The stem cells formed a sac that then folded in half
a couple days later (see image above, courtesy of Nature),
forming the optic cup.

What’s the News: Give a blob of cells the right environment—lots of nutrients, special chemical signals, and a comfy gel cushion—and they just might grow you a body part. In a feat of bioengineering, scientists at the RIKEN Center for Developmental Biology in Japan have grown a retina from mouse embryonic stem cells. Remarkably, much of the development happened spontaneously, indicating that even undifferentiated cells have a blueprint in mind. Researchers hope the work will someday yield transplantable retinas for people with diseases like retinitis pigmentosa.

“When I received the manuscript, I was stunned, I really was,” commented human molecular geneticist Robin Ali (via Nature News). “I never though I’d see the day where you have recapitulation of development in a dish.”

How the Heck: Supported by a gel that mimics cells’ natural environment, the stem cells were immersed in a bath of chemicals that directed their growth into retinal cells. Just as in normal embryonic development, over the course of about a week the cells organized themselves into ...

[Note: this post was published prematurely, then deleted, and is now back.]

Michael Nielsen gave a great talk at TEDxWaterloo about the idea of “open science”:

There’s a great deal of buzz about “openness” in certain sectors of the science community; largely this has passed physics and astronomy by, because we’re already pretty darn open. It’s hard to image something more open than arxiv, where everyone puts their papers up for free even before they’re published in a journal.

But Michael’s talking about something much more ambitious: opening the process of creating science, not just publishing it. For experimentalists this would be difficult, for obvious reasons. (You think people who sweat to build an experiment are going to invite the public in to take a whirl?) For theory it is also hard, but the reasons are more subtle.

The point is that credit in science is given out on the basis of getting your name on published papers. In the arxiv era, the papers don’t necessarily have to appear in a traditional journal — but that’s a topic for another day. The model is set in stone: you have an idea, you work out its consequences to the point where it’s publishable, and you write a paper. Without that last step, you’re not going to get any credit. (Very occasionally you will see references to “unpublished work” or “private communication,” but it’s rare and not really for big-ticket ideas.)

So if I had an idea, I would either work it out myself or start working with students or collaborators. I certainly would not go around publicizing an undeveloped idea; I wouldn’t get any credit for it, and someone else could take it and develop it themselves. I might give seminars in which I mention the idea, but that’s only recommended once it’s to the point where a paper is on the horizon.

Michael and others want to overthrow that model. Their shining example is this blog post by Tim Gowers. Gowers is a mathematician who proposed attacking an open math problem right there on his blog, by asking for comments from the crowd. If they succeeded, they could publish a paper under a collective pseudonym. He next chose a problem — developing a combinatorial approach to the Hales-Jewett theorem — and, several hundred comments later, announced that they had succeeded. Here’s the paper. Buoyed by this success, people have set up a Polymath Wiki to expedite tackling other problems in this way.

Could this work for theoretical physics? I don’t see why not. But note that Michael spends a lot of his time in the talk pointing out the obvious — crowdsourcing doesn’t always work. I could easily imagine ways in which such a project could fail; too much noise and not enough signal, everyone with good ideas deciding they would rather work on them by themselves rather than sharing openly, etc.

Might be worth a shot, though. I’m thinking of suggesting some ideas here on this blog and seeing whether we get any useful input. Let me sleep on it.

The 3-sigma bump reported by Fermilab on Wednesday has garnered a lot of attention. Understandable, since it might be a precious sign of particle physics beyond the Standard Model — but it’s also just a 3-sigma bump, and usually those go away.

Via Matt Strassler and Lisa Randall, here’s a set of plots that helps indicate exactly how hard this game really is. The plots can all be found on this web page at CERN. In comments Matt and Peter note that they were made by Tommaso Tabarelli de Fatis, as explained on Tommaso Dorigo’s blog. Here is the original plot from the CDF paper:

We’re looking at the number of events that produce a W boson and two jets, as a function of the energy of the jets. The bottom plot is all the data, while at the top they’ve subtracted off most of the Standard Model background, leaving only the predicted red curve from WW/WZ events. You see the extra little bump around 150 GeV, that’s what’s getting everyone so excited. It’s unlikely that the data are a good fit to the prediction; the “KS (Kolmogorov-Smirnov) probability” is given as 5×10^-5, which means that it’s not bloody likely.

But, just for giggles, let’s imagine that the energy of the jets wasn’t measured very accurately. Obviously the experimenter worked hard to get it right, and I would trust their judgment over my own any day, but you never know. Jets are complicated things with many particles in them, you can imagine being off by a bit.

So here is the same plot, just scaling the jet energy by two percent:

You see that makes a lot of the excitement go away. The KS probability is now 9×10^-2, which essentially means … the bump has gone away. If we scale by 4%, it goes away almost entirely:

Now the data fit the Standard Model very well. If we keep cranking up the supposed error, we stop fitting again, because the data at very low energies begin to go astray:

There is an animated version of the plot which is fun to look at. Nobody is saying (I don’t think) that this is certainly what’s going on; it’s just an illustration of how difficult this game really is, and why people shouldn’t get too excited about three-sigma events. A little bit of excitement is good, and descending deep into cynicism is bad, but patience is really warranted. Let’s collect more data and see what happens.

What global warming?

What the weather’s like affects some people’s beliefs about global climate change, a new study found: On hot days, they’re all over it, but on cold days, they’re not so sure.

This is not impressive, people. It’s called “global,” meaning not just what you personally felt when you walked out the door this morning. “Climate” also means something different from “weather”, and “change” could mean things will get warmer, colder, or just plain different. On unusually chilly days, these climatically labile folks are 0 for 3.

If only that was the worst of it. A string of studies have shown that people are comically bad at consistently thinking, well, anything when it comes to climate change. Even miniscule differences in what we’re up to at the moment or how we’re asked can have a big effect on what people think of climate change and what they’re willing to do to help. Here are five more ridiculously simple things that get people to change their minds:

What’s on TV. I’m sure you all remember the 2004 hit film The Day After Tomorrow, in which global warming throws Earth into a new ...

What’s the News: Scientists found that periodic fasting may decrease the risk of coronary artery disease and diabetes, and also causes significant changes in heart-disease risk factors like cholesterol, blood-sugar, and triglyceride levels, which hadn’t been linked to fasting before. “We’ve shown it is not a chance finding. Fasting is not just an indicator for other healthy lifestyles,” says lead researcher Benjamin Horne of the Intermountain Medical Center Heart Institute. “It is actually the fasting that is working to reduce the risk of disease.”

How the Heck:

In the first recent study on fasting and heart disease, the researchers surveyed people in Salt Lake City, where a majority of citizens are Mormons and fast once a month for 24 hours. They discovered that the people who answered “yes” when questioned whether they abstain from food and drink for an extended time had a lower rate of coronary disease and diabetes.
In the second study, scientists monitored 230 people ...

I was just reading an interesting study on the politics of intellectuals and postgraduates, and one figure leapt out at me:

The number of graduate and professional degree students grew at a rate of about four percent per year over the past decade (Bell 2010), and data from the General Social Survey (GSS) show the percentage of American adults with advanced degrees has more than doubled since the 1970s, reaching just over 9 percent in 2008.

On Point of Inquiry in February, I somewhat jokingly asked Dan Kahan–who has documented how everybody thinks the experts supports their point of view–whether the problem isn’t simply that there are so damn many experts out there now that you can find one willing to say anything. These data would seem to support the contention, at least with regard to the growing number of experts.

Don’t get me wrong–I know it is very good for our society, in a myriad of ways, to have highly trained, smart people running around. However, I wonder whether one by-product is that it is easier to politicize science, because it is easier to find someone very smart who is willing to argue some strange contrarian position in a very convincing way–and indeed, may even pay the bills by doing so.

This is a pretty neat picture taken by the Lunar Reconnaissance Orbiter: two craters, side by side:

[Click to impactenate.]

What’s cool about it is the obvious age discrepancy between the two craters. The Moon lacks water and air, but it has erosion nonetheless: micrometeorite impacts, solar wind, and even thermal stress cause by the month-long day night cycle slowly wears away at the surface. Old craters have a rounded look to them, while fresher craters are sharp-edged, and show the debris from impact.

The full-res image has a scale of just a meter per pixel, so a lot of the smaller boulders you see around the younger crater on the right are the size of cars. Both craters are roughly 300 or so meters across; you could walk briskly across them in a couple of minutes.

I noticed the young crater has an odd shape, non-circular, almost diamond-shaped. Then I looked at other, nearby craters, and saw the same thing, so it must mostly be due to lighting. However, there is a funny hillock just to the right of the crater, and the boulder field around it is not symmetric; there ...

Answer: When he has Ann Coulter on the air, and somebody has to act responsible:

For a thorough debunking of Coulter, see here.

I like the habit because it makes me
look like the Linux penguin.

From elite hackers, to white-hat hackers, to hacktivists, hackers don’t generally have sterling reputations as upstanding citizens—at least as far as the general public is concerned. That’s why it may come as a surprise that the Vatican has published an essay that redeems computer hackers and even compares hacker philosophy with Catholic theology.

In his article published in the Vatican-vetted Civilta Cattolica, technology expert, literary critic, and Jesuit priest Antonio Spadaro draws similarities between hackers and Catholics (via TechWorld):

Hacker mentality implies a joyful application of intelligence to problem solving, rejecting the concept of work as repetitive, burdensome and stupid, Spadaro wrote. Hacker ethics rejected a capitalistic, profit-oriented approach to work, eschewing idleness but favoring a flexible, creative approach that was respectful of the human dimension and natural rhythms, he said.

In addition, hacker philosophy fosters creativity and sharing, and is both committed yet playful. “Under fire are control, competition, property. It’s a vision that is … of a clear theological origin,” writes Spadaro. He argues (rather vaguely) that many of these characteristics are also, as odd as it ...

“What are the best books for my daughter?” “What kinds of extra curricular programs should my son be enrolled in?”

Dear Parents,

You send so many emails asking, “How do I encourage my child to pursue science?” It’s a noble endeavor, and of course, there’s no end to possible responses. Much depends on what each individual is interested in from marine science to space. While I welcome these inquiries, here’s the best suggestion I can offer: Rather than science specifically, focus on critical thinking!

No matter how advanced a student’s math skills or laboratory technique, it will be her ability to work through problems and develop creative solutions that sets her apart from peers. In other words, parents should do more than going through the motions for standardized test preparation, and begin early. Foster her natural curiosity about the world. Perhaps most importantly, she needs to believe in herself and recognize what she is capable of.

Sure, it sounds a bit cliche, but that doesn’t mean it’s easy. More than ever before, our culture poses formidable social obstacles to success. Joe’s is right that “It’s okay to be Smart,” but “smart” doesn’t always seem adequate. Kids are bombarded with billboards, music videos, television shows, advertisements, and films telling them that they also have to look and act a certain way to be accepted. A cultural firestorm of unrealistic expectations damages self-esteem and, in turn, academic performance. Of course there’s no simple way to counter these harmful false messages, but building confidence is the place to begin.

So that’s what I hope moms and dads will continue to emphasize. And if you’re still seeking a good book to start with, my vote for elementary schoolers goes to Free To Be You And Me. (DVD and audio are even better!). For young adults, books like Tracy Kidder’s outstanding Mountains Beyond Mountains about Dr. Paul Farmer will help them recognize how one individual can have a tremendous positive impact on the world.

Good luck!

Sheril

What’s the News: A gene that makes bacteria resistant to up to 14 antibiotics has been discovered in bacteria in drinking water and street puddles in the Indian capital of New Delhi by a research team from the University of Cardiff in Wales. Scientists were already aware that microbes bearing this gene, which produces an enzyme called NDM-1, were infecting people in India, but it had been thought that such bacteria were mainly picked up in hospitals. This study shows that the gene, which is capable of jumping from species to species, is loose in the environment.

What’s the Context:

NDM-1 is in a class of enzymes that are known culprits in the spread of drug-resistance: the beta-lactamases. The first beta-lactamase, penicillinase, was discovered in 1940 ($, pdf). These enzymes give resistance to antibiotics like cephamycins, carbapenems, and penicillin, which have similar chemical structures. The study is fueling fears that the NDM-1 gene could easily jump into bacteria around the world. Recently, a separate team of scientists showed that Swedish tourists returning from India had bacteria with beta-lactamases in their guts that they hadn’t had before the trip. And as the current study found that the gene for NDM-1 skipped ...

A bill clearly intended to promote and protect antiscience passed in the Tennessee State House yesterday, by a vote of 70 – 23.

Let that sink in. 70 to 23.

The bill is another in a long series of creationist (and broadened into other antiscience topics) wedge bills designed to weaken the teaching of real science in public schools. The summary makes that clear:

This bill prohibits the state board of education and any public elementary or secondary school governing authority, director of schools, school system administrator, or principal or administrator from prohibiting any teacher in a public school system of this state from helping students understand, analyze, critique, and review in an objective manner the scientific strengths and scientific weaknesses of existing scientific theories covered in the course being taught, such as evolution and global warming.

On the surface this sounds like legit science; after all, science thrives on understanding the weaknesses in ideas so they can be improved. But if you read that last part, conservative antiscience rears its head: the two specific cases mentioned are evolution and global warming.

That doesn’t sound like real science is the motivation behind this bill — and

That’s the number. At least according to Public Policy Polling. That seems rather high. So I decided to go back and look at the RACMAR variable in the General Social Survey. Here’s the question:

Do you think there should be laws against marriages between African-Americans and whites?

They kept asking the question for 30 years, but dropped it in 2002. Here’s the reason:

By 2002 it was a consistent finding that less than 10% of Americans would accede to the proposition that interracial marriage should be legally banned. So the finding that that 46% of Mississippi Republicans agree with that position, and that only 40% reject it outright, is somewhat curious. Here’s the question in PPP:

Do you think interracial marriage should be legal or illegal?

The outcomes were:

- 40% said legal

- 46% said illegal

- 14% were not sure

Remember that the sample was limited to Mississippi Republicans. Let’s go back and look at some of the demographic correlates for the responses to RACMAR between 1998 and 2002, when the proportion responding yes and no was relatively constant. I’ll focus on region and politics.

Ban interracial marriage Liberal
7 Moderate
10 Conservative
12 Democrat
10 Independent
10 Republican
11 New England
7 Middle Atlantic
8 East North Central
9 West North Central
9 South Atlantic
11 East ...

The whole Libyan affair seems kind of like a joke, albeit with some serious consequences for the people involved. Gaddafi’s bizarre behavior. Hapless rebels which seem out of central casting for a dark military comedy like Tropic Thunder. An American political class unable to form a coherent message as to the rationale for the intervention. All set against the background of an even more pressing humanitarian crisis in the Ivory Coast.

As Americans are not familiar with Libya at this point the news media has been plying us with many maps which show the locations of the battles. All of them seem distributed along the nation’s coast on the Mediterranean. This makes sense because of the climate of the country, as well as the concentration of oil refineries in this region. But the maps which always seem to show one set of roads hugging the coastline also make me think of South Park. Here’s the clip below which makes my logic clear:

It’s Christmas in Canada
Tags:

What’s the News: On a quest to discover at what size the kooky quantum physics that governs atoms (teleporting!) gives way to the ho-hum classical physics that governs humans (no teleporting), scientists have shown that if conditions are right, a molecule of a record 430 atoms can be in two states at once, like Schrödinger’s infamous cat. For the last three decades, researchers have been watching progressively larger objects under special conditions to see how big of an item they can catch showing quantum behavior. This molecule, which was created by a team at University of Vienna and their collaborators for the experiment and is larger than insulin, is the largest on record.

How the Heck: The researchers shot a beam of molecules through a series of three sets of slits—an updated and modified version of the classic double-slit experiment—and measured exactly where the molecules arrived at the end of the beam. Graphs of where the molecules arrived show a fluctuating pattern indicating interference between the parts of the beam going through different slits. Since the molecules interfered with each other (not something well-behaved classical molecules do) ...

Effect of solar eclipse on microbes.

“OBJECTIVE: A solar eclipse was observed in India on 15(th) January, 2010. It was a total eclipse in some parts of the country, while it was a partial eclipse in other parts. Microorganisms play an important role in various phenomena on the earth. This study was undertaken to know the influence of solar eclipse on nature indirectly, by analyzing certain genotypic and phenotypic variations in prokaryotes and eukaryotes. Since yeast have similar gene expression as that of humans, investigations were pursued on Candida albicans. Hence the study of the effect of solar eclipse on cultures of Staphylococcus aureus, Klebsiella species, Escherichia coli,and C. albicans was performed in the laboratory. The effect of the total or partial eclipse on the microorganism isolated from clinical isolates was investigated during the time period from 11.15 am to 3.15 pm.

MATERIALS AND METHODS: Cultures of S. aureus, Klebsiella species, and E. coli colonies on nutrient agar slants and broth and C. albicans on Sabouraud’s dextrose agar plates and broth. Slants were exposed to sunlight during eclipse and exposure to normal sunlight at Mangalore, Dakshina Kannada district, Karnataka state, India.

RESULTS: There ...

I hadn’t run into this story today (thank God!). John Hawks’ begins a critical post:

I am just about to go crazy today. I just can’t seem to escape the “gay caveman” story.

No, I don’t mean the Geico caveman who likes mango duck breast and who has Talia Shire as his therapist. His sexual orientation I don’t know.

In the sitcom, Cavemen, they were all straight. The main issue in regards to sexuality was that one of the cavemen tended to date sapiens sapiens females, and his girlfriend had a tendency to hook up with cavemen. Another of the cavemen frowned up these “mixed” relationships.

Saw this on Twitter, but I’ve talked to others who have brought up this issue:

It seems the logistic issues are the big problem. How do you validate phenotype? Tight-knit communities could probably work just based on trust, but then how do you scale up the sample size to detect loci of small effect? I think it will come, but I’m not sure when. Though obviously when it comes to disease phenotypes there’s going to be more motivation by interested parties. In the near future we’ll have pretty cheap full sequences, so one could probe differences within families to pick out possible mutations which might account for the variance you see across siblings. But would people really want to know why they’re smarter/stupider or better looking/uglier than their brother/sister? Isn’t the reality enough?

One of the great things about ADMIXTURE is that the population elements shake out of the data through the logic of the program. The worst thing is that it is then left up to you to make sense of the elements. A useful way to use ADMIXTURE and avoid excessive interpretive fogginess is to figure out individual proportions of contribution from X ancestral groups when you have a pretty good idea that an admixture event did occur between very distinct and distantly related population groups. To some extent the whole New World is a good laboratory for this process. Consider, for example, someone from the Dominican Republic or Puerto Rico. There is a good chance that their ancestry will fractionate into three elements:

- An African one

- An Amerindian one

- A European one

These three elements are sampled from very different locations geographically. The ancestral populations have been separated for tens of thousands of years, with little to no gene flow across them. This means that the allele frequencies of the “source” populations should be relatively different (maximizing Fst). A mapping of inferred allele frequencies between abstract ancestral populations generated by ADMIXTURE to concrete allele frequencies of known source populations ...

Sex. Dark chocolate. Nintendo’s Wii. It seems like most anything can be correlated with health and longevity nowadays. Now, some researchers want to add shopping to that list, after they saw a possible link between daily shopping and death age. Not everyone agrees, though, with this “shop so you don’t drop” mentality (surprise!).

In the study, published by the Journal of Epidemiology & Community Health, the researchers followed nearly 2,000, independently living, Taiwanese citizens who were at least 65 years old. The researchers gathered their shopping habits by looking at a 1999-2000 survey that evaluated how often these Taiwanese geriatrics shopped, and then they used national death registries to keep track of the study groups’ deaths until 2008. After correcting for age, gender, health, ethnicity, financial status, and other factors, the researchers discovered that daily shoppers were 27% less likely to kick the bucket than their less shop-happy peers (aka those who shopped only once a week or less). Oddly enough, the best shopping-related survival record goes to the men, who reduced their chances of dying by 28% by shopping; women who shopped daily ...