Similarity Does not Imply Evolution

I have been told many times that similarity does not imply evolution.  At this moment I would like take the time to announce that I resoundingly agree.  Many times after I have talked about similarities between creatures that walk this earth to a Creationist only to be told similarity does not imply evolution.  Please let it be known that I wholeheartedly agree.  If only similarity was observed, that would be insufficient to prove evolution true.  I'll let Talk Origins explain some more

Mere similarity between organisms is not enough to support macroevolution; the nested classification pattern produced by a branching evolutionary process, such as common descent, is much more specific than simple similarity. Real world examples that cannot be objectively classified in nested hierarchies are the elementary particles (which are described by quantum chromodynamics), the elements (whose organization is described by quantum mechanics and illustrated by the periodic table), the planets in our Solar System, books in a library, or specially designed objects like buildings, furniture, cars, etc.

It is possible to classify anything into a hierarchical structure, but the traits used will in the end be weighted subjectively.  This results in a variety of possible orderings for sets not naturally .  Take a set of cars.  We could choose a variety of traits to order the nested result--say first by color, then by manufacturer.  However , the outcome would be colored by our personal opinion about how to classify them best.  In other words no mater what ordering we choose for the cars, any nested hierarchy we choose would be supported by the data.  But only certain things can be objectively classified into a unique nested hierarchy.

Because heredity (and occasional horizontal gene transfer in single celled organisms) are the only known ways that two organisms can share proteins, it can be concluded that the sharing of proteins is indicative of them sharing a common ancestor.  More often than not, two organisms related by this structure share the same errors in their proteins, because heredity passes those down too.  The same is true of any retroviral insertions.

One major example a gene that is broken in humans that controls Vitamin C synthesis.  This gene is also broken in our primate cousins, namely Chimpanzees, Bonobos, Gorillas, and Orangutans.  Additionally our closest cousin, the Chimpanzee has 48 chromosomes.  The gene markers located at the ends of the last two chromosomes in their genes match precisely to the markers located in the middle of our chromosome 46.  Furthermore our cytochrome c's differ by only four base pairs, in addition them to having retroviral insertions at the same spots in our DNA.  Note that retroviral insertions are rare and occur randomly, so the probability of them occurring in two different species in the same place in their DNA is next to impossible.  The only conclusion that can be reasonably drawn is a hereditary relationship.  Not to mention we share about 95% of our DNA.

The evolutionary process is a Markov process, which is simply a system that has multiple states, changing from one state to the next with a certain probability.  The reason for this has to do with the random probability for mutation, combined with the gene inheritance rules discovered by Mendel.  It can be rigorously proven that replicating Markov processes give rise to a nested hierarchy.  Therefore a Markov process that reproduces would invariably give rise to a nested tree structure of offspring.

Modern bioinformatics combined with genomic sequencing of a variety of species has allowed us to molecularly reconstruct the tree of life.  Based on a set of organisms gene sequences we can determine what is the most probable tree for that set.  We can assume heredity based on aforementioned factors; retroviral insertions, errors in the same locations, and similarity if combined with these other factors.  When constructed from the genomic and molecular evidences, the phylogeny obtained match precisely with the same tree constructed by morphological and physiological characteristics.  This provides independent confirmation of the phylogenetic tree from both molecular and morphological evidences.

To reiterate, this isn't about similarity.  This is about the fact that given a set of organisms there is a tree that can be optimally contracted to represent a hereditary relationship between them.  So, unlike the set of cars, where the tree would be arbitrarily drawn based upon the color or manufacturer with no bias toward either, these organisms can be grouped into an optimal tree.

Always Allow Your Views to be Challenged

After losing touch for a great while, a good childhood friend challenged my views on evolution.  After much reflection and research a few astounding conclusions were reached.  Firstly, I realized how little I actually knew about the science behind evolution.  This is probably the result of not being particularly interested in the subject of biology in general throughout my school and college years.  From what I recall, I only took about three courses throughout my entire life on the subject.  Thinking back to life science class in middle school, I vaguely recalled the enzymes used to break down starches.  I have a fuzzy memory of learning something about inheritance and the phylogenetic tree in my high school biology class.  Needing to take a biology course as part of my core curriculum in college, I took human biology, and again have no specific recollection of anything.  The information that was presented, forced me to question my confidence in the subject.  So being one to seek truth on my own, I set out on a quest to find answers.  One of the initial things I realized, as a testament to my initial ignorance, is that I didn't even know what a scientific theory truly was.

This leads to my second astonishment.  Upon actually researching the subject, I indeed did find overwhelming evidence for Evolution and common descent.  Before taking the time to read on the subject, I wasn't aware of the progress that had been made.  I began my journey with the assumption of it being unproven.  Remarkably fast though, by reading the resources available, I was convinced at the sheer volume and quality of evidences from multiple independent sources.

Childhood Memories

I was a remarkably curious child and was always asking questions.  While I don't recall the exact question that was asked in this instance, I remember my father taking out the World Book Year Book and flipping to an article on the work of a Dr. Leakey.  His work featured in that years year book detailed extensive fossil findings in Africa.  It was truly astonishing to learn and actually see that human beings are part of the tree of life, classified as Homo sapiens.  Sapiens is Latin for wise or rational, and homo means man (in Greek homo means same.)  Furthermore, it turns out we are decedents of upright walking primates.  In addition, certain modern primates are extremely closely related and all primates are at least cousins, though quite a few times removed.

Being lucky enough to have a relative in the biological sciences growing up, I was showered with books like The Pandas Thumb.  Honestly I wasn't too keen on the details, but I read and took these ideas for granted.  After all, it seemed so obvious to me.  It never crossed my mind that anyone would doubt what I saw to be sound reasoning and good reading material.  Of course, at that age I didn't have the appreciation for strong evidence that is irrefutable.  Things were read, and assimilated.

Other than these few books, and a couple of biology classes in my lifetime is all my biology education consisted of.  I took these ideas for granted, just like other scientific fields on understanding, like physics or chemistry.  The thought never crossed my mind that there would be anything controversial about them.

My Ideas Challenged

Fast forwarding into my twenties after losing and regaining touch with a good friend of mine.  My friend had recently converted to faith, and we drifted onto the topic of evolution.  Turns out we had some points of disagreement, but I had come to this discussion completely uninformed and unprepared.  Honestly, I had never heard any of the objections he presented, and he pointed me to a web site to refer to.

When I got home and checked the site, the author of the materials seemed to present some very interesting arguments.  Because of my relative lack of background, I didn't have the necessary resources to assess the truth of this individuals claims.  This is when I set out to find answers.  Within a few moments I stumbled upon Talk Origins.  Turns out they had a huge collection of claims made by critics of evolution, where they presented evidence, provided sound reasoning and debunked them.  Not only were the claims of the author that was referred to me listed on the site, but also hundreds of other ones too.  This gave me an opportunity to look at the devil's advocate angle.  I've always believed that being forthright about the claims of your opponents and providing well reasoned, evidence based, plain language responses to debunk them demonstrates intellectual integrity.

Learning came fast and hard, when I realized that I didn't even know what a scientific theory was.  Most people are under the impression that a theory is an unproven idea.  But in a scientific context, I means a description.  Take gravity for example.  The is the phenomenon, or force, of gravity; then there is the Theory of Gravitation that mathematically describes how the force acts on things.  Gravity is a force, and it factually exists.  You might not believe in gravity, but when you jump off a building, it believes in you--hitting the ground at terminal velocity.  The same is true for electromagnetism; there is the force itself--a fact--and the description or theory that describes how the force works.

I realized at this point that the author of the website making these claims was criticizing Evolution based on the fact that it was "just a theory."  The author seems to imply that theories like Evolution aren't legitimate. Gravity is "just a theory" as well by that definition.  Of course it is quite an observable fact.  We can also observe that organisms change over time, and that is a fact (specifically the fact of Evolution.)  The description of how and why they change is the Theory of Evolution.

Reading the evidences for  Evolution on the site, complete with references, images, examples, and sound reasoning convinced me that Evolution is a better description of what we know than I ever thought before.  I learned how there is even powerful molecular evidence now, which is about as strong a proof as you get because it allows gene similarity to be numerically quantified.  One of the problems with Evolution is classifying organisms  phylogenetically.  Based solely on morphology, elements of subjectivity are introduced into the classification.  Thanks to these modern methods using molecular, genomic and protienomic evidence, there is now an objective normalizer to the subjective qualities of morphology.