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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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November 03, 2005

Stay Right There, Mendel

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Posted by Carl Zimmer

mendel.gifBack in March I described a provocative paper that suggested that plants might be able to get around Mendel's laws of heredity. Reed Cartwright, the grad student behind De Rerum Natura, left a comment expressing some deep skepticism. Now he reports that he and Luca Comai of the University of Washington have published a letter in the journal Plant Cell. You can read the letter for free. (There's another paper commenting on it in the journal, but it requires a subscription.)

In the original experiment, scientists bred plants, noting which version of a gene called hothead got passed down to new generations and which did not. Sometimes plants were born with a version of hothead that appeared to have been lost in previous generations. The scientists suggested that somehow the plants were storing a back-up copy of the hothead allele somewhere.

Comai and Cartwright argue that something more conventional was actually happening. Thanks to how the scientists carried out the experiment, they inadvertently caused their plants to mutate much more often than normal plants would. In all those mutations, some happened to alter the hothead gene, changing it back to its ancestral form. Comai and Cartwright propose that pollen grains containing the newly mutated hothead gene could do a better job of fertilizing eggs than the other version. The combined effect of a higher mutation rate and selection produced the strange results that seemed to violate Mendel's laws.

This is turning into a fascinating debate--and one that seems to have some parallels with another debate that Cartwright doesn't appear to have mentioned.

In the 1980s, some scientists claimed to have found evidence of what they called "adaptive mutation." Conventionally, mutations were seen as occurring pretty much randomly, with no influence from the environmental challenges organisms face. It just so happens that some of those mutations help some individuals reproduce more than others. But scientists did experiments that suggested that bacteria could rapidly acquire the mutations they "needed" when faced with a challenge. The classic example of adaptive mutation involved E. coli that was given lactose to eat. But before the bacteria got a chance to enjoy this meal, the scientists inserted mutations in the gene that produced an enzyme that's essential for digesting lactose. Remarkably, the bacteria did not starve. Instead, they rapidly acquired mutations to the lactose-digesting gene that let it function again.

Almost 20 years later, some scientists still argue that this represents a weird and wonderful exception to the conventional picture of evolution. But others have expressed serioius skepticism. It's likely, they argue, that a pretty ordinary series of events produces a seemingly strange result.

Introducing a mutation into the lactose-digesting enzyme cripples it, they argue, but doesn't completely destroy it. On its own, this crippled enzyme can't provide enough food for E. coli to stay alive. But every now and then genes get accidentally duplicated. Extra crippled genes boost a microbe's ability to digest lactose, allowing E. coli to get just enough energy to reproduce. Microbes with extra copies of the gene are strongly favored by natural selection, so that more and more copies spread through the population. And with all these extra copies of the crippled gene floating around the population, the odds are raised that a random mutation will restore it to its normal function. You can read the latest version of this attack on adaptive mutation here.

This kind of evolution may actually matter a lot to E. coli and other microbes in the wild, giving them the ability to adapt to new challenges. The mechanism that Comai and Cartwright propose for plants, on the other hand, may only have bearing on the particular experiment in question. But it's still intriguing in both cases to see how conventional evolutionary biology may be able produce some results that look anything but conventional.

Comments (6) + TrackBacks (0) | Category: Evolution


COMMENTS

1. Reed A. Cartwright on November 3, 2005 10:50 AM writes...

Steve Henikoff's companion paper mentions the "adaptive mutation" debate, as well as some interesting results from Flax.

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2. Carl Zimmer on November 3, 2005 10:55 AM writes...

Thanks Reed. I wish Henikoff's paper was as freely available as yours.

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3. Jim Hu on November 4, 2005 12:23 PM writes...

The E. coli paper you point to is one of nine (!) in that issue of J. Bact, where the three main labs working on the "adaptive" mutation phenomenon were invited to provide their views and then rebut each other. I'd say all sides of both the E. coli debate and the one on Hothead are well within the bounds of conventional evolutionary biology...ironically, the Roth view to explain the E. coli results is arguably closer to Lolle (extra hard-to-detect copies of the genes lurking about) than to Cartwright (hypermutation). In the E. coli case, the extra copies have been detected directly...but as I understand it there is still debate about whether the amplification fully accounts for what's observed.

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4. Anonymous on November 4, 2005 12:30 PM writes...

I saw Bob Pruitt, the author of the original paper describing the oddities of "hothead" present a paper on a conference, recently, where he showed that even deleting hundreds of bases of "hotead" still led to the "reversal" a generation later. how to account for this mechanism?

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5. Ricardo Azevedo on November 5, 2005 12:24 PM writes...

I agree, this is strongly reminiscent of earlier controversies in evolutionary genetics. One correction: the original claims of Cairns, Hall, et al. were of full-blown, Lamarckian-style, _directed_ mutation. _Adaptive_ mutation, its weaker spin-off, came later.

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6. Steve Henikoff on November 11, 2005 04:49 PM writes...

Here's a free link to my Nov. 1 Plant Cell Perspective, "Rapid changes in plant genomes":
http://www.plantcell.org/cgi/content/full/17/11/2852?ijkey=8Yr4/wADywbFU&keytype=ref&siteid=plant

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