Corante: technology, business, media, law, and culture news from the blogosphere
OUR PUBLICATIONS:
Corante is a trusted, unbiased source on technology, business, law, science, and culture that’s authored by leading commentators and thinkers in their respective fields. Corante also produces premium conferences and publications that help decision-makers better understand their industries and the world around them.
Corante Blogs
Corante Blogs examine, through the eyes of leading observers, analysts, thinkers, and doers, critical themes and memes in technology, business, law, science, and culture.
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
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
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
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
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
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
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
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
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
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
Corante Developments
Here you will find the latest news from Corante including updates on upcoming events, new initiatives, product and publication launches, and more.
It was with shock that I returned home from a night out last night to hear the news of Russell's passing. How terribly, terribly sad. Most of all for him, as he'd seemed buoyant, healthier, and content when I'd last seen him several months ago when he was in town - he was happy that work was busy and rewarding and was having fun with it but most of all was thrilled about how things were going with his girlfriend, Ellen.
I've known Russ for what seems like ages now (in a good way) though in fact it's only been about six or seven years since the early days of "commercial" blogging when he started working on various projects at and around Corante. He was a diligent, committed, and prolific journalist who had impressively and more ably than others been able to make the transition from the old-school way of doing things to the new. He had his quirks, as we all do, but I greatly valued that he was good-natured, collegial, reliable, quick to adopt, trustworthy, eager to learn, and earnest in his interest in helping others better understand what he wrote about.
He was also, it should be said, a kind and thoughtful soul and it was the rare conversation in which he didn't ask, with sincerity, about what he knew of my life, e.g. our new babe, and we didn't talk as seemingly old friends about our lives and respective paths. I can't say I knew him very well, of course, but in our half-dozen get-togethers over the years and dozens of conversations I got a good sense of the man: he cared about learning and sharing and his bearing was earnest and ego-less and we'll miss him for that and more.
We wanted to let you know about a discount to New Comm Forum, the annual event event put on by our friends at the Society for New Communications Research. The conference, which runs from April 22-25, will feature many of the field's leading observers and is an important event for those looking, in the words of SNCR, to "better understand new communications tools, technologies and emerging modes of communication, and their effect on traditional media, professional communications, business, culture and society."
Check out the event's website and, if you're interested in attending, be sure to use the code supplied below for a special discount.
EARLY BIRD PRICING - NOW UNTIL FEB. 15th
NewComm Forum Conference - $995.
Pre-conference or post-conference session - $195.
SNCR Jam only - $75.
REGULAR PRICING - AFTER FEB. 15th
NewComm Forum Conference - $1095.
Pre-conference or post-conference session - $249.
SNCR Jam only - $75.
CORANTE READER DISCOUNTS
NewComm Forum Conference - save an additional $100
Use discount code: NCF08100
Pre-conference or post-conference session - save an additional $45.
Use discount code: NCF0845
We've been remiss in letting you know about two new independent blogs we've helped launch in the past month or so.
The first - the ConversationHub - is a companion blog to Supernova 2007, the latest edition of Kevin Werbach's excellent conference on all things connected. As the conference site says: "Supernova examines the effects of an increasingly connected world on business, life, and public policy. As disparate physical and social networks link with one another, a new societal network is rapidly evolving... The New Network is greater than the sum of its parts. It challenges us to re-create everything from the software and hardware we use...to the business models we employ...to the information and entertainment we encounter...to the ways we work and play."
Visit the ConversationHub and you'll find several dozen leading thinkers and doers, led by a few notable ringleaders, weighing in on the themes and trends of the day in technology and business. We encourage you to tune in - feel free to comment and even suggest topics and ideas for posts.
The second blog - Mobile Messaging 2.0 - convenes about a dozen top observers of the mobile messaging space for an intense discussion of the industry and where it's headed. Among its contributors are leading commentators, journalists and players in the field - tune in and you'll find them touching on topics such as mobile device design, messaging platforms, market pressures, user-generated content, interface design, and much, much more.
Also, if you visit the site, which is sponsored by Airwide Solutions, this week, you'll find live coverage and commentary from Global Messaging 2007, to which several of our contributors have traveled to hear about the latest developments from a broad spectrum of the industry's players and providers.
Be sure to catch the Office 2.0 Conference and hear from and engage with leading thinkers and doers in this exciting new market. Find out more here and be sure to use the code "GLDRK" for a special discount for Corante readers.
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline
In March, I wrote a post on some tantalizing new findings about the secrets of human evolution lurking in our genome. In brief, researchers at the University of Pennsylvania studied a gene called MYH16 that helps build jaw muscles in primates. In our own lineage, the gene has mutated and is no longer active in jaw muscles. Perhaps not coincidentally, we have much smaller, weaker jaws than other apes. The researchers estimated that the gene shut down around 2.4 million years ago--right around the time when hominid brains began to expand. They suggested that shrinking jaw muscles opened up room in the hominid head for a larger brain.
It's a cool hypothesis, but it may not hold up. Scientists at Arizona State University have followed up on the initial study by anlayzing much larger pieces of MYH16, both in humans and in other species. All told, they studied 25 times more DNA from the gene. In a paper in press at Molecular Biology and Evolution, they report finding a significantly different date for when the gene mutated. Instead of 2.4 million years ago, they get a much older date: 5.3 million years ago.
If that's true, then you can forget any significant link between the evolution of MYH16 and brain evolution. If the Arizona State team is right, the two events are separated by three million years. What's more, the jaws of hominids also remained relatively large after the mutation of MYH16.
The Arizona State researchers do point out an intriguing clue that may eventually lead to a solution to this paradox. The mutation that the Penn team originally argued that the MYH16 gene became useless when a section of DNA in the middle of its sequence was accidentally deleted. Often, when this sort of deletion takes place, DNA-copying enzymes come to a screeching halt at the site of the mutation. With the gene only partly copied, it cannot be turned into a protein. But the Arizona State researchers found signs that the gene did not shut down entirely 5.3 million years ago. The DNA "downstream" from the mutation--in other words, beyond the point where the enzymes stopped copying the gene--has picked up mutations in a pattern that shows no sign of natural selection at work. That's what you'd expect from DNA that doesn't make a gene, since any change will have no effect for good or bad on its owner. But the upstream DNA--the part of the gene that could still be copied--told a different story. It showed signs of having undergone selection. So perhaps the mutation that occurred 5.3 million years ago didn't actually kill the gene, but just amputated it. What the surviving portion of MYH16 did (or still does) remains unknown.
I would wager that this new paper will unfortunately not attract much press. When scientists first come up with an attention-grabbing hypothesis, they're more likely to get a paper accepted to a high-profile journal, and more likely still to get written up by science writers like me. But follow-up work often ends up in the shadows.
That's a shame, because science is actually not made up of single studies that suddenly overturn everything that came before. It's more of a dialectic, as different groups of scientists search for new evidence in order to put hypotheses to new tests. Some hypotheses--such as the idea that chimpanzees are our closest living relatives--have become stronger over time. Others fall away. It would help if more people understood this process. Unfortunately, it seems that a lot of people think science is like building an elaborate sculpture out of glass. If someone discovers that a piece of research is wrong, then it seems as if the whole sculpture cracks and falls to the ground. Creationists are particularly fond of this tactic. They seize on research about evolution that goes against earlier research, and claim that the entire theory of evolution is a fraud. They conveniently ignore all points on which scientists agree. So, for example, the researchers who have published the new findings on MYH16 do not conclude that humans were intelligently designed, MYH16 and all. Instead, they argue that the gene mutated earlier than once believed, and that the full history of this gene remains to be revealed. Science is more like a sculpture made of clay than glass, continually being molded and reshaped to better reflect reality.
Correction, 10/16/04: Changed "ancestors" to "relatives."
Fantastic post, as is all of the writing on this site! I tried writing a non-technical description of GLUD2 which probably originated by retrotransposition during a time of hominid specialization. I ended up pretty tongue-tied- so now I REALLY admire your efforts!!
There are a number of ways of measuring natural selection on DNA. For example, one way takes advantage of the fact that only some of the "letters" in a gene are actually used to make a protein. So a mutation to this "coding DNA" can have a positive or negative effect on its owner, while a mutation to "non-coding" DNA is almost certain to have no effect. If a gene evolves without strong selection, you'd expect that the coding and non-coding DNA would have acquired equal levels of mutations. If selection is at work, the ratio will not be the same. So, for example, if natural selection favors new versions of the gene, you'd expect more change in coding DNA vs non-coding DNA. Scientists can measure these ratios by comparing versions of the same gene in different species.
Does a mutation to coding DNA ever have 'no effect'?
(Is it possible to tell?)
Does selection ever 'react neutrally' to a mutation? (for example, gene undergoes mutation, codes protein differently, organism as a whole unaffected in terms of interaction with environment)?
Thanks again. I have always loved biology, and I really appreciate this opportunity to learn :)
5. Stan Lyness on October 15, 2004 10:40 PM writes...
Yes, fantastic post & great blog, thanks so much. Maybe here instead of "the idea that chimpanzees are our closest living ancestors" you want to say "closest living relatives"? Regardless of how chimpy the common ancestors may have been, living chimps aren't ancestors.
"Often, when this sort of deletion takes place, DNA-copying enzymes come to a screeching halt at the site of the mutation. With the gene only partly copied, it cannot be turned into a protein."
Just a nit-pick here, but a truncated protein would be the result of a premature termination codon. That wouldn't send any DNA or RNA copying enzymes to a halt; instead, the nascent polypeptide chain being formed on the ribosome would stop synthesis prematurely.
What are the "signs of having undergone selection"?
If the ratio of nonsynonymous to synonymous mutations (dN/dS) is significantly greater or less than 1, it's a sign of selection. A synonymous mutation is one that doesn't change the amino acid sequence of the resulting protein, so we know it's neutral. A nonsynonymous mutation changes the amino acid sequence, and may be beneficial, detrimental, or neutral. If nonsynonymous mutations are being preserved at a greater rate than neutral mutations (when dN/dS > 1), then natural selection must favor the nonsynonymous mutations, indicating positive selection. This means amino acid sequence is evolving in a particular direction. If nonsynonymous mutations are being preserved less often than neutral mutations (when dN/dS against, which indicates purifying selection. That means selection is keeping the amino acid sequence the same. When the rates are the same (dS/dN = 1), then there is no selection. The gene in question is therefore in a state of neutral drift, and probably doesn't do anything important, at least not anymore.
Does a mutation to coding DNA ever have 'no effect'? (Is it possible to tell?)
Oh, certainly. Most mutations will not have any effect. For one thing, there are synonymous mutations, which won't change the amino acid sequence. And then even if the amino acid sequence is changed, many (if not most) mutations won't affect the protein's function, since a lot of amino acids aren't critical, and others can be replaced with similar amino acids without any effect.
Corante: technology, business, media, law, and culture news from the blogosphere
OUR PUBLICATIONS:
Corante is a trusted, unbiased source on technology, business, law, science, and culture that’s authored by leading commentators and thinkers in their respective fields. Corante also produces premium conferences and publications that help decision-makers better understand their industries and the world around them.
Corante Blogs
Corante Blogs examine, through the eyes of leading observers, analysts, thinkers, and doers, critical themes and memes in technology, business, law, science, and culture.
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
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
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
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
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
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
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
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
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
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
Corante Developments
Here you will find the latest news from Corante including updates on upcoming events, new initiatives, product and publication launches, and more.
It was with shock that I returned home from a night out last night to hear the news of Russell's passing. How terribly, terribly sad. Most of all for him, as he'd seemed buoyant, healthier, and content when I'd last seen him several months ago when he was in town - he was happy that work was busy and rewarding and was having fun with it but most of all was thrilled about how things were going with his girlfriend, Ellen.
I've known Russ for what seems like ages now (in a good way) though in fact it's only been about six or seven years since the early days of "commercial" blogging when he started working on various projects at and around Corante. He was a diligent, committed, and prolific journalist who had impressively and more ably than others been able to make the transition from the old-school way of doing things to the new. He had his quirks, as we all do, but I greatly valued that he was good-natured, collegial, reliable, quick to adopt, trustworthy, eager to learn, and earnest in his interest in helping others better understand what he wrote about.
He was also, it should be said, a kind and thoughtful soul and it was the rare conversation in which he didn't ask, with sincerity, about what he knew of my life, e.g. our new babe, and we didn't talk as seemingly old friends about our lives and respective paths. I can't say I knew him very well, of course, but in our half-dozen get-togethers over the years and dozens of conversations I got a good sense of the man: he cared about learning and sharing and his bearing was earnest and ego-less and we'll miss him for that and more.
We wanted to let you know about a discount to New Comm Forum, the annual event event put on by our friends at the Society for New Communications Research. The conference, which runs from April 22-25, will feature many of the field's leading observers and is an important event for those looking, in the words of SNCR, to "better understand new communications tools, technologies and emerging modes of communication, and their effect on traditional media, professional communications, business, culture and society."
Check out the event's website and, if you're interested in attending, be sure to use the code supplied below for a special discount.
EARLY BIRD PRICING - NOW UNTIL FEB. 15th
NewComm Forum Conference - $995.
Pre-conference or post-conference session - $195.
SNCR Jam only - $75.
REGULAR PRICING - AFTER FEB. 15th
NewComm Forum Conference - $1095.
Pre-conference or post-conference session - $249.
SNCR Jam only - $75.
CORANTE READER DISCOUNTS
NewComm Forum Conference - save an additional $100
Use discount code: NCF08100
Pre-conference or post-conference session - save an additional $45.
Use discount code: NCF0845
We've been remiss in letting you know about two new independent blogs we've helped launch in the past month or so.
The first - the ConversationHub - is a companion blog to Supernova 2007, the latest edition of Kevin Werbach's excellent conference on all things connected. As the conference site says: "Supernova examines the effects of an increasingly connected world on business, life, and public policy. As disparate physical and social networks link with one another, a new societal network is rapidly evolving... The New Network is greater than the sum of its parts. It challenges us to re-create everything from the software and hardware we use...to the business models we employ...to the information and entertainment we encounter...to the ways we work and play."
Visit the ConversationHub and you'll find several dozen leading thinkers and doers, led by a few notable ringleaders, weighing in on the themes and trends of the day in technology and business. We encourage you to tune in - feel free to comment and even suggest topics and ideas for posts.
The second blog - Mobile Messaging 2.0 - convenes about a dozen top observers of the mobile messaging space for an intense discussion of the industry and where it's headed. Among its contributors are leading commentators, journalists and players in the field - tune in and you'll find them touching on topics such as mobile device design, messaging platforms, market pressures, user-generated content, interface design, and much, much more.
Also, if you visit the site, which is sponsored by Airwide Solutions, this week, you'll find live coverage and commentary from Global Messaging 2007, to which several of our contributors have traveled to hear about the latest developments from a broad spectrum of the industry's players and providers.
Be sure to catch the Office 2.0 Conference and hear from and engage with leading thinkers and doers in this exciting new market. Find out more here and be sure to use the code "GLDRK" for a special discount for Corante readers.
1. Susan on October 13, 2004 02:39 PM writes...
"But the upstream DNA--the part of the gene that could still be copied--told a different story. It showed signs of having undergone selection."
Can you elaborate on this (or point me somewhere, book or Internet, that explains)? What are the "signs of having undergone selection"?
Thanks.
Permalink to Comment2. gaw3 on October 13, 2004 02:45 PM writes...
Fantastic post, as is all of the writing on this site! I tried writing a non-technical description of GLUD2 which probably originated by retrotransposition during a time of hominid specialization. I ended up pretty tongue-tied- so now I REALLY admire your efforts!!
Permalink to Comment3. Carl Zimmer on October 13, 2004 02:50 PM writes...
There are a number of ways of measuring natural selection on DNA. For example, one way takes advantage of the fact that only some of the "letters" in a gene are actually used to make a protein. So a mutation to this "coding DNA" can have a positive or negative effect on its owner, while a mutation to "non-coding" DNA is almost certain to have no effect. If a gene evolves without strong selection, you'd expect that the coding and non-coding DNA would have acquired equal levels of mutations. If selection is at work, the ratio will not be the same. So, for example, if natural selection favors new versions of the gene, you'd expect more change in coding DNA vs non-coding DNA. Scientists can measure these ratios by comparing versions of the same gene in different species.
Permalink to Comment4. Susan on October 14, 2004 05:32 PM writes...
The answers lead to more questions ...
Does a mutation to coding DNA ever have 'no effect'?
(Is it possible to tell?)
Does selection ever 'react neutrally' to a mutation? (for example, gene undergoes mutation, codes protein differently, organism as a whole unaffected in terms of interaction with environment)?
Thanks again. I have always loved biology, and I really appreciate this opportunity to learn :)
Permalink to Comment5. Stan Lyness on October 15, 2004 10:40 PM writes...
Yes, fantastic post & great blog, thanks so much. Maybe here instead of "the idea that chimpanzees are our closest living ancestors" you want to say "closest living relatives"? Regardless of how chimpy the common ancestors may have been, living chimps aren't ancestors.
Permalink to Comment6. Steve Reuland on October 18, 2004 10:13 PM writes...
Just a nit-pick here, but a truncated protein would be the result of a premature termination codon. That wouldn't send any DNA or RNA copying enzymes to a halt; instead, the nascent polypeptide chain being formed on the ribosome would stop synthesis prematurely.
Permalink to Comment7. Steve Reuland on October 18, 2004 10:28 PM writes...
Susan:
If the ratio of nonsynonymous to synonymous mutations (dN/dS) is significantly greater or less than 1, it's a sign of selection. A synonymous mutation is one that doesn't change the amino acid sequence of the resulting protein, so we know it's neutral. A nonsynonymous mutation changes the amino acid sequence, and may be beneficial, detrimental, or neutral. If nonsynonymous mutations are being preserved at a greater rate than neutral mutations (when dN/dS > 1), then natural selection must favor the nonsynonymous mutations, indicating positive selection. This means amino acid sequence is evolving in a particular direction. If nonsynonymous mutations are being preserved less often than neutral mutations (when dN/dS against, which indicates purifying selection. That means selection is keeping the amino acid sequence the same. When the rates are the same (dS/dN = 1), then there is no selection. The gene in question is therefore in a state of neutral drift, and probably doesn't do anything important, at least not anymore.
Oh, certainly. Most mutations will not have any effect. For one thing, there are synonymous mutations, which won't change the amino acid sequence. And then even if the amino acid sequence is changed, many (if not most) mutations won't affect the protein's function, since a lot of amino acids aren't critical, and others can be replaced with similar amino acids without any effect.
Permalink to Comment8. Steve Reuland on October 18, 2004 10:33 PM writes...
Oops, there was a little truncation there (premature stop codon?)
To recap:
dN/dS > 1: positive selection
dN/dS
dN/dS = 1: neutral drift
Basically the same thing Carl already said, but I had to get nerdy about it.
Permalink to Comment9. Steve Reuland on October 18, 2004 10:34 PM writes...
Arrgh, it did it again. Someone doesn't like my "less than" sign.
Permalink to Comment