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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 22, 2003

Your Loss is Your Gain

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Posted by Carl Zimmer

millepora_a_.jpgEvolution isn't simply about the genes you gain. It's also about the genes you lose.

The word loss has a painful, grieving sound to human ears, and so it can be hard to see how it can have anything to do with the rise of diversity and complexity in life. And until recently, evolutionary biologists didn't pay much attention to lost genes because they were preoccupied with the emergence of new ones. New genes, they found, can be produced in many ways. A gene can get accidentally duplicated, for example, and the copy can mutate, taking on a new function. Or pieces of two separate genes can get fused together, producing a new sort of protein. Or an old gene can get acquire a new switch that turns it on and off according to a different set of signals. As genomes of more and more species have been sequenced, scientists have combed them for new genes. They look for genes that are unique to a species, or some group of species, and are not found in distantly related organisms. They want to sort out the old genes common to much of life and the new ones that created a new body plan in one lineage. Consider the genome of one of the closest living relatives of vertebrates, a delicate sleeve of a creature called Ciona. Scientists found that over 2500 of its genes (a sixth of its entire genome) can also be found in the genomes of vertebrates such as fish--but not in the genomes of invertebrates such as fruit flies or vinegar worms. So here, scientists have argued, may be some of the genes that set us vertebrates apart.

But in just the last few years, evolutionary biologists have also been getting interested in the genes that have vanished. The mutations that erase genes are pretty well understood. A gene may initially get shut down by some disabling mutation. Later, through a copying accident, the gene may get snipped out of the genome altogether. These deletions can be devastating, causing swift death or long agonizing disease. But in some cases, the loss can be borne. Individuals manage to survive without the gene, and over time, more and more of them emerge, until the gene disappears from the species altogether.

Gene loss is particularly important in the evolution of the parasites and mutualists that live within our cells. We depend for our very survival, for example, on oxygen-consuming bacteria that invaded our cells some 2 billion years ago and became mitochondria. Comparisons to their free-living relatives have shown that mitochondria have lost the vast majority of their genes, holding only onto a few they still need to keep up their end of the symbiotic bargain they have with their hosts (us). Losing a gene can actually be an advantage to an organism that live in a host that has genes of its own that produce proteins that serve much the same function as its own. A relative of mitochondria has also stripped down, but for a different reason. Rickettsia, the cause of typhus, can only live inside cells, but it is a deadly pathogen rather than a helpful mutualist.

But free-living organisms have lost their own fair share of genes as well, and those who overlook it may misread the history of life. Case in point: Bacteria can acquire genes not just through heredity, as we do, but grabbing them from other bacteria. (Imagine acquiring someone's DNA through a handshake, your eyes turning from blue to brown. It's a bit like that.) Scientists have been debating how important these two routes of evolution have been for microbes. Do they trade just a handful of minor genes, or can they swap the very core of their genome?

Some new research suggests that much of the evidence for rampant gene trading may actually be an illusion created by lost genes. Think of a cookbook analogy. Imagine that some family in a remote village long ago developed a recipe for a blueberry soup. They keep the recipe a secret, handing down copies of the recipe only to their children. Over time, the children move to surrounding villages, taking the recipe with them and handing it down to their children. But gradually some branches of the family lose it, perhaps in kitchen fires or by accidentally tossing it in the trash. Many generations later, you take survey, recording who still has a copy of the recipe for blueberry soup. You find that most of the people who have it live near one another, close by the ancestral village. But there are also isolated families scattered here and there who also have copies of the same recipe. You might assume that in these cases, the rule of secrecy was broken, and members of the family handed out copies of the recipe to strangers. Only by understanding who had lost it, could you see that the rule had been upheld.

Bacteria have no monopoly on gene loss, though, as a new report in Current Biology makes clear. Australian biologists reported their study of the genome of a coral. Corals belong to one of the oldest lineages of the animal kingdom (a phylum known as Cnidaria, which also includes jellyfish and sea anemones). Cnidarians left fossils almost 600 million years ago, tens of millions before the first fossils of many other animal groups. They are also biologically simpler than most other animals. They lack brains or complex sensory organs, relying instead on nerves that form simple nets. They don't have a mouth and gut running from one end of their body to the other. Only after Cnidarians branched off on their own did new animals emerge with heads and tails, with different sorts of sense organs and neurons, with muscles for swimming and burrowing, and with many other tissues. The Australian biologists decided it would be interesting to compare the genome of a coral (Acropora millepora, the coral in the picture here) to the genomes of animals on younger branches of the animal tree. They compared its genome to ones from both invertebrates (fruit flies and vinegar worms) and vertebrates (humans).

Out of the 1376 genes that the Australian scientists looked at in coral, they found 492 matches in the other animals. But overall, these matches were far more like human genes than of the flies and worms. In fact, 58 of the coral genes (11%) could be found only in the human genome and were nowhere to be found in the other animals. In other words, a sizeable chunk of the genes that existed in the earliest animals have been lost in flies and vinegar worms, while they have survived in corals and humans. These lost genes may change the way scientists understand the evolution of animals. The researchers who used the Ciona genome to identify new vertebrate genes used only fruit flies and vinegar worms as points of comparison. In fact, a lot of these genes may not have all that much to do with the rise of vertebrates at all. Our search for what makes us special will have to turn elsewhere.

Why do species lose genes, and what effects do the loss have on their future evolution? It's puzzling, for example, that humans and corals still carry genes that must date back 600 million years or more--genes that are intimately involved in the development of embryos, for example--and yet fruit flies and vinegar worms (and presumably many other invertebrates) thrive without them. The geneticist Maynard Olson has proposed that losing genes isn't just a mutation organisms can learn to live with, as it were, but actually can offer a big improvement. According to his "less is more" hypothesis, losing a gene can open up a new ecological niche an animal's ancestors never could enjoy.

Olson points out that wild mice have a body clock that senses the changing length of day through the seasons, and uses that information to control when they can have babies. Lab mice have lost this clock, allowing them to breed year-round in their unchanging environment. "Less is more" could be the reason that many animals such as fruit flies and vinegar worms have lost so many genes. It may also one of the things that makes us humans unique. A comparison between humans and mice, for example, shows that 2% of the genes of our common ancestor that lived some 100 million years ago were lost. A closer look our immediate relatives--the apes--shows that we lack a particularly important gene, one that makes a molecule that studes the surface of their cells. It's particularly common on their neurons. And significantly, it appears that our ancestors lost the gene 1.5 mllion years ago, just around the time our brains began to expand dramatically. Scientists speculate that the presence of this surface molecule somehow held back the evolution of more complex brains. Only when it was gone could our ancestors explore their full evolutionary potential. Lose the gene, and you open up a new world.

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


COMMENTS

1. roger on December 24, 2003 01:16 PM writes...

Excellent blog!
I wonder -- one of the stronger arguments against using genetically engineered organisms is the issue of "borrowing" genes. This, at least, is how I have understood the problem with GM potatoes and corn. Hasn't this borrowing been documented? The theory that, instead, an array of genes in a network suffers random attritions that make for concentrations of genes neighboring sets without these genes implies that the borrowing has been illusory.
I wonder what the follow up on this will be.
Yours,
R.
PS. I don't know how to do the trackback thing, but I am going to put a link on my site to your Hamilton post. Again, lovely writing.

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2. Ed van der Meulen on December 25, 2003 03:41 AM writes...

It's a pity people don't look outside theitr own environment. . WEe know the things already a long time, not only growing new synapses but als new neurons taken into use. It looks now Kandel is the first, and that is certainly not too and provabele, But it's your task to look more. Do you tinkk all scientists live in the USA?

This article is not a right one.

Look at this url http://nnw.sourceforge.net/docs.php/intro-layr

And maybe we can talk then again.

Hace a nice day

Ed

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