The study, reported this week in Nature, compared the newly sequenced Y of the rhesus monkey to human and chimpanzee Y chromosomes, and found that the primate Y has been remarkably genetically stable for the past 25 million years.

“This and other evidence suggest that some of these genes are important and have been retained in primate lineages,” said Mark Jobling, who studies the sex chromosome at the University of Leicester in the United Kingdom and was not involved in the research. The Y chromosome does not appear to be decaying away, he said.

But not everyone agrees. “I don’t think this means we can relax about the human Y chromosome,” said Jennifer Graves of La Trobe University in Melbourne, Australia, who was also not involved in the study. Graves has been an outspoken advocate of the rotting Y theory, and, in a 2006 review of the subject, predicted that the Y chromosome will decay in an uneven, jerky process. The new data support that prediction, she argued. “One can’t predict [the degradation of the Y], because it’s a very stochastic process,” she said.

Roughly 300 million years ago, during early mammalian evolution, a segment of the X chromosome stopped crossing over with the Y, causing rapid genetic decay on the Y. This occurred another 4 times throughout the history of mammals, and each time the Y chromosome experienced gene loss. The events were so extensive that today the human Y retains only 3 percent of the more than 600 genes it once shared with the X chromosome.

Prior to the present study, only the human and chimpanzee Y chromosomes had been sequenced, though numerous organisms, from fish to insects to plants, have independently evolved Y chromosomes. Jennifer Hughes, David Page, and colleagues at the Whitehead Institute for Biomedical Science in Cambridge, Massachusetts, sequenced the Y of the rhesus monkey and compared it to the other two sequences. Chimpanzees diverged from humans only 6 million years ago, but rhesus monkeys diverged 25 million years ago, so the new information provides a look at how the primate Y chromosome has changed over a much longer period of time. Genetically speaking, it hasn’t changed much.

The rhesus monkey hasn’t lost a single ancestral gene on its Y chromosome in the past 25 million years, and the human Y has lost just one gene in that period. The Y chromosome’s evolution, therefore, is marked by periods of swift decay followed by strict conservation, said Hughes. And that should put the “rotting Y” theory to rest, she added. “We finally have this very strong empirical evidence that there’s been essentially no change in gene content for 25 million years,” she said. “I’m pretty sure it’s going to be hard to argue with that.”

Yet the study also revealed that the rhesus Y does not have large sections of repeated DNA sequences, called palindromes, that the human and chimpanzee Y chromosomes both have, Graves pointed out. “This means human and chimp lineages must have quite recently gone berserk and made lots of copies,” she said. “To me, that amplification is the last gasp of the Y chromosome.” Two Japanese rice rat species, for example, recently lost their Y chromosomes, and a third has a Y that is now making lots of palindromes. That Y chromosome has “gone bananas,” said Graves, signaling that it will soon disappear as it did in the other two species.

Whether the Y continues to degrade or not, the fact that a core set of genes has stuck around, despite major loss events, suggests that these genes were selected for by natural selection. “The genes that are still on the human Y chromosome have been around for a long time, and that suggests they must actually be doing something useful,” said Jobling. Unfortunately, scientists don’t know what that is. “The Y chromosome has been neglected,” he said. Beyond sex determination, “we really have very little idea” what most of the genes on the chromosome do.

“But we’d love to know,” added Hughes, who plans to follow up the research with functional studies of the conserved genes. The team also plans to sequence Y chromosomes from other animals, including the rat, mouse, and opossum. “They have interesting positions in the mammalian tree and are model organisms,” Hughes said.

J.F. Hughes et al., “Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosome,” Nature, doi:10.1038/nature10843, 2012.

CellTex licenses therapies from RNL Bio, a South Korea-based company that converts patients’ fat cells into patient-specific mesenchymal stem cells, which the company claims can be reinjected to treat conditions like spinal cord injury. To date, no clinical trials have been completed that back these claims.

Though criticism has been leveled at McGee for joining CellTex while remaining at AJOB, observers also wonder whether bioethicists can work in industry at all. McGee has argued that bioethicists have a place in industry, thereby helping bioethics to have a practical purpose. Others, such as Insoo Hyun, a stem-cell bioethicist at Case Western Reserve University in Cleveland, Ohio, are doubtful. Hyun developed patient consent procedure for egg donation for Woo Suk Hwang, the infamous Korean stem cell researcher whose claims of human cloning later proved fraudulent.

“I know firsthand how difficult it is to separate conflict of interest—to maintain the role of bioethicist,” Hyun told Nature. “I know you need to not be too chummy with enterprises trying to speed ahead in stem cells.”

This declaration came to my mind after I experienced three separate occurrences. The first was my application for a European research grant. At the end of the evaluation procedure, the reviewers wrote that my proposal was interesting, I had a good track record of publications, and the project had been well described. Nevertheless, they had to reject my application since I am a “good” but not “outstanding” researcher. This reply was received after I had applied for dozens of research grants without success.

My reading of a comment by John P. A. Ioannidis in Nature (477,529–531 2011) was the second occurrence. He wrote: “…the research behind 30 percent of the pivotal papers from Nobel Laureates in medicine, physics, and chemistry was done without direct funding.” The third occurrence was the refusal by a grad student of mine to enroll in my PhD program. He replied to me: “Thank you for your offer; I am proud of it, but I have to find a way to earn money in a better way. Prestige is not something you can use to pay bills.”

When these three events occurred last year, it made me realize the pervasive problems that exist in the current research funding system. It is obvious that at a time when there is a shortage of funding, only those scientists who are truly outstanding have a good chance of receiving grant awards. I myself know that I am a good scientist, but that there are individuals out there who are better scientists than me. Nevertheless, I do my job to the fullest and make my own contribution to the advancement of science. Funding only the extraordinary may only serve to widen the gap between top laboratories and other scientific institutions and could actually be detrimental for the progress of science. Indeed, there are good researchers from less known facilities who would greatly contribute to the advancement of scientific knowledge if they had access to financial support. To avoid this, reviewers of grant applications should not have a bias toward proposals coming from well‐established and already highly financed labs.

The current funding regime also discourages curiosity‐driven research. We have to write boring applications, always identifying the possible impact on human progress and health. We must precisely indicate what will happen at the end of the research study, and what the short‐ and long‐term expectations are. We have to foresee all the possible pitfalls and caveats. It is true that a research project should have a research plan with expected results, possible alternative plans, and an understanding of the potential impacts on scientific advancement. These, however, are not the only criteria upon which reviewers should evaluate a project. Consider this: if everything goes as we reasonably hypothesize, why do we have to waste time performing research? Science is not done to confirm the obvious. The 2006 Nobel Prize winners Andrew Z. Fire and Craig Cameron Mello, for example, were studying a gene involved in body axis formation when they stumbled upon RNA interference phenomena that have completely revolutionized biology and medicine. It was a curiosity-driven study that produced unexpected results not written in any research proposal.

Day in and day out, modern society is based exclusively on money. Education is considered less important for obtaining and measuring success. The fact that so many individuals without a college degree get paid higher salaries than a competent scientist who has successfully completed a degree in higher education is simply wrong. Why should I be shocked by my student’s reply if at the university level scientists are evaluated by their peers mainly for their ability to get money? Where are the defenders of sheer science? I guess they lost their way.

I do not want to make a useless complaint. Below you will find some proposals that may be amended, ameliorated, or discarded. Additional or alternative ideas are highly welcomed.

1) Equalize the power: If a company or firm holds a position of such economic power that allows it to operate in a market without being significantly affected by competition and engages in conduct that is likely to impede the development or maintenance of effective competition, it is considered an abuse of its dominant position. The same idea should also be applied to scientific institutions, research groups, and individuals. For example, for new grant applications, it should be mandatory to indicate all the research grants and endowments a given person/institution has. If two research proposals have roughly the same scientific value, the grant agency should favor the proposal of the less endowed group/institution, rather than the group with the more impressive track record.

2) Avoid personal bias: As in the case of NIH, all grant agencies should have scientific panels composed of 20‐25 experts whose names are disclosed and not hidden, and the applicant can choose the panel to whom to send his/her application. He or she does not know who among the members of panel will be selected to review his/her grant but, for will be able to avoid panels on which there are persons who may potentially have a bias towards his or her proposal.

3) Reward the “good” ones, too: Usually grant applications require the h‐index and/or impact factor of the principal investigator in order to give a global score to the research proposal. Highly cited scientists take it all. I suggest offering research awards dedicated to “good but not outstanding” scientists, analogous to the awards available to only “young investigators.” This could be done, for example, by accepting applications from only scientists with a good but not outstanding h‐index (track record of papers, etc.).

4) Consider the environmental advantage: Grant agencies also evaluate the scientific environment to see if the research will be carried out in a scientifically encouraging institution. Of course, they claim that the better the institution is, the better the research will be done. Reverse this idea. Do you think it takes the same effort for researchers in less developed countries that do not invest much in research to publish a decorous research in a good journal (say, with an impact factor between 5 and 10), as it does for researches in wealthy nations? Even inside wealthy countries there are inequalities. Do you think it takes the same effort to publish if a researcher works in a prestigious American institutions (Yale, Harvard, Cold Spring Harbor, etc.) or in less known and endowed teaching universities? I believe that those scientists who do objectively good research but who come from an unfavorable environment are the ones who should be awarded the funding.

5) Get to the point: Research application forms must be simple, not like the nightmarish forms of the European Community. Reviewers should focus on the core of the project and not the short‐, middle‐ and long‐term impact on scientific progress.

Umberto Galderisi is a molecular biology professor at the Second University of Naples in Italy and an adjunct professor at the Sbarro Institute for Cancer Research and Molecular Medicine Center of Biotecnology Temple University in Philadelphia.  He is also the president of Stem Cell Research Italy, a young scientific association that gathers more than 200 Italian researchers. He can be reached at umberto.galderisi@unina2.it.

Researchers in the United Kingdom, Japan, and Sweden found that the interaction between two morphogens—fibroblast growth factor and Sonic hedgehog—alternately triggered and hindered cellular activity, leading to the development of ridges, called rugae, in the palates of developing mice. They published their results on the website of Nature Genetics. “There are several theories about how patterns in nature are formed, but until now there was only circumstantial evidence for Turing’s mechanism,” senior author and King’s College London cell biologist Jeremy Green told The Telegraph.

Though researchers had modeled Turing’s theory using computers, “our study provides the first experimental identification of an activator-inhibitor system at work in the generation of stripes—in this case in the ridges of the mouth palate,” Green added. The mechanism is likely to play a role in the development of other patterns seen in animal development, such as spots or stripes on skin.

Turing, who would have celebrated his 100^th birthday this June, was criminally prosecuted with homosexuality, which was a crime in the UK at the time, the month he completed his morphogen paper. He committed suicide 2 years later by eating a cyanide laced apple. “He was a great British genius,” Green said. “He had the confidence to take a completely new field, biology, and ask, ‘What can I add to it?’”

“The same algorithm that is used to understand how Web pages are connected can be used to understand how molecules interact,” said Aurora Clark, a chemist at WSU, in a press release. The team is first applying the software to study hydrogen bonds, since water molecules are ubiquitous in biological processes, including protein folding. Just as Google’s software measures and prioritizes the relevance of Web pages to a user’s search, moleculaRnetworks will predict molecular interactions based on which molecular links are stronger and more likely than others.

Researchers could potentially use the software to design drugs, investigate misfolded proteins, and analyze pollutants, Clark said. The research is described in the 30 March issue of the Journal of Computational Chemistry.

Google execs are pleased with the application, InformationWeek reported. “Our goal in search is to help people expand their knowledge of the world, and we’re delighted to see that our PageRank algorithm is being used to do just that,” said Amit Singhal, Google Fellow and senior vice president.

Poisonous invasive species don’t deter the hungry Australian bluetongue lizard. A new paper in the American Naturalist found that the native lizards that eat toxic mother-of-millions plants are largely resistant to the toxins of the invasive cane toad, which has wreaked havoc on Australia’s ecosystems since being purposefully introduced in 1935 in an attempt to control the native cane beetle, which damages sugar cane crops. Both the plant and toads produce a toxin called bufadienolide. When injected with a non-lethal dose of bufadienolide, bluetongues from areas of Australia without the toxic plant swam 50 percent slower than normal, while bluetongues from areas with the plants swam only 20 percent slower, demonstrating a resistance to the poison.

The researchers hope that resistance will lessen the impact of another potential invader with a similar toxin, the black-spined toad, ScienceNOW reported. The toad has already invaded numerous countries in Asia, and might soon make the leap to Australia.

Ultrasonic cryptography

Philippine tarsiers may be small, but they have a superhero sense of hearing. The little primates, often no bigger than a human hand, communicate using ultrasonic sounds, according to a study published earlier this month in Biology Letters. Only a few other mammals, including cetaceans, domestic cats, and some bats and rodents, send and receive vocal ultrasound signals. The tarsiers’ squeaky calls, well above the vocal range of any known monkey or ape, may keep predators like birds from listening in on their conversations, reported ScienceNOW. The ability to hear the ultrasonic sounds may also help tarsiers zoom in on their prey—small insects that also communicate using ultrasonic frequencies.

Researchers tested the primates for ultrasonic abilities after casual observations that tarsiers occasionally opened their mouths as if to shout, but no sound humans can hear came out. “Philippine tarsiers have often been described as quiet,” co-author Marissa Ramsier, an anthropologist at Humboldt State University in California, told ScienceNOW. But “they’re screaming and talking away, and we just didn’t know it.”

Song of the dead

A 165-million-year-old cricket song has been resurrected. Researchers at China’s Capital Normal University compared the well-preserved wing structures of fossil Archaboilus musicus, a Jurassic ancestor of modern crickets, to contemporary cricket wings, Wired reported, and from that reconstructed what the song might sound like. The low-frequency, high-pitched song may have helped the ancient crickets communicate in the leafy, fern-filled Jurassic forest in which they lived, the authors suggested in a recent PNAS paper.

Bonobo takes up cooking

Kanzi <span>Courtesy of the Great Ape Trust</span>

Kanzi, a famous bonobo at the Great Ape Trust in Des Moines, Iowa, understands 3,000 spoken words and can communicate 500 words by pointing to symbols. Now he’s added another impressive skill to his resume—cooking a hamburger. It is the first time a non-human primate has demonstrated the ability to cook food, the Daily Mail reported.

According to his keepers, Kanzi has always been fascinated by campfires and was encouraged, though never instructed, to build them. In a video taken by the Great Ape Trust, Kanzi builds a fire, toasts marshmallows, and grills hamburgers. Finally, like a good camper, he pours water over the fire to put out the flames when finished. See a video of Kanzi in action.

Hot finger

Note the aye-aye's long twig-like third finger<span>Cenz, Flickr</span>

The Madagascar aye-aye, the largest nocturnal primate, is recognizable for its strange, twig-like middle finger, an extra-long appendage packed with nerve endings and used to tap tree trunks to find beetle larvae. It turns out the aye-aye is able to regulate the temperature of that single digit, according to a paper in the International Journal of Primatology.  Researchers at Dartmouth College in New Hampshire used infrared imaging to examine the finger, and found that it remains cool when not in use but warms by up to 6°C when the animal uses it to forage.

Because of its specialist sense receptors, the finger is costly in terms of energy, co-author Gillian Moritz told BBC Nature. “Like any delicate instrument, it is probably best deactivated when not in use,” she said. How the lemur controls the heating of a single digit remains unknown.

Friendly seas

Wildlife videos typically show species interacting, but usually one species is attacking another. In a heartwarming twist on this typical scenario, researchers recently recorded two separate instances of bottlenose dolphins “riding” humpback whales in Hawaii: the whales lifted the dolphins up and out of the water, and the dolphins slid back down into the surf. Both species seemed to cooperate, with no aggression, in the rarely observed social activity. The interaction was described in Aquatic Mammals and a video of the encounter was recently on display at the American Museum of Natural History.

While the measure could both ensure the productivity of researchers handling multimillion dollar budgets, as well as potentially allow less-established researchers a slice of the money, some are worried about moving away from a purely merit-based system. “It’s a huge sea change,” Howard Garrison, director of public affairs at the Federation of American Societies for Experimental Biology in Bethesda, Maryland, told Nature.

John Tainer, a structural biologist at the Scripps Research Institute in La Jolla, California whom Nature identified as one of the top seven researchers receiving the most NIH grants—added that the measure may end up stifling innovation at established, time-proven labs.

“If you’re a leader and you have momentum and technology, the impact of taking that away and having other people do it at a different level is destructive,” Tainer told Nature.

CORRECTION: In the original version of this story, the term principal investigator was incorrectly written as “private” investigator. The Scientist regrets this error.

On Friday (February 17), several organizations representing scientists and journalists—including the Professional Institute of the Public Service of Canada, which represents 23,000 federal scientists, the World Federation of Science Journalists, and the Canadian Science Writers Association—published an open letter to Prime Minister Harper requesting more freedom.

At the American Association for the Advancement of Science (AAAS) meeting in Vancouver, a panel discussed the problem, which took effect in 2007. “This isn’t about some abstract right that scientists get to chatter about,” said panelist Francesca Grifo of the Union of Concerned Scientists in Massachusetts, according to Huffington Post Canada. “This is about important information that has critical repercussions for our health, our safety, our environment, our world, our future, our children’s future.”

The letter calls for a more transparent policy that allows scientists to respond in a timely matter to journalist requests—such as that in place at the US National Oceanic and Atmospheric Administration, that “even encourages scientists to express their own opinions, provided they indicate that they are speaking personally and not on behalf of the employer,” the letter says.

New York State Health Department investigators have ruled out some environmental factors and infectious agents, including Streptococcus, which can cause a tic-like syndrome called PANDAS or PANS for Pediatric Acute-onset Neuropsychiatric Syndrome.

Although investigators found no contaminants in the air or water within the school, the building is located some 5 kilometers from the site of a 1970 chemical spill that released “cyanide crystals” and trichloroethene (TCE) into the surrounding area, and some worry that this could be affecting the students. Though TCE has been linked to conditions such as cancer, liver damage, nausea, as well as increased risk of Parkinson’s, the development of tics is not listed among the observed symptoms of TCE exposure. TCE levels were not elevated in the school water.

Developed by MIT professors Robert Langer and Michael Cima and scientists at Massachusetts-based biotech MicroCHIPS Inc., this is the first time such chips have proven their worth, Langer said in a press release. Given their wide applicability, the chips may just change how doctors monitor their patients’ medical care.

“You could literally have a pharmacy on a chip,” Langer said in a press release. “You can do remote control delivery, you can do pulsatile drug delivery, and you can deliver multiple drugs.”

The results were reported last week in Science Translational Medicine.