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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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August 29, 2005

The Chromosome Shuffle

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Posted by Carl Zimmer

chromosome.jpg

Our genes are arrayed along 23 pairs of chromosomes. On rare occasion, a mutation can change their order. If we picture the genes on a chromosome as

ABCDEFGHIJKLMNOPQRSTUVWXYZ

a mutation might flip a segment of the chromosome, so that it now reads

ABCDEFGHISRQPONMLKJTUVWXYZ

or it might move one segment somewhere else like this:

ABCDLMNOPQRSTUEFGHIJKVWXYZ

In some cases, these changes can spread into the genome of an entire species, and be passed down to its descendant species. By comparing the genomes of other mammals to our own, scientists have discovered how the order of our genes has been shuffled over the past 100 million years. In tomorrow's New York Times I have an article on some of the latest research on this puzzle, focusing mainly on two recent papers you can read here and here.

One of the most interesting features of our chromosomes, which I mention briefly in the article, is that we're one pair short. In other words, we humans have 23 pairs of chromosomes, while other apes have 24. Creationists bring this discrepancy up a lot. They claim that it represents a fatal blow to evolution. Here's one account, from Apologetics Press:

If the blueprint of DNA locked inside the chromosomes codes for only 46 chromosomes, then how can evolution account for the loss of two entire chromosomes? The task of DNA is to continually reproduce itself. If we infer that this change in chromosome number occurred through evolution, then we are asserting that the DNA locked in the original number of chromosomes did not do its job correctly or efficiently. Considering that each chromosome carries a number of genes, losing chromosomes does not make sense physiologically, and probably would prove deadly for new species. No respectable biologist would suggest that by removing one (or more) chromosomes, a new species likely would be produced. To remove even one chromosome would potentially remove the DNA codes for millions of vital body factors. Eldon Gardner summed it up as follows: “Chromosome number is probably more constant, however, than any other single morphological characteristic that is available for species identification” (1968, p. 211). To put it another way, humans always have had 46 chromosomes, whereas chimps always have had 48.

There's a lot that's wrong here, and it can be summed up up with one number: 1968.

Why would someone quote from a 37-year-old genetics textbook in an article about the science of chromosomes? It's not as if scientists have been just sitting around their labs since then with their feet up on the benches. They've been working pretty hard, and they've learned a lot. And what they've learned doesn't agree with what Apologetics Press wants to claim.

The first big discovery came in 1982, when scientists looked at the patterns of bands on human and ape chromosomes. Chromosomes have a distinctive structure in their middle, called a centromere, and their tips are called telomeres. The scientists reported that the banding pattern surrounding the centromere on human chromosome 2 bore a striking resemblance to the telomeres at the ends of two separate chromosomes in chimpanzees and gorillas. They proposed that in the hominid lineage, the ancestral forms of those two chromosomes had fused together to produce one chromosome. The chromosomes weren't lost, just combined.

Other researchers followed up on this hypothesis with experiments of their own. In 1991, a team of scientists managed to sequence the genetic material in a small portion of the centromere region of chromosome 2. They found a distinctive stretches of DNA that is common in telomeres, supporting the fusion hypothesis. Since then, scientists have been able to study the chromosome in far more detail, and everything they've found supports the idea that the chromosomes fused. In this 2002 paper, for example, scientists at the Fred Hutchinson Cancer Research Center reported discovering duplicates of DNA from around the fusion site in other chromosomes. Millions of years before chromosome 2 was born, portions of the ancestral chromosomes were accidentally duplicated and then relocated to other places in the genome of our ancestors. And this past April, scientists published the entire sequence of chromosome 2 and were able to pinpoint the vestiges of the centromeres of the ancestral chromosomes--which are similar, as predicted, to the centromeres of the corresponding chromosomes in chimpanzees.

Today geneticists sometimes encounter people with fused chromosomes, which are often associated with serious disorders like Downs syndrome. But that doesn't mean that every fusion is harmful. Many perfectly healthy populations of house mice, for example, can be distinguished from other house mice by fused chromosomes. The fusion of chromosome 2 millions of years ago may not have caused any big change in hominid biology--except, perhaps, by making it difficult for populations of hominids with 23 pairs of chromosomes to mate with populations who still had 24. As a result, it may have helped produce a new species of hominid that would give rise to our own.

Just goes to show what 37 years of scientific research can turn up.

Update: Tuesday, 3:30: Thanks to Dr. Paul Havlak for pointing out that some people with fused chromosomes suffer no ill effects. This site at the University of Utah has more information.

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


COMMENTS

1. coturnix on August 30, 2005 09:19 AM writes...

Lovely!

Permalink to Comment

2. Joseph Poliakon on August 30, 2005 11:35 AM writes...

Simply a case of 48...er-r-r...that is 46 Chromosome Monty. Now you count 'em...now you don't.

Permalink to Comment

3. Paul Havlak on August 30, 2005 02:47 PM writes...

Carl,

Thanks for the nice article and blog entry. I enjoy your writing immensely, except sometimes when I'm too tired of your having to explain evolution to people who don't just misunderstand but also abuse the evidence.

You can take the example of chromosomal changes a little further. You mentioned healthy mice with fused chromosomes, but you should also know that developmentally normal people can have chromosomal fusions.

Acrocentric chromosomes have essentially empty short arms, going almost directly from centromere to telomere. When they fuse, that's a Robertsonian translocation. When it's balanced, the individual has fewer chromosomes but all the required genetic material, and matures normally.

This does complicate meiosis and make the individual less fertile, something that would be overcome if all individuals in a population had the translocation.

http://gslc.genetics.utah.edu/units/disorders/karyotype/robertsonian.cfm

Permalink to Comment

4. Joel on August 30, 2005 04:30 PM writes...

Downs can be a fusion, but 95% are trisomy.

There is an extra copy of chromosome 21 caused
most likely by nondisjunction during meiosis.

A trisomy also occurs on chromosome 13 and
18, with even more severe developmental problems.

The centromere remants could be the result of a neocentromere emergence, along with the inactivation of the normal centromere.

What evidence rules out a telomere-telomere fusion, after breakage of chromosome 2, which had aquired telomere ends for stabilization?

Permalink to Comment

5. david tisdale on August 31, 2005 11:52 AM writes...

Any other info on fused chromosomes? Horses and donkeys, for instance?

Permalink to Comment

6. Gary Hurd on August 31, 2005 04:19 PM writes...

I was going to try to write a short explanation this morning of EXACTLY this issue. But, there was a wonderful surprise when I logged on today. Award winning science journalist Carl Zimmer just wrote the very item and posted it to his blog.

Very cool, huh?

Thanks for a very good presentation on a topic that confuses many.

I should have been able to get some of my other work done today, but no. I should have gone fishing, but I am doing that tommorrow.

Permalink to Comment

7. Ediacaran on September 7, 2005 10:26 PM writes...

For those who would like a visual comparison of the chromosomal differences and similarities between the chromosomes of humans, chimps, gorillas and orangutans, see http://www.indiana.edu/~ensiweb/lessons/chro.all.html

The diagram is originally from a 19 March 1982 Science article by Yunis and Prakash, entitled "The Origin of Man: a Chromosomal Pictorial Legacy".

Thanks, Carl.

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