Detecting Truth

Darwin Starts with a Populated Environment

Darwin’s theory of Decent with Modification through Natural Selection does not address how life began. Darwin’s theory attempts to explain how, over time, some members of a well marked species may begin to diverge in organic structure, habits, etc. into incipient (or emergent) species and eventually into an entirely new species. Darwin’s studies, observations, and postulations begin with an environment already significantly populated with organisms. For instance, in The Origin of Species chapter on the Struggle for Existence, the struggle is against numerous other competing species and is a central component to Darwin’s theory on Natural Selection.

Darwin states in The Origin of Species, Instinct chapter:

“I must premise, that I have nothing to do with the origin of the primary mental powers, any more than I have with that of life itself (1).”

Darwin’s definition of Natural Selection

Darwin states, in The Origin of Species:

“Can it, then, be thought improbable, seeing that variations useful to man [under domestic breeding] have undoubtedly occurred, that other variations useful in some way to each being in the great and complex battle for life, should sometimes occur in the course of thousands of generations? If such do occur, can we doubt that individuals having any advantage, however slight, over others, would have the best chance for surviving and of procreating their kind? On the other hand, we may feel sure that any variation in the least degree injurious would be rigidly destroyed. This preservation of favorable variations and the rejection of injurious variations, I call Natural Selection.” (1)

Problem’s with Darwin’s source of variation required by Natural Selection

Darwin spent a lot of time studying variation in the offspring of domestic plants and animals. His observations in this area are discussed in the first chapter of The Origin of Species, Variation under Domestication, and are the basis for his theory. Darwin states:

“The great power of this principle of selection is not hypothetical. It is certain that several of our eminent breeders have, even within a single lifetime, modified to a large extent some breeds of cattle and sheep. … Breeders habitually speak of an animal’s organization as something quite plastic, which they can model almost at they please.” (1)

It is quite apparent, after reading this chapter, the source of variation Darwin was referring to is explained by classical laws of genetic inheritance discovered by Gregor Mendel and not a process of endless variation that Darwin was envisioning. He was simply witnessing the expression of existing genes within the gene pool of the population he was studying. The rate of change in domestic breeding programs cannot be explained by random genetic mutations (more on random genetic mutations later). It should be noted there is ultimately a limit, although very large, on the trait variation available to a breeder. The limit is based on the number of alleles for each gene available in the gene pool represented by the breeding population.

Darwin states in the Origins chapter, Natural Selection:

“Not that, as I believe, any extreme amount of variability is necessary; as man can certainly produce great results by adding up in any given direction mere individual differences, so could Nature, but far more easily, form having incompatibly longer time at her disposal.” (1)

From his observations of domestic breeding, Darwin mistakenly extrapolated variations (traits or genes) can continue to be “selected” endlessly until a new, strongly marked species has emerged from the parent species. The only way additional potential variations can become available is via a random genetic mutation in the parent’s germline (i.e. reproductive) cells that adds a new allele (version of a specific gene) to the gene pool within the breeding population. This will not typically occur during the lifetime of a cattle breeder.

While Darwin was writing his “Origins” abstract, the genesis of modern genetics was being formulated by Gregor Mendel. Gregor published his work in 1866, just seven years after Darwin published Origins. Gregor Mendel’s work was initially ignored, but in the 1900 time frame, his work was rediscovered leading, ultimately, to the discovery of DNA in 1944.

As a result of the creation of the field of genetics and the discovery of DNA, Darwin’s supporters concluded his theory required a new source of variation not constrained by the large but limited pool of genes in a given population.

It quickly became apparent that Darwin’s observations of variation under domestic breeding and his “Laws of Variation” could not explain the variation required by his theory of Natural Selection that leads to new species. As the study of genetics began to mature, it was discovered that genetic material, DNA, can mutate under certain conditions. Supporters of Darwin’s theory soon assigned random genetic mutation the role of providing the variation required by Darwin’s theory of Natural Selection. But, can random genetic mutation fulfill this role? The theory of evolution will live or die by the answer!

Dr J.C. Sanford states in his book, The Mystery of the Genome:

“Darwin’s only truly innovative concept was the idea that the primary creative force in nature might be natural selection. Yet he had no conception of genetics or mutation, and therefore had no conception of what was actually being “selected”. So he was entirely ignorant of all the problems addressed in this book [Dr. Sanford’s book discusses problems with random mutations as the source of variation] … Not until much later did the neo-Darwinists synthesize genetics, mutation, and natural selection – creating the field of Population Genetics.” (2)

Darwin states in Origins, chapter Laws of Variation:

I have hitherto sometimes spoken as if the variations—so common and multiform in organic beings under domestication, and in a lesser degree in those in a state of nature—had been due to chance. This, of course, is a wholly incorrect expression, but it serves to acknowledge plainly our ignorance of the cause of each particular variation.

Darwin acknowledges his lack of understanding of the source of variation. The bulk of the variation Darwin observes and describes is solely due to classical gene recombination during and organism’s reproduction cycle. It should also be noted that Darwin thought that the source of variation was NOT random. Darwin thought the variation was caused by reproductive systems being exposed to “conditions of life”.

Darwin’s Laws of Variation have proven NOT to be a source of variation needed to support his theory, thus creating a dilemma for Darwin’s supporters. There was a period of time when this was a serious problem for Darwin’s theory. However, when random genetic mutation was discovered, it was quickly substituted for Darwin’s Laws of Variation, consequently rescuing his theory.

The Human Genome – An Information Masterpiece

Modern evolutionary theory states that random genetic mutations, filtered through the sieve of natural selection, have built the gnomes of all living things starting with a hypothetical single celled, primordial organism. It should be noted that, unlike the theory of evolution, the scientific community has not rallied around a natural process that can explain the formation of the first living cell.

The human genome is composed of two sets of 3 billion individual “letters” called nucleotides or base pairs represented symbolically as A, T, C, and G. Current understanding of this genome indicates about 30% is functional and the rest is “junk” DNA (2). The functional portion contains genes that code for over 100,000 known proteins in body. Over the past few years, as the level of understanding of the human genome has increased, the amount of DNA that is considered functional has dramatically increased. This trend will likely continue as a deeper understanding of the human DNA develops.

Modern evolution theory implies random genetic mutation and natural selection have progressively increased the information content in the DNA of living organisms from the first living cell to the pinnacle of complexity, the human being. This represents an increase in genetic information from a few thousand base pairs to 3 billion base pairs and is a dramatic increase in the information content from the first genome to the human genome.

Claude Shannon introduced the concept of Information Theory in his studies of communication systems. Although I will not explain his theory in this article, information theory has raised some very substantial problems with the idea that a process (natural selection) involving a random source of data (random genetic mutations) can produce “meaningful” information. Please read Meaningful Information and Artifact by Sean D. Pitman M.D. to learn more about this topic.

What are genetic mutations?

Genetic mutations are typically copying errors that occur during DNA replication when a cell divides. Errors are very rare, but when they do occur it typically involves a single base pair (A,T,C or G) changing to another letter.

The encoding of genes in DNA is considered a form of information analogous to a book. A mutation is analogous to a letter in a word being randomly changed to some other letter. When the letter is changed, either a valid new word is formed or an invalid word is formed. In the former case, the original meaning of the sentence may be changed. In the latter case, the sentence may become meaningless. When such errors reduce (or delete) the information content in a book or DNA they are considered deleterious (or information reducing) in nature.

Mutations can be categorized as follows:

• Positive mutation – helps an organism produce more offspring that survive to also reproduce.
• Negative mutation – reduces an organism’s ability to produce offspring that survive to also reproduce.
• Neutral mutation – has no effect on an organism’s ability to survive and reproduce.

How often do selectable beneficial mutations occur that add information to a genome?

There are many cases where a mutation is considered beneficial. However, in all cases, it has eventually been proven that the mutation did not add new information of the DNA such as a new gene; instead, the DNA information content was reduced. In all cases, there was a modification of existing genes that, for example, reduced the specificity of a protein (loss of information) that produced the beneficial result. Although this was beneficial to the organism, this type of mutation doesn’t represent the gene building, information adding type of mutation required to build vast, complex genomes. (2) (3)

It is accepted in both the evolution and creation communities that beneficial mutations can occur, but most if not all result in information loss in the organism’s genome. It is also recognized that it is theoretically possible for beneficial, information building mutations to occur. However, this has not been unambiguously documented in any research to date.

Dr. Sanford references a study by J. Bergman in his book:

“Bergman (2004) has studied the topic of beneficial mutations. Among other things, he did a simple literature search via Biological Abstracts and Medicine. He found 453,732 “mutation” hits, but among these only 186 mentioned the word “beneficial” (about 4 in 10,000). When those 186 references were reviewed, almost all the presumed “beneficial mutations” were only beneficial in a very narrow sense – but consistently involved loss-of-function changes (hence loss of information). He was unable to find a single example of a mutation which unambiguously created new information.” (2)

Where must mutations occur to be inherited?

Mutations must be inherited by offspring in order for natural selection to work. Additionally, natural selection can only select an entire organism. It has no power to see inside an organism to select only the heart or kidney or a specific mutation of a single DNA base pair. Natural selection simply destroys the less fit organisms and preserves the more fit organisms.

Thus, the only meaningful mutations are those that occur in the reproductive cells. A mutation that occurs in a muscle cell of a bear will die with that bear and not be passed along to any offspring.

Kimura’s “No Selection Zone” (2) (4)

Dr. Sanford references a study by Motoo Kimura that indicates the overwhelming majority of mutations are near neutral and the rest are negative or have “selective disadvantage”. Kimura didn’t show any mutations that have selective advantage (positive mutations) because they are so rare they were not worthy of consideration in his study. (4)

Earlier, it was mentioned that natural selection works at the level of the entire organism. If a mutation occurs in an organism as the first step in a chain of mutations that would potentially benefit the organism in some way, but by itself doesn’t offer any advantage, natural selection will be blind to the change and will not favor that individual organism in the “struggle for existence”. Additionally, if the mutation doesn’t damage the organism, the mutation is considered a near neutral mutation.

Figure 1: Kimura’s Mutation Distribution Curve

Kimura used a rating scale for mutations that ranged from neutral (0) to lethal (1) in a graph of all the mutations he studied. Nearly all mutations are clustered near 0 (neutral) in his graph. A few were spread out towards 1 (lethal) on the “selective disadvantage” side of the graph and none were shown on the “selective advantage” side of the graph.

Kimura is famous for introducing the concept of a “No Selection Zone” close to 0 in his graph. His research and analysis showed that natural selection cannot “see” mutations that don’t clearly give the organism an advantage or a disadvantage in the struggle for existence. As a result, a species may, over time, build up a “load” of neutral or slightly deleterious mutations; sort of like “rusting out” the genome rather than only “preserving and adding up all that is good”. (1) (2)

This contradicts Darwin’s statements in Origins:

“It may be said that natural selection is daily and hourly scrutinizing, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life.” (1)

The implication of Kimura’s research is that natural selection cannot “see” the vast majority of genetic mutations and when the sought after beneficial mutation does occur, it is predicted to be within Kimura’s “no selection zone”, thus never making it into the gene pool of the population.

So, how often does a beneficial mutation add information to the genome? Statistically Never. We will discuss more reasons why this is the case below.

Reasons a beneficial mutation may not get “fixed” in a population’s gene pool

There are numerous reasons why, once the highly sought after and rare beneficial mutation occurs, it may be lost. For example, the organism containing the mutation may die before it is able to produce offspring and pass the mutation along. The mutation could be recessive and never be expressed in the organism. The mutation may be lost from the population due to genetic “drift” in the gene pool of the population before it has a chance to be “fixed” in the gene pool. There are a number of other factors that together represent some statistical probability that a new beneficial mutation will be lost before it is able to take over a population. These and other related reasons that a beneficial mutation may not get “fixed” in to a population are effectively “noise” that interferes with natural seletion’s ability to see the beneficial mutation.

Dr. Lee Spetner’s Calculation (3)

In his book, “Not by Chance”, Dr. Lee Spetner indicates mutations rates are between 0.1 and 10 per billion transcriptions (DNA copying process) (Fersht 1981, Drake 1969, 1991). For other organisms, the mutation rate is between 0.01 and 1 per billion transcriptions. Spetner performs a calculation to determine the probability of random genetic mutations guided by natural selection can produce a new species that requires 500 steps (Stebbins 1966). Stebbins, an architect of modern evolution, estimated it would take 500 steps to get a new species. (3)

Spetner indicates the following information is needed:

1. What is the chance of getting a mutation? (mean mutation rate used is 10e-10)
2. What fraction of the mutations has a selective advantage (i.e. natural selection will see the mutation as beneficial and preserve it)? (0.1% is used in calculation)
3. How many replications there are in each step of the chain of cumulative selection (i.e. how many births will it take to “fix” the new mutation into the population)? (50 million is used in the calculation)
4. How many of those steps there have to be to achieve a new species? (500 steps is used in the calculation)

For a mutation to be a part of a typical step, Spetner sets the following criteria:

• It must have a positive selective value, and
• Add a little information to the genome

Spetner calculates the chances of a new species being produced by this process as 3.6x10e2738 to one. In his book, Spetner works through several examples leading up to a probability that he thinks most people would agree is impossible such as flipping a coin 150 times and each time it displayed heads (10e45 to one). The probability in the new species example is more than 2000 orders of magnitude smaller than that in the coin example. Thus, Spetner concludes that random genetic variation guided by natural selection cannot produce a new species from an existing one.

Dr. J.C. Sanford’s Calculation (2)

According sources referenced in Dr. Sanford’s book, the human genetic mutation rate is between 100-300 mutations (within the reproductive cells) per person per generation (Kondrashov, 2002; Nachman and Crowell, 2000).

Dr. Sanford, using various assumptions used in the field of population genetics calculates it would take 12 million years to “fix” a single base pair mutation into a population. This mutation is only the first of a series of mutations that would be required to create an entirely new gene. He further calculates that to create a gene with 1000 base pairs, it would take 12 million x 1000 or 12 billion years. This is obviously too slow to support the creation of the human genome containing 3 billion base pairs.

Sequence Space Problem for Theory of Evolution (6)

To round out this EXCEEDINGLY LONG article, I recommend you read and essay by Sean D. Pitman M.D. titled Limited Evolutionary Potential that details the sequence space issue facing the evolution of complex amino acid sequences.

REFERENCES

1. On the Origin of Species by Means of Natural Selection, Charles Darwin, 1859
2. Genetic Entropy & The Mystery of the Genome, Dr. J.C. Sanford, 2005
3. Not By Chance, Shattering the Modern Theory of Evolution, Dr. Lee Spetner, 1997
4. Model of effective neutral mutations in which selective constraint is incorporated, Motoo Kimura, 1979
5. Evolutionary Rate at the Molecular Level, Motoo Kimura, 1968
6. The Emporer has No Clothes – Naturalism and The Theory of Evolution, Website, Sean D. Pitman, M.D.