Godspell Follies

Refuting the illogic of "intelligent design" and creationism. An illustrated guide to fallacies of logic.

Biological evolution

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.

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. Bacteria were the first life-forms on the planet, and ruled until the advent of nucleated cells with membranous organelles, such as those of which we are constructed. 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 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.

Since the advent of modern molecular genetics, biological evolution has come to be understood as a change in genotype – a genetic 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 still evolving.

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 change, 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 98% of their DNA.

Along the same lines of modification of genetic expression, the epigenetic mechanism of alternative splicing enables a single gene to give rise to multiple versions of a protein. 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 strawman arguments by focussing their arguments on point mutations, conveniently ignoring the other, more important mechanisms of genetic change.

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.

This brings us to the second type of mechanism operating in biological evolution, the statistical 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.

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Blogger qtr said...

The comment section will be used as a glossary, obviating some of the need to move around the site. If the website’s name shows as blue, you can return to the main page by clicking on “Godspell Follies” or “Home”.

idism = intelligent design theory
idist = intelligent design proponent, for example Behe or Dembski
fodi = fellow of the Discovery Institute, one of the organizations set up for the purpose of promoting intelligent design theory
proid = advocate of intelligent design theory, often an Internet debater

For a full explanation of these terms, see the Illogical Deceit Theory post at: http://refutingid.blogspot.com/2007/12/illogical-deceit-theory.html

3:32 PM  
Blogger qtr said...

Glossary of terms: classification systems and population mechanisms in speciation:

Allopatric speciation occurs when a geographical barrier sub-divides a parent species, resulting in geographic and reproductive isolation such that the descendent species can no longer interbreed upon removal of the barrier.

Anagenesis differs from cladogenesis in that one species progressively transforms into a replacement species when sufficient gene mutations fix in the descendant population. At this point, the ancestral species has become extinct. This mechanism is distinct from the increase in numbers of species generated by cladogenetic branching events.

Cladogenesis is the mechanism of speciation in which one or more lineages (clades) arise from an ancestral line. Such speciation events increase the variety of plants or animals through branching of the phylogenetic tree. Cladogenesis is differentiated from anagenesis, which is the in toto replacement of one species by an anatomically distinct species.

Monophyletic taxon or clade: an accurate grouping of only (opp. polyphyletic) and all (opp. paraphyletic) descendents of a shared common ancestor. A monopyletic group is genetically homogeneous and reflects evolutionary relationships.

Paraphyletic taxon or clade: a monophyletic group that excludes one or more discrete groups descended from the most recent common ancestral species of the entire group. Other descendent species of the most recent common ancestor have been excluded from the paraphyletic taxon, usually because of morphologic distinctiveness.

Phenetic system: groupings of organisms based on mutual similarity of phenotypic (physical and chemical) characteristics. Phenetic groupings may or may not correlate with evolutionary relationships.

Phylogenetic system: groups organisms based on shared evolutionary heritage. DNA and RNA sequencing techniques are considered to give the most meaningful phylogenies.

Phylogenetic separation into evolutionary relationships (clades), based on comparison of genomes is likely to supplant phenotypical (phenetic) taxonomies of the prokaryotes.

Peripatry (paripatry) is a subset of allopatry in which an isolated group has a smaller population than the parent group. Ernst Mayr introduced the term. Peripatric speciation occurs when the smaller sub-group of a species enters a novel niche within the range of the parent species, becoming geographically and reproductively isolated. Peripatric speciation (paripatric) is distinguished from allopatric speciation by the smaller size of the isolate group, and from sympatric speciation, which involves no barrier to breeding.

Polyphyletic taxon: opposite to monophyletic taxon: A polyphyletic group is mistakenly or improperly erected on the basis of homoplasy — characteristics that have arisen despite not sharing a common ancestor. Homoplasy arises because of convergent evolution, parallelism, evolutionary reversals, horizontal gene transfer, or gene duplications. Polyphyletic taxa are genetically heterogeneous because members do not share a common ancestor.

Neontology is a branch of biology that emphasizes the study of modern biota (living or recent organisms) rather than fossilized organisms (paleontology).

Numerical Taxonomies are a common approach to phenetic taxonomy that employ a number of phenotypic characteristics to generate similarity coefficients that may be mapped in dendrograms. Groupings based on numerical taxonomy may or may not correlate with evolutionary relationships.

Taxonomies aim to group organisms according to shared characteristics against the background of biological diversity.

Sympatry involves no geographical separation of sub-populations of individuals. Sympatric speciation events occur most often in plants by the mechanism of polyploidy in which the number of chromosomes is doubled or tripled. John Maynard Smith proposed a model called disruptive speciation, in which homozygotes might have greater fitness than heterozygotes under some environmental conditions.

10:34 PM  

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