This Ebola outbreak seems very different. Perhaps as expected and to be feared.

Ebola Virus 

Sierra Leone doctor who treated scores of Ebola patients dies of Ebola
[Via Boing Boing]

Virologist Sheik Umar Khan is credited with treating over 100 Ebola patients in Sierra Leone. Read the rest


Usually these outbreaks burn  out rapidly because people die quickly. But the mortality rate has dropped from 90% in previous epidemics to 50%.

This now means there is more opportunity for the virus to spread. This loss in virulence is actually what happens with many viruses.

There is a selective advantage for a virus not to kill. Sustaining itself is helped by spreading to others and the most successful viruses are those that do not kill, or kill very slowly. They spread even further.

A ‘hot’ virus like Ebola is under selective pressure to become less deadly, even as the pressure selects for those that spread more easily.

The variants that are less likely to kill will spread further. So, as time goes on, a balance is reached between the virulence of the disease (as well as how many it kills) and how far it can spread. That is, morbidity rates can increase as mortality rates decrease.

At 90% mortality, people die too quickly for the disease to spread. But at 50%, there are greater avenues for spread. Especially since in this outbreak the virus seems to spread by more than just blood-to-blood contact as most of the previous outbreaks saw.

So, in one way the current outbreak indicates that Ebola may be becoming less dangerous, even as it kills more people.  And thus potentially more dangerous. It now becomes much easier for an infected person to get on a plane and send the disease elsewhere.

And that is the really horrible effect, because now it has the ability to disrupt huge swaths of human civilization. The virus is found in fluids, even after death. So funerals are now places for transmission.

How cultures have dealt with death is now being disrupted. This will have social effects for a long time.

Although hard to read, this report from a doctor that was there is both heart-waring and heart-rending.

More cool biology hidden in our guts


Globe-Trotting Virus Hides Inside People’s Gut Bacteria
[Via NPR Science/Health]

New viruses are a dime a dozen.

Every few months, we hear about a newly discovered flu virus that’s jumped from birds to people somewhere in the world. And the number of viruses identified in bats is “extraordinary and appears to increase almost daily,” scientists wrote last year in the journal PLOS Pathogens.

But a virus that has been quietly hiding inside millions of people on three continents — and never been noticed before? That doesn’t come along often.


The drop in cost of sequencing technology (and other tools) now allows us to answer questions we could not even asl 5 years ago. That is how rapidly things are moving.

Many people are just now getting an idea that the microbes that live in our guts have huge impacts on us and our health.

Now we are seeing more and more that viruses inside these gut flora are also important on our diets. This one looks particularly interesting. The strange story of Acanthamoeba polyphaga may be more common than we thought.

I did my postdoc working on genes from bacteriophage, the viruses that infect bacteria. To do that, I have to hand-make oligonucleotides representing the genes, 14 bases at a time. It would take a day to do seven of them at a time.

Putting them together and getting the region sequenced in order to make sure the oligonucleotides had been made correctly would take a couple of months.

It is simply amazing to me how far we have come.

New way to make water into steam from sunlight

Sponge Converts Sunlight Into Steam for Electricity
[Via Discovery News - Top Stories]

A completely new structure heats water and turns it into steam. Continue reading →


If this can be scaled up, it could find some real uses.

The New Agers may have been right – pyramids for a healthier life

dna pyramid

Tiny DNA pyramids enter bacteria easily — and deliver a deadly payload
[Via Eureka! Science News - Popular science news]

Bacterial infections usually announce themselves with pain and fever but often can be defeated with antibiotics — and then there are those that are sneaky and hard to beat. Now, scientists have built a new weapon against such pathogens in the form of tiny DNA pyramids. Published in the journal ACS Applied Materials & Interfaces, their study found the nanopyramids can flag bacteria and kill more of them than medicine alone.


Medicine using nanoparticles to carry a drug holds a lot of promise. But the structural carriers for the drugs can cause health problems.

So, why not use a natural product to construct the carriers? Here they uses small stretches of DNA to create a pyramid which could then carry the necessary machinery/drugs.

While they have not used this in a human being, these researchers did say that using this DNA pyramid to carry an antibiotic substantially enhanced the killing ability of the drug.

Just in time for summer – making healthier hotdogs using olve oil

Summer = Grill = Hotdogs! 

Making a more healthful, low-fat hot dog without giving up texture
[Via Eureka! Science News - Popular science news]

With grilling season upon us, many backyard cooks are turning to more healthful alternatives to their savored but fatty hot dogs. But low fat can sometimes mean low satisfaction. Now researchers are reporting new progress toward addressing the texture problem in low-fat wieners that are made with olive oil rather than pork fat. Their study was published in ACS’ Journal of Agricultural and Food Chemistry.


Removing the pig fat from hotdogs usually makes them less tasty. Here researchers found that they could use olive oil, maintain the taste and reduce calories by 30%.

Sounds…uhh…tastes good.

Climate change might help some plants but it also helps some plant diseases

Soybean Sky

Climate change provides good growing conditions for charcoal rot in soybeans
[Via Eureka! Science News - Popular science news]

With over 100 diseases that can attack soybean crops, why would charcoal rot rise to the top of the most wanted list? University of Illinois scientists cite the earth’s changing climate as one reason that more research is needed on the fungus that causes charcoal rot.


One of the arguments from denialists is that climate change will not be so bad because plants like carbon dioxide. While this is debatable, what is not often discussed is how much better some plant diseases will do.

Here we have a fungus that likes warm, dry weather. And that also infects 500 other plants, including corn and sorghum, besides soybeans. And it loves salty conditions.

So a resistant plant must be one that is heat-, drought -, and salt-tolerant in order to beat the fungus.

Also, in contrast to other disease, charcoal rot not only kills the plant, it lives off the dead tissue. So, it can thrive living off the leftovers from other pathogens that can only use living plants.

At the moment, no soybean plant is completely immune to this fungus. So these researchers are trying to develop varieties that are able to fight off the fungus.

But those varieties also still need to be highly productive. Not an easy task.

MicroRNA directly causes frameshift that regulates protein production

 HIV-infected T cell

Human cells’ protein factory has an alternate operating manual
[Via Eureka! Science News - Popular science news]

Working with a gene that plays a critical role in HIV infection, University of Maryland researchers have discovered that some human genes have an alternate set of operating instructions written into their protein-making machinery. The alternate instructions can quickly alter the proteins’ contents, functions and ability to survive.


Ribosomes read messenger RNA (mRNA) three nucleotides at a time.  But every once in a while it stutters, skips one nucleotide, before starting again.

This causes a frameshift usually resulting in nonsense, producing proteins that are not useful. The protein and the mRNA are then rapidly degraded and things start over again.

So what these researchers found is that the cell actually has a system that directly causes frameshifts, actually controlling protein production by creating nonsense.

How it does this is by using another small RNA – a microRNA or miRNA – that sticks to the mRNA and causes a frameshift at a specific location. The mRNA and resulting proteirn are then targeted for rapid degradation.

So this serves as a negative control loop, decreasing the amount of a specific protein in a cell.

Just another control mechanism in a cell – purposefully inserting errors.

Some interesting epigenetic differences between vaginal and caesarean birth

 Julius Caesar and his pigeon

Cesarean Alters DNA Methylation in Infant Blood Stem Cells
[Via EpiGenie | Epigenetics and Non-Coding RNA News]

There’s no denying that the process of giving birth is an unforgettable experience for those involved but now it seems the labor of love could also be important for programming an infants development. Researchers from the Karolinska Institutet (Sweden) drop some knowledge about the mechanosensitive nature of DNA methylation and show that birth via Caesarean Section (CS) skips the profiles established in blood (hematopoietic) stem cells during labor. 

Here’s the scoop:

  • Blood stem cells (CD34+) from infants delivered by CS are more globally methylated (+2%) than their ‘vaginal peers’.
  • A locus-specific analysis identified 343 differentially methylated regions (DMRs) showing a difference of 10% or more.
  • The majority of these DMRs in infants (76%) are hypermethylated after vaginal delivery.
  • Interestingly, in these infants, the degree of DNA methylation in 3 loci correlates to the duration of labor.
  • DMRs modulate immune system function and metabolism and almost seem to parallel a computer boot up sequence.

Author Mikael Norman shares that “During a vaginal delivery, the fetus is exposed to an increased level of stress, which in a positive way will prepare the unborn baby for life outside the uterus. This activation of the fetus’ defense systems doesn’t occur when a cesarean section is performed before labor begins, which in turn could be a possible cause for the noticed differences between the groups.” So, when it comes down to it, this report suggests that vaginal birth helps give babies an epigenetically programmed ‘jump start’ upon entry into the real world that a CS bypasses, which can lead to some health burdens later in life.


Very intriguing that there are different methylation patterns in the DNA of infants depending on whether they went through the stress of a vaginal birth vs the less stressful caesarean.

Now to see if this results in any physical differences.

Genome editing in the silkworm- I’ve seen this movie

Insectosaurus Invades The World!

Heritable Genome Editing with CRISPR/Cas9 in the Silkworm, Bombyx mori
[Via PLoS ONE Alerts: New Articles]

by Wei Wei, Huhu Xin, Bhaskar Roy, Junbiao Dai, Yungen Miao, Guanjun Gao

We report the establishment of an efficient and heritable gene mutagenesis method in the silkworm Bombyx mori using modified type II clustered regularly interspaced short palindromic repeats (CRISPR) with an associated protein (Cas9) system. Using four loci Bm-ok, BmKMO, BmTH, and Bmtan as candidates, we proved that genome alterations at specific sites could be induced by direct microinjection of specific guide RNA and Cas9-mRNA into silkworm embryos. Mutation frequencies of 16.7–35.0% were observed in the injected generation, and DNA fragments deletions were also noted. Bm-ok mosaic mutants were used to test for mutant heritability due to the easily determined translucent epidermal phenotype of Bm-ok-disrupted cells. Two crossing strategies were used. In the first, injected Bm-ok moths were crossed with wild-type moths, and a 28.6% frequency of germline mutation transmission was observed. In the second strategy, two Bm-ok mosaic mutant moths were crossed with each other, and 93.6% of the offsprings appeared mutations in both alleles of Bm-ok gene (compound heterozygous). In summary, the CRISPR/Cas9 system can act as a highly specific and heritable gene-editing tool in Bombyx mori.


Truthfully, it is pretty amazing that they can make changes in the genome that are carried through the germline  and are inherited.

GMO insects may not be far away.

HIV is even more difficult to eradicate than we thought

 HIV-infected H9 T cell


Why wiping out HIV “reservoirs” is so hard
[Via Ars Technica]


HIV, the virus that causes AIDS, does its damage by decimating immune cells. But it also lies dormant in some cells, creating a reservoir that can restart an active infection long after the active virus has been cleared by treatments. This is apparently what happened to a child from Mississippi who was thought to have been cured of infection following antiviral treatments.

Researchers may now have found one of the reasons that it’s so hard to clear out these reservoirs of infected cells. As part of the infection process, HIV normally inserts a copy of itself into a cell’s chromosomes. By chance, some of these insertions cause the cell to grow faster, ensuring that more copies of the virus are around to cause trouble.

The researchers, who are all based in Seattle, took a pretty simple approach to discover this: they sampled cells from HIV patients who were receiving long-term antiviral treatment, looking for the sites of HIV insertion. In these patients, viral replication was suppressed by the drugs, often for periods of over a decade. Therefore, any viruses researchers found were from those cells that had quiescent viruses inserted into their genome.


In some ways, HIV works like a tumor. Cancer cells have mutations that often affect  cell growth. When we try and hit this with chemotherapy, tumor cells with a selective advantage that allows them to survive will continue to grow.

HIV inserts randomly into a cell’s DNA, sometimes close to a gene. If that gene happens to be one of the growth genes , the HIV will alter the cell’s metabolism much as cancer mutations do. 

So, even when drugs are used to control the HIV, the cells with HIV insertions next to growth genes still manage to survive.

It is not just enough to have drugs that stop HIV from replicating We may have to figure out how to deal with specific insertion points and how to deal with those cells.

High altitude tolerance, Tibet, Sherpas and Denisovan DNA – questions about the Himalayas and Mars

Kathmandu , Nepal,Himalayas,Everest 

Tibetans’ altitude tolerance may have come from our extinct relatives
[Via Ars Technica]

The Denisovans, relatives of the Neanderthals who inhabited Asia before modern humans arrived, are known only from a scattering of small bones and a wealth of DNA data. So far, all of that originates from a single Siberian cave (called Denisova, naturally). Like the Neanderthals, the Denisovans interbred with those modern humans once they arrived. But the modern populations who have the most Denisovan DNA are far from Siberia, occupying southern Asia and some Pacific islands.

Now, a tiny fragment of Denisovan DNA has also been found in a group that’s much closer to Siberia: the Tibetans. And all indications are that it helps them adapt to the extreme elevations of the Tibetan plateau.

Large parts of that plateau are 4,000 meters (2.5 miles) above sea level. The populations native to the area have lower infant mortality and higher birth weights than people who have relocated to the area. In addition, the Tibetans have acclimated to the altitude without relying on increased red blood cell counts, which is how most other people respond after spending time at altitude. Higher red blood cell counts mean a more viscous blood, which creates its own health hazard, so this difference is also likely to be very advantageous.


This explains some really interesting aspects of what has been called a great example of natural selection in human beings. The Tibetans gained this trait in less than 3000 years.The ability to survive at high altitude shows just how dramatically the environment has shaped human genomes.

And now we know that those genes came from non-human sources.

Kind of cool what DNA sequencing is now showing us about our human heritage. Just small amounts of ancient DNA from species we crossbred with still have an impact today.

The Tibetans are healthy at an air pressure that is 60% of what it is at sea level. I wonder just how low the air pressure could go for them to live? The Nepalese sherpas also have the relevant Denisovan genes and are able to survive altitudes on Mt. Everest that others require oxygen to survive. But people in the Andes have a different set of genes.

So I wonder what would happen if someone from Tibet has children with someone from the Andes? Would the children have the abilities to survive at even higher altitudes? And Ethiopians have a completely different set of genetic mutations from Andean or Tibetan sources..

The Armstrong limit is about 19,000 meters or about 12 miles, the point at which water boils at human body temperature. Even the most dense portion of the Martian atmosphere is 6 times less than this. So we would need to do extensive terraforming to raise the air pressure. But would these Tibetans be a likely group to make the first Martian settlers to live unencumbered by pressure suits?

Did Facebook’s unethical research on humans result in suicides?

Dangerous Risk Adrenaline Suicide by Fear of Falling 

Open letter to Mark Zuckerberg: you owe us one hell of an explanation
[Via Scholars and Rogues | Progressive Culture]

As the title of this post indicates, you owe us one hell of an explanation. Indulge me, if you will.

As you are undoubtedly aware, your company, Facebook, recently had a scientific study published online in the Proceedings of the National Academy of Sciences of the United States of America (PNAS). I would naturally assume, social media being your element, that you are aware of a degree of outcry about the ethical lapses that appear evident in your study’s methodology. I doubt you registered my own outrage, so ICYMI, here it is.


The question: In a group of over 600,000 people, what are the chances that someone in the throes of depression was manipulated by Facebook in a way that resulted in suicide?

How many people were possibly harmed by the manipulations Facebook used? How many minors? Did Facebook even consider the possibility?

Who really cares? Certainly not Facebook. Facebook is a corporation that can do unethical things that harm its customers, as long as those things are legal.

But PNAS, as a reputable science journal, should have cared and should have asked the questions. It should not have published this research based on the unethical treatment of human subjects.

As another has written:

Also, there are heads at PNAS that need rolling. As in, first thing tomorrow morning, if not sooner. Human subjects research guidelines can be an unholy pain, but they exist for a reason. How this study got past their reviewers is a mystery of the first order.

I imagine that Susan T. Fiske, the PNAS editor, may have a full inbox on Monday.

Updated: Did PNAS publish a medically unethical paper?

Healthy Human T Cell 

Facebook’s science experiment on users shows the company is even more powerful and unethical than we thought
[Via PandoDaily]

If you were still unsure how much contempt Facebook has for its users, this will make everything hideously clear.

In a report published at the Proceedings of the National Academy of Sciences (PNAS), Facebook data scientists conducted an experiment to manipulate the emotions of nearly 700,000 users to see if positive or negative emotions are as contagious on social networks as they are in the real world. By tweaking Facebook’s powerful News Feed algorithm, some users (we should probably just call them “lab rats” at this point) were shown fewer posts with positive words. Others saw fewer posts with negative words. “When positive expressions were reduced,” the paper states, “people produced fewer positive posts and more negative posts; when negative expressions were reduced, the opposite pattern occurred. These results indicate that emotions expressed by others on Facebook influence our own emotions, constituting experimental evidence for massive-scale contagion via social networks.”

The results shouldn’t surprise anybody. What’s more surprising, and unsettling, is the power Facebook wields in shifting its users’ emotional states, and its willingness to use that power on unknowing participants. First off, when is it okay to conduct a social behavior experiment on people without telling them? Technically, and as the paper states, users provided the consent for this research when they agreed to Facebook’s Data Use Policy prior to signing up, so what Facebook did isn’t illegal. But it’s certainly unethical.


UPDATE: Looks like it is also a poorly designed study also. Unethical and bad science.

Shame on PNAS.

I don’t care about Facebook. PNAS is at fault here. Human experimental protocols without proper informed consent and institutional oversight should never be published. 

Yet here it is.

I read the article and I did not see any discussion of specific informed consent for this example of human experimentation. Human subjects are supposed to be allowed to opt out when given informed consent for a specific research protocol.  To do otherwise is now regarded as medically unethical.

And I did not see mention of any outside review of the protocol by a board tasked with oversight of human experimentation. Failure to do this is now regarded as medically unethical.

Both informed consent and review board oversight are supposed to be part of any research protocol involving human subjects.

Sure, Facebook may legally be permitted to do the research (corporations are permitted to do all sorts of immoral and unethical things, as long as they are legal). However, medically unethical research is not supposed to be published, no matter what the legality.

To my mind, by failing to secure these two important procedures necessary for proper experiments on humans, PNAS has disgraced itself and published a medically unethical paper.

We just went through a lot of controversy regarding HeLa cells and consent. The answer I often heard was that this was back in the primitive days of human experimentation, that today we would get specific informed consent and oversight. 

Yet here we have a published experiment on over 600,000 human subjects apparently without proper consent and no oversight.

How in the world does PNAS publish a report dealing with human subjects that not only did not gain specific  informed consent but seemingly had no oversight from any sort of review board?

Very disappointed in seeing a prestigious scientific journal publish such an unethical and morally obtuse paper.

Especially one that, as discussed in the Pando article, may well be quite weak on its protocol, analysis and conclusions.

Shame on PNAS.

Conservatives acknowledge climate change even as they refuse to believe it

 Smoke art - Cubes to smoke

Conservatives Don’t Deny Climate Science Because They’re Ignorant. They Deny It Because of Who They Are. | 
[Via Mother Jones]

For many years, the US National Science Foundation, more recently with the help of the General Social Survey, has asked the public the same true or false question about evolution: “Human beings, as we know them today, developed from earlier species of animals.” And for many years, the responses to this question have been dismal. In 2006, 2008, and 2010, for instance, less than half of the public correctly answered “true.”

In 2012, however, the NSF and GSS conducted an experiment to try to better understand why people fare so badly on this evolution question. For half of survey respondents, the words “according to the theory of evolution” were added to the beginning of the statement above. And while only 48 percent gave the correct answer to the unaltered question, an impressive 72 percent correctly answered the new, prefaced version.


This work points up the ability of people to ignore facts if it conflicts with their world views. This is seen when we use the word ‘believe’ when discussing science questions: “Do you believe in evolution?”, etc.

I try to never use the word believe when discussing the facts of science, such as evolution or climate change.

Science is not about belief. It is about acknowledging facts. As this study shows, both conservatives and liberals acknowledge the same facts, even as they assert different beliefs. Liberals got the science wrong also when their beliefs got in the way.

If someone refuses to acknowledge that the world is getting warmer, then they are scientifically illiterate and not really worth having as part of a science discussion.

If they do acknowledge facts, then we can begin to discuss why and what might be done.

The discussion on climate change cannot happen if it starts from what people believe. It will only happen when more conservative leaders acknowledge the world is getting warmer.

A single, unusual sugar-amino acid molecule feeds potent Salmonella

Salmonella Bacteria 

Salmonella’s Achilles’ heel: Reliance on single food source to stay potent
[Via Eureka! Science News - Popular science news]

Scientists have identified a potential Achilles’ heel for Salmonella – the bacteria’s reliance on a single food source to remain fit in the inflamed intestine


The nutrient – fructose-asparagine – is required for Salmonella to provoke what we call food poisoning. Blocking this nutrient may help alleviate 42,000 incidents a year.

Salmonella can be 10,000 times less fit if it does not have access to this nutrient. A surprising result but something that may well help us dealign with this illness.


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