Some are simple to answer, but people who have missed their opportunity to be broadly educated sometimes can’t separate the simple queries from the hard. I’m in that group, more times than not.
I rummaged through an old safe the other day. I found its key tucked away and forgotten in the back of a drawer in an antique desk. I asked myself: what might be in that old safe? Why not take a look? What harm could there be in searching a dusty safe for forgotten objects?
I found old papers and school reports. I found Christmas and birthday greetings and expired credit cards. I found a rectangular tin-foil-wrapped object pressed flat and smooth and a quarter-inch thick — a pamphlet of some kind, perhaps.
I would unwrap it later.
I reviewed a report card from the seventh grade. It held up well during the past 58 years. My geography teacher wrote a comment that caught me by surprise. “Billy Lee is a thinker,” he wrote next to the “A” he gave me.
I remembered back. Mr. Holden drove a taxi-cab nights to make ends meet. Memories flooded in.
He complained that teachers weren’t paid enough. Between taxi fares, he read books. He recited titles and authors, but I knew I would never read them. The writers’ names were unfamiliar — foreign, some of them, which I couldn’t remember or pronounce; the titles? — incomprehensible.
How could anyone read books whose content was unconnected to anything they knew or were able to understand? I couldn’t. I was sure of it.
I found a letter from a girl I once loved. She explained why we could no longer be together. Despite all my wonderful qualities, I was needy, she explained. I needed to turn my needs into wants by finding others to fill in the gaps she couldn’t.
It was odd, I thought. I didn’t realize how technically expert was her craft the first time I read her note. Who knows? Maybe today she is a famous author who writes under a pen-name. Stranger things have happened in the history of literature, right?
The writer of Jane Eyre comes to mind. Charlotte Brontë published her novel under the name of Currer Bell. I always thought a writer of her depth might have come up with a better name. I did, and I’m not half the writer Charlotte was. People have to admit, Billy Lee has a nice ring, no?
Lately, I’ve been writing answers to questions on Quora to which no one can possibly know the answers. I call them mystery questions.
Many of the questions remind me of the sailor’s dilemma where a seaman finds himself stranded and adrift on a raft in a vast ocean of swells during a raging monsoon. The man clings to a few pieces of wood and prays to God for deliverance.
He asks God why was he born when it is clear that his life is going to end in terror, alone on a raft in a bottomless sea with no chance of rescue. If God by some miracle answers his prayer; if God saves him and the storm clears, the sun will bake him alive; eventually the sharks will eat him.
Why? Why? Why?
What sin did he commit that drove him to his fate? What decisions did he make that were ill-advised and unwise?
What might he have done differently to avoid the horrid end he knows will befall him in the few moments that remain before his strength is sapped and he loses his grip on the last piece of wood, which will disintegrate once he’s sucked beneath the churn.
Well, one answer that comes to mind is this: he didn’t plan for his birth; once born he didn’t plan for his death. He never really believed that he was doomed to a lonely, fearful death — the destiny of all living creatures; humans are no exception.
The answer to his cry for answers is that there are no answers. No one avoids losing everything they love. It is every person’s fate. No scheme, no matter how cleverly constructed, avoids it.
And yet the sailor begs God. He shakes his fist and screams against the gale: God, why did you forget me? Why my pointless life? Why did I suffer to the very end?
Amen.
Here are six mysteries I will struggle to explain.
Mystery 1 — What caused or initiated the Big Bang, if there was nothing before it?
95% of the mass and energy of the universe that theories and observations say must be “out there”, no one has been able to find, right?
Does anyone anywhere know anything at all about what the universe is or how it works?
The big bang is a verbal “analogy” used to help folks visualize what a few theorists have worked out mathematically to explain a lot of observations that otherwise make no sense.
Here is the hard part: the mathematics is also an analogy; it isn’t real; it’s just numbers. Mathematics cannot make a model that reflects fundamental realities without simplifying a lot of important stuff — and no one as yet knows what the missing stuff is that human speculation and observation is overlooking.
We all know it’s true.
Mathematics is a way of reasoning — like language but minus its ambiguities and textures. An argument can be made that mathematics and language are not adequate to the challenge of describing reality.
Humans seem to be lost in a mystery of existence from which they will never be rescued. They lack certain fundamental tools that they must someday discover and develop to give them any chance at all to climb out of a very dark hole of ignorance.
It might be possible to understand the cosmos — if the secrets of consciousness are unraveled. Consciousness is the magic-water in the desert of ignorance which — when found, understood, and imbibed — could quench the thirst-to-know that every thinking person suffers. That is my hope, anyway.
Consciousness might be fundamental and foundational. Most people won’t accept it, but almost every brilliant person who has thought the problem through seems to have written that it must be so.
Mystery 2 — Assuming we can completely separate religion and faith from pure science and fact, then speaking from a purely scientific point-of-view, what form would life after death take?
The consciousness that people experience today is the consciousness they will experience after death if consciousness is the fundamental foundation of all reality.
Conscious life-forms plug into universal consciousness like televisions plug into the cable network. TVs come and go, but the cable network is forever broadcasting. The conscious experience it creates appears in the televisions that are connected to it and can be observed on their screens by independent observers.
The reality of television comes from its fundamental foundation, which is a broadcasting system — in this analogy. As long as a television is plugged in and turned on somewhere, the reality of the cable network will continue.
Consciousness does not belong to the TV, but is experienced by it. When the TV “dies”, this consciousness will continue to be experienced by other TVs. The unplugged television will never miss it, and the consciousness it shared with other televisions will never die.
This view of reality has been described in analogous ways by Erwin Schrödinger, John Von Neumann, John Archibald Wheeler, and other brilliant physicists.
DNA is a reservoir of bases that RNA draws from to build sequences that are processed in RNA-built structures called ribosomes. From them polypeptide “necklaces” are fashioned which are folded by Golgi structures into proteins. Proteins become the tissues of the body and the catalysts of cell metabolism, right?
In humans, 10% of DNA is used to make the templates of proteins (2%) and catalysts called polymerases (8%). The rest (90%) is not used as far as anyone knows today.
A lot of extraneous chemical structures play at the edges of DNA to influence what is expressed and what is suppressed. It’s called epigenetics and is an active field of research.
DNA is neither a code nor a cipher. It’s not that simple. A lot more is going on that scientists know about and which scientists know nothing about. For example, proteins exist in the body for which no DNA sequencing has been found in the genome. It’s called dark DNA.
Mystery 4 — If the expansion of the Universe is accelerating, won’t it reach infinite speeds? What does an expanding universe mean after the heat death of the universe?
The universe is expanding like a balloon that is being inflated by the force of something that exists inside it, which no one understands. I’ve heard mainstream physicists say that they believe this expansion is uniform and accelerating; it will lead to a “Big Rip.”
The Big Rip will tear apart everything — including atoms and parts of atoms. Energy will dissipate and the universe will flat-line and disappear. It will be as if the universe never existed when the process is complete. Space, time, energy, and matter ripped to shreds will leave nothing behind.
I’ve always thought that the accelerated expansion of the universe is caused by the gravitational tug of trillions of parallel universes that surround our own like a swarm of fireflies. Accelerated expansion is evidence for massive parallel universes, it seems to me.
As seductive as this idea is, no one is proposing it as a serious explanation for the observations of expansion. I don’t know why, but suspect that many of the smartest people don’t think the parallel worlds model clears up enough of the mysteries in the cosmos to be worth pursuing.
Neither does the Big Rip model. It can be argued that the “rip” model explains nothing. It describes what happens when everything is driven apart by an unknown force to its logical conclusion. Somehow, the description doesn’t seem helpful. It doesn’t answer the biggest question of all: how did everything start in the first place?
How did we get here? Where are we? Is anyone in charge? Will the universe live and die without the benefit of any living thing — any conscious life, including itself — understanding the why and how of it all?
How can something on the scale of a universe exist and then cease to exist whose mysteries were forever out of reach — impossible for conscious-life to grasp or comprehend?
Mystery 5 — How could the precursors to the origin of life move or assemble with intent? At what point would this intent become actual life?
Anyone who says they understand how the precursors of life assemble is telling fibs, because no one has any idea how life started. I’ve heard convoluted conjectures about how clays, for example, might have got life started, but they are unconvincing and not reproducible, at least to my way of thinking.
Based on evidence in ancient rocks it seems more likely that comets and asteroids carried prokaryotic cells to Earth. These cells are thousands of times smaller than the eukaryotic cells that are the building blocks of all animals and plants.
Because these cells are small and are, internally, a disorganized mess (no organelles, no nuclei, tiny amounts of RNA & DNA mixed together like scrambled eggs along with everything else they contain), it seems reasonable that prokaryotes could be abundant in the universe and have existed since the first generation of stars and planets.
These cell types were firmly established on Earth (a third generation star) by Earth-Year one-billion. Oxygen didn’t exist, nor did oceans. Some geologists believe Earth was bone-dry at its start.
Now comes the really hard part to understand. It took two-billion years for these tiny cells to branch-off into the much larger and more tightly organized cells called eukaryotes. During that time an onslaught of ice-balls from the outer reaches of the solar-system created a deluge of water on both Mars and Earth.
Earth — having 2.65 times the gravity of Mars and a magnetosphere (which Mars lost when its iron-nickel core froze) — was able to hold onto both its atmosphere and its oceans.
Oceans are probably the incubators where highly unlikely events occurred that made humans possible. Cells grew in size and complexity. Some engulfed prokaryotic granules that became the mitochondria that every eukaryotic cell uses like mechanical batteries to add the energy necessary for big cells to survive.
Somehow these big cells learned how to use sunlight for power. Photosynthesis released oxygen, which poisoned almost every other kind of living cell on the planet. The survivors, the remnant, took another billion-and-a-half years to become space-exploring civilizations of highly intelligent animals who call themselves humans.
It’s a process that, because of its duration and a number of sporadic near-extinctions, seems unlikely to have happened at all, but here everyone is on Earth to prove that the impossible is possible.
Although I agree with Freeman Dyson that prokaryotic life is going to be found to be pervasive in the hundreds-of-thousands of methane-and-water ice-balls in the outer reaches of the solar system (called the Kuiper Belt), it seems unlikely that the much larger eukaryotic cells (or the animals and plants that evolved from them) will ever be found anywhere else but on mother Earth.
It’s possible that intelligent life has evolved in some other place, but the odds are small enough that by the time humans suffer their inevitable extinction it seems unlikely that they will have found and identified beyond Earth any non-prokaryotic life at all.
And now, at last, the final mystery. Mystery number six.
Who forgot what it is?
Remember the foil wrapped object found in the old safe? What was inside, anyway?
Any guesses?
I took the shiny object to my wife, Bevy Mae, and we carefully peeled away the foil to reveal the contents within.
And of course, dear reader, you guessed right. A stack of money is a wonder to behold. It makes living feel real good, at least for a while. A sufficiently large amount provides the freedom to buy any old thing at all.
Will we buy a sailboat and take our thrills from a roiling ocean?
I have hope that someday readers will visit Quora.com to look up me — Billy Lee — to read my answers to hundreds — perhaps one day thousands — of questions asked by every kind of curious person from every part of the world.
I love to read and think about questions from unmet others — to encounter oddities that have never occurred to me to ask or answer.
It’s humbling to be confronted by the knowledge that not only do I not know the answers to thousands of questions, but I lack the breadth of mind to even imagine such questions; I am convicted by my own lack of curiosity and inability to think deeply about an almost infinite number of mysteries that other people of all types and backgrounds wonder about and seek to understand.
Hundreds of years ago, polymaths — the smartest and most energetic of them, anyway — could know and understand all that humankind ever dreamed. Today, the world is too complex; the depth of knowledge required to understand a narrow subject — like juice-carton safety-caps (I hold a patent) — takes years, maybe decades, to acquire.
Is it any wonder that smart people give up and go stupid?
No matter how much a Doctor of Philosophy knows about the rules of logic, he’s a dummy to every certified automobile mechanic he will ever meet — and vice-versa, right?
A way out of the dilemma is to practice the art of pontification. I pontificate based on a lifetime of experience; and reading; and wandering the world; and poking around in my backyard — to ponder why things are the way they seem to be.
Je connais beaucoup demerde, and I know a lot of nothing. When I write it down, well, magic happens. Resonate rings of truth rise which when later read render me reeling.
I’m unsure where-from the magic comes. It seems to fall from heaven to light the world. I’m driven to share with souls known only to God, because I have no way to know who reads my blog. I know only that some folks make the time, because WordPress stats say it’s so.
One of the things on Quora.com that seems to confuse a lot of people is the difference between momentum — a measure of the mass of an object multiplied by its velocity in a particular direction — and kinetic energy, which is a measure of the energy of an object that has been accelerated for a period of time in a particular direction, which enables it to do work.
Momentum is an object’s mass times its velocity; it is a measure of its inertia along a defined direction. It is measured in newton-seconds.
Kinetic energy is released by an object in units of acceleration that were initially induced by newtons of force. It is equal to half the quantity that is calculated by multiplying an object’s mass by its velocity squared. It is measured in units called joules, which are newton-meters.
Of course, spinning objects that aren’t moving in any direction have momentum and kinetic energy, too. The two are wrapped together in a concept called, torque.
Dear God, help me.
Now, I’m confused. Somebody, please, explain to me. I thought I understood until I started writing. I did. Really.
Another source of confusion concerns the nature of photons, which are tiny packets of oscillating electric and magnetic energy — from which light is made, right?
Photons seem to have no mass in the vacuum of space. When they pass through a material like glass, they leave a wake of disrupted electrons in the glass which belch out polaritons. These particles add mass to the photons and slow them down by as much as forty percent.
When photons exit the glass and enter the vacuum of space they leave the polaritons behind, lose their acquired mass, and jump to light speed, instantaneously.
Who knows for sure that it’s true?
Who understands why?
Here is an interesting thought: if humans — limited in understanding by language and mathematics — are unable to ever know why photons exist and behave as they appear to do, then who can? Who does understand?
Is all the complexity of the universe understood by no one? Is it possible that an unlikely universe can exist forever whose fundamentals cannot be articulated and which lies outside the experience and ability to comprehend of any sentient life-form whatever, whenever, wherever?
What kind of place do we live in, anyway?
Calm down. Take a breath.
Reality may not be as hopelessly inaccessible as it seems. Can it?
Here are some questions, which I’ve answered as truthfully as I know how. The answers are assertions of truth.
1 – How did a single cell organism eventually lead to complex life on earth, and does that mean that all life has a common ancestor (the single cell)?
This one is the 64-million-dollar question that no one has ever answered convincingly. Prokaryotic cells were established 3.5 billion years ago on the early Earth. They evolved to become the bacteria and archaea branches in the tree of life that exist to this day.
Here is the amazing part, at least for me: Eukaryotic cells, which are the much larger and more tightly organized cells of all animals and plants, did not emerge until two billion years after prokaryotes. It took a long time to evolve cells capable of conjugating into more complex life.
For the past 1.5 billion years eukaryotic cells have evolved into life forms capable of civilization and space exploration. The time frame is amazingly long.
The thought that a lunatic could in a moment of bad judgment start a cascade of events that extinguishes all life is troubling.
When astronomers look into space they see no signatures of life as advanced as ours. Again, this is troubling, because it might be an indicator that the knowledge possessed by advanced life-forms may approach some asymptotic limit where self-annihilation becomes inevitable.
2 -What evidence would falsify the theory of evolution?
No one knows all the myriad ways that life evolves, only that it does. That life evolved from cells that were fully functional 3.5 billion years ago is an established fact, because of evidence found in rocks.
Scientists know that it took two billion years for these ancient cells to evolve into the much larger and more tightly organized eukaryotic cells that today are the foundational structures of all animals and plants.
No one knows how life as complex as cells was established on a hostile planet like the early Earth, but everyone has an opinion; these opinions are called conjectures and theories.
One scientist might say that life started on Mars and was transferred to Earth on space debris uplifted by a cataclysm on Mars. Another says no; all the stuff necessary to make prokaryotic (primitive) cells existed in abundance on a young Earth — perhaps near hot vents in the ocean floor. Other geologists say the earth was bone dry at one billion years. Oceans came later, so just what the heck does anyone know for sure, anyway?
Many conjectures purport to explain how life changed from unicellular eukaryotic forms 1.5 billion years ago into the space-exploring civilizations of today. Every conjecture thus far has already been falsified either by evidence or by competing conjectures that make as much sense but are different.
For example: some say mutations in DNA drive evolution. The problem is that mutations are too rare. Some say an eco-sphere of processes driven by a halo of molecules that cling to DNA drives evolution. They call it epigenetics. Others say, no. RNA drives evolution like colonies of intelligent ants who build hives. There are other explanations.
None are verifiable or generally accepted due to an insufficient body of proof that is able to overcome alternative ideas that are equally compelling.
Another problem is that no one knows if DNA life is all there is. DNA is a molecule that cannot be seen or worked with until it is amplified into a viewable goo.
Are there other undiscovered molecules no one knows how to amplify?
Understanding of the parameters and limits of life is incomplete and may perhaps mislead researchers. Humans might not yet know enough to figure out the dynamics of genomes. More needs to be discovered and understood.
Is there a shadow biosphere that is in a symbiotic relationship with DNA? Where is the dark DNA that biologists can’t find that is necessary to code for many of the proteins they know exist?
How were cells themselves established so quickly on Earth? It’s a question whose answer is discussed by countless experts and non-experts; no answer fully satisfies.
Darwin’s ideas about natural selection and survival of the fittest have their place. But he was just getting started, and he died a long time ago. Scientists have a lot of work left to do.
3 – Which Bible story is most objectionable when looked at in the context of modern morality?
All Scripture is God-breathed. To love and be loved by both God and people is why we were born; it’s what makes life precious and worth living. No one wants to die; no one wants to be hated.
The sad part is that everyone suffers; everyone is hated by someone; everyone hates someone; everyone dies after a life of blunders and sin. Christ Jesus came to save the lost, which by the looks of this thread is pretty much everyone.
We have hope. It’s something to hold onto as we grow weak and find ourselves ruined at the end of our minutes in the sun on our beloved Earth.
Jesus made a path for us. It cost him everything a human can pay. He somehow survived the Roman crucifixion that killed him to show the poor and overly burdened that in his power is the way, the truth, and the life.
There is a path to paradise; we — everyone of us — can find it by surrendering to the God who loved us, gave us life, and suffered to set right what we put wrong.
4 – People say Newton’s third law, “For every action, there is an equal and opposite reaction,” is not accurate. Is it true?
Einstein said that only mass and energy exist; they are in fact equivalent; they are the same thing; two sides of the same coin. Energy gives rise to all other phenomenon and forces that scientists observe.
Stephen Hawking said that when mass (or energy) comes into existence a negative energy must emerge to balance it so that when added up everything in the universe sums to zero. It appears that Newton’s third law, equal and opposite, is not only accurate — it is a fundamental balancing principle that undergirds existence.
Mass is matter, which can be positive or negative and is referred to as matter or anti-matter.
The Billy Lee Conjecture claims that mass is pixelated (quantized) such that in the contest of emergence within the smallest spherical volume, matter or anti-matter (one or the other) will prevail due to a natural truncation of π in the putative spherical volume of the creation space.
An evenly divided ratio of matter and anti-matter within a spherical creation-space is physically impossible if π is truncated by pixelization. Matter and anti-matter will annihilate until a single piece of either matter or anti-matter remains after the creation event.
To maintain a zero-sum, balancing counter-energy will emerge according to speculation by the late Stephen Hawking.
Over long periods it seems that an extraordinary amount of matter has accumulated inside our own universe by surviving the natural annihilation of matter by anti-matter. This matter seems to have generated an enormous amount of counter-balancing energy — some of which Newton called gravity. Most of the energy remains undiscovered and is referred to as “dark.”
In our own universe, π seems to “round-off” near the precision of the Planck constant.
In universes outside our own — some of which seem to be pulling our universe apart in an accelerating expansion caused, perhaps, by their own gravitational forces — π may truncate to different values to generate in some cases a prevailing anti-matter and opposing energies that manifest qualities different from the energies found in our own universe.
If parallel universes disrupt the zero-sum strategy of our own, it may still be true that the principle of zero-sum or equal but opposite is operational, but humans are too small and the distances are too far for anyone to ever know for sure that it is true.
5 – What are the major foreign policy issues that the United States of America is working on in 2018?
I’m writing this answer just after the meeting in Singapore between North Korea and the United States involving the Korean nuclear arsenal.
The Secretary of State, Pompeo, said yesterday that NK has two years to de-nuke. This delay might tempt the Japanese to convert their stockpile of 47 tons of plutonium into bombs. Japan and North Korea have issues related to the Japanese occupation of Korea from 1910 to 1945.
It takes ten pounds to make one bomb. The Japanese can make as many bombs as they want in as little as 24 hours.
A Japan armed with 10,000 nuclear bombs (they already have the missiles to launch them) is a clear and present danger to China, Russia, and Korea — not to mention the United States with whom Japan has a beef that goes all the way back to World War Two when the USA destroyed 67 of their cities with napalm; two cities by atomic bombs.
The USA has occupied Japan ever since. Some of the Japanese probably hate us — who knows for sure?
6 – Can a photon’s speed be slowed down? I have heard that it can be slowed by a medium, but I have also heard that it is just the velocity being slowed as it “bounces” from particle to particle? I am not talking about Bose-Einstein condensation.
The current thinking is this: when a photon leaves the vacuum to enter a material object, it leaves a wake in its path that vibrates electrons in the medium. These oscillating (or disturbed) electrons generate polaritons, which are photon-like objects that can catch and add mass to the photon. With mass added, the photon slows down — as much as 40% in glass, for example, which enables more polaritons to pile on.
When the photon exits into the vacuum of space, it disentangles from the polaritons, and instantly resumes light speed.
I didn’t make this up.
It’s what some physicists are saying, and it explains a lot and leaves a lot unexplained — like all things physics when folks go just a little deeper into the abyss of understanding.
7 – What is the relation between light and darkness? Can one exist without the other?
Light is the action of certain wavelengths of electromagnetic radiation on structures in the eye, which trigger hallucinations in the brain that humans report as “light.”
An infinite range of frequencies are “out there.” Humans are blind to almost all of them. People who are unable to trigger hallucinations induced by electromagnetic radiation say that they are experiencing “darkness.”
Some frequencies of light are experienced as “heat.” Because the sensation is not accompanied by visual cues, people in hot rooms with no windows believe they are experiencing “darkness.”
The experience of heat is caused by the same electromagnetic waves that induce visual experience, but they are a tiny bit longer in length than those which induce the experience of the color “red” in humans.
The longer waves carry less energy and are invisible to people unless they view the ”infra-red” light through high-tech sensors. Local fire-departments use these sensors to identify ”hotspots” where fires might reignite.
8 – Given an opportunity to pass through one or two slits with no detection, will a quantum object always pass through both?
If the slits are in the right position and are cut to the right size and are at the right distance from the source, a pattern on a detector screen will evolve over time to look as if waves are passing through the slits and interfering in a predictable way with each other.
Of course, it’s not true, because the particles are shot one at a time and the duration of the experiment can be hours to weeks long. The shots land one dot at a time. After thousands of shots, a pattern that resembles what one would expect of waves interfering is formed by the particles as they accumulate on the detector backstop.
9 – Is Jesus a hoax? Jesus has not walked on Earth in 2,000 years. How can a man 2,000 years ago save anyone?
I was hungry and you gave me something to eat, I was thirsty and you gave me something to drink, I was a stranger and you invited me in, I needed clothes and you clothed me, I was sick and you looked after me, I was in prison and you came to visit me.
The righteous will say, ‘Lord when did we do these things?’
My answer will be, ‘Everything you did to help suffering people, you did for me.’
The preceding is a paraphrase of part of Matthew 25, a book in the Bible.
Read it. Why not?
The answer is in the sense that it is not a hoax that the “least of these” walk the earth when we do. How we treat unfortunates is, in the view of Jesus, the way we treat him. He will return to us the same courtesies when finally we give GOD an account of our lives.
RNA, in its many forms, behaves like ant colonies which swarm over the DNA pile to do a number of tasks that seem to involve a lot of decision making.
RNA selects out of billions of bases a few thousand which it strings together to make “genes” that it transfers to ribosomes — which are made almost entirely of RNA and are among the oldest structures in cells.
At a ribosome, the genes are coupled to RNA that carries amino acids; the amino acids are then ejected from the ribosome to be strung together like necklace beads; they are transported to Golgi structures where they are folded into proteins.
A process this complex — and it’s actually far more complex than this summary implies — can be orchestrated without intelligence; it’s possible, but without intelligence of some form, the process seems, at least to me, to border on the miraculous.
After all, what is the result?
It is a conscious thinking life-form who can, in cooperation with others, figure out its own origins.
11 – How do Quantum spins get affected by Quantum entanglement?
All atoms with electron shells that are home to more than one electron have entangled electrons. The spins tend to oppose each other. With bosonic particles, down conversion techniques produce photons that have opposite polarization.
Most physicists think that spin is induced during measurement; the spin is transmitted oppositely to the entangled partner instantly — no matter how far separated.
For this reason, a pair of entangled particles can be envisioned as a single particle that behaves as if one of its dimensions (the distance between its endpoints) is missing.
The distance between the entangled pair behaves as if it is zero — when it is known to be non-zero.
12 – What is the viability of colonies on other planets?
The two planets closest to Earth are the most viable places for colonies simply because they are the easiest to resupply. They are Mars and Venus.
Neither can sustain colonies, because they lack magnetospheres, which are essential for deflecting high energy particles emitted by the Sun (called the solar wind). These particles are deadly to life. The molten iron-nickel cores of Mars and Venus froze millions of years ago on both planets, which collapsed their magnetospheres.
Venus has a highly toxic atmosphere, which is another reason to rule out colonization there.
Beyond Mars are gas giants. Only their rocky moons are candidates for human colonies. All the moons appear to be too cold to operate the machinery necessary to sustain human life. Most lack protection from the solar wind.
Bonus Assertion – Does a photon consist of (f) quantized energy packets each of (h) joules?
A photon seems to be a packet of vibrating electric and magnetic energy, each part of which exerts its energy at a right angle to the other. The energy in the packet is proportional to vibrational frequency alone. A photon has no mass or acceleration. It travels along at a constant speed in space-time. The electric portion of the energy is about seven times the energy of the magnetic portion.
Photons can become more intense (that is, brighter) when they pile up. Pile ups don’t happen to electrons, protons, and neutrons because they obey an exclusion principle that forbids them from occupying the same space at the same time.
Photons can pile up, but their intensity (or energy) can only be transferred into electrons that are in an energy state that resonates with the frequency of the incoming photons. Non-resonate electrons ignore un-matched photons, so photons pass through non-resonate electrons unimpeded.
The energy of an individual photon can be expressed as its kinetic energy and shown to equal Planck’s constant times the photon’s frequency, which always results in a very small number.
When expressed in terms of its wavelength (λ), photon energy equals the Planck constant (h) times the speed of light (c) divided by the wavelength (λ) of the photon. Notice that the mass term is missing due to a simple manipulation of the relevant equations — which anyone who is interested can find in the following link.
Momentum might not be an appropriate metric for a force carrying boson like a photon, because momentum is based on mass, which many physicists say photons in a vacuum don’t possess.
Another reason momentum could be an inappropriate metric is that the velocity of photons in a vacuum is independent of any reference frame, right? Momentum is a vector quantity that is always measured in relationship to a particular reference frame or the momentum of another particle.
There is a theory that claims that photons pick up mass when they pass through materials like glass. They seem to leave a wake that shakes up electrons in the material. The vibrating electrons release polaritons, which by a mechanism analogous to superposition add mass to the photon and slow it down. When the photon exits and returns to vacuum, it sheds the polaritons, becomes massless, and returns to light speed instantly.
Perhaps photons in the vacuum of space acquire mass by interacting with virtual particles that emit virtual polaritons. Notions about the nature of the universe would be changed radically if such a notion were confirmed by evidence.
Because h and c are constants, they can be multiplied together to give a constant that is very close to 2E-25. Dividing 2E-25 by the wavelength of a photon will give its energy in joules. Of course, all units are SI, which stands for standard international units, correct?
Since E = hf or (hc / λ) , the energy is always a multiple of h, which is the Planck constant. The word “multiple” is a simple way to say “quantized”.
So, the energy of a photon bunch or pile can be expressed as a multiple of the number of photons of a certain wavelength in that bunch. The energy in each individual photon is its wavelength (or frequency, if you like) multiplied by the Planck number — a constant equal to 6.626E-34.
It takes a pile-up — or bunch — of about 7 photons with wavelengths close to 2.5 one-hundred-thousandths of an inch long (635 nanometers) to carry enough energy to light up the sensors in a human eye.
How much energy is in those seven photons? It is seven times 2E-25 / 635E-9 — in joules, right?
It’s 2.2E-18 joules. Converted to an easier metric befitting its scale, the energy is nearly 14 electron volts, which is equivalent to the energy held in 14 electrons.
People say that photons with wavelengths that measure 635 nanometers create the color yellow-orange in their minds.
There is no genetic code. Not really. Not in the way most people think. Seasoned, sensible geneticists know it’s true.
Unfortunately, a few immature biologists don’t believe it. They are developing “gene drive” technologies that they hope will enable them to reliably and permanently alter a fragment of “the code” in any life-form that reproduces sexually — to guarantee that the altered piece of “code” will be transmitted to the next generation 100% of the time into perpetuity.
NOTE TO READERS:November 22, 2019: This essay is the longest on the website. To help readers navigate, The Editors asked Billy Lee to add links to important subtopics. Don’t forget to click the up arrow on the right side of the page to return to top.
Deployment of gene-drive technology means that an altered fragment of genetic code can be “injected” into a species, for good or ill, which is permanent and will over a few generations become universal — unable to be suppressed or removed regardless of any natural selection pressures whatsoever — until the end of time.
The changes caused by gene drivers takeover every individual in any species that has been targeted for modification. It takes about 10 generations, give or take. With insects, we’re talking a couple of years; plants, a decade maybe; humans, 300 years or so.
Gene drivers are all about changing an entire species forever and permanently — not just one individual with a genetic disorder, for example, or one generation of plants for another. It’s a higher level of intervention than conventional gene therapies and modifications.
A screw-up can extinguish a species in a relatively short period of time is how I see the danger. Worse, according to the scientists cited by the NYTimes, these genes will migrate into ecological niches, where they will force unintended consequences to the biosphere; worse still, given sufficient time “good” genes are likely to jump species, where they will wreak havoc.
EDITORS NOTE: On 18 September 2020 the website science-news service phys.org published an article titled Biologists Create New Genetic Systems toNeutralize Gene Drives.
According to the article:
The first neutralizing system, called e-CHACR (erasing Constructs Hitchhiking on the Autocatalytic Chain Reaction) is designed to halt the spread of a gene drive by “shooting it with its own gun.” e-CHACRs use the CRISPR enzyme Cas9 carried on a gene drive to copy itself, while simultaneously mutating and inactivating the Cas9 gene.
The system can in principle be placed anywhere in the genome.
The second neutralizing system, called ERACR (Element Reversing the Autocatalytic Chain Reaction), is designed to eliminate the gene drive altogether. ERACRs are designed to be inserted at the site of the gene drive, where they use the Cas9 from the gene drive to attack either side of the Cas9, cutting it out. Once the gene drive is deleted, the ERACR copies itself and replaces the gene-drive.
Both systems have been tested in the lab at a molecular level. The developers have not yet demonstrated that a gene drive screw-up gone wild can be pulled back and eliminated by these systems.
The good news is that scientists are working on the problem. The bad news is that the existence of infant, untested technologies might tempt some to release a gene drive into the wild that will ultimately prove intractable.
EDITORS NOTE: On 6 March 2021 the website science-news service phys.org published an article titled New ‘split-drive’ system puts scientists in the (gene) driver seat. The piece describes new split-gene-drive technology that promises to degrade over several generations to permit engineered genomes to evolve under the rules of natural selection. Such a system, if safely deployed, would help to prevent collapse-of-species and other bad consequences when mistakes are made.
If anybody doesn’t understand what they just read, they shouldn’t worry. By the end of this essay, they will fully grasp why the scientists pursuing this course might be dangerously eager to unleash genetic pollutants that may kill us all — because their love of science makes it difficult to restrain themselves.
Virus stands on cell surface. It will soon inject it’s RNA payload into the cell to take control of its genetic machinery.
These smart people (some might be prodigies for all I know) plan to use gene drivers to exterminate vermin and eradicate insect-borne disease, for starters. They plan to make it impossible for agricultural pests to develop resistance to pesticides.
It all sounds great. But so did using the by-products of nuclear bombs as an energy source for our cities. Ask Japan how their state-of-the-art nuclear energy program turned out. Ask about Fukushima.
Gene-drive technologies are an existential threat to the long-term survival of life on Earth — like those tens-of-thousands of plutonium-loaded thermonuclear missiles, which a number of countries have buried a few hundred feet below the surface of the earth.
The warheads on these missiles are going to rot someday, because no one can take care of them forever, and we can’t get rid of them. Their poisons — the most lethal known; a speck of plutonium dust can kill any human who ingests it — will leach into the soils; over thousands of years percolating plutonium will kill everything.
Genes — bad ones (or very good ones that turn out bad; oops!) — genes that can never die; genes that can’t be suppressed by natural selection; genes that are always passed on to the next generation under every conceivable scenario and every possible pairing of mates (no matter how mismatched) present potential nightmare scenarios for any species that possess them. Errant gene drivers can extinguish some species in a matter of a few years.
It is distressing to think that smart, young adults — I can imagine some younger than 35 who possibly lack basic common-sense — does it matter how smart they are? — might right now be playing around with molecules of DNA they can’t possibly understand fully, because the molecules have a quantum side to their nature that can make their behavior unpredictable; even unknowable.
Young adults are messing around with very complicated structures and processes inside both molecules and cells that they can’t see, even with the best microscopes and the most sophisticated instruments. It’s possible that they might — even with the best intentions; the best lab protocols — screw things up big-time and possibly forever. We need maximum oversight over these researchers and the labs who employ them, now — not tomorrow or next year.
Click on this link to an essay in the science journal Nature, which addresses the issue of gene-driver risk and its management. It is written by someone who seems, at least to my mind, to suggest remedies that are insufficiently robust.
Every biologist knows that “genes” have a mysterious way of migrating between species, crossing boundaries, and behaving unpredictably. They have a way of escaping confinement structures. If folks don’t understand why, what are they doing playing around and calling it research?
Editors Note (May 27, 2017):Here is a link to a May 17, 2017 article in Science News about the role of jumping genes in the expression of genomes, which may be of interest to some readers.
People have claimed for years that recombinant DNA pathogens, retro-viruses and yes, AIDS, escaped from rogue laboratories. Does anyone know for sure? If they do, they aren’t saying.
Anyway, I urge readers to relax for now in the knowledge that they are about to learn some amazing things. I did, writing this essay. And please remember: I am a pontificator, not a scientist.
Links are provided to verify anything written in the essays that people may question. My pledge to readers is, as always, to be as accurate as possible and to correct mistakes should I discover them or find myself corrected by others.
Yes, I can be smart and write good too. Well, I’m trying anyway. Getting it right is important. It’s my highest priority. But sometimes I screw up — usually on some arcane technical detail in an essay about science.
Sometimes the science changes and new facts emerge. When I first published this essay in May 2016 everyone thought the galaxies in the universe numbered 200 billion. As I add this note in May 2018, analysis of the latest pics from telescopes in space suggests that the number of galaxies is closer to two-trillion.
My pledge is to keep my essays up-to-date and to learn enough to fix screw-ups that might be caused by simple ignorance. Readers can help fix errors by sending corrections in comments. Errors in the text will be fixed immediately.
So far, we’ve been lucky. The number of errors identified is amazingly few. In one doozy, I published the picture of a well-known British actress (well-known in Britain) and said it was Rosalind Franklin, the X-ray crystallographer famous for making the images that hinted at the spiral staircase structure of DNA.
Celebrities in Europe (that is, in England) were kind enough to take the time to inform me how wrong I was. I appreciated the feedback and was grateful they didn’t kill me.
I’m joking. The Brits are the kindest and best-behaved people on Earth. I’ve spent enough time in London to know.
The genetic code that everyone talks about lives inside tiny spaces; one way to think about it is to imagine that it lives inside little rooms packed to the ceiling with sacks — bitty-bags stuffed full of strung-together bases — hiding in the center of every cell of every plant and animal (or disbursed throughout the cell in the case of most one-celled microbes).
It isn’t a code at all. It’s a reservoir; an inventory; a collection of templates — most broken into pieces; separated and scattered among the dozens of spiral tentacles in the vast aperiodic-crystal known as DNA.
DNA isn’t exactly a crystal either; not really. Crystals are structures made from regular (periodic) arrangements of molecules. DNA, on the other hand,isa molecule, and it is constructed from strings of chemical bases. It’s found in bundles alongside other DNA molecules. These bundles are called chromosomes.
During part of a cell’s life cycle these DNA strings can sometimes be found tightly wound around little pieces of protein like fishing lines around spinning-reels. It’s a configuration that makes them compact; less intrusive — but easier to see under a microscope when they have been stained.
Inside any particular cell each chromosome of DNA is in some ways a little like a snowflake; within a single cell, no two chromosomes are the same; no two are alike, not even close. But every cell in the body contains the same group of chromosomes; the chromosomes in each body-cell are identical to the chromosomes in every other body-cell, right? It’s not hard to understand.
Bases, by the way, (in case someone might be wondering) are chemical substances that turn into salts when acids are poured over them. Many bases exist in nature, but only four (nucleobases) are found in DNA.
These four bases are essentially one or two rings of nitrogen and carbon atoms with ammonia and vinegar-like side chains attached. Here are links for anyone who wants to look them up: adenine – thymine ; and cytosine – guanine.
A fifth base, uracil substitutes for thymine in RNA, which is a vast assortment of short, single-stranded, DNA-like segments — the cell’s worker-ants who enable cells to perform their many functions. RNA builds genes, moves stuff around, and dramatically speeds up cell chemistry by catalyzing thousands of processes.
Not to digress, but NASA found uracil on the surface of Saturn’s moon Titan in 2012 during a fly-by. It’s something to wonder about.
Caffeine is molecularly similar to the bases adenine and guanine. Bases taste bitter — like the caffeine in coffee. Acids, on the other hand, taste sour — like vinegar. Combine bases and acids (bitter and sour) chemically to make salts, which are substances that taste like the ocean.
This tangled mess is one-celled life, highly magnified. It is varied, imprecise, and invisible to humans. It takes about ten of these microbes (which are about the size of human red-blood cells) to span the width of a human hair; 30 to circumnavigate it. DNA is far smaller. It requires 8,000 tightly wound DNA bundles to span a human hair; 800 to span the length of one of these microbes.
Forgive me for starting simple. Life-sciences are the most complicated sciences of all.
What adds to the difficulty is that in most animals (and all people) the DNA involved in sexual reproduction is configured differently than the DNA in body-cells. It exhibits behaviors a little less like those found in other cells.
In this essay we are talking about animal DNA, usually human, in body-cells — somatic cells; and we are talking about protein production.
A single DNA group inside certain humanbody-cells like liver cells and stem cells (while they undergo the process of replicating and dividing) is composed of ninety-two large molecules called DNA strands, which together warehouse the six billion base-pairs that will populate the genomes of two daughter cells.
During the short-lived interval when cells divide and replicate, dozens of molecules and billions of bases gather themselves into the configuration of chromosome-pairs peculiar to people, which some of us learned about in high school biology.
Most of the time (90% of it anyway) DNA doesn’t divide and multiply; it doesn’t organize itself into easy to recognize chromosomes; in all body-cells except stem cells and liver cells, DNA is the starting material for the making of proteins instead.
Making proteins is the only thing most body-cells do; it starts in the DNA molecules and is the subject of this essay. Cell division and replication is what stem cells do. Links will lead to those subjects for any who might want to learn more.
This essay is not about stem cells, which develop into any and every kind of somatic (body) cell and germ (reproductive) cell. As a pontificator who is not an expert on stem cells, my understanding is that — except for liver cells — somatic cells in mature adults don’t generally divide and reproduce themselves. That function is performed by stem cells, which start at conception and continue through life to replenish the human body.
Stem cells live inside the tissues of adults like seasonings inside cooked beef, is how I imagine it. Check me on this one, experts. Correct me in the comments section. All others read this link on cell differentiation first.
The main point is that human body-cells house 46 chromosomes (called chromatids when they are organized into 23 connected pairs), which contain six billion base-pairs. Reproductive (germination or germ) cells contain 23 unpaired chromosomes that store three billion base-pairs.
Confusing terminology constructed from the Greek language can create stumbling blocks for non-scientists, so I’m reluctant to go there. Terms like diploid, haploid, gamete, and zygote folks can look up and explore on their own. There’s enough that’s fascinating in English. Only tiny, digestible Greek lessons — sparsely sprinkled — will appear in this essay.
Besides unfamiliar vocabulary, another hard concept to grasp is this: inside every animal cell (and plant cell) are hundreds of DNA packed bundles (called mitochondria), where the DNA is not like the DNA in sex-cells or in body-cells either. The DNA in mitochondria matches what one might expect to find in another as yet undiscovered species of bacteria. It’s “coded” differently.
Yes, it’s weird, but there are explanations.
Most scientists today believe that a long time ago cells engulfed bacteria; these foreign migrants from another world (in terms of scale) were simply unable to escape.
Bacteria are small. A thimble-full of dirt can contain 50,000 species. It is amazing to learn that millions of species of bacteria exist in the soils and on the surfaces of plants on the earth.
Thirty-percent of cells in the human body are bacteria. They don’t weigh much, because they are small. It would require as many as 10,000 individuals of some strains to match in size just one of the microbes displayed in the illustration a few paragraphs above.
On average, though, a typical cell in an animal or plant can be visualized as having about 4,000 times the volume of a typical bacterium. The range of volume ratios varies widely, of course. Nothing is simple, especially in biology. Enough said.
Scientists named the trapped bacteria-like life-forms inside cells, mitochondria, afterthe Greek words for threaded granules; these granulesmake the cells they inhabit more robust, because they act like little batteries, boosting the energy in their adopted homes to help power the many tasks that cells do. Click the video link above for an animation by Harvard University that shows how it works.
Click the link above for an easy-to-understand animation of the overall structure of cells; or this link for a YouTube Video designed to transport viewers through an imaginary, animated world that makes real the complexity of a working, living cell.
And here is a link from Wikipedia, if anyone is confused about the numbers of bases and chromosomes in humans, as many folks seem to be, including myself, sometimes.
It’s confusing, because there are different “codes”, different cell-cycle phases, different collections of DNA molecules in body, germ, and stem cells — and I haven’t even mentioned enzyme catalysis or polymerases (and I’m not going to, either — not just yet anyway — because it will open a big can of worms I don’t want to deal with right now).
Don’t worry, we’ll get to some of it later after I’ve laid a little scaffolding.
But let me say this: without all this complexity, life forms as complicated as human beings would be impossible — codes or no codes.
The tools most people use to do science, especially physics, generally depend on mathematics and rigid, predictable rules. The life-sciences aren’t like that; not at all.
Should my essay devolve into complexity, readers are free to bail. I’m going to try to keep the mysteries of DNA understandable to non-technical people. Who knows if I’ll succeed or not?
DNA can be thought of as a collection of pouches or bags stuffed with billions of copies of four basic substances, called bases. DNA is like a roomful of holiday bags, each filled to the brim with four different kinds of unfinished toys like the ones in Santa’s workshops before Christmas.
Each of the four kinds of toys are strung together in-line, one after the other — in no discernible order — in long, tangled spirals. These spirals are unimaginably long, and there are many dozens of them.
The toys in the DNA sacks are unfinished, unpainted, and undecorated. They really don’t look much like toys at all. In this analogy, the four bases might be imagined as four simple blocks of wood, each a different shape and size. And like I said, there are billions of these blocks, at least in human cells.
Is DNA a big molecule? Yes, I already said that it was. It’s huge. But good luck to anyone who tries to find one. Good luck to anyone who tries to look at one. No one has ever seen any molecule. No matter how large, molecules are too small to see, even with microscopes; and that includes DNA molecules, the largest and most complex molecules in biology.
It takes a combination of high-energy light, amplification, and computer-generated algorithms to produce useful pictures of what scientists think molecules look like. A computer-generated image is not the same as a brain-generated image stimulated by the act of looking at reflected light with a pair of human eyes.
X-ray crystallography was the technique used first to unravel clues to the structure of DNA. From the data collected by crystallography, Linus Pauling shared in 1951 compelling ideas about what he thought the structure was, but he turned out to be wrong. He got protein structure right, but his description of DNA had subtle errors. A few years later, others came up with a structure that has thus far stood the test of time.
In soma (body) cells, forty-six molecules (strands or bags or sacks) of DNA contain the six billion base-pairs (or blocks) of the human genome. Most of the time these strands are loose and disorganized; a diffuse mass of hard-to-see chromatin. (Their form depends on what part of its period the cell cycle is in.)
It has to be this way for the worker elves of the cell to gain access to the bases (the unfinished toy blocks) upon which they will do their work. Only during the process of cell division do these forty-six molecules bind together and curl-up into the twenty-three chromosome-pairs that some readers may have learned about in high school biology class.
Researchers have technologies that can amplify what DNA molecules reveal, which they manipulate with computer algorithms to form fuzzy pictures that are helpful to highly trained analysts; but it’s the best they can do, visually.
An early theorist, Erwin Schrödinger, (one of my heroes) said in 1944 — before anyone knew what DNA was — that it must be an aperiodic-crystal. He gave a series of lectures, which later became the famous booklet, What is Life? It can be purchased for fifteen bucks on Amazon.com.
Schrödinger’s booklet changed the world — it’s one of the most prophetic works I’ve ever read. The tract changed my world view anyway; my view of life certainly.
It turns out, Schrödinger was right. DNA bundles store billions of bases in more-or-less random — but frozen — sequences much like crystals.
Just as molecules arrange themselves inside crystals, the bases inside DNA molecules also have an order, yes, an arrangement for sure, but it’s not a code; it’s not even a cipher; it’s merely a starting point for the most chaotic, complex, and messed-up process in nature — the creation of thinking, speaking, conscious-life (and less capable life) — all formed from a relatively few not-so-simple materials.
Here’s another assertion that might be difficult for some readers to accept. Genes don’t really exist. There are no free-standing genes; certainly not in human DNA, anyway. What scientists call genes must be constructed; they must be built; they must be put together; they must be fabricated, collected, and transported by molecules called RNA and by other processes known collectively as epigenetics. More on epigenetics later.
(Click on this old graphic (from 2004) to get a clearer view.) This illustration is a simplified representation of the chaos going on during arguably one of the simplest of the processes (transcription), which is the starting point for encoding other processes (called translation) that will ultimately lead to the fabrication and folding of proteins.
Most graphics and videos on the Internet seem to buy into a tidy notion that DNA is a code (not a reservoir and a starting point for the fabrication of templates). This notion seems to demand laser-precision and machine-like twelve-sigma reliability during protein synthesis.
Don’t believe it.
Yes, there is no argument; we can improve our chances for healthier lives by cleaning up less-than-optimal base-sequences — which are, as often as not, scattered, scrambled hodgepodges — using, hopefully, gene therapies like CRISPR. (Clustered Regularly Interspaced Short Palindromic Repeats)
But until technicians create tools to deal with other processes; until biologists can manipulate RNA itself and learn to change the ”weather” patterns (discussed later) inside cells, physicians will not be able to eliminate many of pathologies that plague our species and lead to diminished health and, for some, death.
RNA in all its forms (and there are many) is itself constructed from scattered templates that are hidden haphazardly like Easter eggs within the billions of bases strewn along the dozens of spirals inside a DNA bundle. RNA first builds itself up by interacting with various sections of base sequences in the DNA and then copies those sequences by borrowing matching freebases, which are floating everywhere in the medium of the cell’s nucleus.
RNA is much shorter in length and less stable than the DNA it models. But it doesn’t mutate as much as folks might expect, because it is also shorter-lived and reproduces less often. It’s more versatile too; more agile, because it is single-stranded; DNA is double-stranded.
RNA, in all its forms, is the workhorse of cell functions; it is both the building material and the construction machinery used in many important cell structures, which perform the yeoman’s task of protein building inside cells.
It seems plausible to me that over a few hundreds-of-millions of years the possibly self-generated RNA sequences may have acquired — through accident, luck, or trial-and-error — the ability to select, copy, paste, and assemble short sections of random DNA bases, which every-once-in-a-great-while actually worked to help build useful proteins that added survival advantages to their evolving hosts.
Maybe RNA designed and built DNA in the first place, which it learned to copy and manipulate. We may never know exactly how.
One thing scientists agree on: one-celled life was already highly developed, complex, and flourishing by the time the new planet, Earth, reached its first billionth year. Earth is four-and-a-half billion years old. Life came on fast during extreme conditions vastly different than now. This fact is amazing. No one understands how.
It has taken an additional three-and-a-half billion years to get to humans and the space-traveling civilizations that seem to dominate the earth today.
Thinking about RNA and DNA can be a frustrating circular process, much like the chicken or the egg problem; which came first? My sense is that most scientists today believe RNA came first, DNA later. Inside our cells, it is impossible to tell, but there is no denying that RNA’s diversity and flexibility make it a most likely candidate.
Many kinds of RNA live inside cells. Some run around doing nothing. They simply try to survive inside the complicated universe that is the typical living cell in every animal, plant, and microbe. They are called selfish RNA.
Most RNA sequences are much less selfish. They are like Christmas elves who work day and night; some to open Santa’s bags to gain access to their contents; others to copy various sections from the strands of blocks inside; others to move the copied sections to an assembly area, where other elves glue the copied segments together to form new sequences — many of which, by the way, are very different from the original sequences that the RNA elves found inside Santa’s gift bags; inside the DNA.
Eventually, messenger elves transport the long strands of little blocks they copied and assembled; they move them away from the center of the cell; out to the gooey regions of the cell beyond its center where other transfer elves are busy assembling (by threes) free-floating blocks (called bases, remember) and attaching these triplet-blocks (called anticodons) to single amino acids. The resulting structures are called transfer RNA (or tRNA, for short).
An amino acid is simply a configuration of carbon atoms with amine (ammonia) stuck to one side and carboxylic acid (vinegar) stuck to another — plus some other simple stuff attached here and there to make each amino acid unique among all the others. Think of an amino acid as a colored necklace bead. Out of the five-hundred or so differently colored beads in nature, transfer elves in humans work with only twenty or so.
Stay with me now. You just read the most difficult sentence in the essay. These amino acids attach themselves like colorized necklace beads to triplet-blocks (called anticodons) according to which of the three blocks (or bases) the transfer-RNA (tRNA) is made from. Watch the video ”From DNA to protein” above to better understand.
In the meantime, while all this other stuff is going on, the messenger elves are directing their long strands of copied-and-pasted blocks (bases) away from the cell’s tiny nucleus (center) toward little triplet-body-handling factories (called ribosomes; ribo for triplet, soma for body), which live in the inner goo (the cytoplasm) of the cell.
Many ribosomes are attached to a winding ribbon-like structure called the rough endoplasmic reticulum. Endo is Greek for inner; plasma is goo; reticulum means network.
At the same time, transfer elves in the goo (cytoplasm) steer their three-blocks-plus-a-colored-beadassemblies — in humans these “three-base” combos and twenty or so colored beads can be arranged forty-eight ways — into the ribosome factories, where they are matched-up to the blocks (bases) in the long strands that are being delivered from the cell’s nucleus (like cars in a choo-choo train) by the messenger elves.
Inside the ribosome factories, the triplet-blocks-plus-one-colored-bead assemblies, which have been constructed and collected by the transfer elves in the cytoplasm, are paired block for block (that is, base for base) to the long train of blocks that were collected, arranged, and carried by the messenger elves from the cell’s center (its nucleus).
As each transfer assembly triplet is matched-up three bases at a time to the blocks in the long messenger train, the single amino-acid bead that the three-block transfer assembly carries is ejected out of the ribosome factory.
Assembly elves — think of them as molecular forces — secure each ejected amino acid bead to the next bead, one after the other — in the exact order demanded by the order (in threes, called codons when located in the messenger RNA) of the bases (blocks) in the messenger sequence — creating as they go an amino-acid-chain, or necklace.
Once the amino acid chain (necklace) is long enough (and remember: there can be as many as twenty-three different colors of amino-acid beads in each necklace, and each necklace can be almost any length at all — up to hundreds or even tens-of-thousands of beads long) elves (molecular forces that work through the micro-scaffolding of the cell) go to work; they transfer the chains to Golgi structures, where they are bundled and folded into the twisted shapes that make them proteins. Like an Amazon distribution center, the Golgi apparatuses deliver the proteins to their destinations.
Like holiday elves, they deliver protein toys to every child’s bedroom in the cell, which in this analogy lie inside the abyss of the cell’s cytoplasm (cyto means cell; plasm means goo).
Some elves might feel compelled to deliver their proteins down the street to other homes (cells) in other neighborhoods by way of certain processes known as cell migrations.
These migrations can bring healing to injured tissues in other parts of the body, among other benefits. However, as I wrote earlier, stem cells that live inside the tissues of the body do the heavy lifting of cell replacement and healing.
Here is a way to visualize a human cell: think of cytoplasm (the cell goo) as the yolk of an idealized egg. A chicken egg is nothing like a human body-cell, but it makes a good model for explanations.
(Click on pic to enlarge.) This drawing is an idealized view of a typical eukaryotic cell, which in this essay is compared to the yolk of a chicken egg. The egg-white is the thin plasma membrane.
The nucleolus (at the epicenter) is a tiny, hard to find collection of proteins, RNA, and DNA at the very center of the nucleus where ribosomes are fabricated, if anyone wonders.
Ribosomes are made entirely from RNA; they are, in fact, one of the most ancient structures in cells; they are essential players in both prokaryotic and eukaryotic (ancient and modern) cells, which I will discuss in more detail soon.
Chromatin (the usually unorganized mess of DNA) lies in the nuclear goo of the nucleus that surrounds the nucleolus.
Remember that ribosomes are the tiny factories, where proteins get their start. Ribosomes themselves move between the nucleolus and the surrounding nuclear goo until they are ejected out of the pores of the nucleus into the goo of the yolk (which in this analogy is the cytoplasm) where many will float freely in an ocean filled with a dozen or more other structures important to cell functions. Many ribosomes attach themselves to the endoplasmic reticulum.
But we’re not concerned about these other structures right now. Proteins are the most essential substances from which our bodies are made.
Some biologists believe that as many as 50,000 different proteins are required to construct a human being. Others say 100,000. The human body is capable of producing two million. Each cell type on its own is capable of making 5,000.
Ribosomes are very important, because it is inside the ribosomes where proteins get started, so we concentrate on them first.
Think of the cell’s membrane as the “white” of the egg. It surrounds and protects the vital cytoplasm, where the making of proteins takes place.
Of course, the chicken egg analogy had to break down. A chicken egg is surrounded by an oxygen-permeable calcium carbonate (CaCO3) shell. Forget about the shells of chicken eggs. Human soma-cells aren’t protected in quite the same way.
In a chicken egg the nucleus is a little white mass that sits on top of the yolk and feeds on it. The nucleolus is inside that little white mass. So the breakfast-egg analogy falls apart pretty darn fast. It might be more confusing than helpful. I hope not.
A lot more is going on. And — I have to say this — the cells of most microbes (one-celled life, like bacteria and archaea) don’t look like the sunny-side-up cells of humans or most other animals and plants. For one thing, they are a lot smaller.
Bacteria and archaea can be from 20 to 10,000 times smaller than the eukaryotic cells of animals and plants. They lack membrane-bound organelles; they lack a nucleus. They look more like little sandwich bags of loosely cooked, scrambled eggs. Scientists call them, prokaryotes. (It’s Greek, meaning before they became fully formed kernels.) They are the ancient cells.
As for the other structures that live inside our own eukaryotic cells (again, it’s Greek, meaning after they became kernels) — they make a fascinating study, but are beyond the scope of this essay.
Eukaryotes are the modern more advanced cells of all plants and animals. It took two billion years for ancient prokaryotic cells to evolve to the modern eukaryotic cells that first appeared 1.5 billion years ago; it is these cells that congregated and evolved to become the plants and animals of today. Click on the links in this essay — such as the links in nearby paragraphs — to access Wikipedia articles, YouTube videos, and other sources to learn more about them.
Phosphoric acid, which people have used for centuries to remove rust and to fertilize crops makes the DNA supports (or strands) on which hang the rungs of billions of bases. Phosphoric acid is the concentrated, clear syrup that makes Coca-Cola sting the tongue (carbon-dioxide bubbles make Coke sparkle). It’s the acid found inside the nucleus of every cell.
Apatite crystal from Mexico.
Hundreds of years ago phosphoric acid was made from the stone mineral apatite (calcium phosphate) and sulphuric acid — by-products of the mining and smelting of ores. Today the production process is more arcane and efficient.
Phosphorus is arguably one of the most important elements of life. Only magnesium is more important to viability, because the ATP that powers all cells will not work unless it is bound to it. Folks who aren’t eating whole wheat, spinach, black beans, almonds, and peanuts should probably be taking a daily magnesium supplement.
People who eat steak consume goodly amounts of phosphoric acid. Early researchers always found this acid in the center of cells, their nucleus. Scientists called it, nucleic acid.
Much later scientists discovered that the DNA sacks were full of bases, crammed together into tangled masses of long, curly chains they called chromosomes (Greek, for coloredbodies).
Chromosomes stained well during lab experiments, which was fortunate for researchers, because color made it easier to see the chromosomes during the short periods of time when the genetic material in the cell’s center took on its distinctive form from out of the shapeless, invisible chromatin, where it lived.
It is by a curious twist of chemical engineering — to my mind, at least — that the bases don’t react with the phosphoric acid that anchors them. The DNA molecules don’t collapse into little piles of salt, like one might expect. Maybe they should; but on Earth, they don’t.
In this sense — the sense in which our DNA is made from acids and bases — we are salt, or could be; we are potentially a very complicated salt, yes, but a salt nonetheless.
A strong argument can be made that proteins and the polypeptide chains that make them are in fact salts. For reasons known only to biochemists, naming conventions hide this reality.
Amino acids, polypeptides, and proteins are thought of as inner salts and given the name zwitterions, of all things. Salt is at the heart of what and who we might become were it not for idiosyncrasies of nomenclature and the miracle that makes life live.
But to get back to phosphoric acid…
Phosphoric acid (phosphate) sacks (or strands) are loaded with toy blocks (bases), so they need something sticky, like sugar, to keep the blocks from falling out. The D in DNA stands for the sticky stuff — deoxyribose, which means sugar.
This simplified graphic shows sticky sugar (deoxyribose) securing the phosphate rails of a DNA strand to the only two kinds of base-pairs found in DNA — thymine / adenine and guanine / cytosine. The sugar, deoxyribose, forms both a link and a buffer between the acid and the bases; otherwise, the molecule would collapse to become a salt. DNA breaks down completely at 374° Fahrenheit, which is just 72° above the melting point of table sugar. An interesting comparison is the melting point of table salt, which is 1474°F.
DNA is deoxyribonucleic acid.
The sugar and acid, together, form the rails of the famous spiral staircase, upon which the rungs of bases are hung. It’s the most incredible structure in nature. It’s called the double-helix. Some people named Watson, Wilkins, and Crick won a Nobel Prize for figuring it out.
To give readers a sense of scale: If someone were to take the longest strand of the double-helix in our DNA (it’s in chromosome-one) and somehow increased its diameter to one-inch (the thickness of a large garden hose), the DNA strand — when pulled straight — would increase in length to 567 miles (about 40 miles longer than the distance between Nashville and Detroit).
The bases (or toy blocks, as we’ve been calling them) would stack in pairs, eight-pairs-to-the-inch, along the entire 567-mile length of the hose. In this single chromosome, each of the nearly half-billion bases it contains (in 247,199,719 base-pairs) would be about the size of a Tic-Tac breath mint; maybe a bit smaller.
At normal scales, the dimensions are too fantastic to believe. A solitary strand of DNA can’t be seen, even with the aid of most microscopes, but if all the DNA in a single cell could be laid out end to end and flattened to remove the kinks, it would stretch to six-and-a-half feet. 6.5 feet is the length of all the DNA in a typical human cell.
According to Siri, 1E14 cells make a human. It’s “one” followed by 14 zeros. It’s 100 trillion. Other sources say no; the number of cells in a human being is between 15 and 70 trillion. A trillion has twelve zeroes, right?
Do the math. It will show that all the DNA in a single human is enough to spin a strand from the earth to the sun and back 99 to 662 times (which is somewhere between 198 and 1324 astronomical units, right?) depending on who is trusted to do the human cell-count. Does anyone believe it?
An astronomical unit (AU) is simply the distance from the Earth to the Sun. It is the distance traveled by light during 499 seconds, which is 8 minutes and 19 seconds. It’s close to 93 million miles, right?
The point is this: strands of DNA are too thin to see, but in humans their total length is on an astronomical scale that spans two-and-half to sixteen-and-a-half times the diameter of the solar system out to Pluto — a diametral orbital distance that is nearly 80 AU.
It’s a lot of DNA, even if the exact amount is uncertain.
Rosalind Franklin (1920-1958). Franklin received her PhD from Cambridge University at age 25. (Her thesis: The physical chemistry of solid organic colloids with special reference to coal.) Franklin spoke several languages, which opened opportunities for her to work in France, where she acquired the skills in X-ray crystallography that enabled her to advance the world to a new understanding of viruses and the molecules of life — DNA.
Rosalind Franklin, the gifted X-ray crystallographer, who did the experimental research that led to the discovery of the double helix, died of ovarian cancer at age 37. The Nobel Prize Committee has a long-standing policy of not awarding prizes to people who have died. It’s why Irish physicist and mathematician John Stewart Bell didn’t receive a prize for his civilization-changing work on quantum-entanglement, after he suffered a brain hemorrhage and perished in 1990.
In Franklin’s case it was doubly sad, because she was also doing important work on the molecular structure of viruses related to polio (funded by the United States Public Health Service) when cancer overtook her. Once again another scientist — this time her partner, Aaron Klug — received the Nobel Prize that she might have shared.
Had Rosalind Franklin survived to receive two Nobel Prizes — one for her work on the double helix and the other on the structure of polio virus — she would be a household name, like Albert Einstein or Francis Crick or Jonas Salk.
Rosalind lived in a generation and a culture that devalued her; she was a woman who competed with men, some of whom may have undercut her and wanted nothing to do with her, a few admitted. It was a different time, the 1950s. Who knows where the truth lies?
For Franklin, fame-and-fortune wasn’t to be. Blame cancer, a disease of the “genes”, which she sacrificed her life to understand by working daily with the deadly X-rays that helped her unlock the secrets of viruses and, most important of all, to finally pull aside the opaque curtain that was hiding the shape of the molecule of life: DNA.
Once the structure of the double-helix became known, the potential to store information in a molecular bundle constructed like DNA was immediately recognized — and it appeared to be unlimited. It is why everyone at first thought that the DNA molecule must be a code, like an old-fashioned computer tape.
I’ve suggested that DNA is not a code; neither is it a cipher. Some researchers view DNA more as a storage device and a starting point for processes — complicated processes — that have taken place inside every living cell for 3.5 billion years.
Yes, a group of three bases and an attached amino acid, properly transformed and manipulated by RNA elves inside little protein-making workshops called ribosomes, can help to fabricate and string together colored beads to make necklaces (chains). Chains of amino acids (polypeptides) — properly ordered and folded, again by RNA elves — can become proteins.
Scattered DNA base sequences inside a cell’s nucleus, its center, are a starting point for an involved and complicated process of selection, duplication, transformation, and fabrication before anything useful can happen; before proteins can be built and released for living.
To think realistically about life, especially human life, people should remind themselves that two-thirds of their bodies is water; two-thirds of what’s left is protein; the rest is mostly fat.
The interior of a cell is a complicated space. The space between cells is other-worldly.
The process that goes on inside cells, instead of being thought of as a precisely executed computer code, might better be compared to the process of weather found on every planet in the solar system.
Each planet can be identified by its surface weather, which starts from a kit of basic materials, and is amplified by an avalanche of environmental conditions and chemistries, much like the bases in chromosomes, which are selected, copied, shaped and reshaped, configured and reconfigured by RNA elves and other characters we have yet to meet (because the science of the evolving genome — the genetic material — and the phenome — what animals and plants look like — is still young, and scientists understand less than the little they think they know about the complete process, at least so far).
The processes used to construct life forms by starting with the bases in DNA are analogous to the processes astronomers observe on the planets of our solar system, where each planet creates its weather from the matrix of materials and thermal conditions that seems to define it. Each planet in the solar system has a characteristic weather profile that depends on a chaotic interplay of materials and environment unique to that planet.
Earth has weather; so does Mars and Jupiter. Those who study planets know immediately which planet is which, simply by observing its weather. From telescopes on Earth, each planet looks like its weather. Each has its characteristic colors and patterns. Weather is a planet’s phenotype; it’s what folks see when they look.
This mammoth storm on Jupiter looks eerily like structures that are found in living cells. The inset is planet Earth, shown for scale.
That’s how it is with life forms, too. Each life form is the result of weather patterns inside cells, which give each animal, plant, and microbe its unique essence; its physical presence in the larger world where it lives.
It becomes conventional wisdom to think this way about life forms, when one considers that identical twins — two humans who share exactly the same DNA — always display a variety of differences when examined closely.
Identical twins never have the same fingerprints, for example. There are systems of weather occurring around their genetic material in every protein-producing region in their bodies. Epigenetics is the technical term for the study of how it is that variations in phenomes occur in organisms that have identical genomes — that is, identical gene sequences.
Click pic for larger view in new window. (from Wikipedia article, Epigenetics)
The outcomes of these storms are never the same; two supposedly identical children do not always receive the same toys from the RNA elves who rummage through their shared bags (strands) of DNA for the bases they will copy and rework into proteins. Things get mixed up and turned around. One toy gets selected; another doesn’t; one is painted green; another purple.
What I find interesting is this: identical twins get less identical as they age. They are easier to distinguish.
How many of the differences are due to variations in the production of proteins, which occur at the molecular level?
How much of the variation is induced by external stresses on the genome caused by lifestyle differences? How much is driven by an unavoidable drift in the statistics of protein production, which emerge and diverge over time in each phenome of the twins regardless of their lifestyle choices?
An animal cannot be constructed from its DNA alone. RNA elves — millions of them, like colonies of ants — must do their work.
It’s a chaotic process that produces life on the earth. It’s a process that cannot be described or predicted by mathematics. If it could, scientists might take the DNA from prehistoric bones to create the original animals. Jurassic Park would be more than a Hollywood fantasy, which is what the book, movie, and sequels were and are.
An animal cannot be constructed from its DNA alone. A lot more is required than a simple collection of sequences formed from four bases and frozen in a molecule of DNA. A lot more of life’s machinery is required. The RNA elves — millions of them, like colonies of ants — must do their work.
When the work is done, and a protein has been made and delivered, the path back is lost, forever. No way exists — or is even possible — to reconstruct the sequence of bases in the DNA that started the process that built the protein. The process is not backward compatible, according to Matthew Cobb, the British zoologist and historian, in his latest book, Life’s Greatest Secret. Not only are the DNA sequences not reachable from knowledge of the proteins alone, but the processing steps that took place between the protein and the DNA are unknowable.
I don’t want to get too Mathy but think about this: sixty-four three-block (or three-base) sequences can in theory “code” for a mere twenty or so amino acids. It means that as many as three or four of those three-base sequences (the transfer elves we talked about earlier) can “code” for the same amino acid.
Reminder: four bases are all the choices DNA offers. Taken three at a time, they are more than enough to “code” for twenty or so amino acids. Get out the calculator, those who don’t believe it. 4 X 4 X 4 = 64. As mentioned earlier, humans have acquired over the eons 48 three-base combinations to work with. Bacteria, for another example, have 31 according to Matthew Cobb. We need less than two dozen.
Amino acid sequences long enough to form proteins can be hundreds to tens-of-thousands of acids long.
Forget about how amino acid chains get folded properly to make proteins. How can anyone work backwards from a protein formed from thousands of amino-acid beads — each one of which was secured to any one of three or four different 3-way combinations of bases (or blocks) — and then go about the task of reconstructing from all those possible combinations the exact sequence of bases (or blocks) in the original DNA, which more than a few random RNA sequences interacted with to make their choices from billions of bases in the first place?
Take a breath. There isn’t enough time in the history of the universe to figure it out for the tens-of-thousands of proteins that it takes to make a functioning animal or plant.
Raise the number “three” (or four, or five, or six, or two; it doesn’t matter) to the thousandth power on a calculator, those who may be having trouble accepting a possibly demoralizing fact. Most calculators will spit out the word, OVERFLOW. The number of possible sequences is impossibly large. It might as well be infinite.
This is the genetic code. I guess I should show it. (Click the pic for a clearer view.) A lot of folks worked on it; it was a pinch point; a roadblock that once slowed progress toward the understanding of what makes life live; how cells behave. Now that it’s known, is anyone sure it is the only code? The answer is, no. Variations have already been found in nature — at least 15 so far with more expected as researchers continue their work.
It seems likely that the ”code” has changed in dramatic ways since the first primitive cells formed 3.5 billion years ago. British zoologist, Matthew Cobb, has suggested that words like ”code” and ”information” might better be thought of as mere metaphors when applied to the machinations of complex molecules like DNA and RNA, which — can we admit? — operate on quantum scales for which we humans have no natural intuition.
There are thousands of chains of all different lengths and folding patterns. No one is going to reverse-engineer the DNA of a life-form as complex as a human being from its proteins; nor from its RNA elves; nor from its essential enzymes and catalysts; not anytime soon; not ever. It goes for dinosaurs, trees, or any other reasonably complex living thing — now or from the distant past.
Why do we have to reverse-engineer? Why not read the instructions right off the DNA itself? By now most readers must be starting to understand that the sequences necessary to build proteins are scattered among billions of bases. We can’t find the right ones in the right order. It’s not possible; not for creatures as complex as humans or dinosaurs.
Even if someone could reverse-engineer DNA sequences from proteins, how would they construct and organize the ant-like colonies of RNA elves that must sort through the DNA bases to select and build the right sequences; how do they identify and isolate the sequences necessary to build and orchestrate, for example, the tens-of-thousands of enzymes that are required to give researchers any chance at all to build a functioning human-being or even a prehistoric dinosaur?
It gets more complicated.
Those who don’t believe it might want to read about CNVs, or copy number variations, that disrupt the probabilities that certain base-sequences in genes can be fabricated in the same way time after time. Click the link.
It’s a form of change that has nothing to do with mutations or inheritance. It is more related to the untidy mess that three billion base pairs make whenever they get together to do anything at all. It’s a genetic Woodstock of variation, where almost anything can happen and sometimes does.
Now might be a good time to mention that there are virus infections that can alter the DNA in cells. These viruses are called retroviruses, because they reverse the DNA to RNA transcription process described earlier by introducing an enzyme into the cells they infect. This process is disease producing — it causes cancer — and destroys the host animal (or person) if left untreated.
The enzyme, reverse transcriptase, has become a tool that molecular engineers now use to modify organisms in experiments. Enough said. The weeds of molecular biology grow thick and deep.
This is the inverse genetic code. I might as well show it, too. (Click the pic for a clearer view.) Tables like this one make the ”code” appear to be comprehensive and far-reaching. Some readers might be surprised to learn that only one or two percent of the bases in human DNA are ever copied by RNA to make proteins.
Tables like the one above make the ”code” appear comprehensive and far-reaching. Some readers might be surprised to learn that only one or two percent of the bases in human DNA are ever copied by RNA to make proteins.
Added to 2% for protein synthesis is 8% to make little pieces of RNA that oversee and coordinate the process of protein-making — like colonies of swarming ants. The rest of the bases (90%) do other things; maybe — many of them — do nothing at all. No one is really sure what they do or don’t do.
Geneticists used to believe they could clone animals from their DNA sequences alone. Yes, there once was a cloned sheep named Dolly. Some readers may have read about her.
After many heart-breaking failures, researchers managed to take the DNA from the mammary gland of one sheep, inject it into the nucleus of an egg from a second sheep, and implant this DNA cocktail into the womb of a third. By some miracle, Dolly was conceived and born, on July 5, 1996.
Dolly (5 July 1996 – 14 Feb 2003). Pic by Tony Barros, Sao Paulo, Brazil.
Sheep live twelve years, on average. By Dolly’s fourth year arthritis crippled her. At year seven researchers euthanized her; she had developed a chronic and incurable lung disease.
Dolly was the recipient of arguably the best healthcare any sheep ever received in the history of veterinary medicine. She didn’t do well. Click this link for an update on the Dolly research.
For the sake of complete accuracy, permit me to admit that no one I know clones sheep anymore. There are too many failures. The failure rate for clones is right around 100%.
Some breeders claim to clone horses, which they sell to folks who hope to increase their odds of winning races. I can argue that their definition of cloning differs from science, and the proof is that the horses have noticeable differences which negatively impact their ability to win.
Clone researchers, as far as anyone knows, have never used DNA alone, anyway. All borrow the enzymes, RNA, ribosomes, and other cell structures of other life forms to incubate the DNA they play with to try to create “artificial” life.
Mitochondrial DNA is unreachable. It is produced only in the ovum of the female. Mitochondrial DNA carried by sperm is miniscule in amount and quickly identified and destroyed in the fertilized egg.
Any technique that involves in vitro fertilization can bypass this natural process and inadvertently scramble the DNA in mitochondria. It can be debilitating, even disease producing.
Any technique that swaps out nuclear DNA while avoiding mitochondrial DNA doesn’t get to the power source of cells — a major enabler of stamina and endurance. In racehorses, the role of mtDNA is probably crucial, it seems to me.
My point is that duplicating a DNA sequence is not enough to produce an identical copy of an animal as complex as a sheep, horse, or human. Too much other stuff is going on during reproduction that is not controllable or even known.
And speaking of enzymes, can we please not go there? I’m reminded of Chris Farley in the 1992 movie, Almost Heroes.
Does anyone remember?
His tutor asks him to learn the symbol for lowercase A. ”What do you want from me?” Chris bellows while rolling his eyes and clawing his hair. ”You want my head to explode?!”
Well, no, of course not. But for those who have to know more, why not push ourselves just a little bit harder? May I point out the obvious? Enzymes speed up chemical reactions. A chemical reaction that might under normal circumstances take years can be reduced to milliseconds by an optimally configured enzyme.
Some enzymes are made from RNA; most are proteins; in fact, most proteins are enzymes; they all get their start from sequences of bases hidden deep within the mountains of DNA inside our cells. These bases are selected, copied, and transformed into their many convoluted shapes for a very special reason: to help accelerate over 5,000 processes inside cells.
Without these highly specialized structures, metabolism would grind to a halt; DNA and RNA would acquire all the mobility of a conga-line of standing stones; cell processes would freeze into a petrified forest of non-living complexity. Life as we know it would be impossible, code or no code.
This is XNA. I’m told it’s less messy and easier to manipulate than DNA. It’s very good at being loaded with code and used as a storage device for information.
Here is a good question: Has any research team ever created artificial life in a laboratory?
Craig Venter, who has been interviewed on 60 Minutes and appeared in several Ted Talks videos, says that he has. He oversees a number of research labs funded by big oil and the government. His labs write computer code to generate base sequences, which they construct and then inject into yeast (among other techniques) to produce life-forms that they hope will someday lead to biofuels and greenhouse gas inhibitors.
Among other accomplishments, one of the labs, the Craig Venter Institute, is known to have introduced a gene from the bacteria, escherichia coli, into the earth’s toughest microbe, “Conan the Bacterium” (Deinococcus radiodurans), to create microbes that can detoxify radioactive wastes at nuclear facilities.
So, the answer to the question about whether anyone has ever created artificial life must be, probably not, not really — not from scratch, anyway. Yes, people have done amazing things. No one has created life without using existing life to do it, though. The process is too complex. On Earth, it has taken 4.5 billion years.
Many argue that life fell to Earth from the stars. Even Earth itself might not have been able to ignite the spark that led to humans and all the life we know.
In 2012 a different group of researchers did find a way to arrange a set of different bases inside DNA-like molecules called XNA. But it was a way of coding sequences only; it didn’t produce or even arrange proteins into anything that could be called, alive.
The “X” stands for the Greek word, Xeno, which means “other.” XNA is other nucleic acid.
An informed reader told me that in fact a protein was made from a sequence of XNA in 2015. If true, the future of genetics could get interesting in coming decades.
XNA is at the very least the precursor, many hope, for long-term storage of massive amounts of information in small, stable molecules — demanded now by data-churning behemoths such as CERN, home of the world’s most powerful particle-collider, located in Geneva, Switzerland.
Just because artificially constructed molecules like XNA can store useful information does not mean that DNA does the same. People have imagined meaning into the bases of DNA, which they simply don’t have — to help better understand their function and to more effectively manipulate them — for good or ill.
Another development in 2012, which some readers may remember, is that researchers learned to use a process known by the acronym CRISPR to change the sequence of bases in stretches of DNA. They adapted an immunization process that bacteria use to kill viruses and defend against subsequent attacks.
Click on the pic to open a more readable image in another tab.
Bacteria use CRISPR to suck the DNA out of an attacking virus, which they store in a kind of library for future reference. If a bacterium survives and the virus dies, somehow the bacteria is able to develop a quick-kill strategy that it will use whenever it is invaded by more DNA that matches a copy in its collection.
Researchers learned to create novel CRISPR DNA based on the system used by bacteria. They then attached RNA guides and cas9 protein shears to the sequences. They learned to deploy the assemblies to search and destroy bad DNA; and to insert designer DNA in its place in the cells of plants and animals; even humans.
These scientists insist that gene “therapies” are necessary, because the fact is: DNA is defective — most of it, anyway. Very few humans are symmetrical, attractive, disease-free, smart, emotionally stable, long-lived, or any other desirable trait anyone might want that is driven by how humans are built, or how they are “coded” at a molecular level.
Crisper video published October 25, 2019 on YouTube.
Gene drivers (mentioned in the first paragraphs of this article) are being developed in coordination with CRISPR techniques to enable changes to DNA molecules that will be permanent and transmittable 100% of the time. Their success will depend on how well lab technicians understand what is going on inside the molecules of life; and inside our cells.
Editor’s note:In January 2018 some researchers admitted that problems related to positional locating have created a roadblock to success for CRISPR technologies. They hope to solve the difficulties soon to avoid a catastrophic failure in the application of this heralded gene-altering process. One process under development that seems to promise more precision and speed is to use electro-magnetic positioning in place of viruses.
I believe we need to slow down and learn more before we unleash immortal genes into the biosphere that no one can pull back and which may turn out to be harmful despite best intentions. Asilomar style conferences that lead to best-practice regulations with the force of international law behind them are desperately needed to control biotechnologies that are quickly getting out-of-hand and beyond the control or understanding of government and politicians.
It is quite certain that PCR technology (polymerase chain reactionamplification), which scientists use to amplify into a viewable goo the molecules of DNA-style life might be misleading folks into believing that DNA-style life is all there is.
Earth could be infested with non-DNA based life, but no one will know until other technologies capable of detecting and amplifying it are developed and perfected.
People need to remind themselves that we are talking about molecules here — molecules of life that can’t be seen — even with help of the most sophisticated microscopes. Everything science knows comes from amplification techniques and mathematical analyses. I hope someday to write an essay on the techniques scientists use to tease out what they know for sure about these next-to-impossible-to-observe molecules.
Serious scientists refer to the possibility for the existence of non-DNA style life as the “shadow biosphere.” If this non-DNA life interacts with our own in a symbiotic way, the potential for harm, it seems to me, increases the more lab technicians play around with molecules they don’t fully understand while they remain oblivious to life they can’t detect, because they lack appropriate laboratory tools and techniques.
An even messier problem is “dark DNA”. It’s DNA that can’t be found, though tests clearly show it must exist for certain cell processes to work right.
Some researchers argue that as many as twenty thousand proteins are manufactured in humans that, when they search the human genome, they can’t find the sequences that are required to be there, somewhere, to enable the proteins to be built. I urge readers to click this link to learn more about this potentially serious inability of sequencers to decode DNA accurately and completely.
No one knows what they don’t know; and what they don’t know can kill us all, if lab workers aren’t cautious. Researchers know they don’t know stuff — important stuff if they intend to play around with gene drivers and CRISPR induced gene sequencing.
Researchers might be walking through a genetic minefield but are so eager to cross that they ignore the dangers of amputated limbs; the loss of sight and hearing; the possibilities for disfigurement to the genomes and phenomes of species like our own, which all people may one day come to regret.
No human is perfect. Sometimes our imperfections are caused not by bad stretches of DNA but by naughty RNA elves who copy less than optimal sections of bases, which they hammer together into less-than-optimal genes, which can screw-up a sequence of amino acids. The RNA elves end up making defective proteins that pollute cells, damage our bodies, and make our lives miserable.
To the extent that these screw-ups are the result of a lousy sequence of bases in our DNA, perhaps these patterns will be able to be altered using CRISPR technology (if anyone can get it to work right), which is likely to increase the odds of inducing better outcomes. But many screw-ups, perhaps most, are not caused by poorly sequenced genes constructed from DNA.
Many problems result from bad choices made by some arbitrary RNA elf, for example, who might have decided, perhaps, to cut and paste a random mix of bad sections it rummaged from the DNA strands; its errors and mistakes might not always be able to be located, identified, and repaired successfully. Renegade RNA elves are hard to track down and kill; at least so far.
Some problems can be caused by all kinds of things not related to DNA, like temperature, quantum effects, and cosmic radiation, including sunlight. The number of things that can go wrong with the weather-environment inside cells is enormous. Copy number variations in gene sequencing is another problem area that I mentioned earlier.
Safety and reliability are probably the two most important reasons why our haystacks of six-billion DNA bases hide a mere twenty-one thousand so-called genes, most of which are scattered in pieces throughout our vast DNA bundled-network.
Those few sequences that are important for survival are less likely to be attacked and mutated if they are surrounded by sequences of little or no value to survival and good health. Base-sequences essential to life hide within chromatin like proverbial needles in a haystack.
Dolphins have noses but can’t smell; they lack olfactory lobes. Sequences in their DNA have been identified that resemble corrupted versions of sequences related to olfactory lobes in other mammals.
Big chunks of DNA are thought to be junk — relics left behind by billions of years of evolution and change. Junk DNA could be a legacy of screw-ups and obsolescence. Dolphins, for example, have noses, but can’t smell. They seem to have a lot of corrupt DNA sequences related to smell, which are broken and don’t work due to neglect and disuse.
Humans are no different. We have DNA we no longer use. Through disuse, our base sequences, some of them, get corrupted over time, some think, and become unusable. The base sequences don’t get up and go anywhere, though. They just hang around, paralyzed, doing nothing. They become unrecognizable to the RNA elves, who learn somehow to avoid them.
Mitochondria and bacteria don’t seem to have much, if any, junk DNA, but humans, like other animals and plants, have almost no nuclear DNA that isn’t junk. It’s kind of mysterious.
A Russian agronomist from the Soviet era, renown in his time as an expert on the cultivation of wheat, Trofim Denisovich Lysenko, believed that plants and animals which were unlucky enough to find themselves subject to environmental stresses could draw on reserves from a pool of what is today called junk DNA to change their hereditary direction and enhance their survival odds. His idea has yet to be discredited.
The simple onion has 16 billion base pairs in its DNA. The loblolly pine tree — it’s an important source of lumber, which thrives in southern swamps — houses 22 billion. Humans have 3 billion.
EDITORS NOTE:As of January 2018, a Mexican salamander that can regrow limbs (the axolotl) has been sequenced. It is known to have 32 billion base pairs.
What do all these bases code for? They code for nothing, apparently. Maybe they are a warehouse of survival tools left behind as the distant past of billions-of-years ago gradually transforms itself into now; our miraculous present.
Another compelling idea that occurred to me as I wrote this essay is that the tangled mess of unused DNA in every plant and animal might have grown both in volume and complexity during ancient times — quite apart from environmental pressures on the life-forms themselves.
Could massive DNA growth have preceded evolution to enable and accelerate biodiversity during unforeseen environmental catastrophes?
It’s important to find out, because statistical studies on the rate of mutations seem to support the idea that mutational frequency cannot be the primary driver of species differentiation. Mutation rates are too low; the process is a snail’s pace compared to what is needed to transform a chimpanzee for example into an orangutan; or primates of any kind into humans.
Is it possible that mammoth reservoirs of disorganized and unused bases grew and multiplied inside the nuclei of ancient cells — like molds in petri dishes — to fuel bio-explosions of diversity and complexity when conditions were right? It’s a thought.
An abundant supply of unused DNA combined with aggressive colonies of swarming RNA segments might help to explain rapid, diverse bio-blooms (and even account for absences in fossil records) that seem to have occurred during the Cambrian era — to cite one example out of many.
The world’s smartest people are just getting started in the field of molecular genetics. Despite all that others have learned, much remains to know; more, much more, remains to discover and understand. Secrets hide in the complexity that are certain to better explain how biodiversity bloomed on planet Earth.
DNA bases are not a code, it seems to me; they are simply a platform for departing mRNA trains that, when properly coupled, can become assembly templates for chains of amino acids — complex assemblies of molecules that depend on very many processes and structures to have even the remotest chance of being transfigured by ribosomes into a seeming infinity of unlikely proteins — matrices of proteins and other structures, which have risen from the dust and the seas like the miracles of angels; an endless froth of bubbles; a deluge of structures that have over eons shaped the messy, sometimes ugly, often beautiful human beings and all other life on our planet; our home; our beloved Earth.
Adam Rutherford, the British geneticist said, ”This is the definitive history of arguably the greatest of all scientific revolutions.”
Life’s Greatest Secret is a must read for anyone who is interested in the science and history of the human genome. We strongly advise our readers to buy and read this important book. Billy Lee has read it twice, marking it up each time with magic-marker and margin-notes. It is a science blockbuster; a fantastic book written in an engaging, easy-to-understand style.
This February marks the 71st anniversary of the lecture series What is Life? presentedat Trinity College in Dublin, Ireland by quantum physicist Erwin Schrödinger — best known today for his Schrödinger’s Cat thought experiment.
In these lectures Schrödinger correctly described — ten years before James Watson and Francis Crick published their work on the structure of DNA (for which they won the Nobel prize in 1962) — many of the important and essential markers of the yet undescribed and undiscovered molecule that we now know determines everything about us and all other living things.
The lectures are remarkable for their prescience and clarity — they have an almost prophetic quality about them — but what I found most interesting (and it’s all interesting to me) are Schrödinger’s observations in the Epilogue, which he labeled On Determinism and Free Will.
After some warm-up remarks he says:
But immediate experiences in themselves, however various and disparate they be, are logically incapable of contradicting each other.
So let us see whether we cannot draw the correct, non-contradictory conclusion from the following two premises: (i) My body functions as a pure mechanism according to the Laws of Nature. (ii) Yet I know, by incontrovertible direct experience, that I am directing its motions, of which I foresee the effects that may be fateful and all-important, in which case I feel and take full responsibility for them.
