Have You Heard of the Protein-Folding Problem?

I had planned to highlight the top ten scientific achievements in 2021 on this New Year’s Day, but one achievement stands out so significantly that I’m devoting my blog to the solution of the protein-folding problem.

The human body has around 100 million proteins, which govern much of how our bodies work. Some transport messages between cells; some break down or create molecules like fats, proteins and sugars; some control blood pressure; some replicate DNA; some respond to stimuli, some provide cell structure, and others have different roles. They are the body’s workforce. The shape of the protein molecule determines its job. They are made up of chains of amino acids, which uniquely determine the shape. Biologists have long lusted over the ability to predict shapes from the chains involved, labeling it the folding problem. I had to dig to understand why they used the word folding. The best analogy I could find is to view the given amino acids as ribs on Christmas ribbons. Folding becomes similar to taking a blade of a scissors and dragging it along the ribbon in several places. You end up with those lovely curls, shaped like a helix. Somehow the chain of amino acids dictates where the curls occur.  However, the number of possible shapes from a given chain of amino acids, the order and the number of each, is so large that programming a computer to test all shapes to compare with the given protein is infeasible.

One of the reasons that understanding the relation between the chain and the corresponding protein molecule is that misfolding is responsible for some diseases such as alzheimers, parkinsons, and diabetes. Scientists have been able to associate the shape to function only in a small fraction of the 100 million protein molecules, but using AI, Alphafold, a division of DeepMind, a British company acquired by Google, they can determine the shape from the amino acid chain. Understanding the structure of proteins is said to have tremendous consequences  for designing drugs, controlling disease, designing enzymes to break down plastic, finding ways to capture carbon, and “?.” Further, AlphaFold is making use of their discovery freely available for such purposes.

Let’s view this as hope for a better New Year and an ultimate cure for future pandemics.

PS So far so good for the James Webb telescope’s journey to the far side of the moon.

Mystery on the Moon and Other Notable Science News

  • The Chinese not so long ago succeeded in landing on the far side of the moon. Click and scroll down to see the mysterious picture of the horizon from Yutu, China’s name for their rover, Something that looks like a hut perches in the center of the photo. While, it will take months for the rover to rove over (alliteration intended) to check it out, scientists speculate it’s likely a boulder. However, it has a perfectly cubical shape, unlikely for a boulder, but anything else would be groundbreaking excitement.
Troposphere–bottom layer

Another curiosity due to global warming is that the bottom layer of atmosphere called the troposphere around our Earth is expanding. According to to NASA: “Closest to the surface of Earth, we have the troposphere“Tropos” means change. This layer gets its name from the weather that is constantly changing and mixing up the gases in this part of our atmosphere.”


As the world turns to electricity to slow Earth’s warming, demand increases for  lithium and cobalt to power vehicle batteries, and  these precious metals like all of our resources are limited. It was unclear how successful recycling the metals could be, but it turns out that the recycled products work even better than those made from the newly mined sources.

I need longer legs in this wind!

According some studies, climate change is causing animal (and plant?) species to evolve to survive in the new environment. Not surprising that some species are migrating to different habitats, bears fattening at different times of the year, and conifers shifting growth to different areas. However, it was interesting that some lizards are growing longer limbs to help them stay on leaves in stronger winds.

Hubble is about to become history!

According to a writer for the Science Times, what astronomers are eating these days is their fingernails. The diet will continue through Christmas Eve when the James Webb telescope will launch for the dark side of the moon. Maybe it’ll beat the rover to the myserious hut. It is a bigger and better replacement for Hubble. The potential for learning more about our universe is momentous, but the fear that one of many maneuvers may go astray and put the mission in peril is considerable. Let’s hope the auspicious date of the launch will bode well. OTOH, Rudolph will be too busy to help.

Merry Christmas!

Does The Future of Humanity Depend on Colonizing Mars?

It’s commonly known that our sun will die someday, but if you’re like me it’s of no concern. It’s not expected until about five billion years from now. My worries regard the humans in this century and whether the human race will survive not only climate disasters but the aftermath of shortages to water, food, and energy, which affects our very way of life.

Thus, when visionary entrepreneurs like Elon Musk talk about humans needing to find a home other than Earth and suggesting establishing life on Mars, I’ve rejected the idea as an infeasible solution to Earth’s decline in habitability due to climate change. In my thinking, colonization to any extent simply cannot happen fast enough if at all. I am now reading a book whose title is embedded in this blog’s title that made me realize the concern is over the very long term future.

I was surprised to learn how much thinking and research has gone into ways of making Mars habitable. There are ideas about how to melt ice a few feet under the surface and the ice caps for water for normal use, and for extracting oxygen to replace the atmosphere of carbon dioxide. Other plans exist to warm the planet from its bitter temperatures. Solar would provide energy. Further, rockets bringing cargo could be refueled for the return by fuel created via solar energy making room for more cargo. Eventually, they believe the soil could support agriculture using human waste as manure. All of this, not surprisingly, would take centuries. Scientists are considering having the enormous amount of work done or assisted by robots.

While Mars will also suffer if our sun dies, it is thought that humans might be able to hopscotch to outer planets in perpetuity using the technology developed to terraform Mars.

Besides climate disasters and a dying sun, there are other threats to our home. Eventually there will be an ice age—in tens of thousands of years as opposed to billions. A major collision by an asteroid could be disastrous. I’m glad scientists are paying attention. There is a project planned to nudge an asteroid out of its orbit to test the feasibility in case a large one is ever discovered heading toward us.

After the 2008 recession, interest in funding NASA waned, and President Obama asked private industry to take up the enterprise. Indeed, the amount of precious metal in asteroids if harvested could make space travel profitable. One of several TV series about colonies living on Mars provoked an interesting question regarding ownership. One colony was government funded, the other by industry whose goals of research and profit were in conflict. That’s a likely conflict in the future given our history.


Was COP26 a COP-OUT?

It was a Bad News/Good News scenario..

Bad News: (I always like the bad news first.)

1.The pledges fell short of meeting the need identified by climate scientists of containing Earth’s warming to 1.5 degrees centigrade by 2030.

2. There is no means of accountability for keeping the pledges.

3. The Paris pledge of developed countries to collectively provide 100 billion dollars per year to developing countries was not met.

4. The carbon emitting sources were divided into sectors about which resolutions were made with only 6 resolutions of  97 beginning with “decides”and the rest beginning with words like “urges, welcomes, invites, encourages, …”

5. There was no resolution to provide reparations to island  nations and other small countries who have been hurt by climate change. A leader from Tuvalo, one of the Pacific Islands gave an address standing knee deep in ocean water which a few years ago was beach.

6. Independent investiagtions indicate that a number of countries under reported their net carbon output.

7. Some sectors like agriculture admittedly received short shrift.

Good News:

1. Early days of the climate conference were more promising than previous COPs in that gone were the arguments over whether climate change was human caused. They could settle down to arguments over what to do about it. They passed significant resolutions provided countries actually feel urged to act.

2.The pledges made were also signficant A.Halt and reverse deforestation in 85% of the world’s forests, and land degradation by 2030. 100 countries B. Dedicate 8.5 billion to help South Africa decarbonize its coal-heavy energy system. U.S., U.K., France, Germany, & EU C. No new coal power for decades. 190 countries D. End public financing of overseas oil, gas and coal projects by the end of 2022. 25 countries including the U.S., U.K., Denmark, Canada, Italy & the European Investment Bank.E.. Cut carbon emissions to net zero and increase renewable energy by 100 gigawatts by 2070. India F. Various private individuals & organizations pledged 3.5 billion for various projects. An alliance of private & global organizations plan to tackle access to renewable energy across Africa, Asia, & Latin America.G. End building coal-fired power plants. China in abstentia.

3. There will be a COP27 in a year.

4. Satellites will be more involved in measuring and monitoring results and inhibiting under reporting carbon emissions.

5. While not mentioned by name there is an organization GFANZ (Glasgow Financial Alliance for Net Zero) made up of 450 investment institutions in 45 countries who aim to achieve net zero carbon among the companies they invest in and provide capital from private investors for companies to do the work of meeting the commitments of COP26 and beyond. There may be other parties willing to finance and share solutions. Governments alone cannot or will not be able to supply the necessary capital.

My Conclusions

Whether Cop26 is a failure or a success depends on what happens next. If the world conducts business as usual, it will be a failure. If, however each of the following happens it will be a success: All pledges met, all resolutions taken seriously, sufficient capital to support innovative solutions which are shared among countries, along with a worldwide spark of “let’s get this done together,” which carries into COP27.

Climate Change Fighters

There are a myriad of efforts to halt the warming of Earth and its consequences in different ways. Accordingly, there is a plethora of organizations working on the issues.

Getting off dependence on fossil fuels: The use of fossil fuels—coal, oil, natural gas is why we are where we are. Planes, cars, factories, homes spewing poison into the air. Climate scientists have long called for reduction in use. Attempts to improve fuel efficiency, turn to renewable energy, reduction of consumption have dominated early efforts. They must be stepped up. We need to:

  • get out of our cars by using public transportation, carpooling, working from home when possible, flying less, stop building more highways and lanes
  • electrify our cars and homes and sign up for electricity from renewable sources like  solar, wind, and hydrothermal. Improve energy storage.

Carbon Capture: We’ve waited too long, and done too little to stem the warming by less carbon pollution. The above efforts won’t happen fast enough on their own. Scientists are seeking ways to remove carbon from the air and to capture carbon as it’s produced in industry.

Special Attention to our Oceans:

Our oceans produce 70% of our oxygen via plankton, whose numbers are threatened by the warming of Earth. Oceans also absorb large amounts of carbon dioxide. Heatlhy oceans are critical to our survival. Above are only two of many who see the problem. Also, critical to the planet’s survival are wild animals. Other organizations are fighting for them. Their success in reintroducing keystone species to their former habitats has regenerated the areas and proof of Climate Scientists’ claim that humans need to move from exploiting nature to protecting nature and regenerating any areas we overuse.

Legal Means and Political Will:

  • Organizations like Earth Justice support environmental laws and sue corporations for damage to the environment that affects public health, etc. I like their slogan “Because Earth Needs a Good Lawyer.”
  • Big Money talks loudest in our political system, and many fossil fuel industries and industries that pollute in their manufacturing processes work hard to conduct business as usual. Individuals must pressure their politicians to step up to stem the damage from climate change.
  • Organizations like 350.org apply even more pressure from the size of their membership. EDF tries to work with companies on ways to improve their carbon footprints.
  • This year’s climate disasters have changed the mindset of the peoples of the World. Few doubt now that we are in trouble. The COP26 discussion has changed from arguments over human causation to the best means of dealing most quickly with the crisis. While 100 countries have pledged to stop deforestation and other promises, Greta Thunberg isn’t convinced.

Today’s Climate Action Plan Can’t Become Tomorrow’s “Shoulda, Woulda, Coulda!”

It’s not only about your grandchildren and children any longer regarding concern over climate catastrophes. It’s also about whether you think you will still be alive in 2030. Unfortunately, there are two camps who are motivated to do nothing. One doesn’t believe human behavior is causing our current disasters. The other believes we’re already doomed so why bother. I guess there is a third faction who are so wealthy, they and their descendants will be able to afford livable places and don’t care how costly water and food become. OTOH, who will provide basic services such as security, maintenance, entertainment, mobility, etc.? Corporations are buying up land in South America and probably other places rich in ground water. Sadly, they legally stole land formerly dedicated to native South Americans who have been on the land since the beginning of time. Meanwhile, drought in South America is bankrupting farmers and increasing migration.

I can relate to the second camp as it’s clear that much of what we’ve done can’t be undone and we will continue to suffer consequences. However, it is still a question of how bad, which now needs to be addressed. My favorite saying is that I’m glad I’m old. It’s the only thing that keeps me going. I’ll be lucky if I’m around  in 2030, or is it unlucky?

No matter your campground I highly recommend the book Under the Sky We Make by Kimberly Nicholas, subtitled  How to be Human in a Warming World. The author’s  nutshell message : It’s warming, it’s us, we’re sure, it’s bad, we can fix it. She also points out, however, that once in our atmosphere carbon is essentially forever, and we need to get to zero carbon pollution by 2030 to stabilize the climate. She describes how humans have approached nature to exploit it for the betterment of their lives, and the need to turn from the exploitation mindset to a regenerative mindset. (I would make an exception for indigenous people, who understand the need to leave enough in nature for future generations.)

The book has specific suggestions for how individuals can lessen their carbon footprint, naming the three largest sources of carbon are due to flying, driving gasoline cars, and eating meat. The author would probably agree with a recent article that the problem is no longer solvable by individual behavior. Governments must act. No financial incentives/disincentives, but outright bans. It’s a stitch in time saves nine time. Fema is rapidly becoming a larger part of the federal budget.

Perhaps the best individual behavior is to pressure your government representatives to act for the good of us all and for the future of those to come.

Every LItter Bit Hurts

I recently discovered that sending even a one-word email uses 4 grams of CO2 emissions. Further, storing emails uses energy. The accumulative effect is scary. Check it out. You’ll be blown away. I send many emails, and I let old ones pile up. I do try to unsubscribe, but it’s a never-ending chore. I can only take pride in not hitting Reply All merely to say “That’s great” or “Thanks” to the sender.

When I thought about the bigger picture of energy use I thought about all the other small energy usurpers. I take so long to drink my morning cup of coffee that I keep it on an individual coffee warmer. Then I routinely forget to turn it off along with lights around the house. I get up in the middle of the night, and I don’t need to turn on anything since tiny blue, white, and red lights guide me to the kitchen for a drink of water. Hard drives, speakers, electric clocks, Wi-Fi boosters, microwaves, stoves, sidewalk lights, and more all beam “We’re here.” At least I don’t use bitcoin, which uses an insane amount of energy.

It doesn’t matter that we have signed up for a 100% renewable electricity program or that sometimes we feed the grid from our solar panels. If we used less electiricity, we’d be able to feed more solar into the grid. We have a long way to go to be free of fossil fueled electricity. If everyone used less, the difference would be substantial.

Stay tuned to hear about a remarkably well-written book about climate change in my next blog. I’m only about 1/3 of the way through Under the Sky We Make-How to be Human in a Warming World by Kimberly Nicholas. She manages to inject a bit of humor along with personal grief in the doom & gloom portion of the book and explains in concrete terms what we can expect depending on the actions we take.

How Does Any Vaccine Find the Bad Guys?

Given all the unfortunate hullabaloo about Covid vaccines, I’m reminded of a vague question that has lived at the back of my brain for some time. How does a vaccine get to the places it needs to be to hunt down the small beasts hoping to take us over as their private home? We are filled with harmless invaders who mind their own business in our guts. Some of them even carry their weight by making us healthier. So how does the vaccine get to the ones determined to make us seriously ill?

My curious thoughts: Why not inject into a vein? It would easily travel through our blood circulation system. A needle would more easily pierce fat than muscle, so why not stick us in our pudgy places? I had to dig deep to discover the answers.

If injected into a vein for some reason, a vaccine is vulnerable to destruction. No explanation found.

Muscle unlike fat evidently has a great supply of blood, which helps disperse the vaccine at a measured rate according to  immunology researchers.  Muscle holds and captures dendritic cells that scoop up injected antigens. (An antigen is anything that stimulates an immune response, most commonly dead virus cells or a small amount of living virus cells of the targeted disease.) These cells then migrate to lymph nodes, and take up residence. Our lymph node system is like the body’s built-in vacuum cleaner. The system filters and cleans the lymphatic fluid of any debris, abnormal cells, or pathogens. When the altered dendritic cells encounter white blood cells in the system such as T and B cells—defenders of our bodies from pathogens—they present them with the injected antigen, saying “See this guy? Go get him.”  

I understand the mRNA vaccines work slightly differently. mRNA controls the production of proteins in our body. Many are desirable essential proteins, but not all. For example, Alzheimer’s disease is associated with buildup of particular proteins. Covid cells are coated with a particular and recognizable protein. mRNA vaccines train our cells to go after any guy wearing the signature protein coat, but the vaccines are injected into the muscle and are distributed into the lymph node system in the same way.

With any vaccine, you may have a sore or red arm, slightly enlarged lymph nodes, but this is evidence that the vaccine is working.

I understand Covid nasal spray vaccines are being researched and developed, but I haven’t heard much about them besides the fact that the nose is the entry point for Covid, making the idea seem worth a look.

Can We Brave Our New World?

Given this year’s fires, smoke, floods, hurricanes, and drought, there can be little doubt that we are suffering under the effects of climate change. In fact, we’ve reached a point of no return according to climate scientists in terms of melting ice in our poles. To wit, we could stop using all fossil fuels, and the ice would continue to melt. The question is now how bad things will get. Since we cannot turn off the fossil fuel switch overnight, scientists and others are turning more attention to the question of how to mitigate the damage. They are stepping up such efforts, which previously were not advertised lest people become complacent about the need to stop spewing greenhouse gases. Here are some hopeful ideas.

Carbon Capture,which may involve storage or utilization,

Plant life consumes carbon dioxide, but once it dies the CO2 is released into the atmosphere. Biologists are working on creating plants that store the carbon dioxide in the roots, which will remain sequestered in the ground. This is only one of many efforts to capture carbon and store it.

Some companies that create carbon dioxide in manufacturing processes capture and utilize in more products; such as plastics, concrete or biofuel; while retaining the carbon neutrality of the production processes. (Don’t get me started on plastics, however.)

Severe climate events not only destroy many homes annually, but create power outages that harm and threaten lives. Putting transmission lines underground is the ultimate solution, and PG&E recently announced plans to put 10,000 miles underground over several years. Presumably, areas at most risk for fires will be targeted. The process is expensive, and one company is working on lines above ground supported by structures that collapse without creating a domino effect. While power will still be interrupted, it will be restored much more quickly because of fewer collapses, diminishing the effect on the dangerous disruption to families and loss of food.

In South Korea solar panels shade bicycle paths between highway lanes. A win-win: it gets people out of their cars and provides solar energy.

These are the kinds of efforts that must be stepped up in order to protect quality of life while we battle to live in a way the preserves our planet’s sustainablity .

And here are a couple of visual unrelated amazing video treats:

Check out these clever bees: https://twitter.com/i/status/1435362486811861005 and

a seal hugging a diver: https://twitter.com/i/status/1435408292872740867

Use Hydrogen for Energy? Not so fast!

Should we use hydrogen for energy given that it burns clean. It depends on the color!

Green Hydrogen: Yes, it is produced by using energy from renewable sources.

Brown Hydrogen: Hell no! It’s made by gasifcation from coal releasing carbon dioxide along with the hydrogen, and there is pollution from the mining of coal.

Gray Hydrogen: No! It’s made by reforming methane in natural gas with high carbon dioxide emissions, and of course, natural gas is a fossil fuel whose extraction risks polluting the atmosphere

Blue Hydrogen: Still no! it’s made like gray hydrogen with carbon capture but doesn’t prevent unburned fugitive methane from escaping.

The latter three sources seem convoluted to me. What’s the point of turning fossil fuel energy into a different kind of energy? Granted the burning of hydrogen in our cars means less carbon down our canyons of freeways, but creates new low income areas with undesirable air quality where the hydrogen is produced.

The reason this is of interest is that the sorely needed pending one trillion dollar infrastructure bill includes several billion for hydrogen research. I’m campaigning that in the implementation, the research is for green hydrogen. The best way for that to happen is for the word green be inserted as an amendment.