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Creation Science ResourceA New Look at Genetic Recombination

by Christopher W. Ashcraft M.S.

Abstract

Homologous DNA recombination occurs in all organisms, and is at the heart of genetics. Since its discovery, these reactions were assumed to occur randomly along the length of chromosomes. However, recent findings have revealed that meiotic recombination is not the random process it was originally assumed to be, and controlled by highly organized regulatory systems. In addition, a clear connection between this process, and the production of new genetic information has been established through in vitro, and in vivo studies. Recombination is the principal source of genetic variability driving evolution, and therefore a critical area for future intelligent design theory and research.

 


When Charles Darwin formulated his theories regarding evolution, he proposed that random mutations were responsible for varieties such as the finches on the Galapagos Islands before population geneticists determined that genetic recombination alone is responsible for this quantity of change. Although the Origin of Species was published in 1859, the participation of the cell in the production of the variability he described was not established until Gregor Mendel's work, which was not published for several years later, and largely ignored until 1900. Mendel determined that characteristics such as size, shape, and color would be distributed to offspring in fixed patterns showing cellular mechanisms were instead responsible, and he is now considered the father of modern genetics.(1) Following a century of genetic studies, it is now thoroughly understood the features possessed by organisms are intentionally varied during reactions called homologous DNA recombination. Despite this well-known fact, the theory of evolution remains reliant upon a source of new genetic information that is independent of cellular mechanism to explain diversity before proteins were present to catalyze these reactions. Ultimately Darwinian evolution is an attempt to explain the unintentional development of life on earth, and requires a random mechanism for generating new genetic information.

"Mutation is the ultimate source of all genetic variation found in natural populations and the only new material available for natural selection to work on." Ernst Mayr. Populations, Species, & Evolution. 1970, p.102

Review of Genetic Recombination

The bacteria (E. coli) has been the prime experimental organism for studies on homologous recombination, and investigations of meiosis have mostly been performed using lower eukaryotes such as the baker's yeast (Saccharomyces cerevisiae), and fruit flies (Drosophila). More recent work with mutated mice has also provided information on these reactions in mammals. This research has shown that substantial differences exist between unicellular and multicellular organisms, but like most cellular mechanisms, the basic details of homologous recombination appear conserved throughout all cell types.(15) Decades of genetic, morphological, and molecular investigations have now established without question that internal mechanisms are altering the genomes of each cell used for sexual reproduction, and yet the reactions that are occurring remain unknown. Despite the absence of specific knowledge regarding the products of recombination, random mutations are credited for all changes to gene sequence.

Fig 1. Meiosis
During these stages of meiosis, homologues pair-up along the cell axis while recombination takes place, then the genetically unique chromosomes are pulled apart into daughter cells. Although the exact changes remain theoretic, it is from these differences that nature selects, and through which evolution occurs. Another division will separate the sister chromatids, and generate gametes with only half of the genetic material possessed originally.

During sexual reproduction, an organism is formed from the fusion of two gametes (egg, sperm, pollen) that are produced during a unique cell division process called meiosis.(Figure 1) It is during this portion of the cell life cycle where the parental genomic DNA is recombined by cellular mechanisms to introduce genetic variability. The entire nuclear genome condenses during meiosis into organized units called chromosomes that interact as distinct pairs. These paired homologous chromosomes possess sequences that are very similar, and code for variations of the same characteristic like sex determination. Prior to the division of DNA into new daughter cells, the homologous pairs of chromosomes are cleaved and spliced together at multiple locations. During these interactions DNA is exchanged, but the exact details remain unknown. Figure 2 shows a general formation produced during homologous recombination in prokaryotes and eukaryotes called a Holliday formation. This splice junction is formed from a duplex of complementary stands derived from each parental DNA molecule. The duplex junction has been shown to extend large enough to cover an entire gene, and ensures exact alignment allowing recombination to occur under precise control. Many genes involved in homologous recombination are conserved among all organisms, and in particular, the duplex joints are formed through reactions mediated by the commonly found RecA/Rad51-family of proteins.(14)

Fig 2. Holliday Junction
Recent work has added further substantiation to the existence of a DNA formation known as the Holliday junction. During recombination the junction exists as a series of intermediates during the cascade of reactions involved with the formation of the recombinant DNA.

Genes typically exist within a population as a number of varieties (alleles), and as a result the features they produce are polymorphic or are present in more than one form. Offspring variations are largely produced by the intentional recombination of alleles during meiosis, and it was the regulation of this process that was demonstrated by Mendel's experiments. Mendelian genetics, and selective breeding histories have answered a great portion of the mystery behind heredity. However, the relationship between meiotic recombination, and the selectable phenotype remains far from understood.(9) No two offspring are ever the same because the gametes generated for sexual reproduction are always genetically unique (i.e. DNA fingerprinting). A relatively short history of recombination, and artificial selection has led to a tremendous variety of domestic breeds such as the dogs. Since their discovery, it has been largely assumed recombination events create these differences by simply rearranging genes into other combinations, and any new alleles (variations of genes) are believed to be the result of unintentional mistakes such as replication errors, or through exposures to external mutagens.

In addition to sexual reproduction, the recombination of homologous DNA sequences is induced or shut off as a programmed cell function during differentiation, development, and is also stimulated in response to a wide variety of environmental stresses. It is also well recognized that recombination is controlled by highly organized regulatory systems.(6) The induction of meiotic recombination is reliant upon several genes, and is regulated by a complex network of cellular signaling mechanisms.(14) Furthermore, a cascades of specific macromolecule interactions has been recognized to coordinate and regulate catalysis.(10)

Since their discovery or that of genetic mapping it was assumed that homologous crossing-over during meiosis occurred at regular intervals along the chromosomes, however, these presumptions have been largely shattered by a variety of discoveries indicating that differential recombination rates and patterns exist. For example it is now well-known recombination frequency is not constant in any one particular cell. Reactions occur more frequently in some regions of the genome than in others, with variations of several orders of magnitude observed. These hyperactive regions have been termed "hot spots" and as opposed to inert "cold spots" where little to no nucleotide exchange is found.(3) The process of recombination is likewise recognized to be significantly different when comparing somatic and germ-line cell types, and events during meiosis are known to generally occur at a much higher frequency than in mitosis. For example mitotic recombination frequencies in the fungus Ustilago maydis have been estimated at 2.9 x 10-7, whereas in meiosis the rates are closer to 1.9 x 10-3. Sex-specific differences in recombination frequency are now also relatively well elucidated. Standard linkage analysis was used to confirm that females have a higher recombination rate than males, and males recombine preferentially in the distal regions of the chromosome. These and other techniques were separately used to establish the existence of significant inter-individual variation in recombination over short intervals.(13) Still other researchers demonstrated background effects on the frequency of recombination using immunostaining techniques to assess meiotic exchange patterns. It was found in this case and many others that crossover events were non-randomly distributed and displayed positive interference.(2)

A New Look from Intelligent Design Theory

The ability of the cell to intentionally modify the genome through homologous recombination deserves considerable analysis from intelligent design theorists. It has become clear from a variety of sources that indeed organisms possess new genetic information. Prokaryotes are known to readily uptake polynucleotides, and all major taxa are able to exchange genes across species barriers through homologous recombination.(19) It was in fact the genetic transformation of bacteria in the late 1920's that finally led to the discovery of DNA as responsible for the heredity of life. Biotechnologists have now also learned they can easily transform eukaryotes with foreign DNA, and routinely use this ability to create genetically modified organisms such as herbicide resistant crops. Many of the procedures used to transfect plant and animal tissues simply stress the cells or breech the plasma membrane in the presence of DNA, and some will uptake the genetic material. (Figure 4) It is now apparent that all cell types can be genetically transfected with little difficulty, and any extracellular sequences will be incorporated into the genome if there is sufficient homology.

Fig. 4 Gene Gun
Biolistics or the "gene gun" is the most commonly used technique for performing genetic transformations. It employs a high pressure delivery system to shoot tissue with gold or tungsten particles that are bound by DNA. Although the propulsion is now most typically accomplished using a gas such as helium, the original variation of this system from Bio-Rad was equipped with a 22 caliber pistol. Following a shot with the gene gun, some of the cells will transport the sequences into the nucleus and splice them into the genome.

Genetic samples from living populations have also shown that closely related species possess an extremely high percentage of polymorphic DNA. The number of alleles discovered to date is in fact so high it proves without question they are variations of preexisting genes. For example the cystathionine -synthase gene locus has been intensely studied in humans due to vascular, skeletal, and nervous system problems resulting from deficiencies in protein activity. Exon 8 in particular has been found with a high frequency of sequence repeats or single base variations, and it is estimated that about 5% of human Caucasians possess alterations in this region.(18) While it is true random mutations are not likely to accomplish any significantly advantageous modification, the machinery within the cell has been overlooked as a source for this new genetic information. The incorporation of foreign DNA, interspecies gene transfer in bacteria, and the genetic variations produced during meiosis are all the result of cellular-performed homologous recombination. These reactions were intelligently designed to produce these genetic changes, and are widely known to modify the physical nature of biological organisms through this process.

Homologous recombination is indeed most important for its ability to create the offspring variability from which nature selects, and through which evolution occurs. Following cell division we cannot determine whether homologous recombination or mutations were responsible for changes to gene sequence, and yet it has been simply assumed that any alterations to a reading frame are an unintentional consequence of these and other DNA manipulations such as replication. (Figure 5) Environmental adaptations are indeed the result of natural selection upon individuals with genetic differences, but it is extremely unlikely that random changes to a complex genetic code could produce any significant usefulness or evolutionary assistance to an organism. Despite this rather obvious fact, the theory of evolution requires random mutations as the ultimate source of new genetic information, and yet within the last few years the scientific communities best example has collapsed. The mitochondria were previously thought to offer evidence that new alleles form through mutation alone because it was believed the organelle's genome was obtained exclusively from maternal contributions. However, it has been recently reported in the journal Science that recombination between parental genomes also occurs in mitochondrial DNA. Evidence of mixing of paternal with maternal DNA in the mitochondria was evident, and it was concluded there had been recombination between the parental genomes.(4,5)

Fig 5a. It is believed the intended function of recombination is to leave existing genes unchanged by crossing over between reading frames.
Fig 5b. Crossovers within genes are able to create new alleles, however it has been assumed any changes to sequence are the result of unintentional modifications.
 

Although the exchange or movement of alleles from one homologue to another does occur during meiosis, it is now well recognized that recombination is not just limited to these procedures. In addition to creating genetic diversity in offspring, recombination is involved in error-free DNA repair, and is stimulated by double-stranded breaks during any stage of the cell cycle. The repair function of recombination maintains the integrity of the genome through the accurate correction of several different types of DNA damage.(14) In fact homologous recombination is now known to be induced by a wide variety of environmental stresses such as nutrient deprivation, high cell density, and a great many carcinogens. These reactions are also believed to be involved with editions such as deletions, duplications, and translocations between dispersed homologous sequences.(12) The ability to induce homologous recombination during times of stress would also provide obvious survival advantages through the introduction of new genetic information. Mutations would be clearly disruptive in their affect, however homologous recombination is theoretically able to use portions of preexisting genes to assemble novel proteins in a systematic manner.

"The ability to induce homologous recombination in response to unfavorable environmental changes would be adaptive for each species, as it would increase genetic diversity and would help to avoid species' extinction. Homologous recombination would be more efficient for evolution than random mutagenesis or nonhomologous recombination. Although the latter two will mostly disrupt previously existing genes rather than creating new ones, homologous recombination can use previously existing genes as building blocks, thus enabling the creation of new proteins with more complex functions in a step-by-step manner. " Proc. Natl. Acad. Sci. U.S.A. 98(15):8425-8432 (2001) 

Whether mutations are responsible for the development of any significant useful information is unclear, but the machinery within the cell cannot be excluded from theoretically possessing the ability to assemble new gene constructs from portions of native and foreign sequences. Recently the rapid acquisition of new functional proteins by homologous recombination was demonstrated in laboratory experiments, and was shown to be much more efficient than simple random mutations. Using a technique called DNA shuffling, a pool of mutated genes was fragmented and reassembled by a self-priming polymerase chain reaction (PCR). Although not exactly the same as cellular recombination, it incorporates the formation of a duplex joint through complementary strands. Using this technique it was demonstrated that recombination directed the evolution of a gene product with a significant increase in comparison to simple mutagenesis techniques. Also, when a mixture of DNA from related organisms was used as starting DNA, the efficiency of the directed evolution of the gene(s) was extensively enhanced.(16)

In addition to crossing-over or the exchange of alleles, there is an entirely new class of homologous recombination only recently recognized that may share common mechanisms. During the process of gene conversion, homologous pseudo genes are used to create gene variations, and are easily distinguished from cross-overs because only one of the pairs of homologous sequences are altered. During gene conversion, no other part of the active genome is altered, but instead regions typically referred to as junk DNA are used in the production of this variabilty.(Figure 6) DNA repair through conversion is performed when the regions flanking the damage are replaced by an intact copy from the sister chromatid or homologous chromosome. It has been documented that mitotic recombination via gene conversion is able to create genetically altered cells, and suggested that conversion can generate a gene with novel functions by rearranging various parts of the parental open reading frames.(11)

Crossing over VS Gene conversion 
Fig 6. Two Classes of Homologous Recombination
"While meiotic crossing over is supposed to create genetic diversity by producing new combinations of alleles derived from parents and the genetic diversity may help cell to adapt to such unfavorable conditions, the significance of meiotic gene conversion has not been well understood" Quote and figure reproduced from: Functions of Homologous DNA Recombination. Takehiko Shibata. Riken Review 41:21-23 (2001)

Without a doubt the immunity system provides the best example of the ability of the cell to generation new genetic information through homologous recombination. Antibody specificity for foreign substances is now known to be due primarily to gene editions that alter the antigen-binding site. It is typically assumed that any gene variations or alleles are the result of random mutations, and the changes on the antibody (V-regions) have been largely attributed to such unintentional alterations. Contrary to these assumptions, the V-regions on immumoglobulin were first demonstrated to be participating in gene conversion in chickens, and these reactions are now known to be the mechanism responsible for V-region alterations in most mammals.(21) The variable region of the antibody gene is altered through repeated rounds of intrachromosomal gene conversions that occur between the variable gene, and a pool of homologous pseudogenes that are being used as donor sequences.(17) In many vertebrates including humans, the V-region is altered by a different mechanism that makes single base pair substitutions instead of through the use of template pseudo genes as previously mentioned. These alterations have also been assumed to be due to mutations resulting from relaxed replication fidelity; however, a clear connection was established this past year between these numerous individual changes termed "hypermutations", and the process of gene conversion. A putative RNA editing enzyme (AID - activation-induced cytidine deaminase) was already known to be required for hypermutations to occur in the V-region, and has now been recognized as necessary for gene conversion also. This fact suggests that AID plays a pivotal role as master controller of antibody gene modifications.(20) Although the mechanisms of gene conversion within the V-regions remain unknown, these gene changes are clearly due to cellular mechanisms which produce these variations with intent.

Conclusion

Current creation science concepts of genetic heredity are based on early assumptions that are now known to be incorrect. It has become clear that crossovers do not occur at random intervals along the chromosome, and likewise that recombination is also involved with DNA repair and gene conversion. The real function of recombination during meiosis likely remains misunderstood because secular science is assigning the tasks they are performing to a source that is independent of cellular design (mutations). It has been broadly assumed that genetic variability such as the changes responsible for antibody specificity are the result of random errors, and yet in most cases they appear the result of intentional cellular reactions. Suggestions of randomness in the development of antibody specificity are also argued strongly by the fact that vaccinations produce certain outcomes. When a vaccine is effective in a particular species, it will completely eradicate a disease from the population because every single individual will develop immunity when inoculated. There are many examples of viruses such as Polio and Small Pox that have been completely eliminated from the face of the planet because it is unquestionable that functional antibodies will be assembled following an exposure to almost any foreign substance. This acquired immunity is largely produced through alterations to the genes that produce antibodies, and random genetic changes cannot with certainty produce a positive outcome.


The theory of evolution requires an abiotic mechanism to create new genetic information, and therefore secular science holds steadfast to Darwin's assumptions despite evidence to the contrary, and assumes that all new alleles were formed unintentionally. The undisputed function of these reactions during meiosis is to recombine parental DNA, and thereby produce offspring variability. Subsequent selection upon these recombinants has led to the variety of domestic breeds commonly used by humans today. In nature these changes provide adaptive capability, therefore the function of genetic recombination is unquestionably to drive evolution. Although gene shuffling clearly occurs as a result of this process, it is now well recognized that foreign or altered genetic codes(alleles) are being used by various organisms today. Homologous recombination is also now known to produce genetic diversity through gene conversion, and it is not illogical to assume the cell is designed to intentionally modify genes during these reactions. Unfortunately it is largely assumed by most creation scientists that mutations were responsible for any new alleles. In fact, a great many creationists do not believe new alleles are produced as a result of design, and the evolution of groups such as the canine breeds was simply the result of shuffling preexisting genes.(7, 8)

"Recombination explains why children look different from their parents. This shuffling of the genes can produce superior combinations of different genes. However, because we see that mutations are incapable of supplying useful variation, the useful genes that are there to be shuffled must have been created at the beginning." The History of Life. Lane P. Lester. Creation Research Society Quarterly 31(2) 1994 p96 

However, recent evidence has adequately illustrated that organisms are uptaking foreign DNA, and using modified native genes. The percentage of unique alleles found present in closely related eukaryotes such as humans is certain proof that indeed we are using altered DNA.(18) We also know all cell types are able to uptake and incorporate foreign DNA into their genome, and interspecies gene transfer occurs readily in all major taxa of bacteria through homologous recombination.(19) There are still further examples of organisms that appear to have acquired or developed new genetic information such as in the cases of bacterial antibiotic resistance. In fact many instances have been found where an organism possesses a unique gene, which gives it the ability to tolerate an otherwise toxic environment. This fact has on numerous occasions allowed very important genes to be isolated, and used for research or medical purposes. For example the bacteria, (Thermus Aquaticus) was found thriving in Yellowstone hot springs at temperatures greater than it previously thought possible for life to exist, and it was therefore recognized to possess proteins that are stable at higher temperatures than all other cells. The enzymes isolated from these organisms are now widely used in laboratory reactions throughout the world for copying polynucleotides using PCR. Such highly adapted organisms are often found to possess genes not present outside the habitat in question. This frequent pattern suggests the genes responsible were either lost in all other related organisms, or were constructed through a history of recombination while under regional-specific selection. It is not unreasonable to suggest the latter may be true at times, and the cell was designed to purposefully modify genes or create new code to accomplish these evolutionary adaptations.

The adaptation of an organism to a particular habitat or niche involves largely uncharacterized modifications of the genome, and much of what we know about genetic heredity has come from science that does not recognize the intelligence behind the design of the cell. Without intelligent design theory, random mutations are the only other explanation for continued genetic diversity, and are therefore a theoretic requirement for Darwinian evolution. Despite the discovery of Mendelian genetics, and recognition that homologous recombination is responsible for offspring variability, Darwin's original theories are still taught as fact. Indeed many people today assume varieties like the finches on the Galapagos are the result of unintentional changes almost one hundred years following discoveries to the contrary.

Mutations are a theoretic necessity for the theory of evolution; therefore, the function of the cell regarding the production of novel genetic information has been overlooked. The purpose of genetic recombination is to edit the genome in a largely uncharacterized manner, and therefore any alterations found to exist are probably the result of these reactions. This simple logic has escaped scientists who instead require mutations to be ultimately responsible for evolutionary adaptations. Creation science perspectives concerning the existence, and use of new information have also been affected by erroneous Darwinian assumptions. However, the existence of new alleles indicates the cell has the ability to generate continued diversity through recombination, and intelligent design theorists should therefore closely investigate the ability of the molecular machinery to purposefully assemble new reading frames from portions of native and foreign DNA. Although it is clear that many organisms possess and are utilizing foreign or altered DNA, the participation of the cell in these processes is unequivocal.

"It is a considerable strain on one's credulity to assume that finely balanced systems such as certain sense organs (the eye of vertebrates, or the bird's feather) could be improved by random mutations. This is even more true of some ecological chain relationships. However, objectors to random mutations have so far been unable to advance any alternative explanation that was supported by substantial evidence". {Harvard biologist Ernst Mayr, SYSTEMATICS & THE ORIGIN OF SPECIES, 1942, p.296}

Article References

(1) Evolutionary Biology. Eli Minkoff. Addison-Wesley Publishing. (1984)

(2) Genetic control of Mammalian meiotic recombination. I. Variation in exchange frequencies among males from inbred mouse strains. Koehler KE, Cherry JP, Lynn A, Hunt PA, Hassold TJ. Genetics 162(1):297-306 (2002)

(3) Meiotic recombination hotspots. Lichten, M. & Goldman, A.S.H. Annu. Rev. Genet. 29:423-444 (1995)

(4) mtDNA Shows Signs of Paternal Influence. Strauss. Science 286:2436 (1999)

(5) Linkage Disequilibrium and Recombination in Hominid Mitochondrial DNA. Awadalla, Philip; Eyre-Walker, Adam; and Maynard Smith, John. Science 286:2524-2525 (1999)

(6) Hierarchic Regulation of Recombination. Kunihiro Ohta. RIKEN Review 41:28-29 (2001)

(7) Genetics No Friend of Evolution. Lane Lester. Creation Ex Nihilo 20(2):20-22 (1998)

(8) The History of Life. Lane Lester. Creation Research Society Quarterly 31(2):95-97 (1994)

(9) The Growth of Biological Thought: Diversity, Evolution, and Inheritance. Ernst Mayr. (1982)

(10) Cascades of Non-covalent Protein-protein and Protein-DNA Interactions for Homologous DNA Recombination. Takehiko Shibata. RIKEN Review 46: (2002)

(11) Functions of Homologous DNA Recombination. Takehiko Shibata. RIKEN Review 41:21-23 (2001)

(12) Homologous Recombination as a Mechanism for Genome Rearrangements: Environmental and Genetic Effects. Alexander Bishop. Human Molecular Genetics 9(16):2427-2434 (2000)

(13) Counting Cross-overs; Characterizing Meiotic Recombination in Mammals. Terry Hassold. Human Molecular Genetics 9(16):2409-2419 (2000)

14) Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: a possible advantage of DNA over RNA as genomic material. Shibata, T., Nishinaka, T., Mikawa, T., Aihara, H., Kurumizaka, H., Yokoyama, S. & Ito, Y. Proc. Natl. Acad. Sci. U.S.A. 98(15) 8425-8432 (2001)

15) Regulation of meiotic recombination and prophase I progression in mammals. Cohen P.E. & Pollard J.W. BioEssays 23:996-1009 (2001)

16) Rapid Evolution of a Protein In-Vitro by DNA Shuffling. Stemmer, W.P.C. Nature 370(6488):389-391 (1994)

17) The chicken B cell compartment. Weill JC, Reynaud CA. Science 238(4830):1094-8 (1987)

18) High prevalence of a mutation in the cystathionine -synthase gene. Tsai MY, Bignell M, Schwichtenberg K, Hanson NQ Am.J.Hum.Genet. 59:1262-1267 (1996)

19) Homologous recombination in procaryotes. Smith, G.R. Microbiol. Rev. 52:1-28 (1988)

20) AIDing diversity. Jennifer Bell. Nature Reviews Immunology 2, 223 (2002)

21) Immunoglobulin diversity, B-cell and antibody repertoire development in large farm animals. J.E. Butler Rev. sci. tech. Off. int. Epiz., 17(1):43-70 (1998)

 

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