These are the sorts of tools that change things

by Beige Alert

New players in sequencing debut at AGBT
[Via Genetic Future]

The main theme of this year’s Advances in Genome Biology and Technology meeting should come as no surprise to regular readers: sequencing. Generating as many bases of DNA sequence as quickly, cheaply and accurately as possible is the goal of the moment, and the number of companies jostling to achieve that goal is growing rapidly.

The meeting saw impressive performances from established players in the field, especially Illumina: their new HiSeq 2000 instrument seems to have dug in as the platform of choice for generating vast amounts of high-quality short-read data. Life Technologies seem to be slowly abandoning the research genomics market (already dominated by Illumina) with their SOLiD platform, focusing instead on capturing the clinical sequencing market; they showed some impressive accuracy improvements for their technology.

As I mentioned in my previous post, PacBio largely underwhelmed the audience with their theatrical unveiling of a massive box with quite limited applications, although we’ll have to wait and see how much its specifications improve over the next couple of years. Meanwhile, Complete Genomics gave an understated but seriously impressive series of presentations on their human genome sequencing service; I’ll have more on them in a day or two.

Anyway, in this post I want to focus on the two brand new platforms announced in the emerging technologies session on the last day of the conference: the newcomer Ion Torrent, and Life Technologies’ futuristic quantum dot technology.

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One machine may be cheap enough to do quality control tests on samples before subjecting them to very high-throughput DNA sequencing devices while the other holds the promise of DNA reads on single molecules that extend for the whole molecule – a single read on a single molecule.

We are approaching the era where these can really be clinical lab technologies rather than only research lab tools. That could have a huge affect on how we interact with the medical profession.

[Listening to: Deacon Blues from the album "Citizen Steely Dan 1972 - 1980 disc 4" by Steely Dan]

The fifteen years that shook the world . . . and you were there

by psd

The fifteen years that shook the world . . . and you were there
[Via Effect Measure]

Fifteen years isn’t a long time. Most of us can remember what we were doing 15 years ago. Often it’s the same thing we are doing now, job-wise. Sure our kids were just kids, not adults. But 15 years isn’t a historical epoch. At least not when you are living through it. But the fact is we have gone through a revolution in that period that will seem as profound as the 50 years from 1450 to 1500, the half century after Gutenberg and the invention of moveable type.

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I mentioned earlier about how far we have come in 5 years. Here is a peek at 15 years back. Some people got it totally wrong, laughingly wrong.

How awkwardly incorrect we will be trying to predict what the world will be doing with technology 15 years from now? Web 5.0?

And the gnashing of teeth will begin in

White House Meets With Non-Theists
[Via Dispatches from the Culture Wars]

The Obama administration became the first presidential administration in American history to hold an official meeting and policy briefing with a non-theist organization. The Secular Coalition for America, a meta-organization that includes the Center for Secular Humanism and American Atheists among others, met on Friday with White House officials on matters of concern to the non-religious community.

This is a very good thing and a very welcome development.

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Three. Two. One. The cry that the secular organizations are getting special treatment is ludicrous, as the administration has met with many, many religious groups. As stated, this appears to be first time a coalition of secular Americans has had such a meeting.

I love that In God We Trust.org kept throwing out “Madalyn Murray O’Hare”, who was murdered in 1995 and whose last name was actually “O’Hair”.

But I don’t expect the moaning to extend very far into the consciousness of most Americans. They have more important things to worry about these days.

Scientists singing about science

Snow Day Special: Warbling Scientists on the Newest Symphony of Science

[Via Discoblog]

Scientific superstars like Carl Sagan and Richard Dawkins are sounding better and better. In the series Symphony of Science, creator John Boswell uses the auto-tune program so beloved by R&B and pop stars to tweak such nerdy delights as Carl Sagan’s monologues from “Cosmos,” and sets them to electro-funk music. The result? Highly watchable videos of Sagan and other guest scientists expounding on the magic of the cosmos and our place in the universe. Boswell has put four videos out previously, but here is his latest offering, “The Poetry of Reality.”

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The Symphony of Science series has been amazing to watch and listen to. And it is a amazing display of what creativity can do using modern tools. He remixed videos, added music, made the scientists ‘sing’, and then put the results up for everyone to examine. He now uses Twitter to help him find new pieces of video or to suggest topics. You can even purchase the music on iTunes.

Five, years ago, this would not have been possible. What will another 5 years bring?

A sign that our courts may not have a clue about the proper place of copyright

US Postage Stamp Found To Be Infringing On Copyright Over Statues In US Korean War Memorial
[Via Techdirt]

Last year, we wrote about the appeal in a case involving a US postage stamp which was based on a photograph of the US’s Korean War Memorial in Washington DC. You can see the sculpture and the stamp below:

There were a variety of issues involved in the case, including who actually owned the copyright, but in the end, the interesting question is whether or not this was fair use. The lower court had ruled that this was clearly quite transformative, different in nature, and did not harm the commercial value of the original work (which even the sculptor admitted). Thus it was fair use. To us, and many other experts in fair use, it seemed hard to question that logic, but when it comes to copyright, you can always be surprised by how judges interpret the law.

The Federal Circuit has ruled on the appeal and stunningly decided that this isn’t fair use, claiming that it’s not, in fact, transformative. I’m somewhat amazed — as is law professor Peter Friedman in the post linked here. The two works are quite clearly extremely different, but the court felt that since they both were designed to honor soldiers killed in the Korean War, it couldn’t be seen as transformative. The fact that the photographer took hundreds of images before settling on this one apparently didn’t matter. On top of that, the fact that the snow totally changes the character of the image was dismissed by the court as being just “nature’s decision.” Update: That “nature’s decision” line was really bugging me, and Friedman has updated his post to show it’s bugging him too, so I wanted to write a bit more. If “nature’s decision” makes something non-copyrightable, then it can be argued that all nature photography is not covered by copyright — which goes against pretty much every precedent out there. It’s hard to see how CAFC can make this argument.

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This really seems to mess of the idea of fair use. And, as the post mentions, how in the world can the government spend public money on a memorial and not be the ones that hold any copyright on the memorial?

That is messed up.

OS X will rule the world

by raneko

Ten Myths of Apple’s iPad: 10. It needs Mac OS X
[Via RoughlyDrafted Magazine]

Daniel Eran Dilger Here’s segment ten in my series taking on iPad myths: no the iPad doesn’t need to run Mac OS X. Ten Myth of Apple’s iPad: 1. It’s just a big iPod touch Ten Myth of Apple’s iPad: 2. iPad needs Adobe Flash Ten Myths of Apple’s iPad: 3. It’s ad-evil Ten Myths of Apple’s iPad: 4. It [...]

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I have loved reading Daniel’s work for a long time. This column has some of the best reasoning explaining why the Mac OS can be found on such a wide range of very popular devices while other OS, such as Windows or Linux, simply are not successful.

It is a great demonstration of why creating a ‘best of breed’ product can provide a more resilient item than trying to just get something that works. MS has always been this way, bolting Windows onto DOS, or onto a mobile DOS. It’s one attempt to create an all new OS, Windows NT, simply was unable to remove the stranglehold Windows has, even within MS.

Apple consistently removes the barriers legacy software and hardware put in its way. MS has really never found such a path, opting for the easy approach of simply bolting on a new veneer onto old technology.

While Apple, because it started with the idea of having the best, not the just good enough, has an OS that is flexible enough to change with the world without too much disruption.

Because the world will always change. Apple can adapt but MS seems to always have some problems.

Our everlasting fight against bacteria

by BertBeckers

Rising Threat of Infections Unfazed by Antibiotics
[Via NYT > Health]

A minor-league pitcher in his younger days, Richard Armbruster kept playing baseball recreationally into his 70s, until his right hip started bothering him. Last February he went to a St. Louis hospital for what was to be a routine hip replacement.

By late March, Mr. Armbruster, then 78, was dead. After a series of postsurgical complications, the final blow was a bloodstream infection that sent him into shock and resisted treatment with antibiotics.

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As I wrote yesterday, our use of antibiotics is probably making bacteria much better are getting around all the different barriers we put up. Now we have bacteria we have not been targeting with antibiotics causing problems.

INterestingly, the report comments on several people who were able to fight off the infection.

Our immune systems protect us against infection by being adaptive, changing our response depending on how the infectious agent adapts. Perhaps we should also look at finding ways to enhance our immune responses.

The other thing is for hospitals to do a better job with their own sanitation procedures. Lack of proper hand washing and cleansing is a big problem.

The publishers should be the frantic ones, not Apple or Amazon

by austinevan

Amazon frantically phoned publishers as Steve Jobs unveiled iPad
[Via AppleInsider]

Apple chief executive Steve Jobs was still standing on stage addressing an auditorium full of media reps last month when higher-ups at Amazon began phoning publishers in an effort to extract details on the deals they were given to supply content on the new iPad device he was touting.



The move came as the online retailer and eBook reader pioneer was pressing its publisher partners to agree to long-term licensing deals that would guarantee Amazon Kindle owners would always be afforded the lowest possible price for content, in exchange for publishers seeing higher revenues from each sale, according to the New York Times.

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This just creates such wonderful visions in my head. Because this means that two smart companies, Apple and Amazon, are going to compete head-to-head but will keep the publishers caught in the middle.

Just like the record companies, and the movie companies, and the TV companies, the print media will try to exercise control and keep their high-priced models around (Who will really spend as much for an ebook as for the real thing?) I expect the smart guys at Apple and Amazon, who understand much more the new world we inhabit, to run rings around these guys.

And, just like with digital MP3 downloads, they will have large effects on what we get to download, even as it turns out when all the dust settle, that Amazon and Apple were really not head-to-head after all. That is, they sell similar things in slightly different ays and to different people.

In the end, the customer is the one who wins. As it should when capitalism works correctly.

Guessing voices

How Well Do You Know Celebrity Commercial Voices?

[Via TV Squad]

There are a lot more celebrities doing voice overs than you might think. Sure, we can all instantly recognize David Duchovny when he plugs dog food, but there are a lot of other celebrities doing ads and you probably don’t even realize it as you’re watching the commercials (if you still watch commercials and don’t speed through them on DVR).

TV.com has a quiz to see if you can guess which voice is on various commercials (don’t read the comments on that page because they give away some of the answers). They show you the commercials and then you type in the actual name of the person (no multiple choice with this quiz, sorry).

A few of the voices will be familiar to you right away while some of them are going to leave you scratching your head a bit. I only got six out of fifteen, though all of the voices sounded familiar to me. I’m really angry at myself for missing number three…

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This was a fun quiz. I did pretty well, considering they did not use some of the easiest ones, such as Donald Sutherland. Give it a try. A nice relaxing thing to do on a Saturday.

Apps on the desktop

by sciondriver

Former Apple Senior Engineer says OS X could adopt Front-Row-style iPhone OS implementation in future version | Cult of Mac
[Via Cult of Mac]

After January 27th’s unveiling of the iPad, it became abundantly clear that Apple has meaningful plans for iPhone OS outside of the smartphone arena. In fact, given the App Store’s runaway success, it’s just good business sense for Apple to try to get iPhone apps on as many devices as possible: not just phones, portable media players and tablets, but more traditional laptop and desktop machines as well.

The question is, then, when will OS X and iPhone OS begin to converge? When will OS X become compatible with iPhone OS?

In a recent New York Times blog post, Nick Bilton examines this very question, and talks to a former senior Apple Engineer to get to the bottom of whether or not iPhone apps could run natively on OS X one day.

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iPhone Apps on the Mac. I wonder just how useful those would be. They would definitely need to multitask. It would certainly open up a lot of possibilities.

I guess some of the apps could be pretty big. Lots more memory and real estate to deal with. It would be interesting to see what comes up.

The idea of getting some pretty nice bits of software for 10s of dollars instead of hundreds is appealing also.

DNA is not everything and could be misleading

DNA links Everett man to second cold-case slaying
[Via The Seattle Times: Local News]

A 73-year-old Everett man arrested by Seattle police in connection with a cold-case murder from 1972 was ordered held without bail Friday during a brief hearing that the ailing defendant declined to attend.

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DNA’s Dirty Little Secret
[Via Political Animal]

DNA’S DIRTY LITTLE SECRET…. Is DNA evidence, a forensic tool known for exonerating the innocent, being used to put them behind bars? That’s what lawyer and journalist Michael Bobelian argues in the new issue of Washington Monthly. DNA has a…

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Too many people think that DNA is total proof. Read the comments to the Seattle Times article. They have already convicted the guy and want him dead.

But read the second article and discover how the statistics they so often use to try and make DNA testing sound so strong can simply fall apart when looking at cold cases where the DNA is the only evidence.

Degraded DNA. Incomplete markers. These rapidly reduce the statistics. If there is a 1 in a million chance of something and you search for it in a database of 10 million people, chances are you will find several matches just by random chance.

So, if they search a database of 333,000, they have a 1 in 3 chance of finding someone just by random. If there is nothing else to put the person at the scene of the crime, should they be convicted by a 1 in 3 chance?

The prosecutor himself said that there were 18 other people in California at the time that would have the same DNA profile. So, if they had a database of everyone in California, they would have had 18 suspects.

Lucky for them they had a much smaller database.

The horrible thing is that the defense lawyers are often prevented from bringing this point up. They also are often not permitted to do independent tests because all of the original sample was used up in the first test.

How in the world can someone be put in prison e=because of faulty statistics, a fact that they are not even allowed to present in their defense.

Apple versus Flash

★ Yet More on the Unfolding Future-of-Flash-and-the-Web Saga
[Via Daring Fireball]

I love this whole unfolding future-of-Flash saga because it’s a wonderful mix of politics and technology. It’s complex and multivariate, but not too complex to get a handle on the basic gist. It occurred to me this week, after both reading and writing quite a bit regarding Flash Player’s performance issues, that the whole performance angle is a distraction from the fundamental issues at hand.

I linked to this piece by Jeffrey Zeldman three weeks ago, but it’s worth a re-link. His first paragraph nails it:

Lack of Flash in the iPad (and before that, in the iPhone) is a win for accessible, standards-based design. Not because Flash is bad, but because the increasing popularity of devices that don’t support Flash is going to force recalcitrant web developers to build the semantic HTML layer first. Additional layers of Flash UX can then be optionally added in, just as, in proper, accessible, standards-based development, JavaScript UX enhancements are added only after we verify that the site works without them.

I.e. if you think people using iPhone OS devices are an important segment of your intended audience, you can no longer build a Flash-dependent web site. (And if you don’t think people using iPhone OS devices are an important segment of your intended audience, you’re probably wrong.)

Flash’s performance problems on Mac OS X and mobile devices are very much real. (As of today, note that there still is no shipping version of the full Flash Player for any major mobile platform.) And I do think these performance issues are a factor in Apple’s decision not to include it in iPhone OS. But I believe the larger issue goes beyond performance. Apple sees the web as a platform based on open standards. Flash isn’t part of that.

So at the moment, Flash’s performance issues provide Apple with a good apolitical explanation for why Flash Player isn’t included with iPhone OS. It’s a way for Apple to argue that they can’t rather than that they won’t.

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Flash appears to have some real problems for mobile devices. And using it on touch screens seems to offer some further difficulties. Adobe is a smart company. Can they come up with something that works before HTML5 takes over?

And i think this point is the heart of the matter.

From Apple’s perspective, when it comes to software platforms, theirs is best (Cocoa/Cocoa Touch), because they have complete control. Everyone’s is good (the web), because Apple has control over their own implementation and can influence the future direction of the standards. What Apple doesn’t want is someone else’sproprietary platform, where they have no control at all. That’s what Flash is.

Flash is one of the major proprietary bits of the web that Apple has no ability to control the implementation. That is what really concerns Apple, and probably should concern most companies.

If your ability to provide the best experience for your customers is dependent on what another company decides to do, you should be concerned.

The world turned upside down

by Richard0 – Catching

Noble: Let’s Have Perpetual War, But No Earmarks, Please
[Via Eunomia]

His dovish stance on the war on terror and his support for earmarking (the gateway drug to huge spending) won’t wear well with newly inspired activists worried about federal spending and the debt. Either you are a fiscal conservative, or you’re not. Unfortunately, Ron Paul is not at the most basic level. ~Sean Noble

This nicely captures the incoherence of the Republican anti-Paul critique. In this view, Paul is far too hostile to the warfare state and the tremendous costs it imposes on the public, which are not just fiscal but extend to lost civil liberties as well. Somehow, this is seen as incompatible with being “worried about federal spending and the debt,” as if military spending had nothing to do with either one. Despite his career of voting against pretty much every expansion of government and constantly voting for spending reductions, Paul is deemed insufficiently fiscally conservative because he has defended the use of the dreaded earmark. Earmarks are the targets of people who like to pretend they care about spending so that they can avoid advocating genuinely unpopular spending cuts. So-called fiscal conservatives who obsess over earmarks but ignore real entitlement reform, which would be almost all of them in Congress, have no business lecturing anyone about fiscal responsibility or fiscal conservatism. Obviously, if Ron Paul does not qualify as a fiscal conservative, no one does.

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I started as a Republican 34 years ago and have been a moderate most of my life. One of the things I really disliked about Bush was he, along with the neocons, somehow made me a liberal because i was against the war, against the huge increase in military-industrial complex spending, against the lack of oversight of the Executive branch, against subversion of the Bill of Rights, against torture, against the corrupting influence of corporations in the political process.

Daniel and I may disagree on many things. I am not a Ron Paul fan at all. But we absolutely agree on this point:

It has never made much sense to me that there can be people who are furious with “big government” for excessive spending but who simultaneously have no problem vesting the same government with virtually limitless power to seize, detain, wiretap, attack and kill just about anyone it wants to target. [...] Noble’s “worried” activists are people who are very familiar with the old line about a government big enough to give you everything you want, but they seem not to understand that the same danger of unchecked power is even greater when it applies to the government’s power to spy on communications, imprison and mistreat suspects, and start wars.

If more of the GOP wrote like this, I could see much greater areas of overlap in our political discourse. Unfortunately, so very few of the conservative leadership seems to want to do this.

Restoring fertility something to be optimistic about

Woman’s fertility restored after chemo

[Via Health News from NHS Choices]

An experimental technique has allowed a woman to successfully have two children after chemotherapy, several newspapers have reported.

The mother, Dr Stinne Bergholdt of Denmark, had part of her right ovary removed and frozen prior to chemotherapy for a rare bone cancer. Although the powerful anti-cancer drugs made her infertile, she was later able to conceive two children once the frozen tissue was thawed and re-implanted. Dr Bergholdt and her two daughters, born in 2007 and in 2008, are reported to be healthy.

This research is encouraging as it is said to be the first time that a woman has had two separate pregnancies following the transplant of ‘frozen and thawed’ ovarian tissue. Dr Bergholdt’s doctor, Professor Claus Yding Andersen, told The Times that the result “should encourage the development of this technique as a clinical procedure for girls and young women facing treatment that could damage their ovaries”.

However, it is important to remember that this is only a single case, and questions remain over how successful or safe this technique might be for other women. Only time will tell whether further cases of ovarian tissue re-implantation will be as successful as in this interesting but very early research.

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There are a lot of procedures that destroy fertility. Using homologous transplantation to restore the ability to have children is a wonderful step forward.

I just wonder how expensive this will be and whether only rich people will be able to use it.

‘Nature, red in tooth and claw’

by jelleprins

Scientists reveal driving force behind evolution

[Via Eureka! Science News]

The team observed viruses as they evolved over hundreds of generations to infect bacteria. They found that when the bacteria could evolve defences, the viruses evolved at a quicker rate and generated greater diversity, compared to situations where the bacteria were unable to adapt to the viral infection. The study shows, for the first time, that the American evolutionary biologist Leigh Van Valen was correct in his ‘Red Queen Hypothesis’. The theory, first put forward in the 1970s, was named after a passage in Lewis Carroll’s Through the Looking Glass in which the Red Queen tells Alice, ‘It takes all the running you can do to keep in the same place’. This suggested that species were in a constant race for survival and have to continue to evolve new ways of defending themselves throughout time.

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I hate interesting press releases that contain no link to the paper itself. Luckily, the lab’s website is totally up to date (a short search revealed thanks to Google) and not only had the paper listed but also a link.

Antagonistic coevolution accelerates molecular evolution is a great title. What they showed is that organisms do not evolve simply due to environmental conditions (i.e. climate), but also are under tremendous pressure from every other organism in the same environment. Whether it is infectious organisms, predators or simply those that want to eat the same foods, the species that have the greatest chance for survival are those that have the greatest diversity, allowing them to respond to all the different pressure of natural selection.

The greatest diversity occurs when the organism is under direct pressure by other organisms. Without this selective pressure, overall diversity is greatly reduced, decreasing the ability of the population to respond to changes.

Thus, in this very specific experimental set up, when only the virus could evolve, its genetic responses were less robust than when the bacteria could also evolve. Then the virus had to keep finding new ways around the protection that the bacteria kept coming up with – the Red Queen’s Race. In order to just keep surviving, the population had to constantly change.

This constant struggle to overcome bacterial changes actually resulted in a viral population that was able to get around many different barriers the bacteria could erect.

Sequencing the viral DNA at different points revealed that these changes were actually selective in nature and not simply some sort of demographic or global change. such as more rapid generation time or higher mutation rates.

Under these conditions, the viral population developed much larger genetic diversity. They evolved at twice the rate as those that did not have to respond to changes in the bacteria. And the genes in the virus that showed the greatest diversity were those involved with infecting the bacteria.

Importantly, the paper showed that this diversity produced by the coevolution of viruses and bacteria allowed the resulting viral populations to infect a wide range of bacterial mutants. No matter what barriers the bacteria erected, there were always some number of viruses in the population that could still infect.

In contrast, the viruses that simply evolved by themselves were totally unable to infect any of the bacterial mutants.

Thus, having to fight with a metaphorical tooth and claw, actually made the viral populations more fit and more able to survive whatever the bacteria could come up with.

This is a nice real world example of something that had been postulated several decades ago. It should also have some impact on our use of anti-viral medications or antibiotics.

Not only could we be selecting for organisms that can get around some of the barriers we erect, we are possibly creating populations that can get around all the barriers we could erect.

Anyone who thinks a single anti-disease approach will always work is looking at the world too simplistically. We will always be fighting. If we ever have to stop, it would make us actually less able to deal with new infectious agents,

The fight is what makes us better.