Critiques of Arsenic-DNA paper published in Science

Almost 6 months later from the publication of the original paper.

Eight critiques!

Another case of peer review out in the open.

When nasty peer review goes into the open...

in the august journal Langmuir, over the concept of the Gibbs adsorption isotherm (GAI).

It started with a paper (a group from Eindhoven) commenting on these 2 papers (by a group at Emory), and which then elicited a response from the Emory researchers.

The opening salvo (as the paper abstract no less) from Eindhoven:

Recently, some arguments were published that cast doubt on the validity of the Gibbs adsorption isotherm. The doubt was on whether the often visible linearly declining part in the surface tension versus logarithm of concentration plot of a surfactant solution, just before the critical micelle concentration, really represents a situation of constant adsorption. Those published arguments are partly of a conceptual nature and partly based on experimental evidence. The conceptual arguments appear to be based on a misunderstanding of the theory, while the arguments based on experimental evidence stem from an inaccurate treatment of these data. Our conclusion is that none of the relevant arguments put forward are valid. The experimental evidence, if properly treated, is in line with the Gibbs theory.

Ouch. Surely you won't expect the Emory group to take such a punch in their face without a counterpunch of their own. And so they did:

In the preceding paper, Laven and de With defend the classical Gibbs analysis. If one ignores their ad hominem comments (see, for example, their abstract), then what remains is a deceptively authoritative text devoid of any additional experimental data. In response, there is no need for us to repeat in detail all our experimental evidence.Only two experiments, based on conductivity and monolayer data, will be discussed briefly to illustrate the general tenor of the Laven and de With arguments.

Wow. The knives are out in the open for blood. I see nasty peer reviews all the time, but this is the first time I have seen such reviews become publicly archived and indexed as articles on a reputed peer-reviewed journal.

Who reviewed those two papers, and the Editor went ahead and have them both published with such word choices? Most of us tend to think of journal papers as the type to read in order to fall asleep, but this goes to show they can be exciting in a way...

The Confucian way (and lack thereof)

Confucius Statue Vanishes Near Tiananmen Square

Unrepentant Maoists celebrated the move on Friday. “The witch doctor who has been poisoning people for thousands of years with his slave-master spiritual narcotic has finally been kicked out of Tiananmen Square!” one writer, using the name Jiangxi Li Jianjun, wrote on the Web site Maoflag.net.

For those who have been heartened by the government’s embrace of Confucian values, news of the statue’s removal was devastating. Guo Qijia, a professor at Beijing Normal University who helps run the China Confucius Institute, said that only Confucian teachings could rescue China from what he described as a moral crisis.

“Students come home from school and tell their parents, ‘One of my classmates got run over by a car today — now I have one less person to compete against,’ ” he said. “We have lost our humanity, our kindness and our spirit. Confucianism is our only hope for becoming a great nation.”

and commenters on Lucky's blogpost

Let me tell you what is very wrong here. If a high income man marries a foreign wife, his wife can get citizenship or PR easily and will be entitled to things like subsidised medical care (class "C" wards)etc. However, if a poor man marries a foreign wife, he may not even get a LTVP and his marriage will be strained and have a higher chance of failing. If he manages to get a LTVP (which has to be renuewed annually), his wife can stay to help look after the children but without citizenship or PR, he has to pay substantially more if his wife gets sick - unnecessarily increasing his financial strain.

One of the commenters replied:

The case Lucky cited - Damien Koh the security guard who earns only $1.5k a month and who insisted on having two kids with an uneducated vietnamese woman.

Even if their mother is granted Singapore PR, what can she work as? Cleaner earning $1k a month? Is this enough to live by in Singapore?

In the end, who suffers the most? Their two kids!

Sometimes you have to be cruel to be kind. Damien Koh should not be allowed to marry the vietnamese woman in the first place, and that was what the government tried to do.

From The Straits Times (Apr 30):

On complaints that last-minute PAP candidate Chia Shi-Lu became an MP overnight because he was fielded in his Tanjong Pagar GRC which had a walkover, MM Lee said: 'He's not an untested person, we've interviewed him. He's a president's scholar, he scored straight A's.'

What is "peer review"?

Boingboing has an excellent write-up.

Yay

:D

I am now motivated to tie up my loose ends here as a postdoc and write my remaining papers. Then pack my bags, get onto a plane and start a new adventure (to be on the other side of the fence).

The best quote ever (modified slightly):

The biggest problem at this point is trying to fit my whole life into two suitcases and a backpack. Not a simple task, as it turns out. But there is something incredibly cathartic about shedding most of your worldly possessions for the sake of hopping on a plane and starting anew, bringing only my research and teaching skills, my laptop and some souvenirs of my past life as a postdoc. I’m pretty stoked that my life is going in this direction now; I hope it’s as fruitful as it is exciting and new.

I now feel like Charlie, having just won a coveted Golden ticket to the Chocolate Factory.

Willy Wonka: "Now, hats, coats, galoshes over here. But hurry, please, we have so much time and so little to see. Wait a minute! Strike that. Reverse it. Thank you."

It has been quite a month.

"How do you get a TT position?"

It's very easy. You first excel as an undergraduate to earn a place in a top-tier graduate program. You then spend roughly 5-7 years in penury while learning one's craft and honing one's research skills, and then writing a doctoral thesis. [...] And no, this does not mean cutting and pasting from wikipedia. Then another couple of years slaving away in someone else's lab broadening your skillsets. Finally you must compete with several hundred equally qualified candidates for one of the dwindling numbers of tenure-track positions.

So yeah, it's very easy. ... Really. It only takes a decade or more of effort and a fair amount of brain power.

Last but not least, it helps to be a fox rather than a hedgehog these days when hunting for academic and industrial jobs, especially in the hot fields like nanotechnology, energy and green technology.

Scientific research in 3 different countries

Pick your choice of poison:

China:

For most scientists, publishing an article in a prestigious journal is likely to be recognized and rewarded with attention from one’s peers.

In China, however, scientists are also rewarded with cash, and the more prestigious the journal, the larger the sum, according to a new paper published in the April issue of Learned Publishing.

*

The theory is simple and pure economics. Money motivates: pay people to publish in good journals and they try to do so. Monetary rewards are the best; money is a universal reinforcer.

*

Because of limited international circulation of Chinese journals, there is a real push to have one’s work appear in an international index, such as the Science Citation Index (SCI), Engineering Index (EI), or the Index to Scientific & Technical Proceedings (ISTP). But it doesn’t stop there. Institutions like Zhejiang University rely on a detailed accounting sheet that lists specific monetary rewards for articles according to the journal’s Impact Factor.

(Converted to US$:)

* Indexed in ISTP — $92
* Indexed in EI — $275
* Impact factor < 1 — $306
* 1 ≥ IF < 3 –$458
* 3 ≥ IF < 5 — $611
* 5 ≥ IF < 10 — $764
* IF ≥ 10 — $2,139
* Published in Science or Nature – $30,562

Singapore

In a 5-year plan launched this month, Singapore will boost public spending on research by 20% compared with spending during the previous 5 years. This largesse comes with a price: The government is demanding more economic bang from its research bucks. The drive to make science pay is falling hard on bioscience institutes under the Agency for Science, Technology and Research (A*STAR). Their core budgets will be cut and A*STAR's bioscientists, accustomed to assured funding, must compete for grants decided in part by the likelihood of an economic payoff. In contrast, government funding for research at the universities would increase steadily.

The sudden change has left many A*STAR scientists confused and chagrined. “Planning for the change has been rushed, the execution has been disappointing, and the messaging to the scientific community problematic,” says Edison Liu, director of A*STAR's Genome Institute of Singapore. Some are packing up. Two high-profile scientists who arrived here with great fanfare 5 years ago—cancer researchers Nancy Jenkins and Neal Copeland—will return to the United States in September. Others say they are mulling exit strategies.

*

NRF and the Education Ministry, meanwhile, are supporting the National University of Singapore (NUS) and Nanyang Technological University in their quest to become global research university powerhouses. Over the past decade, both schools beefed up their faculties and research, and expanded graduate programs.

USA

With a possible government shutdown only a few days away, the National Institutes of Health (NIH) appears to be ready to send in a skeleton staff to care for patients and maintain animals and experiments at the agency's Bethesda, Maryland, campus. But accompanying the plans is a strange sense of secrecy.

As lawmakers and the Obama Administration continue to clash over the depth of budget cuts, leaders are now acknowledging that the federal government could shut down Monday barring another stopgap measure to fund government operations for a fiscal year that began last October. University-based scientists may not notice at first, as temporarily closing the offices that distribute most of NIH's $31 billion budget to outside investigators won't immediately affect these extramural grants. But about 10% of the agency's budget goes to its intramural program, which has over 1000 principal investigators (PIs), 4000 postdocs, hundreds of labs, animal facilities, and many clinical studies. Much of this can't just shut down and be left unattended.

*

Although government shutdowns are not uncommon, most recently in late 1995 and early 1996, the culture seems different this time around. While in the past many people, especially postdocs, came into work and were eventually paid, this time, "the impression I have is that you will have to show you're on some list" to enter a building, one lab chief said. Another investigator was told there will be fines for violators. This time, NIH staff members aren't even supposed to log into e-mail from home, a source said.

Moving on, but where?

My current postdoctoral grant will end in a few months' time. (In other words, I have to find a new job soon.) My advisor was unable to get my funding extended, in spite of the excellent results (5 research papers in high impact journals of my sub-field and 1 patent) that have come out of it. Seasoned readers of this blog can probably figure out the reasons.

But that is not all. As a faculty candidate, I had earlier this year made it onto the final (on-campus) round of a well-regarded Midwestern university in a state that has been making the news for the wrong reasons with regard to 'fiscal responsibility'. Then came the following email from the department chair:

Hello takchek,
The (state) legislature has announced plans to cut (the university's) funding by $XX million as part of the 2011-12 state budget proposal. The university has decided to put the hiring of faculty on hold for now and it is not clear when we can resume the process. I will keep you informed of any changes in the near future.

Regards,

A one-two punch in the span of a week. How is that? Just when I thought things cannot get "curiouser and curiouser", the advisor received two separate emails (also in the same week) from different collaborators asking if he can recommend grad students or postdocs to work in their labs.

I have issues with both. The first lab is based in the Middle East, in one of the Gulf states. With the current upheaval in the Arab world, my folks are strongly dissuading me from going.

The plus side is the money. I will see a pay jump of about 2.5 times of my current income, and it is tax free. Work for a few years, then take the money and decide what to do next.

The total compensation package includes a tax-free 12-month base salary, and a benefits allowance that covers relocation, housing, initial furnishings, utilities, transportation (automobile purchase loan), health insurance, child(ren) education, end-of-service benefit and annual leave travel.

The research theme in the second lab will be on the sesquestration, removal and storage of radionuclides from contaminated waters. While there are the obvious health issues of working with radiation, the skills acquired will be highly valuable as shown by the ongoing nuclear crisis in Fukushima.

Or I should just quit research now. Am sick and tired of this dog and pony show.

There is really a journal called Nature and Science

And I leave it to you readers to judge its quality.

Someone should start another journal called "Cell, Nature and Science". Talk about being a shameless ripoff.

Hat tip: Retraction Watch.

Nature tua kee

One of the neighboring lab's graduate students is defending her PhD thesis next week. Her advisor sent out the dissertation defense notification to the whole department with a pdf attachment of the student's Nature Nanotechnology paper.

It seems to me that the student has just one publication to show for her PhD work. If that is really the case, then it isn't impressive at all frankly speaking (Nature Nanotech notwithstanding).

Yeah, call this a case of Nature envy.

Nevada Public Higher Ed Going Bust?

I wonder how the whole situation is going to play out for UNLV-Singapore if the University of Nevada system is to declare bankruptcy.

More details here and here.

Faculty Senate President Cecilia Maldonado had prepared a statement to read. In it, she said she was sad and angry and sick.

She said she was sick of political ideology. Sick of people who attack faculty salaries. Sick of hearing that Nevadans don't value education. Sick that this same debate about whether higher education is a "cost" or an "investment" has been going on for 20 years.

"I'm sick that we never seem to learn our lessons," she said.

Maldonado said the cuts will make it difficult to recruit and retain talented faculty and students.

She began to cry, then composed herself and continued, saying the higher education system should impose cuts elsewhere to save UNLV.

The room broke into applause when she was through.

Hat tip: Leiter Reports.

Incidentally, I watched Idiocracy on DVD last night. It scared the hell out of me because that really seemed to be the way the whole society is moving towards, with the all too frequent assaults on academia (see above, and my previous posts) and a rising anti-intellectual movement.

Virginia's state government seems to be bucking the trend of higher education cuts though.

The plan, which has broad support in the state's General Assembly, is meant to fulfill his goal to increase the number of Virginians with college degrees by 100,000 during the next 15 years, and in particular the number who earn degrees in science and technology.

"These reforms will help us attract new employers to Virginia and better prepare our citizens to fill the jobs that already exist in the state today," Mr. McDonnell, a Republican, said at a news conference in January, announcing the proposal. The cost of the legislation, which has not been determined, is an investment in the state's economic future, the governor said, arguing that higher education returns more tax revenue to the state than it costs.

When Scientific Research and Higher Education become just Political Football

A mere two years after the passage of the economic stimulus package by a Democratically-led Congress, the now Republican-controlled House of Representatives have started swinging their budget cutting axe at scientific research and higher education.

One point stood out in the midst of all this "fiscal responsibility" talk:

The House bill does not specify cuts to five of the Office of Science's six programs, namely, basic energy sciences, high-energy physics, nuclear physics, fusion energy sciences, and advanced scientific computing. However, it explicitly whacks funding for the biological and environmental research program from $588 million to $302 million, a 49% reduction that would effectively zero out the program for the remainder of the year. The program supports much of DOE's climate and bioenergy research and in the past has funded much of the federal government's work on decoding the human genome. - Science , 25 February 2011: Vol. 331 no. 6020 pp. 997-998 DOI: 10.1126/science.331.6020.997

Do the terms Big Oil, Creationism/Intelligent Design come to your mind?

In other somewhat related news, tenure rights are being weakened in Louisiana and state legislatures are trying to have greater control over how colleges are run. It is hard not to see that there seems to be some sort of a coordinated assault against academia (presumably since many academics are seen by the Republican right as leftist liberals).

Lawmakers are inserting themselves even more directly into the classroom in South Carolina, where a proposal would require professors to teach a minimum of nine credit hours per semester.

"I think we need to have professors in the classroom and not on sabbatical and out researching and doing things to that effect," State Rep. Murrell G. Smith Jr., a Republican, told the Associated Press.

Are they attempting to turn research universities into trade/vocational schools? Or are they confused about the different roles the educational institutions play? There are research-focused universities and primarily teaching colleges.

Adieu to the Middle Class, and the Rise of Wee Shumin-ism in America

My previous post talked about the protests by faculty and graduate students in Wisconsin over the dismantling of collective-bargaining rights by public worker unions (and of course the worsening academic job market despite soaring tuition and enrollment in US universities).

What is at stake is more than just that, as Paul Krugman and George Lakoff had helpfully pointed out:

For what’s happening in Wisconsin isn’t about the state budget, despite Mr. Walker’s pretense that he’s just trying to be fiscally responsible. It is, instead, about power. What Mr. Walker and his backers are trying to do is to make Wisconsin — and eventually, America — less of a functioning democracy and more of a third-world-style oligarchy.

and

The central issue in our political life is not being discussed. At stake is the moral basis of American democracy.

The individual issues are all too real: assaults on unions, public employees, women's rights, immigrants, the environment, health care, voting rights, food safety, pensions, prenatal care, science, public broadcasting, and on and on.

Budget deficits are a ruse, as we've seen in Wisconsin, where the governor turned a surplus into a deficit by providing corporate tax breaks, and then used the deficit as a ploy to break the unions, not just in Wisconsin, but seeking to be the first domino in a nationwide conservative movement.

But I digress. I want to point out a few paragraphs in Lakoff's essay that caught my eye (the parts in italics).

...But deficits are not what really matters to conservatives.

Conservatives really want to change the basis of American life, to make America run according to the conservative moral worldview in all areas of life.

Conservatives believe in individual responsibility alone, not social responsibility. They don't think government should help its citizens. That is, they don't think citizens should help each other. The part of government they want to cut is not the military (we have 174 bases around the world), not government subsidies to corporations, not the aspect of government that fits their worldview. They want to cut the part that helps people. Why? Because that violates individual responsibility.

But where does that view of individual responsibility alone come from?

The way to understand the conservative moral system is to consider a strict father family. The father is The Decider, the ultimate moral authority in the family. His authority must not be challenged. His job is to protect the family, to support the family (by winning competitions in the marketplace), and to teach his kids right from wrong by disciplining them physically when they do wrong. The use of force is necessary and required. Only then will children develop the internal discipline to become moral beings. And only with such discipline will they be able to prosper. And what of people who are not prosperous? They don't have discipline, and without discipline they cannot be moral, so they deserve their poverty. The good people are hence the prosperous people. Helping others takes away their discipline, and hence makes them both unable to prosper on their own and function morally.

The market itself is seen in this way. The slogan, "Let the market decide" assumes the market itself is The Decider. The market is seen as both natural (since it is assumed that people naturally seek their self-interest) and moral (if everyone seeks their own profit, the profit of all will be maximized by the invisible hand). As the ultimate moral authority, there should be no power higher than the market that might go against market values. Thus the government can spend money to protect the market and promote market values, but should not rule over it either through (1) regulation, (2) taxation, (3) unions and worker rights, (4) environmental protection or food safety laws, and (5) tort cases. Moreover, government should not do public service. The market has service industries for that. Thus, it would be wrong for the government to provide health care, education, public broadcasting, public parks, and so on. The very idea of these things is at odds with the conservative moral system. No one should be paying for anyone else. It is individual responsibility in all arenas.

Do they remind you of a particular (wealthy) South-East Asian country's style of governance?

"You die your own business" and "Please, get out of my elite uncaring face".

March of the Teachers

Protests in Wisconsin

Very appropriate for current faculty candidates. The (always awful) academic job market is getting worse, and many universities nationwide are either instituting hiring freezes or continuing more layoffs. (A proposed bill in Utah goes further - banning tenure.)

The brightest star burns out the fastest

One of my undergraduates (let's call him D) sent me an email over the weekend announcing that he will be taking a leave of absence from the university starting this week for the rest of the academic year. Apparently he has trouble coping with the stress of school and the college had recommended that he take a break from campus. D is the best among the undergrads in my lab - meticulous in record-keeping, dedicated, smart and hardworking. He is strong in both understanding the theoretical concepts and a hands-on person with good tactile sensitivity (especially with thin-tissue slicing). Everyone has high hopes on him graduating with honors and continuing to medical school.

Perhaps I should have known. He changed somewhat after coming back from the Christmas/New Year holidays - started growing a goatee, taking unannounced breaks from the lab during critical experiments, and wearing differently. His choice of clothes has somehow switched from light colored T-shirts with jeans to black shirts and pants (with an accompanying trench coat).

In light of the recent events in Arizona, the university has also started a more aggressive approach towards reporting of students, staff or faculty who show critical signs of mental stress to the campus mental health services. I wonder if that office had played a role in him taking a break from class. I hope he gets well soon.

Why read

For the love of books
Letter from Preeti Athavle
05:55 AM Feb 07, 2011
TODAYonline

The letter by Chng Hee Kok ("More help for less well-known schools?", Jan 26) was an eye-opener for me. For the first time, I realised how children from low-income families might not be able to visit libraries as their parents might be too busy to bring them.

There are also other children who don't read much. Either they don't know what books to read or their parents don't inculcate the habit in them as they do not consider it important. I'd like to suggest some solutions.

Some local schools have reading programmes (often assisted by parent volunteers) for Primary 1 students who may be lagging behind. Why don't we extend that to higher levels?

We could have a parent volunteer who comes in after school, and reads a chapter or two from a good book (like a Book Reading Club). A good story could ignite interest in some children to actually borrow that book from the library and read. Even if just 10 per cent of the children become willing to read more, it would be worth the time and effort.

I am impressed with the National Library's amazing collection of books and its e-systems that let you renew or search for a book online, for instance.

What is interesting is that in the children's section, you can check the computer for books and authors that have won awards.

For parents and children who don't know which books to read, this provides an easy reference, thereby not restricting the children to Geronimo Stilton, Harry Potter and other such popular books, but also exposing them to the beautiful works of Andrew Clements, Betsy Byars, Cynthia Rylant and many more.

There are parents who think books are a waste of time and their kids should do workbooks instead. But when their child reaches P4/P5, he or she struggles with the harder vocabulary in comprehension passages. Schools could stress to parents from the start that reading books will help their children.

Many a time my son, who is in the Gifted Education Programme, returns from his English exam expressing the desire to read a particular book, his curiosity having been ignited by the comprehension passage which was taken from that book.

Books are our window to the world. They expose us to beautiful writing, historical events, different cultures and much more. But with the growing pervasiveness of TV, computers and video games, children are losing the patience to sit down and read a book. If not cultivated early, a child might never develop this interest.

1. Improve your knowledge,
2. Understand more about life, society and yourself
3. Have Fun,
4. Make your imagination fly,
5. Find new ways to express your ideas,
6. Expand your vocabulary.

Alka Selzer: Acceptance Letter Ad

Funny ad on TV. College is expensive, and tuition costs have been rising more than inflation.