by AlexWitherspoon
The $4400 Genome:
[Via ScienceNOW]

The cost of sequencing an entire human genome continues to plummet. Complete Genomics, a Mountain View, California-based biotechnology company last year claimed it would soon be able to sell full human genome sequences for as little as $5000 apiece. That now appears within reach. In tomorrow’s Science, the company will report that it sequenced three human genomes for about $4400 each, at least in the cost of reagents. Such cheap sequencing could vastly accelerate studies designed to pinpoint genes underlying complex diseases.
[More]

And they claim to be able to do it in a day! I’d like to see how accurate the data is but it does represent a huge decrease in time and money:

The rapid fall in sequencing prices may give genomics an equivalent of Moore’s Law, which describes how the number of transistors on computer chips doubles every 18 months, steadily driving down the cost of computing power. In 2003, the cost of sequencing a human genome was an estimated $300 million. That was down to $1 million in 2007 and $60,000 last year.

It is now dropping about an order of magnitude every 18 months or so. So by the end of next year, we could be looking at $500 genomes. As i said below, buy stock in hard drive makers.

Technorati Tags: Bioinformatics

What’s in an Illumina GA run directory?:
[Via PolITiGenomics]

One of the main things that differentiates genomics from other endeavors that use a lot of disk space is that genomics file systems tend to have a lot of files (millions). This was true with Sanger sequencing, and it seems to be even more true with next-generation sequencing technologies, especially Illumina/Solexa and AB SOLiD. This large number of files and the parallel access of these files by large computational clusters tends to give most storage solutions great difficulty.So what, exactly, is in an Illumina run directory? Well, to get breakdowns of file statistics there is a nifty little tool called fsstats. It is just a simple Perl script that crawls through a directory stat’ing files and reporting metrics. For example, when you run it on an Illumina GA IIx 2×100, high cluster density run after the primary analysis has completed, you get the following information about the distribution of file sizes. (I have rearranged and condensed the information to make it fit.)

total 7.46 TB used to store 7.46 TB user data, overhead 0.04%
count=991227 avg=8076.50 KB
min=0.00 KB max=13128679.30 KB
size range    count   %tot  %tot cum       total size   %tot  %tot cum
[       0-       2 KB):   4019 ( 0.41) (  0.41)       3009.03 KB ( 0.00) (  0.00)
[       2-       4 KB):      2 ( 0.00) (  0.41)          6.99 KB ( 0.00) (  0.00)
[       4-       8 KB):    981 ( 0.10) (  0.50)       5964.82 KB ( 0.00) (  0.00)
[       8-      16 KB): 193351 (19.51) ( 20.01)    2588619.88 KB ( 0.03) (  0.03)
[      16-      32 KB):   2656 ( 0.27) ( 20.28)      58586.79 KB ( 0.00) (  0.03)
[      32-      64 KB):    901 ( 0.09) ( 20.37)      31369.79 KB ( 0.00) (  0.03)
[      64-     128 KB):   2893 ( 0.29) ( 20.66)     303872.38 KB ( 0.00) (  0.04)
[     128-     256 KB):      2 ( 0.00) ( 20.66)        345.34 KB ( 0.00) (  0.04)
[     256-     512 KB):      4 ( 0.00) ( 20.66)       1222.53 KB ( 0.00) (  0.04)
[     512-    1024 KB):      1 ( 0.00) ( 20.66)        622.26 KB ( 0.00) (  0.04)
[    1024-    2048 KB):      2 ( 0.00) ( 20.66)       3199.89 KB ( 0.00) (  0.04)
[    2048-    4096 KB):     12 ( 0.00) ( 20.66)      41779.69 KB ( 0.00) (  0.04)
[    4096-    8192 KB): 776654 (78.35) ( 99.02) 5863161178.18 KB (73.24) ( 73.28)
[   16384-   32768 KB):     21 ( 0.00) ( 99.02)     487156.46 KB ( 0.01) ( 73.28)
[   32768-   65536 KB):   3856 ( 0.39) ( 99.41)  163552521.17 KB ( 2.04) ( 75.32)
[   65536-  131072 KB):   3825 ( 0.39) ( 99.79)  307535341.32 KB ( 3.84) ( 79.17)
[  131072-  262144 KB):    133 ( 0.01) ( 99.81)   32458046.12 KB ( 0.41) ( 79.57)
[  262144-  524288 KB):   1787 ( 0.18) ( 99.99)  658830514.46 KB ( 8.23) ( 87.80)
[ 2097152- 4194304 KB):     16 ( 0.00) ( 99.99)   47898262.36 KB ( 0.60) ( 88.40)
[ 4194304- 8388608 KB):     64 ( 0.01) (100.00)  432084134.39 KB ( 5.40) ( 93.80)
[ 8388608-16777216 KB):     47 ( 0.00) (100.00)  496603147.67 KB ( 6.20) (100.00)

So the total size of the run directory is nearly 7.5 TB and there are almost one million files. The average size of a file in the run directory is about 8 MB and the maximum size is over 13 GB. The images (represented in the 4096-8192 KB range), comprise over 78% of the files and 73% of the total size of the run directory. This significant penalty can be avoided by using RTA and not transferring image files. The largest files are the alignment (ELAND) outputs and the FASTQ files in the GERALD directory. Speaking of directories, here is a breakdown by number of files in each directory.

[More]

7.5 terabytes! One million files! That just boggles the imagination. I love how the sizes are still in kilobytes. 1 terabyte is over a million kilobytes. or 1000 gigabytes. A blue ray disk can store up to 50 gigabytes on a dual layer disk so 1 terabyte would take 20 of these disks.

With all the sequencing going on, there will be lots of huge storage centers to hold all the data. I wonder how long it takes to back up several terabytes of information?

Technorati Tags: Health, Science, Technology

by stevechasmar

NIAID scientists propose new explanation for flu virus antigenic drift

[Via EurekAlert! - Infectious and Emerging Diseases]

(NIH/National Institute of Allergy and Infectious Diseases) Influenza viruses evade infection-fighting antibodies by constantly changing the shape of their major surface protein. Now, researchers from NIH/National Institute of Allergy and Infectious Diseases have proposed a new explanation for the evolutionary forces that drive antigenic drift.

[More]

Pretty cool little experiment here. Using a mouse model, they showed that the response of the flu virus to people already immunized against it was to increase the binding of one of its coat proteins to a receptor found on human cells. By doing this, it shielded this protein from the very antibodies that had been developed to neutralize the virus.

Evolution in action.

But if the virus produced mutants that bound too tightly, it was rendered less infective. The virus gets stuck to cells in the nose and never makes it to the lungs. Wonderful

What was really interesting was that when these mutated viruses were put into naive mice that had no antibodies to the virus, the virus tended to revert back to normal binding activity and the virus bound the receptor with a low affinity.

It usually did this by making new mutations in other areas of the protein involved in binding to cells. But because the viruses retained the original mutations, they still retained a greater ability to evade antibodies than the original flu viruses.

From their paper:

  

The blue shows the cell binding ability in each round while the red represents the ability to evade detection by the immune system.

What they found was that each round of pressure-release generated sets of mutations that altered the affinity for the receptor and that also resulted in escape from antibody recognition. When pressure was released, new mutations occurred that reduced the receptor binding back to normal. But the ability of these new forms of the virus to escape detection from antibodies remained higher than before.

SInce each round tended to result in different mutations, the cumulative effects after several rounds were to have a virus which was substantially able to escape antibody detection, even in immunized humans. eventually enough mutations would accumulate for the virus to completely evade the immune system, even in vaccinated humans.

The authors postulate that this is a major cause for antigenic drift, the small changes that are seen in the flu virus from season to season. Moving from selective pressure in vaccinated humans to unselected naive humans and back again creates a push me-pull you effect, driving rapid change in the virus.

This drift would be what causes new forms of flu to be seen each year. This process increases the chances that new mutations will occur that escape antibody detection, resulting in a new seasonal flu outbreak.

Putting organisms under selective pressure, then removing that pressure, then reapplying it has been shown to drive very rapid genetic changes. This often results in mutants that can elude the selective pressure. This is often why antibiotics fail when they are not used properly. It is the iterative process of pressure, release, pressure, release that can often create mutants that evade whatever the selective pressure is, such as our immune system.

The key to preventing this would then be to come up with a way to prevent the release of the selective pressure being applied by the immune system. The pressure needs to constantly be applied.

The authors suggest that increasing herd immunity by increasing the vaccination of the major pools for the virus, such as children, will provide the virus with fewer places to revert and mutate. This would keep the pressure up enough to prevent the sorts of antigenic shift that we see.

The virus would then be under continuing pressure to stick really strongly to the receptor and maybe never make it to the lungs at all. At least this would greatly reduce the ability for antigenic drift to occur, reducing the need to come up with new seasonal vaccines each year.

It is a nice hypothesis. It implies that greater vaccination would reduce the drift we see each year, making it less likely that the seasonal outbreaks would keep occurring. Thus we would only have to get one (or a few) vaccinations in our lifetimes. Until an antigenic shift occurred and we needed a new vaccine.

by robstephaustralia

SuperFreakonomics Ignores the Business Case for Sustainability
[Via HarvardBusiness.org]

Stephen Dubner and Steven Levitt’s SuperFreakonomics has certainly gotten a lot of people worked up. The point of contention is a chapter about global warming which makes the case that Al Gore and others are getting us way too worked up about the climate problem because the only way to solve it is to convince people to “put aside their self interest and do the right thing even if it’s personally costly.”

The authors go on to explain their solution — geoengineering — which purportedly isn’t going to require us to cut back on our energy use or rethink the way we do business. But what they have completely failed to address — and what the (ahem) lively discussions on the topic have missed as well — is what the benefits of tackling climate change might be, instead of just the costs.

The authors have missed a major economic issue: the process of shifting our economy to a low-carbon one has enormous upsides completely aside from the benefits to climate balance.

I’m not going to try and take apart their arguments or judge the soundness of their climate science as a whole; there are some others who are already doing a detailed job of that. If you like your climate discussions hot and sarcastic (which can be entertaining), see Joe Romm’s posts on his Climate Progress blog. Or if you like the cool, dispassionate analysis, I’d recommend the Union of Concerned Scientists or the well-respected journalist Eric Pooley’s take on how the authors — who he says are friends of his — “flunk” the science.

There’s also been a fascinating back and forth which includes the authors and Nobel laureate economist Paul Krugman. In short, Krugman is not pleased and he lays out some devastating concerns about the mental exercise the authors have undertaken (“We’re not talking about the ethics of sumo wrestling here; we’re talking, quite possibly, about the fate of civilization. It’s not a place to play snarky, contrarian games”).

The brouhaha is truly unfortunate on many levels. It’s not that having a discussion of geo-engineering is a bad thing — we should explore and assess many options. But the real problem is that the authors of SuperFreakonomics — and even the big critics who have gotten sucked into it — seem to have taken too narrow a view of the problem. While the authors clearly believe that there is too much climate-change hype, there is some agreement that there’s a warming problem (or why propose a solution — the main point of the chapter — at all?). But the focus of the discussion is entirely on a way to counteract the effects of greenhouse gases, as if there are no other issues related to our reliance on fossil fuels.

Instead, let’s just think about the business benefits of changing our products and processes to reduce carbon emissions, regardless of the atmospheric benefits. How will changing to a lower-carbon economy help companies? Well, there’s real money involved here — energy and other resources are getting fundamentally more expensive over time as demand around the world rises and supply gets harder to find. Oddly, the SuperFreakonomics authors acknowledge this Econ 101 supply problem in passing with the statement: “In just a few centuries, we will have burned up most of the fossil fuel that took 300 million years…to make.” So why wouldn’t we want to move away from a declining resource?

[More]

Steven Levitt is one of the authors of Superfreakonomics and an economic professor at the University of Chicago. Yet according to this article, he seems to have taken off his economic hat in the chapter on climate change. Or at least he decided to wear his hat somewhat askew.

Moving away from fossil fuels has very strong economic implications, particularly since these fuels are a dwindling resource which will become more expensive over time.

The countries and companies that decouple themselves from fossil fuels will slash their costs and increase profits mightily. In fact, as Robert Kennedy, Jr. pointed out in a speech recently, the countries that have already reduced their reliance on fossil fuels — such as Iceland, with its geothermal energy, and Sweden, with a carbon tax driving down energy use as the country grew — have made their economies richer and more stable. (Yes, Iceland then bet its wealth on bad investments at the heart of the financial crisis in 2008 and bankrupted itself, but that’s another story.)

As many have repeatedly argued, we also place ourselves at great risk globally by continuing to pour money into oil markets. We send hundreds of billions of dollars a year to parts of the world that don’t like us very much. And we place ourselves at personal risk — the National Academy of Sciences just estimated, conservatively, that fossil fuels cost $120 billion per year in health costs and cause 20,000 premature deaths (that’s more than six 9/11s if you’re counting).

In their admiration of geoengineering, which only covers up the effects of burning fossil fuels, the authors appear to ignore the benefits that moving away from fossil fuel use engenders.

So, not only did they mess up in several ways when it came to the solutions to climate change, they also missed the economic implications of continuing to burn fossil fuels. I guess being contrarian was more important than fundamental economics. It helps sell more books, I guess.

Al Gore’s Climate Choice

[Via Dot Earth]

Al Gore’s new book finds the core of the climate challenge, and solutions, in the human brain.

[More]

I bought the book and have started reading it. Revkin provides a nice viewpoint but the comments are full of people who are spouting the same drivel that has been shown to be either wrong or misleading.

But it does appear that there are a lot more who agree with Gore’s perspective. Perhaps some day soon we will make some real progress.

Open Source Science? Or Distributed Science?:
[Via Common Knowledge]

I was asked in an interview recently about “open source science” and it got me thinking about the ways that, in the “open” communities of practice, we frequently over-simplify the realities of how software like GNU/Linux actually came to be. Open Source refers to a software worldview. It’s about software development, not a universal truth that can be easily exported. And it’s well worth unpacking the worldview to understand it, and then to look at the realities of open source software as they map – or more frequently do not map – to science.

The foundations of open source software are relatively easy to track. In the beginning, there was free software and Richard Stallman. RMS didn’t just invent the GPL as a legal, he wrote crucial foundational software for writing software, notably the GNU compiler collection, GNU Debugger, and the original Emacs. So from the beginning, there was not only a free legal tool, but tools for coding that were better than other systems at the time.

Simultaneously, we can see that the emergence of microcomputers and ubiquitous access to the internet expanded the number (and interconnectivity) of potential programmers. Suddenly there were tens of thousands of programmers with computers at home and at work. The explosion of the Web saw the creation of infrastructure like code repositories, version control systems, and coding communities. Thanks to object-orientation, software was also very amenable to being broken into defined, modular chunks and tasks. One coder could work on a kernel function, another on a user interface function, a third on an application, and they could be reasonably sure that as long as they all followed the standards, their work would snap together into the growing distribution. The phrase “open source” can sort of be a shorthand for this kind of innovation, which we also see in wikipedia and other community built projects.

Open source, if we view it through a different lens, is really more about a distributed methodology for software development. The burden of creation is widely distributed across a massive community with more-or-less equal access to tools and systems. In this context, the role of the legal tool is more akin to an enzyme. It was an essential piece of a puzzle, but it was not the only piece. In fact, without the rest of the infrastructure (connectivity, tools, and people) the legal tool on its own would not have led us to GNU/Linux.

[More]

A really nice discussion of the differences between Open Source approaches in high tech and the need for Distributed Sources in science. There have been an lot of overlap in the development of new high tech tools and those seen in biotech.

After all, the Web was created at CERN to deal with distributed science.

Technorati Tags: Science, Web 2.0

The Hidden Economic Carnage in Science and Education

[Via The Scholarly Kitchen]

Economic statistics don’t measure science or training well. Our fields are being hurt inordinately, but the damage isn’t being measured. What will it mean long-term?

[More]

Anyone who thinks things are getting better needs to read this. Because it is often the best trained, most intelligent ones who are being forced to leave. We are beginning to provide much fewer rationales for people to spend so much time becoming well trained and very educated.

Especially if those people are let go because their expertise costs too much money. We already treat airline pilots as bus drivers with some working at regional carriers making $22,000 a year, the poverty line for a family of four.

Because our current system does do really want to pay for expertise.

I love the last paragraphs:

So, the next time you hear that perhaps the recession is lifting, that halcyon days are on the horizon, remember that the numbers being used for those rosy projections are based on items that are easy to measure, slower to grow, of decreasing value, and not vital for future growth.

This could be a lesson in how intangibles become tangible, I’m afraid.

It will be a long time before employment levels are back up to what they were, especially for those with the most training.

by dog ma

The Sea Change That’s Challenging Biology’s Central Dogma

[Via Discover Magazine | RSS]

For decades, RNA was seen as a simple slave to DNA. Newer research shows it has an active and critical role in every disease from Alzheimer’s to cancer.

[More]

This is a great story about how a small group of focussed people working on a seemingly obscure problem can sometimes provide incredible insight. The author provides some really great insight into the path the research took, including the fact that the researcher who first published on this work, who was one of the key instrumental scientists involved, did not initially get tenure.

His work was viewed as too obscure.

The article does an excellent job of portraying these researchers as flesh and blood humans, rather than Promethean geniuses or lone wolfs.

The only thing a little off is that this work’s challenge to the Central Dogma (i.e. DNA to RNA to Protein) is a little more subtle than simply overturning it. It is more like the effect of Relativity on Newtonian mechanics.

It provides a more sophisticated explanation while leaving much of the framework intact.

In the Central Dogma, proteins are the really important things. They determine just what a cell does. DNA is simply the memory and RNA the transmitter. But proteins are the key.

The big challenge this work provides, where it does some real overturning of paradigms, are to some of the hypotheses regarding so-called junk DNA. Many people have had a feeling that this supposedly unused DNA might actually have a use. It has just been hard to figure out what it is. Now we have an idea of what some of it does.

It is there for a reason.

And what it does is really important. One area where the Central Dogma is influential is with the idea of genomic sequencing as an insight into disease. ‘If we want to know what the protein sequence is, we can look at the DNA sequence.’

However, it is really hard to determine the sequence of a protein, while it is easy to get DNA sequences. So genomic sequencing has been a surrogate for having protein sequences. The Dogma suggests that there is a one-to-one mapping of DNA sequence and protein sequence. With some small exceptions, this remains true.

This makes sense since mutations in DNA often produce alterations in proteins. A change in quality of one is seen in a change in the quality of the other. So we have been hearing a lot about getting everyone’s DNA sequenced. Then we will know what diseases they are likely to be susceptible to. At least in a simple world.

This is a leftover of the Central Dogma’s proposal that changes in proteins are reflected in changes in DNA sequences. But I have already discussed how epigenetic factors (here, here, here, here, here ) can break this relationship, producing different disease states without changing the genetic sequences.

Proteins are still important. But simply knowing what their sequence is – indirectly from DNA – does not describe fully the complex nature of a cell. More than just protein sequence is used to determine what a cell does.

The work on microRNA demonstrates that simply knowing a person’s genomic sequences does not tell the whole story. These RNAs are critical for controlling the amount of different proteins found in each cell.

And the quantity may be just as important as the quality.

Along with epigenesis, microRNAs show us that disease can be caused by the wrong amount of a protein.

So, the dogma of DNA to RNA to Protein is still present. Things are just a little more complex. What a cell does is not just determined by the quality of protein, its sequence that then determines its structure and activity.

It is also determined by the quantity of the protein. Some cells may have a protein that can prevent disease. But if microRNAs prevent it from being produced, then we have disease. Knowing the DNA sequence might not really help us much in this case.

Having too much or too little of a particular protein in a specific cell may well be the cause for many of the diseases we see today. Sometimes it will be because the protein itself is ‘wrong’ and sometimes it will be because the amount of protein present is wrong.

Knowing the genomic sequence of a person will be really important and useful to have. But it will be critical to know how much protein is produced. Knowing how microRNAs work will be critical for understanding this.

by Hey Paul

Can a GOP walkout really stop the climate bill?

[Via Congress Matters]

No.

I’m posting from the road, on my phone, so this won’t be as comprehensive and link-rich as it should be, but here goes.

It’s been pointed out that there’s a rule in the Senate Environment and Public Works Committee that requires the presence of two minority side Senators for a markup to go forward. But like most such rules, it’s probably not “self-executing,” meaning that in order for it to have an effect, someone needs to show up to point out that there aren’t the requisite number of minority Senators in attendance. A majority side Senator could certainly do that, but why? The job of protecting minority rights belongs chiefly to the minority. Let them do it. And when they do, you politely point out that if you’re present enough to object, then you’re present enough to count towards a quorum.

Now, this particular rule requires two minority Senators, not just one. That sounds like a rule designed by someone who had been burned by the one-Senator rule before. So technically, one Republican can show up, point out that there aren’t two, and try to invoke the rule. And if that happens, what can the chair do about it?

Well, one way around it is the way the Judiciary Committee traditionally deals with a similar rule. They ignore it.

Another would be to bypass the formal use of the committee entirely, and use Rule XIV to move the bill to the floor when they’re ready. That is, Chairwoman Boxer could convene a meeting of anyone who’s on the committee and who wants to participate in the process, and in effect simply ask them, “If this were a committee markup, what amendments would you offer, and how would you vote on them?” Then she could alter her draft bill accordingly, and either try to move it to the floor under Rule XIV, pass the resulting document on to the next committee of jurisdiction for its consideration, or set it aside for whatever future merger process the leadership may have planned for it.

[More]

I wrote about this the other day.The Republican members of the committee were going to vanish, making it impossible to continue because 2 minority members were required for markup to continue.

But it requires someone to be present to ‘notice’ that the minority members are absent. If no one ‘notices’ then things are fine. What an perfectly diabolic way to get around a rule.

And then if someone from the GOP does show up to ‘notice’ well, the majority just says that this is not a real committee meeting. “We just happened to get together to talk about the bill. Want to join us?”

Parliamentary procedure at its best!

by epicharmus
Lawsuit against gene patents can proceed: judge:
[Via Reuters: Science News]

NEW YORK (Reuters) – A lawsuit challenging patents on two human genes associated with hereditary breast and ovarian cancer can move forward, a U.S. federal judge ruled on Monday.

[More]

This is where health and business clash. Myriad holds the important patents that permit a test to be done. hey do not license the test to anyone else, doing it themselves. They can charge whatever they want, as there is no possible competition, on a test that is absolutely critical for the prognosis of many women.

The ACLU filed suit. The basis is that the patents are based on natural products, that already occur in the world:

The U.S. Patent and Trademark Office (PTO) has granted thousands of patents on human genes – in fact, about 20 percent of our genes are patented. A gene patent holder has the right to prevent anyone from studying, testing or even looking at a gene. As a result, scientific research and genetic testing has been delayed, limited or even shut down due to concerns about gene patents.

As a result of the PTO granting patents on the BRCA genes to Myriad Genetics, Myriad’s lab is the only place in the country where diagnostic testing can be performed. Because only Myriad can test for the BRCA gene mutations, others are prevented from testing these genes or developing alternative tests. Myriad’s monopoly on the BRCA genes makes it impossible for women to access other tests or get a second opinion about their results, and allows Myriad to charge a high rate for their tests – over $3,000, which is too expensive for some women to afford.

That’s right. Since no other test is allowed, there is no way to get a second opinion. You just have to hope that Myriad does the tests rights and has the right process. And no one can look for a different or better test because myriad holds the patent on the genes themselves, and on anything those genes could be used for.

We fill figure this all out eventually. Perhaps creating monopolies from some health products is not the best approach.

Technorati Tags: Economy, Science

by simone.brunozzi
The must-read solutions book — “Our Choice: A Plan to Solve the Climate Crisis” by Al Gore.:
[Via Climate Progress]

The long-awaited sequel to An Inconvenient Truth comes out Tuesday. If you want a preview, Gore and the book are featured in an excellent Newsweek cover story, The Thinking Man’s Thinking Man.

In September, Nature Reports Climate Change asked me (and several others) to suggest three books to read ahead of the Copenhagen conference. Of those, they then asked me to review Gore’s new book, Our Choice: A Plan to Solve the Climate Crisis:

When your last work led to an Oscar and Nobel Prize, anticipation is high on the sequel. And former US Vice President Al Gore’s new book delivers. Our Choice, due out in November, is a wonderfully readable treatise on climate solutions.Whereas An Inconvenient Truth framed the crisis that climate negotiations are tackling, this followup spells out what needs to be done.

Based on 30 of Gore’s ‘Solutions Summits’ as well as one-on-one discussions with leading experts across multiple disciplines, the book aims, in Gore’s words, “to gather in one place all of the most effective solutions that are available now”. Gore naturally focuses on energy, the source of most anthropogenic greenhouse gas emissions, and discusses many underappreciated strategies such as concentrated solar thermal power and cogeneration. He also devotes a full chapter to soil, a major carbon sink that is gradually degrading. Farming strategies for restoring soil carbon are described, including biochar, a porous charcoal that can potentially enhance the soil sink while providing a source of low-carbon power. And like its PowerPoint-based predecessor, Our Choice is replete with lush photos and simple but powerful charts. This [is] a must-read book for those who want a primer on all the key solutions countries will be considering at Copenhagen.

[More]

Here is a guy who held summits with people from many walks of life in order to gather information for this book, who has altered his opinions as new data emerges, and I bet many people will just ignore him. While two guys who have no background in this issues and really talked to very few people (apparently mischaracterizing those they did talk with) will make the best seller lists.

I expect his ideas will be more useful and achievable, with lower overall costs , than those of Superfrteakonmics. They will most likely actually be based in reality.

Technorati Tags: Environment, Government, Politics, Science, Sustainability

Rep. Jay Inslee slams SuperFreakonomics: “People are still trying to write books to deceive the American public” on climate science.:
[Via Climate Progress]

This is a repost from Wonk Room.

Yesterday, Rep. Jay Inslee (D-WA) rebuked the authors of SuperFreakonomics for participating in a “continuing effort to deceive the American public” on the science of climate change. During an investigative hearing on forged letters sent by the coal industry to oppose climate action, Inslee condemned the industry’s effort to “hoodwink, defraud, and deceive the American public now to cover up the toxicity to the world environment” of global warming pollution. Inslee then turned to Steven Levitt and Stephen J. Dubner, criticizing them for “absolute deception” in their work on global warming:

The second thing I want to note is this is not the only continuing effort to deceive the American public. I want to note a book called Freakonomics, or SuperFreakonomics, that some authors wrote, that basically said or asserted we don’t have to control CO2, we’ll just pump sulfur dioxide up into the atmosphere and that will solve the problem. They purported to quote a scientist named Ken Caldeira from Stanford who’s one of the predominant researchers in ocean acidification to suggest that Dr. Caldeira didn’t think we should control CO2. Which is an absolute deception. Dr. Caldeira I’ve spoken to personally. He’s told me we have to solve ocean acidification. You can’t solve ocean acidification without controlling CO2 and yet people are still trying to write books to deceive the American public. And we ought to blow the whistle on them, we’re blowing the whistle on one today, we’ll continue to do it, because ultimately science is going to triumph in this discussion.

[More]

Deception and mischaracterization of the science are typical tools used by those hoping to obfuscate the debate. It is nice to see Inslee, who represents my district, get a chance to have a few words.

Well, at least some people.

Technorati Tags: Environment, Government, Science

by fireflythegreat

Healthcare provision seeks to embrace prayer treatments

[Via LATimes]

I’m hoping this does not make it to the final bill. One of the big things that is being done for health care reform is to actually do some research to find out what procedures actually work and how well. It turns out that there has actually been little systematically done to examine this, at least compared to the multitude of just-so stories and personal anecdotes.

Having insurance companies pay for pseudo-scientific methods completely negates this approach and means that cost savings, by not doing things that really do not work, will be reduced.

And this opens up all sorts of abuses and unintended consequences.

We might possibly have something that pays for spiritual prayer healings but does not pay for legitimate medical procedures or practices.

Starting a High Tech Business: No Cold Hires:
[Via Phil Windley's Technometria]

Image via Wikipedia

I’m starting a new business called Kynetx. As I go through some of the things I do, I’m planning to blog them. The whole series will be here. This is the twenty-first installment. You may find my efforts instructive. Or you may know a better way–if so, please let me know!

In the past two weeks Kynetx has doubled in size. There’s lots to do and the resources to make it happen, so getting more people became a priority. Getting the right people became the most important thing Steve and I could do for the long term health of the company.

I’ve been in lots of hiring situations before–at iMall we grew from three people to over 125 in a little over 16 months. I’ve learned a few things. The most important being that mistakes in hiring can cause untold grief later on down the road. You definitely want to get this right the first time–iterating to a solution is too expensive.

I’m in firm agreement with Joel Spolsky on what constitutes getting it right: hire people who are “smart and get things done”. That’s not easy; the good people aren’t usually out looking for jobs. They’ve already got jobs where they’re respected and well compensated because they’re “smart and get things done.”

One good rule of thumb for getting good employees is “no cold hires.” Four out of the five people we hired this past week are good friends who Steve and I have worked with in multiple ventures in the past. The fifth was someone who had worked closely with another key member of the team in mutliple ventures. We know these people well: we know their personality, we know their strengths, and we know their weaknesses. And…they know ours. Most importantly, we know they’re “smart and get things done.”

[More]

This is one reason why answering ads and sending out resumes are only a small part of looking for a job. They are necessary because they can work but sometimes only indirectly.

The hires may not be hot but lukewarm can make a big difference in this economic climate.

Technorati Tags: Economy, Government

Draft report on openness in higher ed.:
[Via Open Access News]

The Committee for Economic Development, a longstanding American business-led think tank, has released a draft of its report, Harnessing Openness to Improve Research, Teaching and Learning in Higher Education. See e.g. the table of contents for chapter 5, “Openness in Higher Education: Changes in Research”:

Resistance to Greater Openness
Openness and Open-Access Journals
Digital Repositories
Educating Faculty Members on Their Intellectual Property Rights
Openness and Commercial Support of Research
Access to Government-Funded Research Results
Openness and University Libraries
Openness and Academic Presses
Openness and Technology Transfer

[More]

Increasing openness will be required for higher education institutions. Rapid and easy access to information will be a requirement for a successful university. Not only teaching will be changed.

How we educate ourselves will determine how well we manage to live. Just one of the many changes going on.

Technorati Tags: Education, Sustainability, Web 2.0