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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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February 29, 2004

Networks Under Construction

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Posted by Carl Zimmer

protein_map.gifAs biologists figure out more about how life is, they can then figure out how it got to be that way. First there were genes. Mendel noticed that somehow the wrinkles on wrinkled peas could be transmitted down through the generations, even if some of those generations had no wrinkles at all. It turned out that the wrinkles were the result of a gene; a different version of the gene produced smooth peas. For much of the twentieth century, evolutionary biologists worked out how changes in genes produced evolutionary change. A mutation that alters one position in a gene (or chops out a whole chunk of it) can alter the protein it encodes. As the proteins on a virus mutate, for example, their shape becomes harder for an immune cell to recognize.

But towards the end of the twentieth century, it became clear that the protein-coding sequence is not the whole story. For example, many genes are equipped with on-off switches. Only if other proteins toggle these switches on will a gene produce its own protein in a particular place and time. A slight tweak to one of these switches can produce a drastic change--adding or subtracting legs from a segment on an insect's body for example. Other proteins destroy other proteins, while others enhance their supply. Some genes create proteins that can only work when they fuse to proteins made by a different gene. You can think of the genes as pieces of a complicated circuit, evolutionarily wired for some particular job, such as sensing a molecule or telling time.

How then do networks evolve? At first this can seem like an insurmountable problem. Consider a network of three genes that can only do a job if all three genes are working together. How then could the network evolve from two genes, let alone one? This is the basic "irreducible complexity" argument you sometimes hear from the Intelligent Design camp. They'd like you (or at least your local board of education) to think that you can't get there from here, and that someone must have designed the network from scratch. In reality, many scientists are now probing genomes to figure out how networks evolve, generating detailed hypotheses, testing them, and publishing their results--yet never once finding the need to utter the phrase Intelligent Design.

The key to network evolution lies in yet another way genes can mutate. Instead of just a small segment of its DNA changing, it's possible for an entire gene to get duplicated. Gene duplication happens a lot, judging from the many families of similar genes both in our own genome and those of other species. A copied gene would initially play the same role in the original network. But as it gradually mutates, it can take on a new function. Can it take up a new role in a new network? One clue that the answer is yes is that many networks are made up of related genes. Some researchers have proposed that all the genes in a network (perhaps even an entire genome) have to get duplicated at once in order to create a new network. But this large-scale copying may come with its own trouble: somehow, all the copied genes would have to stop interacting with the old network.

In the current issue of EMBO Reports, scientists at the University of Manchester in Great Britain offer a more humble way to build a new network. They suggest that it can happen one duplicated gene at a time. Imagine that one gene in a three-gene network gets duplicated. A mutation prevents it from interacting with the original three. Then it gets duplicated in turn, and these two genes start interacting in a tiny network of their own. Another duplication, and there are three genes at work in a fully-functional network that's completely isolated from its parent.

It would have been vaguely interesting if the scientists had stopped there, but then they figured out a way to test their hypothesis. They studied a family of genes that produce molecules called basic helix-loop-helix proteins (bHLH). These genes form several networks in our own bodies and in those of other animals. By linking with one another in different combinations, they can do all sorts of work in the cell, from sensing signals from the environment to keeping cell division under control. The history of these networks, the researchers realized, should be preserved in the genealogy of the genes. Say that some ancestral bHLH network was copied all at once. Then each gene of the new network should be most closely related to the gene playing the same part in the old network. But if, as the scientists propose, new networks are built a gene at a time, then all the genes in a new network should be closely related to each other, and only distantly to the old network. When they drew the bHLH family tree, that's what they found.

What's particularly remarkable about this work is what it means about the way new networks evolve. Each one budded off from an old network as a single duplicated gene. But over time, as the new network expanded with additional gene duplications, the new network came to look and act a lot like the old one. Each network, for example, is organized around a hub of a few genes that can interact with a constellation of other genes. Stephen Jay Gould famously asked whether life would take the same form it has today if you replayed the tape. Gould thought that there were so many contingencies that could push life off on another path that the answer must be no. But when it comes to gene networks, it appears that the tape may play just about the same.

(Update, 3/1/04 8 am: Link to paper fixed, along with a few typos.)

Comments (2) + TrackBacks (0) | Category: Evolution


1. Paige on March 1, 2004 11:59 AM writes...

Thank you for the excellent explanation of biology and evolution in action.

This testing hypotheses idea, what a great concept! Someone should tell the creationists about it.

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2. V.Pawar on April 16, 2004 07:54 AM writes...

To begin with how genes come into existence and when they came into existence what were the processes that ensured plant life, insect life, animal life and human life.Is there any literateure throwing some light on the subject?

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