Evolution: As Simple As Possible

The modern definition of Evolution is:

evolution can be precisely defined as any change in the frequency of alleles within a gene pool from one generation to the next. - Helena Curtis and N. Sue Barnes, Biology, 5th ed. 1989 Worth Publishers, p.974

An Allele is simply a particular gene variant.

When a genetic scientist speaks of "microevolution" or "macroevolution" (which is rarely the case) they are talking about the exactly same underlying phenomena over different scales of time. They are not making a distinction between the cause of those changes, as uninformed evolution-deniers often like to incorrectly imply (this is a common dishonest tactic).

Microevolution: allele changes within organisms or populations of organisms; studies that look at individual genetic changes, or allele changes within a population over small periods of time (up to roughly 100 years).

Macroevolution: evolution on a scale of separated gene pools over geologic time; studies that look at the effects of accumulated allele changes between groups of organisms that are no longer biologically/genetically interconnected (over periods of 10,000 years or greater).


Here are the high-level facts regarding Evolution.

• We know for an absolute fact that many major biological components and structures are determined by DNA & RNA.
  
  Tens of thousands of genes have been specifically mapped out, we understand the proteins they produce, how those proteins are further modified and ultimately used. These are directly observed phenomena. We've taken spider-silk protein genes from spiders and inserted them into goats, the goat then produces this protein, in their milk glands as it turns out. There are thousands of studies on everything from pigmentation, to morphology (see, HOX gene complex), to cell specialization, etc. Thousands of confirmed, observed, direct links between the genetics and our biology.
  
  Hox Genes in Development: The Hox Code
  Spider Goats
  Hox patterning of the vertebrate rib cage
  Pearson, J. C., et al. Modulating Hox gene functions during animal body patterning. Nature Reviews Genetics 6, 893–904 (2005)

• We know for an absolute fact that entire genes can be accidentally duplicated during replication.
  
  We also know that this isn't even required because some genes produce RNA strands that can actually modify other proteins to adapt them to new purposes.
  
  Evolution by gene duplication: an update (pdf)
  Gene Duplication: The Genomic Trade in Spare Parts
  An Abundance Of RNA Regulators
  In Evolution, the Sum Is Less than Its Parts (epistasis)
  epistasis

• We know for an absolute fact that individual nucleotides in the genetic sequence can be inserted, deleted, replaced or translocated via mutations.
  
  And we know that mutations are fairly common. It is absolutely NOT true that most mutations are harmful (most have almost no effect). The average human has some 150 mutations in their genome. Truly harmful genes are weeded out by Natural Selection. Seemingly harmful mutations (e.g., sickle-cell) can have benefits (resistance to malaria) that can cause them to be prevalent in a population despite their detriment to the organism (assuming the organism can still live to reproduce).
  
  Nature: Genetic Mutation
  DNA Replication and Causes of Mutation
  Charcot-Marie-Tooth Disease Type 1A -- Association with a Spontaneous Point Mutation in the PMP22 Gene

• We know for an absolute fact that our genetic material is recombined (where nucleotides are broken and then joined to a different location, especially during meiosis), where it facilitates chromosomal crossover and gene conversion. The crossover process leads to offspring having different combinations of genes from those of their parents, and can occasionally produce new alleles.
  
  Genetic recombination
  Evolutionary Origin of Recombination during Meiosis
  Mutations not considered harmful, FAQ at Talk.Origins

• We know for an absolute fact that chromosomes can be joined together or broken apart and experience inversions and duplications.
  
  Origin of human chromosome 2: an ancestral telomere-telomere fusion
  Chromosome 2 (human)
  Comparison of the Human and Great Ape Chromosomes as Evidence for Common Ancestry
  Chromosomal inversion
  Check out the genome size of Polychaos dubium! Amoeboid genome 200 times larger than the human genome

So, in summary:

1. We know that DNA drives pretty much everything that makes us, well, us.
2. We know how the genome can grow (gene duplication/chromosome duplication).
3. We know how the genome can and DOES change (nucleotides inserted, deleted, or substituted), with great frequency (~150 mutations per individual).
4. We know that the genome changes from individual to individual.

We observe all these changes happening in real organism. Microorganisms are the most studied because they replicate faster and generally have smaller genomes to study. It's all there - we see things changing over time with EVERY type of change necessary to change a bacterium into a human being - given enough time. And the amount of time you would estimate from the observables above (and in more scientific detail) are exactly what we find. The radiometric dates (from fossils) align with the molecular clock dates we would expect to an astonishing degree (remember this is a stochastic process so we do not expect perfect clockwork changes) over a wide range of phyla and different time periods.

Yes, it requires many steps - but remember, each of those steps are filtered through Natural Selection. Natural Selection is the key process.

Imagine you thoroughly shuffle a deck of cards and, without looking at them, deal them into 4 piles. The odds that you have 4 Royal Flushes is as close to impossible as we can imagine. But with a subtle change of the rule, imagine that you turn the cards over and simply Select the next random card into the right piles. 4 Royal Flushes becomes a mundane result. Natural selection is Nature looking at the cards and selecting them based on survival. Survival itself is an extremely complex subject and it is NOT simply survival of the fittest, organism often develop complex relationships with one another (food, predator, host, symbiotic, parasitic, etc). If one species depends upon another, it is not in that species best interest to utterly destroy the other species, at other times species may compete for common resources. But the interplay between all of these relationships cannot be so easily summed up.

Evolution is a fact, it's happening all around you in every single organism.

This is why results like Escherichia coli evolving the genes necessary to process Citrate is such strong confirmatory result (Proceedings of the National Academy of Sciences (DOI: 10.1073/pnas.0803151105)). If you read all the papers from Lenski and his team on this you can find the exact genetic changes that gave this result, so they know EXACTLY what changed in the genome to enable this new function.

Evolution is Happening. That is the undeniable conclusion from the above set of facts. There is no way to avoid it if you look at the facts and apply even a modicum of basic reasoning. If you want to deny it, show me exactly which genetic change cannot happen that would get us from point A to point B. Creationists want to claim 'macro evolution' can't happen -- well show me which step can't happen. At the genetic level there is NO SUCH THING as a species, species is an arbitrary category that humans apply because some set of things is "different enough" from another set of things. There are some 10 million species alive today. There is a fantastic series of gradations of life from the lowly bacterium to human. Hundreds of different kinds of eyes (including eyes that are no longer eyes at all, like our own pineal gland, which literally functions in some reptiles as a "third-eye").

There are many other reasons we could go into as well, eg., the observation that everything is made of similar cells (with a few major groupings) goes to common origins, we've observed single-cellular organisms evolve the ability to stick together and form multi-cellular clusters - and the beginnings of specialization, how more essential genes are highly conserved. All these factors just support the facts outlined above.


Another important thing to note is that bacteria have survived for billions of years, the genome of the modern bacteria is NOT the same as the ancient bacterium. It has stabilized itself as it adapted for survival in the environments in which it survives so it's not likely that a modern bacterium would suddenly turn into a squirrel. That just isn't going to happen, if it was that likely to happen we would probably have trillions of species and not merely the millions see today. You would need the EXACT genetics of the ancient bacterium and the exact conditions under which it mutated. But what we do expect to see is a continual, long-term evolution. Just as we've observed in populations where human selection has resulted in massive and sometimes incredible changes in just a few hundred or thousand of years (eg, in dog, horses, cabbages, pigeons, avocados, peas, lettuces, etc).

Think of the tiniest dog and the largest dog - HUMANS did that in just a few hundred years. Because of the limited time-period the claim that "it's still just a dog" is really irrelevant - you are missing the significance of the amount of actual change we know has occurred. Nature still has to provide the mutations (short of genetic manipulation of course).


NOTE: I'll enhance the references as time goes along (I would like to link to definitions for all the terms as well), feel free to comment and suggest key papers and articles to be added. Meanwhile, the reader is encouraged to do their own research to validate the claims. They are VERY simple claims and easily confirmed in numerous scientific journals and popular science publications. Hint: use Google Scholar

There are an estimated 5 × 10³⁰ Prokaryotes (bacteria and the like) on earth today, that's a lot of parallel mutation going on.

For tons more information explore the talkorigins site and this video: