And by biometrics on the iWatch, he means health data

Apple’s iWatch to come in late 2014 with focus on biometrics, analyst says
[Via AppleInsider]

Noted KGI Securities analyst Ming-Chi Kuo believes Apple’s much-rumored iWatch will hit store shelves late next year, not in 2013 as many market watchers expect, with a 1.5- to 2-inch screen, focus on biometrics and deep integration with existing iOS devices.

[More]

Generation of personal health data is going to explode in the next year. As I wrote yesterday, Scanadu will provide a ton of data.

With biometrics, the iWatch can better safeguard an owner from unwanted user access, while providing advanced healthcare features

What happens if we can wear the device that gets our walking data – like the FitBit does – and heart rate and who knows what else? And that data is communicated wireless to the iOS device in our pocket?

It may well be that the reason for the 2014 date is not only due to its development. It may, just as the Scanadu Scout must, have to pass some FDA approval processes if it can act as a medical device.

We shall see.

Molecular paleontology is so cool

by Patrick Feller

The sea shall give up her dead
[Via john hawks weblog]

I really like this ScienceNOW account by Traci Watson of new work that has uncovered ancient DNA in deep-seafloor contexts: “Ancient DNA Found Hidden Below Sea Floor”. The article covers two studies, including one looking at 11,400-year-old DNA from the abyssal plain, another comparing more ancient and recent Black Sea seafloor samples. The latter study may help to redate the last time the Black Sea basin was flooded from the Mediterranean:

One type of marine fungus, for example, first appeared in the sediments roughly 9600 years ago—exactly when some forms of freshwater plankton and a freshwater mussel vanish, the team reports this week in the Proceedings of the National Academy of Sciences. That suggests that marine waters started to invade the lake roughly 600 years earlier than thought. The team also found DNA from a form of marine alga in 9300-year-old sediments, though the alga doesn’t show up in the fossil record until 2500 years ago, says molecular paleoecologist Marco Coolen of the Woods Hole Oceanographic Institution in Massachusetts and an author of the Black Sea paper.

What a neat project it will be, to explore seafloor DNA for unexpected inclusions. There’s a good reason to fund much more work here, given that the 11,400-year horizon where this is already practical is so near the Younger Dryas. We need a fleet of tiny autonomous vessels to find the interesting stuff — we can call them, “Glomar Venters”!

[More]

We are gaining greater and greater expertise in deriving genomic DNA sequences from life that died ten thousand or more years ago. And sequencing becoming cheaper, allowing greater investigation of these questions.

Here we have investigation of the DNA molecules found in silt from the Black Sea. They tell us when the Black Sea changed from a freshwater lake to a salt water sea. Because the types of life seen changed.

And they found DNA from life whose fossils were not found from that time. I wonder if similar things can be done using territorial soil samples instead of marine?

Homeless have 400-fold increase in head injuries

by theeruditefrog

Researchers say they are shocked by new statistics on head injuries among people who are homeless
[Via EurekAlert! - Business and Economics]

(St. Michael’s Hospital) Men who are heavy drinkers and homeless for long periods of time have 400 times the number of head injuries as the general population, according to a new study by researchers who said they were shocked by their findings.

[More]

These numbers are starling. 300 times the normal rates of bleeding in the brain is tremendous. These are not slight little things but injuries that require a lot of medical care – and cost – to deal with.

 In the normal population 12 out of 10,000 men have a head injury per year. For the homeless population this becomes  4800 out of 10,000 every year.

And the average time between injuries decreases the longer the person is homeless.

With the increasing focus on concussions and the its impact on CTE, this work is important. The numbers in the study “suggest that head injuries are causing physical changes such as dizziness, memory loss, impaired cognitive functions and mental health issues, which lead to more head injuries.”

Working to prevent brain injury among the homeless could have substantial public health effects.

Reducing the distortion from journal impact factors

by webtreats

Scientific insurgents say ‘Journal Impact Factors’ distort science
[Via EurekAlert! - Business and Economics]

(American Society for Cell Biology) An ad hoc coalition of unlikely insurgents — scientists, journal editors and publishers, scholarly societies, and research funders across many scientific disciplines — today posted an international declaration calling on the world scientific community to eliminate the role of the journal impact factor in evaluating research for funding, hiring, promotion, or institutional effectiveness.

[More]

JIF were developed to help librarians make subscription decisions.  They have morphed into a requirement for tenure.

They have a lot of problems, can be gamed by authors and have little transparency regarding their determination.

The document makes several recommendations Tey generally fall along these lines:

• the need to eliminate the use of journal-based metrics, such as Journal Impact Factors, in funding, appointment, and promotion considerations;
• the need to assess research on its own merits rather than on the basis of the journal in which the research is published; and
• the need to capitalize on the opportunities provided by online publication (such as relaxing unnecessary limits on the number of words, figures, and references in articles, and exploring new indicators of significance and impact).

For example, a researcher can actually receive higher marks by writing a review article on other people’s research than writing about their own. That is because many researchers reference review articles much more often than original papers. So, write an review article on a hot topic and your metrics can go way up.

The fact that old guard journals such as Science are working with new fangled publications like PeerJ suggests that this might have some legs.

Used to be that attacking science was a career killer

by kevin dooley

Climate science denier appointed President of New Mexico State Univ.
[Via Leiter Reports: A Philosophy Blog]

What an embarrassment. (Thanks to Lawrence Torcello for the pointer.)

[More]

Now you get to run a University. Isn’t America wonderful?

Skeptics of AGW a disappearing breed – except in politics and the media

Zombie climate sceptic theories survive only in newspapers and on TV | Graham Readfearn
[Via Science news, comment and analysis | guardian.co.uk]

Study finds overwhelming scientific consensus that humans have caused global warming, but media still hasn’t caught up

Here’s the news from 1991 – a vanishingly small number of peer-reviewed studies in science journals argue that humans aren’t the cause of global warming.

Here’s the news from 2013 – since 1991, less than two per cent of all peer-reviewed studies say climate change is caused by something other than human activities (that’s burning fossil fuels and digging up forests, to you and me).

Both the news from 2013 and the news from 1991 come from new research published this week in the journal Environmental Research Letters.

[More]

The paper – Quantifying the consensus on anthropogenic global warming in the scientific literature – is Open Access.

Here is the take home figure:

 

What is interesting is not that there really are no papers the reject AGW. It is the increase in number that take no real position. This took place rapidly in the late 90s and has stabilized.

The paper looked at some of the possible reasons for this and came to the conclusion that scientists were taking no position because it was simply understood that AGW was happening. By 2000 or so, they no longer felt they needed to state the obvious and were more concerned with new problems, not with restating what was already known.

There have been millions of dollars invested to make people think there is not a scientific consensus regarding climate change. As the conclusions state:

A key strategy involved constructing the impression of active scientific debate using dissenting scientists as spokesmen (Oreskes 2010). The situation is exacerbated by media treatment of the climate issue, where the normative practice of providing opposing sides with equal attention has allowed a vocal minority to have their views amplified (Boykoff and Boykoff 2004). While there are indications that the situation has improved in the UK and USA prestige press (Boykoff 2007), the UK tabloid press showed no indication of improvement from 2000 to 2006 (Boykoff and Mansfield 2008).

The data show otherwise.

 

Could the Gaboon viper’s scales help create better solar panels?

by Life As Art

The Gaboon Viper Has Ultra-Black Scales So You Can’t See It
[Via Phenomena » Not Exactly Rocket Science]

“It’s like, how much more black could this be? And the answer is none. None more black.” – Nigel Tufnel, This is Spinal Tap.  

The Gaboon viper is a fairly docile creature, and that’s where the good news ends. It also has the longest fangs of any snake—2.2-inch-long weapons that swivel forwards like switchblades. The fangs are connected to such huge glands that they deliver more venom than any other snake—a cocktail of toxins that thin the blood, trigger massive internal bleeding, and can stop hearts.

And to make things much, much worse, the Gaboon viper is virtually impossible to see.

From above, its head looks like a dead leaf. Its five-foot-long body is patterned with rectangles and hourglasses, and shaded in cream, yellow, brown and black. Against the leaf litter of its forest home, the viper simply fades away.

Now, Marlene Spinner from Kiel University has discovered one of the secrets to the Gaboon viper’s exceptional camouflage: The black on its body is really, really black. Not just black, but black. Ultra-black. None more black.

[More]

The article – Snake velvet black: Hierarchical micro- and nanostructure enhances dark colouration in Bitis rhinocero – is Open access, so you can look at the pictures.

The upshot is that the highly patterned viper has black areas that reflect such little light that the deep blackness confuses our eyes.

WHen the scales from these black areas are examined under an electron microscope, unusually small ridges were found. When regular scales are coated in a metal in preparation for use in an electron microscope, they take on the color of the metal. Because light is reflected back to our eyers.

But the black scales remain back, even after coated. Light does not get reflected back.

It appears that these very small ridges bounce any incoming light around so it cannot reach our  eyers. It appears black because there is little light coming from them. And it does not matter which direction we move our etes too. 

It is like once light enters, it cannot escape.

Turns out this is something that solar panels would love to be able to do. We want to use all the light energy and let little of it escape. We would like the panels to look black. We have created some materials that are even more efficient than viper scales in holding onto light but they are brittle and hard to work with.

Perhaps something like these scales will be helpful.

Harboring parasites for protection

by siamesepuppy

Ladybird Invader Carries Deadly Parasite as Biological Weapon
[Via Phenomena » Not Exactly Rocket Science]

When Europeans arrived in the New World, they brought devastating diseases like smallpox, which killed more native Americans than guns and other weapons. Infections go the other way too: When grey squirrels from North America arrived in the UK, they brought a squirrel pox virus that decimated the local red squirrels. Time and again, animals have invaded new regions and killed the locals by inadvertently bringing biological weapons with them.

Now, Andreas Vilcinskas from Justus-Liebig-University of Giessen has found that one the world’s most invasive insects—the harlequin ladybird—also belongs in the biological weapons club.

It hails from central Asia, but was willingly introduced to Europe, North America, and other parts of the world, by people who were seemingly undeterred by the outcomes of bringing cane toads to Australia or mongooses to Hawaii. Like those other invaders, the harlequin has brought ruin to local ladybirds, many of which have declined dramatically since its incursion.

[More]

Luckily I knew that a ladybird was the same thing as a ladybug.

While not all the science is in, it does look like the invasive harlequin ladybird has some built in defenses which may explain why it is taking over habitat.

It’s circulatory system is awash in a mix of anti-biologics and other molecules. These do not seem to have any effect on the health of other ladybirds. WHat does affect them is a single-celled parasitic fungus. The fungus has no effect on the harlequin ladybird – perhaps because all of the anti-biologics.

But when native ladybirds are exposed to the parasite in the lab, they die. 

Now the researchers have to show that this transfer happens in the wild. If so, then we will know that some organisms carry around their own biologic weapon, one that removes their competitors.

Interesting new data on the orgiins of agriculture

New discovery of ancient diet shatters conventional ideas of how agriculture emerged
[Via EurekAlert! - Biology]

(University of Leicester) The use of new analysis techniques provides food for thought about how people lived 5,000 years ago.

[More]

It has been believed that agriculture in China  did not really get going until the cultivation of rice.

But new research indicates that milling of starchy nuts from palms may have started 5000 years ago.

The tricky thing is whether the plants used were taken from formally created acreage by a sedentary population or just fortuitously use by a nomadic one.

More research needed.

Great “Into Darkness” review: “too much stuff”

 by Horia Varlan

BA Review: Star Trek Into Darkness
[Via Bad Astronomy]

So, Star Trek Into Darkness. The new Trek movie. Big summer blockbuster. Lots of box office, lots of buzz.

Yeah, that. I didn’t like it.

Now, I didn’t hate it. It was fun, and entirely watchable. But, well, I just didn’t actively like it. It was OK for a fast-paced action movie where you can just watch and go along for the ride, but as a Trek movie it fell short. I think this reboot series still has a lot of promise, but this movie, for me, was just marking time.

Here’s why. Obviously, there are big fat spoilers here, and the movie does ride on a lot of the mysteries. So if you don’t want the flick ruined for you, go look at something else for a while. Also obviously, what follows are opinions. A lot of my friends are saying they liked or even loved this movie. That’s great! It just didn’t strike me the same way. Fairly warned be thee, says I.

Cap’n! THERE BE SPOILERS HERE.

[More]

I’ve heard this a lot. A fun movie but really not a Star Trek movie. It has lost a lot of what made Star Trek such a phenomenon.

Just like the latest Total Recall was not Total Recall. Or the latest Rollerball was not Rollerball. Or I, Robot was not I. Robot.

In their latest incarnations, they have lost all the stuff that made the original different.

Star Trek is supposed about exploration and the things we find. And how we deal with it.

But now Star Trek is just a good excuse to have lots of stuff happen, preferably across rooftops and with explosions.

The Original Series and the Next Generation inspired people to greater heights, having effects on what we did in many important ways. ask most people working in aerospace.

The new Star Trek will have as much impact as a James Bond movie.

Instead of Wagon Train to the stars, it is now Goldfinger in Space.

Specialists required in any revolution. I’m the third type.

by Stifts- och landsbiblioteket i Skara

The Three Types of Specialist Necessary for Any Revolution
[Via Daring Fireball]

Kottke, quoting Vonnegut.

[More]

Could just three types of specialists really be responsible for any successful revolution? Even a scientific one?

First type – a true genius: “a person capable of having seemingly good ideas not in general circulation.” By themselves they are just lunatics.

Second type – a thought leader: “a highly intelligent citizen in good standing in his or her community, who understands and admires the fresh ideas of the genius, and who testifies that the genius is far from mad.” By themselves they are unsatisfied.

Third type – the integrator: “a person who can explain everything, no matter how complicated, to the satisfaction of most people.” By themselves they are ignored.

But together they change the world. At least that is the idea.

And I think there is a germ of an idea.

I fit in the third type and I am really good at it. But I’ve recognized that my skills often only have real impact when I connect with those of type 1 and 2.

By myself, I am often ignored. Any calls for change are put aside, the fear of change is too great.

But when my words are put into the mouth of the right person – often a thought leader – they get heard and acted on. And when I take the ideas of a genius and make them understandable for the group, miraculous things get done. The group wants change, they want a revolution.

Let’s figure out a way to connect these three together and see what happens. What important and useful changes could we produce?

Let’s revolutionize revolution! Who wants to help?

The quacks gravitate to Angelina Jolie and her late breasts

by John5199

The quack view of preventing breast cancer versus reality and Angelina Jolie
[Via Respectful Insolence]

I should have known it. I should have known that the reaction wouldn’t take very long. I should have known it based on prior history. The news story to which I am referring is, of course, the revelation yesterday in the New York Times editorial page by Angelina Jolie that she had decided to undergo prophylactic bilateral mastectomies (removal of both breasts) because she had learned that she was a BRCA gene mutation carrier, and the particular mutation that she apparently carried portended an 85% lifetime risk of breast cancer. The reaction to which I am referring is, of course, the same sort of despicable reaction that we see all the time from one of the crankiest of quackery-promoting quacks, Mike Adams, publisher of NaturalNews.com.

[More]

This is the first in a two parter, not strictly about the medical rationale behind Jolie’s decision (which I’ve had some discussions about), although there is some of that.

It deals with the ‘alternative’ medicine guys who decry the maiming of her body when it could have been saved if she had only listened to them and their snake oil dreams.

Some of the real danger from her public approach is the huge pushback from those selling their own non-reality based treatments. Reading what some of them have written – seeing how they get simple biology wrong – is quite scary.

Having them jump out of the woodwork at this is not surprising at all. They have something to sell.

But the article highlights another problem – that many women are choosing preventative mastectomy even if they do not have a high risk for breast cancer, such as the BRCA1 mutation. From the NYT:

For women’s health advocates, the trend toward double mastectomies in women who do not have mutations is frustrating. Studies in the 1970s and 1980s proved that for many patients, lumpectomy was as safe as mastectomy, and the findings were seen as a victory for women.

Even so, there is increasing demand for mastectomy. Dr. Morrow says that she has often tried to talk patients out of it without success. Some imagine their risk of new or recurring cancer to be far higher than it really is. Others think that their breasts will match up better if both are removed and reconstructed.

Patients demanding surgeries they do not need seems to me to arise from the impreciseness of how we do medicine. Illness rates, drug effectiveness and much of the rates are based on statistics of populations. They say nothing about the real chance of an individual to get the disease or react to the medication.

In many ways health numbers are like the decay of a radioactive material. We know with exact precision what the half life of such an element is. In X amount of time, half the molecules will have decayed. But we have little idea of which specific molecule will.  we could look at one and it might decay faster than the half-life or slower.

Our numbers only work for the group not for the individual. I believe as we gain more data, information and knowledge about an individuals personal health – genomic, metabolomic, miRNA, etc. – we may get a clearer picture.

Until then, I expect to see  even more confusion with women who really do not need the surgery demanding it from doctors and medical snake oil sellers telling women who might need the surgery that they have a miracle herbal/lifestyle cure.

Our cells have different genomes: genomic sequencing and mosaics

by DaveFayram

A cautionary tale on genome-sequencing diagnostics for rare diseases
[Via Eureka! Science News - Popular science news]

Children born with rare, inherited conditions known as Congenital Disorders of Glycosylation, or CDG, have mutations in one of the many enzymes the body uses to decorate its proteins and cells with sugars. Properly diagnosing a child with CDG and pinpointing the exact sugar gene that’s mutated can be a huge relief for parents — they better understand what they’re dealing with and doctors can sometimes use that information to develop a therapeutic approach. Whole-exome sequencing, an abbreviated form of whole-genome sequencing, is increasingly used as a diagnostic for CDG. But researchers at Sanford-Burnham Medical Research Institute (Sanford-Burnham) recently discovered three children with CDG who are mosaics — only some cells in some tissues have the mutation.

[More]

As we do more and more sequencing of the genome, we are going to see more of this – some people have a mixture of cells with totally different genomes in them. If we only look at one cell type, sya blood cells, we may thing someone has one genome when in fact their liver’s genome might be very different.

Or their liver might be a mixture of genomes. Or all sorts of complicated stuff.

In fact, work published at the end of last year demonstrated that most of us are a mosaic of different genomes. Different sin cells have a different genomic content than other skin cells. Blood cells were different than brain.

Not just in the DNA that was expressed but in the actual DNA present.

And, as this paper, above showed, the mosaic cells can even disappear. The cells with the genomes that were causing the problem actually vanished.

The team then went back to the three original children and examined their transferrin again. Surprisingly, these readings, which had previously shown abnormalities, had become normal. Freeze and his team believe this is because mutated cells in the children’s livers died and were replaced by normal cells over time.

Diagnosing genetic disease will get a lot more complicated before they get easier.

SCANning single chromatin molecules to determine epigenetic state

by Libertas Academica

SCANning Single Molecules to Pinpoint Co-Occurrence of Epigenetic Marks
[Via EpiGenie | Epigenetics and Non-Coding RNA News]

Just because two people live on the same street doesn’t necessarily mean they live that close to each other or in the same house, yet that’s what you often have to assume when using ChIP to detect epigenetic modifications. Either that, or you have to use tons of sample and/or a labor-intensive method to figure that out more definitively. Now, a team reports that they can tell where multiple epigenetic marks are located simultaneously, quantitatively, and quickly.

We’ve been keeping an eye on this method, called Single Chromatin molecule Analysis in Nanochannels (SCAN). We first told you about it way back in 2009 when Paul Soloway of Cornell University told us about his plan to do something similar to flow cytometry to detect epigenetic modifications on single chromatin molecules in nanochannels.

[More]

The paper is entitiled Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells and is free to read.

The oritein-DNA complex of a chromosome – called chromatin – contains many modifiction that control gene expression. However, current approaches could only look at a population of chromatin pieces. So we could see that 70% of the chromoatin examined had one modification and that 20% had another. BUt it was very difficult to determine exactly how much of the chomatin had both modification and how many had none, because single pieces could not be examined.

It’s like saying that 7 out of 10 shirts in a drawer are red and 2  out of 10 have a pocket. How many are red with a pocket? we cannot know unless we look at every single shirt.

What is interesting in this paper is that they have developed a technique to look at these  modifications in a single piece of chromatin. So now they can actually measure which modifications occur with which other ones or never do.

They found that some specific modifications often co-located. and that these modifications are altered during the cell immortalization process often seen in tumors. This holds some real promise, especially since such small amounts of material needs to be used.

RNA can be methylated to control gene expression

by dullhunk

Dynamic RNA Methylation Emerges as New Player in the Epigenetic Landscape
[Via EpiGenie | Epigenetics and Non-Coding RNA News]

Methylation is a hot topic in the field of epigenetics whether it’s occurring on the cytosines of DNA or its histone protein friends. With a relatively well-known set of enzymes, methylation marks are dynamically modified in order to regulate gene expression.

However, the revisiting of a RNA modification discovered in the 70’s has come to show that post-translational modifications to RNA have the potential to influence the epigenetic landscape just as well.

Methylation of N6-methyladenine (m⁶A) is the most prevalent internal modification on mRNA and long non-coding RNA. Recently, Dr. Cuan He’s team at the University of Chicago (Go Bulls) have made some groundbreaking discoveries. Here are the highlights of their recent findings:

[More]

It is becoming more and more obvious that we still live in an RNA World, just one with DNA and protein adjuncts.

Methylation of DNA has been known for some time to be involved in epigenetics – the control of gene expression through non-genetic means. The level of methylation can determine whether a gene is active or not. So simply the presence of a gene does not mean it is actually doing anything, depending on epigenetic factors.

RNA is being seen more and more as something beyond just a transition between the DNA of the gene and the protein the gene codes for. It turns out that all sorts of RNAs are involved in controlling gene expression. And now we see that those RNAs can be actively methylated to control the way they control gene expression.

RNA becomes more  important every day.