothesis, performed research, accumulated evidence, and began what was certainly a long hard slog to convince the doubters that they were onto something. In short, unlike the creato-designoids, they DID SCIENCE.

We have a standing joke over at Panda's Thumb--if you think you've got the killer evidence with which you can REALLY dethrone evolutionary biology's core understandings, PROVE IT and you're on the short road to a Nobel Prize.

Hey, evolution skeptics, it may be funny, but WE'RE NOT KIDDING! And this story is the proof. Scientific evidence will eventually trump scientific "dogma."

But you've gotta do the work, you've gotta track down the evidence, and you've gotta be right. All things the creato-deezdoids never seem to get around to. Heck, you'd think they don't really WANT that Nobel that badly after all...

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2. ScienceNerd on October 4, 2005 11:54 PM writes...

Yeah, these Great Scientists not only "rolled their sleeves up and went to work" but also drank their findings to fulfill Koch's 3rd and 4th postulates. Let that be a lesson to all of us!

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3. Noumenon on October 6, 2005 07:12 PM writes...

That aside about intestinal worms protecting from allergies is one of the most interesting things in the post...

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4. Courtney Gidts on January 26, 2006 12:27 PM writes...

I've managed to save up roughly $75601 in my bank account, but I'm not sure if I should buy a house or not. Do you think the market is stable or do you think that home prices will decrease by a lot?

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