Biological Evolution

A collage of fossils.Scientific theories of evolution seek to explain the mechanisms of the observable fact of biological evolution.

Yes, organisms have indeed evolved over time – most former species are now extinct, many species remain much as they are in the fossil record, and new species continue to evolve. Before the discoveries of science, it was intellectually excusable to believe that a God planted all those bones, but to believe so nowadays is a sign of ignorance.

Historically, scientists observing biological evolution first sought to explain observed morphological (body shape) changes over time – the phenotypic evidence of changes in body structure found in the fossil record.

Microfossils dating from more than 3 billion years ago demonstrate that bacteria were the first life-forms on the planet. Bacteria and Archaea, both prokaryotic, ruled until the advent of nucleated cells with membranous organelles, such as those of which we are constructed (eukaryotic cells). The earliest known fossilized evidence of early life forms are found in stromatolites – large reef structures created by communities of Cyanobacteria. Mistakenly called ‘blue-green algae’, the Cyanobacteria are bacteria that evolved relatively late. They are believed to have “invented” oxygenic photosynthesis over 1 billion years ago. As oxygen levels rose, organisms were forced into endosymbiotic unions as – to them – toxic levels of oxygen threatened their continued existence. (Anaerobic bacteria, which are killed by oxygen, persist to this day in environments with very low levels of oxygen.) These serial endosymbiotic transfer events paved the way for evolution of eukaryotic cells, which in turn enabled multicellular assemblages.

Since the advent of modern molecular genetics, biological evolution has come to be understood as a change in genotype – a genetic variation resulting from mutation and alteration in the intergenerational frequency of alleles in populations. That is, an alteration in the frequency of alternative forms of genes between generations. By this definition, the human species is demonstrably still evolving.

The term 'microevolution' refers to small-scale evolutionary events that involve changes in allele frequencies from one generation to the next, and that results in slight changes in affected organisms. The term 'macroevolution' refers to that accumulation of microevolutionary events that is associated with the origin, diversification, extinction, and interactions of organisms. Macroevolution, being cumulative, involves large scale evolutionary change such as the evolution of new species, genera, and families (or even higher taxa). Some creationists favour the ridiculous, fallacious straw man argument that microevolution occurs, but that macroevolution could not have occurred by the same mechanisms, or is impossible.

Biologist Ersnt Mayr suggested that a biological species be defined by its inability to produce fertile offspring when mated with another species. Mules are an example of such a mating – between a horse and a donkey. Mules do rarely produce offspring, but the gene-based, phylogenetic classification of species remains more useful than taxonomies based on physical characteristics. Molecular geneticists are able to compare the genomes, the total complement of nucleic acids, of different species and to estimate the evolutionary distance between species. This is time since the compared species last shared a common ancestor.

Speciation depends upon genetic mutation and alteration of allele frequencies, yet morphologic changes may reflect alterations in the regulation of genetic expression without a major alteration in genotype – body type may appear very different without considerable change in genes.

If this seems unlikely, just consider the considerable differences that selective breeding has wrought in size and configuration within one canine species. Mechanics might prevent the union of a Chihuahua with a Great Dane, but such a union could produce fertile offspring.

Similarly, the paramount importance of gene regulation almost certainly explains much of the morphological difference between humans and chimps – two species who share more than 98% of their DNA. Just a comparatively few regulatory genes are responsible for the developmental changes that render us distinct from our closest relative.

Along the same lines of modification of genetic expression, epigenetic mechanisms, such as alternative splicing or alternative promoters, enable a single gene to give rise to multiple versions of a protein. Thus, through epigenetic mechanisms, the biological complexity confered by genes is greatly expanded. Proteins are much, much more variable in structure, and hence in biochemical activity, than are nucleic acids such as DNA and RNA. Formed from amino acids, proteins regulate cellular metabolism (as enzymes), regulate genetic expression (cofactors), and regulate communication between cells (ion channels, pumps, receptors). Structural proteins form the cytoskeleton that supports cells, and specialized transport proteins move materials and organelles within cells and effect muscular contraction.

There are two basic types of mechanism involved in biological evolution. First are the genetic causes of alteration of genes within the genotype of individuals. Most genetypic alterations are not the result of point mutations, which may, or may not result in abnormal proteins through alteration of a single nucleobase in the genetic code. Creationists create fallacious straw man arguments by focussing their arguments on point mutations, conveniently ignoring the other, more important mechanisms of genetic change, such as duplications.

Single nucleotide polymorphisms, as point mutations are correctly termed, as well as alteration of longer segments of DNA may be neutral, beneficial, or deleterious. Clearly, neutral or beneficial alterations, whatever their genetic mechanism, will persist while deleterious alterations will ultimately be eliminated if they render the organism less capable of reproductive success. Gene duplications, while guaranteeing a functional copy of a gene also provide duplicate copies of the gene that may be altered without destroying the organism's viability, thus providing opportunity for the accumulation and transmission of a variety of mutations.

This brings us to the second type of mechanism operating in biological evolution, the statistical population mechanisms that determine the fate of an altered gene. These are the mechanisms that increase or decrease frequency of an allele – an alternate gene at a particular chromosomal position –within a population. Natural selection, the Darwinian explanation for biological evolution, remains one of the mechanisms acknowledged by biologists, yet not the only recognized mechanism. Genetic drift, gene flow, and horizontal gene transfer in prokaryotes have also been demonstrated to have operated in bringing about evolutionary change. Creationists typically focus their fallacious straw man attacks on "Darwinian" evolution, avoiding dealing with the much stronger "Modern Synthesis of Evolution", which combines understanding of population genetics and molecular genetics.

"Darwin made it possible to be an intellectually fulfilled atheist." ~ Richard Dawkins, The Blind Watchmaker.
"No intervening spirit watches lovingly over the affairs of nature (though Newton's clock-winding god might have set up the machinery at the beginning of time and then let it run). No vital forces propel evolutionary change. And whatever we think of God, his existence is not manifest in the products of nature." ~ Stephen Jay Gould

Inner Life of the Cell



Video from studiodaily.


"The animation opens with the rolling adhesion of a leukocyte within a blood vessel. The surfaces of two cells are shown adhering at contact points between adhesion molecules (selectin-saccharide).


We enter the cell and see a lipid raft, with its embedded sphingolipids and phosphatidyl choline(cholesterol+proteins), floating within the plasma membrane. Next we see a multi-protein focal contact, and then the cytoskeleton. After glancing back at the sub-plasma membrane 'geodesic' microfilaments, we pass down throught the cytoskeletal lattice and see actin microfilaments assembling, then depolymerizing after attachment of a protein (gelsolin?).

Next we see assembly and disassembly of tubulin. This interesting sequence is followed by my favorite segment, which is kinesin dragging an endosomal vesicle along a microtubule as kinesin-bigfoot 'walks' along the tubulin that is radiating from a centriole pair. A fellow kinesin, in the background, actively transports an endosome in the opposite direction.

Next, we approach the nuclear envelope with its embedded nuclear pore complexes. Several mRNA molecules with attached proteins exit the nucleus through the pores and assemble into loops within the cytoplasm, where the mRNA is scanned for a start codon, and is then translated into new polypeptide/protein chains by a ribosome. Globular proteins dimerize and tumble toward a mitochondrion.

Further translation injects a nascent protein chain through a pore into the endoplasmic reticulum as 'bigfoot' continues to clomp along tubulin, dragging a vesicle behind. Next, we see the Golgi apparatus budding vesicles before our plodding kinesin reaches the plasma membrane and proteins are released into the ECF by exocytosis. The newly synthesized integrins float on a lipid raft before unfolding into their active conformation, whereupon they snare a passing leukocyte and induce extravasation."


From here.

Mutation

Genetic mutations involve structural, usually transmissible change in DNA or RNA within a cell or organism.

Somatic mutations affect the cells of an organism, yet are not trasmitted to the next generation unless they affect the germline, those cells, such as ova and sperm that are committed to reproduction.

Cells have evolved complex molecular machinery committed to replication, transcription, repair, and translation of genetic information. Viruses subvert the nuclear machinery of infected cells to bring about replication of viral DNA or RNA and to generate packaging and shedding of newly manufactured virions.

Damage to DNA can be caused by mutations such as replication errors or incorporation of mismatched nucleotides (substitution errors – transitions and transversions). DNA can suffer single or double-strand breaks. DNA damage can result from unintentional and intentional environmental mutagens such as oxygen radicals, hydroxyl radicals, ionizing or ultraviolet radiation, toxins, alkylating agents, and chemotherapy agents, particularly anti-cancer drugs.

Cells have evolved mechanisms for repair of DNA, and all organisms, prokaryotic and eukaryotic, utilize at least three enzymatic excision-repair mechanisms: base excision repair, mismatch repair, and nucleotide excision repair.

Transmissible mutations affect the germline or result from errors during replication and cell division. Gene mutations have small-scale effects on sequences of nucleic acids, while chromosomal mutations involve larger-scale disruption of genetic material. Sequence mutations result from nucleotide alterations, insertions, deletions, or re-arrangements of gene segments, while, on a larger scale, chromosomes are altered during replication and cell division by deletion, duplication, inversion, recombination, translocation, transposition, and non-disjunction.

Depending upon their effects upon an organism within a particular environment, mutations may be neutral, beneficial, or deleterious. The commonest mutations affect single nucleotides (point mutations or SNPs). Because the genetic code is redundant, many single nucleotide substitutions are neutral. Insertion of mobile genetic elements, transposons and retrotransposons, increases genetic variability. The human genome, for example, includes approximately 500,000 Alu elements located within introns, and 25,000 of those could become new exons, coding for polypeptide sequences, by undergoing a single-point mutation.

As a result of alternative splicing, mutations that alter a splice site or a nearby regulatory sequence can have subtle effects by shifting the ratio of the resulting proteins without entirely eliminating any form. Alternative splicing also generates new polypeptide combinations from already existing code. Recently, researchers have demonstrated that modification of regulation of a single gene has enabled rapid phenotypic speciation in sticklebacks.

Natural Selection

Evolution by Natural SelectionCharles Darwin recognized that selection is the most important mechanism acting upon variability to bring about long-term, intergenerational change. Individual organisms that are better adapted to an environment are more likely to survive and reproduce.

Darwin accurately predicted that his theories would evoke skepticism from scientists and ridicule from the religious. Happily, scientists came to accept his ideas, and his breakthrough insights have proved highly influential. Unhappily, those biblical literalists who insist that Biblical Book of Genesis is an accurate description of life's origins, continue to unjustly vilify Darwin's theories.

“Can it, then, be thought improbable, seeing that variations useful to man have undoubtedly occurred, that other variations useful in some way to each being in the great and complex battle of life, should sometimes occur in the course of thousands of generations? If such do occur, can we doubt (remembering that many more individuals are born than can possibly survive) that individuals having any advantage, however slight, over others, would have the best chance of 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 favourable variations and the rejection of injurious variations, I call Natural Selection. Variations neither useful nor injurious would not be affected by natural selection, and would be left a fluctuating element, as perhaps we see in the species called polymorphic.” Darwin, "Origin of Species", Ch. 4

Summary of Darwin's observations and his Theory of Evolution by Natural Selection:
1. Most animals have such high fertility rates that their population size would increase exponentially if all individuals were to reproduce.
2. Yet, except for seasonal fluctuations, populations remain relatively stable in size.
3. Because environmental resources are limited, individuals compete for resources, limiting survival and reproduction.
4. Individual characteristics vary within populations and those members of a population that are better adapted for survival in the face of competition are more likely to pass their characteristics on to the next generation.

Conclusion: 5. Thus, species gradually accumulate inherited adaptations that best suit them for their environment, passing these on to progeny. Speciation involves gradually accumulated differentiation of characteristics.

Subsequent evolutionary theorists first disputed Darwin's concept of gradual evolution. Gould and Eldredge introduced the concept "phyletic gradualism " which they discredited through the concept of punctuated equilibria. The Theory of Punctuated Equilibria was proposed in order to explain patchiness in the fossil record and the the localized adaptive radiation of species observed following extinction events. This stage of thinking about evolutionary mechanisms has been termed "Neo Darwinism".

The modern synthesis of evolutionary theory combines an understanding of the genetic mechanisms (genotype and regulation of expression) that determine phenotype, and population genetics explains the fate of genetic variability (alleles) within populations of organisms.

In their attempt to discredit evolutionary science, creationists and defenders of "intelligent design" creationism commonly attack a straw man depiction of Darwinism or Neo-Darwinism as representing current thinking. It is important for any person wishing to defend evolution-as-fact and modern evolutionary theories to attain a thorough understanding of modern evolutionary theory as well as fallacious creationist arguments. For example, creationists who attack evolutionary theory in the vain hope that this will "prove" the existence of a "God" are creating a false dichotomy and relying upon a fallacious argument from ignorance.


Science

Much experimental science is conducted with the laboratory, whereas observational science is conducted in the field.The commonest misconception about science involves equating science with the areas in which scientific method is applied. Thus, people mistake the topics investigated by scientific techniques as being the sum total of science. Biology, for example, is a science, but "biology" does not delimit the meaning of science.

In fact, science is a method by which knowledge about the physical world is attained. Scientific 'knowledge' inheres both observed, empirical data and the best possible explanation regarding the mechanisms by which the observed phenomena came about and the prediction, where appropriate, of any future manifestations that can reasonably be expected. The scientific method is most appropriately applied to natural, physical phenomena, so it defines the subject areas appropriate to investigation.

Scientific method, methodological naturalism, is akin to formalized skepticism in that it ideally proceeds by rigorous scrutiny of falsifiable hypotheses. To achieve this, postulated explanations for observed phenomena must be expressed in such a way that they can be tested and disproven. An analogy would be determining whether a suspect in a crime has an alibi – if the suspect can be demonstrated to have been in Beijing at the time that a stabbing was committed in San Francisco, then the suspect cannot have perpetrated the stabbing (unless, that is, the suspect had impossibly long arms).

Any hypotheses that are demonstrated to be faulty will be discarded, and alternate explanations for empirical observations will be formulated and tested. (Expanding the analogy, another suspect will be sought for the stabbing.) Eventually, any reasonable hypotheses that are not disproven will be regarded as so acceptable as to be elevated to the level of scientific theory.

Scientific predictions, however, represent a subset of experimentation and are propositional – if this hypothesis is correct, then we will observe such and such a phenomenon. Failure to observe the predicted phenomenon might be taken to disprove the hypothesis. However, the failure might be a result of experimental or observational error, or might result from faulty predictions based upon a reasonable hypothesis. Alternatively, the hypothesis may be incorrect, but the predicted phenomenon is observed because of a mechanism not yet hypothetically considered.

For these reasons peer-reviewed scientific papers include analyses of current thinking, descriptions of methods, and statements of results so that other researchers might evaluate conclusions and attempt replication or alternate experimentation. In science, unlike the case for mathematics, proof is not possible, while disproof – falsification – is possible. For this reason, hypotheses to be experimentally tested are ideally framed in such a way that they may be disproved – falsifiable hypotheses. When an empirically-based, logical hypothesis, which has not been disproved after repeated testing, is deemed satisfactory by consensus within the scientific community, then the hypothesis graduates to the status of Theory (capitalized to differentiate the scientific term from its vernacular usage).

In practice, much of science proceeds upon positive results – repeated observations of a phenomenon under particular conditions. In the softer sciences, such as the social sciences, statistical analyses of results play an important role. Some sciences, such as paleontology are by their nature outside the possibility of experimentation – we cannot resurrect dinosaurs or recreate meteor impacts – and must proceed on the basis of accumulated empirical evidence.

We all toss around vernacular 'theories' – unproved ideas or theoretical speculations that are not necessarily even so well formulated as scientific hypotheses. Even some elaborate theories, such as intelligent [sick] design theory have considerably less conceptual merit than their promoters will ever acknowledge. For biblical literalists, such a 'theory' may have emotional appeal, but in terms of speculation concerning reality, ‘intelligent [sick] design theory’ has no more merit than the belief system of the Lambayeques.

Ȣ biological evolution Ȣ evolution Ȣ mutation Ȣ natural selection

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