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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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January 05, 2006

Cat-Blogging from Deep Time

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Posted by Carl Zimmer

cat%20collage.jpg

As the proud owner of a fine cat, Tino, I'm happy to join the ritual of cat-blogging. I was inspired after reading a new study that sorts out Tino's kinship with other cats. Now I know that a cheetah is more closely related to Tino than it is to a leopard (right and left, respectively).

The evolution of cats has been a tough nut to crack. While it's no great mental feat to tell the difference between Tino and a tiger, it's not so easy to figure out exactly which species are most closely related to domesticated cats and which are more distant relatives. The oldest cat-like fossils date back 35 million years ago, and since then they've rapidly evolved into many lineages that have spread across all the continents save Antarctica. When evolution moves fast, it is hard to reconstruct its path. Making things harder is the fact that cat lineages have repeatedly evolved into similar forms to take advantage of similar ecological niches. This pattern isn't unique to cats. Mammals with placentas (including cats, dogs, bears, bats, cows, primates, and rodents) underwent a massive evolutionary explosion, driven in large part by the extinction of big dinosaurs 65 million years ago. The evolutionary picture of this entire group has long been blurry. Over the past few years, a network of scientists have forced that picture into focus by gathering gene sequences from a wide range of mammal species and comparing them with statistical methods that can only be carried out on big computers. The major branches of the mammal tree are much clearer now.

The researchers (who come mainly from the Laboratory of Genomic Diversity at the National Cancer Institute) have now turned their attention to some of the branches on the mammal tree--such as cats. They looked at 22,789 base pairs of DNA from all living cat species. They used several different methods, based on the different ways in which DNA can evolve. Among the most common mutations are changes to single base pairs. The researchers calculated the most likely course evolution had taken to produce these sorts of mutations in the various lineages of living cats. Less common are mutations that move large chunks of genetic material from one part of the genome to another. When a group of species share the same massive mutation, scientists become more confident that they share a close common ancestor. And finally, by looking at the fossil record of cats and other mammals, the scientists constructed a molecular clock that they used to calculate when the lineages branched off from each other.

The scientists were able to reconstruct the evolutionary tree of cats with a great deal of statistical confidence. Their results are published in this week's Science (link to come here). I've put the illustrations from the paper at the bottom for those who like to revel in the gorey details. What's particularly neat about the paper is that it offers a hypothesis for how cats spread around the world. The researchers came up with this hypothesis by looking at where cats are today, and then mapping their locations onto the evolutionary tree.

The common ancestor of all living cats, according to their results, lived in Asia about ten million years ago. This cat's descendants split into two branches. One led to lions, jaguars, tigers, leapards, snow leopards, and cloud leopards. The other branch gave rise to all other cats. These early cats remained in Asia until 8.5 million years ago, when new lineages moved into the New World and Africa. The New World immigrants gave rise to bobcats, couggars, lynxes, ocelots, bobcats, and other species found in the Western Hemisphere today. The African migrants were the ancestors of today's servals and other small cat species.

But cats have a way of wandering. The ancestors of domestic cats moved back from North America back into Asia around 6.5 million years ago. Lynxes moved back as well about 2 million years ago, spreading west until they reached Spain. The ancestors of today's mountain lions in the New World also produced another lineage that moved back into Asia and eventually wound up in Africa, where it became today's cheetahs. Other big cats moved into Africa at around the same time--the cousins of tigers and snow leopards in Asia moved through the Sinai peninsula and evolved into African lions. But close cousins of the lions moved into the New World, evolving into jaguars.

It's a cool study, but I was struck by the fact that all seven authors are geneticists, without a single paleontologist in their ranks. That's pretty typical these days. Geneticists are busy publishing evolutionary research as they get their hands on vast new supplies of data. When they do glance at the fossil evidence, they mainly do so to calibrate their molecular clocks. But paleontologists have dug up lots of fossil cats all over the world, all of which have something to say about the evolution of these creatures. How, I wonder, do they fit into the pictures below?

Still, this DNA evidence is important for suggesting just how fast cats could migrate, and how splendidly they could adapt to all sorts of new niches, from the cliffs of the Himalayas to the canopy of South American cloud forests to the Sahara. Conservation biologists are rightly concerned about the introduction of cats to Australia and remote islands, where they're wiping out endangered animals. But it turns out they've had plenty of practice at being invasive species, without help from us.

Update: 1/6 2 pm: I contacted an expert on cat fossils, Blaire Van Valkenburgh of UCLA, for her thoughts on the paper. She just replied. While she is impressed by the cat tree, she's not so pleased with the way they use it to interpret the migrations of cats without consdering the fossils.

"The problem of ignoring extinct species and their potential influence on the tree produced is huge," she writes, " and they can only get away with it because it is impossible to get DNA from such ancient material. Their biogeographic hypotheses are provocative, but not at all convincing. One of my main problems with the paper is the lack of a causal explanation between sea-level shifts and cat speciation rates. In one case, they point out that an increase in within-lineage divergence is associated with higher than present sea levels (6.4-2.9 ma) and then in another case, they point out that rapid speciation is associated with lower sea levels (3.1-0.70. So what is the driving mechanism? I think they would have been wiser to look for associations between global cooling and drying as well as grassland expansion to explain some of these patterns."

By the way, the paper is now online.

cat%20tree%20small.jpg

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Comments (13) + TrackBacks (0) | Category: Evolution


COMMENTS

1. Tanya Perkins on January 5, 2006 02:19 PM writes...

It's fascinating how geneticists are doing so much heavy lifting in terms of reconstructing evolutionary pathways, but Carl raises an intriguing question (and doesn't answer it, alas), that is, how does the fossil record dug up by all those persevering paleontologists compare? Does it tell the same story or at least a supporting story? And how can I find out?

Permalink to Comment

2. Xerxes on January 5, 2006 02:19 PM writes...

This is confusing to me. According to the diagram from this study, servals and domestic cats are pretty distantly related (8.5My). But according to Wikipedia (and a NYT article I recall), it's possible to interbreed servals with cats to get a hybrid called a "Savannah". How distantly related can two animals be if they are able to interbreed?

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3. Anonymous on January 5, 2006 02:56 PM writes...

Some googling suggests that Savannahs are fertile so they manage one better than mules. Horses and donkeys aren't terribly similar and they don't even have the same number of chromosomes (that's why mules are usually, though not universally, sterile) but they manage it. I guess it's just a matter of the right little details not changing (some light googling suggests horses and donkeys diverged 2-4 million years ago, fwiw).

Heck, I've seen speculation that human and chimpanzee could cross-fertilize but I guess some crazy Soviet scientist tried it in the 1920s and it didn't work, though he didn't have modern IVF methods available. I doubt anyone trying today would ever admit to it.

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4. Brent Michael Krupp on January 5, 2006 02:57 PM writes...

Oops, that anonymous was me. Didn't mean to do that. Not that anyone is likely to care, but direct scorn or criticism this way.

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5. Babbler on January 5, 2006 04:08 PM writes...

I was just wondering about domestic cat evolution.

Interesting...

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6. Bob on January 6, 2006 02:39 AM writes...

Are the sabre tooths an earlier branch?

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7. Bob on January 6, 2006 05:52 AM writes...

re : 2, Xerxes

I found this link with cool pictures of big cat hybrids:

http://www.lairweb.org.nz/tiger/hybrids.html

Permalink to Comment

8. Thomas R. Holtz, Jr. on January 6, 2006 08:57 AM writes...

I have to agree with Carl on this one: the paper *DESPARATELY* needed the contribution of a paleontologist. Even leaving aside the issues of entirely extinct cat lineages (whose effect on the tree topology can only be guessed), there is the matter that present geographic ranges of the extant species are considerably different than their historic and prehistoric ranges. Take lions, for instance: today limited to Africa and a pocket in South Asia, but once broadly distributed in Europe, Africa, much of Asia, and North America (assuming P. atrox is indeed P. leo atrox). I'm not a fossil cat worker (my critters were much older...), so I don't know which region has the oldest specimens of P. leo. The authors might be overcounting or undercounting dispersal events.

Paleo-cat fans should definitely check out A. Turner and M. Anton's The Big Cats and Their Fossil Relatives (Columbia Univ. Press, 1997). Excellent illustrations.

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9. dearkitty on January 6, 2006 11:31 AM writes...

More on cat ancestry here.

Permalink to Comment

10. Davvid B Benson on January 6, 2006 06:18 PM writes...

Re: #6

A quick check in wikipedia indicatess that all
saber toothed and simitar toothed cats diverged
early from all other cats. None of these, being
extinct, appear in the 'live DNA' analysis.

Permalink to Comment

11. Biopolitical on January 7, 2006 10:12 AM writes...

"Mammals with placentas (including cats, dogs, bears, bats, cows, primates, and rodents) underwent a massive evolutionary explosion, driven in large part by the extinction of big dinosaurs 65 million years ago." The story that the extinction of dinosaurs left an ecological void that was then filled by the radiation of mammals is, to the best of my (scant) knowledge, just that - a story. Clades come and go and we know very little about the causes.

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12. jessica on January 19, 2006 06:25 PM writes...

cats are so cute

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13. Van Stoffer on February 8, 2006 11:00 AM writes...

Thinking of cat evolution, I wondered why they all compulsively lick and wash themselves even at the risk of hairballs? The question then is what evolutionary advantage does this behavior confer? It seems most likely that it is to reduce oder to prey or predators. It is probably much easier for a clean cat to sneak up on a mouse than a smelly one! I have never read of an explanation for this behavior but would like to hear any alternative ideas.

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