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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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March 12, 2004

The Wisdom of the Mailbox

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Posted by Carl Zimmer

I have been grievously mum in response to the many comments that readers have been sending to the Loom. My silence is not hostile--it is the result of way too much traveling, too much magazine writing, and the standard sleep deprivation that comes with life with two young daughters. In fact, reading comments is one of the favorite things I like about this blog.

As a case in point, today Nick at talkdesign.org explored the link between the subject of two recent posts: the ongoing adaptation of bacteria to manmade pollutants and the ongoing pollution of biology education with creationist distractions:

[snip]

Well, I don't have a poem, but I would like to mention that the evolution of catabolic pathways is the perfect example of the evolution of "irreducible comlexity" in modern times, which as you will recall is exactly the thing that the Intelligent Design folks say can't evolve.

(1) These catabolic pathways typically break down "xenobiotic" compouds that humans have only recently introduced into the environment

(2) These compounds are typically environmentally persistent toxins. Sometimes they are pesticides or herbicides, or by-products of other nasty compounds like explosives. Much of the the research on the evolution of the degradation pathways is done by military-funded labs, because the military has a big problem with polluted ground on military bases where chemical weapons, explosives, etc. were stored.

(3) The degradation pathways typically have multiple required proteins in the breakdown process. Often the compounds contain e.g. aromatic rings protected by tightly-binding atoms such as chlorine, and stripping off the chlorines and then breaking open the rings are all required before a non-toxic "eat-able" carbon chain is produced.

Some example papers:
* Copley, S. D. (2000). Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends in Biochemical Sciences V25(N6): 261-265. Source: http://www.sciencedirect.com/science/journal/09680004

* Johnson, G. R., Jain, R. K. and Spain, J. C. (2002). Origins of the 2,4-Dinitrotoluene Pathway. Journal of Bacteriology 184(15): 4219-4232. Source: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12107140&dopt=Abstract

* (Atrazine pathway evolution) Sadowsky, M. J., Tong, Z., de Souza, M. and Wackett, L. P., 1998. AtzC is a new member of the amidohydrolase protein superfamily and is homologous to other atrazine-metabolizing enzymes. J Bacteriol. 180 (1), 152-158. URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9422605&dopt=Abstract

* (Atrazine pathway evolution) Seffernick, J. L. and Wackett, L. P., 2001. Rapid evolution of bacterial catabolic enzymes: a case study with atrazine chlorohydrolase. Biochemistry. 40 (43), 12747-12753. URL: http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi011293r

The McAdams et al. Nature Reviews Genetics paper you linked to mentions studies like these, and also last year's paper in Nature by Lenski et al. that did a computer simulation of the evolution of an "irreducibly complex" system. McAdams et al. don't miss the chance to take a swipe at Intelligent Design:

====
These experiments are particularly valuable as they show how straightforward evolutionary mechanisms of mutation and selection can produce steady increases in organism complexity without invoking ‘intelligent design’.
====

So far, the ID folks seem to be saying that the computer simulation is irrelevant for [insert obscure hair-splitting here], and they seem to hope that if they completely ignore the studies on the evolution of catabolic pathways for xenobiotic compounds, the studies will just go away. I would not bet on their strategy over the long term. But then again, the ID folks appeal entirely to the public and avoid discussions with the relevant scientific experts like the plague, and their strategy seems be having some success lately. I'm glad that there are at least a few people like Carl Zimmer around to help get the word out.

Nick

[snip]

Thanks for the connection and the sources, Nick.

Comments (5) + TrackBacks (0) | Category: Evolution


COMMENTS

1. Blake on March 12, 2004 10:58 AM writes...

Carl, I hate to be cynical, but do the facts really matter to people who believe in Intelligent Design?

Who's the audience for these kinds of critiques, which, while useful and pointed, seem self-evident to me?

Is Gregg Easterbrook going to read something like this and say, "You know what, maybe I'm just full of it after all..."

Permalink to Comment

2. Carl Zimmer on March 12, 2004 11:05 AM writes...

The audience, in my opinion, are people who are read about attacks on evolution in the newspaper and want to find out the ways in which evolution is actually deeply embedded in modern biology. I suspect there are a lot of folks who fit that category.

Permalink to Comment

3. Dano on March 12, 2004 12:45 PM writes...

I agree with your comments Carl, but I would like to add I have a dear friend in Ohio, very smart, but conservative and religious and she thinks ID in Ohio is just fine - evolution is 'just a theory' and what about those flies and such?


The point being she doesn't want to take the time and has made up her mind - she's listening to the church people's rhetoric. She doesn't see anything to fight for.


So there have to be proxies in the fight, and I appreciate Carl's (and other's) efforts.


D

Permalink to Comment

4. Nick on March 12, 2004 02:27 PM writes...

Wow, I made Carl Zimmer's blog! Thanks! BTW, we've added your blog to the Good Evolutionist Blogs page at EvoWiki, the Evolution Education Wiki.

For a recent example of Intelligent Design silliness, see today's post by William Dembski wherein he accusses all evolutionists of laziness. In support of this he appends a news article on drug development that doesn't seem to have any particular connection to evolution as far as I can tell. We report, you decide...

Permalink to Comment

5. Nick on March 12, 2004 02:29 PM writes...

Forgot to add links:
*EvoBlogs
*EvoWiki

Permalink to Comment


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