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kottke.org posts about Carl Zimmer

Vaccines May Help End the Pandemic. But Realistically, It’s Not Even Halftime Yet.

posted by Jason Kottke   Oct 13, 2020

We’re all so goddamned tired of this fucking pandemic and so people are looking at the development and distribution of a vaccine as the thing that’s going to get us out of this (and quick). But realistically, that’s not what’s going to happen. Carl Zimmer wrote about some of the challenges with Covid-19 vaccines.

The first vaccines may provide only moderate protection, low enough to make it prudent to keep wearing a mask. By next spring or summer, there may be several of these so-so vaccines, without a clear sense of how to choose from among them. Because of this array of options, makers of a superior vaccine in early stages of development may struggle to finish clinical testing. And some vaccines may be abruptly withdrawn from the market because they turn out not to be safe.

“It has not yet dawned on hardly anybody the amount of complexity and chaos and confusion that will happen in a few short months,” said Dr. Gregory Poland, the director of the Vaccine Research Group at the Mayo Clinic.

See also Dr. Fauci’s belief that our best case scenario for returning to something close to normal life in the US is late 2021.

On Twitter, Zimmer also commented on something that I hadn’t really thought about: that all of these vaccines in development in the US are only for adults:

I wrote last month that no trials for kids had started. Update: still no US trials for kids. The goal of having shots ready for them by fall 2021 may be slipping further away.

From Zimmer’s article on the development of a kids’ vaccine:

Only if researchers discovered no serious side effects would they start testing them in children, often beginning with teenagers, then working their way down to younger ages. Vaccine developers are keenly aware that children are not simply miniature adults. Their biology is different in ways that may affect the way vaccines work. Because their airways are smaller, for example, they can be vulnerable to low levels of inflammation that might be harmless to an adult.

These trials allow vaccine developers to adjust the dose to achieve the best immune protection with the lowest risk of side effects. The doses that adults and children need are sometimes different — children get smaller doses of hepatitis B vaccines, for example, but bigger doses for pertussis.

You probably hate reading these kinds of articles; I know I do. But facing up to the reality of our situation, particularly here in the US where our political leadership has utterly failed in protecting us from this virus, is much better than burying our heads in the sand — that’s just not mentally healthy.

A Scientific Portrait of the SARS-CoV-2 Virus

posted by Jason Kottke   Oct 12, 2020

A model of the SARS-CoV-2 virus

This is a great piece from Carl Zimmer about how much scientists have learned about SARS-CoV-2 through imaging, including how the virus works and prospects for treatment and a vaccine.

Thanks to the work of scientists like Dr. Li, the new coronavirus, known as SARS-CoV-2, is no longer a cipher. They have come to know it in intimate, atomic detail. They’ve discovered how it uses some of its proteins to slip into cells and how its intimately twisted genes commandeer our biochemistry. They’ve observed how some viral proteins throw wrenches into our cellular factories, while others build nurseries for making new viruses. And some researchers are using supercomputers to create complete, virtual viruses that they hope to use to understand how the real viruses have spread with such devastating ease.

I’ve been watching the lectures for MIT’s online Covid-19 class and the thing that has struck me most is just how much scientists have learned about the SARS-CoV-2 virus in such a short amount of time. To be clear, there are many things that they still do not understand about it (and viruses in general), but scientists know this thing upside down and backwards. The depth and breadth of their knowledge is so impressive and I wish more people were aware of it.

How to Read a Scientific Paper

posted by Jason Kottke   Jun 03, 2020

With the Covid-19 pandemic and the reams of research scientists are producing in trying to understand it, many people are reading scientific research papers for the first time. Long-time science writer Carl Zimmer, who estimates he’s read tens of thousands of them in his career, provides some useful guidance in how to read them.

When you read through a scientific paper, it’s important to maintain a healthy skepticism. The ongoing flood of papers that have yet to be peer-reviewed — known as preprints — includes a lot of weak research and misleading claims. Some are withdrawn by the authors. Many will never make it into a journal. But some of them are earning sensational headlines before burning out in obscurity.

In April, for example, a team of Stanford researchers published a preprint in which they asserted that the fatality rate of Covid-19 was far lower than other experts estimated. When Andrew Gelman, a Columbia University statistician, read their preprint, he was so angry he publicly demanded an apology.

“We wasted time and effort discussing this paper whose main selling point was some numbers that were essentially the product of a statistical error,” he wrote on his blog.

Developing research-reading skills can also be helpful for activists attempting to drive change using data about policing & racism in America. (Just be aware that recent scientific studies have shown the limitations of facts in changing human minds.)

Mosaicism, or DNA differences from cell to cell (not just person to person)

posted by Tim Carmody   May 25, 2018

Science writer Carl Zimmer has a new book on genetics and heredity called She Has Her Mother’s Laugh. The New York Times published an excerpt this week focusing on mosaicism — an unexpected but surprisingly common condition where different cells in the same organism display different DNA (sometimes strikingly, fatally different).

Dr. Walsh and his colleagues have discovered intricate mosaics in the brains of healthy people. In one study, they plucked neurons from the brain of a 17-year-old boy who had died in a car accident. They sequenced the DNA in each neuron and compared it to the DNA in cells from the boy’s liver, heart and lungs.

Every neuron, the researchers found, had hundreds of mutations not found in the other organs. But many of the mutations were shared only by some of the other neurons.

It occurred to Dr. Walsh that he could use the mutations to reconstruct the cell lineages — to learn how they had originated. The researchers used the patterns to draw a sort of genealogy, linking each neuron first to its close cousins and then its more distant relatives.

When they had finished, the scientists found that the cells belonged to five main lineages. The cells in each lineage all inherited the same distinctive mosaic signature.

Even stranger, the scientists found cells in the boy’s heart with the same signature of mutations found in some brain neurons. Other lineages included cells from other organs.

Based on these results, the researchers pieced together a biography of the boy’s brain.

I’ve always been drawn to the idea that each of us are many people, an assembly of mismatched parts, manifesting themselves in different times and contexts. It’s striking to see that reflected, albeit in a refracted way, in our array of possible genomes.

Oldest homo sapiens fossils found in Morocco, dating back 300,000 years ago

posted by Jason Kottke   Jun 08, 2017

Oldest Human Jawbone

The oldest known fossils of homo sapiens have been found in Morocco. The bones date back to ~300,000 years ago, more than 100,000 years earlier than previous fossils found. Here’s Carl Zimmer reporting for the NY Times about the paper in Nature:

Dating back roughly 300,000 years, the bones indicate that mankind evolved earlier than had been known, experts say, and open a new window on our origins.

The fossils also show that early Homo sapiens had faces much like our own, although their brains differed in fundamental ways.

Until now, the oldest fossils of our species, found in Ethiopia, dated back just 195,000 years. The new fossils suggest our species evolved across Africa.

“We did not evolve from a single cradle of mankind somewhere in East Africa,” said Phillipp Gunz, a paleoanthropologist at the Max Planck Institute for Evolutionary Anthropology in Liepzig, Germany, and a co-author of two new studies on the fossils, published in the journal Nature.

The previous oldest fossils were found clear across the continent in Ethiopia, in eastern Africa. From a New Yorker article on the discovery:

And the specimens in question were found not in East Africa, which has become synonymous with a sort of paleoanthropological Garden of Eden, but clear on the other side of the continent — and the Sahara — in Morocco. “We’re not claiming that Morocco is the cradle of modern humankind,” the lead author, Jean-Jacques Hublin, of the Max Planck Institute for Evolutionary Anthropology, said at a press conference yesterday. Rather, he added, our emergence as a species was pan-African. “There is no Garden of Eden in Africa — or if there is, it’s Africa,” Hublin said. “The Garden of Eden is the size of Africa.”

Studying climate change with small self-contained ecosystems

posted by Jason Kottke   May 17, 2017

Carl Zimmer reports that a team of Australian scientists have developed a useful way of studying the effects of climate change: they’re building small-scale ocean ecosystems in the lab and manipulating different variables and studying the outcomes. The approach is a middle-of-the-road effort to minimize the number of variables typically present in a real-world ecosystem like a coral reef while having the habitats be large enough to observe the effects they’re looking for without oversimplifying.

To test the effects of climate change, Dr. Nagelkerken and his colleagues manipulated the water in the pools. In three of them, the researchers raised the temperature 5 degrees - a conservative projection of how warm water off the coast of South Australia will get.

The scientists also studied the effect of the carbon dioxide that is raising the planet’s temperature.

The gas is dissolving into the oceans, making them more acidic and potentially causing harm to marine animals and plants. Yet the extra carbon dioxide can be used by algae to carry out more photosynthesis.

To measure the overall impact, Dr. Nagelkerken and his colleagues pumped the gas into three of the pools, keeping them at today’s ocean temperatures.

In three others, the researchers made both changes, heating up the water and pumping in carbon dioxide. The scientists left the remaining three pools unaltered, to serve as a baseline for measuring changes in the other nine pools.

Monet’s ultraviolet vision

posted by Jason Kottke   Apr 17, 2012

In a review of the Color Uncovered iPad app, Carl Zimmer highlights something I hadn’t heard before: Claude Monet could see in ultraviolet.

Late in his life, Claude Monet developed cataracts. As his lenses degraded, they blocked parts of the visible spectrum, and the colors he perceived grew muddy. Monet’s cataracts left him struggling to paint; he complained to friends that he felt as if he saw everything in a fog. After years of failed treatments, he agreed at age 82 to have the lens of his left eye completely removed. Light could now stream through the opening unimpeded. Monet could now see familiar colors again. And he could also see colors he had never seen before. Monet began to see — and to paint — in ultraviolet.

The condition is called aphakia.

The human body’s microbial ecosystem

posted by Jason Kottke   Jan 27, 2012

In this transcript of a talk given to the attendees of the Joint Summits on Translational Science, Carl Zimmer highlights an important aspect of understanding the human body and how to treat its many maladies: the ecosystem of microbes.

The microbes in your body at this moment outnumber your cells by ten to one. And they come in a huge diversity of species — somewhere in the thousands, although no one has a precise count yet. By some estimates there are twenty million microbial genes in your body: about a thousand times more than the 20,000 protein-coding genes in the human genome. So the Human Genome Project was, at best, a nice start. If we really want to understand all the genes in the human body, we have a long way to go.

Now you could say “Who cares? They’re just wee animalcules.” Those wee animacules are worth caring about for many reasons. One of the most practical of those reasons is that they have a huge impact on our “own” health. Our collection of microbes-the microbiome-is like an extra organ of the human body. And while an organ like the heart has only one function, the microbiome has many.

When food comes into the gut, for example, microbes break some of them down using enzymes we lack. Sometimes the microbes and our own cells have an intimate volley, in which bacteria break down a molecule part way, our cells break it down some more, the bacteria break it down even more, and then finally we get something to eat.

Another thing that the microbiome does is manage the immune system. Certain species of resident bacteria, like Bacteroides fragilis, produce proteins that tamp down inflammation. When scientists rear mice that don’t have any germs at all, they have a very difficult time developing a normal immune system. The microbiome has to tutor the immune system in how to do its job properly. It also acts like an immune system of its own, fighting off invading microbes, and helping to heal wounds.

While the microbiome may be an important organ, it’s a peculiar one. It’s not one solid hunk of flesh. It’s an ecosystem, made up of thousands of interacting species.

NASA study of arsenic-based life flawed?

posted by Jason Kottke   Dec 07, 2010

Carl Zimmer in Slate:

Redfield blogged a scathing attack on Saturday. Over the weekend, a few other scientists took to the Internet as well. Was this merely a case of a few isolated cranks? To find out, I reached out to a dozen experts on Monday. Almost unanimously, they think the NASA scientists have failed to make their case. “It would be really cool if such a bug existed,” said San Diego State University’s Forest Rohwer, a microbiologist who looks for new species of bacteria and viruses in coral reefs. But, he added, “none of the arguments are very convincing on their own.” That was about as positive as the critics could get. “This paper should not have been published,” said Shelley Copley of the University of Colorado.

(thx, anil)

Killer carnivorous plants

posted by Jason Kottke   Feb 19, 2010

Writing for National Geographic, Carl Zimmer on the fascinating plants that eat animals. Like the Venus flytrap, “an electrical plant”:

When an insect brushes against a hair on the leaf of a Venus flytrap, the bending triggers a tiny electric charge. The charge builds up inside the tissue of the leaf but is not enough to stimulate the snap, which keeps the Venus flytrap from reacting to false alarms like raindrops. A moving insect, however, is likely to brush a second hair, adding enough charge to trigger the leaf to close.

Volkov’s experiments reveal that the charge travels down fluid-filled tunnels in a leaf, which opens up pores in cell membranes. Water surges from the cells on the inside of the leaf to those on the outside, causing the leaf to rapidly flip in shape from convex to concave, like a soft contact lens. As the leaves flip, they snap together, trapping an insect inside.

See also the accompanying photo gallery.