US pollsters argue over public view on climate
change

post from New Scientist - Environment on 10 June 2010 12:50:00 PM. © New Scientist - Environment

A new survey suggests that climate science scandals don't bother people in the US much – but hot words have been exchanged about global warming polls

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Autism and the search for simple, direct answers

post from Pharyngula on 10 June 2010 12:17:03 PM. © Pharyngula

Coming up with simple, one-size-fits-all answers to serious problems is so tempting and so satisfying. Look at autism, for instance: a mysterious disease with a wide range of expression, so wide that it is more properly called Autism Spectrum Disorder (ASD), and the popular press and various celebrities all want it to be pegged to a simple cause: it's vaccines, or it's mercury, or it's the dose of the vaccines, and all we have to do to fix it is not vaccinate, or reduce the number of vaccinations, or use chelation therapy to extract poisons, and presto, a cure! This is magical thinking, pure and simple, and it doesn't work.

ASD isn't simple, it's not one disease, it doesn't have one cause, and vaccines are definitely not the cause: if there's one thing the research has done, it's to thoroughly rule out the idea that giving kids shots at an early age causes autism. What we're actually discovering more and more is that ASD can be traced to genetic variation.

Again, though, the causes aren't simple. There is no single mutation to which ASD can be pinned.

For example, one hot spot for an association of genes with autism is the long arm of chromosome 22; cases of developmental delays and autistic behavior have been associated with partial deletions in chromosome 22, and the problems have even been narrowed down to one specific gene, SHANK3, which is expressed in neurons and localized to synapses. We know that if you've got a broken copy of this particular gene, you're likely to have ASD.

How many ASD individuals have this specific genetic change? 0.75%. It is a cause in less than 1% of all affected individuals, but it cannot be the sole cause of ASD in all cases. We have to get out of this mindset that tries to find single causes for complex phenomena; ASD is a case where we have a complex range of disorders with multiple, complex causes.

So how do we get a handle on ASD? This is where the work gets interesting: just because something is multi-causal does not mean that science can't get a grip on it and that we can't learn anything interesting about it. We've got lots of new tools for analyzing broad properties of genomes now, and one promising line of attack are methods for measuring and identifying copy number variants in individuals and populations.

Copy number variants (CNVs) are surprisingly common. If you've had any biology instruction at all, you're probably familiar with the Mendelian concept that we have two copies of each chromosome, and two copies of each gene. As it turns out, that is an oversimplification: sometimes, a piece of a chromosome is accidentally duplicated, and then you'll carry two copies of the associated gene on one chromosome, and one copy on another chromosome, for a total of 3 copies. And in some cases, these duplications have occurred often enough that you'll have many more than 3; the median number of copies of the amylase gene (an enzyme that breaks down starch) in European American populations is 7, with a range of 2 to 15 in different individuals. Get used to it, this kind of variation in copy number seems to happen fairly often.

Now in the case of amylase, the effect of this variation is mild — individuals with more copies of the gene produce more of the enzyme and break down starchy foods faster. It does have evolutionary effects, since cultures with diets rich in starch contain individuals who have, on average, more copies of the gene than individuals where starches are less common in the diet. But what if these chance variations in copy number affect genes involved in the function of the brain? We might see more profound effects on behavior or cognitive ability. The defect in SHANK3 mutations is an example of a reduction in copy number of that gene; what if we could screen populations of ASD individuals not for a specific gene variant, but for the more general occurrence of frequent variations in copy number of any genes…and then we could ask which genes are often affected?

It's being done. A new paper in Nature describes a screen of control and ASD individuals to identify rare copy number variants associated with autism. It worked! In fact, it worked maybe a little too well, since we now have an embarrassment of riches, a great many genes that may be related to ASD.

The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable (~90%), the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4?×?10^-4). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.

They analyzed both affected individuals and their parents, and found both familial transmission — that is, the child with ASD had received a copy number variant from a parent who was a carrier — and de novo events — that is, the child had a spontaneous, new mutation that was not present in either parent. There is no one single gene that can be tagged as the cause of autism: they identified 226 de novo and 219 inherited copy number variants in affected individuals. No one individual carries all of these variants, of course — the results tell us that there are many different paths to ASD.

Oh, no, you may be tempted to wail, autism is hundreds of diseases, with even more possible combinations of variants, and every individual is unique — this is no way to get a handle on what's actually happening to autistic kids! Don't despair, though, this is just the start. Although there are many genes involved, we can try to ask what all of them have in common functionally. There may be common consequences from all of these different genes, so maybe we can identify the common errors in the process of building a brain that lead to ASD.

Here's a first stab at puzzling out what these genes do. The genes that have been identified as being deficient in ASD individuals are mapped out by known functions, and what jumps out at you is that the hundreds of specific genes fall into a smaller number of functional categories. Many of them cluster in a few functional roles: cell proliferation (genes that affect the number of cells in a tissues) and cell projection (particularly important in neurons, where cells will extend long processes that project into target regions), and a specific class of cell signaling molecules, RAS-GTPases, which are involved in how cells communicate with one another and are particularly important in synapses, or the linkages between neurons.

(Click for larger image)
Enrichment results were mapped as a network of gene sets (nodes) related by mutual overlap (edges), where the colour (red, blue or yellow) indicates the class of gene set. Node size is proportional to the total number of genes in each set and edge thickness represents the number of overlapping genes between sets. a, Gene sets enriched for deletions are shown (red) with enrichment significance (FDR q-value) represented as a node colour gradient. Groups of functionally related gene sets are circled and labelled (groups, filled green circles; subgroups, dashed line). b, An expanded enrichment map shows the relationship between gene sets enriched in deletions (a) and sets of known ASD/intellectual disability genes. Node colour hue represents the class of gene set (that is, enriched in deletions, red; known disease genes (ASD and/or intellectual disability (ID) genes), blue; enriched only in disease genes, yellow). Edge colour represents the overlap between gene sets enriched in deletions (green), from disease genes to enriched sets (blue), and between sets enriched in deletions and in disease genes or between disease gene-sets only (orange). The major functional groups are highlighted by filled circles (enriched in deletions, green; enriched in ASD/intellectual disability, blue).

The second map above ties the various copy number variants to previously known disease genes involved in ASD, and what catches my eye is the dense cloud of variants associated with central nervous system development. That tells me right there that it is inappropriate to treat ASD as something that is switched on or off by simple causal factors: ASD is the product of long-developing, subtle changes in the growth of the nervous system in embryos and infants.

So the conclusion, as expected, is that ASD is a multi-factorial disorder with a strong genetic component — but definitely not single-locus inheritance, as many different genes are involved.

Our findings provide strong support for the involvement of multiple rare genic CNVs, both genome-wide and at specific loci, in ASD. These findings, similar to those recently described in schizophrenia, suggest that at least some of these ASD CNVs (and the genes that they affect) are under purifying selection. Genes previously implicated in ASD by rare variant findings have pointed to functional themes in ASD pathophysiology. Molecules such as NRXN1, NLGN3/4X and SHANK3, localized presynaptically or at the post-synaptic density (PSD), highlight maturation and function of glutamatergic synapses. Our data reveal that SHANK2, SYNGAP1 and DLGAP2 are new ASD loci that also encode proteins in the PSD. We also found intellectual disability genes to be important in ASD. Furthermore, our functional enrichment map identifies new groups such as GTPase/Ras, effectively expanding both the number and connectivity of modules that may be involved in ASD. The next step will be to relate defects or patterns of alterations in these groups to ASD endophenotypes. The combined identification of higher-penetrance rare variants and new biological pathways, including those identified in this study, may broaden the targets amenable to genetic testing and therapeutic intervention.

There aren't any simple answers. There are some hints of hope for future treatment, though, in the recognition that there are a few functional modules that are being commonly impaired by these many different genes — it at least focuses the direction of future research in to some narrower domains.

One fact is so obvious that it's unfortunate I have to mention it: no external agent, such as a vaccine, can generate a consistent pattern of duplication and deletions in an affected individual's cells. These data say it's an error to chase down transient environmental agents given relatively late in life to people.

Pinto D et al. (2010) Functional impact of global rare copy number variation in autism spectrum disorders Nature doi:10.1038/nature09146.

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Federal Aviation Administration Exploring
Possibilities of Unmanned Commercial Flight

post from CR4 - Recent Blog Entries on 10 June 2010 12:14:24 PM. © CR4 - Recent Blog Entries

From Popular Science - New Technology, Science News, The Future Now: The Federal Aviation Administration wants you to fly the robot-friendly skies, 1but the regulatory overseer has more than a few challenges to overcome before it can extend that invitation in earnest. The FAA today

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Solar Cells: Coming to a Window Near You

post from CR4 - Recent Blog Entries on 10 June 2010 11:21:00 AM. © CR4 - Recent Blog Entries

From CNN.com - Technology: A professor who invented low-cost solar cells that may be incorporated into energy-producing windows has been awarded the Millennium Technology Prize. Finland's Technology Academy on Wednesday awarded Swiss professor Michael Gratzel with the prize, wh

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Gulf Spill: Ideas Bubble To The Surface

post from Science Ain't So Bad on 10 June 2010 11:17:23 AM. © Science Ain't So Bad

It's THEIR move now.

THROW A FEW IDEAS AT IT

My sweet wife can’t look at the photos of gooey pelicans. “I’d like to grab the guys behind this and stuff THEIR heads in a barrel of oil”.

My sweet wife.

PLEASE don’t hate MISTERScienceAintSoBad for saying this, but there’s good.

You’re NUTS, Mister SASB. Name one good thing.

Sure.

It’s a GOOD thing that SO many creative people’re chiming in to with ideas. It’s inspiring.

People care.

And they want to help.

When we’re not screwing up the environment, we can be awfully smart and good hearted hominids.

As you know, several “official” solutions were tried and tossed before the “top hat” version which seems to be doing an OK job with the oil flow till that well can be properly euthanasized (probably with a “bottom kill” of heavy fluids followed by cement pumped into the lower portion of the casing).

However it’s the ideas from “out there” that’re flowing faster than the black mucky stuff.

Maybe you heard about Kevin Costner’s Ocean Therapy machines ? Large centrifuges that can separate oil and water in the quantities required for a spill like this? And John Hofmeister (used to run Shell Oil Company) has been all over the place with a plan to suck the oil into supertankers.

A professor of engineering from the University of Pittsburgh came up with a reusable cotton filter that gets coated with an oil blocking polymer. Works great. There’s even a video. Di Gao says that large filters made of this material could be dragged through the Gulf, capturing the surface oil.

The many other proposals include some for WAY cool explosives to seal the thing, including some VERY exciting ones to use nukes. Ya want science, ya gotta be willing to experiment a little, right?

MISTERScienceAintSoBad still thinks there’s hope for our clumsy human race. We’ll get through this disaster, somehow.

You’ll see.

Attribution for above photo:
This work is licensed under a Creative Commons Attribution 2.0 Generic License.

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Are dead cancer cells feeding cancer's spread

post from Machines Like Us - Science at the speed of thought on 10 June 2010 11:01:20 AM. © Machines Like Us - Science at the speed of thought

Researchers with the University of Alabama at Birmingham (UAB) Comprehensive Cancer Center and UAB Department of Chemistry have won an $805,000 grant from the U.S. Department of Defense Breast Cancer Research Program to study whether dead cancer cells left over after treatment encourage cancer?s spread to other parts of the body.

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Today's Mystery Bird for you to Identify

post from Living the Scientific Life (Scientist, Interrupted) on 10 June 2010 10:59:45 AM. © Living the Scientific Life (Scientist, Interrupted)

tags: birds, mystery bird, bird ID quiz

[Mystery bird] photographed at Bolivar Peninsula, Galveston County, Texas. [I will identify this bird for you in 48 hours]

Image: Joseph Kennedy, 26 April 2010 [larger view].

Nikon D200, Kowa 883 telescope with TSN-PZ camera eyepiece 1/1000s f/8.0 at 1000.0mm iso400.

Please name at least one field mark that supports your identification.

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Mystery Bird: Red Knot, Calidris (Tringa) canutus

post from Living the Scientific Life (Scientist, Interrupted) on 10 June 2010 10:59:45 AM. © Living the Scientific Life (Scientist, Interrupted)

tags: Red Knot, Calidris canutus, Tringa canutus, birds, mystery bird, bird ID quiz

~~[Mystery bird]~~ Red Knot, Calidris (Tringa) canutus photographed at Bolivar Peninsula, Galveston County, Texas. [I will identify this bird for you in 48 hours]

Image: Joseph Kennedy, 26 April 2010 [larger view].

Nikon D200, Kowa 883 telescope with TSN-PZ camera eyepiece 1/1000s f/8.0 at 1000.0mm iso400.

Please name at least one field mark that supports your identification.

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