A Rational Approach to Science Funding

The problem with science research today is that everyone wants to fund the next Einstein, and no one wants to fund a thousand crackpots whose ideas will lead only to dead ends—but none among us is smart enough to tell the difference.

We have to give up on the idea that we can manage research the way we manage an efficient business.

We have to give up on the idea that we have a solid foundation or understanding nature’s workings, and the job of scientists is to fill in the details.

— Josh Mitteldorf

image: https://upload.wikimedia.org/wikipedia/commons/thumb/2/20/Nikola_Tesla%2C_with_his_equipment_Wellcome_M0014782.jpg/318px-Nikola_Tesla%2C_with_his_equipment_Wellcome_M0014782.jpg

Nikola Tesla, with his equipment

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Biodegrading Plastic Bottles

About 1 million plastic bottles are purchased every minute.  Only 14% of these are recycled worldwide.  The rest end up in landfills or, worse, pollute the ocean.  PET is inert by design, and lasts millions of years.

In 2016, a species of bacteria was genetically engineered to eat plastic.  The bacteria use an enzyme (a biochemical catalyst) that breaks down the plastic and turns it into liquids that can be used like kerosene or gas.

Tweaking the enzyme, a group of University of Portsmouth scientists stumbled on a form that is more efficient than what the bacteria used.  It can break down PET in just a few days.

“It is a modest improvement – 20% better – but that is not the point,” said McGeehan. “It’s incredible because it tells us that the enzyme is not yet optimised. It gives us scope to use all the technology used in other enzyme development for years and years and make a super-fast enzyme.”

Guardian article

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Sentience of Trees

Trees do most of the things you do, just more slowly. They compete for their livelihoods and take care of their families, sometimes making huge sacrifices for their children. They breathe, eat and have sex. They give gifts, communicate, learn, remember and record the important events of their lives. With relatives and non-kin alike they cooperate, forming neighborhood watch committees — to name one example — with rapid response networks to alert others to a threatening intruder. They manage their resources in bank accounts, using past market trends to predict future needs. They mine and farm the land, and sometimes move their families across great distances for better opportunities. Some of this might take centuries, but for a creature with a life span of hundreds or thousands of years, time must surely have a different feel about it.

 

 

— Barbara Kingsolver, writing in the NYTimes,
reviewing The Overstory by Richard Powers

 

Bacteria can Learn

Bacteria have individual lives, and also collective lives. They can form films that support a communal existence, protecting one another at a cost in individual autonomy.

UCLA press release

In this study published last month, bacteria remember the surface they were attached to and pass this information along to their offspring. This is learning, combined with inter-generational memory. Bacteria are the smaller kind of one-celled orgnisms, and science has no understanding of how memory is stored. The article doesn’t describe a mechanism. The most likely candidate would be epigenetic. In other words, markers on the DNA that tell what genes to turn on and off are persistent, and can be passed to offsring when the DNA is copied.

James Shapiro has written a book describing how bacteria modify their own DNA. This is full Lamarckian adaptation.

Six-inch mummy

Nearly two decades ago, the rumors began: In the Atacama Desert of northern Chile, someone had discovered a tiny mummified alien.

An amateur collector exploring a ghost town was said to have come across a white cloth in a leather pouch. Unwrapping it, he found a six-inch-long skeleton.

Despite its size, the skeleton was remarkably complete. It even had hardened teeth. And yet there were striking anomalies: it had ten ribs instead of the usual 12, giant eye sockets and a long skull that ended in a point.

Ata, as the remains came to be known, ended up in a private collection, but the rumors continued, fueled in part by a U.F.O. documentary in 2013 that featured the skeleton. On Thursday, a team of scientists presented a very different explanation for Ata — one without aliens, but intriguing in its own way.

Ata’s bones contain DNA that not only shows she was human, but that she belonged to the local population. What’s more, the researchers identified in her DNA a group of mutations in genes related to bone development.   — NYTimes article

The body was mummified just a few decades ago.  Most skin is still there.  Internal organs are identifiable.

This is a unique specimen, of unique interest.  I’m sure there are dozens of labs around the world that would leap at the opportunity to study it.  But one lab at Stanford has held onto this specimen for 5 years before publishing anything or even issuing a press release.

What I find suspicious is that the explanation they have put forward is the most conventional, and that it is taken as “Science has spoken!”  There is only one explanation, and it is fantastically improbable, but it has been selected for us from among many other fantastically improbable explanations.  Science Daily tells exactly the same story as NYTimes.

Sanchita Bhattacharya, a researcher in Dr. Butte’s lab, searched for mutations in Ata’s DNA and identified 2.7 million variants throughout the genome. She whittled this list to 54 rare mutations that could potentially shut down the gene in which they were located.

Here’s the journal article.  Their analysis begins with the assumption that the specimen is human, and doesn’t consider other possibilities.  Their conclusion involves a co-occurrence of many rare mutations.   They attribute the large amount of DNA that doesn’t match human to DNA damage that has occurred in the mummy.  But full genomes have been extracted from much older samples than this one.  Damage can be differentiated from genome variation because damage is different from one cell to the next, whereas variation is consistent.

My  hope is that this is the beginning of an open-ended scientific discussion, and that many labs around the world have a chance to do their own analysis.

— JJM

How Old is Life?

On the one hand, experiments tell us that the gap between non-living and living matter is even wider than naïve observation would lead us to believe.  The origin of life seems to require vast amounts of space and time and astronomically good luck.  On the other hand, life appeared on the primeval, Hadean Earth pretty much as soon as the Earth was cool enough that it wouldn’t be cooked.  In this latest fossil discovery, there was not just life but complex, multi-celled life at a time when Earth was still in its Hadean age.

A sliver of a nearly 3.5-billion-year-old rock from the Apex Chert deposit in Western Australia (top). An example of one of the microfossils discovered in a sample of rock from the Apex Chert (bottom).

As that story goes, in the half-billion years after it formed, Earth was hellish and hot. The infant world would have been rent by volcanism and bombarded by other planetary crumbs, making for an environment so horrible, and so inhospitable to life, that the geologic era is named the Hadean, for the Greek underworld. Not until a particularly violent asteroid barrage ended some 3.8 billion years ago could life have evolved.

But this story is increasingly under fire.  Many geologists now think Earth may have been tepid and watery from the outset. The oldest rocks in the record suggest parts of the planet’s crust had cooled and solidified by 4.4 billion years ago. Oxygen in those ancient rocks suggest the planet had water as far back as 4.3 billion years ago. And instead of an epochal, final bombardment, meteorite strikes might have slowly tapered off as the solar system settled into its current configuration.

Rebecca Boyle writes for Quanta Magazine