The Origin of Life: Programmatically Predestined?

Cross-posted from www.futureandcosmos.blogspot.com
 
Let us now look at one of the great mysteries of the universe, the mystery of the origin of life, something that took place more than three billion years ago.

Some readers may be thinking along these lines: That's not such a mystery. Given a primordial soup and millions of years of time, there developed some self-replicating molecule. Once you had that, the development of everything else was just a case of things evolving from the simple to the more complex.

But such a glib explanation glosses over the great difficulties involved in explaining the origin of life on the early Earth. The fact is that there are huge difficulties in explaining how life began on our planet billions of years ago. In recent decades scientists have made relatively little progress in solving this problem.

Consider the progress of astronomy during the past 50 years. Since the year 1963 we have seen the discovery of the Big Bang, the discovery that the expansion of the universe is accelerating, and the discovery of more than 1000 extrasolar planets. But without doing a Google search, can you name one bit of progress that has been made in the past 50 years regarding the origin of life? You probably can't. When most of us think of scientific work on the origin of life, we think back to the Miller experiments involving amino acids, but they were done in the 1950's.

We can divide up the problem of the origin of life into three different problems: a necessary components problem, a combinatorial problem, and a computation problem.

The Necessary Components Problem

The basic units of life (below the cellular level) are things such as RNA, DNA, and proteins. Proteins are made of building blocks called amino acids. Some proteins are extremely complicated molecules built from very many amino acids. It was calculated long ago that the chance of some of these proteins forming from random combinations of amino acids is incredibly low, even given billions of years. But that's not necessarily a problem, because proteins are formed using the instructions in DNA. A DNA molecule is like a library of recipe books, with each of the recipes being a recipe for making a particular type of protein.

So if there is a mechanism for producing DNA from a chance combination of chemicals, we might have a way of explaining how all those complicated proteins came into existence. Unfortunately it seems DNA molecules appear to be way too complicated to have arisen from a chance combination of their constituent elements of nucleotides (which consist of sugars, phosphates, and nitrogenous bases), without assistance from something more complicated than nucleotides.

So the current leading hypothesis is that the first self-replicating molecule was not DNA but something simpler, presumably some version of RNA. This idea is called the RNA World hypothesis. The idea is that first there was RNA, and that DNA evolved later. However, the RNA World hypothesis is on shaky ground.

One problem is the difficulty of explaining the origin of all the necessary building blocks. The table below shows the various types of building blocks. As indicated below, there are reasons for doubting that the ribose sugars, purines, and nucleotides would have existed in sufficient quantity for DNA or RNA to originate.

	Components
RNA, DNA	Ribose sugars Harvard science web site: "In experiments ribose could not be made at the necessary quantities that would explain its abundance on early Earth because it was highly unstable." Wikipedia article: some scientists have concluded that "the backbone of the first genetic material could not have contained ribose or other sugars because of their instability." Phosphates Pyrimidines (type of nitrogenous base) 2009 paper (Powner et. al) suggests possible path for abiotic origin. Purines (type of nitrogenous base) More complex than pyrimidines. According to this paper, hard to explain abiotic origin, in a way compatible with formation of ribose sugars. Nucleosides (combination of ribose sugar and pyrimidines or purines) and nucleotides (a nucleoside plus a phosphate) Wikipedia article: “No known chemical pathways for the abiogenic synthesis of nucleotides from pyrimidine nucleobases cytosine and uracil under prebiotic conditions."
Proteins	Amino Acids Found in a meteorite. Miller-Urey experiment produced amino acids from gases and continuous electricity.

The Combinatorial Problem

The combinatorial problem is the problem of getting anything like RNA or DNA to appear from the building blocks listed above. This scientific paper by Joyce and Orgel refers to the difficulty of joining together nucleosides (a combination of ribose sugar and pyrimidines or purines) and nucleotides (a nucleoside plus a phosphate). The wikipedia article on the RNA World hypothesis notes that “Joyce and Orgel further argued that nucleotides cannot link unless there is some activation of the phosphate group, whereas the only effective activating groups for this are 'totally implausible in any prebiotic scenario', particularly adenosine triphosphate.”

Well-known scientist Freeman Dyson has stated, “The results of thirty years of intensive chemical experimentation has shown that prebiotic synthesis of amino acids is easy to simulate in a reducing environment, but prebiotic synthesis of nucleotides is difficult in all environments...If it happened, it happened by some process that none of our chemists have been clever enough to reproduce.”

RNA is made of nucleotides, which are made of ribose sugar, phosphates, pyrimidines, and purines. Scientists have not been able to synthesize RNA through a simulation of the early earth, and in such simulations have not been able to make the simpler nucleotides either. As discussed in the table above, there are difficulties in assuming the availability of even some of the building blocks of the building blocks of RNA.

The Computational Problem

Perhaps the biggest problem involving the origin of life is the problem of accounting for the origin of the genetic code. The genetic code is a symbolic representation system used by all earthly life. It has been called a kind of miniature programming language. 

 The Genetic Code

It is fairly easy to explain the basics of how the code works. In the spiral staircase structure of the DNA molecule, the “steps” of the staircase are chemicals called nitrogenous bases: either purines (adenine or guanine) or pyrimidines (cytosine or uracil). Various combinations of three of these chemicals stand for different amino acids (the building blocks of proteins). For example, if there are three consecutive “steps” in the spiral staircase, and the first is cytosine, the second adenine, and the third guanine, that stands for the amino acid glutamine. There are 63 other cases where a sequence of three nitrogenous bases stands for a particular amino acid. (In the diagram above, the chemicals around the four edges of the square are the amino acids.)

Imagine if you liked to write down recipes, but you needed to write down many of them on a single piece of paper. You might invent a little “recipe language” in which MK1 stands for a half a cup of milk, MK2 stands for a full cup of milk, FL1 stands for a half a cup of flour, and so forth, with a total of 64 different three-character symbols (and some other characters standing for “end of recipe”). You might then write out recipes very concisely using this little language. That's quite similar to what the genetic code does, except the recipes are stored in the DNA molecule, and the recipes are instructions for making proteins from the building blocks of amino acids.

The big question is: how did this genetic code ever originate? It's hard to imagine it arising through anything like Darwinian evolution, as the genetic code seems to be required from the very beginning of biological evolution.

The genetic code can be considered an example of code, the term software developers use for the symbolic instructions they create. The baffling question is: how did nature go from chemicals to code? Code seems like something fundamentally different from chemicals, and the two seem as unrelated as an apple is to a bicycle.

The issue was highlighted by a paper by biologists J.T. Trevors and D.L. Abel:

"Peer-reviewed life-origin literature presupposes that, given enough time,
 genetic instructions arose via natural events. Thus far, no paper has provided
 a plausible mechanism for natural-process algorithm-writing...There is an
 immense gap from prebiotic chemistry and the lifeless Earth to a complex DNA  instruction set, code encryption into codonic sequences, and decryption
 (translation) into amino acid sequences...How did inanimate nature write
(1) the conceptual instructions needed to organize
metabolism?
(2) a language/operating system needed to symbolically
represent, record and replicate those instructions?
(3) a bijective coding scheme (a one-to-one correspondence
of symbol meaning) with planned redundancy
so as to reduce noise pollution between triplet codon
‘‘block code’’ symbols (‘‘bytes’’) and amino acid
symbols?
We could even add a fourth question. How did
inanimate nature design and engineer
(4) a cell [Turing machine? (Turing, 1936)] capable of
implementing those coded instructions?" -- Trevors and Abel

In this article the widely read physics professor Paul Davies has discussed other difficulties in the “code from chemicals” scenario, the assumption that the genetic code arose from some kind of chemical evolution: 

"The language of genes is digital, consisting of discrete bits, cast in the language of a four-letter alphabet. By contrast, chemical processes are continuous. Continuous variables can also process information – so-called analogue computers work that way – but less reliably than digital. Whatever chemical system spawned life, it had to feature a transition from analogue to digital. The way life manages information involves a logical structure that differs fundamentally from mere complex chemistry. Therefore chemistry alone will not explain life's origin, any more than a study of silicon, copper and plastic will explain how a computer can execute a program." -- Davies

This problem of the origin of the genetic code recently got even more difficult to explain, because scientists recently announced the discovery of a second genetic code buried in DNA. Apparently many of the triple sequences have a double-meaning. Explaining one genetic code was a nightmare -- how can we explain two of them?

A New Approach to the Origin of Life

We might get around these difficulties by imagining that the origin of life on Earth required external intervention by a divine agent or perhaps extraterrestrials. But that would raise the question: why should our ordinary little rock have deserved such a special blessing? After all, modern astronomy tells us that planets are as common as apples in an apple orchard.

A more intellectually attractive idea is the daring concept that the origin of life was programmatically predestined. We can boldly postulate that long, long before there arose the programming in the genetic code, there was a more general programming woven into the fabric of the universe, a programming that drives the evolution of the universe, causing the frequent occurrence of things that might otherwise have very little or no chance of occurring. Under such a scenario, we can think that life is appearing throughout the universe, because that is the way the universe is programmed to behave. Under such a concept, we no longer have to imagine the origin of the genetic code by supposing a farfetched case of “code from chemicals.” We can instead plausibly imagine the origin of the genetic code as a case of “code from code” – the genetic code being a product of a more general cosmic software that is influencing cosmic destiny, propelling the universe forward towards desirable outcomes.

I speak here of the theory explained in other posts on this site: the theory of a programmed material universe. For more details, see my post The Theory of a Programmed Material Universe and my post Nature's Computation Needs Imply a Programmed Material Universe.

We Do Not Understand How the Universe Came to Look This Way

Cross-posted from www.futureandcosmos.blogspot.com

From the time of the Big Bang nearly 14 billion years ago, the universe has undergone an amazing evolution. Imagine if you had been there at the beginning, to witness the hot smooth density, in which supposedly all of our universe was packed into a microscopic size. If you knew nothing about the eventual outcome, you would not have been optimistic about what would have resulted from this explosive event. Your best bet might have been a mess of disorganized space junk, with no more order than the debris resulting from a hydrogen bomb explosion.

But almost 14 billion years later, we have a universe of remarkable order. Matter is organized into superclusters of galaxies consisting of clusters of galaxies consisting of galaxies consisting of solar systems. A large fraction of the galaxies are the particularly beautiful type called spiral galaxies. Do scientists really have a firm grip on how this improbable evolution occurred?

Difficulties in Explaining the Seeds of Structure

Scientists say that the current structure of the universe evolved from what are called primordial density fluctuations. They can see tiny fluctuations in the cosmic background radiation, which is uniform to about 1 part in 100,000. But how did those fluctuations get there?

Cosmic Background Radiation

The most common explanation is that the fluctuations began as quantum fluctuations (matter popping into existence in accordance with Heisenberg's uncertainty principle), and that these quantum fluctuations were then amplified by a period of cosmic inflation (exponential expansion) that occurred for a fraction of a second when the universe was less than a second old.

The difficulties in this explanation are many. For one thing, no one has ever actually observed a quantum fluctuation that caused matter to appear out of nowhere, not even a fluctuation big enough to produce an atom. Secondly, there are currently serious credibility issues associated with the theory of cosmic inflation, issues that have been highlighted by Princeton physicist Paul Steinhardt in this review. Among those issues are what Steinhardt calls an “unlikeliness” problem, plus the problem of creating an inflation theory that both begins and ends an inflation phase while remaining consistent with observations. Cal Tech physicist Sean Carroll says here, “When perturbations are taken into account, inflation only occurs in a negligibly small fraction of cosmological histories,” and then spells that out as a fraction less than 1 in 1.000,000,000,000,000,000,000,000,000. The leading cosmologist Roger Penrose has described cosmic inflation as a thermalization process, and has stated, “There is, however, something fundamentally misconceived about trying to explain the uniformity of the early universe as resulting from a thermalization process.” He states that any thermalization process doing anything would have “been even more special before the thermalization than after” (The Road to Reality, page 755).

Third, the inflation theory requires a severe fine-tuning of its model parameters in order to perform the trick of inflating these quantum perturbations to be the right size. As one scientist puts it here:

A lumpiness of about 10^-5 is essential for life to get a start. But is it easy to
arrange this amount of density contrast? The answer is most decidedly no! The
various parameters governing the inflating universe must be chosen with great
care in order to get the desired result.

In short, we do not yet have a good plausible explanation of how these “seeds of structure” appeared. The only explanations are ones that resort to extensive parameter tweaking, rather like in the graphic below.

Explaining the Growth of Structure: More Nebulous Fudge Factors

Scientists have done calculations regarding the formation of galaxies and the preservation of galactic structure, and have come up with the resounding conclusion that the gravity of visible matter is completely insufficient to explain the origin and persistence of galactic structure.

Consequently cosmologists have come up with some “fudge factors” to help explain things. The two biggest fudge factors are called dark energy and dark matter. Scientists say that dark matter is a mysterious type of matter that is invisible. Dark energy is supposed to be a mysterious unseen energy that pervades all of space. Scientists guess that the universe's mass-energy is 68% dark energy, 27% dark matter, and 5% regular matter.

Total unambiguous observations of dark matter: 0
Total unambiguous observations of dark energy: 0

It's not as if scientists haven't tried. They have spent many dollars and much time with some very fancy observation techniques, but have still come up short. But that hasn't stopped cosmologists from creating a “lambda cold dark matter” theory (called LCDM) designed to explain cosmic structure.

Besides the fact that it relies on dark matter (the existence of which has not been verified), there are problems in this LCDM theory. One of the main problems is that it predicts way too many satellite galaxies. The paper here describes the problem. According to this link the LCDM theory predicts that our galaxy should have thousands of satellite galaxies, but instead it only has about 26.

Another problem with the LCDM theory is that it predicts that almost all galaxies should have have large bulges in the center or be spherical. But between 58% and 74% of disk-shaped galaxies do not have a bulge.

Another problem with the LCDM theory is the difficulty of getting it to produce not just galaxies but a universe with as many beautiful spiral galaxies as we have in our universe.

A spiral galaxy

As this site says, "Cosmological evolution simulations do not generally produce universes containing large spiral galaxies. Rather they produce clumps of matter making up roughly spherical amorphous galaxies without anything like the broad disks and extended arms of a typical spiral galaxy." 

Strange Anomalies

In this story a scientist comments on strange findings he has discovered by studying deep space:

"The dark matter seems to 'know' how the visible matter is distributed. They seem to conspire with each other such that the gravity of the visible matter at the characteristic radius of the dark halo is always the same...It's like finding a zoo of animals of all ages and sizes miraculously having identical, say, weight in their backbones or something...It is possible that a non-gravitational fifth force is ruling the dark matter with an invisible hand, leaving the same fingerprints on all galaxies, irrespective of their ages, shapes and sizes."

Perhaps this is some strange cosmic conspiracy, or perhaps just a reason why we may need an explanation other than dark matter. Another strange finding is the discovery of a Vast Polar Structure (VPOS), which is basically about 26 dwarf galaxies above and below our galaxy, without any matching structure on the other two sides of our galaxy. This structure does not at all seem to be what we would  expect from a dark matter theory of the origin of structure (and may be hard to explain even with alternate theoretical models). If gravity alone is creating structure, why don't these companion galaxies exist in more of a sphere around our galaxy?

The limits of our understanding of cosmic structure may also have been highlighted by the recent discovery of the planet HD 106906 b, a planet 11 times the mass of Jupiter. HD 106906 b orbits its star at a distance 650 times the average distance between Earth and the Sun. That puts the planet 20 times farther away from its star than the planet Neptune is from the Sun. This finding seems to be quite incompatible with current theories of solar system formation. HD 106906 b is being called “the planet that shouldn't exist.”

Particle Physics Makes the Situation Even Worse

When we look in the world of particle physics for help with these problems in explaining large scale structure, we get no help.

The prevailing theory of large structure formation (the Lambda Cold Dark Matter theory) is based mainly on the hypothesis of dark matter, but dark matter is totally unaccounted for in the Standard Model of physics. Dark matter has no place in that model. That leaves dark matter as a kind of nebulous “some kind of something.” Do we know how many dark matter particles there are, or how much mass any dark matter particle has? We sure don't.

Modern quantum physics does predict that dark energy should exist. The problem is that quantum field theory predicts that the dark energy should be at least 10⁶⁰ times (a trillion trillion trillion trillion trillion times) larger (and probably 10¹²⁰ times larger) than the maximum value that it can be, according to observations. This is known as the vacuum catastrophe problem or the cosmological constant problem. Quantum field theory predicts that every cubic meter full of vacuum should contain more energy than the maximum amount that the observable universe can contain.

In light of all these considerations, the graphic below summarizes the current very shaky state of our current understanding of the formation of cosmic structure. 

The difficulties of explaining the origins of cosmic structure are one of the reasons I have advanced the theory of a programmed material universe explained in other posts on this site. By postulating that the universe has had built-in programming from the beginning, we can more plausibly explain the origin of galaxies, life, and Mind.

Why “Nature Has Math” Leads to “Nature Has Software”

It has long been recognized by many scientists that in a fundamental way nature seems to have mathematics embedded within it. One widely discussed essay that commented on this was a paper entitled The Unreasonable Effectiveness of Mathematics in the Natural Sciences, written by the physicist Eugene Wigner in 1960. Wigner pointed out numerous cases where scientists took to using mathematical formulas to describe some little understood feature of nature, and such an approach ended up being successful beyond their wildest dreams. An example is Isaac Newton coming up with the formula for gravitation based on earthly experiences and a few astronomical observations, a formula which has been used ever since, and still holds up today as we study distant galaxies (notwithstanding the additional complications of general relativity). Another example is Maxwell coming up with some equations to describe electricity and magnetism, which also proved to be the right equations for radio waves, which were not even discovered until decades later.

Wigner stated, “The miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve.”

This paper provoked widespread comment, and since then it has widely been stated that nature has math within it in some fundamental way. Let's use this as the starting point for a line of reasoning.

Premise 1: It is widely recognized by scientists that in some fundamental way, nature has mathematics kind of embedded within it, as shown by countless cases in which mathematical formulas are the correct way to describe fundamental regularities in nature.

There are numerous fundamental formulas of physics that could be cited to support this statement, such as Newton's law, Coulomb's law, the Schrodinger equation, Einstein's equation for time dilation, and Einstein's famous equation e= mc². The nature of our universe is critically dependent upon such formulas.

Three formulas that dominate our universe

For an example of how impressed modern physicists are by the math within nature, you can look at this piece by physicist Max Tegmark entitled "Is the Universe Made of Math?"

Now let us consider: just what is mathematics? Mathematics is a very general term, which can refer to numbers, elements of geometry such as the circle and the circumference, and also simply logic, in the sense of mathematical algorithms and procedures. Most of what you learn in school when you study mathematics are procedures and algorithms for solving particular math problems.

In fact, mathematics seems to be mainly logic. Some famous philosophers such as Bertrand Russell and Alfred North Whitehead have argued that all mathematics can be reduced to logic, basically taking the position that math is just logic. A major branch of the philosophy of mathematics is called logicism, which maintains that all or most of math is just logic. So it therefore seems justified to state the next premise:

Premise 2: Very much of the math that we see operating within nature is a kind of logic.

If you doubt this premise, simply consider that almost every mathematical formula that appears in a physics text book can be stated in terms of logical statements such as “if/then” statements or algorithmic statements. For example, something such as Newton's law of gravity, which can be mathematically expressed by the formula shown above in the visual, can also be expressed by a logical statement such as “If two particles are separated by a particular distance, then the gravitational force of attraction between them is directly proportional to the product of their masses and inversely proportional to the square of the distance between them, and also proportional to a universal constant G.”

Now let us consider: what type of logic is it nature is applying as it behaves the way we observe it to behave? The answer is that nature uses a very precise logic of complete regularity. By way of contrast, consider the way logic is used by an entity much less regular, for example, a bigoted Southern sheriff of the 1960's. Such a person might have used logic in all kinds of irregular and unpredictable ways, perhaps applying the rule “If I see someone littering, I'll arrest him” if the person aroused the sheriff's prejudices, or if the sheriff was in a bad mood, but completely ignoring the rule if the person was someone who looked like the sheriff, or the sheriff was in a good mood. But nature doesn't act in that kind of mercurial or unpredictable way. When it comes to things such as gravitation, electromagnetism, and the Pauli Exclusion principle, nature applies logic in a completely regular, invariant, precise, and predictable way. The Apollo moon landing in 1969 depended critically on gravitation acting in a completely regular, invariant, precise, and predictable way. The mission designers knew there was absolutely zero chance that the astronauts would ever suffer from a “bad gravity” day caused by gravitation working in an irregular way.

Another aspect of the logic used by nature is that it uses constants, certain fundamental numbers that are always the same. Below are some of the most fundamental constants used by nature.

Some fundamental constants of nature

So we must then state the next premise:

Premise 3: The logic we see operating within nature is a highly regular, invariant, precise, and predictable kind of logic, involving heavy use of fixed numerical constants.

Now we need merely ask ourselves: what are we talking about when we speak of the application of logic in a highly regular, invariant, precise, and predictable way, using numerical constants? This is not behavior that corresponds to the application of logic by human beings. Human beings are notoriously wavering and hard to predict, applying logic in all kinds of variant, biased, unpredictable, and inconsistent ways. The same political leader who will claim to be operating under fixed principles will then operate according to some other principles whenever it suits him politically.

But we do know of one type of system within our cities that does operate according to a highly regular, invariant, precise, and predictable kind of logic, making use of numerical constants. That system is a computer program. That leads to the next premise:

Premise 4: The application of logic in a highly regular, invariant, precise, and predictable kind of way, using fixed numerical constants, is a hallmark of programming.

This is the way computer programs operate. If I have a computer program that adds 1 to a total every time I press a key, the program will keep doing that with great regularity and predictability. It won't just do it 99 times out of 100. Computer programs also make use of fixed numerical constants, and all of the main programming languages have syntax support for declaring a constant within a program. For example, a computer program may have a line such as “const int AgeOfMajority = 18” which declares AgeOfMajority as a numerical constant. Then that constant will be used within the logic of the program, perhaps in a phrase beginning “if (AgeOfMajority >= 18).” 

It is a fair statement that nowadays when we see the application of logic in a highly regular, invariant, precise, and predictable kind of way, using fixed numerical constants, it is usually programming that we are seeing. 

Premise 5: It therefore seems that nature has programming.

This premise follows from premises 3 and 4, not as a matter of perfect certainty, but at least as a kind of likelihood (which is why I have used the word “seems”).

Now let's consider software. Is software something fundamentally different from programming? No. Most full-time software developers are called both computer programmers and also software developers. There's really no difference. So we can state this premise:

Premise 6: Software and programming are essentially the same thing.

Now from premise 5 and premise 6, this conclusion follows:

Conclusion: It therefore seems that nature has software.

This conclusion does not quite follow with metaphysical certainty, but this line of argument will do as a fairly simple bit of reasoning to support the claim that nature has built-in software.

For more elaborate arguments in support of the same conclusion that the universe must have built-in software, see my post The Theory of a Programmed Material Universe and my post Nature's Computation Needs Imply a Programmed Material Universe. 

As I explain in the first of these posts, once we realize that nature has built-in software, we can make much use of this idea as part of an explanatory framework, to help explain our universe's improbable evolution from an explosive beginning of supposedly infinite density to a place of fantastic harmony and order where life and Mind exist.