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@madgeneticist
The development of antimalarial drugs is fascinating – it is often driven by war and conquest. When human beings got busy trying to kill each other (during the era of colonial expansion, WWII, the Vietnam War), they often found themselves face to face with an even deadlier foe.
Check out my animation that explores this incredible history.
Read more about the 2015 Nobel Prize in Physiology or Medicine.
Scientists discover new system for human genome editing with potential to increase power and precision of genome engineering
A team including the scientist who first harnessed the revolutionary CRISPR-Cas9 system for mammalian genome editing has now identified a different CRISPR system with the potential for even simpler and more precise genome engineering.
In a study published today in Cell, Feng Zhang and his colleagues at the Broad Institute of MIT and Harvard and the McGovern Institute for Brain Research at MIT, with co-authors Eugene Koonin at the National Institutes of Health, Aviv Regev of the Broad Institute and the MIT Department of Biology, and John van der Oost at Wageningen University, describe the unexpected biological features of this new system and demonstrate that it can be engineered to edit the genomes of human cells.
CRISPR systems help bacteria defend against viral attack (shown here). These systems have been adapted for use as genome editing tools in human cells. Image by Ami Images/Science Photo Library.
Kennewick Man
If anyone is looking for the Nature article on the new Kennewick Man DNA analysis, open access to it is available here.
'Kennewick Man' sequencing points to Native American ancestry.
I like this article; I think the most important and striking part is this: "“We really have to change the top-down approach, where we come to people and say 'these are our research questions and you should participate, because — SCIENCE',” says Jennifer Raff, an anthropological geneticist at the University of Texas at Austin."
I don't think science ever really benefits from a top-down hierarchical approach. I think science benefits most from creativity, collaboration, and curiosity. And I think many if not most communities would be better served by a more "holistic" approach to science. Namely, as an anthropologist, even if you are most interested in using DNA evidence to map ancient human migrations, you really do need to spend time first engaging diverse groups in your research, talking to them, figuring out what /their/ questions about their origins are. Incorporating those questions into your research. That way, everyone's curiosity is driving the research, not just yours.
Obviously, this wouldn't work with the (colonialist...) idea that (usually white) scientists are beings of pure reason and (usually brown) indigenous groups are fluffy spiritualists content in their superstition. But that is an idea that is holding science back. It is something to be fought against. And I think that efforts to work with native groups in a respectful way are a first step towards fighting back against that narrative. So, you know, props to Hank Greely for pointing out that this evidence could be used to bolster the case that the remains should be given back to the native groups, to be buried (or studied. Or whatever.) And extra props for noting that "Hey, we've gotten what we want, we have this genome sequence, we figured out they were right, let's do what they asked."
As to the scientist who discovered the remains, and says he'd "hate to see one of the most complete North American skeletal remains be put back into the ground for political reasons," well, first of all, let's push back on the idea that a museum is a totally understandable place for the remains to stay. Or that there's no middle ground between "respectful of the desires of the descendants" and "available for science and study". Or that there isn't anything we could do (i.e. take another tiny sample to hold in reserve, take a cast of the bones) to study it while the original remains are given back. (Note: Or that we couldn't have done that to begin with? Maybe?) But mostly I really don't see why being sensitive towards the desires of this group of people is really stifling any science at all. (Like Greely points out, the science was done. 700 pages worth of science.) Or that it's motivated by 'politics' and not, like, basic human empathy.
Sure, most white people (myself included) would feel less identification with a set of 8,500 year old remains found in Germany. We would probably /want/ them to be put in a museum. But that's a function of white supremacy and colonialism. Since "white" is the default, since we "don't have an ethnicity", we don't feel as strong a connection to our past. But we shouldn't label the fact that other groups do feel a connection to their distant ancestors strange or unreasonable -- especially when we were the ones who brokered that connection and identification by classifying their cultures as somehow "primitive". When we weren't, you know, invading their land and murdering them.
Why do we teach “statistics” without communication?
This week I have been dealing with some puzzling gaps in my education, going back over and learning best practices (in particular re: scripting in R). And as a result I have been thinking a lot about my statistics education, and the biases inherent in it. To wit: I took several classes in R, but these always focused on calculations rather than the presentation of data.
Which seems backwards to me since so much of what makes statistics crucial is that they allow you to present data in a way humans can understand, and so much of what makes R an exceptionally powerful tool are specialized packages that let you present data beautifully.
I was never encouraged to use Rstudio. I am entirely self-taught on ggplot2. No one mentioned R markdown files. Or R project files. Or, really, anything that required the use of specific packages or platforms outside of the base class.
I wish I had learned any of those things rather than (for instance) spending my time scripting a replacement for R’s built-in standard deviation function; especially given the fact that the built-in function was guaranteed to be more optimized and the exercise was more “figure out how to script in R and remember what a standard deviation is” than actually-useful.
Largely, I get it. I do need to know what a standard deviation is and how it is computed. I also need to know how to do calculations in R. These are, in fact, essential skills and I think any scientist with an undergraduate degree should be able to do them. (Require statistics classes, folks!) What I don’t think, however, is that scripting a standard-deviation function in R is a particularly good way either to understand what a standard deviation is or to learn how to do calculations in an analysis platform like R or to figure out how R works.
(For standard deviations, I suggest interpretive dance. For the others, I have more boring suggestions.)
This came up again in a codecademy course on Python, wherein I spent time doing addition and subtraction in binary in my head before I was deemed “ready” to learn “complex” things like file input an output. But that’s a slightly different matter and might be suitable for another post.
My basic question is: for people learning and teaching R, why don’t you start from an editor like Rstudio and using things like markdown files? Why isn’t ggplot2 just required for everyone anymore? I know it’s not in the core functionality (requires more packages, etc). But a huge part of what makes R so powerful is our ability to get and use packages other people have created. It seems like a big advantage for teachers: getting problem sets in nicely-formatted outputs rather than cobbled together documents. And a bigger advantage for students: knowing how to easily document code and create presentations, which is really why most people use R to begin with.
Is it the mercury or the malaria?
Or maybe it’s something else entirely that’s making people sick in the Peruvian Amazon.
Those questions are bedeviling researchers from Duke University who have been studying gold mining in the region. Illegal mining has exploded in the area in the past decade, and the people living downriver have a variety of medical issues, from malaria to anemia to high blood pressure.
Researchers have documented that mercury used in illegal gold mining ends up hundreds of miles downstream from the mines, and it eventually ends up in fish — a major local source of protein.
But you can’t see or smell mercury in fish.
So it’s hard to measure the impact on residents. One of the main effects of mercury is that it causes developmental delays in children. Toxic exposure can cause severe fatigue, headaches and vomiting. Those symptoms could be the result of mercury. Or not. There’s very little data on all the other things that could be responsible for health issues in the area.
They’re Going Door To Door In The Amazon To See Why People Get Sick
Photo credit: Jason Beaubien/NPR
(Image caption: An embryonic mouse forebrain shows the genetically modified neurons in the neocortex (orange/yellow). Cortical stem cells and neurons in other brain regions remain unaltered)
Brain cells capable of “early-career” switch
Scientists at the Salk Institute have discovered that the role of neurons–which are responsible for specific tasks in the brain–is much more flexible than previously believed.
By studying sensory neurons in mice, the Salk team found that malfunction of a single molecule can prompt the neuron to make an “early-career” switch, changing a neuron originally destined to process sound or touch, for example, to instead process vision.
The finding, reported May 11, 2015 in PNAS, will help neuroscientists better understand how brain architecture is molecularly encoded and how it can become miswired. It may also point to ways to prevent or treat human disorders (such as autism) that feature substantial brain structure abnormalities.
“We found an unexpected mechanism that provides surprising brain plasticity in maturing sensory neurons,” says the study’s first author, Andreas Zembrzycki, a senior research associate at the Salk Institute.
The mechanism, a transcription factor called Lhx2 that was inactivated in neurons, can be used to switch genes on or off to change the function of a sensory neuron in mice. It has been known that Lhx2 is present in many cell types other than in the brain and is needed by a developing fetus to build body parts. Without Lhx2, animals typically die in utero. However, it was not well known that Lhx2 also affects cells after birth.
“This process happens while the neuron matures and no longer divides. We did not understand before this study that relatively mature neurons could be reprogrammed in this way,” says senior author Dennis O’Leary, Salk professor and holder of the Vincent J. Coates Chair in Molecular Neurobiology. “This finding opens up a new understanding about how brain architecture is established and a potential therapeutic approach to altering that blueprint.”
Scientists had believed that programming neurons was a one-step process. They thought that the stem cells that generate the neurons also programmed their functions once they matured. While this is true, the Salk team found that another step is needed: the Lhx2 transcription factor in mature neurons then ultimately controls the fate of the neuron.
In the mouse study, the scientists manipulated Lhx2 to make the switch in neuronal fate shortly after birth (when the mouse neurons are fully formed and considered mature). The team observed that controlling Lhx2 let them instruct neurons situated in one sensory area to process a different sense, thus enlarging one region at the expense of the other. The scientists don’t know yet if targeting Lhx2 would allow neurons to change their function throughout an organism’s life.
“This study provides proof that the brain is very plastic and that it responds to both genetic and epigenetic influences well after birth,” says O’Leary. “Clinical applications for brain disorders are a long way away, but we now have a new way to think about them.”
“Since this study was conducted in mice, we don’t know the time frame in which Lhx2 would be operating in humans, but we know that post-birth, neurons in a baby’s brain still have not settled into their final position–they are still being wired up. That could take years,” Zembrzycki says.
However, the findings may be an ingredient that contributes to the success of early intervention in some very young children diagnosed with autism, adds Zembrzycki. “The brain’s wiring is determined genetically as well as influenced epigenetically by environmental influences and early intervention preventing brain miswiring may be an example of converging genetic and epigenetic mechanisms that are controlled by Lhx2.”
Stunning Timelapse Shows the Aurora Borealis From Space
“The European Space Agency recorded a timelapse video of the Aurora Borealis as seen from the International Space Station. The latest video taken from the International Space Station is short, but it’s about as gorgeous a shot of the glowing phenomenon as one can hope to get.”
Check out the stunning full video from the washingtonpost.
Allergy sufferers are often told to eat local honey. This builds up your tolerance to local pollen, the theory goes, and it would make sense except for one inconvenient fact: Honey comes from flowers, and you aren’t allergic to flower pollen.
It doesn’t take a brain injury to have headache, dizziness and cognitive impairment
A team of researchers based at McMaster University has developed a new understanding of post-concussion syndrome, answering questions that have been plaguing researchers in the field.
Their study, published in the medical journal Brain, Behavior and Immunity, provides an explanation for why many people with even very trivial head injuries, or even injuries to other parts of their bodies, experience incapacitating post-concussion like syndromes.
These symptoms include headaches, dizziness, cognitive impairment and other neuropsychiatric symptoms such as irritability, anxiety and insomnia.
“It’s inflammation that they have in common,” said Michel Rathbone, a professor of medicine for McMaster’s Michael G. DeGroote School of Medicine and a lead author of the paper. “Rather than a concussion, we’d like to propose a unifying umbrella term of post-inflammatory brain syndromes or PIBS.”
He added that the research will encourage scientists to open up new lines of research into understanding the cause of post-concussion symptoms in the absence of obviously visible brain injury on conventional imaging and into the treatment of these symptoms by targeting inflammatory mediators. For example, people who have a very subtle genetic change in a certain inflammatory protein have poorer recovery after brain injury.
It also explains why many social factors appear to play a role in development of symptoms: “We know that the immune system can be modulated, or sensitized by the current and even the previous environment an individual was in. These social factors, such as preexisting stressors, depression or anxiety, may actually be, in a way, biological factors.”
Rathbone added that this will provide hope for individuals with cognitive dysfunction after major infections, surgeries and traumas, as it suggests that current and future treatments for concussion may hold a benefit for these individuals.
“This research opens many doors for so many different patients. We are excited to be starting a totally new approach to the field, and we look forward to making a difference for the patients of the future.”
Rats forsake chocolate to save a drowning companion
A new study shows that rats will rescue their distressed pals from the drink—even when they’re offered chocolate instead. They’re also more likely to help when they’ve had an unpleasant swimming experience of their own, adding to growing evidence that the rodents feel empathy.
Researchers at the Kwansei Gakuin University in Japan tested the rat’s altruistic behavior by devising an experimental box with two compartments divided by a transparent partition. On one side of the box, a rat was forced to swim in a pool of water, which it strongly disliked. Although not at risk of drowning—the animal could cling to a ledge—it did have to tread water for up to 5 minutes. The only way the rodent could escape its watery predicament was if a second rat—sitting safe and dry on a platform—pushed open a small round door separating the two sides, letting it climb onto dry land.
Within a few days, the high-and-dry rats were regularly aiding their soaking companions by opening the door, the team reports online today in Animal Cognition. They did not open the door when the pool was dry, confirming that the rats were helping in response to others’ distress, rather than because they wanted company, Mason says. Rats that had previously been immersed learned how to save their cagemates much more quickly than those who had never been soaked, suggesting that empathy drove their behavior, she adds. “Not only does the rat recognize distress, but he is even more moved to act because he remembers being in that situation.”
Given a choice between eating chocolate and helping a pal, rats make the noble decision. Sato, N. et al., Animal Cognition (2015)
What does “Probably Cause Cancer” actually mean?
Grist asked: “Hey Risk Bites guy, the WHO just said that the herbicide in Roundup probably causes cancer – what’s the deal with that? It seems like every month we find out that something else is probably giving us cancer. Should we be worried?”
http://grist.org/science/watch-stick-figures-explain-what-probably-causes-cancer-even-means/
By: Risk Bites.
there are actual people out there who want to genetically modify carnivores so they no longer eat other animals
im going to fly away from this planet goodbye
yeah let’s just fuck up the entire ecosystem because i’m uncomfortable with the fact that nature doesn’t conform to my world-views.
Okay kids gather round while Aunty Amber tells y’all a story that her 10th grade Biology teacher told her. When his wife was in college, she was a Vegan. She and her vegan friends rallied and protested for their little town to stop hunting the surrounding deer. Fast forward a few years, and that’s just what happened. So I want you to think for a moment. What happens to a population when their main predators stop hunting them? They grow. What happens to a population when they grow? They use up more resources. Fast forward a few more years. Deer are everywhere. Literally, everywhere. In the streets, in peoples yards, at schools. You know what’s not everywhere? Vegetation, because the deer population grew so large that they were eating everything and anything. This also grew to them being more violent, trying to compete for resources. Not only were there too many deer, but they were hella malnourished. Lack of food = bony-as-fuck deer. The town finally allowed the hunters to start hunting again, and it only took a few months for things to start going back to normal. Healthy deer, plenty of vegetation, streets filled with people and not with deer. The point is, if you take out a predator, everything it hunts will multiply, and resources will diminish. Don’t be stupid, let these animals hunt.
Seriously, we’re reintroducing predators in some places because after they had been hunted into extinction, the food web was torn apart.
plus deer carry deer ticks, which carry lyme disease, which can kill people
check out this video about wolves at yellowstone for examples of repairing the ecology of a place via reintroduction of an apex predator. (Also amazing landscape shots)
A promising technique for making brain tumors glow so they’ll be easier for surgeons to remove is now being tested in cancer patients.
Eighteen months ago, Shots first told readers about tumor paint, an experimental substance derived from scorpion venom. Inject tumor paint into a patient’s vein, and it will actually cross the blood-brain barrier and find its way to a brain tumor. Shine near-infrared light on a tumor coated with tumor paint, and the tumor will glow.
Now, after successful tests on dogs, surgeons have used tumor paint on a about a half dozen patients with brain tumors.
Doctors Test Tumor Paint In People
Photo Courtesy of Blaze Bioscience
Passive exposure to bleach in the home is linked to higher rates of childhood respiratory and other infections, suggests new research.
I am dubious of this; it seems like there are a lot of potential confounding variables that weren’t even mentioned. Mostly related to reporting bias -- a germophobe parent will be more likely to use bleach, and also more likely to notice an illness in their child that might otherwise pass unnoticed. It seems a difficult thing to control for, unless you get an external measure for both bleach use and childhood illness.
But the general idea that microbes are not by nature unhealthy, that we must be more targeted in our disinfecting, and that irritants in cleaning products can lead over time to serious harm, resonates. Worth thinking about.
A test that uses gold nanoparticles to detect early-stage prostate cancer costs less than $1, returns results in minutes and is more accurate than standard PSA screening, pilot studies show. The new technique leverages the ability of gold nanoparticles to attract cancer biomarkers.
