How Many Macromolecules Can Dance on the Head of a Pin

Here’s a very interesting discussion of Levinthal’s paradox.  In a nutshell, the paradox is related to the almost infinite possibilities in the ways that a macromolecular protein can fold into its primary, secondary and tertiary shape versus the effortless way that proteins function in living thing.  The author says the degrees of freedom inherent in a large protein molecule have been modelled and there are supposed to be 10300 different shapes that the protein could assume.  Now the point is that this number is so absurdly large that the chance of any particular protein molecule assuming the shape it needs in order to perform its biochemical function in a living cell within a short enough time to sustain the metabolic requirements of life seems impossible.

Well I must admit that is a ridiculously large number.  Someone did a guess at how many separate atoms there are in the observable universe and he came up with 1082.  So that gives you a feel for the absurdity of 10300 .

Basically this argument is supposed to demonstrate the unlikeliness of the genesis of life occurring again elsewhere in the universe.

I guess I’m not sure what I think of this.  While the large size of macromolecules render their physical properties subtle and hard to predict, nevertheless, they do possess these properties and these are exactly the properties needed to sustain life in the world we live in.

If they occur on Earth then they could occur elsewhere.  Now the point really is how could life occur in the first place if the exact sequence of amino acids and nucleic acids needed to make up the macromolecules of life are so absurdly complicated and the random forces involved in creating these exact molecules would be so blind?

It seems what the paradox is hinting at is God.  Well, I won’t argue with that.

Turtles All the Way Down

Over the last few months, I have been reading and listening to a bunch of physics.  Particle physics and cosmology.  The micro and the macro of the attempt to understand the universe.  Limitless vistas of space with super clusters of galaxies and more exotic objects that stretch back to the alleged Big Bang.  And inside the proton are the ephemeral quarks and gluons flashing in and out of existence in (I kid you not) a yoctosecond.

And all of this hyperactivity of nothingness just to make it possible for me to push on the keys of my laptop to write this post.  All of those electrons and quarks following all these conflicting forces at various distances; the strong force, weak force, electro-magnetic force and gravity just so that reality can be felt and tasted.  All of these incredibly complex concepts and the mathematics that tries to describe it.  And the weirdness of quantum mechanics and its inherent and explicit ruling out of determinism.  All of this and how far we’ve come from Galileo and Newton.  And all we’ve achieved in technology.

And yet…

What are quarks made of?  What are gluons made of?  What happened five minutes before the Big Bang?  What happens five minutes after the End of the Universe?

There is no bottom.  There is no top.  There is no start.  There is no finish.

The human mind cannot encompass the infinite.  If we find something beneath quarks, I am sure there will be something under that.  And when the successor to the James Webb Space Telescope is put into service in twenty years at a cost of $100 billion or so I’m sure it will show us even further wonders that defy our ability to explain.  And so will the telescope after that.

And as the man said, “Not that there’s anything wrong with that.”  But that’s the part you have to wrap your head around.  Thinking that scientists have the ultimate truth is a misnomer.  All they have is the latest and greatest explanation as to how things work.

But they’ll never be able to tell you why you’re here or why you should care.  Each of us has to do that all by ourselves.

It’s remarkable.  Five hundred years after the Renaissance put us on the trajectory of man is the measure of all things and God is dead, we come right back to the same place.  The universe isn’t a big windup toy that means nothing and will return to nothing.  And after science tried to convince us that Earth is nowhere and humans are less than nothing it turns out that life is really the only thing with inherent value.  And human life is the miracle that we started out with before we killed God.

The more we study life the more in awe we are of its complexity and miraculous properties.  The more we study humans the more we discover about their potential.

I do not mean to disparage science.  Wresting the secrets of the universe from Nature is a noble endeavor.  And done with proper humility it is one of the finest works that can be achieved by the human mind.  But surely by now all the best minds in the world must be aware that an infinite universe cannot be defined by finite beings.  God built this nursery for us and it’s built to hold us while we grow up.  I can’t imagine we’ll find the door to the nursery unlocked.  At least not on this side of reality.

Sunnyside Saturday

It’s Saturday and that’s the happiest day of the work week (in my opinion).  And so today can’t be doom and gloom day.  No end of the world stuff or triumphant deep state conspiracy theories for me today.

I was just watching a YouTube video about why commercial nuclear fusion is fifty years away and always will be (ha ha).  And of course there were no surprises there.  The sheer magnitude of the temperatures, pressures, magnetic flux and energy consumption needed to make this process work is beyond daunting.  It’s technical lunacy.  When you look at where nuclear fusion does exist (a star), what you realize is that this is an environment where gravity can compete against the electromagnetic force head-to-head.  That is not going to happen in our labs and factories.  So, we have to pay for magnetic containment and we pay by the gigawatt-hour.  It’s not a good trade-off.

When I try to imagine what practical controlled nuclear fusion would look like I conjure up a tiny gun shooting tritium nuclei, one at a time, into a target of heavy water and boiling the heavy water to make steam.  It’s my version of the “Back to the Future,” Mr. Fusion engine that runs Doc Brown’s time machine at the end of the movie.  The breakthrough is that I’m able (by magic) to keep the energy expenditure for the tritium gun down to the level of what I can extract from a USB cable on my MP3 player.  Of course, where I get the radioactive tritium from and how I keep myself from being irradiated while riding in my fusion powered car are at this point undetermined.

Now, don’t get me wrong.  Given a thousand years I think we’ll make real progress on commercial nuclear fusion or find out it’s not feasible.  And I think research on it is a very good idea, if for no other reason than that it will spawn innumerable amazing technological byproducts that may be even more beneficial than the primary problem.  But I think we should all put aside any dreams of living in a world powered by nuclear fusion (unless some wise guy figures out that cold fusion is an actual thing).

But all of this is just the intro to my main thought.  And that is what would life on Earth be like if energy really were essentially free.  Now I don’t mean free, free.  The infrastructure for breeder reactors and handling their waste products will be an incredibly complicated and expensive industry that will employ a good chunk of the technically minded part of the population.  And maintaining a power grid and the other allied industries that will grow up around very cheap electricity (e.g., syn-fuel) has always been a big piece of modern life.

But imagine if you can what kinds of problems would be solvable if essentially limitless power were available.  For instance, what if desalination of sea water could be accomplished at a scale to be able to farm the Sahara Desert?  Think of the engineering projects that become feasible if power is no longer a problem.

And all chemical synthesis is available if the power to provide the potential to run the reaction in your direction is provided.  We could even start making cars out of metal again.  I’ve always dreamed of having a car that was immune to road salt corrosion.  Hastelloy C, Tantalum, or boring old titanium?

But the best part of all is imagining that my electric bill for my home heating and cooling and lighting is zippity doo dah all the way up to some pretty impressive electrical usage.  Hell, even I would give up my oil heat and use resistance heating just for the sake of getting rid of that damn furnace that’s always breaking down.  And I want them to throw in free fuel for my car up to let’s say a couple of thousand miles worth a week.  Ah, what a wonderful world it could be without technophobes.

Alright, all optimism for the week officially used up.

Actual Progress

Over the last decade or so Peter Thiel has made a point of claiming that other than computer automation, technological progress has been at a standstill.  And he’s essentially correct.  From about 1900 to 1960 we went from horse power to nuclear power.

From 1960 to 2020 we went from nuclear power to wind power.  This is not technological progress.  It’s surrender.

And this is mostly a psychological problem we’re facing.  We haven’t hit any quantum barrier that forbids us from improving almost every aspect of our technology.  Even the make-believe problems we create have solutions that are neglected by the dim-witted “technologists” that preside over our decline.  A good example is the farce called recycling.  Currently we are all forced to dutifully separate “recyclables” in a separate pail from the rest of our trash as if this was a magical process that allowed these paper and plastic waste products to somehow become usable materials.

But in reality, the majority of this material is landfilled along with the non-recyclable garbage that we collect in the other pail.  And the reason is simple.  Crude oil is a cheaper and better raw material for making plastic than plastic scrap.  Maybe in the far future when petroleum runs out, our landfills will become plastic mines that we’ll tap for a feed stream in our manufacturing process.

Of course, another thing it’s good for is as fuel.  Paper and plastic are mostly hydrogen and carbon and as such they make incredibly good combustion fuels.  Buring these materials in a garbage incinerator associated with a turbine generator would be the most efficient use of these waste materials.  But, you know, Gaia.

But let’s assume that at some point in the next twenty years, first world people are going to get tired of being forced into third world squalor.  At that point I’m guessing that the first direction selected for energy production will be nuclear fission steam turbine generation plants.  Sure, maybe they’ll have to pay lip service to global warming pieties.  Maybe they’ll even build solar powered carbon sequestration projects to please Gaia.  But at some point, people will demand to have the amenities they’ve become accustomed to; reliable electrical distribution and convenient transportation.  In the long run what the source of that power will be is yet to be determined.  My theory is that geothermal energy will supplement and maybe replace nuclear in the long run.

One thing I’m not sure of is what will be the fuel for transportation.  Many people have said that hydrogen is too hazardous.  Maybe they’re right.  It does tend to go boom when trapped in an enclosure.  Well, it’s cheaper and easier to make than octane but with unlimited electrical energy from something like widespread nuclear or geothermal I don’t see a problem with an octane synthesizing plant.  Carbon dioxide and water are available in endless supply so all that’s needed is cheap power.  And there’s a lot to be said for a really well-built internal combustion engine car.

But this is all just getting back to where we were in 1960.  What will real technological progress look like?  Ironically, I think that there will be an emphasis on Gaia!

I think quality of life innovation will be the future.  Research into the detrimental effects of all the chemicals that we add to our foods and come in contact with our bodies will begin shaping the products our industries produce.

And likewise with containers.  Maybe bottles will start being made of glass and metal again.  Some of the older materials were safer and newer alloys and other materials can be tested and whatever the healthiest choices can be substituted for things that may be harming us.

So better living through chemistry may become something more than just an empty slogan.

With all the talk of AI I’d be remiss if I didn’t mention the progress, we can expect from the ongoing computer automation revolution.  Eventually all automobiles will be subject to traffic control in densely crowded traffic.  Despite our strongest resistance, this will happen in many jurisdictions.  The nanny-state is just too strong in places like California and New York.  For many people this will be welcomed.  It will relieve them of the responsibility of driving.

Artificial intelligence will eventually make large scale industrial economic planning much more efficient.  Supply chain coordination for a whole network of companies producing a multitude of products will be optimized and trends and changes tracked and compensated for.  How this will effect capitalism remains to be seen.

Maybe the greatest use of AI will be in bioresearch and medicine.  The enormous complexity of living systems and the almost infinite number of chemicals that need to be tested for toxic and other detrimental effects cries out for the brute force that artificial intelligence can bring to bear on bioresearch and development.  I can see a future where the oncologist is a computer that scans the DNA of a cancer cell and chooses a custom antibody coded precisely to attach to and kill only the cancer cells and nothing else.

And the final area of progress is a sentimental one for me and one I’ll never see.  Mankind should send an unmanned probe to Proxima Centauri.  I guess HAL 9000 will be in charge of this mission.  It will require an enormous tank of water that will be used as rocket mass.  A fission reactor will be used to boil the water as a jet to provide acceleration.  Maybe it can get up to .3c and so the round trip will be something less than a century.  It can take readings and photos and see if there are any little green men there and come back and let us know.  Now that’s progress.

Quantum Mechanics, Consciousness, Intelligence and Life

Roger Penrose is a Nobel prize winning mathematical physicist whose most important contribution was work on black holes in relation to the theory of general relativity.  But he’s getting old and so he decided to think about the nature of consciousness and he has come to the conclusion that the phenomenon of human consciousness is caused by quantum effects generated in the cells of the human brain.

Wow!

 

 

If you watch the video, you’ll get a little information how the flow of chemicals in the microtubules or even the shaping of the atoms in the tubulin that makes up the tubules might be responsible for the quantum effects that provide the indeterminacy necessary to make human brain more than just a computer running a program.  Penrose equates that quantum indeterminacy with the basis of human consciousness.

Wow!

Okay, maybe that’s an interesting idea.  Is it true?  Damned if I know.

But I do like the fact that it gives us a way of saying that computers won’t have consciousness.  Lots of people think that if we just make a computer big enough, then it will suddenly develop consciousness because humans have consciousness and we have the best brains in the biological hierarchy.

Of course maybe if we can build indeterminacy into computers maybe they’ll become conscious.  Will that happen when the size of the circuits on the chips become so small that the actual paths that the electrons take become indeterminate?  I guess that’s possible.  We can make the AI as flawed as we ourselves are.  Maybe we’ll be able to make them neurotic or bi-polar or even psychotic if we want.  That’s kind of what happened to HAL 9000.  He became psychotic because he was forced to lie about the mission that was such an important part of his self-image.

And maybe that’s possible.  But somehow I don’t think complexity makes consciousness.  We “know” we have consciousness.  But is that because we have giant brains?  Dogs don’t have giant brains but try to convince any dog owner that his pet isn’t conscious.  He’ll laugh you out of the room.  I don’t think consciousness is a synonym for intelligence.  I think consciousness is a synonym for life.  We’re conscious.  Dogs are conscious.  Even mice are conscious.  Are mosquitoes conscious?  How about protozoans.  What about our individual cells?

I’m guessing the all are.  Obviously, a rotifer isn’t spinning around a pond saying, “I rotifer, therefore I am.”  But I think he knows he’s there in some sense.  Does that mean he has indeterminate microtubules providing him with agency?  Well, maybe it has nothing to do with quantum effects but for whatever reason, In some minimal sense, I think the answer is yes!  Consciousness equals life.

Now don’t ask me if viruses have consciousness.  I’m not going to bring this down to individual DNA and RNA molecules.  That would make my head hurt.  But I believe that life is life and it is all of a piece.  And whatever we have that is called consciousness is only the most exquisite version of what every other creature has writ small.

Whether God created quantum mechanics to allow us to have agency or whether the actual mechanism of our souls is completely impossible to reverse engineer by any human intelligence is unknown and probably unknowable.  What has already become apparent over the course of the last four hundred years of scientific investigation is that the more we learn the more we learn that we know absolutely nothing.

Isaac Newton “knew” what kept the Moon in orbit and how to calculate the orbits of the planets to whatever accuracy he needed.  He had discovered God’s textbook for his creation.

James Clarke Maxwell knew what the equations were that governed electromagnetism and ushered in the modern age of electric power.

Albert Einstein decoded time-space and “corrected” Newton’s laws.

But a generation later, Heisenberg’s Uncertainty Principle forever locked the door on our knowledge of the quantum world.  We invented quarks and gluons and muons and who knows what else.  But every time we learn something new we find out that ten other things are just illusions.  Dark matter and dark energy and string theory and who knows what else crowd around the dark corners of the forefront of our knowledge and we still know less than nothing about ourselves and why we’re here.

Well, I’m okay with that.  Just as long as we’re not kidding ourselves about where we stand with respect to our dogs.  They’re our friends meant to keep us from taking ourselves too seriously.

Oppenheimer (2023) – A Movie Review

I finally got around to watching this movie.  This won’t be a full review because I don’t think I can be completely fair to the movie.  Christopher Nolan has been a big-time director for a good long while.  His Batman trilogy earned gazillions of dollars and was actually very good.  Now this movie is a very different animal.  I don’t think it is supposed to be entertainment in the same way.  It’s a biopic and a historical recreation of a very important event, the Manhattan Project; the invention of the atomic bomb.

As the story of the Manhattan Project, it is fascinating and compelling.  The biopic is a combination of experiences.  Oppenheimer himself is very odd duck.  From his own admission he was not a great physicist like Fermi, Einstein or Bohr.  He was a dilettante who found himself surrounded by the generation that invented quantum mechanics and became their interpreter and project manager in shepherding all the pieces needed to allow the US military to get the a-bomb in 1945.

And we hear his history as a retrospective because the movie is really the story of how Oppenheimer; this critical individual in the ushering in of the nuclear era, loses his US government security clearance due to his former association with communists and other less reputable individuals in his circle of friends.  We are also led through the less than honorable path of his love life.  And we see how his concerns about the dangers of nuclear weapons seem somewhat inconsistent depending upon where his role in producing the bomb stands.  While ensconced in the project he seems not at all conflicted.  But once he and his colleagues have handed over the bombs to the Army and the spotlight is no longer on him, his qualms grow exponentially.  As a viewer of the story, this seems clear.

The movie is populated with famous names and faces, some of them very hard to recognize.  Robert Downey Jr. is Lewis Strauss, Oppenheimer’s implacable foe who hounds him out of the government circle of influence.  Emily Blunt is Kitty Oppenheimer, his wife.  Matt Damon is Gen. Leslie Groves, director of the Manhattan Project.  Josh Hartnett is Ernest Lawrence, a Nobel-winning nuclear physicist.  Kenneth Branagh is the brilliant physicist Niels Bohr.  Tom Conti is Albert Einstein and weirdest of all Gary Oldman is Harry S. Truman.

And there’s all kinds of good acting.  I especially enjoyed the “physicists seemingly engrossed in the endless details of making a weapon out of their incomprehensible mathematical equations.  There is a critical scene where Edward Teller, the father of the H-Bomb stops the project when his calculations seem to indicate that there is a very high probability that setting off a fission bomb could ignite the whole atmosphere of Earth and end all life on the planet.  That is a pivotal scene where eventually even Einstein is consulted.

And the climactic Trinity test scene in the desert is very effective.

But it’s a three-hour movie and that means we see quite a bit of J. Robert Oppenheimer and I have to admit I didn’t find him the most sympathetic character to follow for that three-hours.  It’s a good movie.  But I ended it wishing it had been more about Matt Damon’s character and that’s an odd feeling for me.

Once in a Billion Years

In the 4-billion-odd-year history of life on Earth, primary endosymbiosis is thought to have only happened twice that we know of, and each time was a massive breakthrough for evolution. The first occurred about 2.2 billion years ago, when an archaea swallowed a bacterium that became the mitochondria.

The second time happened about 1.6 billion years ago, when some of these more advanced cells absorbed cyanobacteria that could harvest energy from sunlight. These became organelles called chloroplasts.  

And now, scientists have discovered that it’s happening again. A species of algae called Braarudosphaera bigelowii was found to have engulfed a cyanobacterium that lets them do something that algae, and plants in general, can’t normally do – “fixing” nitrogen straight from the air, and combining it with other elements to create more useful compounds.”

Endosymbiosis.  That’s a good name for it.  The article says this process has been going on for a 100 million years and is still probably a work in progress.  These nitrogen fixing cyanobacteria haven’t reached the advanced state of dependence that mitochondria and chloroplasts now display.

Well, the biologists will be playing around with this experiment in progress for the next hundred years and I expect they’ll learn plenty.  One day we’ll probably have chloroplasts of our own and spend a few hours in the sun every day to improve our green complexions.

Sawdust and Forever Wars

Well, the boys from the road crew were back today and finished off the job, but good.  A tractor trailer was blocking my driveway and the trailer was an open topped box that was rapidly filled by an enormous wood chipper that ate whole sections of tree trunks that were ten feet around.  The noise that came off of this thing was considerable and the hounds were incensed.  The chipper finished off the big white pine in less than an hour and that included all the scraps that they had trimmed off the trunk.

Then they moved on and took care of the two ash trees.  These were smaller but the hardness of the wood gave the machine a different sonic tone as it spat the sawdust into the trailer.  And the wood was a lighter, cleaner looking stream as it flowed into the box.  And soon they were gone too.  Of course, gone didn’t include the debris that the crew left far and wide.  Between sawdust, small branches and pine needles I’ll be cleaning up the tree bits for the whole of the spring.

But I’ll have to say I’m impressed by the state of the art in robotic forestry.  It sort of reminded me of a Dr. Seuss book where some absurdly complicated string of machines reprocesses some thing into a completely different substance.  The only thing missing were the absurdly bright primary and secondary colors along with Thing One and Thing Two running the machinery.  And come to think of it, the foreman did look a little like the guy who didn’t want to eat the Green Eggs and Ham.

Well, after they finished, I went to work and when I got back home the temperature had dropped down into the forties and it was once again raining cats and dogs.  You know I’m pretty sick and tired of the rain.  Last year it rained endlessly from April to the end of June.  I dream of kidnapping Camera Girl and dragging her to Southern Utah.  When I was there, there was a little snow but the ground looked like a desert and at this point that would be A-OK with me.  But the lure of the grandkids is too powerful for her.

So, I heard a little while ago that Israel counterattacked in Iran and some other places.  Well, that’s a little disturbing.  The way Joe Biden has been talking I think maybe they’re ready for some really bad things.  I can’t say I’m terribly surprised.  I guess I’m just sick and tired of the forever wars.  Maybe I’m so tired of it I’m willing to see it all blow up now.    Just fire them all and let God sort it all out.  It sounds right.

But then I think of the kids and the grandkids and of course I don’t want that to happen to them.  So apparently, I’ll have to let the morons we have running our foreign policy continue on with their insane games and their demented strategies.  Ukraine, Iran, Israel, Syria, China.  All that crap.

Humans are the most remarkably clever animals. Look at those machines I saw working today. Reducing those trees to dust was an acceleration over nature of many orders of magnitude. They reduced the work of twenty or fifty years of natural processes to machine minutes. We are that paragon of animals that Shakespeare mentions. But simultaneously we are led by gibbering idiots. They could reduce the whole human race to dust in minutes. So, there it is.

Who Will Own the Future?

The earliest civilization that archeologists have identified is Sumer.  Located in the southern portion of the Tigris-Euphrates basin the Sumerians invented irrigation agriculture, domesticated several of the familiar farm animals and formed the first empire.  Their technological advances allowed them to grow their population until it probably included a million people.  Pretty good for six or seven thousand years ago.

So why aren’t we all speaking Sumerian and praying to Enki and Enkidu (Enki see, Enki do)?

Well as it turns out, using the Tigris and Euphrates as an irrigation source for hundreds of years eventually raises the salinity of the soil to the point where agricultural yield falls way off.  That’s right.  The technology that made their civilization possible was eventually unsustainable.

Sustainability is a buzzword that Gaia worshippers love to bandy about.  And typically, they’re talking about fossil fuels as being “unsustainable.”  But more and more the sustainability of things like wind and solar energy systems have begun to be questioned.

As an example, down in Texas a hail storm destroyed a significant part of a 4,000 acre solar panel array.  And local people are worried about the damaged equipment leaking harmful chemicals into the groundwater.  And this is far from the first occasion when hail has destroyed these arrays.  And wind turbines have been having their own problems.  Maintenance has been found to be more expensive and frequent than estimated.  And the impact on bird life has been shocking for the wildlife lovers among the green energy crowd.  Dead eagles and other raptors are a common sight around these installations.

But the main complaint about these supposedly sustainable technologies is that they have significant environmental costs compared to the limited power production they represent.  In other words, replacing the current power generation capacity with these sustainable technologies would create enormous ecological impact from the production of the equipment and from the sheer size of the area needed to contain this capacity.  Imagine a landscape covered for miles and miles with wind turbines.  And the whole area littered with bird carcasses.

The current green energy technologies remind me of the compact florescent bulbs that the Obama administration tried to push on us.  It was a technology that had more problems than the technology it was supposed to replace.  Basically, it was a pretend solution to a situation that was being presented as a critical problem but was actually a manufactured crisis.

Now here’s the thing.  Problems with technology occur.  One problem that we have anticipated for a long time is what to do when fossil fuels run out.  Now whether that’s a hundred years in the future or a thousand years there will most probably will be a point where we’ll run out of recoverable coal, oil and gas.  And long before that time comes mankind should have a plan to replace this energy source with something else.

But the answer can’t be going back to living in caves as the green energy people want you to believe.  And if this country and the rest of Western Civilization decide that following the lead of the Greens is the answer then someone else will find the better way and move forward without us.

Will it be the Chinese, the Russians, the Indians?  It’s very hard to know who.  But it will happen.  And if we allow ourselves to be bullied by the likes of Greta Thunberg and John Kerry then we’re going to doom our children to living like stone age people and eventually be displaced by more rational societies.

I’m hopeful that the great experiment with green energy that California has pioneered will soon bear fruit and cause some horrific catastrophe.  Maybe a huge number of electric cars will get stuck in a traffic jam out in the desert and thousands of stranded motorists will die of heat stroke.  Something like that could allow rational people to realize how stupid the Greens truly are and return people to a sane way of thinking about energy and its place in our lives.

Well, Enki see Enkidu.

Cthulhu Attempts to Swallow the Sun and Fails Badly

The First Selectman was miffed about something.  Maybe his shadow appeared a little too portly or his reflection in a dank lake was a little too unflattering.  Whatever it was he attempted to swallow Earth’s star.  Luckily he’s not the Elder God he used to be.  All he got was a nasty burn around his mouth tentacles, a case of butthurt and a dose of reality.

I collected this shot at the moment of maximum effort.