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The Science of Mind-Reading: SVMs Extract Intentions from Neural Activity (video) [Developing Intelligence]

For the basics about multivariate fMRI "mind-reading" techniques, see the video below. Some of it is based on this 2007 Haynes et al paper from Current Biology, described in more detail following the video.

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Benni Hemm Hemm [Dynamics of Cats]

Benni Hemm Hemm

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Dita Von Teese's The Science of Sexy... [On Becoming a Domestic and Laboratory Goddess]

Dr. Isis commenter and friend of the blog Eppendork just left this video in the comments section of another post. It is so amazing I thought it warranted its very own post.

Video 1: This is exactly what I imagine it will be like when I make the big breakthrough that gets me the cover of Science and my Nobel. Fantastic shoes and all.

Eppendork, you're amazing and you can work in Isis's lab any day. But, you had better bite your damned tongue next time you think of writing:

Dr Isis - I do believe she out does you on the shoes this time!

Them's fightin' words, little missy.

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Quick. What’s pink and has stripes? [Stranger Fruit]

Ed reports on a putative new species of iguana that has been found on the Galapagos archipelago. Darwin saw two species (one marine and one land). We now have two additional land species, the Barrington land iguana Conolophus pallidus and this new one which is found only Volcan Wolf, the northernmost volcano of Isabela Island.

Paper is in press with PNAS (DOI: 10.1073/pnas.0806339106).

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Vote early, vote often... [Respectful Insolence]

...for me as Best Medical/Health Issues Blog.

At the very least, put me past Junkfood Science!

While you're at it, vote for the Best Science Blog. There are two fellow ScienceBloggers (PZ and Greg Laden) in contention, as well as one of my blog buds, Steve Novella of Neurologica and another of my favorite blogs, Bad Astronomy. A tough choice.

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Ping-pong with a creationist [Pharyngula]

Would you believe that Nick Lally has responded — well, reacted might be the better word — to our criticism of his silly letter? This is a reply to one of the editors to whom he had sent his original mail.

Dear "Yo", for lack of a name....since you have not yet given me yours while you put me out there for others to read.

With the exception of a few bright guys who challenged my facts, the rest of the responses were lame, personal and disrespectful. So typical of you atheists.

But I must admit, I did get a laugh of myself for miss-typing "Louis Pasteur".

But for now, allow me to explain my position on only one of the responses I read....and later I will respond to the other responses that are worthy:

Your writer wrote: "Actually, we do have transitions between single-celled and multi-cellular organisms. We do have transitions between invertebrates and vertebrates -- look up protochordates sometime. Your ignorance of these basic facts is not evidence"

I tell you the following about Choanoflagellates: These one cellular animals are designed with a propulsion system that is similar to an outboard motor. They have a propeller (whip) shaft, etc, etc. Just look at this diagram and you would think you were looking at a motor. [he included a standard cartoon of the bacterial flagellum]

Now, just take away any one part of this motor and ask yourself: Could this machine work? The obvious answer is "no". So my question to you atheists is simple: How could a one cellular animal that houses a complex design come into existence with all its parts working simultaneously through a natural process called mutation and natural selection?

Isn't it clear to you that this machine was designed instantaneously by intelligence with a futuristic purpose...and a finished product in mind?

Yo, I tell you the truth: There is a designer. His name is God. I may not understand all there is to Him right now, but one day we all will understand.

Typical creationist, we should say. Note the usual evasion, focusing on the disrespect given to him rather than the content. Note also the goal-post shifting. He said there were no transitions between single-celled and multicellular organisms; I gave him one, the choanoflagellates, so what does he do? Ducks and runs and throws out a different claim, in this case falling back on the tired old ID claim that the bacterial flagellum could not have evolved (it certainly could have: it has homology to other organelles, and there are pathways by which it could have evolved).

Oh, wait…bacterial flagellum? Choanoflagellates do NOT have the rotary flagellum of bacteria. They have the eukaryotic flagellum (also called an undulopodium) which is completely different. Eukaryotic flagella do not rotate, instead consisting of a bundle of fibers that slide past one another to generate a bend in the whole structure.

He really doesn't know what he's talking about. And he was a science teacher?

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The dangers (?) of public funding of drug trials [Neuron Culture]

Ezra Klein relays Jim Manzi's worry that public funding of drug trials

exposes you to the inverse problems of the current system. Namely, "bureaucrats and politicians tend to have enormous career risk from an unsafe drug introduction, but almost none from a rejected drug that would have been effective had it been introduced...[it] would likely result in fewer new drugs being brought to market."

There's a bit to this. But it misses something important: The biggest problem with the present system may not be that deeply unsafe drugs are approved but that too many drugs that carry modest safety issues (and most drugs carry some safety issues) but little if any benefit are approved because their benefits are overstated. The risk-benefit ratio gets misrepresented, in other words, not so much because risks are understated (though that is done too) as because the benefits are oversold.

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Linnaeus' Legacy No. 15: Sorting it all out [Greg Laden's Blog]

This is my favorite web carnival, and this is the best version of it yet, owing to the outstanding submission we have this month!

Welcome to the 15th Monthly edition of the blog carnival Linnaeus' Legacy. I thought about being cute and fancy for this edition of the carnival, but instead, I decided to be very systematic.

(de - dum - dum)

So we will work our way from foundations to theory to taxonomy, and within the taxonomic sphere we will sort out all the organisms by type and deal with them as such appropriately. And then, we will have one little item related to extinction. The place where diversification ends.

On with the show:

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Adolph Hitler: So cute you just want to pinch his fat little cheeks.... [Greg Laden's Blog]

Heath and Deborah Campbell had three children. They named them:

• JoyceLynn Aryan Nation Campbell
• Honszlynn Hinler Jeannie Campbell
• Adolf Hitler Campbell

That, right there, would be child abuse. Do you not agree?

The story is making the rounds (h/t: McDuff) because it is little Adolph's third birthday and the local shop-rite (supermarket) refuses to provide the family with a cake enscribed "Happy Birthday Adolph Hitler."

The story can be found here and here.

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Quick Isis Facts.... [On Becoming a Domestic and Laboratory Goddess]

There's a lot on the brain of the domestic and laboratory goddess and so much I'd like to blog about. Unfortunately, I am giving a seminar Friday and have an abstract due this week for a meeting I have been itching to attend, so you will have to make do with a quick post from me tonight. Rest assured that I have an "Ask Dr. Isis" post in the works that is going to blow your mind. It's already been blowing my mind and it's not even done.  In the meantime, here are a few fast facts about my day:

• This morning I completely lost my shit with Mr. Isis.  I feel kind of bad about it.  I feel even worse that, while I was losing my shit, Little Isis was unsupervised, got into the nightstand, and filled his right ear with KY.
• I think my punishment for not properly supervising my child has been some science failures.  Things that seemed like great ideas at 9 am ended up being poor ideas at 9 pm.  Crap.
• I have been in my running clothes for about an hour now and I promised myself I would run today.  Seriously, I'm going to.
• Last night I ate about 1400 calories worth of Raisinets.  The aftermath of 1400 calories worth of Raisinets is very, very similar to a hangover.

Alright.  I am going to run.  Really, I am.  Really.
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Zombie French Fries from Hell [Greg Laden's Blog]

Well, from McDonald's, actually.

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42nd Street Times Square Mezzanine Subway Art, Detail 4 [Living the Scientific Life (Scientist, Interrupted)]

tags: Times Square, 42nd street Times Square, Times Square Mural, subway art, NYC through my eye, photography, NYC

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Pram Good, Stroller Bad...What? No wonder this is a "report". [DrugMonkey]

A recent post up at the Frontal Cortex points approvingly to a study of strollers, prams, toddlers and parental conversation. Jonah Lehrer concludes:

It would be nice to see this research filter down to stroller manufacturers, so that even cheap plastic strollers allow the infant to interact with the parent.

Very interesting. Must be strong evidence, no? And after all, we all want our little wackaballoons to be as smart and advanced as possible, do we not?

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Tecnology Tidbits [Greg Laden's Blog]

Two killer items for you today:

Create your own personal font

Check out the new Google Hacker Search:

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The Senator Larry Craig Gay Sex Bathroom Stall Is NOT For Sale! [Greg Laden's Blog]

This important story was broken by the Minnesota Independent.

The agency that runs the airport refused an apparently serious offer to buy the men's room stall made famous by Craig's 2007 conviction for disorderly conduct in a sex-solicitation sting operation by the airport police. The Metropolitan Airport Commission (MAC) spurned the $5,000 offer, which arrived by certified mail, according to MAC spokesperson Patrick Hogan.

Details are here.

And here is some related video content. Includes explicit demonstration of gay sex solicitation toe tapping.

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...you can check out any time you like, but you can never leave... [A Blog Around The Clock]

Hotel Scienceblogs, that is. Do you remember David Dobbs and the blog Smooth Pebbles here on Sb? Well, David left the Borg, blogged for a while at his own non-Sb version of Smooth Pebbles and now he's back - with a new blog and a new title - Neuron Culture.

Welcome back, SciBling!

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Water Protection and 2008 in Pictures [Chaotic Utopia]

Well, here it is the first Monday in 2009, and judging by my inbox, which suddenly jumped to life, it is definitely time to get back to this poor site update. I was ready to dive in, anyhow, since the holidays are finally past, and my son returns to school tomorrow. (Yay!) Besides, tomorrow is Chaotic Utopia’s birthday--my first blog post was January 6, 2006. So, as a present to my blog, I’ll be giving it that much needed facelift. (I’ll admit, I was stymied by a few design choices, but I’ve finally moved past that and know what I want to do.)

In the meantime, check out this series of photographs compiled by the Boston Globe. The entire collection of 120 pictures is incredible. Some are amazing, others shocking, but all are excellent works of photography. This one was my favorite:

In this photo by Irfan Khan (AP), workers are releasing the first of four million black balls into Ivanhoe Reservoir, in order to prevent a chemical reaction between chlorine from water treatment, natural bromide, and good old California sunshine. Thus, they are hoping it will protect the Los Angeles water supply from the carcinogenic product: bromate. It reminds me of a giant plastic pool covering, separated into individual bubbles.

You can find many more great photos in these three articles.

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Today's carnivals [A Blog Around The Clock]

20th Carnival of the Blue is up on Biomes Blog

Carnival of the Green #161 is up on Tao of Change (a blog very local to me, here in Carrboro, NC).

Cabinet of Curiosities #12 is up on Walking the Berkshires

Edition #12 of Berry-Go-Round is up on Foothills Fancies

Festival of the Trees # 31 is up on Rock Paper Lizard

Encephalon #61 is up on SharpBrains

Change of Shift Volume Three - Number Thirteen is up on Nurse Rached's Place

Four Stone Hearth the New Year edition is up on Testimony of the spade

Gene Genie #41 is up on ScienceRoll

Cancer Research Blog Carnival #17 is up on Blind.Scientist

Carnival Of Space #83 - The Antipodean Edition is up on Astroblog

The 46th Carnival of Mathematics is up on Walking Randomly

Medicine 2.0 Carnival #35 is up on ScienceRoll

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Call for submissions for 'Praxis' and 'The Giants' Shoulders' [A Blog Around The Clock]

The next edition of Praxis will be arriving on January 15th 2009 at Pod Black Cat.

The 7th edition of The Giant's Shoulders will be held on January 15th 2009 at The Questionable Authority.

Start submitting your entries.

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Conservatives in 2009: As Scroogish as they were last year [Thoughts from Kansas]

Ned Ryun, baby boy of the discredited and disreputable former Congressman Jim Ryun, wonders "do we really need 600,000 new govt. employees?":

Appears that Obama is promising 600,000 new government employees. That is just slightly troubling.

Ryun is currently employed at a conservative group that trains people to run for public office, so if he's really troubled by all that government out there, he might reconsider his current profession. And I will mention only in passing that George W. Bush, for whom Ned used to work as a writer, is the first president since World War II to see government job growth outpace private sector job growth. But my issue is not Ryun's hypocrisy.

My issue is his apparent willingness to elevate partisan ideology over human compassion. Because those 600,000 new jobs that he doesn't think we need represent less than half the jobs that have been lost in just the first ten months of the last year of the Bush administration:

The government reported more grim news about the economy Friday [November 7], saying employers cut 240,000 jobs in October - bringing the year's total job losses to nearly 1.2 million.

According to the Labor Department's monthly jobs report, the unemployment rate rose to 6.5% from 6.1% in September and higher than economists' forecast of 6.3%. It was the highest unemployment rate since March 1994.

"There is so much bad in this report that it is hard to find any silver lining," said Morgan Keegan analyst Kevin Giddis. …

With 1,179,000 cuts, the economy has lost more than a million jobs in a year for the first time since 2001 - the last time the economy was in a recession. With most economic indicators signaling even more difficult times ahead, job losses will likely deepen and continue through at least the first half of 2009.

"It's pretty clear that we're in a recession," said Robert Brusca, economist at FAO Economics. … "We may be in a severe recession, in which case these job numbers are not even big yet," he said, suggesting monthly job loss totals could grow in excess of 300,000 an unemployment could rise to around 7%.

Heck, those 600,000 jobs lost represent only slightly more jobs than those lost in November, 2008, when nonfarm payroll employment fell by 533,000:

Job losses were large and widespread across the major industry sectors in November.

Both the number of unemployed persons (10.3 million) and the unemployment rate (6.7 percent)continued to increase in November. Since the start of the recession in December 2007, as recently announced by the National Bureau of Economic Research, the number of unemployed persons increased by 2.7 million, and the unemployment rate rose by 1.7 percentage points.

Now, Ned is entitled to think that the size of the government should decrease. I happen to think that the size of the government isn't so important as what it does. I also care a lot less about the question of whether we need 600,000 new government employees than I do about whether we should have 600,000 more people with jobs. When the economy is shedding jobs at a record pace, hiring people makes all kinds of sense.

From his cushy place on wingnut welfare, Ryun can afford to place ideology over the needs of millions of people. Unfortunately for the millions of people suffering through the second Bush recession, ideology doesn't put food on the table, it pays poorly and the benefits stink.

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Franken is the man [Pharyngula]

The state canvassing board certified the results this afternoon; Al Franken is our senator, by 225 votes. Also, the Minnesota supreme court has denied Coleman's request to reconsider some rejected ballots, but of course he's going to sue.

Forget all that, though, and welcome our new senator. Not many can do this:

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Bailing out the sciences [Thoughts from Kansas]

Science's policy blog reports:

[T]he House Democratic Steering and Policy Committee has invited not only noted economists Martin Feldstein, Mark Zandi, and Robert Reich [to discuss the economic recovery bill] but also Maria Zuber, a professor of geophysics of the Massachusetts Institute of Technology and principal investigator on GRAIL, a NASA mission to measure variations in the moon's gravitational field.

House Speaker Nancy Pelosi, who will kick off the discussion, has made it clear that "investing in technology and innovation should be part of any economic recovery plan," says a spokesperson for the committee, a message that Zuber is expected to emphasize. Also making that point will be engineer Norman Augustine, former CEO of Lockheed-Martin and author of the well-regarded 2005 National Academies' report Rising Above the Gathering Storm: Energizing and Employing America for a Brighter Economic Future that called for a $20 billion investment in science education and research.

This makes ten tons of sense. Not only do research labs employ keep a lot of hooligans safely off the streets, the research that comes from those labs has a huge effect on future economic growth. While there can be a long lag between when you spend a dollar on research and when you get the payoff, it's important to be looking past the immediate crisis. Boosting labs in academia and in industry will keep a lot of people employed, and will create the innovations that will require the factories and industries of tomorrow. We also need to pour money into SUPERTRAINS and bridges and weatherizing houses and erecting wind and solar farms. Those big construction projects will employ a lot of people, but once we've built SUPERTRAINS and bridges and weatherized millions of homes, there have to be new, well-paid, secure jobs for people to go into.

And that's what investing in science gives you.

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Intriguing [Zooillogix]

A little background here: Japanese squid monster moisturizer tentacle woman video. Yup.

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The Minnesota Recount is Over [Greg Laden's Blog]

As many of you have already heard, the recount process in Minnesota to determine the outcome of the Senatorial race is over, and Al Franken has been certified as winner.

There is now a review period of seven days during which any voter in the state of Minnesota. Including me, Al Franken, whomever, can sue for an Election Challenge. Although both Secretary of State Ritchie and I have expressed the opinion that Norm Coleman, who lost the race, is unlikely to issue such a challenge, the press and even Coleman's lawyers have suggested that a challenge will in fact be filed by three o'clock tomorrow (Tuesday) afternoon.

However, you know the following is true: The best chance Coleman has to turn what he calls Franken's "Artificial Lead" around is from a set of 650 as yet uncounted rejected absentee ballots. There are two things working against Coleman in regards to these ballots. First, the process is over and they were not counted. Asking for them to be counted is not a matter of bringing in something new. They have already been not-counted by a process determined by the same court to which Coleman would issue the challenge, and some members of that court were also on the canvassing board that certified the election this afternoon. So the chances of a challenge being accepted by this court is easily estimated at zero point zero zero zero. Or less.

Second, in order for Al Franken's official 225 vote lead to be erased by counting these absentee ballots, there would have to be a very strong bias in these 650 ballots that Coleman wants counted. I calculate that there is about a two to three percent probability that counting these votes would change the outcome in Coleman's favor. That may seem like a lot, but the chances of having the votes being counted to begin with is about zero.

Coleman really has two choices: Proceed with the challenge and end his political career or don't proceed and have a chance of continuing in Minnesota politics.

Which, I would guess, would involve his run for governor in two years. As a democrat, of course.

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Dolphins Wear Sponge Nose Guards to Forage [Zooillogix]

In the 1980's female dolphins were first seen using sponges as a foraging tool to protect their noses while digging at the ocean floor for prey. New research, however, conducted by a team from Georgetown University (go Hoyas, biotches!) has taken a much more comprehensive look at this use of tools by dolphins.

So they can use tools. But this dolphin has clearly not yet mastered the use of female contraception.

Professor Janet Mann of Georgetown looked at a population of bottlenose dolphins in Shark Bay in Western Australia to observe the sponging behavior. Only female dolphins were witnessed using sponges as a means to protect their noses while disturbing the ocean floor, and only 11% seemed to display this behavior. When they located prey, the dolphins would drop the sponges and attack it, only to pick back up their tools when they were finished. Professor Mann concluded that females learned this behavior while still weaning (while male dolphins preferred to socialize during this time). She also found that the female dolphins who used sponges (spongers), "were more solitary, spent more time in deep water channel habitats, dived for longer durations, and devoted more time to foraging than non-spongers."

Previously, chimpanzees were the only vertebrates observed habitually using tools to hunt for prey, so this study has significant ramifications. In fact, Professor Mann told the Daily Mail that the spongers spend "more time hunting with tools than any nonhuman animal." Probably more than some human animals as well!

Her research can be found in December's issue of PLoS ONE.

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Oxford is better than Cambridge [Stoat]

To look at, anyway.

[ps: for anyone who watched while I put this together: apologies!]

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The pink Galapagos iguana that Darwin never saw [Not Exactly Rocket Science]

One hundred and seventy-four years ago, Charles Darwin first set foot on the Galapagos Islands aboard the Beagle. Since then, the islands and the unique species they house have been a source of inspiration for many an evolutionary biologist. Even so, it is gratifying to see that even now, on the bicentennial of Darwin's birth, the Galapagos have not yet finished yielding their secrets.

During Darwin's five-week stint on the Galapagos, he observed two types of iguana. One was a marine version that, uniquely for lizards, swam and fed in the ocean, and the other was a cactus-eating landlubber, which we now know to be two separate species. But Darwin's adventures never took him as far north as Volcan Wolf, the northernmost volcano of the large Isabela Island. And that's why he never described the distinctive pink land iguana that lives only on that volcano.

To be fair to Darwin, even scientists who actually visited Volcan Wolf failed to spot the pink land iguana for the better part of a century. Despite its striking pink head and black-striped flanks, it was only discovered when park rangers accidentally stumbled across it in 1986. They must have thought that they were the victims of some elaborate practical joke.

Atheists will no doubt chuckle at the existence of a pink animal that's so hard to find it may as well be invisible. The fact that it lives in the Galapagos of all places is just the icing on the irony-cake. But I digress.

The elusive iguana has since been christened the "rosada" form, after the Spanish word for "pink". And according to Gabriele Gentile, it's a species in its own right, genetically distinct from the more common yellow versions. Gentile's team of international scientists from Italy, the USA and Ecuador have analysed the pink lizard's genes to show that it is a relict, older even than many of the current Galapagos Islands themselves.

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Voodoo fMRI [The Frontal Cortex]

I just wanted to draw attention to two fantastic blog posts that describe a new paper by Edward Vul, a grad student at MIT, and colleagues at UCSD. The first post comes from Vaughan over at MindHacks:

I've just come across a bombshell of a paper that looked at numerous headline studies on the cognitive neuroscience of social interaction and found that many contained statistically impossible or spurious correlations between behaviour and brain activity.

Social cognitive neuroscience is a hot new area and many of the headline studies use fMRI brain imaging to look at how activity in the brain is correlated with social decision-making or perception.

This new analysis, led by neuroscientist Edward Vul, was inspired by the fact that some of these correlations seem to good to be true, and so the research team investigated. The abstract of their study is below, and it's powerful stuff - indicating that many of the results are due to flawed analyses.

If you're not familiar with neuroimaging research it might be useful to know that what a 'voxel' is before reading the abstract.

Essentially, brain scanners digitally divide the scanned area into a block of tiny boxes and each one of these is called a voxel (think 3D pixel).

This allows the scans to be analysed by comparing the activity or tissue density in each voxel to another measure - which could be the same voxel during another scan, or it could be something entirely different, such as a measure of emotion or social decision-making.

The Neurocritic has much more. One noteworthy aspect of this paper is that it calls out a few dozen brain scanning studies for very public criticism. (Vul is a brave grad student.) After reading his analysis, I'm rather amazed that these many of these studies got through the peer-review process, and ended up getting published at such eminent journals!

This latest paper continues what might be called the "fMRI backlash," although the backlash is really being driven by people within the brain scanning field who are simply trying to improve the quality of the average fMRI paper. Here's how I described the backlash in a Globe article earlier this year:

The scanners, these critics say, excel at measuring certain types of brain activity, but are also effectively blind when it comes to the detection of more subtle aspects of cognition. As a result, the pictures that seem so precise are often deeply skewed snapshots of mental activity. Furthermore, one of the most common uses of brain scanners - taking a complex psychological phenomenon and pinning it to a particular bit of cortex - is now being criticized as a potentially serious oversimplification of how the brain works. These critics stress the interconnectivity of the brain, noting that virtually every thought and feeling emerges from the crosstalk of different areas spread across the cortex. If fMRI is a window into the soul, these scientists say, then the glass is very, very dirty.

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Obama and Self-Inflicted Negotiation: More of the Same? [Mike the Mad Biologist]

Democrats won the election handily. Why are we rolling ourselves? I thought Obama would be smarter than the usual Democrat and not negotiate against his own position on behalf of the Republicans. Apparently, I was wrong, since that seems to be the impetus behind making 40% of the 'stimulus' tax cuts:

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Can sign language really help babies get along better? [Cognitive Daily]

Baby sign language is all the rage these days. Upscale day-care centers and nanny services promote it as a better way of understanding what babies want. Babies have been known to reliably produce signs as young as 5.5 months, and studies have shown that they reliably produce signs significantly earlier than spoken words. As we've reported here, there is no evidence that teaching sign language delays spoken language development.

But is formal sign training effective? Some studies about baby sign language have been quite informal, with parents and caregivers inventing makeshift signs to "talk" to their babies about bodily functions, favorite toys, desires for comfort, and so on. Other studies have focused exclusively on laboratory settings, with little follow-up to see if the signs acquired in the lab have any practical use.

A team led by Rachel Thompson has now combined these two approaches to explore whether formal laboratory training can have a positive impact on real babies' lives -- and their parents and caregivers.

The researchers systematically taught a modified ASL sign to Heather, a 10-month-old with Down syndrome. Heather learned to say "please" to ask for a toy. A 6-month-old normally-developing child, Betty, was taught a different sign, "more," to ask for more food.

The training for each baby was similar, but I'll take you step-by-step through Betty's training. Remember, a six-month-old is just barely able to sit up on her own, much like Nora in this photo:

In fact, I think Nora's a little older than six months here -- but this photo was still taken several months before she uttered her first word.

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Dad - 5 Years On [The Quantum Pontiff]

It is nearly impossible for me to believe that five years have passed since you passed away.

And hey, we're still waiting for Mt. Shasta to explode, could you get working on that?

One day, when I was an undergraduate at Caltech, I received a package in the mail from my father. In it was a small yellow squash with red dots painted onto it along with a strip of paper which read "what is this?" Well, Caltech is full of some pretty smart people, so we spent a few days trying to reason what this strange package that my father sent was. Small. Yellow. Squash. With red dots. Huh? After a few days I gave up and gave him a call. Okay, dad, what is that damn thing? "Oh, that's simple," he said, "It's an itsy bitsy teeny weeny yellow polka dot zucchini!"

We miss you. Even your bad jokes.

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Beliefs, Knowledge, Articles, Databases. [Common Knowledge]

I've been working on some text for a series of papers lately. I'm writing the core of a book proposal and working through the ideas around the knowledge web and the knowledge economy, and thought I'd post some interim thoughts here.

Knowledge is a funny thing. Philosophers have spent eons debating it. I'm not going to figure it out here - in fact, the conclusion that I wasn't going to figure it out played a big role in my choosing not to go to graduate school. But on the web, we have these things that are kind-of-knowledge. Databases. Journal articles. Web pages. Ontologies.

Taken together, these things are somewhere in the epistemological chain. But the act of digitizing them does some strange things...they start to form an observable, computable network, a knowledge web of sorts. And in a knowledge web, we have to understand a important conceptual transformation that knowledge itself needs to be treated as something similar to software, something upon which computing happens and depends - and the implications of that transformation.

The great revolutions of the internet, the web, and free software were all predicated on access to sources and standards - a mix of technical and legal access. The internet didn't really have to deal with the law, as TCP/IP didn't really affect copyright. The web ignored copyright from a legal perspective, but actively encouraged viewing and copying from a technical perspective. Free software embedded legal freedoms inside the technical access concept.

But knowledge is different, as the vast majority of the canon is already embedded in creative works protected by copyrights. Thus, we have to unlock some content if we're going to reformat it into something that can in turn be treated as an interim step along the way to knowledge, and then used as cyberinfrastructure. This is why Open Access is so crucial. Whatever knowledge is, a lot of it is locked behind paywalls, copyright licenses, or trapped in lousy formats from a machine perspective.

But - if we have access - if we can take the individual facts described in papers and turn them into modelable knowledge, or at least precursors to knowledge, we convert those facts into infrastructure for construction into something bigger, for composition into structures that software can use.

This transformation is already under way in the life sciences. Most of the valuable CI data in the life sciences has been hand-curated out of journal articles into more structured sources like the Kyoto Encyclopedia of Genes and Genomes, or the Human Protein Reference Database, or the Information Hyperlinked Over Proteins, and on and on.

This needs to be accelerated and industrialized, as the human-readable paper is the least valuable format of knowledge from a cyberinfrastructure/CI perspective. But this requires an understanding of access to the knowledge canon as a fundamental lever of CI construction in a knowledge web. Unfortunately most of these databases tend to have copyright or contractual restrictions that make it impossible to build on them as infrastructure (particularly non-commercial restrictions or restrictions on redistribution in federated or integrated knowledgebases). That's why open access to databases is essential as well.

We are lucky to have vast amounts of public domain databases that are, from a CI perspective, un-networked. The scientist needs to open a dozen or more tabs in a browser and use her own mind to integrate the results. That's lousy. But it's a natural outcome of the web not integrating databases the way it integrates documents, and at least the legal terms let us start to integrate.

There are competing philosophies about how to deal with the integration - I follow the one that believes again that software is the right metaphor for dealing with knowledge integration, and that data integration is a plausible first place to start working on knowledge integration. It's certainly better than getting stuck in an infinite loop arguing about what knowledge is. It's a funny place to come back into ontological realism after nearly 20 years away from the academy but this approach indeed demands a certain amount...because you're dealing with database records that need to be reconciled, not ideas like "gene" and so on, and if you're going to write code about them realism helps. But I digress. Back to software integration.

The way we integrate software in free software is via the *distribution* - a community using a standard set of kernel interfaces to knit together multiple software packages. This is a model for data integration, and the SC Neurocommons project is the first one that I know of - released in October 2008 - and we're already seeing some encouraging early returns (I love the version that a user installed on the Amazon cloud). The idea is to let users who like our modeling and ontological work simply expose a version of their database using our standards, and then any user or community that wants to add that database to the distribution can do so with minimal effort, just like adding a new software package to a linux distribution.

Note that we are assuming from the beginning that everyone has a different idea of knowledge - people will disagree with our models, and we've pre-emptively guaranteed the right to "fork" knowledge like software so that each community can craft its own solution based on our kernels.

This is all a way of trying to leverage techniques we've seen work in the service of complex systems creation by distributed inputs. It might work - I hope it does. It might also be an evolutionary step along the path. But clearly we need some evolution away from the human-readable paper and the standalone database as containers for the things we know, or the things we believe. The information space is simply too big for any one brain to process any more, and Google simply isn't as efficient for science as it is for culture...

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Carnivalia [Living the Scientific Life (Scientist, Interrupted)]

The latest Carnivalia has been published for you to dig your teeth into.

Bobo Carnival of Politics is weird: the host spends a fair amount of space telling me that I am wrong about Bush being history's worst president by claiming that Bush will be recognized as one of the best presidents -- OMG. Seriously. Just like the religious wingnuts among us, this guy has an obvious fantasy life that overrides all reality and reason. Anyway, be sure to go over there and chew him a new one!

Movie Monday, issue 88. This blog carnival links to everything about film!

Europe Travel blog carnival, where they link to one of my photoessays from Finlandia. Seeing that photoessay reminds me to continue publishing these photoessays (along with my London photoessays) now that I have some flickr space to store my hosted images.

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Horrible English weather [Stoat]

Its all rather manky here: cold, thin snow semi-melted by rain and refrozen. Urgh.

Which brings up the obvious question: if I could suddenly make the world, or at least this little bit of it, 2 degrees warmer all year round, would I be better or worse off? I'm just thinking of direct response, mind you, so leaving out any ecological problems and assuming no change in precipitation. +2 oC would mean that we never had snow and hardly ever had frosts. That latter would make breaking up the soil each winter a bit harder (and would have lots of ecological repercussions, but I'm ignoring them, only thinking of me). But it would make the summers too hot. They already are a bit too hot, every other year has a week (ish) when its hot enough to make it unpleasant to sleep at night. But on balance, I think it would be an overall gain: there is more unpleasantly cold winter than there is unpleasantly hot summer.

Saying things like that inevitably makes me suspected of being an evil septic (even folks at work have started to comment) so I suppose I'll take a stab at sketching out my position (again). My last go was I'd like us to slow down, step back and take a far longer term perspective on life and values. Vast swathes of things that we currently do simply don't need to be done at all. I'd like us to do this because we could all be happier, and the environment less damaged. But I don't see any real chance of this happening, absent some external shock, because sitting quietly tends to get overwhelmed by doing. On the CO2 front, my position is still that a "vast geophysical experiment" is a bad idea: we know enough to know that we don't know what is going to happen to a sufficient degree of accuracy to know that we're safe. I think that's pretty clear. Its a slightly weaker version of what mt has been saying ever since the days when sci.env was worth reading (or posting to). But this is, obviously, a much weaker position than "we're all going to die/become homeless/be flooded by refugees/become poor from rising sea levels real soon now" or somesuch. I'm sure I had a post somewhere looking at the top reasons why we should worry about climate change, but I can't find it now, so you'll have to be content with these ramblings (somewhere in the middle, about Bali).

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Is This Cute Video Just a Rat Loving a Cat, or the Beginning of the End of Toxo [Culture Dish]

A lot of people probably look at the video I've posted below and think, Awh, it's a hilarious rat who just loves his friend the cat! But when I watch it, I can't help imagining something evolutionarily larger.

Some background information: The parasite Toxoplasma infects many species (including an estimated 60 million people in the US), but it can only undergo sexual reproduction in cat digestive tracts. Evolutionarily speaking, this means toxo's survival depends 100% on its host being eaten by a cat (even if its host is human; more on that below the jump). So toxo has evolved a complicated system for taking over its hosts' brains to increase the likelihood that they'll be eaten by cats (for example: it rewires rat brains so they're actually attracted to the smell of cat urine). Knowing this, I ask you: Is this rat just friends with this cat? Or is it actually in a toxo induced frenzy and trying to get eaten? If so, then this video is an example of a cat kicking toxo's ass (to a hilarious soundtrack):

If all cats were like this one, toxo would eventually cease to exist.

Now, on a more human note ...

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Drug Addiction Dualism is Harmful, Not Just an Interesting Philosophical Navel-Inspection [DrugMonkey]

A recent post from PalMD notes that discontinuation from clinical treatment with modern anti-depressant drugs such as the Selective* Serotonin Reuptake-Inhibitors (SSRIs; Prozac/fluoxetine and the like) can result in unpleasant effects.

When many of the newer classes of antidepressants are abruptly discontinued, there is a constellation of symptoms that many patients experience, including headache, dizziness, muscle aches, and nausea. This isn't one of those "iffy" adverse drug events, for example when a patient treated with a statin complains of a backache and blames the drug. This is a predictable reaction to stopping or skipping a dose of medication.

PalMD then asks a question that is most fascinating to YHN.

In other words, stopping these medications can cause a withdrawal syndrome. Why don't we just call it that? What's with this "discontinuation syndrome" thing?

It all comes back to the stigma associated with dependence on recreational drugs and a persistent misconception that it is all merely "psychological" in nature. The overwhelming connotation of "psychological" in the context of substance dependence is a dualist connotation. In this case the notion expressed quite widely from the average layperson to the medical doctor to certain lay areas of substance dependence treatment (AA for example) that substance dependence is a matter of personal willpower or morality. It follows that all that is wrong with the substance dependent person is a deficit of will or morals and that the solution is to support will-power and moral rectitude.

This is pernicious and harmful nonsense.

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Snowy Burrowing Owls [Living the Scientific Life (Scientist, Interrupted)]

tags: Burrowing Owls, Speotyto cunicularia, wildlife, nature, image of the day

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Why I've Gone Back to Seed - or 'Why I Blog More Happily Now' [Neuron Culture]

With this post, and with pleasure, I bring the blog formerly known as Smooth Pebbles -- now Neuron Culture (mark your RSS readers!) -- back to Scienceblogs.

Seventeen months ago I said farewell to this Scienceblogs home, at least for a time, because I had not found blogging a comfortable fit. Since then, however, as I blogged off in the hinterland, I've come to better see how this slippery but flexible form can hold a valuable place in both my own writing and in the changing world of journalism.

I've been particularly swayed by the work of bloggers innovatively exploiting the immediacy, constancy, and scalability of this weird form, both in science writing and elsewhere -- among them Carl Zmmer, Jonah Lehrer, Vaughn Bell, Tyler Cohen, Cory Doctorow, Philip Dawdy, the people at Wall Street Journal Health Blog, and Alex Ross, to name a few.

Of all, however, the Atlantic's Andrew Sullivan, through both his example and his treatises on blogging, has been foremost in helping me see how I might blog more happily and productively,. There's an irony in Sullivan's influence: The biggest page hit I ever got while at Scienceblogs before was when Sullivan blogged my farewell post. It was his post that got me reading him more regularly and closely and thinking about just what he's really doing at the Daily Dish: not just reporting, explaining, and opining -- the reach of most blogs -- but both stimulating and (co-)curating a set of discussions.

Sullivan's blog and others have also shown me that blogging (for which, truly, I wish there were a prettier word) lets you track changing issues in a way that longer-form and more traditional journalism does not. As someone fond of the long form -- of immersing myself in a story and then working it till it's just so before sending it out -- I had (and still have) some trouble getting comfortable with the idea of writing more quickly on subjects I care about. Yet the blog form -- more quickly launched, more scaleable -- lets you examine issues more steadily, repeatedly, and collaboratively than traditional journalism does, and these advantages hold an increasing attraction to me.. Some my key subjects seem especially ripe for this approach.

Consider, for instance, the almost operatic crisis growing within psychiatry right now, as scandals embarrass the discipline and the drug-dominated monoamine hypothesis of depression is transformed from a badge of empiricism to a contradiction of it. I could write a book on the convolutions psychiatry is undergoing right now, and may yet do so. Yet the blogosphere is already shaping public discussion of this issue as much as more traditional newspaper and magazine stories do -- partly because blogs can visit the issue(s) more steadily and (over time) more thoroughly, and partly because the blogosphere can mix both the first-rate, invaluable mainstream reporting of people like Gardiner Harris and the digging, personal perspectives, and inside dish from people like Daniel Carlat, Philip Dawdy, Liz Spikol, and the folks at Pharmalot.

Same thing can be said for the growing momemtum for school reform, health care reform, and universal health care; the conflict in medicine between empiricism and research driven by commercial interests; and the revision of psychiatry's Diagnostic Statistical Manual.

I hope to use this space to track and contribute to all those discussions and also to track the less complicated and laden puzzles pleasures of science and medicine, like how the brain works -- not to mention music, sports, literature, and odd bits of culture.

Enough treatise. You actually came here for links? Okay: Below the fold, a few things I might have blogged on this past week had I not been enjoying the holidays, doing the drudge techy work of transferring this blog over from Typepad, and writing this:

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C.I.A. Director Panetta [The Intersection]

Ocean champion Leon E. Panetta will take over the Central Intelligence Agency.

In disclosing the pick, officials pointed to Mr. Panetta's sharp managerial skills, his strong bipartisan standing on Capitol Hill, his significant foreign policy experience in the White House and his service on the Iraq Study Group, the bipartisan panel that examined the war and made recommendations on United States policy. The officials noted that he had a handle on intelligence spending from his days as director of the Office and Management and Budget.

Details at The Caucus Blog...

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Little Miss Bleeeeeeeeeep [The Quantum Pontiff]

Anyone else catch Little Miss Sunshine on USA this weekend? The scene where the brother Dwayne breaks his vow of silence has to be one of the longest silence bleeps of all time. Anyone know of of a longer one (for one word, not for a string of words)?

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Could DIY biologists tackle problems with pollutants? [Discovering Biology in a Digital World]

Some of the things that are attracting people to DIY biology are:

• the idea of doing science with others for fun
• the possibility of doing something that might be beneficial to society
• being part of larger movement

All of those notions appeal to me and since I've been involved with biotech for many years, I have lots of project ideas. After thinking about the yogurt and melamine detection project, I started to wonder if a DIY project could even have a bigger impact, and say, develop a cheap test for heavy metals like arsenic or lead.

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True love lasts a lifetime as demonstrated by fMRI (bleh!) [Pure Pedantry]

Seriously, when I read the headlines to this article, I wanted to wretch retch. (Ed. I need to learn how to spell.)

Scientists discover true love

Scientists: True love can last a lifetime

I can feel it welling up now...eh...OK, I feel better.

Just to be clear, I didn't want to wretch retch because I am a deeply cynical person who scoffs at the notion of true love. (That is true, but not why I wanted to wretch retch.) I wanted to wretch retch because scientific research like this inevitably results in the worst kind of popular tripe when communicated in journalism. We are talking the most shameful, smaltzy fluff pieces -- complete with pictures of swans and anecdotal references to the journalist's own marriage.

So, what I am going to do now is save you from all of that. (You can thank me later.) We are going to have a serious discussion of this article complete with criticism. There is serious science to be discussed, and -- by Jove -- I mean to do it without personal allusion or description appropriate only for a Valentine's Day card.

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The French are different: L’Affaire Madoff [Gene Expression]

Madoff Investor Awaits 'Imbecile' or 'Dupe' Verdict:

Patrick Littaye, co-founder of Access International Advisors, lost his savings after investing with Bernard Madoff, expects to lose his house in his hometown of Saint-Malo, France, and says he'll canvass investors over the next few weeks to see whether he has also lost his business.

Littaye, 69, invested all of his own money with Bernard L. Madoff Investment Securities LLC last year, enticed by the firm's positive returns as other hedge funds slumped. His error was compounded because he borrowed money to increase the return on his investment, leaving him with $4 million in personal debts, Littaye said in telephone interviews from Jan. 2 through Jan. 4. He declined to specify the amount he had lost.

"I'm going to sell everything I have and start over," Littaye said from Brussels, adding that he planned to subsist on his French social security payments. "For Access, we'll go to our investors over the next couple of weeks and we'll see what they think of us."

And some candor:

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I get email [Pharyngula]

A while back, I posted some email from Debra Rufini that had been forwarded to me — a long list of stupid arguments for creationism. Now, almost 6 months later, she has discovered my posting, and she is hoppin' mad.

Hello there Mr. Myers,

I must say that I'm incredibly flattered that you've gone to all the trouble to 'attempt' to tackle my 50 points. One would assume that seeing as tehy were so ridiculously stupid, that you'd rather fob me off as yet just another 'religious fool'. Had I written to you (Which I hadn't even done), representing the Flat Earth Society, I could guarantee that you wouldn't waste your time on a response. If you did, you'd look pretty stupid.

It's obvious that you really loathe me without even knowing me, and to be honest with you, I reckon I'd be a pretty miserable, angry person with a chip on my shoulder if I also believed that I was no more than worm meat at the end of the day. I do find it interesting that almost all athiests tend to have this angry & patronising streak in them. If only you would find the love of Christ, and it would all be gone.

It's not a very professional approach to call people rude names, simply because tehy don't agree with you, is it?! Sounds like you were the sort of child who threw a tantrum whenerver he didn't get his sweeties. I would have respected you far more, had you given an adult approach, and responded in a civil manner, in the process not making yourself look so immature.

This 'thick as bricks' author has the commpon sense to believe that a mind is responsible for the complexity of life, as opposed to a vast volume of mindless time. Unaided time alone cannot be the great magician that you seem to believe is the case.

It takes a fool to believe that a randomly chewed up piece of chewing gum plus a whole load of time - hey presto; da da - results in a fully functioning Porshe!

Jesus called us to love those who persecute us, so that's exactly what

And it just kind of ends there.

If you look at my original post, you'll notice that I didn't waste any time on it — I just posted her list with little attempt to address the flamboyantly obvious inanity of her arguments. It was like a letter from the Flat Earth Society.

I am not surprised that atheists in the vicinity of Debra Rufini seem angry and patronizing. They're probably also annoyed and exasperated.

Raise your hand if you think chewing gum for a long time will produce a fine German-engineered automobile…

Yes? You in the back? Oh, you were just scratching your nose.

Hmm. Guess there aren't any fools here. OK, is there anyone here who thinks biologists believe in gum-to-car transmutation?

Debra! Of course! OK, there is one fool here. Maybe she'll give us the joy of her commentary in the thread down below.

---

Hang on! I just got the remainder of her message!

Sorry, something happened there - don't know what!

I was just saying that as Jesus taught us to love those who persecute us, I shall do the same. I pray for you, just as he did for those who crucified him.

Kind regards,

Debra.

P.s. This was typed in a rush, so should there be any spelling mistakes, it's not because I have the intelligence of a flea. I would like to also point out to you that should this get put on your website, (as I'm sure you'd like to rip me to shreds even further), I shall be deleting any abusive or hate mail I receive either from yourself or any of your other bitter friends.

What a relief. It just wouldn't be creationist hate mail without the "kind regards" signoff.

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The Downside of Monomania [Science After Sunclipse]

So, there's this video. It's apparently for a German electronics retailer whose motto is, roughly translated, "We hate expensive".

Phil thought it looked really kewl. P-Zed agreed, but he said that it portrayed evolution as a linear progression along a Great Chain of Being, and that this is the sort of bad media which fosters misconceptions about evolution.

All of that was somewhere in my head when I first watched it, but I must confess my initial reaction was more like the following: "Cyborg women? Robots? Evolving robots? Misconceptions about evolution? At the risk of sounding all Denyse O'Leary — I wrote about that in my book!"

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Kids' books! [Pharyngula]

Everyone is also asking me for a list of children's books on evolution, and it's always hard to come up with any titles. I am now saved: Charlie's Playhouse has a list of 89 kids' books on evolution!

You know, Darwin Day is coming up, and we could create a new tradition of educating young'uns on 12 February…

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Not the Raptor Post I Was Expecting to Write [Science After Sunclipse]

Today's xkcd was insufficiently nerdy for me.

Yes, that's right.

In order to make the comic adequately reflect what I do on a daily basis, I have at least to modify the temperature conversion chart:

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Ian Musgrave piles on Luskin [Stranger Fruit]

From here:

Casey also chides Miller for not doing any knock-out experiments on blood clotting systems. This is heavily ironic as no ID proponent, not even Behe, has done any experiments on the blood clotting system. As I point out in my post Behe vs Lampreys, it's the evolutionary biologists that have been doing all the heavy lifting in regard to understanding the clotting system. In fact I issued a challenge to the ID proponents, the Amphioxus genome had just been published at http://genome.jgi-psf.org/Brafl1/Brafl1.home.html. Amphioxus is a primitive chordate, more primitive than lampreys, that clot their haemolymph. I challenged the ID proponents to predict which coagulation factors are present in Amphioxus, search the Amphioxus genome database and report on whether the genes found match their predictions.

Since then, silence. I can tell you one thing for sure. The Amphioxus has no gene for fibrinogen, the final step in the modern clotting cascade, yet it still clots its haemolymph. So the very basis of the "Irreducible Core" that Casey goes on about is absent in these animals, and one of Behe's iconic pathways is exposed as reducible.

Of course, we expect none of this to have any effect at all on Luskin and the DI. They will still spout the same-old-same-old in an effort to animate the undead corpse that is intelligent design. Luskin is, after all, a lawyer.

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Walt Ruloff: Nazis > Science [erv]

Via PZ, a quote from Walt Ruloff, producer of EXPELLED:

The first version of Expelled leaned heavily on computer-generated images of cells, illustrating how their development relied on more than random mutation.

But alas, Ruloff said, "When we first watched that movie it was verrrrry boring."

So, with the help of Abbotsford screenwriter Kevin Miller, they made a more controversial film -- by splicing provocative black-and-white images in between Stein's punchy interviews with various scientists.

The final version of Expelled includes chilling reels of the Berlin Wall, of soldiers, of machine-guns, of scolding school principals and of extermination camps where "inferior" people, the disabled and Jews, were slaughtered.

HA!
HA!

Okay, ignoring the fact the animations were 'reduced' due to the fact they were STOLEN, not because they were 'boring'-- lets pretend Ruloff isnt a lying piece of shit that had no problems stealing from Mr. Rogers. Lets pretend comparing scientists to NAZIS isnt an ancient Creationist tradition, and wasnt EXPELLEDs original intent. Lets pretend he really did alter EXPELLED drastically 'because science is verrrrry boring'.

WHAT???

ROFL!!!

Spoken like a true D-student, Ruloff!! 'Its not my fault I flunked biology! The teacher was an ATHEIST! And biology is boring anyway!' LOOOOOL!!!!

LOOOSER!

LOOOOOOOOOSER!!!

HAHAHA!

This isnt an intelligence thing-- As I hope ScienceBlogs is showing, you dont have to be a super genius to understand cutting-edge science. Science isnt just for egg-head nerds. Its cool! Its fun! Its exciting!

Unless you are an intellectually lazy bastard named Walt Ruloff.

What a fucking loser.

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