Chose a new project

from Wikipedia.

I think Stephen may have to start on another film:

In the July 2009 issue of Fantastique magazine, director Sommers had the following to say in an interview: “Steven Spielberg and I have a great script for When Worlds Collide. We just have to wait now because of Roland Emmerich’s 2012. It’s too close a project.”

2012 already did his movie and it will be almost impossible to top. It is too close a project.

[Some small spoilers follow]

I just got back from 2012 and it was so much better than I could have imagined. A great disaster movie has to have great special effects. 2012 does have those, with entire cities falling into the oceans.

But the good movies usually present something else. They present a series of postulates and provide examples to answer them.

How we as people should deal with the world when it completely changes, when things alter so far that they can not be the same again? Do we all panic and run around screaming? Or do we try and find something constructive to do?

Do we sit around pissing in our pants? Do we climb over everyone else and devil take the hindmost? Do we try and maintain our humanity or descend into purely animalistic violence?

All great questions for society today as we change from one phase to another, from Industrial Age to Information age, from fossil fuels to green energy, from exponential growth to sustainability.

2012 is a really well done lightweight movie but it does try and present some answers to these questions. That is why I think it may have a longer term impact than a simple popcorn movie might.

And as I was watching it, I was reminded a lot of When Worlds Collide. The causes of civilization’s destruction are different in the two movies and the scope of the special effects are not on par (the difference between an ‘A’ movie with 10s of millions to spend and a ‘B’ science fiction movie).

We have Danny Glover, as the President, suggest that perhaps they should have held a lottery to determine who gets a seat. That is exactly how ‘When Worlds Collide’ did it. 2012 took a different route to populate the arks. So it seemed to me that there was a wink at “When Worlds Collide” in 2012.

But a lot of the tropes are really similar. We have scientists who know what is happening, politicians dealing with the crisis, corrupt businessmen throwing their money, children in peril and a good-looking lead to sympathize with. We have arks to carry the survivors to a new world. We have love triangles.

The general sweep of the narrative is very close. The questions are similar, although answered slightly differently.

And in neither does the businessman make it on the ark while the good looking lead does. The third wheel of the triangle dies nobly. That is not a spoiler. We knew that was going to happen. There is a reason they are cliches.

But the reason 2012 may have any impact has to be more than simply great effects destroying the world. I mean, it does a great job doing that but it is the personal stories that really matter. Besides simply destroying everything, the reason for this sort of movie can rise above mediocrity is by how it answers those questions, what is the right way to react in the face of such terrible change.

Our stories are lessons, teaching us what our society expects of its members. 2012 does a remarkably good job presenting very strong examples of how to act through world-shaking change.

We can have the competent courage of John Cusack or Chiwetel Ejofor, the quiet dignity of Danny Glover, or the weaselly shouting of Oliver Platt. We can have John Billingsley, playing a minor scientific character, step up in his moment and utter the few words that allow the entire course of the narrative to shift 180 degrees. We can have George Segal, trying to call his estranged son for the last time or Johann Urb competently saving people’s lives while putting his a extreme risk.

The new ‘When Worlds Collide’ may have different special effects and a slightly different plot, but it will really cover the same narrative ground. Same questions and similar answers. Only it will be second and possibly travel on the same path that 2012 has blazed.

So I think it could end up like Deep Impact vs. Armageddon.

Not that either of those is as great a film of their type as 2012. But everyone remembers the narrative sweep of Armageddon while few do for Deep Impact. Similar narrative arcs are present in both, but Armageddon does so in ways that viscerally affect us while Deep Impact does not.

I’m afraid something similar would be in line for a remake of ‘When Worlds Collide.’ It is really hard to see how it could engage our senses with even better special effects for the end of the world, while doing a better job with its personal narrative.

What I would suggest is not to remake ‘When Worlds Collide” but to make the movie of the sequel, After Worlds Collide. No one has made a modern disaster movie that deals with the aftermath. In 2012, the three arks that carry the people left of humanity sail to Africa. Fade out. Independence Day – one final speech and fade out. The Day After Tomorrow – transfer everything to Mexico and fade out.

Tell us what happens next.

Tell us of how they manage to survive.What type of courage will be needed AFTER tremendous changes have altered the world? How does civilization actually survive and how does it look?

Tell us how that story should go. Because someday we are going to get past the problems we face. What should that world look like and what types of people do we want to be in it?

[Yes, I can not believe I wrote this much about a movie that should have been as slight as 2012. It is not meant to be a really deep movie and many characters are stereotypes. But they are cliches in the grand tradition of Jung and Joseph Campbell. There is a reason their actions become so important to us and why it is important to understand somewhat the overarching rationales for the narrative we are presented.]

[And yes, it is my ability to write these sorts of things about movies that helped raise my GPA at CalTech. Two quarters of classes where we watched movies and wrote about them. I got very good grades!]

Technorati Tags: General

A very useful parable

by jaycross
SuperFreakonomics and the “parable of horseshit”
[Via CEJournal]

In a review of the book in The New Yorker, she starts with what she calls a “parable” of malodorous patties. It’s the story of “horsecars” that once plied the byways of New York City on iron rails. This early form of mass transportation became wildly popular — too much so:

By 1880, there were at least a hundred and fifty thousand horses living in New York, and probably a great many more. Each one relieved itself of, on average, twenty-two pounds of manure a day, meaning that the city’s production of horse droppings ran to at least forty-five thousand tons a month. George Waring, Jr., who served as the city’s Street Cleaning Commissioner, described Manhattan as stinking “with the emanations of putrefying organic matter.”

[More]

She also notices something that others have seen:

To be skeptical of climate models and credulous about things like carbon-eating trees and cloudmaking machinery and hoses that shoot sulfur into the sky is to replace a faith in science with a belief in science fiction. This is the turn that “SuperFreakonomics” takes, even as its authors repeatedly extoll their hard-headedness. All of which goes to show that, while some forms of horseshit are no longer a problem, others will always be with us.

[Listening to: Precious and Grace from the album "The ZZ Top Six Pack" by ZZ Top]

A very long time to be around

from Wikipedia

Are Gross, Whalebone-Eating Worms Actually Older than Whales?
[Via Discover Magazine]

If ever a species got the disgusting name it deserved, bone-eating worms would be the one. Robert Vrijenhoek’s team discovered them five years ago eating the bones of a dead gray whale off California, and since then they’ve shown up in whalebones around the world. The worms don’t have mouths or anuses—instead, they rely on their bacteria to handle nutrient uptake and waste disposal. And according to a new study by Vrijenhoek in BMC Biology, there’s more to these strange sea-dwelling scavengers: They might have been around since before whales even existed, and are probably more numerous than we thought.

[More]

Perhaps they were once plesiosaur-eating worms? Someone check out some fossils.

They have some pretty disgusting scientific names, also. The Monterey Bay Aquarium has more.

I think Bradbury and Blish covered this

from Wikipdedia

Beyond Darwin: Vatican Conference on Aliens:
[Via The Sensuous Curmudgeon]

THINGS are out of this world at the Daily Telegraph, which has the ninth largest daily circulation among UK newspapers. A few days ago one of their stories inspired us to write Darwin, Evolution, and Alien Life.

Now, from that same source we bring you: The Vatican joins the search for alien life. Here are some excerpts, with bold added by us:

The Pontifical Academy of Sciences is holding a conference on astrobiology, the study of life beyond Earth, with scientists and religious leaders gathering in Rome this week.

For centuries, theologians have argued over what the existence of life elsewhere in the universe would mean for the Church: at least since Giordano Bruno, an Italian monk, was put to death by the Inquisition in 1600 for claiming that other worlds exist.

Alas, Giordano Bruno got torched for committing Thoughtcrime. For lots of the people we write about, those were the good old days. Let’s read on:

Among other things, extremely alien-looking aliens would be hard to fit with the idea that God “made man in his own image”.

Furthermore, Jesus Christ’s role as saviour would be confused: would other worlds have their own, tentacled Christ-figures, or would Earth’s Christ be universal?

There are people who truly worry about such issues. We continue:

However, just as the Church eventually made accommodations after Copernicus and Galileo showed that the Earth was not the centre of the universe, and when it belatedly accepted the truth of Darwin’s theory of evolution, Catholic leaders say that alien life can be aligned with the Bible’s teachings.

[More]

Some of my favorite science fiction stories deal with this same topic. In “The Man“, Ray Bradbury wrote of men landing on a new planet and finding out that Christ-like figure had just left. Seems he traveled from planet to planet bringing the gospel.

Probably the most ambitious story was written by James Blish, – A Case of Conscience. For if Christ exists on different planets, then so must the devil. Could the devil have created an alien race to bring destruction to mankind? Could the devil actually be creative rather than just working with what God had provided? Is Satan co-equal with God? This book is where I first heard of the Manichean heresy, something that provides continuing questions for mankind.

Even more so if there are other intelligent life in the Universe. I think it is great that the Catholic Church is at least addressing the idea. But what if an alien race has no god, is essentially atheistic. What happens then?

As for me, I’d just be happy to see some aliens.

Technorati Tags: General, Science

Dover stll ruffling feathers

Discovery Institute: Dover Derangement Syndrome:
[Via The Sensuous Curmudgeon]

THAT picture was first used here: Casey Luskin is Behe’s Parakeet, and it’s time to deploy it again.

Casey Luskin is our favorite among the neo-theocrats at the Discovery Institute’s Center for Science and Culture (a/k/a the Discoveroids), and his latest article at the Discoveroid blog only enhances our opinion of him: Misrepresenting the Definition of Intelligent Design.

The article is typical of Casey’s Discoveroid writing, long and agonizingly twisted, so we’ll excerpt only a small portion that contains the essence of his message. As most of you will recognize, his references to the “Dover trial” refer to the creationist fiasco resulting in the superbly reasoned opinion by Judge John E. Jones III, issued on 20 December 2005, in the case of TAMMY KITZMILLER, et al., Plaintiffs, v. DOVER AREA SCHOOL DISTRICT, et al., Defendants. That’s the 139 page opinion (pdf file). You may want to look at this Wikipedia article about the case, which has a great deal of worthwhile background information.

[More]

It is one of the odd ironies that the Discovery Institute, harbinger of so much creationist IDiocy, resides in liberal Seattle. Oh well.

The legal case being discussed in 4 years old. The legal position of the ID proponents was pretty much destroyed. But they continue to try and rehabilitate other aspects of ID.

But as the Curmudgeon’s post shows, they just do not really have a logical leg to stand on. ID is still built on negatives, as is most creationism. ‘If we do not know exactly every step involved for an explanation using natural means, then it MUST be because ID was involved.”

Read the whole post for some very nice discussion of the inability of ID to provide positive evidence. Because it really can not.

Technorati Tags: Science

Carl gets an award!

Congrats to Carl Zimmer!:
[Via Bad Astronomy]

My fellow Hive Overmind blogger Carl Zimmer just won the American Association for the Advancement of Science’s Kavli Science Journalism Award for writing in large newspaper, specifically the New York Times.

Yay!

Carl Zimmer won in the large newspaper category for a trio of articles he wrote for The New York Times on aspects of genetics and evolution. “I sometimes feel a little embarrassed that I like to write articles about the kinds of basic questions my kids ask me,” Zimmer said. “For the three stories I submitted, the questions were, “What’s a virus?” “What’s a gene?” and “Why do fireflies flash?” I had a marvelous time talking with scientists about the complex answers to those simple questions, and now, thanks to this award, I don’t have to feel at all embarrassed.” Zimmer previously won in the online category in 2004.

And he shouldn’t be embarrassed, because it’s exactly those kinds of questions that should be written about! Engaging the public is what more scientists should do, and if they did it as well as Carl the world would be a better place.

[More]

This is great news. Carl is one of the journalists who is not only a great writer but does an extremely good job connecting the world of science with the world the average person inhabits.

However, he has another trait that is even rarer. He makes science interesting to scientists.

Science writing can be very hard. Not only must one be able to synthesize work that one is not necessarily proficient in, one must also make it all worth reading. But what Carl so often does is to also capture why the science is interesting. He presents the excitement of the work in ways that can resonate well with other scientists. He does a wonderful job of exposing the human behind the science.

That is why Carl’s blog, The Loom, has been on my RSS aggregator since we were both writing blogs at Corante. (You can see some of my blogposts at my old Corante blog, Living Code, in the categories at the left)

Technorati Tags: Science, Web 2.0

Bugs in the stomach

from Wikipedia

Helicobacter pylori’s unconventional role in health and disease.:
[Via PLoS Pathogens]
Related Articles

Helicobacter pylori’s unconventional role in health and disease.

PLoS Pathog. 2009 Oct;5(10):e1000544

Authors: Dorer MS, Talarico S, Salama NR

The discovery of a bacterium, Helicobacter pylori, that is resident in the human stomach and causes chronic disease (peptic ulcer and gastric cancer) was radical on many levels. Whereas the mouth and the colon were both known to host a large number of microorganisms, collectively referred to as the microbiome, the stomach was thought to be a virtual Sahara desert for microbes because of its high acidity. We now know that H. pylori is one of many species of bacteria that live in the stomach, although H. pylori seems to dominate this community. H. pylori does not behave as a classical bacterial pathogen: disease is not solely mediated by production of toxins, although certain H. pylori genes, including those that encode exotoxins, increase the risk of disease development. Instead, disease seems to result from a complex interaction between the bacterium, the host, and the environment. Furthermore, H. pylori was the first bacterium observed to behave as a carcinogen. The innate and adaptive immune defenses of the host, combined with factors in the environment of the stomach, apparently drive a continuously high rate of genomic variation in H. pylori. Studies of this genetic diversity in strains isolated from various locations across the globe show that H. pylori has coevolved with humans throughout our history. This long association has given rise not only to disease, but also to possible protective effects, particularly with respect to diseases of the esophagus. Given this complex relationship with human health, eradication of H. pylori in nonsymptomatic individuals may not be the best course of action. The story of H. pylori teaches us to look more deeply at our resident microbiome and the complexity of its interactions, both in this complex population and within our own tissues, to gain a better understanding of health and disease.

[More]

We are used to thinking about bacteria on our skin, in our mouths or in our intestines. However the ability for bacteria to not only live in the acid of our stomachs but to also cause disease was a huge paradigm shift for researchers.

Helicobacter pylori is just such an organism. The researchers (Marshall and Warren) that demonstrated that this organism was responsible for stomach ulcers not only one the Nobel prize but also took part in one the the great examples of self-experimentation in modern history.

In order to demonstrate that Helicobacter was responsible, Marshall drank a beaker of the bacteria. He became very ill within a few days and the presence of the bacteria was found in his stomach. A course of antibiotics not only reduced his gastritis but also removed the bacteria.

This story is one of the great examples of how researchers can go against conventional wisdom. They went up against dogma that people had learned for almost a century. They were originally ignored. They did very good, basic work, published in peer-reviewed journals, changed everyone’s minds and won the Nobel Prize.

Whenever anyone tries to say that there is a conspiracy of researchers preventing the truth from coming out, all I do is think of Marshall and Warren. If you have the data, if you are right, you will overcome any conventional wisdom. That is how science works,

And you could probably win the Nobel Prize and have your career set for life. Wouldn’t you think that some young hotshot out there would try to do just that?

But the key is that they have to have the data. Simply being contrarian will not work.

Technorati Tags: Science

Cassava genome in hand

by Tatters:)
Researchers complete draft genome sequence for cassava:
[Via EurekAlert! - Biology]

(University of Arizona) A $1.3 Million grant from Bill & Melinda Gates Foundation will fund the next phase of research that is critical to global food security.

[More]

The cassava is a very important foodstuff. However, it requires a tremendous amount of processing and does not keep well.

Having its gene sequence will be very helpful in developing varieties that are more useful. With so many sequencing technologies out there all looking for a convenient way to demonstrate their worth, I expect we will see a lot more of these sorts of sequencing projects.

Technorati Tags: Science

Vito, you’re still blocking

by Yury Cortés
The New York Times Columnist Who’s Helping To Ruin The Future [Monday Hate]
[Via io9]

Why is John Tierney so skeptical, and yet so gullible? The New York Times’ science columnist is one of the most vocal global-warming doubters in the media, but when it comes to Ray Kurzweil’s Singularity and geo-hacking, he’s suddenly wide-eyed.

People often lump Tierney together with George Will, as global-warming doubters at major newspapers who use somewhat specious arguments to downplay the scientific consensus that we’re slow-cooking our planet. But Tierney’s position as the Times’ science columnist gives him more authority than Will’s as a random TV pundit. But also, the thing I find fascinating about Tierney is that even as he goes to great lengths to paint the evidence about global warming as mere hype, he’s also eager to buy into the hype whenever there’s a claim that new technology will deliver us to a beautiful future, without having to make any hard choices. It’s hard not to believe the two things are related.

Reading Tierney’s columns and blog posts on global warming, a few things become clear. He’s a global warming skeptic, rather than an out-and-out denier. (In one blog post, he says he believes there’s “some risk” that global warming will be a danger.) But he’s given tons of exposure and legitimacy to outright deniers, including some groups with ties to the oil industry. And he’s done a lot to paint the scientific consensus on global warming as pure hype and conformism.

In Tierney’s world, the reason the majority of scientists agree that global warming is a worsening crisis is dick-measuring. In a column on Obama’s science advisor, John Holdren, Tierney spends most of the column quoting Roger Pielke, a climate researcher who’s been one of the most vocal critics of the idea that the polar ice caps are melting. According to Pielke, scientists present conclusions about global warming as definitive not because the data supports them, but just to boost their own “authority in the political debate” and tarnish their opponents.

[More]

I have noticed this also. People who dispute climate change but accept all sorts of ‘woo’ with very little scientific underpinnings.

Here he ignores a lot of hard data to follow along with one of those ‘theories’ that posits exponential curves continuing forever. That is a fun thought experiment but there is nothing to believe that this particular curve will continue.

But it sure is fun speculating. And that is what attracts some people where actually dealing with real science does not. Science tends to abhor pure speculation because it has to deal with reality.

We saw the same thing in Superfreakonomics, where fun speculation with geoengineering was touted more than the hard facts of climate change. It is the old Tinkerbell Effect, where if we just beleive hard enough,the World, I mean Tink, will get better.

We all know about wishes, horses and beggars. Trying to ignore the hard thoughts of realty with the wistful joys of speculation is not a way to fix things. It just stifles our real efforts to find solutions. It makes for fun comedy but not for good policy. I think someone is blocking their true feelings about the Tattaglia Fami…, I mean climate change.

[Listening to: Something in the Way (Live) from the album "MTV Unplugged in New York: Nirvana" by Nirvana]

Keep on screening

by KaCey97007

Rethinking cancer screening?
[Via Respectful Insolence ]

Here we go again.

I see that the kerfuffle over screening for cancer has erupted again to the point where it’s found its way out of the rarified air of specialty journals to general medical journals and hence into the mainstream press. This is something that seems to pop up every so often, much to the consternation of lay people and primary care doctors alike, often trumpeted with breathless headlines along the lines of “What if everything you knew about screening was wrong?

It isn’t, but some of it may be. The problem is the shaking out process. I’ll try to explain.

Over the last couple of weeks, articles have appeared in newspapers such as the New York Times and Chicago Tribune, radio networks like NPR, and magazines such as TIME Magazine pointing out that a “rethinking” of routine screening for breast and prostate cancer is under way. The articles bear titles such as A Rethink On Prostate and Breast Cancer Screening, Cancer Society, in Shift, Has Concerns on Screenings, Cancers Can Vanish Without Treatment, but How?, Seniors face conflicting advice on cancer tests: Benefit-risk questions lead some to call for age cutoffs, and Rethinking the benefits of breast and prostate cancer screening. These articles were inspired by an editorial published in JAMA last month by Laura Esserman, Yiwey Shieh, and Ian Thompson entitled, appropriately enough, Rethinking Screening for Breast Cancer and Prostate Cancer. The article was a review and analysis of recent studies about the benefits of screening for breast and prostate cancer in asymptomatic populations and concluded that the benefits of large scale screening programs for breast cancer and prostate cancer tend to be oversold and that they come at a higher price than is usually acknowledged.

Read the rest of this post… | Read the comments on this post…

[More]

It is easy to read the headlines and think that screening does not work. It does but we also need to recognize that just doing more screening does not necessarily help if we do not really understand all the facets underlying the disease being screened for.
It turns out that a significant minority of breast cancers resolve on their own. We really do not have a good way of knowing which ones have to be treated now and which would resolve without treatment. Some cancers might be very slow growing and present a very small chance of mortality. But, again, we can not really tell the difference, so all get treated the same.
As the blog post states:

So what’s the solution? Should we give up on screening?

I’ll answer the second question with an emphatic absolutely not. There is no doubt that screening can save lives; the problem is that we’re doing it “bigger” and “badder” and not necessarily better or smarter, using more or less a one-size-fits-all approach when a more tailored approach might actually be necessary. Also, we’re using 20th century technology, when 21st century technology might be able to find a way out of these conundrums. Here’s where I (mostly) agree with Esserman et al. We need to change how we screen for common cancers using the latest advances in biochemistry, molecular biology, and technology to differentiate which lesions are most likely to be cancer and which are not, which cancers are likely to progress to the point of threatening a patient’s life in their remaining lifespan and which ones are not.

We need to improve our screening approaches by having a better understanding of all the biology involved, including the specific biology that an individual possesses. We will get there but it may be a little confusing until then.

The comet’s the thing

<i>by Charleston (South Carolina) County School District CAN DO Project.
it’s a comet! it’s a meteor! no, it’s a piece of rna!
[Via Research Blogging - Biology - English]

What do you get when you take pyrimidine molecules, freeze them in a vacuum to -340°F, then expose them to ultraviolet radiation you’d find in space? Think about it for a second. If you took a few extra credits in a college biology class, you may remember that your DNA contains purines and their chemical [...]…

Nuevo, M., Milam, S., Sandford, S., Elsila, J., & Dworkin, J. (2009) Formation of Uracil from the Ultraviolet Photo-Irradiation of Pyrimidine in Pure H

O Ices
. Astrobiology, 9(7), 683-695. DOI: 10.1089/ast.2008.0324   Formation of Uracil from the Ultraviolet Photo-Irradiation of Pyrimidine in Pure H

O Ices

[More]

It is really interesting to read about organic chemistry that can take place in the vacuum of space, at such low temperatures and under UV irradiation at levels that should be very destructive to most complex molecules.

Yet, in this experiment, some very important biomolecules could be formed. The key seems to be the presence of water, which not only protects the molecules from UV but also permit the reactions to occur.

Perhaps Fred Hoyle’s panspermia hypothesis has some real validity for the appearance of Earth-bourne life.

[Listening to: Humanoid Boogie from the album "The Doughnut In Granny's Greenhouse (Remastered)" by Bonzo Dog Band]

Science is wonder-full (not a misspelling)

byNASA, ESA, The Hubble Key Project Team, and The High-Z Supernova Search Team
License to Wonder
[Via Olivia Judson]

Yes, science relies on facts, but also on speculation and inspiration.

[More]

This is a really nice discussion regarding two, somewhat divergent aspects of doing scientific research. Most people are used to the inductive reasoning aspects of science – understanding the specific in order to understand the general.

An large part of science is made up of assembling the millions of small facts and data points into a cohesive understanding of the world around us. The answer is methodically arrived at by the slow accumulation of information.

But sometimes, and this is often where the wonder of science comes from, deductive reasoning takes precedence. Here we go from ‘general’ principles to the specific. We can make up an answer and see how well it fits the data.

In the example used by Judson, Watson and Crick took the general principles of chemistry to create a structure first, and then saw if it could explain the specific data from X-ray crystallography, while Franklin was trying to use the data only. With each wrong structure, they got closer to the right one.

In some ways it is a backwards way to go to get the accurate description of Nature. It can not always be used, as our imagination so often comes up with all sorts possibilities that are simply wrong. It requires scientists with very good understanding of general principles. And it usually requires extremely good data of the highest order to reveal Nature’s secrets in this fashion.

Watson and Crick had the internal knowledge to keep their conjectures within realistic bounds. And they had access to data no other speculator had. They ‘won’ the race because they had access to Franklin’s data while Linus Pauling did not. Thus their conjectures could be self-corrected in ways that no one else’s was.

Darwin is an example of someone who displayed both aspects of science in one tremendously important person. He collected data of the highest order. HIs understanding of the principles permitted him to see the general aspects of natural selection, which permitted him to gather even more data to support the specific ramifications of the theory.

Science often moves in contrapuntal cycles of inductive and deductive reasoning, traversing from specific to general to specific and so on, each cycle moving us closer to a fuller description of the world around us.

This is the fascinating wonder of science. To move from close-up to panorama and back again, each time gaining new knowledge of Nature.

Isaac Asimov said:

The most exciting phrase to hear in science, the one that heralds new discoveries, is not ‘Eureka!’ (I found it!) but ‘That’s funny …’

But the real thrill to a scientist is when we can complete the ellipsis by stating. “Oh, so that’s how it works” as we get a little chill down our spine realizing that Nature is just so amazing! That is when science is just so full of wonder. (Thus my choice for a title.)

[Listening to: Francene from the album "Rancho Texicano: The Very Best Of ZZ Top (Disc 1)" by ZZ Top]

Make it a pub

by gailf548
Participation Value and Shelf-Life for Journal Articles:
[Via The Scholarly Kitchen]

Discussion forums built around academic journal articles haven’t seen much usage from readers. Lessons learned from the behavior of sports fans may provide some insight into the reasons why.

[More]

The scientific discussions that many researchers have found the most productive are often those sitting around a table in a informal setting, like a pub. These discussions are often wide-ranging and very open. They often produce really innovative ideas, which get replicated on cocktail napkins.

Some of the best ideas in scientific history can be found on such paper napkins. Simply allowing comments on a paper does not in any way replicate this sort of social interaction. But there already online approaches that do. We call them blogs.

Check out the scientific discussions at RealClimate, ResearchBlogging or even Pharyngula. Often the scientific discussions replicate what is seen in real life, with lots of open discussion about relevant scientific information.

If journals want to create participatory regions in their sites, they might do well to mimic these sorts of approaches. David Croty at Cold Spring Harbor has such a site. Although it has not reached the popularity of RealClimate, it is a nice beginning.

I would think that research associations, with an already large audience of members, would have an easier time creating such a blog, one that starts by discussing specific papers but is open to a wide ranging, semi-directed conversation.

Technorati Tags: Open Access, Science, Web 2.0

Fun to read

Book reviews by email. Slate has been doing this while, printing emails and responses about books. This one, dealing with the excellent new book, Denialism, is really very interesting. It reminds me of some of the best correspondence exchanges form the 19th Century.

I have not been a big fan of Mooney’s book, Unscientific American, because I think his focus is misplaced. But his dialog with Spector is quite fun to read. The ‘dueling’ emails, with some really great insights, allowed each other to respond in ways that were not only fun to read but extended the discourse.

Producing swine flu vaccine

by themissiah

Barbara Ehrenreich on the swine flu supply problem

[Via Effect Measure]

I first read Barbara Ehrenreich in 1971 when she wrote The American Health Empire: Power, Profits, and Politics with her (then) husband John Ehrenreich (Health PAC, 1971). She was by then a PhD in cell biology (Rockefeller University) and anti-war activist. We traveled in the same circles and I knew her slightly at the time. Her next book, Witches, Midwives, and Nurses: A History of Women Healers (with Deirdre English) was a new reading of women in medical history. It was an influential text in the emerging women’s health movement. Since then she has published many books, several making the best seller lists and throughout an astute and still influential observer. Now she has penned a brief comment on the the alleged swine flu vaccine supply problem and who’s to blame. And I find myself in complete agreement with her:

[More]

There is a really nice discussion in the comments about many aspects of the shortage and the place for Pharma in vaccine production. The big problem with the delivery of so many doses is actually one that most Big Pharma could have answered honestly 6 months ago with a ‘gray’ answer, rather than the black and white one we all wanted.

First, the normal seasonal vaccine had to be made. This is already a massive enterprise, one that has resulted in shortages in years past when things got messed up in the process.

Second, an additional 120 million doses needed to be made and packaged using the H1N1 virus. While the process should have been just like normal seasonal flu, there was one problem, one that has popped up before and resulted in some shortages – the production of vaccine per egg was lower than normal So it required even more specially treated fertilized chicken eggs to produce the large number of doses than normal.

Most research personnel, when asked what they could produce, might have said 120 million, assuming things remain the same as usual. The assumption gets removed by the time upper management hears it and the government does not really want to hear the full answer. Everyone has an incentive to say “yeah. 120 million doses.”

Sometimes, yields are not as expected. This can usually be overcome by just using more eggs. But I would expect that there really were no more eggs available in the timeframe needed.

So, when things start heading south, people do what people do. Hope something fixes the problem. Make sure they are not the ones who get the blame. One way to do that would be to extend the effectiveness of the doses by using adjuvants or reduced doses.

And we have seen attempts at both of those. I think they really hoped that they could get an effective 120 million doses by using such measures. It was only in the last month of so that they realized that even these would not be effective.

As often happens in human endeavors, hope was the plan.

One big problem is that market forces for vaccine development are not always useful for producing the best vaccine for the public. Millions of cheap doses are not something that is attractive to many companies. And they have little incentive to develop new and better technologies which can cost billions and take a long time for their costs to be recouped.

Thus we are still using 50 year old, or more, technology for almost all of our vaccines. This needs to change.

Because someday, an avian flu virus will produce a pandemic. And little vaccine will be able to be produced.

Avian flu kills birds. Chicken eggs are from birds. Trying to produce flu vaccine in chicken eggs using avian flu results in very, very (if any) vaccine. Luckily, the current pandemic flu permits some vaccine to be produced, even at lower levels.

If it was avian flu, we might not be able to produce any vaccine in chicken eggs at all.

We need some of the better approaches that are wending their way through approval.

[Listening to: Skateaway from the album "Private Investigations - The Best Of" by Dire Straits]