Creating Synthetic Life

Environmental & Science Education
STEM
Medicine
Society
Culture
Philosophy of Science
Art and Environment
Edward Hessler


Sean Carroll is a theoretical physicist (CalTech), a writer (several popular books as well as a basic text on general relativity), and producer of the podcast--Mindscape: Science, Society, Philosophy, Culture, Arts, and Ideas.

The release, hard to believe that this is #56--on July 22, 2019 features a conversation with University of Minnesota's Kate Adamala, Department of Genetics, Cell Biology and Development. This is the short blurb:

Scientists can’t quite agree on how to define “life,” but that hasn’t stopped them from studying it, looking for it elsewhere, or even trying to create it. Kate Adamala is one of a number of scientists engaged in the ambitious project of trying to create living cells, or something approximating them, starting from entirely non-living ingredients. Impressive progress has already been made. Designing cells from scratch will have obvious uses is biology and medicine, but also allow us to build biological robots and computers, as well as helping us understand how life could have arisen in the first place, and what it might look like on other planets.

A transcript of the conversation is available if you prefer reading, as are links to Dr. Adamala's U of M webpage, lab web site, Google scholar publications, a talk on synthetic life, Twitter feed, and information about the international collaboration, Build-A-Cell.

Google's 2018-2019 Science Fair Winners

Environmental & Science Education
STEM
Science Fairs
Edward Hessler

Google has announced its 2018-2019 Science Fair winners.

A few details:

Participants are 13-18 years old.
The program is global.
179 prizes awarded.
The grand prize awardee receives a $50,000 academic scholarship.
There are travel based prizes sponsored by Lego, Virgin Galactic, National Geographic, and Scientific American.
The field is divided into global finalists, regional finalists, and state and territory winners.
There is an entry for each awardee which includes a summary, the question/proposal, research, method/testing and redesign, results, conclusion, about me, and a conclusion
The Grand Prize was awarded to Fionn Ferreira, Ireland. Here is the abstract:

This project investigates a new method for the extraction of microplastics from water using ferrofluid, a nontoxic magnetic liquid that consists of oil and magnetite (iron oxide powder). In the presence of water, the ferrofluid attracts the microplastics because of the nonpolar properties of both. I investigated this extraction method on 10 different types of microplastics. The concentration of plastics before and after was measured using a homebuilt spectrometer and a microscope. The results supported my hypothesis of 85% extraction.

What an incredible range of projects and approaches. Here is a small sample of the diversity: Averrhoa bilindi: A Natural Coagulant For Rubber Latex; Alteration Of Bicycle Handlebar Grips To Decrease Impacts As Measured By Penetration Into Ballistic Gelatin; An Electric Sole For The Foot
That Prevents Muscles From Shrinking In Children With Cerebral Palsy; and Digital Agriculture Module Designed To Harvest Tree Vibration For Energy.

I hope you take a look.
 

Death With Dignity: One Of The Problems of Lifetime

Environmental & Science Education

STEM

Medicine

Death

Edward Hessler

I've referred, perhaps too often, to a paper by Rodger Bybee in which he discussed science education for an ecological society. The paper, one of two focusing on the this topic, was republished in Reforming Science Education (Teachers College Press 1993). 

There is a sentence in one of Bybee's papers that has stuck with me, one that I still find useful. "We are clearly concerned with problems of lifetime (conception, abortion, birth control, death with dignity), lifespace (pollution, crowding, urban decay), and lifestyle (affluence, poverty, consumption, conservation)." (Emphasis added)

I was reminded of Bybee's essay when I read an essay by Colorado thoracic oncologist D. Ross Camidge (Huffington Post) titled "Why I Wrote The Rx That Helped My Cancer Patient Die."  Colorado is one of seven states and the District of Columbia that have death with dignity acts.

Camidge writes about his experiences with three patients. Two of them never used the prescription. One told Camidge when asked on whether she had taken the pills, "No. Not yet. I just like to have them sitting in the bathroom cabinet, to be honest. It makes me feel calmer. More ... in control." She died on her own, pills still in the cabinet. His second case, a patient with small cell lung cancer, was unable to self-administer the prescription and died on his own in a coma.

Camidge struggled following these two deaths, losing "sleep over both of them," because the process of Medical Aid in Dying (MAID) seemed "to be 'giving in' instead of fighting for every good day."  He found the experience "different and unsettling" from his regular practice, training and commitments as a physician. (Doctors are trained to extend life with little regard to other factors--financial cost and the informed wishes of patients. In addition, there are the advances in technology designed to extend life.) And then, several months later, a patient, Bobbie, "a tiny, talkative Italian American woman" brought up the option of MAID, "and this time everything was different." 

In the essay, Camidge describes treating Bobbie for three years--their arguments, their honeymoon periods, their "last dance" (Bobbie's attention to details, her penchant for circular discussions), his work with a team (and how one of them helped Bobbie decide but especially Camidge "to get it."), the options (including cost and how the drugs work), and the setting of the date (Camidge asks an interesting question: "What do you do on your last day on earth?" and expresses some of his hopes for how she spent that day.).

This essay is a sensitive, respectful and personal story about death with dignity. Camidge closes by writing, "Bobbie, on behalf of your team, I want you to know how much you are missed, despite all the endless conversations in busy clinics. How much you were loved, for you laughter, your attention to detail and your style. And above all, how grateful we are for your courage in showing us if not the way for everyone, at least one way that was, in the end, the right way for you."

A death with dignity.

Finding Out How Cats Spend Their Time

Environmental & Science Education
STEM
Behavior
Biodiversity
Edward Hessler


Two British researchers, Maren Huck (University of Derby) and Samantha Watson (Metropolitan University) placed small cameras on 16 cats, "following them for up to 4 years as they prowled their neighborhoods."

David Grimm who writes for the science journal Science interviewed Maren Huck "about the challenges of getting cats to wear video equipment and how the research might dispel some common misconceptions about felines." 

The interview includes a video which includes snippets of a few of the rambles with various behaviors labeled. If you have been around cats you will recognize the first image: stare.

Grimm asks Dr. Huck about why she acknowledges the cats in the paper she and Watson published. "I always acknowledge the animals I work with. I’ve been doing that since my Ph.D. thesis. I do feel thankful because if the cats didn’t oblige us, we couldn’t do the study."

Studying Two Dangerous Natural Hazards

Environmental & Science Education
STEM
Earth Science
Geology
Nature of Science
Edward Hessler

Volcanoes

There is always more to know about the natural world, especially natural hazards.  NPR's Maddie Sophia calls attention to an obvious example: volcanic eruptions.

Volcanoes are not easy to study, are dangerous and the conditions of volcanic events are not predictable. Sophia reports on one method to study them: volcanic simulations that involve physical processes.

A (safe) place to do this is at the University of Buffalo's Geohazards Field Station, a location dedicated to large-scale ("too large for a lab") experiments on hazardous processes. Volcanoes meet that criterion.

You can read Sophia's report here which includes a video of scientists doing some manageable experiments under controlled conditions. One of the features that appeals to me about these experiments is learning how earth scientists design experiments to better understand how volcanoes work.

Wildfires 

In late June 2019 forest fire researchers will study a large fire (900 hectares or ~2224 acres) from ignition to fire's end.

"If all goes to plan," Alexandra Witze reports in the scientific journal Nature, "a helicopter will hover above a thickly forested slope in Utah and set it ablaze. the goal is to clear out dead conifer trees to allow quaking aspen (Populus tremuloides) to regain a foothold in this high-altitude national forest."

The Fire and Smoke Model Evaluation Experiment will study this fire through the use of drones, radar and other equipment. "Researchers plan to monitor every step--from mapping the types and nunmber of trees that will burn, to measuring how much of that fuel actually gets consumed during the fire. ... Tripods laden with instruments will video-tape the flames and measure the temperature as the forest burns. Laser and radar equipment will probe the shape and density of the smoke plume as it rises, while a series of drones will attempt to fly directly into the plume."

One of the research questions is about how plumes form and evolve while "the detailed inventory of the fuel on the ground should reveal how the quantity of fuel burnt translates to smoke produced.  The amount of smoke, and what noxious chemical it contains, depends on the types of trees or shrubs that are burning." Additionally, the drone will collect data from "smoke at night-time--when its chemistry changes, and it cools and sinks, meaning that people can more readily breathe it in."

Witze's essay about this research may be found here. It includes more details as well as information on other studies this year designed "to gather data from wildfires in western North America as they happen."

Friday Poem

Environmental & Science Education
Poetry
Art and Environment
Edward Hessler

The sweet and bitter of lives, a moggie and her humans is what today's poem is about. It is as gray as the poem's title and is from Garrison Keiller's, The Writer's Almanac.

Gray was written by the late Philip Deaver.

A Revealing Close-Up On Clinical Trials

Environmental & Science Education
STEM
Health
Medicine
Edward Hessler



How might a bird see drug research and development?  Details would come into view that are presently obscured.

Spencer Phillips, writing for STAT, notes that "statistics about waste are illuminating, and the suggestions offered for improvement are reasonable, they present a very high-level picture of the research and development enterprise — what might be called the 30,000-foot view. But there may be important patterns or properties of the research enterprise that can be seen only by zooming out and adopting something more like a bird’s-eye view."

Phillips analyzed (this seems a tour de force to me) "all of the registered clinical trials from 10 large — AbbVie, Bayer, Gilead, GSK, Johnson & Johnson, Merck, Novartis, Pfizer, Roche, and Sanofi — over (the) past 20 years or so."  What this translates into is a giant graph based on 13,749 trials including some 6 million patients. Phillips provides two ways to see and interact with it: a dedicated website and a video. I include the link to the dedicated website which includes directions for using it.

The original article in STAT provides a guide to the graph. Nodes correspond to a registered trial and if you click on a node it opens the trial's registration page. Trials are organized from oldest to newest on the x-axis; the y-axis organizes by patient population or disease. The node colors refer to companies. Node circles are completed studies. Node triangles are recruiting studies. Studies that have been terminated have an "X" through them. Node size represents the number of patients enrolled.

If anything you are likely to be struck by the sheer volume and quantity of the studies. You may have to remind yourself that this is for 10 companies, not all of them. It is too bad costs of these trials are not available which is in the millions. Phillips raises some interesting questions about, e.g., company activity, distribution of effort, differences in trial size, gaps in trial activity, reasons why some trials were stopped. He observes that answering these kinds of questions could lead to efficiencies in the clinical trial enterprise.

Another thing that strikes Phillips are questions such a graph raises about power, i.e., "the power and responsibility to intervene and intervene to alter the patterns." Those with little power include patients, clinical investigators, researchers. Those with power include funders, governmental regulators, big pharma, and investors.

Phillips notes that "every node in this figure--should be ethically justified by an assumption that it will offset its social costs and the burdens it imposes on the research subjects by producing valuable gains in scientific knowledge." Why do these trials make sense in the research and development landscape? Are the recruiting studies the right ones?  The visualization makes these quuestions much more explicit?

Spencer Phillips is at the Harvard Center for Biothics and Brigham and the Program on Regulation, Therapeutic, and Law at Brigham and Woman's Hospital (Boston).

Fireflies

Environmental & Science Education
STEM
Behavior
Biodiversity
Art and Environment
Edward Hessler

Photographer Richard Sherman was in eastern Iowa during late June and early July--"firefly season."  He made several short time lapse videos and firefly closeups in local corn and soybean fields.

When I was a kid fireflies were mostly known as "lightning bugs," a very appropriate name here because Sherman's videos include some incredible lightning storms (more than 100 miles from where he was shooting ). And on the 4th of July he not only shot fireflies, and a lightning storm, but also fireworks in the same time lapse. And as a bonus, a white moggie is seen sitting in one of the fields.

The close-up photographs are lovely too, so scroll down to the bottom. 

If you've not seen a firefly (Photuris lucieresens) close-up take a look at the Wiki entry which also includes a link on how these insects make light, light known as cold light since it is chemical. The process has one of those words to roll of the tongue: bioluminescence.  The chemistry and behavior have been well studied, e.g., see here.

For more about fireflies here are 14 facts from Smithsonian.

Poet Robert Frost wrote a lovely poem about fireflies, one not to be missed.

h/t Molly who writes "(I) still have just a few more years in our suburban back yard...which feels like such a gift."

Jodrell Bank Observatory: A New UNESCO World Heritage Site

Environmental & Science Education
STEM
Astronomy
Cosmology
History of Science
Edward Hessler


Jodrell Bank Observatory, part of the University of Manchester, UK, has been named a World Heritage Site. Scientific research began there in 1945.

The BBC has a great article about Jodrell with photographs and links.  Here are a few quotes from their report.

--The site pioneered the then new science of radio astronomy, which used radio waves instead of visible light to understand the universe.

--The site's new accolade marks the end of a decade-long bid to gain World Heritage status, following a 2010 application to be included on the UK's nominations shortlist.

--The Lovell Telescope, which was the world's largest telescope when it was completed in 1957, is now the third largest. 

--The observatory is among 32 sites in the UK - including Stonehenge and the Giant's Causeway - to receive World Heritage status and joins a list of 1,100 sites worldwide.

--A University of Manchester spokeswoman said the observatory fulfilled the judges' criteria, which included being "a masterpiece of human creative genius", due to its scientific achievements.

And here a short BBC video on Jodrell's World Heritage status.

Couscous: Intangible Cultural Heritage UNESCO Application

Environmental & Science Education

STEM

Culture

Food 

Biodiversity

Edward Hessler

In April, four countries--Morocco, Mauritania, Algeria, and Tunisia--filed a joint submission to have Couscous recognized for UNESCO Intangible Cultural Heritage status. Two of the countries, Algeria and Morocco have a long history of bitter rivalry, described as an "endless cold war."

The Wiki entry provides information about this dish formed of tiny, hard pellets made from durum wheat semolina which are steamed and served with a stew on top. The stew recipes vary and the Wiki  includes entries for Algeria, Morocco and Tunisia. Mauritania is not mentioned specifically but this Wiki entry on Mauritania includes a mouth-watering photograph of a camel meat couscous on a very large platter. There meals are regularly served from large communal dishes.

UNESCO defines intangible cultural heritage as "traditional, contemporary, and living at the same time; inclusive; representative; and community-based." These phrases/terms are explained at the UNESCO site.

France 24 reported that "the application will be examined at the next meeting of UNESCO's World Heritage Committee in Columbia's capitol Bogota in December."

Will a new world begin following this meeting? I think of a poem by poet Laureate of the United States, Joy Harjo, a poem which includes beginning and ending. "At this table we sing with joy, with sorrow. We pray of suffering and remorse. We give thanks."

Kinetic Sculptures

Environmental & Science Education
STEM
Engineering
Art and Environment
Edward Hessler

Kinetic sculptures the likes of which I've never seen.

Artist/designer/engineer Anthony Howe talks about it and his business. The link will take you to more of his sculptures and also a bio.

Friday Poem(s)

Environmental & Science Education
Poetry
Art and Environment
Edward Hessler

Today's poem or poems, three short poems by Wendell Berry.

Goldman Environmental Prize 2019

Environmental & Science Education

STEM

Sustainability

Miscellaneous

Edward Hessler

The Goldman Environmental Prize honors grassroots environmental heroes from the world’s six inhabited continental regions: Africa, Asia, Europe, Islands & Island Nations, North America, and South & Central America. The Prize recognizes individuals for sustained and significant efforts to protect and enhance the natural environment, often at great personal risk.

The Goldman Prize views “grassroots” leaders as those involved in local efforts, where positive change is created through community or citizen participation in the issues that affect them. Through recognizing these individual leaders, the Prize seeks to inspire other ordinary people to take extraordinary actions to protect the natural world.

--Alberto Curamil Chile/South and Central America--Organized his Mapuche community to stop the construction of two hydroelectric projects on the sacred Cautín River in Chile. The projects would have diverted hundreds of millions of gallons of water each day, harming a critical ecosystem and exacerbating drought conditions. In 2018, Curamil was arrested and remains in jail today. Colleagues believe that he was targeted because of his activism.

--Linda Garcia United States/North America--Organized her community to stop construction of the Tesoro Savage oil export terminal in Vancouver, Washington. By preventing North America’s largest oil terminal from being built, Garcia halted the flow of 11 million gallons of crude oil per day from North Dakota to Washington.

--Jacqueline Evans Cook Islands/Islands and Island States--Led a five-year campaign to protect the Cook Islands’ stunning marine biodiversity. Because of her persistent organizing, the Cook Islands enacted new legislation—Marae Moana—to sustainably manage and conserve all 763,000 square miles of the country’s ocean territory, designating marine protected areas (MPAs) around all 15 islands.

--Ana Colovic Lesoska North Macedonia/Europe--Led a seven-year campaign to cut off international funding for two large hydropower plants planned inside of North Macedonia’s Mavrovo National Park, thereby protecting the habitat of the nearly-extinct Balkan lynx.

--Bayarjargal Agvaanttseren Mongolia/Asia--Helped create the 1.8 million-acre Tost Tosonbumba Nature Reserve in the South Gobi Desert—a critical habitat for the vulnerable snow leopard—and persuaded the Mongolian government to prohibit all mining within the reserve

--Alfred Brownell Liberia/Africa--Stopped the clear-cutting of Liberia’s tropical forests by palm oil plantation developers. His campaign protected 513,500 acres of primary forest that constitute one of the world’s most important biodiversity hotspots. For his safety, he is living in temporary exile in the United States.

Information about the Goldman Prize, full biographies with videos are found here.

Emperor Chicks and a Petrel or Prey and Predator

Environmental & Science Education
STEM
Behavior
Biodiversity
Edward Hessler

On their walk to the sea, emperor penguin chicks are attacked by a formidable enemy, a petrel. They know how to deal with it although the defense is problematic. And then....

This is an amazing glimpse into the natural world about which there is to much yet to learn. The film is from BBC Earth.

The Chalk Race

Environmental & Science Education
STEM
Maths
History of Science
Nature of Science
Edward Hessler

I've written about the preference that many physicists and mathematicians have for an important tool in their somewhat limited armamentarium: chalk.

Here is a lovely video about a chalk that is regarded as the best in the world: Hagoromo. It is made in Japan. You will hear mathematicians referring to it as the "Rolls Royce of chalk" and as "made from the tears of angels."  You will learn that it has become scarce and some mathematicians decided to hoard it and sell it at cost, I think (!), to colleagues.

Watching the video reminded me of writers who prefer pen and a paper pad or a notebook for their first drafts. It is about the feel of instrument/tool on the medium.

A Potential Model Organism

Environmental & Science Education
STEM
Biological Evolution
Nature of Science
History of Science
Models
Edward Hessler

In its useful entry on the use of model organisms in science, Wikipedia begins with a definition: A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms.  

The reason for using model organisms is based in evolutionary history. All organisms "share some degree of relatedness and genetic similarity."

Or to put it as Theodosius Dobzhansky wrote an essay first published in American Biology Teacher (1973) with this title: Nothing in Biology Makes Sense Except in the Light of Evolution.

There is a new potential model organism on the block--the world's smallest primate. The critter is the mouse lemur (Madagascar).  A first step in the process is developing a genetic library, using non-invasive techniques. Mouse leumurs have some obvious advantages. They are more closely related to us than another famous model animal, the mouse and like the mouse is small, reproduces rapidly and produces relatively large litters.

This short Nature video is an introduction to mouse lemurs and to the research. The critters are terminally cute. 

Nature published an essay about the mouse lemur as a potential research organism by Leslie Roberts. Here are a few reasons on why you should consider reading it.


--You will learn how Stanford's Mark Krasnow found this critter. His daughter and friends, high school students,  had been pestering him to work in his Stanford lab.  He didn't relent easily but when he gave in (2009), Krasnow gave three of them an assignment, a real job: find "a new genetic model organism that was a closer mirror of human biology than a mouse."  Among the animals they looked at, the mouse lemur stood out in terms of characteristics such as "time to sexual maturity, litter size and conservation status."  In 2011, a "first-ever mouse lemur conference was held." Participants were enthusiastic but there was a research divide between field biologist and laboratory biologists regarding genetic modification. As Roberts notes, "a scientific strategy emerged that aimed to use powerful genetic tools in a minimally invasive way."

--It is never the case that if you've seen on organism in nature you've seen them all. The article has a gallery of "mouse lemur mugshots" that "reflect the animals' unique personalities." Think the large V, variation. This is also reflected in "the names the researchers have given them." Feisty. Murderface. Blinky. Stoic.

--A new animal model is not a shoo-in. There have to be evidence-based reasons for a researcher to make the switch for it represents a significant change in ongoing research programs. According to Roberts, one researcher "doesn't see researchers switching from macaques or baboons, the most widely used primate models, or marmosets, which are coming up fast, because so much is already known about them."

--Krasnow has an interest in school biology education (citizen science) in Madagasgar. He would like "students to explore what he calls the 'living laboratory' right outside." Students can learn how to screen "mouse lemurs in their own backyards and then sequence their genomes, greatly expanding the databases."

--Research techniques and design, e.g., how to measure a mouse lemur's strength (there is a wonderful picture showing a strength test), analysis of their gait, and how mouse lemurs are collected and released.

--Nature of science or how scientists go about their day-to-day work.

# 480: Otis the Brown Bear

Environmental & Science Education
STEM
Behavior
Nature
National Parks

# 480 (Otis) is the oldest bear using the Brooks River in Katmai National Park and Preserve.

We meet him and learn about how he as adapted to growing old--he is a patient bear--in this short feature video from Katmai.

Regular watchers of BearCam were concerned this spring, as usual, about him when he failed to show up  but then he is known for lingering in bed. There was a collective sigh of relief when he was reported.

It was great to know that he is back for another season of fishing.

Rene Favaloro Honored With a Google Doodle

Environmental & Science Education
STEM
Medicine
Health
Society
Edward Hessler


Today's Google Doodle celebrates the achievements of Argentinian cardiac surgeon Rene Favaloro who would have been 96 today.

Like me you may wonder who he is and why his birthday is the subject of a Google Doodle.

Forbes has an article about the Doodle as well as Favaloro. Forbes contributor Bruce Lee tells us why when he says, "When you think of Favaloro, think of CABGs, which is pronounced cabbages but has little to do with the vegetable. CABG is short for coronary artery bypass graft. While you may think that all your heart needs is some love, what it really needs is oxygen to function and survive. 

Coronary arteries are the blood vessels that provide blood and thus oxygen to your heart." The surgery is the most common heart surgery in the world.

There are two videos linked in Lee's essay. The first is to a short (~5 minutes) Cleveland Clinic video about CABGs, "the surgery," Lee reminds us, "and not the vegetable." The second video is from The Independent (< 1 minute).  I appreciated Lee's warning and you might, too. The video has "a tremendous amount of bass in the background music."

As usual please read Lee's article. He ended his essay by writing, " Thus, if you have a heart, you may want to say Happy Birthday to the late Dr. Favaloro."

Happy Birthday!