A devastating response

by SophieG*
An open letter to Steve Levitt:
[Via RealClimate]

Dear Mr. Levitt,

The problem of global warming is so big that solving it will require creative thinking from many disciplines. Economists have much to contribute to this effort, particularly with regard to the question of how various means of putting a price on carbon emissions may alter human behavior. Some of the lines of thinking in your first book, Freakonomics, could well have had a bearing on this issue, if brought to bear on the carbon emissions problem. I have very much enjoyed and benefited from the growing collaborations between Geosciences and the Economics department here at the University of Chicago, and had hoped someday to have the pleasure of making your acquaintance. It is more in disappointment than anger that I am writing to you now.

I am addressing this to you rather than your journalist-coauthor because one has become all too accustomed to tendentious screeds from media personalities (think Glenn Beck) with a reckless disregard for the truth. However, if it has come to pass that we can’t expect the William B. Ogden Distinguished Service Professor (and Clark Medalist to boot) at a top-rated department of a respected university to think clearly and honestly with numbers, we are indeed in a sad way.

By now there have been many detailed dissections of everything that is wrong with the treatment of climate in Superfreakonomics , but what has been lost amidst all that extensive discussion is how really simple it would have been to get this stuff right. The problem wasn’t necessarily that you talked to the wrong experts or talked to too few of them. The problem was that you failed to do the most elementary thinking needed to see if what they were saying (or what you thought they were saying) in fact made any sense. If you were stupid, it wouldn’t be so bad to have messed up such elementary reasoning, but I don’t by any means think you are stupid. That makes the failure to do the thinking all the more disappointing. I will take Nathan Myhrvold’s claim about solar cells, which you quoted prominently in your book, as an example.

As quoted by you, Mr. Myhrvold claimed, in effect, that it was pointless to try to solve global warming by building solar cells, because they are black and absorb all the solar energy that hits them, but convert only some 12% to electricity while radiating the rest as heat, warming the planet. Now, maybe you were dazzled by Mr Myhrvold’s brilliance, but don’t we try to teach our students to think for themselves? Let’s go through the arithmetic step by step and see how it comes out. It’s not hard.

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This article, which uses simple math, destroys one of the points from the book. Since many of the other points in the book are also based on just as much ‘just-so science’ , the post serves as a good example of what to look for.

If he was so wrong with his point of view on something that was so easily examined, how far off is he on all the other things he discusses? Why should we believe anything he says about geoengineering if he is misleading on other approaches?

One of the things a contrarian should do is not use misleading ideas. Getting people to look at problems from a different perspective can be very helpful. But forcing a new perspective by using distortions does not accomplish anything helpful at all.

Technorati Tags: Environment, Science

British stiff upper lip

There is something to be said for the phlegmatic nature of the British. I imagine that if I were attacked by a lion, even if it was only playing, I’d be screaming my head off. Of course, I’d then probably be dead.

Here, the attacked reporter is actually more excited about getting some stitches, which he is around to get because he was so very calm as the lion bit him, while clawing his back. Why don’t we have any reporters in America as interesting?

Drumline of the gods

Awesome to the corps

[Via Bad Astronomy]

When I was in high school I was a marching band dork. Shocker, I know. But let me tell you something: we were good. Very good. We won a lot of competitions, and we hosted a drum and bugle corps competition at our school that pulled in the best from around the country. To this day, all these decades later, it’s still the loudest thing I have ever heard.

We humans have incredible talents: imagination, cleverness, dexterity, and musical abilities that are truly astonishing. Don’t believe me? Then behold:

Un. Flipping. Believable.

Those guys have major talent. Watch the bit from 4:50 to 5:10 again, and call those guys dorks. Holy mackerel, they rock.

Tip o’ the chapeau to Fark.

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Why I love the Internet. I played drums in the marching band in high school. We won state but never had a drum line like this. The Top Secret Drum Corps are from Basel. Switzerland. According to Wikipedia, they were one of the fist non-military groups to appear at the Edinburgh Military Tatoo in 2003, giving a performance that made them a little famous.

The performance from Bad Astronomy is from the Basel Tatoo, which was started in 2006, is now the second largest tatoo, and whose producer is the leader of the Top Secret Drum Corps.

But, if you want to be amazed, watch their performance from just this last August at the 2009 Edinburgh Military Tatoo. Flaming drum sticks and exploding bass drums!!

Changing the culture

[Crossposted at SpreadingScience]

Loose coupling and biopharma:
[Via business|bytes|genes|molecules]

A few days ago, via the typical following of links that is typical of a good search and browse section on the interwebs, I chanced upon a discussion about a presentation given by Justin Gehtland at RailsConf. The talk was entitled Small Things, Loosely Joined, Written Fast and that title has been stuck in my head ever since. Funnily enough, what was in my head was not software, and web architectures, cause today, I consider that particular approach almost essential to building good applications and scalable infrastructures, and most people in the community seem to understand that (not sure about scientific programmers though). What I started thinking about was if that particular philosophy could be extended to the biopharma industry.

Without making direct analogies, but without suspending too much disbelief, one can imagine a world where drug development is not done in today’s model, but via a system consisting of a number of loosely coupled components that come together to combine cutting edge research and products (drugs) in a model that scales better and does a better, more efficient job of building and sustaining those products. One of the tenets of the loose coupling approach to scalable software and hardware is minimizing the risk of failure that is often a problem with more tightly coupled systems and in many ways the current blockbuster model is very much one where risk is not minimized and one failure along the path can result in the loss of millions of dollars. I have said in the past that by placing multiple smart bets, distributed collaborations and novel mechanisms (like a knowledge and technology exchange), we can reboot the biopharma industry, reducing costs and developer better drugs more efficiently. I don’t want to trivialize the challenge, the numerous ways in which the process can go wrong, and the vagaries of biology, but resiliency is a key design goal of high scale systems, and is one we need to build into the drug development process, one where the system chooses new paths when the original ones are blocked.

How could we build such a network model? I know folks like Stephen Friend have their ideas. Mine are ill formed, but data commons, distributed collaborations, and IP exchanges are a key component especially in an age where developing a drug is going to be a complex mix of disciplines, complex data sets and continuous pharmacavigilance. I can’t help but point to Matt Wood’s Into the Wonderful which does point to some of those concepts albeit from a computational perspective

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Designing great and awesome tools for researchers to use will be critical for successful drug development. But there also has to be a cultural change in the researchers themselves and the organizations they inhabit.

One is that the tools have to work the way scientists need them to, not what works well for developers. This is actually pretty easy now and many tools are really starting to reflect the world views of researchers in biotech, who, more times that expected, are somewhat technophobic.

This leads to the second area- researchers often need active facilitation in order to take up these sorts of tools. They need someone they trust to actually help convince them why they should change their workflows. Most will not just try something new unless they can see clear benefits.

Finally, the last thing is better training for collaborative projects. Most of our higher education efforts for training researchers makes them less collaborative. They are taught to get publications for themselves in order to gain tenure. Plus, with the competition seen in science, letting others know about your work before publication can often be harmful Large labs with many people often can quickly catch up to a smaller lab and its work.

Like in the business world, being first to accomplish something can be overtaken by a larger organization. So, many researchers are trained to keep things close to the vest until they have drained as much reputation as possible form the work.

But many of the difficult problems today can not be solved by even a large lab. It can require a huge effort by multiple collaborators. Thus, there is a movement towards figuring out how to deal with this and assign credit.

Nature just published a paper by the Polymath Project, an open science approach to the discovery of an important math problem. They addressed the problem of authorship and reptation:

The process raises questions about authorship: it is difficult to set a hard-and-fast bar for authorship without causing contention or discouraging participation. What credit should be given to contributors with just a single insightful contribution, or to a contributor who is prolific but not insightful? As a provisional solution, the project is signing papers with a group pseudonym, ‘DHJ Polymath’, and a link to the full working record. One advantage of Polymath-style collaborations is that because all contributions are out in the open, it is transparent what any given person contributed. If it is necessary to assess the achievements of a Polymath contributor, then this may be done primarily through letters of recommendation, as is done already in particle physics, where papers can have hundreds of authors.

We need to come up with better ways to design useful metrics for those that contribute to such large projects. Researchers need to know they will get credit for their work. As we do this, we need to also help train them for better collaborative work, because that is probably what most of them will be doing.

Technorati Tags: Open Access, Science, Web 2.0

For really small splinters

Optical Tweezers

[Via Bench Marks]

Light carries momentum, so an object that reflects or refracts a beam of light experiences a force. This force is very small, but still strong enough to manipulate objects, such as a polystyrene bead. Using light focused through a lens, beads can be “trapped” near the focus. These optical traps, or “optical tweezers” have become an important tool that allows researchers to manipulate individual molecules or molecular complexes. High-resolution optical trapping techniques can now detect movements on the scale of a single base pair of DNA, 3.4 angstroms. The October issue of Cold Spring Harbor Protocols includes a series of articles detailing the concepts behind optical trapping, the components of an optical trapping system and the single-molecule experiments in which they are used. Carlos Bustamante, Yann Chemla, and Jeffrey Moffitt provide an introduction to High Resolution Dual-Trap Optical Tweezers with Differential Detection, and subsequent articles on Managing Environmental Noise, Instrument Design, Data Collection and Instrument Calibration, Minimizing the Influence of Measurement Noise and Alignment of Instrument Components.

Optical Tweezers are really cool, not only to think about but to actually use. There are some nice experiments that can be done with them, as seen below:

Who says science is all work.

[Listening to: Every Little Thing from the album "Beatles For Sale" by The Beatles]

Priority on the internet?

A solution to Darwin’s ‘mystery of the mysteries’ emerges from the dark matter of the genome

[Via Eureka! Science News - Popular science news]

Biological species are often defined on the basis of reproductive isolation. Ever since Darwin pointed out his difficulty in explaining why crosses between two species often yield sterile or inviable progeny (for instance, mules emerging from a cross between a horse and a donkey), biologists have struggled with this question. New research into this field by basic scientists at Fred Hutchinson Cancer Research Center, published online Oct. 22 in Science Express, suggests that the solution to this problem lies within the “dark matter of the genome”: heterochromatin, a tightly packed, gene-poor compartment of DNA found within the genomes of all nucleated cells.

[More]

Naturally I read my feeds in reverse time order. So this was posted at 11:23 AM while my previous post was up at Eureka Science at 6.28 PM. While the previous work only describes in generalities the regions in the chromosomes responsible for reproductive isolation, this paper not only gives more specific information on the regions but identifies some of the proteins involved.

At a quick glance, I would say that this paper may have more impact in the long run, as it provides an actual mechanism with the possible culprit for rapid creation of new species.

Time will tell.

[Listening to: The Word from the album "The Beatles]

No gene flow. New species.

by Image Editor

Researchers discover mechanism that prevents two species from reproducing

[Via Eureka! Science News - Popular science news]

Cornell researchers have discovered a genetic mechanism in fruit flies that prevents two closely related species from reproducing, a finding that offers clues to how species evolve.

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This is potentially a very important finding, if it carries over to other species and not just fruit flies. Reproductive isolation is often an important aspect of species formation.Once the flow of genes has stopped between two groups, the ability for them to evolve separately occurs.

Alterations in certain areas of the sex chromosomes might be important first steps in reproductive isolation. These areas can diverge fairly rapidly; they develop mutations and additional repetitive sequences very quickly compared to normal regions of the chromosomes.

Thus two isolated groups could develop fairly rapidly. Once separate, they are free to develop much larger changes in their genetic material because there is really no way for them to ever breed again. Thus the genetic sequences diverge even more, with entire regions becoming altered, even those that where mutation accumulate at a slower pace.

It is almost as if the drive it to create species rapidly when gene flow decreases between groups. Create new species rapidly and often.

I wonder how many generations with no gene flow it takes to create a new species by this route?

[Listening to: Tomorrow Never Knows from the album "The Beatles]

Making mistakes

by Johnny Jet
Plimer the plagiarist

[Via Deltoid]

Eli Rabett has been investigating Ian Plimer’s claim that climate scientists were coking the books on the CO2 record. Plimer wrote:

The raw data from Mauna Loa is ‘edited’ by an operator who deletes what is considered poor data. Some 82% of the raw data is “edited” leaving just 18% of the raw data measurements for statistical analysis [2902,2903]. With such savage editing of raw data, whatever trend one wants can be shown. [p 416 of Heaven and Earth]

The raw data is an average of 4 samples from hour to hour. In 2004 there were a possible 8784 measurements. Due to instrumental error 1102 samples had no data, 1085 were not used due to up slope winds, 655 had large variability within 1 hour but were used in the official figures and 866 had large hour by hour variability and were not used.[2102] [p 418]

This drew a correction from NOAA’s Pieter Tans:

To illustrate how misleading Plimer is I made a plot of 3 years of all hourly data, with 2004 in the middle because Plimer discussed 2004. … In the plot, “selected” data means that we have used it in constructing the published monthly mean because those hours satisfy the conditions for “background” measurements. The red stripes are extremely close to the published monthly means. … Also plotted in purple-blue are all non-background data. If one constructs monthly means from ALL data, incl. non-background, one obtains the purple-blue stripes. The differences are only slight, with the seasonal cycle becoming a bit larger due to upslope winds, esp. during the summer.

Tans concludes that Plimer is a con man, but the story doesn’t end there. Plimer’s reference 2102 is ftp://ftp.cmdl.noaa.gov/ccg/co2/in-situ/. I analyzed the 2004 Mauna Loa data from there and found there were some minor errors in Plimer’s numbers: In fact, due to instrumental error 1103 samples had no data, 1097 were not used due to up slope winds, 655 had large variability within 1 hour and were not used and 881 had large hour by hour variability and were not used.

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One of the easiest way to tell plagiarism is when mistakes are carried forward by the plagiarist. In fact, some people actually put errors into such things as the Index or other sorts of databases. Then is the error is copied, they know that their database was copied also.
In this case, the error appears to come from a paper that directly refutes the exact point Plimer is trying to make. Awkward.
When people try to accuse researchers of manipulating data, data that others have been able to examine for years, they had better make sure they know what they are doing. There is no grand conspiracy of scientists because if these data had been manipulated to get certain results, other researchers would have gone “Great. Now I can get a paper demonstrating that they did it wrong.” We live for publications and being able to demonstrate where someone else went wrong is a great way to make a career.
The fact that this data has been vetted by others and found to hold up makes Plimer reasoning even more off kilter.

[Listening to: She Said She Said from the album "The Beatles]

I’ve been drinking it

If Dr. Seuss Designed Produce…

[Via Cosmic Variance]

…he would have invented the dragon fruit.

Look at it! It’s fantastic! And when you cut it open:

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Dragonfruit is in the Vitamin Water I have been drinking, at least one of the types. I had been a little afraid to check out hat it was but this is really a nice thing to see.

There are plants available. I wonder how well they would do in the Pacific NW?Protect from frost but I wonder if they could really grow.

[Listening to: Komm, Gib Mir Deine Hand from the album "The Beatles.]

Bad histones

from Wikipedia

Antibody ‘fixes internal bleeds’

[Via BBC News | Science/Nature | World Edition]

US scientists say they have discovered an antibody that could minimise the damage caused by major traumas.

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Histones are necessary for proper packaging of the very long chromosomes in the very small nucleus. They are also important in controlling gene expression. But I have to point out an error in the report that makes me want to search out the real paper.

It regulates the DNA, causing it to fold and form the characteristic double helix.

Histones have nothing to do with DNA and the double helix. DNA forms that structure by itself. Histones deal with higher oder packing of the DNA as it wraps around the histones.

So let’s look at a couple of other reports, as this BBC one has lost ,y confidence that it is reporting accurately. ScienceDaily gives us the actual press release, which does provide some better information.

Histones released from dying cells damage the lining of blood vessels. this may be the cause of some of the major problems we see following various traumas – internal bleeding into the surrounding tissue.

In fact, this sort of damage is what drives things such as sepsis. Sepsis can kill very rapidly, often from the huge response the body makes to try and fix things.

Few things have been found to be very effective against sepsis once it gets going. It can kill very rapidly and most of the therapy is palliative in nature, keeping the patient alive long enough for their body to deal with the damage.

An antibody therapy would be pretty straightforward. Infusion with the antibody would soak of the histones and thee damage they do would be reduced.

If this actually helps in a meaningful way, it could be a real breakthrough. Let’s just see what happens in humans.

To me, the really amazing fact is that histones do so much damage. I wonder just what the mechanism is. I’m waiting for this to turn up on CSI – the victim was injected with large histones which mimicked sepsis, resulting in the death of the victim.

Living by rumor

Making Stuff Up:
[Via Eschaton]

Get used to a neverending stream of horseshit.

Getting like the 90s again.

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What do facts matter when rumor is so much more useful? Some people will just spread any old rumor without giving any thought at all to its veracity. Some of them are even called journalists. But not by anyone who actually cares about things like the truth.

And these lies will stay with a whole lot of people because a supposed authority figure told them it was true. Even when revealed to be false. But you can be sure that emails detailing this thesis will be making the rounds.

I guess Snopes.com will always exist to deal with this sort of matter, as if any of these guys ever check the facts. Reality-based views of the world apparently just do not work for a sizable fraction of Americans.

Technorati Tags: Politics

If you kick an anthill, don’t whine about getting bit

Rules for Contrarians: 1. Don’t whine. That is all:
[Via Crooked Timber]

I like to think that I know a little bit about contrarianism. So I’m disturbed to see that people who are making roughly infinity more money than me out of the practice aren’t sticking to the unwritten rules of the game.

Viz Nathan Mhyrvold:

Once people with a strong political or ideological bent latch onto an issue, it becomes hard to have a reasonable discussion; once you’re in a political mode, the focus in the discussion changes. Everything becomes an attempt to protect territory. Evidence and logic becomes secondary, used when advantageous and discarded when expedient. What should be a rational debate becomes a personal and venal brawl.

Okay, point one. The whole idea of contrarianism is that you’re “attacking the conventional wisdom”, you’re “telling people that their most cherished beliefs are wrong”, you’re “turning the world upside down”. In other words, you’re setting out to annoy people. Now opinions may differ on whether this is a laudable thing to do – I think it’s fantastic – but if annoying people is what you’re trying to do, then you can hardly complain when annoying people is what you actually do. If you start a fight, you can hardly be surprised that you’re in a fight. It’s the definition of passive-aggression and really quite unseemly, to set out to provoke people, and then when they react passionately and defensively, to criticise them for not holding to your standards of a calm and rational debate. If Superfreakonomics wanted a calm and rational debate, this chapter would have been called something like: “Geoengineering: Issues in Relative Cost Estimation of SO2 Shielding”, and the book would have sold about five copies.

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Being truly contrary is a lot of work, something these guys seem to have missed. If you actually misrepresent what people say and believe, you should not be to surprised if they come back hard.

And if you try to go up against something with a lot of factual data behind it, you had better get your facts straight. Their apparent approach to being contrary – where they take a conventional wisdom and reflexively say it is not true, gee whiz, darn it – reminded me of this other exercise in taking a contrary position:

Technorati Tags: Environment, Science

Why Fox News needs fact checking

by Rob Lee

Fox News Outfoxes Itself:
[Via Talking Points Memo]

If you’ve had Fox News on today, you’ve seen them cranking up the indignation machine over a supposed new incident between the network and the White House. The claim is that the White House denied Fox the same access other networks had to a press briefing at the Treasury Department yesterday. But we’ve looked into it, and it turns out that’s not what happened. Christina Bellantoni has the details on how a miscommunication over the TV pool feed has Fox playing First Amendment victim.

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Fox News, and a ton of reporters that never bothered to find out what happened, spent Friday claiming foul. Yet, according not only to the White House but also to people who were there, it was nothing of the kind.

Looks like some MSM were punked. Like Rush and Obama’s thesis. Or it would seem so unless you also had a better memory.

What is amazing to me is how many so-called journalists just fell in line with Fox, needing no other verification, yet, when the Bush white House was excoriating MSNBC, the crickets made more noise than the MSM.

I would rather believe that most reporters are simply incompetent rather than they take their marching orders from their corporate owners. I think one reason the MSM are failing is that they no longer select for good reporters. Edward R. Murrow, Cronkite, Huntley, Brinkley etc. got to the top because they were good reporters.

No more. Actually being good is more likely to get you a quick boot out the door. Read a book called Good Work or follow the Good Work Project. They show again and again that the veteran journalists, the ones who mainly got into the field because of the work of the earlier great reporters, who wanted to help create an informed citizenry, are finding those principles are no longer wanted in their business.

What is wanted is a focus on the bottom line, on bread and circuses. Thus we get hours devoted to something that was an obvious hoax to many at the time, with no real investigation into that possibility at all during those hours. The only reason it took off was the admission of a child hours later.

Shiny sells. And explaining does nothing for the bottom line. In fact, outright lying works much better. Not too many years ago, Fox won an appeal in which they stated that they had a First Amendment right to lie. That there was no law forcing hem to tell the truth.

Fox fired two reporters who refused to allow statements that they knew to be false into a telecast. They were fired. They sued for unlawful termination, winning in a jury trial. But they lost on appeal. The court said that there was nothing illegal with Fox presenting falsehoods!

It is enough to make you think that anyone who believes Fox is a legitimate news channel also believes wrestling is a legitimate sport.

They have a right to be viewed as the entertainment channel they mostly are. But just as we would not follow WWE because it represented an unfiltered view of an athletic endeavor, Fox should not be viewed as an unbiased source of news.

‘The reality of a world without Princess Di’

On Today’s Edition of ‘Onion or CNN’ …:
[Via First Draft]

Horrific 120-Car Pileup A Sad Reminder Of Princess Diana’s Death
A.

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Satire seems more mainstream every day. So few people seem able to tell the difference. This was just too close to what CNN, Fox, etc. do almost every week.

Technorati Tags: General

More bad acid, man

by Sea_daddy
Climate Change – what’s worse than the heat?:
[Via Observations of a Nerd]

**A post about Climate Change as a part of Blog Action Day 2009**

When people talk about climate change, they, more often than not, talk about global warming. Yes, the effects of increased temperature will be diverse and generally bad for most creatures on Earth, including us. But the most dramatic effect of climate change won’t be due to the heat – it will be due to ocean acidification. I might seem biased (being a marine biologist and all), but trust me, the addition of carbon dioxide to the ocean and its subsequent effects will be far worse in the long run than a change in temperature. Not so sure? Let me explain.

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This is a great discussion of the science behind carbon dioxide and water. We could perhaps survive the heat but the acid could be far deadlier.

I’ve written about ocean acidification before (here, here, here, and here). This is more than just disappearing coral reefs. It is about the disruption of the ocean’s food chain from the bottom. The inability of plankton and other organisms to properly form a calcium shell has huge ramifications.

This Nature paper, from 2005, states:

In our projections, Southern Ocean surface waters will begin to become undersaturated with respect to aragonite, a metastable form of calcium carbonate, by the year 2050. By 2100, this undersaturation could extend throughout the entire Southern Ocean and into the subarctic Pacific Ocean. When live pteropods were exposed to our predicted level of undersaturation during a two-day shipboard experiment, their aragonite shells showed notable dissolution. Our findings indicate that conditions detrimental to high-latitude ecosystems could develop within decades, not centuries as suggested previously.

This is well within the lifetimes of many people alive. The ability of these organisms to properly grow and thrive will have impacts all the way up the food chain. How far is almost too scary to contemplate.

Because these organisms are a big part of the biological side of the carbon cycle. They also generate a lot of oxygen in our atmosphere. The loss of them would effect many of the normal cycles of the planet that we depend on.

We might survive but who really knows? Why take the chance?

Technorati Tags: Environment, Science