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Monkey Wrench

We need to know what happened to CRISPR twins Lulu and Nana

Kiran Musunuru
technologyreview.com
Tue, 03 Dec 2019 14:54 UTC
gene editing
© MS TECH Peggy Peterson
The unpublished research paper by He Jiankui about the creation of the babies shows proof of attempted gene editing gone awry.

It's been a year since He Jiankui announced that he'd made the world's first gene-edited human babies, twin girls with the pseudonyms Lulu and Nana. Widespread condemnation of his actions followed the announcement. But the facts of the case remain unclear, because he has not been transparent about his work.

In his single public appearance following his announcement, at the Second International Summit on Human Genome Editing in Hong Kong in November 2018, He presented his work by racing through about 60 slides in just 20 minutes. Although he showed data about what he had done to the twins' genes, it was blink-and-you'll-miss-it, and not enough to convince anyone of his claim that he'd safely edited the genomes of the human IVF embryos that became Lulu and Nana.

Comment: The CRISPR baby scandal gets worse by the day

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Blue Planet

Granny killer whales pass along wisdom — plus extra fish — to their grandchildren

Eva Frederick
Science Magazine
Mon, 09 Dec 2019 21:55 UTC
orca calf mother killer whale
© NOAA Fisheries
A mother orca and her calf near Port Renfrew, British Columbia.
Many human grandmothers love to spoil their grandchildren with attention and treats, and for good reason: Studies have shown that having a living grandmother increases a child's chance of survival. Now, new research shows the same may be true for killer whales. By providing young animals with some freshly caught salmon now and then — or perhaps with knowledge on where to find it — grannies increase their grand-offspring's chance of survival.

The new study is the first direct evidence in nonhuman animals of the "grandmother hypothesis." The idea posits that females of some species live long after they stop reproducing to provide extra care for their grandchildren.

"It's very cool that these long-lived cetaceans have what looks like a postfertile life stage," says Kristen Hawkes, an anthropologist at the University of Utah in Salt Lake City who has dedicated much of her career to studying the grandmother effect; she was not involved in the new study.
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Fish

MBARI: Thousands of holes discovered on seafloor off California coast

Aristos Georgiou
Newsweek
Wed, 11 Dec 2019 07:42 UTC
Big Sur
© GlobalLookPress/ZUMAPRESS.com/Joanna Glikeson
Pacific Ocean, Big Sur, California
Researchers have discovered thousands of mysterious holes or pits in the seafloor — measuring 36 feet across and three feet deep on average — off Big Sur, California.

A team led by Eve Lundsten from the Monterey Bay Aquarium Research Institute (MBARI) discovered the so-called "micro-depressions" during a survey of North America's largest pockmark field.

Pockmarks are similar to micro-depressions albeit much larger, measuring around 600 feet across on average and 16 feet deep in this particular field. Since 1999, MBARI scientists have uncovered more than 5,200 of these almost-circular and evenly-spaced pockmarks across an area of around 500 square miles off Big Sur.
Pockmark locations
© 2019 MBARI
Pockmark locations
For their latest survey, the Lundsten and colleagues wanted to investigate this pockmark field because there are proposals to build a wind-energy farm in the area.
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Info

Electrons flowing like water imaged for the first time


Weizmann Institute of Science
Mon, 09 Dec 2019 17:53 UTC
River of Electrons
© Weizmann Institute of Science
A “river” of electrons flowing in a graphene channel. The viscosity generated by the repulsion between electrons (red balls) causes them to flow with a parabolic current density, illustrated here as a white foam wavefront.
We often speak of electrons "flowing" through materials, but in fact, they do not normally move like a liquid. Such "hydrodynamic" electron flow had been predicted, though, and Weizmann Institute of Science researchers recently managed, with the help of a unique technique to image electrons flowing like the water flowing in a pipe. This is the first time such "liquid electron flow" has been visualized, and it has vital implications for future electronic devices.

Electrons usually move through conductors more like a gas thana liquid. That is, they do not collide with one another, but rather, they tend to bounce off impurities and imperfections in the material. A fluid flow, in contrast, takes it shape - be it waves or whirlpools - from frequent collisions between the particles in liquid.

To make electrons flow like a liquid, one needs a different kind of conductor, and the team turned to graphene, which is a one-atom-thick sheet of carbon, and which can be made exceptionally clean. "Theories suggest that liquid electrons can perform cool feats that their non-liquid counterparts cannot. But to get a clear-cut proof that electrons can, indeed, form a liquid state, we wanted to directly visualize their flow," said Prof. Shahal Ilani head of the team in the Institute's Condensed Matter Physics Department.
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Fish

Predators may make prey get smart and grow more brain cells

Chelsea Whyte
New Scientist
Wed, 11 Dec 2019 07:23 UTC
fish
© U.S. Geological Survey, Bugwood.org
Where predators are common, this fish has more brain cells
Sometimes stress can be good for a fish. When there are more predators around, killifish in Trinidad grow more brain cells than those that face no predators, and they do so even into adulthood.

"I was surprised to find this because in previous studies, we found that predators inhibit the production of brain cells," says Kent Dunlap at Trinity College in Connecticut. It seems that killifish swim their own way.

Dunlap and his colleagues examined the brains of a type of wild caught killifish (Rivulus hartii) from three streams on the Caribbean island. In each stream, they gathered about eight adult fish from a location with a high number of predators and about eight from a location with little to no predation. They only used males because previous research on these fish showed that predation affects male but not female brains.

The researchers measured the size of the males' brains as well as the density of newly grown cells. They found that fish from both spots in each stream had brains similar in size relative to their bodies, but those that had to fight off more predators had nearly double the amount of new brain cells. Dunlap says this may mean that instead of fairly static brains that respond to predators in a timid way, the new brain cells could allow for more responsive behaviour.
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Satellite

Asteroid Bennu is shooting out rocks - and NASA isn't sure why

Chris Ciaccia
Fox News
Tue, 10 Dec 2019 17:04 UTC

Comment: So what you're saying is... when you're 'tracking' an incoming asteroid, it could have split into a wide debris field by the time it 'passes' us?

Oh boy...


asteroid Bennu ejecting particles from its surface on Jan. 6, 2019
© NASA/Goddard/University of Arizona/Lockheed Martin
This view of asteroid Bennu ejecting particles from its surface on Jan. 6, 2019, was created by combining two images taken by the NavCam 1 imager aboard NASA's OSIRIS-REx spacecraft: a short exposure image, which shows the asteroid clearly, and a long-exposure image (five seconds), which shows the particles clearly.
Asteroid Bennu, which could provide answers to questions about the origins of our solar system, is mysteriously launching particles into space and NASA isn't sure why.


Comment: There it is again! Every single MSM article about asteroids/comets opens with 'could provide answers to the origins of our solar system!'

What is UP with that?!

How about solving the 'mystery' of why asteroids/comets periodically wipe out civilization??


Since reaching the massive space rock in December 2018, NASA has observed multiple particle-ejection events, including three major ones on Jan. 6, Jan. 19 and Feb. 11. The researchers found that the particles either orbited Bennu and fell back to its surface or escaped its orbit and went into space. The largest event, which took place on Jan. 6, saw "approximately 200 particles" get ejected from the asteroid, NASA wrote in a blog post.

The particles traveled as fast as 10 feet and ranged in size between less than an inch to 4 inches. The mysterious ejection could be caused by three different reasons, according to the NASA blog post: meteoroid impacts, thermal stress fracturing and released water vapor.


Comment: All of which are regulated by electric charge differential as the asteroid interacts with near/distant bodies like other asteroids/planets...


Comment: See also:

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Sun

Plants thrive when climate warms, study of last ice age shows

Paul Voosen
Nature
Tue, 10 Dec 2019 01:40 UTC
baffin island
© Zach Montes/Orijin Media
CF8, a 40-hectare lake on Baffin Island in Canada, holds a DNA record of the surrounding ecosystem that may go back 125,000 years.
High in the Canadian Arctic on Baffin Island, beneath 10 meters of water and many more of mud, sits a refrigerated archive of Earth's past life. The deep sediments in a small lake called CF8 hold ancient pollen and plant fossils. But it now appears that the mud harbors something else: ancient DNA from as far back as the Eemian, a period 125,000 years ago when the Arctic was warmer than today, left by vegetation that otherwise would have vanished without a trace.

"We feel confident that we are getting authentic results," says Sarah Crump, a paleoclimatologist at the University of Colorado in Boulder who is presenting the work here this week at the annual meeting of the American Geophysical Union. She acknowledges the finding needs to be confirmed. But if it holds up, it could open a window on the ecosystems that flourished in the high Arctic at a time when temperatures were a few degrees warmer than today. It would also attest to the power of sedimentary DNA, as it's called, to show how Arctic plants responded to past climate shifts — hinting at how they might respond in the future. "We are now at the point that this is a really useful signal for reconstructing biodiversity," says Ulrike Herzschuh, a paleoecologist at the Alfred Wegener Institute in Potsdam, Germany, who uses the technique to study how the larch forests of Siberia in Russia reacted after the end of the last ice age some 12,000 years ago.

Comment: As would be expected. Too bad, this time, our planet is entering an ice age.

See also:

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Microscope 1

Jonathan Wells was right: Non-coding 'junk' DNA continues to show function


Evolutionary News
Tue, 10 Dec 2019 18:02 UTC
junk dna
In his 2011 book The Myth of Junk DNA, Jonathan Wells called the notion of junk DNA a science-stopper. Noting discoveries already made by 2011, he said these are "exciting times," predicting that ongoing research would continue to discover functions that were not yet imagined. As the following papers show, he was right.

Cistromes

In PNAS, Dongyin Guan and Mitchell A. Lazar commented on work by Fei et al., concluding that "noncoding mutations in enhancers and other, less well-characterized, TF [transcription factor] binding regions also have large effects on cell survival and proliferation." Their review, "Shining light on dark matter in the genome," begins,
The complexity of multicellular organisms requires the genome to be transcribed in a cell-type-dependent manner that is responsive to signals, such as hormones, from the internal environment. This is mediated by the epigenome, which decorates and organizes the genome in a web of modified histone proteins functioning in nucleosomes and chemical modifications to genomic DNA arranged 3-dimensionally in the cell nucleus. Functional features of the epigenome such as acetylation of histone lysine residues are "read" by specialized proteins such as those containing bromodomains. Likewise, the genome itself is read by proteins known as sequence-specific transcription factors (TFs), which recognize and bind to specific motifs in genomic DNA. The totality of these sites for a given transcription factor in a given cell is known as its "cistrome". Most of these binding sites occur in the ∼99% of the genome that does not encode for proteins. [Emphasis added.]

Comment: It is a shame that most conventional microbiology seems to start with the unspoken assumption that Nature is wasteful and arbitrary whenever it comes up against something it doesn't immediately comprehend. Hence the terms 'junk' and 'parasite' for misunderstood DNA structures. How much quicker would the science progress if they took the stance as Paul Nelson has: "If it works, it's not happening by accident."

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People 2

Fooling ourselves: Even with accurate info, humans 'self-generate their own misinformation'

Christopher Carbone
New York Post
Tue, 10 Dec 2019 17:18 UTC
communication social media graphic
© iStockphoto
Although social media giants such as Facebook and Twitter have taken heat for spreading misinformation, it turns out that we — all of us — may be our own worst enemies in the battle against the scourge of fake news.

A new study found that people given accurate statistics on controversial topics tend to misremember those numbers in order to fit their own commonly held beliefs.

In the study, when people were shown that the number of Mexican immigrants in the United States declined recently — which is true but has gone against most people's beliefs — they tended to recall the opposite.

Comment: More from the Ohio State researchers:
The researchers found that people usually got the numerical relationship right on the issues for which the stats were consistent with how many people viewed the world. For example, participants typically wrote down a larger number for the percentage of people who supported same-sex marriage than for those who opposed it - which is the true relationship.

But when it came to the issues where the numbers went against many people's beliefs - such as whether the number of Mexican immigrants had gone up or down - participants were much more likely to remember the numbers in a way that agreed with their probable biases rather than the truth.

"We had instances where participants got the numbers exactly correct - 11.7 and 12.8 - but they would flip them around," Coronel said.

"They weren't guessing - they got the numbers right. But their biases were leading them to misremember the direction they were going."

By using eye-tracking technology on participants while they read the descriptions of the issues, the researchers had additional evidence that people really were paying attention when they viewed the statistics.

"We could tell when participants got to numbers that didn't fit their expectations. Their eyes went back and forth between the numbers, as if they were asking 'what's going on.' They generally didn't do that when the numbers confirmed their expectations," Coronel said.

"You would think that if they were paying more attention to the numbers that went against their expectations, they would have a better memory for them. But that's not what we found."

In the second study, the researchers investigated how these memory distortions could spread and grow more distorted in everyday life. They designed a study similar to the childhood game of "telephone."

For example, the first person in the "telephone chain" in this study saw the accurate statistics about the trend in Mexican immigrants living in the United States (that it went down from 12.8 million to 11.7 million). They had to write those numbers down from memory, which were then passed along to the second person in the chain, who had to remember them and write them down. The second person's estimates were then sent to a third participant.

Results showed that, on average, the first person flipped the numbers, saying that the number of Mexican immigrants increased by 900,000 from 2007 to 2014 instead of the truth, which was that it decreased by about 1.1 million.

By the end of the chain, the average participant had said the number of Mexican immigrants had increased in those 7 years by about 4.6 million.

"These memory errors tended to get bigger and bigger as they were transmitted between people," Sweitzer said.

Coronel said the study did have limitations. For example, it is possible that the participants would have been less likely to misremember if they were given explanations as to why the numbers didn't fit expectations. And the researchers didn't measure each person's biases going in - they used the biases that had been identified by pre-tests they conducted.

Finally, the telephone game study did not capture important features of real-life conversations that may have limited the spread of misinformation.

But the results did suggest that we shouldn't worry only about the misinformation that we run into in the outside world, Poulsen said.

"We need to realize that internal sources of misinformation can possibly be as significant as or more significant than external sources," she said.

"We live with our biases all day, but we only come into contact with false information occasionally."


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Info

C-section would increase risk of obesity in a child debunked by Swedish study


Karolinska Institutet
Mon, 09 Dec 2019 10:28 UTC
C-Section Study
© Karolinska Institutet
Women who have C-sections are no more likely to have children who develop obesity than women who give birth naturally, according to a large study by researchers at Karolinska Institutet in Sweden published in the journal PLOS Medicine. The findings contradict several smaller studies that did find an association between C-section deliveries and offspring obesity but did not consider the numerous maternal and prenatal factors that the researchers did in this study.

Cesarean or C-section deliveries have soared in recent years, from 6.7 percent globally in 1990 to around 19.1 percent in 2014, according to earlier reports. The jump has sparked intense research into the long-term consequences of C-section on offspring health, and several studies have linked cesarean deliveries with increased risks for asthma, various allergies and obesity. The association with obesity has, however, mainly been confirmed in smaller studies that were unable to account for a wide array of possible confounders or differentiate between types of C-sections.

The researchers in this study set out to investigate if indeed increased C-section births could explain part of the rise in obesity also seen in the last decades, and whether this potential association held true once they accounted for maternal and prenatal factors known to impact offspring weight. They compared the body-mass index (BMI) of nearly 100,000 male 18-year-olds and divided them into categories depending on whether they were born through vaginal delivery, elective C-section or non-elective C-section.
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