Lab Notes

Short stories and links shared by the scientists in our community

🌋 What's in a name? Mount Taranaki

Shared by

Brittany Ward

Geochemistry and Paleoclimatology

University of Waikato

Volcanoes of New Zealand are important figures in Māori (New Zealand's indigenous people) culture. When European exploration of New Zealand began in the early 1700's many places and landmarks were renamed, replacing their original Māori names. One such name change was Mount Taranaki, a volcano central in Māori legends with other mountains in the Tongariro National Park. Taranaki was renamed Mount Egmont by a Dutch explorer in 1770, and was taken by the British Crown in 1865. In 1986, Mount Taranaki (then Mount Egmont) was officially renamed "Mount Egmont or Mount Taranki" by the Lands Minister at the time, although the New Zealand Geographic Board had unanimously voted to return its name to Mount Taranaki months prior. In December 2017, eight iwi (people or nations of New Zealand) Taranaki officially signed an agreement with the Crown to begin the process of giving Mount Taranaki legal personality, meaning Mount Taranaki would have legal ownership over itself. Upon legalization, Taranaki will join Te Urewera and the Whanganui River, both of which have had legal identity since 2014.

What we know, and still don't know, about the CRISPR-modified twins

Shared by

Devang Mehta

Genomics

University of Alberta

What we know:

  • Dr. Jiankiu He, a scientist in China claims to have edited the genome of two human embryos, which were then implanted and given birth to by their mother as twins, dubbed Lulu and Nana.
  • Dr. He says he edited the CCR5 gene, in order to provide the embryos with resistance to HIV infection. Jiankiu He says he did this because the father of the twins carried HIV. A version of CCR5 (CCR5-Δ32), mainly found in Northern European genomes, is known to confer immunity to certain variants of HIV. 
  • Based on Dr. He’s presentation at the 2nd International Summit on Human Gene Editing this week, one of the two embryos did not have all its cells edited, as a result it is not clear that this baby will have resistance to HIV. The other embryo has only a single-copy of CCR5 edited (humans have two copies of all genes), and the resulting edited gene is not yet known to confer resistance to HIV. It is possible that neither of the two babies will have resistance to HIV. It would certainly be unethical to test this!
  • There are other ways, such as sperm washing during IVF, to prevent HIV transmission from father to off-spring.
  • Dr. He also detected an “off-target” edit, i.e. another region of the genome that was edited by the CRISPR technology used. He suggested that this was unlikely to result in any adverse medical outcomes.
  • He’s experiment was performed in secrecy. His former employer has denied involvement in the trial. 
  • The informed consent form used by Dr. He appears to be misleading in terms of the risks involved.
  • Dr. He claims to have followed the recommendations of the US National Academies report on human gene-editing. However, his trial doesn’t seem to have followed several of these recommendations (highlighted below) and may yet ignore others. 

Restrictions on human germline editing (NASEM, 2017). Highlights showing points not met by Jiankiu He’s experiment.

  • Dr. He says he’s in the process of submitting a scientific manuscript for publication.
  • His experiment drew immediate criticism in China, with over a hundred scientists signing a letter decrying his work as unethical.

What we don’t yet know:

  • The role of He’s collaborator, Michael Deem, a professor of bioengineering at Rice University in the US.
  • There are media reports of a PR firm hired by He, but there’s no clarity about the role of this firm.
  • As of now it is still unclear which research institutions, which medical doctors, and which hospitals were involved in this project. 
  • The funding for the trial is still unclear. It appears to have been funded through He’s personal funds as well as funding from the Shenzhen Science and Technology Innovation Commission according to the clinical trial registration in China. The commission however has claimed to have never funded this project. 
  • Documents showing ethics approval from the Shenzhen HOME Women’s and Children’s Hospital appeared on social media. However the hospital seems to have lodged a complaint suggesting this form was forged. We need to learn more about the ethics and approvals pipeline followed by He. 
  • Dr. He has pledged to follow up with the health of the babies for the first 18 years of their life, however there is no information about who would be involved in this effort, nor what kind of tests this will involve, or how the results would be reported.
  • We do not yet know if the edits on the genome of the two babies will have any adverse effects. Some scientists have suggested that the method He used to screen the embryos for off-targets were insufficient. We will just have to wait and hope the babies do not suffer due to the editing. 

External Link MIT scientists invent an ion-drive powered plane with no moving parts

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Devang Mehta

Genomics

University of Alberta

From Nature:

Researchers from MIT have flown a plane powered by an ‘ion drive’ for the first time. The drive uses high powered electrodes to ionise and accelerate air particles, creating an ‘ionic wind’. This wind drove a 5m wide craft across a sports hall. Unlike the ion drives which have powered space craft for decades, this new drive uses air as its accelerant. The researchers say it could power silent drones.

Check out this video featuring Steven Barrett, the researcher who led the team:

This first flight made it about as far as the Wright brothers' first flight at Kitty Hawk. While it seems infeasible for passenger flights, it does have the potential to create a new class of small, silent, and clean drone aircraft.

External Link USDA and FDA announce that they'll both regulate cellular agriculture, but at different stages

Shared by

Dan Samorodnitsky

Biochemistry

Carnegie Mellon University

In the US, food regulation is split in two. As they put it, the Food and Drug Administration (FDA) regulates most "food or food additives" in the US, including the production, packaging, labeling, and sale of food besides meat and poultry. Meat and poultry are regulated by the US Department of Agriculture (USDA). The USDA regulates the production, slaughter, and sale of all meat and meat products. These agency's joint decision on cell-based meats will treat these new products as different things at different points along the process of turning cells into meat.

The FDA will oversee the growth and production of cells. At harvest time, when the cells are collected to be turned into meat, regulation will transfer to the USDA. The decision can be seen as a win for the companies that make cell based meat, which advocated for a similar set up in a letter to the White House in August.

To learn more about the growing field of cellular agriculture, read Massive's free report on the state of this research.

Cephalopalooza!

Shared by

Allan Lasser

Co-founder and CTO, Massive Science

Last month the scientific exploration ship Nautilus has discovered the largest deep-sea octopus nursery, with over 1,000 octopus. 

"We went down the eastern flank of this small hill, and that's when - boom - we just started seeing pockets of dozens here, dozens there, dozens everywhere," King told National Geographic.

It's wonderful to hear the un-self-conscious enthusiasm of these researchers as they discover the nursery.

Follow along with the Nautilus on Twitter and their ship's ongoing livestream.

External Link The EPA Can’t Wait to Reopen the Mine That Poisoned North Idaho

Shared by

Nadja Oertelt

Co-founder and CEO, Massive Science

This is a great piece:

“In 1983, the U.S. Environmental Protection Agency declared the Bunker Hill Mine and smelter complex the nation’s second-largest Superfund site. The agency has been a presence in the valley ever since. Today, after 35 years and almost $900 million in cleanup costs, Bunker Hill’s tailings heap still oozes 400 pounds of toxic metals a day into the South Fork of the Coeur d’Alene River. Tundra swans still flap and stagger in the marshes. After picking up more mine waste downstream, the river dumps almost 400 tons of lead and 700 tons of zinc into Lake Coeur d’Alene every year.”

Meanwhile, in England, extremophile microbiologist and Consortium scientist Dr. Rose Jones is figuring out how to clean up toxic mining waste with microbes.

💩 The human microbiome

Shared by

Yewande Pearse

Neuroscience

LA Biomed

Our microbiome, the collective genomes of the microbes that live inside our digestive systems, has been linked to multiple facets of our health, from cancer to depression and everything in between. However, before you go recommending one probiotic over another, you might want to read ahead.

Large studies have revealed significant variation between the gut microbiome of both healthy individuals and those with health conditions, making it hard to identify associations between the gut microbiome and a person’s health. However, thanks to two recent studies (one in Amsterdam and one in Guangdong, China), the reasons for this variation are now clearer. The two studies showed that both ethnicity and geography are key factors in determining the gut microbiome. It gets even more complicated: most of the current knowledge about the connections between the microbiome and health come from studies of European and North American populations.

This new research highlights the importance of being careful when applying data about the gut microbiome to different groups of people: clearly, one size does not fit all. However, researchers still don’t know why differences in the gut microbiome are associated with ethnicity and geography. We’ll need to untangle the influence of genetics, cultural norms, and diet if we want to develop personalized microbiome-based treatments.

Researchin' with urchins

Shared by

Dan Samorodnitsky

Biochemistry

Carnegie Mellon University

Purple sea urchins are eating all the kelp in California. But in Pittsburgh, hundreds of miles from the ocean, we order them in the mail.

They arrive wrapped in wet newspaper with pieces of seaweed to snack on. We keep them in tanks, next to some sea star buddies, and study how they grow skeletons. When we're done, we bleach them (the university considers them a biohazard) and save them as extremely fragile decorations.

External Link Just Months of American Life Change the Microbiome

Shared by

Kevin Pels

Chemical Biology

The Scripps Research Institute

Immigrants’ gut bacteria “westernize” soon after they move to the U.S., which might influence obesity in immigrants and Americans alike

External Link Bruno Latour, the Post-Truth Philosopher, Mounts a Defense of Science

Shared by

Devang Mehta

Genomics

University of Alberta

He spent decades deconstructing the ways that scientists claim their authority. Can his ideas help them regain that authority today?

Some spooky Halloween Archaeology facts from Massive Consortium member Darcy Shapiro

Shared by

Darcy Shapiro

Evolutionary Anthropology

Rutgers University

💀 You can estimate a person’s age from their skeleton (specifically, from how many/which bones have fused growth plates) — and the more skeletal bones you have, the better your age estimate! 

🧛🏼‍♂️ Bioarchaeologists recently excavating a 17th-18th century cemetery in Poland have found graves of “suspected vampires” — people the locals interred with iron sickles or with rocks under their chins, to keep them from rising and feeding on the living. 

🔪 Paleoanthropologists have found cut-marked Neanderthal bones at a number of Neanderthal sites. The placement of these marks suggests that individuals were dismembered and de-fleshed — a likely indicator of cannibalism. 

👻 Happy Halloween! 🎃

🌋 Mount Ngauruhoe, aka Mount Doom 🌋

Shared by

Brittany Ward

Geochemistry and Paleoclimatology

University of Waikato

One of the most famous volcanoes of New Zealand is Mount Ngauruhoe, which some may recognize as Mount Doom from Lord of the Rings. The largely accepted translation of its Māori (New Zealand's indigenous people) name is "throwing hot stones," characterizing its active volcanism. Ngauruhoe isn't actually a volcano on its own, but rather a cone of the larger Tongariro Volcanic Complex, which resides in the Tongariro National Park.

Ngauruhoe is a stratovolcano, which means its built of alternating layers of lava and ash. The type of lava that erupts from Ngauruhoe cools and hardens relatively quickly after eruption and piles closely around the volcano, a behavior that gives Nagauruhoe and other stratovolcanoes their iconic cone shape.

Recent studies suggest Ngauruhoe began forming 7,000 years ago. There is a long Māori verbal record of eruption activity and 60 events since written records began in 1839. Ngauruhoe was erupting roughly every 9 years until its last eruption in 1975. Today New Zealand-based research teams actively monitor the seismic and chemical activity of Ngauruhoe. 

Did climate change cause Hurricane Florence?

Shared by

Gabriela Serrato Marks

Marine Geology

Massachusetts Institute of Technology

The short answer is no. Our planet's changing climate did not cause Florence to form, but it's definitely not making things any easier. Because of increased air and water temperatures, hurricanes can carry more rain onto land than they used to. That makes flooding an even more pressing threat. In addition to being wetter, hurricanes are also larger: a brand-new (not yet peer-reviewed) analysis released yesterday showed that the diameter of Florence is 50 miles (80 km) larger because of the influence of climate change. Analyses completed after landfall will have more information about how warming temperatures are influencing big storms, but for now, scientists will continue to watch and wait.

External Link Giant Squids, Giant Eyes, but Rather Small Brain Lobes

"This is the first time we get to have any information about what the world might look like to a giant squid, and that’s just super cool."

External Link The Giant Squid’s Biggest Mystery

Deep below the sea surface, giant squid fight off predatory sperm whales–stirring legendary tales of epic battles. Yet for all it’s infamy, discovering how many of these enormous cephalopods are lurking in the ocean has remained impossible…until now. Using simple arithmetic, Elizabeth Shea, Curator of Mollusks at the Delaware Museum of Natural History, along with colleagues at the Smithsonian Institution try to solve the mystery – with unfathomable results!

External Link Love, Octopus-ly

It’s small. It’s striped. It’s looking for love. Meet the lesser Pacific striped octopus. Full-time biologist—part-time cephalopod matchmaker, Richard Ross invites us into his secret home lab where he studies the mating rituals of these tiny cephalopods.

External Link Do Stars Fall Quietly into Black Holes, or Crash into Something Utterly Unknown?

Astronomers at The University of Texas at Austin and Harvard University have put a basic principle of black holes to the test, showing that matter completely vanishes when pulled in. Their results constitute another successful test for Albert Einstein’s General Theory of Relativity.

External Link Starving Prostate Cancer With What You Eat for Dinner

When you dine on curry and baked apples, enjoy the fact that you are eating something that could play a role starving — or even preventing — cancer.

External Link Has lithium-battery genius John Goodenough done it again?

Researchers have struggled for decades to safely use powerful—but flammable—lithium metal in a battery. Now John Goodenough, the 94-year-old father of the lithium-ion battery, is claiming a novel solution as a blockbuster advance.

External Link Octopus: The Footed Void

Their intelligence is all the more striking because it has evolved completely independently of the line that gave rise to us: our last common ancestor—perhaps some simple, slug-like creature—lived well over 540 million year ago.

External Link Other Minds by Peter Godfrey-Smith review – the octopus as intelligent alien

"If we can make contact with cephalopods as sentient beings, it is not because of a shared history, not because of kinship, but because evolution built minds twice over."

External Link The Mind of an Octopus

Eight smart limbs plus a big brain add up to a weird and wondrous kind of intelligence.

External Link Watch cuttlefish apparently pretending to walk just like crabs

It could be a strategy to deter predators by making them think soft cuttlefish have a hard shell, or trick prey into thinking they're harmless.

External Link The Scandalous Life of Nurse and Adventurer Kate Marsden

She spent 11 months trekking to Siberia to find a cure for leprosy, but her love life overshadowed everything.

External Link People With Leprosy Were Exiled There—Should It Be a Tourist Destination?

Kalaupapa, Hawaii, is a former leprosy colony that’s still home to several of the people who were exiled there through the 1960s. Once they all pass away, the federal government wants to open up the isolated peninsula to tourism. But at what cost?