RESEARCH ARTICLE: Limits of Natural Selection

RESEARCH ARTICLE: Limits of Natural Selection

In order to understand natural selection and how it affects populations, it is necessary to understand something about genetics. I used some terms in the previous chapter which I did not define, but which bear strongly on the natural selection issue. Therefore, this chapter will include a basic primer on genetics, and how genes are transmitted from one generation to the next.

Genetic information is contained within the DNA of an organism. DNA is perhaps the most iconic structure in science. Computer generated imagery has made it possible to view the three-dimensional structure of DNA at a vastly enlarged scale, leading to it being easily recognized by the general public. However, DNA is far more than an interesting structure.

Genetic Overview

In an ultimate sense, DNA is a code, containing all the information necessary for life. This information must be translated from that code. Before discussing the translation process, it would be helpful to understand what DNA is.

DNA, known to science as deoxyribonucleic acid, is a molecule made of three components.  The first part is a sugar, known as deoxyribose sugar. This molecule serves as the backbone of the DNA strand.  Deoxyribose is formed of a D-ribose sugar[1] with a single oxygen molecule removed. The chemical structure of this molecule is C5H10O4. D-ribose has a sugar removed by a special enzyme called ribonucleotide reductase to create deoxyribose[2]. This deoxyribose sugar, as the backbone, provides the support structures for the DNA strand.

The deoxyribose sugar is only half of the backbone, however. The deoxyribose sugars have to be held together by something and, in the DNA strand, the “glue” that holds the strand together is the phosphate group. The phosphate group is comprised of a single phosphate which is bonded to four oxygen molecules. Two of these oxygen molecules bind to the deoxyribose sugars, one at each end. These keep the DNA strand together. These binding sites serve as the link to keep the lengthy strand of DNA together.

The final piece of the DNA strand is the internal connecting links, known as the nitrogenous bases. There are two forms of these nitrogenous bases; pyrimidines and purines. There are three types of pyrimidines and two purines.  Two of each type are found in DNA itself, while the third pyrimidine is found in DNA’s counterpart, RNA.  Normally, pyrimidines will only bond to purines and vice versa.  In fact, there is a specific 1:1 correlation between a specific purine and a specific pyrimidine on the DNA strand. It was this correlation that helped Watson and Crick solve the DNA structure enigma.   There is one exception to this, adenine, a purine, will bond to two pyrimidines, thymine and uracil, though only one at a time. Uracil only exists on RNA strands which are formed from DNA strands (more on that in a moment). These three parts form the entire DNA strand and provide the entire structure of the DNA double helix[3].

Just having DNA is not enough though. The information must be stored in a mechanism called codons[4]. Codons are three letter terms in the DNA which each code for a given amino acid. Amino acids are the building blocks of proteins. However, the codons on the DNA do not directly code for amino acids. Instead, the codons are mirrored as part of the production of RNA. RNA is produced as part of the transcription process. Transcription is catalyzed by special enzymes called RNA polymerases[5]. These enzymes unzip the double helix by breaking the bonds holding the nucleotides together. It then pairs the appropriate nucleotides on the RNA strand to the DNA. While this is happening, a proofreading enzyme checks for mistakes[6].

RNA is then split from the DNA. The DNA is then zipped shut and the RNA packaged to leave the nucleus. Numerous types of RNA are possible, depending on the needs of the cell.  Once it is formed, it is sent out of the nucleus of the cell and, if it is messenger RNA (mRNA), it will go to a special structure called a ribosome where it is translated into a chain of amino acids[7]. These amino acids will be folded into proteins and these proteins will be used to assemble cells and multi-cellular structures.

Because codons code for, eventually, multi-cellular structures, it is important to know these codons are transmitted from one generation to the next. This process is known as heredity. These DNA codons are stored in groups called chromosomes. These chromosomes are packages that contain a portion of an organisms DNA.  Generally, at least in eukaryotes, chromosomes are paired and are passed to the offspring, who inherits one copy of a chromosome from the mother, and one from the father. Organisms with two paired chromosomes are referred to as diploid. While chromosomes are often paired, they are rarely identical in the information they contain.  This permits a significant amount of variation in offspring[8].

Because information is not always identical for a given trait on paired chromosomes, but only one outward expression of that trait is possible, there has to be a mechanism to determine which version of the trait is expressed. Gregor Mendel, the scientist and monk who discovered the principles of heredity, pointed out that this was due to dominance and recessiveness of given traits[9].  When a dominant and recessive trait are present, the dominant trait is the only one expressed. The recessive trait only appears when it is the only trait present. On some occasions, codominance occurs, in which two alleles are equally expressed. This can result in a blending between the traits when they are expressed, or the two together may make an entirely different version of the trait.

Often multiple codons make up an allele and sometimes multiple alleles are involved in the expression of a trait.  Natural selection does not select for codons. Nor does it directly select for alleles.  Instead, natural selection can only see the phenotypes that are expressed by an organism. In other words, natural selection is blind to the genome. It can only see the outward manifestations of the genome. This means that a recessive allele can only be seen by natural selection if it is expressed.  Thus natural selection is, in two-thirds of instances, is blind to half of the genetic potential of the organism by default.  In other words, approximately one-third of the genome that codes for traits is completely invisible to natural selection at all times.

This is incredibly significant. If one-third of the genetic potential of an organism is simply invisible to natural selection, natural selection has much less potential to work with than evolutionists believe.  Worse still, this means any mutations that occur in these blind regions are also invisible to natural selection. This means that one-third of all mutations are completely useless to natural selection. They simply fail to appear. They cannot be selected for or against in a generation.  Only several generations later do they appear and, when they do, often they contribute to a weakened fitness of the population.

The remaining two-thirds of the genome is not always visible.  The environmental influence on selection means that selection can only select against the negative. It cannot select for the positive, something even Richard Dawkins acknowledged “Natural selection, the blind, unconscious, automatic process which Darwin discovered, and which we now know is the explanation for the existence and apparently purposeful form of all life, has no purpose in mind. It has no mind and no mind’s eye. It does not plan for the future. It has no vision, no foresight, no sight at all,[10]” While Dawkins thinks natural selection can explain the origin of diversity, he correctly recognizes that natural selection cannot see the benefit of a slightly positive trait. It can only remove traits which are excessively bad.

Removing excessively bad mutations is a very good thing. It helps keep a population from going extinct. However, removing bad mutations is not evolution. For natural selection to actively improve a population, it must not just remove negative mutations. It must also actively seek positive mutations and select strongly for them to advance the population up the evolutionary tree of life.  This is not what we observe, nor is it what Dawkins, one of the foremost evolutionists of our time, believed natural selection is doing.

Information Theory

 Natural selection has significant limitations. Perhaps the largest one is the introduction of information.  Explaining the origin of information is a significant problem for evolutionists.  Information has been defined varying ways in the scientific community so determining what is meant by information is important and tends to vary depending on the field. Within certain sections of the scientific community, information theory has become widely accepted. This is particularly true within the computer science community. However, it has received some attention within biology as well.

Defining information is incredibly difficult.  One author writing on the topic described information as follows. “More generally, information measures the amount of correlation between two systems, and reduces to a difference in entropies in special cases.[11]” This is using terms from physics with slightly altered meanings.  Entropy in physics refers to potential energy. In biology, it refers to differences in potential information. Thus, this definition of information attempts to say that how much relationship there is between two systems is equivalent to the amount of information present. The more similarity there is between two systems, the less difference there is in potential information. Therefore, they are more similar in information content.

That might sound a bit confusing. In practice, what it meant is much simpler.  Information exists in the genome as the blueprint for what makes the organism.  Potential information in the genome is information which is not expressed but is present. Later in the same paper, the author writes “Information is always about something. (emphasis his)[12]” In other words, information always conveys a message. The message is what is meant by the sender (more on that in a moment.)

Another important facet of information is that it is coded. In other words, information is always presented in a coded form[13]. This should come as no surprise to anyone. After all, if someone who spoke no English were to attempt to read this book, they would fail to understand most of it. Why? Because the English language is the code in which the information in this work is presented. In order to understand the message of the information, one must understand the code in which it is sent.  This analogy applies neatly to DNA, because like English, DNA is also a code[14]. In order to understand the information contained in the DNA code, you must be able to translate it into a form you can understand.  This applies to the cell as well. The cell must be able to translate the DNA code into a form it can recognize.  It does this by means of RNA and ribosomes which was discussed above.

Another extension of information theory is that information, by default, cannot be material. Gitt formulated this well. “It should now be clear that information, being a fundamental entity, cannot be a property of matter, and its origin cannot be explained in terms of material processes.[15]” In other words, because information is, by its very nature, a message, it cannot be material.  While the physical medium used to convey the message may vary, the actual ideas that the message conveys cannot be reduced to matter.  Matter cannot explain the genesis of information.

If matter is not the source of information than what is? As noted above, information is always a message and a message is always conveying information from a sender. Therefore, the very existence of information implies an intelligence greater than the contents of the information. Since even humans themselves are made from incredibly specific, complex information, by extension, humans must have arisen as the result of higher intelligence.  As an analogy, consider a computer.  Computers are composed of highly specific, integrated information and demonstrate a high degree of intelligence.  Yet creating a computer requires a team of incredibly intelligent team of programmers, designers, and developers.  The computer’s information is a product of the information that originated with the team that designed it. The information in the computer did not originate in the computer.  In the same vein, the information in humanity did not come from humanity. It had to come from a source of information much higher than mans.

The implications of this idea are significant. If matter cannot explain the origin of information, and DNA is an information code, then matter cannot explain the origin of DNA. Logically, by extension, if DNA could not have originated solely through matter, then purposeless chance evolution is ruled out by definition.  Note that this does not rule out evolutionary processes by default. It is possible, in a historical science sense, that God could have used evolution, however badly this mangles the Scripture.  All that information being immaterial proves is that there must be an informer.  Information is the stake through the heart of atheism.

In fact, information theory is so damaging to the evolutionary worldview, even articles in secular peer reviewed journals have been forced to admit it since the 1980s! “It is found that self-organization must yield only genetic message ensembles of information content much too low to constitute a genome. It is shown that the statistical structure reflected in “the instructions in the amino acids themselves” is an impediment to the generation of genetic information not a source of it. It is concluded that at present there are no scientifically valid origin of life scenarios.[16]”  This is not buried in the lower third of the paper. This is in the abstract of a paper published in 1981.  And, in case you are thinking there have been a lot of advances since then, a paper in 2018 discussing the origin of DNA said much the same thing, admitting they were “stuck” on the origin of DNA[17].

While evolutionists have acknowledged in the past that information is crippling to their dogma, they still talk about information theory quite frequently. This disconnect is only explainable two ways. Either there is a massive cognitive disconnect in their brains, which happens on occasion, or they have developed a rescuing device.  In this particular instance, they do have a rescuing device that they deploy regularly to explain the origin of information. Their rescuing device is mutations.

Mutations

As mentioned above, DNA is the information for life. The DNA strand of an organism contains all the information needed to produce that particular organism.  Different organisms have DNA strands of different sizes. The DNA is stored in special structures called chromosomes. Chromosomes generally are paired, with sections called genes that code for variants of the same trait on each pair.  Genes themselves are poorly defined.  The original Mendellian idea claimed that genes directly coded for traits though the term “gene” was not coined until 1909[18]. However, since then, it has been discovered that single segments of the genome code for multiple traits. “We have amassed tremendous knowledge, which has forced a reconsideration of the question of what genes are. Not only might coding regions be transcribed in both directions in different ways, but they are variously spliced in ways that may be context specific, so that a classical “gene” can code for multiple proteins used in multiple pathways.[19]”  In other words, genes no longer are believed to code for a single trait.  Instead, many of these genes code for multiple traits and can be read backwards and forwards, and from multiple starting points.

The implications of this view of genes are significant, but we will pass over them for the moment. We will return to them once we have established what is meant by mutations. To the Neo-Darwinists, mutations are the source of all new variation.

Mutations are any change in the sequence of the DNA strand.  Because of DNA’s complexity, mutations are generally considered deleterious and, according to information theory, represent a loss of potential information. To the evolutionists, however, mutations are the answer to the evolutionary problem. These changes in the DNA strand come in numerous types.  Without going through all the types of mutations, which are immaterial to this book,  mutations can be regarded as the primary mover in the evolutionary dogma.

Evolutionists argue that mutations we observe in the present represent a gain of fitness. However, this is entirely different from a gain of function. Though it may seem paradoxical, it is possible that a loss of function will result in a gain of fitness.  To my knowledge, every mutation that evolutionists postulate to provide fitness represents a loss of function that confers a situational advantage. Several common examples are cited, from antibiotic resistant bacteria, to HIV resistance in humans. In every instance, there are significant drawbacks, which the evolutionists have acknowledged in at least some instances. “In the absence of the selecting drugs, chromosomal mutations for resistance to antibiotics and other chemotheraputic agents commonly engender a cost in the fitness of microorganisms.[20]” According to the evolutionists, antibiotic resistance is a loss of information and hurts the bacteria unless antibiotics are present.  The same goes for HIV resistance. Recent research has demonstrated that people with the mutation conferring HIV resistance reduces lifespans on average by 21%[21].

Even if no beneficial mutations are observed in the present, evolutionists still postulate that beneficial mutations in the past were the source of all the variation we observe in the present.  This being the case, it behooves us to ask whether natural selection and mutations can drive the evolutionary process.

Natural Limits

As defined in the previous chapter, natural selection has significant limits.  It is blind to neutral mutations or mutations that are only slightly deleterious.  It only removes outliers.  If a mutation is slightly deleterious, it could persist in the population, as discussed above. As noted above, beneficial mutations are either extremely limited or non-existent.  Since beneficial mutations are essentially non-existent, natural selection can only select for deleterious mutations.  Over time, this would result in degradation of a population’s genome and eventual extinction.  This is known as genetic entropy, something well known to creationists[22].

Genetic entropy predicts that the genome of humans, along with all other living organisms will break down over time. This is expected and observable. We know that mutations tend to increase in a population over time. This is demonstrated in human Y chromosomes which accumulate up to 200 new mutations per generation[23].  Since the vast majority, if not all of the mutations are deleterious, there will, logically, be a steady increase in deleterious mutations in a population.  Eventually, these mutations will so cripple a population that it will go extinct.

So what exactly does natural selection have to work with? From what has been written so far, it appears the materials for natural selection to operate on are a mountain of deleterious mutations. The loss of function in these mutations eventually builds up to the point where the animal goes extinct. Natural selection cannot counteract this. Since natural selection only works as a conservative force, it cannot replace the slightly neutral mutations. It actually conserves them. Thus indirectly, natural selection contributes to the extinction of organisms by not removing the deleterious mutations.  On the flip side, natural selection moderates the rate of extinction by removing the worst mutations and leaving only the slightly damaged and untouched genes in the population.

This brings us back to the implications of the gene being able to be read backwards, forwards and from random points within the reading frame.  When humans, with all our knowledge and foresight, write books, we write them to be read left to right, at least in English.  If you were to attempt to read an English book right to left, as DNA does, it would read like utter gibberish. Just consider the following example from Genesis 1:1. Read normally in English it reads “In the beginning God created the heaven and the earth.” Trying to read it as DNA does would result in the following gibberish. “Htrae eht dna nevean eht detaerc dog gninnigeb eht ni.”  While there are two English words in there (DNA and dog) the sentence no longer makes any logical sense whatsoever.  Even if you split randomly in the middle of Genesis 1:1 you still end up with garbled information. Splitting at the tenth letter and stopping at the thirtieth yields this absurdity: “ning God created the hea”.  This simply does not work.

Now evolutionists might argue that, even though we do not understand them, the other readings of Genesis 1:1 are still information.  Or, they might argue that this is not an example of mutations and that mutations can alter the DNA code in such a way that it can produce legitimate new information. I will address both of those in turn.  Neither objection is valid.

Are the other readings of Genesis 1:1 still information? They are not. Attempting to put the reversed Genesis 1:1 into Google translate yields a suggested language of Estonian. However, the translation into English yields a mashed up, senseless collection of letters.  So it is not Estonian. And even if it was Estonian, or any other language,  it would not matter. It needs to be legible in the same code in which it is written. DNA does not flip from coding in nucleotides to coding in something completely different when read in reverse. It still codes in nucleotides. Therefore, the analogy presented above is perfectly acceptable and accurate.

Evolutionists may also argue that the analogy presented above did not accurately present mutations. In that, they are correct. However, we can present that as well using Genesis 1:1 and the outcome will still be the same. For example, consider this reading of Genesis 1:1, with an insertion mutation from Genesis 1:2. “In the beginning God crwithout form andeated the heaven and the earth.” Parts of the verse still make sense, but the meaning is lost. It has been garbled. Perhaps a substitution mutation would help. “In the beginning God created the hemann and the earth.” That substitution does not help. In fact, even though the substitution was information, it still no longer makes clear sense.  Deletion mutations are no better. “In the eated the heaven and the earth.” Again, the mutation does not create new information. All it does is garble existing information. The final type of mutation, the frame shift, does no better. “In theeginnin gGo dcreate dth eheave nan dth eeart h.” The frameshift mutation in this example occurred on the word “beginning” removing the “b” and changing the syntax of the sentence.  Because of the mutation, the sentence is no longer readable.

The above paragraph should demonstrate just how destructive mutations are. Just one mutation applied to Genesis 1:1 butchers the meaning and syntax of the sentence. Given that DNA is far more complex than the English language Genesis 1:1 is presented in here, what must one mutation do to DNA?

Since mutations cannot, by default produce new information, as has been demonstrated by the above examples, the evolutionists have no mechanism to produce new information.  Therefore, there are limits to how much the genetic code can change and still be functional. This means that natural selection is limited in what it works with. It cannot work with something that does not exist. Until the information exists in the genetic code, natural selection cannot operate on it or influence it at all.

Conclusion

This is a significant problem for evolutionary dogma. Natural selection is promoted as the primary mechanism of evolution. However, evolution requires unlimited change from a single celled progenitor to create all the variety we observe in the world.  As we have demonstrated above, natural selection is limited by the availability of information in a population. If natural selection is limited, then it cannot be the mechanism that produces the variety we observe.

Even worse, the evolutionist’s mechanism for providing new information, mutations, are completely unworkable, given the specified complexity of the genome.  The ability of the genome to be read in multiple directions and from multiple starting points means that a mutation no longer can be believed to affect just one trait. Instead, even if it were to be beneficial in one trait, the change that is made would also be deleterious to all the other traits involved in the reading frame. In other words, mutations represent a net loss of potential information and a net loss of function.  While not all mutations are created equal, in that some of them do extensive damage, while others are nearly completely neutral, all mutations do degrade the genome.  Further, as pointed out previously, unless the mutations are significant, in that they produce a phenotype that is either much more survivable, or much less survivable than the rest of the population.  We only observe the latter. Therefore, populations should be running downhill, and in fact, they are.  Natural selection and mutations are not the answer for evolution.

 

References

[1] There are two forms of ribose. D-ribose is the naturally occurring form of ribose. L-ribose, its mirror image, is only produced in laboratory conditions so I will just use ribose for D-ribose in this book for simplicity.

[2] Pete Reichard and Anders Ehrenberg. “Ribonucleotide Reductase­–A Radical Enzyme.” Science Volume 221, No.4 (1983) Pages 514-519. https://www.jstor.org/stable/1691206?seq=1#page_scan_tab_contents

[3] Kevin Beck “What Are the Four Nitrogenous Bases of DNA?” Sciencing August 14,2018 Accessed November 14, 2018. https://sciencing.com/what-four-nitrogenous-bases-dna-4596107.html

[4] James D. Watson and Andrew Berry. DNA New York: Alfred A. Knopf, 2003.

[5] Richard R. Burgess, Andrew A. Travers, John J. Dunn, and Ekkehard K.F. Bautz. “Factor Stimulating Transcription of RNA Polymerase.” Nature Volume 221 (1969) Pages 43-46. https://www.researchgate.net/profile/Richard_Burgess3/publication/18286739_Factor_Stimulating_Transcription_by_RNA_Polymerase/links/00463518b9f4384d35000000/Factor-Stimulating-Transcription-by-RNA-Polymerase.pdf

[6] Margaritis Voliotis, Netta Cohen, Carmen Molina-Paris, and Tanniemola B. Liverpool. “Backtracking and Proofreading in DNA Transcription.” Physical Review Letters Volume 102, No. 258101 (2009) Pages 1-4.  https://www.researchgate.net/profile/Netta_Cohen2/publication/26721248_Backtracking_and_Proofreading_in_DNA_Transcription/links/0fcfd5102732597be2000000/Backtracking-and-Proofreading-in-DNA-Transcription.pdf  

[7] Michael Ibba and Dieter Soll. “Aminoacyl-tRNA Synthesis.” Annual Review of Biochemistry Volume 69 (2000) Pages 617-650. https://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.69.1.617

[8] Samuel Levy, Granger Sutton, Pauline C. Ng, Lars Feuk, Aaron L. Halpern, Brian P. Walenz, Nelson Axelrod, Jiaqi Huang, Ewen F. Kirkness, Gennady Denisov, Yuan Lin, Jeffrey R. MacDonald, Andy Wing Chun Pang, Mary Shago, Timothy B. Stockwell, Alexia Tsiamouri, Veneet Bafna, Vikas Bansal, Saul A. Kravitz, Dana A. Busam, Karen Y. Beeson, Tina C. McIntosh, Karin A. Remington, Josep F. Abril, John Gill, Jon Borman, Yu-Hui Rogers, Marvin E. Frazier, Stephen W. Scherer, Robert L. Strausberg, and J. Craig Venter. “The Diploid Genome Sequence of an Individual Human.” PLOS B (2007) https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050254

[9] Gregor Mendel (translated William Bateson)“Experiments in Plant Hybridization” Verhandlungen des naturforschenden Vereines in Brunn Bulletin 4 (1865) Pages 3-47. http://old.esp.org/foundations/genetics/classical/gm-65-a.pdf

[10] Richard Dawkins, The Blind Watchmaker (New York: W.W. Norton & Company, Inc. 1996)

[11] Christoph Adami “Information Theory in Molecular Biology.” Physics of Life Review Volume 1, no. 1 (2004) Pages 3-22. https://www.sciencedirect.com/science/article/pii/S157106450400003X

[12] Ibid

[13] Gitt, 2005.

[14] Adami, 2004.

[15] Gitt, 2005.

[16] Hubert P. Yockey “Self organization of life scenarios and information theory.” Journal of Theoretical Biology Volume 91, no. 1 (1981) Pages 13-31. https://www.sciencedirect.com/science/article/pii/0022519381903702

[17] Adam Kun and Adam Radvanyi. “The evolution of the genetic code: impasses and challenges.” BioSystems Volume 164 (2018) Pages 217-225. http://real.mtak.hu/73375/1/KunRadvanyi-GeneticCode-Manuscript_Formatted.pdf

[18] Wilhelm Johannsen The elements of heredity (Elemente der exakten Erblich-keitslehre) Jena, Sweden: Gustav Fischer; 1909.

[19] Anne V. Buchanan, Samuel Sholtis, Joan Richtsmeier, and Kenneth M. Weiss. “What are genes “for” or where are traits “from”? What is the question?” Bioessays Volume 31, no. 2 (2009) Pages 198-208. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807122/#R27

[20] Bruce R. Levin, Veronique Perrot, and Nina Walker. “Compensatory Mutations, Antibiotic Resistance and the Population Genetics of Adaptive Evolution in Bacteria.” Genetics Volume 154 (2000) pages 985-997. http://www.genetics.org/content/genetics/154/3/985.full.pdf

[21] Xinzhu Wei and Rasmus Nielsen. “CCR5-D32 is deleterious in the homozygous state in humans.” Nature Medicine Volume 25 (2019) Pages 909-910.

[22] John C. Sandford Genetic Entropy New York: Feed My Sheep Publications, 2005.  

[23] Yali Xue et al. “Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree.” Current Biology Volume 19, Issue 17. (2009) Pages 1453-1457. https://www.sciencedirect.com/science/article/pii/S0960982209014547

 

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