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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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December 06, 2004

Resurrecting Genomes

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Posted by Carl Zimmer

mammaltree.gifIn tomorrow's New York Times, I have an article about how to reconstruct a genome that's been gone for 80 million years. The genome in question belongs to the common ancestor of humans and many other mammals (fancy name: Boreoeutheria). In a paper in this month's Genome Research, scientists compared the same chunk of DNA in 19 species of mammals. (The chunk is 1.1 million base pairs long and includes ten genes and a lot of junk.) The researchers could work their way backwards to the ancestral genetic chunk, and then showed they could be 98.5% certain of the accuracy of the reconstruction.

There are some pretty astonishing implications of this work. For one thing, it should be possible to synthesize this chunk of DNA and put it in a lab animal to see how it worked in our ancestor. For another, the scientists are now confident that they will be able to use the same technique to reconstruct the entire genome in the next few years, if the sequencing of mammal genomes continues apace. Could scientists some day clone a primordial Boreoeutherian? It's not impossible.

On the down side, this method will not work for just any group of animals you want to pick. Mammal evolution was rather peculiar 80 million years ago: a lot of branches sprouted off in different directions in a geologically short period of time. That makes the 19 species the scientists studied like 19 different fuzzy images of the same picture. Other groups of species had a very different evolutionary history, and one that may make genome reconstruction impossible. If you yearn for the day when Jurassic Park becomes real, you will have to conect yourself with a swarm of shrew-like critters. If they did somehow manage to break out of a lab, I suspect they would get eaten by the first cat to cross their path.

Comments (8) + TrackBacks (0) | Category: Evolution


COMMENTS

1. Tim Ogilvie on December 7, 2004 10:45 AM writes...

Seems like the species with the smallest changes in this gene would have similarly small changes throughout the genome. So I would expect that the species most resembling the ancient ancestor (rodents), would have the smallest amount of loss.

Instead, it appears that they have the most loss. Humans and horses have the least loss, and seem physically very different. What am I missing? (apart from a degree ;-))

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2. Carl Zimmer on December 7, 2004 10:57 AM writes...

A lot of evidence indicates that relatively small changes to DNA can produce dramatic changes in body size, etc. That's because many genes come with tiny switches that determine when and where they will make proteins. Change the switch, change the role of the gene. So the link between the number of nucleotides that change and visible differences in bodies is a complicated one.

Permalink to Comment

3. otey on December 7, 2004 01:31 PM writes...

Your links on the right are over-lapping your text in the middle of the page. Please adjust your macros.

Thanks. Enjoy your blog. I am a regular visitor and read your stuff when I can see it through your links.

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4. William Gruzenski on December 7, 2004 02:32 PM writes...

A journey back through time to a point where we can find out who we are. Can this be done? Indeed, it is being done--by all of us. Life itself is but the retracing of our steps on a journey that was over the moment it began. Do not believe for a second that this results in a fence we call the body that wards us off from an imaginary external world. "Is the cat dead or alive," asked Schroedinger in one of his famous thought experiments on the theoretical implications of Quantum Mechanics. 'Neither' was his answer. It has a tendency, a probability of being when the observer looks. Possible, probable and, in the end, the undoing must be certain.

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5. Sarah Dempsey on December 7, 2004 03:55 PM writes...

Is it possible to retrace the same steps in reverence, remembrance and hope to remind children of days past? What we should be doing is encouraging them to embrace the power of their dreams and tell them to lead with their heart. God has everything planned for us, regardless of what it looks like in any given moment. So the real question is how do we return from a journey? We don't. We carry it with us journey forever. Let's face it, anything is possible if you believe.

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6. vernaculo on December 7, 2004 09:26 PM writes...

Carl, your reply to Tim Ogilvie was a perfect example of what it is I come here to find. Clear, unbiased science news, in relatively non-technical lucid prose.
And in mozilla your links don't overlap at all.

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7. Steve Russell on December 8, 2004 07:41 PM writes...

I don't have a relevant degree either, :=), but I have heard that a parent language "evolves" more radically over time in the languages's homeland than the daughter languages do as the speakers migrate further from home. Thus, to find the most "conservative" languages, the ones that have changed least by comparison with the parent language, you want to investigate the communities of speakers that have migrated furthest from the center. I've heard a similar "rule" for human genetic history: that the greatest genetic diversity is found in the populations remaining in the ancestral homeland and that this is one piece of evidence validating the Out of Africa hypothesis. I wonder if there might be a similar "fringe" versus "center" conservation rule applying to genomes? If so, then the descendant population that has continued to exploit (approximately) the same niche as the common ancestor may exhibit the greatest number of "random" (non-adaptation driven) genetic changes, while the populations that have changed niches the most may exhibit fewer changes of this kind.

Permalink to Comment

8. coturnix on December 9, 2004 06:01 PM writes...

Off-topic, but, speaking of genomes, this is really cool:

http://sciencepolitics.blogspot.com/2004/12/do-we-also-taste-just-like-chicken.html

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