How Life Originated

It’s time to write about one of the greatest mysteries of the Universe—how life originated—because we know enough, today, to solve the mystery. But there are problems.

The greatest problem is that, despite an army of Nobel prize winners and lesser  biologists working heroically to synthesize a living cell, the net result, so far, is zero.

So what can I add to the thousands of articles and books that have been written about the first living cell? A few years ago, I proposed a theory about why it seems to be impossible to get that first cell going. Therefore, this essay consists of two parts: 1) How that first cell came into being, and 2) Why we can’t repeat that magic in a modern biological laboratory.

Part 1) My thesis is that the first living cell came into being because certain atoms and molecules stick to each other. As an example, look at a human being: obviously, except for liquid media and gases, the skeleton and muscles are constructed out of cells that stick to each other; those cells, in turn, are made out of atoms and molecules that are surrounded by an individual membrane in each cell.

It is impossible for us to “visualize” something as small as an atom. But we have to, at least, learn some of the language. The most convenient unit of length is a nanometer, or nm. A water molecule (H2O, of course) has a diameter of 0.3 nm, and green light has a wavelength of around 520 nm. One thousand nm is equivalent to one micrometer (a micron) – a length that remains invisible to the bare human eye. Finally, 1000 microns are equivalent to something we can relate to – a millimeter. And 1000 mm, of course, equal one meter.

Add up all of the zeros, and we get 1 nm = 10-9  meter, or 1 m = 109 nanometers = one billion nm. Today, with trillions being bandied about by politicians, I am grateful that I need not go beyond billions. Also today, there is a huge effort by engineers and physicists to “make things that work” at nanometer dimensions (1 to 100 nm).

With respect to how life originated, we seek the smallest ensemble of atoms that will form a valid deoxyribonucleic acid (DNA) molecule. Why DNA? A DNA molecule itself is not alive—it doesn’t wiggle if it is placed into a jar of water—but it is the blueprint upon which the genetic code of all living bacteria, plants, and animal cells is imprinted.

I should mention that ribonucleic acid (RNA), a close relative of DNA, was probably synthesized first. Also, there are large organic molecules—enzymes—that are not really alive, but some of them take part in metabolism by using ambient sources of energy. They are the precursors of plants. But they, too, with a cargo of thousands of atoms, have survived a great deal of evolution.

In what follows, to simplify matters, I will only refer to DNA.

The machinery of a living cell requires a minimum amount of volume. The smallest bacterium has a diameter of 100 nm. A typical atom has a diameter of 0.1 nm. The following arithmetic is trivial: for a spherical cell, atoms are so tiny that 1000 of them, sitting side-by-side, can reach from one side of the cell to the other side. It may sound weird but, very approximately, the total number of atoms in the smallest cell is 10003  = 109, or one billion. This includes the atoms that constitute a coiled-up DNA molecule.

My “bible” on the subject is Cradle of Life, by J. William Schopf, Princeton Univ. Press, 1999. He serves up biology in a painless manner, diluting it with history and personal stories about Aleksandr I. Oparin, Salvador Dali, and others. According to the subtitle, the book is about The Discovery of Earth’s Earliest Fossils, but it also has pertinent information about the Earth’s living creatures.

Three types of chemical bonds occur in the reactions in an organic environment: namely, covalent, ionic, and hydrogen bonds:

Covalent bond: This is the stable balance of attractive and repulsive forces between atoms when they share electrons. For example, methane (CH4).

Ionic bond: This is the bond formed by the attraction between two oppositely-charged ions. For example, sodium chloride (NaCl).

Hydrogen bond: This is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen, or fluorine. For example, acetylacetone.

There is not enough room here to further give the details of the chemical bonds, but one can refer to Google or Wikipedia. The main point, of course, is that atoms and molecules stick together, forming larger and larger ensembles.

As the above examples illustrate, the bonds are restricted to certain atoms and molecules. This is most fortunate; if there were no restrictions, the resulting ensembles would be a hopeless hodge-podge of every conceivable combination. Furthermore, there is a tendency for helical structures, such as is found in DNA-RNA, to form, so random constructions frequently contain helixes.

And we also know about the basic CHON elements – Carbon, Hydrogen, Oxygen, and Nitrogen – that are the foundation upon which organic structures are built. The list includes water and carbon dioxide, of course, but we also have carbon monoxide (CO), methane(CH4), ammonia (NH3), hydrogen cyanide (HCN), formaldehyde (H2CO), and so forth.

A “simple bacterium” is a microbe known as a prokaryote because it does not contain a nucleus; eventually, some 1.9 billion years ago, much more complicated eukaryotes, that contain a nucleus, appeared. The question really is—how do we go from a few CHON compounds to the DNA molecule of the simple bacterium?

Today, the DNA molecule has become part of our culture. One can no longer plead ignorance about DNA—in fact, nowadays, it is used to convict people who plead innocent (and to sometimes free those who have been convicted). Deciphering the DNA blueprint and gene functions, for all animals and plants, has become one of the great cottage industries of the 21st century. My main point here is that this “simple” primitive cell contains one billion atoms of carbon, hydrogen, oxygen, and nitrogen, plus a sprinkling of other atoms such as sodium and chlorine (as if they add flavor to the soup).

The genetic code consists of a sequence of only four nucleotide bases: They are A = Adenine, C = Cytosine, G = Guanine, and T = Thymine. The code portion of a DNA molecule consists of two approximately parallel strands that tend to form a helix – hence, DNA is called a “double helix.” Along the parallel strands, A is always cross linked with T, and C is always linked with G, so the same message (which is the code for amino acids) is duplicated since each strand fully determines the sequence of the other strand. The bases along a strand are around 0.34 nm apart in an axial direction, and there are 10 base pairs per single turn of each helix. The outer diameter is 2.0 nm. A backbone or scaffold is provided by groups of atoms that form phosphate and deoxyribose.

Just how many nucleotide bases are there in a DNA molecule? This depends, of course, on the animal or plant. From the simplest of animals, a bacterium, to the most complicated of humans, all  are programmed by a DNA molecule. In every bacterial cell, and in every cell of the mammalian body, there is a string of A, C, G, and T nucleotides characteristic of that organism. Isn’t that remarkable – that all living cells are defined by the same four nucleotides?

Is it possible that other types of “nucleotides” existed when life first began? If so, they fought it out, and the present nucleotides won the battle (on a geological time scale of 400 million years), as discussed below. Furthermore, the principles of biochemistry indicate that A teams up with T, and C with G, because these combinations are more stable than the only other four possibilities: AC, AG, CT, and GT. But this has literally far-reaching consequences – to the end of the Universe, in fact. If after 400 million years the nucleotides A, C, G, and T survived, then DNA molecules everywhere are made of AT and CG base pairs. This sounds like a great unsubstantiated leap into the unknown. But is it really so farfetched? The “everywhere” conclusion is strengthened by the fact that spectroscopic examination of simple molecules that populate space outside the solar system shows the same simple CHON molecules that are found here on Earth. Since, after a tremendous effort, nobody has succeeded in demonstrating how life began on Earth, what is the missing ingredient? Is it time? If they begin today, our organic chemists may, in 400 million years, duplicate what nature hath wrought?

The chronological background against which life evolved is as follows: The earth was formed 4550 million years ago (or, using the standard abbreviation for “millions of years ago,” 4550 Ma). For the next 650 Ma, until 3900 Ma, the earth was bombarded by asteroids and meteorites. This bombardment released a tremendous amount of energy. Until 3900 Ma, mainly as a result of these collisions, the earth was too hot (temperature greater, everywhere, than the boiling point of water) for life to exist as we know it. Then, according to Schopf, in “only” 400 million years, by 3500 Ma, life was “flourishing and widespread” (p 167). (With our ever-greater ability to detect asteroids, if not fictitious UFOs, we have become aware that some bombardment, although rare, is unavoidable.)

But 400 million years is an enormous chunk of time. Please, Dr. Schopf, can you tell us when, during this period, did life begin? No, because the fossil record is missing, and that is the only reliable way to date the prokaryotes. As Schopf says (p 99), “The very first forms of life … probably didn’t even have fossilizable cell walls, … and were made of chemicals far too fragile to be geologically preserved.”

Only the bacteria (such as escherichia) are actually pertinent to the present essay. Presumably, if we can synthesize the simplest of living creatures, the more complicated ones are sure to follow. The question boils down to—how did a random process assemble the 4,000,000 base pairs of the “first” bacterium?

Does it really take four million base pairs to define a simple living ensemble? Perhaps the first living assembly had only 400,000 base pairs? Is there an error here somewhere? Probably no. Superficially, the cell consisted of some “cytoplasm” surrounded by a thin membrane. The DNA blueprint had to direct the construction of the membrane. It had to distinguish food from undesirable chemical combinations. It had to convert food into its internal mixture of thousands of proteins, in reasonably proper proportion. It had to define a mixture of internal proteins that can take in energy and use it to power living processes. When it reached a certain critical size, having taken in a sufficient amount of nutrient material, it slowly divided into two daughter cells via a process called asexual reproduction. The important point is that this “simple” cell, which doesn’t have much to do except eat and achieve immortality by dividing in two, is anything but simple. It contains the DNA molecule, and lots of associated genes, perhaps 1000 different proteins, and so forth. If somebody asked you to build a mechanical contraption that could do all of the above, how many small parts would you need? Evolution’s answer – four million—is quite believable.

Let’s consider the construction of a DNA molecule. Forget about its physical size for the time being. How do we make a nucleotide, A, C, G, or T? It turns out that they are similar to each other, so one can talk about an average nucleotide: It has 5 Cs, 4 Hs, 1 O, and 4 Ns for a total of 14 atoms. They do not form a linear array, which would be around 1.4 nm long but, instead, are squeezed into a ball. So we start out by mixing together carbon, hydrogen, oxygen, and nitrogen in a flask, and add a mild source of energy to “stir the pot.” Energy is the least of our problems – there are plenty of troublemakers, such as geothermal hot spots, cosmic rays, X-rays, ultraviolet rays, lightning, and so forth. If we leave out the minor details, that is essentially what Stanley L. Miller did in a famous Ph.D. thesis experiment in 1953, which has been repeated any number of times since then. (See Schopf’s book for the details.) What do we expect? A simple (and simple-minded) approach is to say that, with four different elements and a total of 14 atoms, the total number of molecules that can be formed is 414, or 268 million. This is simple-minded because chemistry doesn’t work that way. Only a very few of the 14-atom molecules that can be formed from CHON are stable, held together by hydrogen and other bonds.

The great excitement that followed Miller’s experiment was that he was able to generate simple organic molecules using vey simple apparatus. Furthermore, the spectrum of light from the stars and galaxies shows that these relatively simple CHON molecules exist everywhere in the Universe.

In recent years, however, an important hint of which molecules are stable has emerged via “reverse engineering”: In order to read its genetic ACGT code, some of the DNA molecules of a particular species are broken down, by chemical or other means, into many relatively short sections. Each short section is tractable; that is, its code can be determined. By matching identical and overlapping sections, with a great deal of assist from computers, the entire original DNA sequence can be revealed.

The system modeled here took place in 400,000,000 years. That is an awfully long time. What were the environmental specifications under which life developed in this time? It had to be fluid because the pre-viable molecules were not alive; since they couldn’t move from one place to another, their surrounding material had to slowly change. Liquid water is probably too fluid, too dilute. A high-viscosity mud, or what I like to call “goo,” full of CHON molecules of various complexities, is a more likely environment. The temperature was high – close to the maximum tolerable that avoids instability – because thermal agitation literally moves small molecules from one location to another. [This is also known as Brownian movement. Robert Brown (1773-1858), a botanist looking at pollen grains in a microscope, was the first to notice the incessant random motion of minuscule particles.] In a high-viscosity fluid, movement is very slow, but with a span of 400 million years, there is no need to rush along with inter-molecular alliances.

What about pressure? Here there is a common misconception that high pressure kills. Yes – if you take an organism that has air spaces and drop it from the top of the ocean to a high-pressure depth, the air spaces become compressed, and the resulting physical distortion can be fatal. But if the organism spends its entire life under high pressure, atoms are slightly closer together than on the surface of the earth, but this has only a minor effect on physiological processes. In other words, the goo can be very far underground—underneath deep oil wells, or beneath the seas, for example.

The exciting conclusion that logically follows is that the simplest pre-viable molecules are evolving right now, probably in goo deep inside the earth, on land, or underneath the sea. Not too deep—just deep enough to be hot, but not past the boiling point of water. Alas, pre-viable molecules are evolving but, as soon as they are formed, they are “eaten” by bacteria, so they are not around in detectable quantities. In other words, since time immemorial, primitive bacteria have been plundering the planet by consuming CHON pre-viable molecules. They sound positively human!

Another exciting concept is that pre-viable molecules are evolving everywhere in the Universe. Since when is the earth the only place fortunate enough (or unfortunate, considering what we are doing with it) to have primordial goo?

Despite the negative prognosis, there is always the chance that some useful information will turn up.  What should we be looking for? It would be nice to find something around 300,000 bases long. Translated into meters, with a DNA length of 0.34 nm per base, we should be looking for molecules that have a physical length of 100,000 nm, or 0.1 mm. Unfortunately, there is something unrealistic with regard to this calculation: A 300,000-base molecule, consisting of a string of A, C, G, and T nucleotides, would be folded into something that approximates a ball. That is how it really is with a viable DNA molecule. Perhaps the pre-viable molecules can be unfolded. All of this seems to require high-magnification electron-microscope work, perhaps with special containers that can preserve the temperature and pressure conditions of pre-viable goo. A great deal of useful feedback can come from the people that break up DNA molecules; it certainly seems logical for them to try to reverse the process and reconnect the pieces to get the original DNA molecule. (When life’s origins are thus revealed, one can expect a storm of protest from religious and conservative groups as they strive to deny the scientific evidence.)

Let’s dig deeper. Or, better still, above ground in the sterile laboratory of some clever organic chemist, perhaps Stanley Miller’s experiment can be speeded up by a factor of 100 million, so that pre-viable molecules can be synthesized in the lab, but in much less than 400 million years. It would be great for a Ph.D. thesis, or even a Nobel prize or two.

The above displays the logic of evolution: Survival of the fittest. Chemical bonds are restricted to a relatively few organic atoms and molecules, and there is a tendency to form helical structures. In due time (400 million years?) a single viable cell arose in a suitable goo.

Part 2) of this essay is based on the work of cosmologists Frederick Rothwarf and Sisir Roy, “Quantum Vacuum and a Matter-Antimatter Cosmology.” Their manuscript (R-R) derives a Universe that is spectacularly different, in its past embodiment, from the accepted “establishment” version of the history of our Universe.

Frederick Rothwarf, frothw@ieee.org, is in the Physics Dept. of George Mason Univ., Fairfax, VA 22030. Sisir Roy,sisir@isical.ac.in, is in the Indian Statistical Institute, Calcutta, India.

The R-R manuscript is, in turn, a continuation of the work of physicist Allen Rothwarf (1935-1998, Frederick’s brother). Allen Rothwarf’s magnum opus, “An Aether Model of the Universe,” was published by Physics Essays, vol. 11, no.3, Sept. 1998, pp. 444-466.

Allen Rothwarf’s model is a Universe filled with aether particles (EP’s). An EP  consists of an electron-positron pair. This immediately gives the mass of an EP as twice the mass of an electron, or 1.822 X 10-30 kg. Since it has mass, an EP is gravitationally attracted to other masses. Furthermore, the EP model led to a set of calculations that concluded that the velocity of light, c, is inversely proportional to the square root of time, t, where t is taken as zero at the Big Bang:
c = k/t 0.5 

where k is a constant. This has a singularity at t = 0 (that is, c becomes infinite), but the equation is applicable only after a period of “inflation” following the Big Bang.

Using the present-day values of c = 2.998 × 108 m/s and t = 13.7 billion years, we get

c = 3.509 × 1013/t 0.5

where the units of c are m/s, and those of t are years.

Several interesting features show up using this equation:

(1) There is only a relatively short time between the “Earth formed” and “Now,” 4.55 billion years later. The velocity of light when the Earth formed is 3.668 × 108 m/s, or a decrease of 18.28% since then.

(2) Is there a chance that, during one of our lifetimes, we can measure the change in velocity of light? We get

dc/dt = – c/(2t).     

At the “Now” point, then, dc/dt = – 0.01094 m/s/year, or – 1.094 m/s in 100 years. This raises the exciting possibility that the decrease in the speed of light, if it exists, can be measured with very accurate instruments.

(3) At t = one billion years, the velocity of light is 11.10 × 108  m/s. At the other end, where the Universe is 100 billion years old, the velocity is 1.110 × 108 m/s. From “Now” at t = 13.7 billion years to t = 100 billion years, the velocity decreases by a factor of only 2.70.

Allen Rothwarf also pointed out that “If c is a function of time, e [electron charge], h [Planck’s constant], and m [rest mass of an electron] may also be time dependent.” This may invalidate the “official” age of the Universe.

But let’s, for now, ignore the time scale given above. Consider, instead, the following four Phases. I conjecture that the natural “constants” change with time, so that the chemical, physical, and biological processes with which we are familiar also change with time. That is:

In Phase 1, life as we know it could not exist. In this early phase of the Universe, the structure of CHON atoms were such that it was impossible for these atoms to stick together, in proper sequence, to form anything like a DNA  molecule. Other complex molecules could form, but none of them were viable.

In Phase 2, during which the Earth formed, it was easy and natural for CHON atoms to stick to each other. Eventually, given the millions of places where a proper “soup” formed, and millions of years for molecules to grow as their atoms stuck together, the simplest of DNA molecules formed. Without any predators, the first living cell multiplied until all of the available chemical “food” or energy was consumed. Then the species-building process of mutation, and survival of the fittest, began.

In Phase 3, the phase in which we now find ourselves, mutations and survival of the fittest have, after some 4 billion years, given birth to homo sapiens. These creatures are very intelligent, and they know a great deal about DNA molecules, but they cannot synthesize the most primitive of viable cells. The reason is that the CHON atoms are different from what they were in Phase 2. They don’t stick together in a manner to form the simplest of living cells. There’s not much that can be done about it, because one cannot take a bottle filled with Phase 3 aether particles, and compress them to duplicate Phase 2 conditions. In other words, my conjecture is that all of Part 1 of this Essay existed in Phase 2, but the most elementary, basic steps in “how life originated” have been absent in Phase 3.

In Phase 4, the natural “constants” will change to the point where life becomes impossible. A living cell, in Phase 4, will not be able to function. Gradually, as the Earth goes from Phase 3 to Phase 4, the population of complex biological forms will decrease. Finally, even the simplest of cells will fail to reproduce. Life will end because CHON atoms will not be capable of forming viable combinations. Again, complex molecules can form, but none of them will be viable. (This may or may not occur before the sun explodes.)

There is a message here for the Intelligent Design (ID) people. The notion that some kind of intelligent force molded the Universe is a most nonsensical idea. The ID argument is that the natural “constants” could never, by themselves, allow living cells to form. But my conjecture is that, as the Universe expands, as the density of aether particles changes, the natural “constants” likewise change. They enter a biologically viable Phase 2, where living cells can evolve, and eventually enter a biologically deadly Phase 4, where life becomes impossible. An Intelligent Designer is an unnecessary invention in the history of the Universe.

Finally, the R-R calculations are sensational because they yield 9.24 billion years for the age of the Universe rather than the “establishment” value of 13.7 billion years. Furthermore, they indicate that the expansion of the Universe is decelerating, whereas conventional wisdom (since 1998) has it accelerating.

In due time, when the cosmologists come to accept the natural aether fluid that defines the Universe, they will be able to check the R-R calculations.

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