evidence of stasis

Protein degradation

It is well known that proteins inside the cell are constantly changing. New proteins replace old, broken down ones. Some cellular proteins have degradative properties as explained by Hershko and Ciechanover (1982). They say that the long-lived proteins have a slow turnover rate; the short-lived proteins a fast turn over rate; and the abnormal proteins, which are the result of occasional mutations or errors in RNA/protein synthesizes, decompose even faster than short-lived proteins.

E.g. in E-coli if incomplete beta-galactosidase chains are synthesized they break down in few minutes (Zubay, 1988).

If in the newly forming hemoglobin an amino acid valin, is inserted, the new polypeptide will break down within ten minutes.

This protein degradation occurs because cells have "very efficient mechanisms to recognize and quickly degrade damaged proteins." (Zubay 198: 968) The ubiquiton polypeptide and the protease La enzyme are known to perform the functions of hydrolyzing proteins to peptides (protein degradation), that means degrading nonsense polypeptides, proteins, abnormal proteins and DNA sequences which do not do what they are supposed to. For example, Ubiquiton, also known as CoQ10, is found in all the cells of the body and its function is especially beneficial for heart and gum tissues.

Protein degradation obviously has an important function in the cell. It preserves its usual condition. It challenges the idea of transformation on the molecular level. Protein degradation does not occur immediately after the extra gene is generated. This extra gene is at first inactive, only after undergoing some mutations and becoming ready for new functions does the process of protein degradation begin by which the new gene is eliminated. Some argue that the new gene can escape protein degradation, but the new gene would be not be functional because it was redesigned by chance.

There are great doubts about the reactivation of genes. Li (1983: 29) writes: The probability of reactivation would still be very small...because a pseudogene often contains multiple major defects such as frame-shifts, which cannot be corrected easily.

From above difficulties we can see that there are great obstacles after gene duplication occurs.

To overcome the problems of random change and reactivation some propose the idea of constant functioning of the extra duplicated genes even during mutation. However, in this case the new gene would be continuously subject to protein degradation. Generally, proteins are spherical, and any change of form requires an unfolding and refolding process which will precipitate degradation.

Protein degradation, with its highly specific action, protects the molecular structure from change and thus preserves its required function. Resistance to proteases (enzymes that break peptide bonds between the amino acids of proteins) is increased by decreasing the changes in protein structure. That means if the protein changes are small the probability of activation of protein degradation will be also small.

In order to produce abnormal proteins (such as in gene duplication) the organism will require additional energy. Such additional energy will be required for gene mutation and for gene degradation. (Ciechanover et al., 1984). An organism where these processes are occurring will have an energy disadvantage compared to organisms, which minimize such events.

It is difficult to conceive how new useful proteins could be produced by chance over periods of thousands of years, when abnormal proteins are degraded in minutes. How can the abnormal proteins be the new building blocks of evolution?

Another obstacle to the development of new functional proteins is the DNA repair processes expressed in gene conversion.

Gene Conversion

Theorists say that by gene duplication new proteins are created that can take up new functions. However, there is an obstacle, gene conversion. Recent studies show that gene conversion is a very common in various genomes, and there is evidence that duplicated genes are homogenized by gene conversion(s). In other words during the gene duplication mutations are quickly removed by gene conversion.

Before proceeding let us consider multi gene families and the multiple copies of genes. When there are multiple copies of a gene there is a potential problem for evolution. The mutation for improved function will have a diluted effect. For example, if the improved version results in 10% faster growth. However, if there are ten copies of genes and nine of them are the old one, recombination can destroy the new version (even while it makes further variations).

The Xenopus frog, for example, has roughly 600 copies of the rRNA genes (Ribosomal RNA which is involved in protein synthesis). When Fristrom and Clegg, (1988: 677) mapped and sequenced the genes it was discovered that the multiple copies within the species were almost equal in every respect. We would expect that by accumulation of mutations obvious differences would be created but this did not occur. How could these 600 genes not change their structure but rather preserve a great similarity?

First, any change in the essential rRna genes would cause great harm to an organism. If any mutation occurs does natural selection removes it? Because of the huge number of these genes this suggestion is hard to accept. It is difficult to see how selection could work to eliminate new mutations. Any mutation in one gene making it non-functional would have no observable effect, its functions being replaced by hundreds of functional gene products.

The generally accepted operative system that preserves the similarity of the various gene copies is gene conversion (Li et al., 1985). When a DNA double helix forms from single strands, each from different sources; if there is a sequence difference between the strands, or in other words the double-strands do not show perfect base matches that is called heteroduplex. There are unpaired regions of single strand loops or bubbles. Gene conversion occurs to rectify the disorder. Interaction between the two DNA sequences ensures their diversity becomes homogeneity and gene conversion helps to maintain that homogeneity of repeated sequences. This means that gene conversion is there to eliminate diversity from a mutated copy of duplicated gene. As Li et al. (1985: 72) wrote: "If there are only two repeats on a chromosome, a single intrachromosomal gene conversion will lead to homogeneity of the repeats on the chromosome."

This statement is not an assumption. It is observed that the rate of gene conversion is "clearly higher then the frequency of mutation" (Klein and Petes, 1981).

E.g. Jureerat Chamnanpunt, Wei-xing Shan,* and Brett M. Tyler of Department of Plant Pathology at the University of California, Davis, wrote : "We report here that in particular hybrid strains of Phytophthora sojae, an oomycete pathogen of soybean, high frequency mitotic gene conversion rapidly converts heterozygous loci to homozygosity."

Further, Mark D. Baker and Leah R. Read from the department of Molecular and cellular biology at the University of Guelph, Guelph, Ontario, wrote: "Gene conversion is also thought to be important in maintaining similarity between repeated eukaryotic genomic DNA sequences variation of trypanosome surface glycoproteins, somatic diversification of the avian immune system, mammalian variable and constant region gene segment evolution, and the diversification of the mammalian major histocompatibility complex locus."

Actually, an average gene mutates at the rate 10-5 per generation and according to the experiments the frequency of gene conversion is about 10-2 per generation. (Klein and Petes, 1981; Klein, 1984).

The evidence shows that gene conversion takes place thousand times more frequently than mutation. Therefore, it is highly unlikely that any duplicate gene would escape gene conversion.

In conclusion, gene conversion maintains the original allele. If, by gene conversion, a mutation spreads to both alleles then selection removes such changes.

We have to note that in gene duplication one gene will possess the same essential qualities while the other one can accumulate changes. However, when gene conversion spreads the mutation this feature is eliminated.

When a segment of wild type of DNA is recombined with another mutant segment of DNA the location of the mutation would be a mismatch. As both strands are methylated or have CH3 molecules attached to the DNA structures, the repair system cannot eliminate the mismatch and the whole segment has to be converted to either wild type or mutant form. This is the typical gene conversion, which seems to be at work. It not only sustains homogeneity but also removes differences created by gene duplication and thus has a crucial role in maintaining stasis. If there is some change, it is obvious that the essential molecules can bear changes.

Ivica Tamas, Lisa Klasson, and others in their work titled - '50 Million Years of Genomic Stasis in Endosymbiotic Bacteria' give a clear analysis how in Buchnera aphidicola bacteria no chromosome rearrangements or gene acquisitions have occurred in the past 50 to 70 million years, despite substantial sequence evolution and the inactivation and loss of individual genes. (The brief report of this discovery can be found at http://www.genomenewsnetwork.org/articles/07_02/models.shtml).

Other scientists also come to similar conclusions "for millions of years species remain unchanged in the fossil record", "stasis is data" as Stephen Jay Gould of Harvard (1991) said in his "Opus 200" Natural History, August, p. 16.

According to Modern Synthesis, evolution is gradually moving on as small changes are accumulated over many millions of years. We can see from the fossil record the resultant steadily advancing lineages. But the great problem is that most of paleontologists find the principal feature of the fossil record to be stasis or no change. Even Francisco Ayala the main proponent of Modern Sythesis in the USA declared: "We would not have predicted stasis from population genetics, but I am now convinced from what the paleontologists say that small changes do not accumulate."

There have to be different mechanisms for stasis because mutations in the structures of the genes can have an overwhelming destructive effect. Different "developmental mutations" can damage an organism or even cause its death. This proves that biochemical systems are irreducibly complex and there are many examples: aspects of protein transport, blood clotting, closed circular DNA, electron transport, the bacterial flagellum, telomeres, photosynthesis, transcription regulation, and much more. Michel J. Behe defined this irreducible complexity in the following way "A system which meets Darwin's criterion is one which exhibits irreducible complexity. By irreducible complexity I mean a single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning."

Therefore all the different evolutionary theories, like for example, punctuated equilibrium, are not complete since they do not provide detailed models for intermediates in the development of complex biomolecular structures and moreover they give rise to more questions than they answer.

Over the last ten years there has been no discussion of detailed models for intermediates in the development of complex biomolecular structures in scientific journals like Proceedings of the National Academy of Science, Nature, Science, the Journal of Molecular Biology etc. Out of 886 papers published in the Journal of Molecular Evolution, 95 discussed the chemical synthesis of molecules thought to be necessary for the origin of life, 44 proposed mathematical models to improve sequence analysis, 20 concerned the evolutionary implications of current structures, and 719 were analyses of protein or polynucleotide sequences. There were no papers discussing detailed models for intermediates in the development of complex biomolecular structures. This not peculiar to JME; there are no papers to be found that discuss detailed models for intermediates in the development of complex biomolecular structures in the Proceedings of the National Academy of Science, Nature, Science, the Journal of Molecular Biology or, to my knowledge, any journal whatsoever. (Michael J. Behe, Molecular Machines)

Again considering some more mechanisms promoting stasis: The DNA repair enzymes - because the DNA undergoes many chemical modifications, the genetic information has to remain uncorrupted so any change must be rectified. Around 130 DNA repair products have been described and it is likely more will be in future.

Some factors that can damage DNA are: Gamma radiation, a short-wave electromagnetic radiation which is emitted by radioactive substances, is very penetrating and not appreciably deflected by a magnetic or electric fields. The prevailing view is that they are non-periodic ether pulses differing from x-rays only in being more penetrating;

X-rays are short-wave electromagnetic radiation able to penetrate solids;

Ultraviolet rays, especially UV-C rays (~260 nm) that are absorbed strongly by DNA but also the longer-wavelength UV-B that penetrates the ozone shield. It has been estimated that under the strong sunlight typically encountered on a beach, an exposed cell in the human epidermis develops about 40 000 damaged sites in one hour, primarily from absorption of UV radiation by DNA;

Highly-reactive oxygen atoms known as free radicals produced during normal cellular respiration as well as by other biochemical pathways;

Environmental chemicals and pollutants, different types of hydro carbons of which some are found in cigarette smoke.

Natural products with DNA-damaging activity like sesquiterpenes, diterpenoids, steroids and alkaloids.

Chemicals used as agents in the treatment of disease especially in treating cancer.

There are claims that exposure to DNA damaging chemicals increased in the 20th century due to military operations and treatment of diseases with chemicals or drugs.

The damage caused can be repaired in several ways:

Direct reversal

This repair process is the most efficient but it repairs only few common DNA injuries, such as pyrimidine dimers and alkylated guanine residues. The Pyrimidine dimers are the main type of damage caused by UV light, which distorts the double helix structure of DNA and blocks transcription or replication past the damaged site. The damage is repaired by photoreactivation, a mechanism of DNA repair in which solar energy is used to split pyrimidine dimers. In the direct reversal repair mechanism the original pyrimidine bases (thymine (T) and cytosine (C) of DNA) are restored and remain in the DNA.

While the prokaryotes and eukaryotes like E-coli, yeast, and several plants and animals can repair pyrimidine dimers by photoreactivation, many species, including humans do not have this repair system. For them other repair systems rectify DNA damage.

Base Excision Repair (BER)

It is estimated that premutagenic damage in the genomic DNA occurs so often that the DNA glycosylase has to make some 20,000 repairs a day in each cell of our body. This repair system of enyzmatic reactions also works to prevent mutations. BER often corrects damage that arises spontaneously, due to the inherent instability of DNA, from alkylation of DNA or damage generated by anti-cancer agents and environmental mutagens which generate free radicals (such as ionizing radiation and radiomimetic antibiotics). BER thus deals with damage that is produced "every day". In all organisms, DNA bases are subject to chemical modifications causing cell death and/or genetic change (mutagenesis) if left unrepaired. Such damage can be enzymatically repaired by the base excision repair (BER). The repair is initiated by removal of the modified base by a DNA glycosylase. In other words, in base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Presently 8 human genes are known to encode different DNA glycosylases each enzyme responsible for identifying and removing a specific kind of base damage.

Nucleotide Excision Repair (NER)

The different steps of the complex NER process, which uses different enzymes, are as follows:

(i) recognition of a DNA lesion;

(ii) separation of the double helix at the DNA lesion site;

(iii) single strand incision at both sides of the lesion;

(iv) excision of the lesion-containing single stranded DNA fragment;

(v) DNA repair synthesis to replace the gap and

(vi) ligation of the remaining single stranded nick.

NER can eliminate a broad range of structurally unrelated cdamage from DNA, including those from UV-induced damage and some chemical damage. Defects in a single piece of the NER can cause genetic diseases like sensitivity to UV radiation and predisposition to skin cancer such as xeroderma pigmentosum (XP) and Cockayne syndrome (CS).