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Preview: Being Human - Short Sharp Science

Being Human - Short Sharp Science



A New Scientist blog



Updated: 2012-10-11T04:17:31Z

 



Cheap genome sequences demand new rules on privacy

2012-10-11T04:17:31Z

In the age of the $1000 genome, people's genetic information will need protecting from prying eyes Peter Aldhous, San Francisco bureau chief In the era of the $1000 human genome, new rules will be needed to protect people's genetic privacy. So warns the US Presidential Commission for the Study of Bioethical Issues, which is calling for a ban on unauthorised genetic sequencing - citing New Scientist's 2009 investigation into genome hacking as evidence of a looming threat. The US government and individual states should harmonize a mish-mash of laws to ensure a basic "floor" of genetic privacy protection across the nation, however the data information was obtained, the commission adds. For instance, if a volunteer has their genome sequenced for research, the information should have similar protection from prying eyes as if the analysis had been ordered by a doctor for diagnostic purposes.  "In order to make full use of whole genome sequencing, which holds out enormous promise for human health and medicine, we're going to have to figure out how to protect people's privacy and avoid harms that can come from the misuse of this very personal data," says commission chair Amy Gutmann, president of the University of Pennsylvania in Philadelphia.Breaches in security of DNA sequence data held on computer systems are the most obvious threat. But in 2009, New Scientist pointed to another danger by simulating the surreptitious analysis of my genome: a colleague used commercially available services to extract DNA from a glass from which I had drunk, and analyse it for my genetic predispositions to disease.We ordered a scan of about 1 million letters of my genetic code, but plummeting prices and advancing technology will soon make it feasible to obtain a full genome sequence in a similar way, at modest cost. The new report comes down firmly against surreptitious genome sequencing: "[P]olicies should protect individual privacy by prohibiting unauthorized whole genome sequencing without the consent of the individual from whom the sample came." In an earlier article in the same series, New Scientist teamed up with the Genetics & Public Policy Center in Washington DC to look at variation from state to state in laws covering surreptitious genetic testing.This is part of a larger patchwork of regulation on genetic privacy that the bioethics commission wants to see overhauled.One big split is between research and clinical medicine. A patient's medical records come under the federal Health Insurance Portability and Accountability Act, which provides criminal penalties for knowingly disclosing medical records containing personally identifying information, such as people's names and social security numbers.  However, it remains unclear whether genome sequences ordered for diagnosis would themselves be protected as personal information under HIPAA.Geneticists taking samples for research are not covered by HIPAA, but separate rules covering informed consent and the protection of research subjects. Researchers are usually careful to protect volunteers' privacy, but if breaches were to occur, those responsible would not be subject to the same criminal prosecution.Without clear and consistent guidelines to protect personal genetic information, the bioethics commission fears that people could suffer harm - in part by keeping secret information that could help their doctors provide better treatment.As a cautionary example, the report notes the case of Victoria Grove, whose story was revealed in a 2008 article in The New York Times. For nearly three years Grove kept secret from her doctors that she had tested positive for a genetic condition called alpha-1 antitrypsin deficiency, worried that she might be denied health insurance. It was only when Grove developed a bout of pneumonia that she knew could lead to permanent lung damage for people with the condition that she broke down, explaining in a tearful phone call to a clinic why she needed an urgent prescription for antibiotics.However, in[...]



Global project reveals just how active our 'junk' DNA is

2012-09-06T15:49:04Z

The reams of "junk" DNA that make up the majority of our genetic code appear to have a purpose after all, according to the latest results from a global research collaboration Jessica Hamzelou, reporter (Image: Laguna Design/SPL/Getty)The reams of "junk" DNA that make up the majority of our genetic code appear to have a purpose after all, according to the results of a global research project. The DNA within all of our cells makes RNA, which in turn makes proteins. But only 1.2 per cent of our DNA provides the protein-making instructions. Exactly what the rest of our DNA is doing has been something of a mystery. The leading theory, although this has been on shaky ground for a while now, has been that the non-coding, junk DNA didn't really do anything at all. But this idea has finally been laid to rest by the new findings of a massive research effort. In 2003, the US National Human Genome Research Institute launched the Encyclopedia of DNA Elements project (ENCODE), a consortium of over 400 researchers from 30 or so labs whose aim was to work out exactly what different parts of the human genome do. The researchers' first results - based on an analysis of 1 per cent of the human genome - were published in 2007. The group found that some so-called junk DNA appears to be transcribing or making RNA, although this RNA doesn't then make new proteins. Since then, the collaboration has widened its research with the aim of getting to grips with the entire human genome. In the latest study, the group analysed 147 types of cells - including cancer, liver and bone cells - and observed which sections of DNA were transcribed to RNA, and what the RNA might be doing. They found that, across the genome, about 19 per cent of our DNA may code for RNA switches that turn genes on or off. "We see way more switches than we were expecting, and nearly every part of the genome is close to a switch," project coordinator Ewan Birney of the European Bioinformatics Institute in Cambridge, UK, told New Scientist. The switches also appear to be spread out over the genome, with some being located at a distance from the gene they are controlling. Around 95 per cent of the genome appears to be very close to a switch, suggesting that almost all of our DNA may be doing something important. While the team do not yet know exactly what the switches are doing, the researchers hope that further study might reveal how some diseases are inherited. "Most of the changes that affect disease don't lie in the genes themselves; they lie in the switches," team member Michael Snyder at Stanford University, California, told The New York Times. So does this mean that "the term junk DNA must now be junked" as Birney told the BBC News? Not so fast. As New Scientist points out, this may not be the end of the story. It has yet to be shown that the DNA previously known as junk gets selected for because it confers any evolutionary benefit. To read more about the many research papers published this week in Nature and other journals, see our in-depth feature, "The ever deepening mystery of the human genome", and accompanying editorial "Don't junk the 'junk DNA' just yet". [...]



ESP evidence fails key test of repeatability

2012-09-05T14:44:02Z

Controversial claims about precognition are crumbling to dust as replication attempts mount Peter Aldhous, San Francisco bureau chiefWe cannot see the future. That's the conclusion from a meta-analysis of studies attempting to replicate astonishing findings on "precognition"  - which suggested that people's behaviour is influenced by events that haven't yet happened.The original findings, revealed in 2010 by Daryl Bem of Cornell University in Ithaca, New York, would have turned established views of causality and human perception on their head. New Scientist's bet at the time was that most attempts to repeat the experiments would fail to replicate Bem's results.Bem's experiments were disarmingly simple: he ran well-established psychological experiments - for instance those showing that typing selected words from a presented list facilitates their later recall - in the reverse order. In this case, student volunteers were better at remembering words that they would later type. Several groups have reported previously on their attempts to repeat Bem's work, with most failing to replicate his findings. In the new paper, a team led by Jeff Galak of Carnegie Mellon University in Pittsburgh not only conducted their own experiments on the word-recall tests, but also ran a statistical analysis combining results from their work, Bem's studies and 10 other experiments.That's important, because such meta-analyses are considered the best approach when assessing a body of scientific evidence - used, for example, to combine the results of multiple clinical trials to determine whether a medical treatment works.The Journal of Personality and Social Psychology, in which both Bem's research and the new paper appeared, had earlier been criticised for failing to publish a failed attempt to repeat Bem's work. At the time, journal editor Eliot Smith, a psychologist at Indiana University in Bloomington, said he was open to publishing a meta-analysis."It seems that the normal practices of scientific research and journal publication can effectively correct claims that turn out to be incorrect or overstated," wrote Smith in an email to alert reporters to the new paper."An effect is not an effect unless it is replicable," conclude Galak and his colleagues, who nevertheless praise Bem for encouraging other researchers to repeat his work. [...]



When do life crises strike? Help us find out

2012-02-08T17:46:54Z

Scientists want to find out exactly when and why life-changing crises occur - and who is most likely to succumb. Find out how you can help

Jessica Griggs, careers editor

Psychologist Dan Levinson once remarked that he had never met anyone who had not gone through at least one major crisis during their adult life.

While films, sports-car cliches and personal experience may back up his comment, the questions of when and for whom crises occur have received little academic attention. Well, not for much longer.

Last year, New Scientist reported on the phenomenon of the quarter-life crisis; the re-evaluation and dramatic change of direction that sometimes occurs during early adulthood.

This was based on research carried out by researchers at the University of Greenwich who interviewed 50 young people about their emotional experiences during this time. The work established that the quarter-life crisis exists (as corroborated by the comments on our news story) but the sample wasn't large enough to determine how common it is or when it occurs.

Now, the innermost secrets of the crisis are to be laid bare. The Greenwich team are conducting an online survey of British adults which will probe the link between crisis episodes, age and life stage across a diverse group of adults.

The researchers are looking for adult volunteers to participate in the study. You can take part here (and be in with the chance of winning a cash prize for your efforts).

Stay tuned as New Scientist will exclusively report the findings later this year.





Brain scans should not be used in court... for now

2011-12-13T18:10:02Z

Neuroscience should be used to raise age of criminal responsibility, but it's too soon to scan the brain to spot benefit cheats, liars and psychopaths Jessica Hamzelou, contributorShould an offender's sentence be decided on the basis of a brain scan? A group of neuroscientists have put together a report for the Royal Society to assess this issue and other ways that progress in brain science might impact the law.Neuroscience is already making waves in court: an Italian woman convicted of murder recently had her sentence reduced on the grounds that her behaviour could be explained by abnormalities in her brain and genes. The authors on the Royal Society panel, led by Nicholas Mackintosh of the University of Cambridge, also flag up research that suggests the brains of psychopaths are fundamentally different. This raises the question: should individuals with the brain anatomy of a psychopath have their sentence reduced on the ground of diminished responsibility, or should brain scan evidence be used to keep dangerous individuals locked away? Perhaps one day we may also be able to find neurological clues that help predict whether a criminal is likely to reoffend. The report only goes so far as to suggest that such information may be useful in conjunction with other evidence. Another key issue is that of the age of criminal responsibility. In England, the age at which a child can be tried as an adult is ten - this is too low, say the report's authors. Recent research into brain development suggests that crucial brain regions - such as the prefrontal cortex, which is important in decision making and impulse control - don't actually finish maturing until the age of around 20. Neuroscientists claim to be able to identify certain patterns of brain activity that are associated with lying, a finding that has raised the possibility of brain scan-based lie detection. But many remain skeptical that such an approach can ever be useful in the legal setting. Lie detection research is often based on students telling untruths that are unlikely to have any impact on their lives - a situation that's difficult to compare to a criminal who might be lying for his life, not to mention that of a cunningly deceptive psychopath. Moreover, as the report points out, if such lie detection were possible, it wouldn't detect when a person was telling a falsehood they believed was true, or whether a person had learned how to trick the system. "In one experiment, the success rate for distinguishing truth from lies dropped from 100 per cent to 33 per cent when participants used countermeasures," say the authors. They conclude that "for the foreseeable future reliable fMRI lie detection is not a realistic prospect." In the same vein, attempts to measure the amount of pain that a person is in - perhaps to catch people who cheat on health insurance payouts - could also be foiled by individuals who learn how to simulate the brain activity associated with the experience of pain, the authors say. And then there's that old chestnut: "my brain made me do it". In some cases it seems the argument can be made. For one man, paedophilic tendencies appeared and disappeared with a tumour in his orbitofrontal cortex - a region linked to judgement and social behaviour. Most cases aren't so clear cut. The report concludes by recommending that neuroscientists and lawyers from around the globe meet to discuss the latest in each discipline once every three years. In the meantime, the authors recommend that the legal system consult with groups such as the British Neuroscience Association to assess how lawyers currently access scientific expertise. The authors also reckon it would be useful for law degrees to include some background in neuroscience, and for neuroscientists in training to consider the societal applications of their science. [...]



Science 'geniuses' win $5 million

2011-09-21T10:59:05Z

Nine scientists and a science radio host have each won $500,000 MacArthur "genius" grants intended to help them "advance their expertise" Lisa Grossman, reporter Nine scientists and a science radio host are among the 22 people to receive $500,000 MacArthur "genius" grants this week. Each year the MacArthur Foundation gives the no-strings-attached awards to innovative thinkers "to advance their expertise, engage in bold new work, or, if they wish, to change fields or alter the direction of their careers". This year, the honours went to: Jad Abumrad, co-host and producer of the radio show "Radiolab," which explores the mystery and wonder of science through playful, curious and deeply thoughtful conversations with scientists and experimental soundsmithing. Elodie Ghedin, a parasitologist and virologist at the University of Pittsburgh in Pennsylvania who uses genomic sequencing techniques to attack human pathogens, from tropical parasites that cause diseases like elephantitis and sleeping sickness to the rapidly-mutating influenza A virus. Markus Greiner, a condensed matter physicist at Harvard University who is developing ways to trap thousands of ultra-cold atoms in order to study quantum phenomena like superconductivity under well-controlled conditions. Kevin Guskiewicz, a sports medicine researcher at the University of North Carolina, Chapel Hill, who has developed new ways to diagnose and treat sports-related concussions by placing accelerometers in the helmets of young football and hockey players. Matthew Nock, a clinical psychologist at Harvard, who studies suicide and self-injury in adults and adolescents and is seeking to disentangle the neurobiological aspects of self-harming behaviours from those that are dependent on cultural context. Sarah Otto, an evolutionary geneticist at the University of British Columbia who studies questions like why some species reproduce sexually and why some have more than one copy of each gene. Shwetak Patel, a computer scientist at the University of Washington in Seattle who invented a series of sensor systems that let people track their water and energy use in their homes. Melanie Sanford, a chemist at the University of Michigan, who is developing ways to use metal-based agents like palladium to modify specific carbon bonds in complex molecules, while leaving other bonds untouched. The work could streamline the reactions necessary to produce molecules useful for pharmaceuticals, while increasing their yield. William Seeley, a neuropathologist at the University of California, San Francisco, who studies the origins of frontotemporal dementia, which is the second most common cause, after Alzheimer's, of early dementia. Yukiko Yamashita, a developmental biologist at the University of Michigan, who studies stem cell division to figure out which ones go on to replace specialised cells that are infected or worn out, and which ones maintain a reservoir of stem cells for future use. [...]



Belly button biomes begin to blossom

2011-06-30T21:35:23Z

A project to explore the bacteria present in the human navel has revealed over 600 microbes that may be new to science Peter Aldhous, San Francisco bureau chief The human navel should be designated as a bacterial nature reserve, it seems. The first round of DNA results from the Belly Button Biodiversity project are in, and the 95 samples that have so far been analysed have turned up a whopping total of more than 1400 bacterial strains. In 662 cases, the microbes could not even be classified to family, "which strongly suggests that they are new to science", says team leader Jiri Hulcr of North Carolina State University in Raleigh. The project was conceived as a light-hearted exercise in science communication, but is making a serious contribution to the understanding of microbial diversity. Since New Scientist wrote about the initiative in April, samples of bacteria taken when volunteers swabbed their navels with Q-tips have had their "DNA barcodes" read by sequencing the gene for 16S ribosomal RNA, widely used in studies of bacterial evolutionary relationships. My own sample was among 10 per cent of those in the first round in which reactions to amplify the DNA present failed - so the next installment of the comparison of my belly button biome with that of fellow science writer Carl Zimmer will have to wait for another day. Still, Zimmer has already been having some fun with his results, finding among other things that his belly button hosts Georgenia bacteria, previously found in Asian soils. Results like this reflect our ignorance of microbial diversity, Hulcr suggests: the inhabitants of our navels seem weird because biologists haven't sampled sufficiently extensively to document the full diversity of microbial life in a variety of habitats. He likens reactions to the first round of belly button results to the astonishment of the first European explorers seeing African big game - which today seem commonplace. "Now you're expecting rhino and elephants," Hulcr says. Also, identifying bacteria to species is difficult. Noah Fierer's team at the University of Colorado, Boulder, classified them into "operational taxonomic units" having 16S ribosomal RNA gene sequences that differed by 3 per cent or less. Apply this standard to mammals, Hulcr explains, and dogs and cats would be lumped together. It means that a "match" between a belly button strain and a species known from the deep ocean, for instance, may actually represent two microbes separated by several million years of divergent evolution. Although the total number of strains recorded was large, the results so far indicate that a small group of about 40 species accounts for around 80 per cent of the bacterial populations of our belly buttons. "It is tempting to think of the abundant species as the good, core biome of bacteria and the rare ones as transients, struggling to take hold, sometimes at our expense," says Rob Dunn, author of The Wild Life of Our Bodies, and head of the lab in which Hulcr works. Confirming that theory will require studies on a new scientific frontier: belly button ecology. [...]



Skin cancer treatment: Biggest breakthrough in 30 years

2011-06-06T16:48:53Z

Two new drugs for an advanced form of skin cancer are being hailed as the biggest breakthrough for cancer of the last 30 years Jessica Hamzelou, reporter Two new drugs for metastatic melanoma - the deadliest form of skin cancer - are being hailed as the biggest breakthrough therapies for cancer in the last 30 years. The drugs reduce tumour size, significantly increasing survival rates. Although melanoma can be cured if caught early enough, individuals in the late stages of the disease are only expected to survive for an average of six months. One of the two drugs - vemurafenib - works by inhibiting the effects of a mutated form of the BRAF gene, which is thought to accompany around half of the cases of malignant skin tumours. Early trials of the drug had shown that around half of patients with the mutation responded to the treatment. Now, Paul Chapman at the Memorial Sloan-Kettering Cancer Center in New York and colleagues have shown that vemurafenib outperforms dacarbazine - the most commonly prescribed chemotherapy drug for metastatic melanoma. In a study presented this week at the American Society of Clinical Oncology annual meeting in Chicago, and published in the New England Journal of Medicine, Chapman's team compared both drugs on 672 patients with late stage, inoperable melanoma and a mutation in the BRAF gene. The group found that 48 per cent of those receiving vemurafenib responded to the treatment, while only 5 per cent of patients responded to dacarbazine. At 6 months, survival was 84 per cent in the group taking vemurafenib compared to 64 per cent in those taking dacarbazine. The results were so impressive that the team stopped the trial early in order to switch all the participants to vemurafenib. Hal Barron, head of global development at Roche, who funded the study, said in a statement: "We are greatly encouraged by the results, which showed that vemurafenib not only extended life and reduced the risk of disease worsening, but also led to significant tumour shrinkage, an important result for this devastating cancer." Yet more encouraging results were presented at the meeting by a group hoping to boost the effects of dacarbazine by combining it with another drug - ipilumumab - developed by pharmaceutical company Bristol-Myers Squibb. Ipilumumab is an antibody that works by boosting the immune system's response to a tumour. Caroline Robert at the Gustave Roussy Cancer Institute in Villejuif, France, and her colleagues compared the effects of the drug in combination with dacarbazine to a placebo in people with late stage, inoperable melanoma. Robert's team found that 28.5 per cent of the 250 patients who received combination therapy survived for two years - a marked improvement on the 17.9 per cent of those taking dacarbazine alone (New England Journal of Medicine, DOI: 10.1056/NEJMoa1104621). The US Food and Drug Administration approved the drug for late stage melanoma back in March after an early viewing of the study results. Now, the European Medicines Agency has recommended the drug for approval in Europe - a decision that the European Commission will make before August. The success of the trials is being met by overwhelming enthusiasm from the cancer research community. Peter Johnson, chief clinician at Cancer Research UK told the BBC: "For the first time, we have effective treatments becoming available for melanoma. Both [studies] show how the research we have been doing is feeding through into help for patients". Lynn Schuchter at the University of Pennsylvania's Abramson Cancer Center told the Associated Press:"This is really an unprecedented time of celebration for our patients." She says that the new drugs are not by themselves cures, but "the future is going to be to build upon the success" by testing combinations of these newer drugs. And that's just what the two [...]



Moody men are more attractive than happy men

2011-05-25T14:32:52Z

A new study claims to have identified the emotional expressions that are most likely to attract the opposite sex Helen Thomson, biomedical news editor (Image: PhotoAlto/Frederic Cirou/Getty) A man walks into a bar, catches a girl's eye, and immediately looks gloomy, moody and averts his eyes. The woman is overcome with sexual attraction. Not your usual love story but maybe a more realistic one. Turns out, a winning smile isn't the way to a woman's heart; men who swagger and look gloomy are more likely to set pulses raising. That's according to Jessica Tracy at the University of British Columbia, Canada, who asked more than 1000 adults to rate the sexual attractiveness of hundreds of photos of the opposite sex. The images showed men and women in various displays of happiness, with big smiles and puffed out chests or shameful glances, lowered heads and averted eyes. In an interview with UK newspaper The Daily Telegraph, co-author Alec Beall, also at British Columbia said: "We did not ask participants if they thought these targets would make a good boyfriend or wife - we wanted their gut reactions on carnal, sexual attraction." The study found that women were not attracted to smiling, happy men, preferring those who looked proud and powerful or moody and ashamed. In an interview with Reuters, Tracy said: "To the extent that men think that smiling is a good thing to do if they want to be found sexually attractive our findings suggest that's not the case." The researchers say that smiling has been linked with a lack of dominance. Tracey reckons moody guys show that they are flawed, but "know it and are tortured by it". Displays of shame, Tracy says, have been associated with an awareness of social norms and appeasement behaviours, which elicits trust in others. On the other hand, men's reaction to women was just the opposite - they absolutely love a smile, says Tracey: "Women who smile are very attractive. That was by far the most attractive expression women showed." She emphasises that the study explored first impression, and the team are not recommending men adopt a no-smile policy for a long-term relationship. "We're not saying don't be a nice guy," she says. But don't worry if you haven't quite perfected "broody" - there are plenty of other ways to attract the girls. Making out that you've got a partner could help. Apparently us girls are a sucker for the married man. And make sure you choose the perfect chat-up line too. And if all else fails, you could always just change your name. Journal reference: Emotion, DOI: 10.1037/a002290 [...]



Half of world's stillbirths are preventable

2011-04-14T11:40:46Z

Half of the 2.6 million stillbirths occurring around the world each year could be prevented with simple interventions and little financial cost Jessica Hamzelou, reporterA mammoth study conducted by a team of international researchers has estimated that over 2.6 million stillbirths occur around the world each year, with the UK having the highest rate of all high-income countries. Ten simple interventions could halve this number, say the authors in a series of papers published in The Lancet today. The research groups adopted the World Health Organisation's definition of a stillbirth - the death of a fetus in the uterus after 28 weeks gestation. Around 7000 lives are lost in stillbirths on a daily basis - more than AIDS and malaria combined, says study co-author Joy Lawn of Save the Children's Saving Newborn Lives programme. To reach this estimate, Simon Cousens at the London School of Hygiene and Tropical Medicine and his colleagues in America, Switzerland and South Africa collected data from stillbirth registrations, national surveys and published studies. The team estimated that 2.64 million stillbirths occurred globally in 2009. According to the estimate, the worldwide stillbirth rate has dropped by 14.5 per cent since 1995. But this rate of decline is still too slow, says Lawn:Still births are coming down at a rate of 1.1 per cent per year, while maternal death is going down by 2.5 per cent per yearCurrently, the bulk of stillbirths - a whopping 76 per cent - are occurring in South Asia and Sub-Saharan Africa. However, the study also revealed surprisingly high figures in high income countries. A study by Vicki Flenady at the Mater Medical Research Institute in Brisbane, Australia and her colleagues suggests that stillbirth rates in high income countries - Australia, Canada, the Netherlands, the UK and the USA - have shown "little or no improvement over the last two decades". Of the five countries, the UK had the worst rate. At a press conference, Steve Hale, chair of Sands, a UK-based stillbirth and neonatal death charity said:Eleven babies every day in the UK are stillborn. That's more than the number that die on the roads So is there anything we can do to cut this figure? One problem with stillbirths is the widespread misconception that these events are "just one of those things", say the authors. Obesity, high blood pressure, smoking and advanced maternal age are all known to be risk factors for stillbirths, making some preventable. In a separate paper in the series, Zulfiqar Bhutta at Aga Khan University in Karachi, Pakistan and colleagues highlighted 10 interventions that, if implemented, could cut the global number of still births by around half.The interventions include folic acid supplementation before and during pregnancy, detection and treatment of syphilis, prevention of malaria and improved obstetric care. "None of these interventions are remarkably new science," says Lawn. An additional study by Robert Pattinson at the University of Pretoria in South Africa and his colleagues comes to the conclusion that such interventions would cost a mere $2.32 per person per year - a small price to pay to avoid the grief and devastation associated with stillbirths. [...]



UFO search engine for those who want to believe

2011-04-13T10:47:00Z

The FBI's Vault contains documents released under FOIA rules and could spawn a raft of UFO theories Paul Marks, senior technology correspondent A photo from declassified FBI archives - OK, not really, this is an exhibit at the International UFO Museum and Research Center in Roswell (Image: Robin Loznak/ZUMA Press/Corbis)Gird yourself for a whole new wave of alien conspiracy theories: the FBI has placed hundreds of pages of information on its past UFO investigations online in a new, searchable database. It means that documents on UFO sightings - and the feverish correspondence between concerned members of the public and the bureau - can now be easily mined for fine-level data. Called the Vault (I can almost see Fox Mulder yanking its door open as Scully looks on), the FBI's new site gathers together documents frequently requested via the Freedom of Information Act - and is designed in part to reduce costs in answering such FOIA requests. It covers many popular subjects - from Al Capone to Marilyn Monroe - and the UFO info is under the heading "unexplained phenomena". The Vault does not contain any previously unreleased information, an FBI spokesman told New Scientist today. So what's really new (and powerful, in my view) is the ability to search the unstructured, often handwritten and/or smudgily typed text. What immediately grabbed news media attention today is a 22 March 1950 memo about an incident in Roswell, New Mexico in June or July 1947: an FBI special agent called Guy Hottel cites an unnamed US air force (USAF) source revealing the recovery of three flying saucers - each crewed by 3-foot-tall humanoids dressed in "metallic cloth". I also played with the Vault myself. Entering "Socorro" in the search box brings up a 147-page document in which the 1964 case of police patrolman Lonnie Zamora in Socorro, also in New Mexico, is mentioned. Zamora saw an O-shaped UFO on the ground with two beings in white coveralls beside it. They disappeared by the time he parked, whence the craft supposedly departed. The detail people will now be able to glean with this facility will doubtless spawn new theories. Similar information releases in the UK and France have added fuel to the fire, too. The balance of probabilities is not really on the side of the UFO believers. In USAF's final Project Blue Book report, it revealed how many "UFO" sighting it had investigated between 1947 to 1969, in the white heat of the Cold War. Of 12,618 sightings only 701 could not be explained. But of course, that's just a conspiracy. [...]



Belly button biome is more than a piece of fluff

2011-04-01T10:00:53Z

Peter Aldhous engages in a spot of scientific navel-gazing - and finds surprising biodiversity hitching a ride on his belly button Peter Aldhous, San Francisco bureau chief No one likes to be accused of navel-gazing, but in the name of science I'm going to take that risk. Yesterday I received an email informing me that this image of microbial cultures grown from a swab taken from my belly button is now online for all to see: In late February, I visited Rob Dunn's lab at North Carolina State University in Raleigh, where a team led by Jiri Hulcr has launched the Belly Button Biodiversity project. The project was conceived as a device to interest the public in microbiology, and to counter the common view that bacteria are nothing but causes of disease. "This fear is based on a lack of awareness that we live in a microbial world," says Hulcr, who notes that even some "self-described germophobes" have confronted their anxieties and given swabs. Hulcr also aims to extend a scientific frontier: researchers are realising that the human "microbiome" - the diversity of microorganisms that inhabit our bodies - is a key influence on our health and physiology. The skin remains poorly explored territory, and the belly button is an ideal sampling point because it doesn't get as scrubbed and sprayed with chemicals as much other, more accessible parts. Like most volunteers, I was initially most interested in comparing my samples with those of others. This, for example, is what grew from the Q-tip that science writing luminary Carl Zimmer poked into his navel when Hulcr's team set up shop at the Science Online 2011 conference in Raleigh in January: The number of colonies, rather than the size of each one, is what reveals the density of microbes in the original swab - competition for nutrients keeps each colony smaller if there are more on the petri dish. But according to Hulcr, the fact that my swab (sample #1203) yielded more colonies than Carl's (#944) doesn't necessarily mean that his personal hygiene is superior to mine. Other factors, including how rigorously we both swabbed (that must be it!), or inherent differences in the habitat provided by our skin, will also come into play. Judging from their appearance, Hulcr expects most of the colonies in my culture to be Staphylococcus epidermidis, the most common species found on human skin. Other cultures grown from the roughly 300 volunteers who have provided samples so far suggest the presence of different microbes. For example, the streak-like colonies seen in the sample pictured below are a telltale sign of bacteria that can propel themselves along using whip-like flagella, such as species of Pseudomonas: And this culture reveals the aftermath of microbial chemical warfare, with two colonies of Aspergillus fungus having wiped out almost everything else through the release of natural antibiotics: While it's possible to extract some information from the overall appearance of the cultures, the real science will start in a couple of weeks' time, when samples from an initial batch of 96 volunteers - hopefully including Carl and I - will be subjected to genetic analysis. Specifically, Hulcr's team wants to record the sequences of the gene for 16S ribosomal RNA, which acts like a "barcode", allowing the bacteria present in the swabs - including those that don't grow well in culture - to be identified to species and strain. Hulcr told me: I would hope that in a few weeks I can tell you what lives on you New Scientist will bring you the next installment in this tale of comparative human microbial diversity as soon as the results are in. [...]



Humans came from southern Africa – maybe

2011-03-09T14:45:58Z

A study of hunter-gatherer genetics suggests that modern humans emerged from southern Africa, not the east as archaeologists have long claimed. Who is right? Michael Marshall, environment reporter If reports this week are to be believed, the entire anatomically modern human population descends from ancestors who lived in southern Africa. This flies in the face of a mass of evidence that the cradle of humanity was east Africa, probably somewhere near the famous Great Rift valley. So where did we really come from? The idea of a southern Africa origin comes from a study of the genetics of African hunter-gatherer groups. Brenna Henn of Stanford University in California and colleagues genotyped people from seven groups, including Khoisan-speakers from the Hadza and Sandawe populations in Tanzania and click-speaking ǂKhomani Bushmen of South Africa, and found many differences. Nature News explains: These sorts of differences have allowed geneticists to calculate relationships and moments of evolutionary divergence... The team used the geographic locations of the genetically diverse groups of people to determine where humans might first have emerged. The researchers found genetically diverse groups in central and eastern Africa, but most were in the south of the continent. As Henn told the BBC: Populations in southern Africa have the highest genetic diversity of any population, as far as we can tell. So this suggests that this might be the best location for [the origins] of [anatomically] modern humans. We already knew that humans elsewhere in the world have lost much of their diversity, partly because the population crashed 70,000 years ago and many rare genes were lost, and partly because most humans are descended from farming populations, which tend to be low in diversity. So the finding that African hunter-gatherers retain so much diversity is pretty uncontroversial. It's one thing to use the genetics to work out how the different hunter-gatherer groups, and indeed the rest of humanity, are related. In that regard, everyone I spoke to this week agreed that Henn and colleagues' work is important. Hans-Peter Uerpmann of the University of Tübingen in Germany calls it "serious research and solid results". But it's another to try to work out where the ancestral modern human population lived based on where humans live now. Anatomically modern humans began expanding out of Africa between 125,000 and 60,000 years ago. We simply don't know whether the ancestors of Bushmen now living in southern Africa were there all that time, or if they moved there fairly recently. Sarah Tishkoff of the University of Pennsylvania in Philadelphia says: Genetic studies like this can teach us a lot about the demographic histories of African peoples, but we have to be extremely careful when making inferences about their geographic origin. Modern populations may not have originated in the location where they are currently living. It is important to combine archaeological, linguistic, and genetic data to obtain a complete picture of modern human origins. Uerpmann agrees: I am sceptical with regard to the conclusions drawn from recent patterns of genomic variability. In particular the geographic distribution of hunter-gatherers was greatly affected during the Holocene by the spread of pastoralists. Southern Africa is sort of a "refugium" for these peoples, which may have lived farther north at the time under consideration for the first occurrence of "moderns". I put this to Carlos Bustamante of Stanford University, one of the authors of the paper. He said: It's a fair question. We took care to remove any known migrations from the last few thousand years. For instance, the Bantu migration had a large i[...]



Plague scientist dies of... the plague

2011-03-07T20:40:00Z

A bizarre turn of fate left a plague researcher vulnerable to bacteria that couldn't normally even kill mice Debora MacKenzie, reporter  It must be a recurrent nightmare for researchers who work with deadly microbes: being killed by your own research subjects. Microbe hunters know better than anyone else just how nasty infectious disease can be, and they spend much of their professional lives wielding bleach and maintaining stringent lab protocols to keep the objects of their fascination at bay. But sometimes one jumps the fence. Just such a tragedy caused the death in 2009 of Malcolm Casadaban, aged 60, a respected plague researcher at the University of Chicago. But how it did so was a mystery, until now. Plague has a fearsome reputation, being blamed (unfairly, some believe) for the medieval Black Death. But the bacteria are far harder to catch than many lab pathogens - in nature you must inhale lots of bacteria, or have them injected by a flea bite. The plague bacteria Casadaban was working with were deliberately weakened, and unlike ordinary plague, they aren't even on the US list of potential bioweapons bugs. Medical investigators later found they couldn't even kill mice with the bacteria that killed the scientist. So how did Casadaban die? It turns out his death was a medical coincidence worthy of the hit TV series House, in which crack diagnosticians try to figure out tough cases. Their patients typically have unusual combinations of conditions, something Casadaban unfortunately fell prey to.Casadaban's lab bugs were weak because they have trouble taking up iron, which they need to make crucial enzymes. Unfortunately, unbeknownst to him, Casadaban had haemochromatosis, a genetic disorder in which people accumulate high levels of iron in their blood and organs. When the weakened bacteria somehow hit Casadaban's blood, they suddenly received an influx in iron and regained their strength. There are several tragedies here, besides the loss of a good scientist. One, the bacteria may have entered his bloodstream because, like many experienced researchers, he occasionally didn't take all the safety precautions, such as rubber gloves. Why bother, with such safe bacteria? This is one more reminder that nature can bite in ways we don't always expect. Readers, if you work with microbes - wear the gloves. Worse, Casadaban initially went to the doctor with the classic "flu-like symptoms" typical of nearly every early infection, but sought no further treatment. He then went back three days later as it got worse, and was dead 13 hours after that.The bacteria were only identified when a hospital doctor learned by chance where the patient worked, and someone tested for plague - five days after he died. Yet plague would have been readily curable with the right antibiotics. Casadaban never told his doctors he worked in a plague lab. Maybe he feared unleashing the kind of panic experienced by other plague scientists over misplaced fears of bioterrorism. Who knows how many unusual afflictions like this are never diagnosed at all? Surely we can devise the technology to do a better job of diagnosing infections.  [...]



Do casual words betray warlike intent?

2011-02-21T15:31:15Z

Statements from al-Qaeda groups and national leaders provide clues to their future behaviour, says Peter Aldhous Peter Aldhous, San Francisco bureau chief (Image: Rex Features) What do George W. Bush and Osama Bin Laden have in common? Both may have unwittingly revealed their decisions to launch violent actions through subtle shifts in their use of language. "It doesn't matter which team you're on," James Pennebaker, a psychologist at the University of Texas at Austin, claimed at the annual meeting of the American Association for the Advancement of Science. "If your team is going to war, there are these linguistic shifts." Pennebaker is one of several researchers working with the US Department of Homeland Security on the Comparative Case Studies of Radical Rhetoric project, which is analysing English translations of statements issued by al-Qaeda and al-Qaeda in the Arabian Peninsula, alongside those released by two groups with similar radical Islamic philosophies, but which have not resorted to violence. The ultimate goal is to help intelligence analysts predict impending acts of terrorism. Pennebaker's insights come not from the main "content words" in each document, mostly nouns and verbs, but the everyday "function words" that surround them. These include pronouns, articles like "the" and "a" and a host of other common words such as "this", "upon", and "by". There were fairly clear differences between the two terrorist groups and their non-violent counterparts, Hizb ut-Tahrir and the Movement for Islamic Reform in Arabia. The violent groups used more personal pronouns, and words with social meaning or which convey positive or negative emotions. By contrast, the two non-violent groups had a more stilted and passive style. The real value of the project will come not from distinguishing between the rhetorical styles of violent and non-violent groups, but if it can help predict when a terrorist group is about to strike. The strongest potential signal came during the period two to six months before a major attack, when Pennebaker found an increase in the use of function words associated with honesty in statements from the Islamic terrorist groups. Pennebaker has been able to apply similar analyses to the statements of political leaders who have led their nations into war, including Adolf Hitler and Franklin D. Roosevelt. George W. Bush provided a particularly revealing picture, thanks to his frequent press conferences. Twice during his presidency, Bush suddenly began using "I" less frequency. Once was in the immediate aftermath of the 9/11 attacks, when he instead used "we" - presumably reflecting a feeling of national unity. The other came in 2002, when the decision to go to war in Iraq the following year was taken behind closed doors. This time there was no corresponding upswing for "we". Can such patterns reliably reveal aggressive intent? Some in the audience were sceptical, and even Pennebaker admits that his method can only provide modest probabilistic predictions. "It's going to be pretty crude, but it's a pretty crude business we're in," he says. [...]