Most people work the greater part of their time for a mere living; and the little freedom which remains to them so troubles them that they use every means of getting rid of it.

- Johann Wolfgang von Goethe

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The 24th edition of the Four Stone Hearth is up on Moneduloides

Gene Genie Edition #40 is up on Human Genetics Disorders

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A nice article in the HHMI Bulletin:

Slowly, however, the culture is changing, not only through blogs but also by means of open notebooks, open publishing, and other interactive models. Those involved call it Science 2.0, an effort to harness the capabilities of the Internet to help scientists communicate better among themselves as well as to the public at large.

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And, while on the topic of "Science by press release", it struck me that announcing intentions of future research is a Good Thing. Isn't that what we are all talking about - Open Science?

If you signal in advance that you are working on something, you allow others to either move on to something else so as not to duplicate the effort, or to speed up their work in order to scoop you, or to give you a call and offer to collaborate. The second option is likely to be rare and localized in a few research fields that are hugely competitive (e.g., cancer research). The first and the third options are much more likely.

I think the problem is that the researchers are doing it wrong. They are placing those announcements in wrong places using the wrong mechanism. When you go to a press release page of a University, or to Eurekalert or ScienceDaily, you expect to find press releases about the stuff that has been already done and published. The meaning of the word "published" may be completely different in 50 years, but it is not today. So, when you browse press release you expect to find only reports on published work. Seeing that a press release is about work yet to be done in the future is, of course, going to be jarring. Not because it is not nice to know what people are up to, but because they are using a wrong venue to do this - an article about an intention is masquerading as an article about a done deal.

I think researchers and their press officers need to figure out a different method and venue for publishing intentions. A blog?

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We are in the final stretch! The submissions have been trickling in all year, and a little bit more frequently recently, and many more over the past couple of weeks, so, if you have not done it yet, it is high time now to dig through your Archives for your best posts since December 20th 2007 and submit them. Submit one, or two, or several - no problem. Or ask your readers to submit for you.

Only submissions received through this form are valid.

Then take a look at your favourite bloggers and pick some of their best posts - don't worry, we can deal with duplicate entries. Do not forget new and up-coming blogs - they may not know about the anthology - and submit their stuff as well.

As we did last year, we encourage you to also send in original poems and cartoons.

Keep in mind that the posts will be printed in a book! A post that relies heavily on links, long quotes, copyrighted pictures, movies, etc., will not translate well into print.

The deadline is December 1st, 2008. - just two weeks to go!

Below are submissions so far. Check them out and get inspired. If you see that one of your posts is at an old URL and you have since moved, re-submit with the new URL (perhaps re-post it if necessary).

Posting URLs in the comments does not work. Go down to the bottom of this post (or to the sidebar of this blog) and click on the "Submit to OpenLab2008" button. Or click here.

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One time I went to a museum where all the work in the museum had been done by children. They had all the paintings up on refrigerators.

- Steven Wright

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There are 13 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:

Mass Mortality of Adult Male Subantarctic Fur Seals: Are Alien Mice the Culprits?:

Mass mortalities of marine mammals due to infectious agents are increasingly reported. However, in contrast to previous die-offs, which were indiscriminate with respect to sex and age, here we report a land-based mass mortality of Subantarctic fur seals with apparent exclusivity to adult males. An infectious agent with a male-predilection is the most plausible explanation for this die-off. Although pathogens with gender-biased transmission and pathologies are unusual, rodents are known sources of male-biased infectious agents and the invasive Mus musculus house mouse, occurs in seal rookeries. Molecular screening for male-biased pathogens in this potential rodent reservoir host revealed the absence of Cardiovirus and Leptospirosis genomes in heart and kidney samples, respectively, but identified a novel Streptococcus species with 30% prevalence in mouse kidneys. Inter-species transmission through environmental contamination with this novel bacterium, whose congenerics display male-bias and have links to infirmity in seals and terrestrial mammals (including humans), highlights the need to further evaluate disease risks posed by alien invasive mice to native species, on this and other islands.

GP-9s Are Ubiquitous Proteins Unlikely Involved in Olfactory Mediation of Social Organization in the Red Imported Fire Ant, Solenopsis invicta:

The red imported fire ant (RIFA), Solenopsis invicta, is an invasive species, accidentally introduced in the United States that can cause painful (sometimes life-threatening) stings to human, pets, and livestock. Their colonies have two social forms: monogyne and polygyne that have a single and multiple functional queens, respectively. A major gene (Gp-9), identified as a putative pheromone-binding protein on the basis of a modest amino acid sequence identity, has been suggested to influence the expression of colony social organization. Monogyne queens are reported to possess only the GP-9B alleles, whereas polygyne queens possess both GP-9B and GP-9b. Thus, both social forms are reported to express GP-9B, with GP-9b being a marker expressed in polygynes but it is absent in monogynes. Here, we report two types of polygyne colonies, one that does not express GP-9b (monogyne-like) and the other expressing both proteins, GP-9B and GP-9b. Given their expression pattern, GP-9s are hemolymph proteins, which are more likely to be involved in the transport of lipids and small ligands within the homocoel. GP-9B existed in two forms, one of them is phosphorylated. The helical-rich content of the protein resembles the secondary structures of a beetle hemolymph protein and moth pheromone-binding proteins. An olfactory role is unlikely given the lack of specific expression in the sensillar lymph. In marked contrast to GP-9s, a chemosensory protein, SinvCSP, is demonstrated to be specifically expressed in the antennae. Within the antennae, expression of SinvCSP is restricted to the last two segments, which are known to house olfactory sensilla.

The Neural Basis of Object-Context Relationships on Aesthetic Judgment:

The relationship between contextual information and object perception has received considerable attention in neuroimaging studies. In the work reported here, we used functional magnetic resonance imaging (fMRI) to investigate the relationship between aesthetic judgment and images of objects in their normal contextual setting versus images of objects in abnormal contextual settings and the underlying brain activity. When object-context relationships are violated changes in visual perception and aesthetic judgment emerges that exposes the contribution of vision to interpretations shaped by previous experience. We found that effects of context on aesthetic judgment modulates different memory sub-systems, while aesthetic judgment regardless of context recruit medial and lateral aspects of the orbitofrontal cortex, consistent with previous findings. Visual cortical areas traditionally associated with the processing of visual features are recruited in normal contexts, irrespective of aesthetic ratings, while prefrontal areas are significantly more engaged when objects are viewed in unaccustomed settings.

A Green Fluorescent Protein with Photoswitchable Emission from the Deep Sea:

A colorful variety of fluorescent proteins (FPs) from marine invertebrates are utilized as genetically encoded markers for live cell imaging. The increased demand for advanced imaging techniques drives a continuous search for FPs with new and improved properties. Many useful FPs have been isolated from species adapted to sun-flooded habitats such as tropical coral reefs. It has yet remained unknown if species expressing green fluorescent protein (GFP)-like proteins also exist in the darkness of the deep sea. Using a submarine-based and -operated fluorescence detection system in the Gulf of Mexico, we discovered ceriantharians emitting bright green fluorescence in depths between 500 and 600 m and identified a GFP, named cerFP505, with bright fluorescence emission peaking at 505 nm. Spectroscopic studies showed that ~15% of the protein bulk feature reversible ON/OFF photoswitching that can be induced by alternating irradiation with blue und near-UV light. Despite being derived from an animal adapted to essentially complete darkness and low temperatures, cerFP505 maturation in living mammalian cells at 37°C, its brightness and photostability are comparable to those of EGFP and cmFP512 from shallow water species. Therefore, our findings disclose the deep sea as a potential source of GFP-like molecular marker proteins.

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Malcolm Gladwell has a new book out and critics all home in on different aspects of it....

MICHIKO KAKUTANI:

Much of what Mr. Gladwell has to say about superstars is little more than common sense: that talent alone is not enough to ensure success, that opportunity, hard work, timing and luck play important roles as well. The problem is that he then tries to extrapolate these observations into broader hypotheses about success. These hypotheses not only rely heavily on suggestion and innuendo, but they also pivot deceptively around various anecdotes and studies that are selective in the extreme: the reader has no idea how representative such examples are, or how reliable -- or dated -- any particular study might be.

Louis Bayard:

The problem with having your theory in hand from the beginning is that you have to slough off whatever data don't fit. There is, in fact, a small-print proviso attached to each of Gladwell's theoretical constructs: "Except when it doesn't." "The Tipping Point": A small-scale social shift can generate sweeping societal change ... except when it doesn't. "Blink": Great decision making happens on impulse ... except when it doesn't. (Or, in the case of racial profiling, shouldn't.)

STEPHEN KOTKIN:

Academic journals brim with disputes as theories are contested by opponents. Mr. Gladwell revels in the flaws of Lewis Terman's hoary work on I.Q. -- because it argues for innate ability -- and he gives voice to Terman's critics. But he omits discussing objections to the work of the social scientists he chooses to rely upon. As in a magic trick, he wows the audience, using bold claims and exquisite storytelling, but we see no arguments that would detract from his brilliant spectacle.

Michael Nielsen:

Given these examples, how should we think about the relationship between great achievement and the 10,000 hour rule?

It's certainly clear that great achievement is possible without putting in 10,000 hours of deliberate practice. Indeed, I'd go so far as to suggest that it's perhaps even relatively common among the greatest discoveries within science, and would not be surprised if this were also true in some areas of technology.

I believe it's a mistake to focus on building up 10,000 hours of deliberate practice as some kind of long-range goal. Instead, pick a set of skills that you believe are broadly important, and that you enjoy working on, a set of skills where deliberate practice gives rapid intrinsic rewards. Work as hard as possible on developing those skills, but also explore in neighbouring areas, and (this is the part many people neglect) gradually move in whatever direction you find most enjoyable and meaningful. The more enjoyable and meaningful, the less difficult it will be to put in the time that leads to genuine mastery.

Amanda Marcotte:

Still, there's no way around it---the books sounds foremost like a dissection of privilege. And he shoved it into a space that's usually hostile to that message, that successful people owe it more to their background than their inherent superiority over people who aren't as successful, but likely as smart and creative. Unfortunately, according to this review, Gladwell indulges his urge to wank off on pet theories a little too much, using rice paddies to explain why some Asian nations best the rest of the world in math scores. I think the likelier explanation is more mundane, which is that Asia began to rise in the world markets at precisely the time that economies started to be driven more and more by science and technology, and they reacted to that environment by putting the focus on math in schools. Americans, alas, just don't care as much. But I'm curious to read the book and see if Gladwell makes his case.

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Specialization Does Not Predict Individual Efficiency in an Ant:

Social insects, including ants, bees, and termites, may make up 75% of the world's insect biomass. This success is often attributed to their complex colony organization. Each individual is thought to specialize in a particular task and thus become an "expert" for this task. Researchers have long assumed that the ecological success of social insects derives from division of labor, just as the increase in productivity achieved in human societies; however, this assumption has not been thoroughly tested. Here, I have measured task performance of specialized and unspecialized ants. In the ant species studied here, it turns out that specialists are no better at their jobs than generalists, and sometimes even perform worse. In addition, most of the work in the colony is not performed by the most efficient workers. So the old adage "The Jack of all trades is a master of none" does not seem to apply to these ants, suggesting that we may have to revise our understanding of the benefits of colony organization.

A Novel Gene Family Controls Species-Specific Morphological Traits in Hydra:

Closely related animal species share most of their genes, and only minor morphological differences allow us to tell them apart. The genetic basis for these differences may involve minor changes in the spatial and temporal activity of transcription factors--"regulator" genes--which are surprisingly conserved throughout the animal kingdom. However, every group of animals also has a small proportion of genes that are extremely variable among closely related species or even unique. Such genes are referred to as "novel," "orphan," or "taxonomically restricted." Their functions and origins are often obscure. We have found that a family of novel genes is responsible for morphological differences between two closely related species of fresh water polyps called Hydra. A secreted protein encoded by a novel gene regulates the way in which tentacles develop. Our data indicate that novel genes may play a role in the creation of novel morphological features, thus representing one way how evolution works at the genus level. Appearance of novel genes may reflect evolutionary processes that allow animals to adapt in the best way to changing environmental conditions and new habitats.

The Making of a Compound Inflorescence in Tomato and Related Nightshades:

Among the most distinguishing features of plants are the flower-bearing shoots, called inflorescences. Despite a solid understanding of flower development, the molecular mechanisms that control inflorescence architecture remain obscure. We have explored this question in tomato, where mutations in two genes, ANANTHA (AN) and COMPOUND INFLORESCENCE (S), transform the well-known tomato "vine" into a highly branched structure with hundreds of flowers. We find that AN encodes an F-box protein ortholog of a gene called UNUSUAL FLORAL ORGANS that controls the identity of floral organs (petals, sepals, and so on), whereas S encodes a transcription factor related to a gene called WUSCHEL HOMEOBOX 9 that is involved in patterning the embryo within the plant seed. (F-box proteins are known for marking other proteins for degradation, but they can also function in hormone regulation and transcriptional activation) Interestingly, these genes have little or no effect on branching in inflorescences that grow continuously (so-called "indeterminate" shoots), as in Arabidopsis. However, we find that transient sequential expression of S followed by AN promotes branch termination and flower formation in plants where meristem growth ends with inflorescence and flower production ("determinate" shoots). We show that mutant alleles of s dramatically increase branch and flower number and have probably been selected for by breeders during modern cultivation. Moreover, the single-flower inflorescence of pepper (a species related to tomato, within the same Solanaceae family) can be converted to a compound inflorescence upon mutating its AN ortholog. Our results suggest a new developmental mechanism whereby inflorescence elaboration can be controlled through temporal regulation of floral fate.

The Chilling Effect: How Do Researchers React to Controversy?:

Can political controversy have a "chilling effect" on the production of new science? This is a timely concern, given how often American politicians are accused of undermining science for political purposes. Yet little is known about how scientists react to these kinds of controversies. Drawing on interview (n = 30) and survey data (n = 82), this study examines the reactions of scientists whose National Institutes of Health (NIH)-funded grants were implicated in a highly publicized political controversy. Critics charged that these grants were "a waste of taxpayer money." The NIH defended each grant and no funding was rescinded. Nevertheless, this study finds that many of the scientists whose grants were criticized now engage in self-censorship. About half of the sample said that they now remove potentially controversial words from their grant and a quarter reported eliminating entire topics from their research agendas. Four researchers reportedly chose to move into more secure positions entirely, either outside academia or in jobs that guaranteed salaries. About 10% of the group reported that this controversy strengthened their commitment to complete their research and disseminate it widely. These findings provide evidence that political controversies can shape what scientists choose to study. Debates about the politics of science usually focus on the direct suppression, distortion, and manipulation of scientific results. This study suggests that scholars must also examine how scientists may self-censor in response to political events.

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On the Seed Magazine site...:

ScienceBloggers discuss the advantages of open science and debate the necessity of the current peer-review system.

Nice! But of course I'd say that. Just to emphasize, in case the article does not make it clear enough, Open Access and changes in peer-review will both be a result of the Age of the Web, but the two are not necessarily tied to each other in each individual instance of a publishing venue. Different journals, pre-print sites, etc., are experimenting with OA and with changes in peer-review in different ways and at different rates, the two processes being independent from each other at this stage in history.

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How To Make A Barometer In Few Easy Steps With Household Items - Celebrity bloopers here

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ObamaCTO (independent of the Obama transition team) is a site for recommending ideas to Obama's new Chief Technology Officer. You can go and suggest ideas or vote on ideas already there.

I just voted for this suggestion - "Require open access for publicly-funded research". You should vote for it as well and add a comment if you care about this issue (and I bet most of my readers do).

See also Moving Toward a 21st Century Right-to-Know Agenda: Recommendations to President-elect Obama and Congress, report (pdf)

(via)

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Growing up, we (meaning: kids growing up in Yugoslavia) all learned about the strangest animal of our country - the cave-dwelling White Olm Proteus anguinus, that we called Man-fish (Covecja ribica).

But what do I know? Darren Naish knows much more about it - and after reading his post (an updated version of his older post) you will see for yourself what a cool and crazy animal this is.

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The geriatric leaders of the government of Italy are making fools of themselves by trying to regulate bloggers, i.e., get them to register with the government, pay taxes, be liable for what they write, etc.:

The law's impact would turn all bloggers in Italy into potential outlaws. This could be great for their traffic, I realise, but hell on the business aspirations of an Italian web start-up, not to mention any tech company that wants to sell its blog-publishing software in Italy, or open a social network here. In addition to driving out potential tech jobs, the stifling of free speech also can have a dramatic chilling effect on all forms of free expression, the arts and scholarship.

Or, to keep it simple:

Only someone who is utterly clueless on how the internet works, or even what it is, could come up with such an idea.

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If I had to select one quality, one personal characteristic, that I regard as being most highly correlated with success, whatever the field, I would pick the trait of persistence. Determination. The will to endure to the end, to get knocked down seventy times and get up off the floor saying, 'Here comes number seventy-one!'

- Richard M. Devos

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There is quite a lot of chatter around the intertubes about changes in the communication environment that happened between the last and this election and how those changes may be affecting the way the new White House communicates to people as well as how the new White House will receive communications from the people.

A lot of people are impatient - they want to see everything in place right this moment. Easy, guys! The inauguration is on January 20th. Until that time, Bush is the President and the Obama communications folks have time to think through, design and implement communication channels that we will definitely NOT see until the inauguration or a little bit later. So, you can pore over Change.org all you want in search for hints of the future, but it is unlikely you will see anything truly informative until January 20th at the earliest.

But in the meantime, speculation abounds.

This NYTimes article lays down the arguments pro and con (and check out the FriendFeed discussion as well - quite telling to see how some techie folks do not understand this is not a technological problem at all).

The problem is this: if a President says or writes something that is recordable - and technology is irrelevant, it could be handwriting, a magnetophone or an 8-track - it can be subpoenad by Congress. The article explores the tensions between the need for a President to have confidentiality about important matters of the state, and the need to open up new mode of communications fit for the 21st century mindset of the Facebook generation (Note: "facebook generation" has nothing to do with the actual Facebook site, or with a particular age - it is a frequently-used shorthand term for a mindset of continuity and openness in communication).

This is why Bush stopped using e-mail the day he became the President. Everything that the President says or writes becomes official record. New technology allows one to communicate too much and too informally. Chatting with friends over e-mail becomes a potential liability for the officials of such high ranking.

What is new is that Obama is the first President with that "facebook generation" mindset of constant, open communication, as opposed to a bubble-boy, smoke-filled back-rooms, secretive types that the previous 43 Presidents were. The laws, customs and trappings of his new job are going to be conflicting with his modern instincts towards openness. And people are starting to talk about a potential need to alter these out-dated laws in order to allow Obama to lead a more transparent government.

We shall see what actually happens, but we can expect, at least until/unless there are legal changes, that all the e-mailing will be done by staffers and not Obama himself. He is also going to be the first President in history to keep a laptop on the Oval Office desk (doesn't this sound quaint?)! He will likely use the computer not to broadcast or communicate anything himself, but only to get informed (perhaps via an RSS Feed).

Another confusion in online chatter about potentially new communication is that people do not make a distinction between centrifugal (broadcasting, outwards) communication and centripetal (listening, inwards) communication.

The best example is probably this Slate article. I think Disckerson is confused. The new Prez will experiment with a number of new ways to communicate. Some of it is inside out, some is outside in. Posting the radio address on YouTube is the part of inside out. It is not the only tool and should not be looked at in isolation. Yes, it is part of his PR, but it is targeted to a set of people who past Presidents did not and could not reach: exactly the same people who are the most likely to use OTHER channels of communication to talk back to him. What Dickerson did in this text was sorta like focusing on a Food Chain and not seeing the Food Web (or forest for the trees, choose your own metaphor) - a lack of ecological thinking by a member of an old media class that thinks too linearly.

Brian Solis has collected probably some of the best ideas on the entire issue, and you should also read the various links and ideas in Josh Bernoff's post and Lidija Davis' post.

Obama's first radio address was also filmed. The movie was posted on Change.org, and also on YouTube:

People like Dan Farber and Allen Stern are worried about favouritism - why YouTube and not other video services? Answer: if the only place they place a video is Change.org, then someone else will put it on YouTube, perhaps edited, with open comments, who knows what else. By posting it on YouTube themselves, the Obama comms folks are putting a degree of control over the message. In the next few months, they may decide to do the same on several other video-hosting services. This was just the first address, and YouTube, being such an 6000lbs gorilla (or is it an elephant in the room?), is the obvious place to go and test the waters first before embarking on a more ambitious program.

Also, a more ambitious program requires building the communications team. Which requires hiring people, including a Chief Conversation Officer, perhaps this guy (or me - I can do it, that's my job right now anyway). That process has just started. People like Secretary of State are much more important positions to fill first. So, have some patience....

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More movies here

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Democrats had the means (a majority in both Houses, committee chairmanships, investigative powers) to launch one investigation after another of George W. Bush and his cronies between 2007 and the end of 2008, on violation of constitutional protections against cruel and unusual punishment, not to mention international law, and even to introduce impeachment legislation. But they showed remarkable restraint. Andrew Sullivan: Any reasonable person examining all the evidence we have - without any bias - would conclude that the overwhelming likelihood is that the president of the United States authorized illegal torture of a prisoner and that the evidence of...

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