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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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July 08, 2005

Tangling the Tree

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Posted by Carl Zimmer

net tree.jpg

I've been fascinated by this picture since I first saw it over the weekend. It's a hint of how we may be visualizing life in years to come.

As Darwin was trying to figure out how new species could evolve from old species, he began to think of evolution as a tree. He scribbled some simple branches in a notebook, and then published a more elaborate one in The Origin of Species. Darwin didn't actually put any animals or plants on the branches of these trees; he was just thinking about the process itself. Today, though, evolutionary trees are a common sight in scientific journals, whether scientists are reconstructing the origin of a new strain of HIV or are trying to figure out how animals evolved from single-celled ancestors.

But scientists have also realized that drawing trees is harder than it once seemed. Evolution, at its heart, is about changes to DNA. For some organisms, like ourselves, DNA changes almost entirely as the result of mutations when parents bequeath their genes to their offspring. But it is possible for genes from one organism to hop to another. This happens most often in microbes. A bacterium may jam a needle into another bacterium and inject some genes. In other cases, viruses may pick up the genes of one host and bring them to a new host. Once a gene makes this jump, it may then get carried down through normal heredity to the receiver's descendants, spreading into new species that evolve from it.

Scientists are trying to figure out how important this kind of species hopping has been over the history of life. In a sense, scientists are asking what is the shape of the tree of life? Is it for the most part an ordinary tree as Darwin pictured it, with a few vines representing jumping genes? Or are the vines so dense that they obscure parts of the tree altogether? This debate is not a huge issue when it comes to the evolution of animals (although viruses have shaped our genome). Most of the evidence for these vines comes from bacteria and other microbes, which are very promiscuous with their genes. Most of the diversity of life is microbial, and microbes were the only game in town for the first couple billions years of the history of life. So the stakes of this debate are big.

This picture is a splendid representation of this debate. Scientists at the European Bioinformatics Institute created it by comparing 184 microbes. The scientists first identified genes that the microbes all inherited from a common ancestor that they then passed down in conventional parent-to-offspring fashion. By comparing their different sequences, the scientists were able to draw a conventional tree of the sort Darwin had in mind. Next, they scanned the genomes of these microbes for jumping genes. They drew the jumpers as vines from one branch to the next. They then produced this three-dimensional picture.

As you can see, the branches rise from a common ancestor, but they are enmeshed in vines. What's particularly fascinating about it is the way in which the vines connect the branches. It is not a random mesh. Instead, a few species are like hubs, with spokes radiating out to the other species. This is the same pattern that turns up in many networks in life, from the genes that interact in a cell to the nodes of the Internet. These hubs can bring a vast number of nodes into close contact. It's why you can play Six Degrees of Kevin Bacon. In the microbial world, this network allows genes to move quickly through the tree of life, whether those genes provide resistance to antibiotics or allow microbes to cope with some other change in the environment. The Kevin Bacons of the microbial world, at least in the current study, seem to be species that live in habitats where they may come in intimate contact with other species, such as in plant roots. They then act as gene banks from which other species can make withdrawals.

Of course, 184 species of microbes represent a vanishingly small sample of the diversity of life on Earth. It remains to be seen if the Kevin-Bacon structure survives as more branches and vines get added to this picture. But this is an important step forward in how we envision life. Perhaps in the future, this tangled tree will take its place alongside Darwin's notebook scribbles.

Comments (7) + TrackBacks (0) | Category: Evolution


COMMENTS

1. MJ on July 8, 2005 05:01 PM writes...

What does the Kevin Bacon analogy mean?

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2. it on July 8, 2005 06:04 PM writes...

mj, take a look at http://en.wikipedia.org/wiki/Six_Degrees_of_Kevin_Bacon it's a play on the six degrees of seperation

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3. Torbjorn Larsson on July 8, 2005 09:27 PM writes...

So one can actually have an interesting life without sex. How shocking!

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4. Matt on July 9, 2005 09:51 AM writes...

For more on the Kevin Bacon reference, see http://www.cs.virginia.edu/oracle/

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5. Brian on July 13, 2005 03:10 AM writes...

Can you link a larger version of the graphic. I cannot make out the writing.

Great piece of writting. Kevin would have liked it if her read it.

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6. John Wilkins on July 13, 2005 02:03 PM writes...

It is my view that lineage recombination, from full hybridisation through to occasional lateral transfer, is going to become more and more important in our phylogenies. Moreover, there is a tradition of being concerned about lateral recombination from Aristotle onwards. This is not new, but we are finding that it made more sense to view evolutionary phylogeny as a tree first, and then refine it with horizontal links as the diagram shows, than to assume everything is a cyclic graph and work out which bits aren't.

But I am wondering how this will affect our ways of reconstructing phylogenies.

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7. ask on July 15, 2005 04:52 PM writes...

I see an analogy with linguistic archaeology, in which scientists attempt to reconstruct "Proto-Indo-European", say, from extant languages. This is confused by problems of loan words and debates over how language spreads from one region to another.

Similar difficulties arise here. And I thought molecular reconstruction of evolutionary history was already complex!

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