Lenski's Evolving E. coli & A Rebuttal to Answers

In 2009, Richard Lenski produced some of the most detailed documented evidence of the production of new novel traits through natural selection.  In this case, E. coli bacteria developed the ability to transport citrate through their cell wall in oxygenated conditions before metabolizing it.  The mutation chain that occurred was documented in detail and the experiment is notable in giving biologists a much better understanding of the role of potentiating mutations.

These mutations don't produce benefit alone, but are necessary intermediates in the production of new traits.  It is of importance to note that when bacteria containing the potentiating mutation that led to the citrate transport trait were frozen, they retained the ability to re-evolve it.  That demonstrated that the potentiating mutation is a necessary intermediate, providing further verification for the causal chain of mutations.

In addition to the potentiating mutation, subsequent mutations occurred that provided increasing benefit.  The initial ones allowed the bacteria to metabolize a small amount of citrate.  Eventually though, the mutations  greatly improved the function, allowing those bacteria to consume the food source, outcompeting their neighbors.

This experiment isn't about a single chance mutation leading to some benefit.  It is the complete evolution of a new trait through a series subsequent mutations.  The addition of a new feature.  Again the premise of evolution is very simple.  Given a set of organisms, and a set of environmental conditions and states, a certain number of organisms will survive.  The ones that survive will continue to produce offspring and pass on their genes, the others perish and do not.  Random mutation provides some variety to the mix.  Change over time driven by the selection of a given set of organisms over another set that are better able to survive in an environment.

In the following I present Answer's In Genesis's (AIG) response to the results of the experiment, and my rebuttal to their response.

Many evolutionists state that the bacteria are experiencing “adaptive evolution.” However, this is not evolution but rather adaptation. Molecules-to-man evolution requires an increase in information and functional systems. Instead, these bacteria are likely experiencing a loss of information and functional systems as has been observed in other mutant bacteria in Lenski’s lab. While these changes are beneficial in the lab environment, they do not lead to a net gain that moves bacteria in an upward evolutionary direction.

The bacteria in question didn't lose anything.  The E. coli actually gained the ability to transport citrate through its cell wall.  That is not a loss of any kind.  They go on to quote a study on how E. coli can transport and metabolize citrate in low oxygen conditions

Previous research has shown that wild-type E. coli can utilize citrate when oxygen levels are low.⁶ Under these conditions, citrate is taken into the cell and used in a fermentation pathway. The gene (citT) in E. coli is believed to encode a citrate transporter (a protein which transports citrate into the cell).⁶ When oxygen levels are high, it is thought that the citrate transporter does not function or is not produced (even though they still possess the enzymes necessary to utilize citrate).

Lenski's paper itself, also points this out.

The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions.

The evolved trait is not the ability to utilize citrate, but to transport it through its cell wall.  This involves several mutations, and each of them in the chain was documented by Lenski's experiment.  In fact, by freezing different strains at various points in the evolutionary chain, Lenski was able to restart the process at different points repeatedly, and demonstrate the causal chain conclusively.  He reconfirmed the link between the mutation and trait.  The AIG response is simply speculating about what might have happened, which they need not do since reading Lenski's paper, the precise mutation chain is laid out.

Lenski’s lab has not yet identified the genetic alterations of the Cit+ E. coli line, but he believes that there are multiple mutations involved. Studies of the “fossil record” of this line indicate that one or more mutations occurred around generation 20,000 which he terms “potentiating” mutations that were necessary before additional mutations around generation 31,500 led to Cit+ cells. Lenski thinks that the mutations may have activated a “cryptic” transporter

Lenski's lab has found the genetic alterations.  AIG's response is old, so I grant them the benefit of the doubt here.  There have been further publications from Lenski on the subject further confirming the results.

While the fitness of the bacteria has increased (as compared to the starting bacteria), it has come at a cost. For example, all the lines have lost the ability to catabolize ribose (a sugar).³ Some lines have lost the ability to repair DNA.⁴ These bacteria may indeed be more fit in a lab setting, but if put in competition with their wild-type (normal) counterparts in a natural setting, they would not stand a chance.

Let's quote Lenski's paper for context.

Previous analyses of this experiment have shown numerous examples of parallel phenotypic and genetic evolution.All twelve populations underwent rapid improvement in fitness that decelerated over time (2, 3, 22, 23). All evolved higher maximum growth rates on glucose, shorter lag phases upon transfer into fresh medium, reduced peak population densities, and larger average cell sizes relative to their ancestor (22–26). Ten populations evolved increased DNA supercoiling (27), and those populations examined to date show parallel changes in global gene-expression profiles (4, 28, 29). At least three genes have substitutions in all 12 populations (30, 31), and several others have substitutions in many populations (27–30), even though most loci harbor no substitutions in any of them (32). At the same time, there has also been some divergence between populations. Four have evolved defects in DNA repair, causing mutator phenotypes (3, 33). There is subtle, but significant, between population variation in mean fitness in the glucose-limited medium in which they evolved (2, 23). In media containing other carbon sources, such as maltose or lactose, the variation in performance is much greater (34). And while the same genes often harbor substitutions, the precise location and details of the mutations almost always differ between the populations (27–31).

I don't see where Lenski states they lost the ability to catabolize ribose, but citation 31 is a reference to documented instances where the ability was lost in E. coli. (Cooper VS, Schneider S, Blot M, Lenski RE (2001) Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of E. coli B. J Bacteriol 183:2834–2841.)  I have bold-faced the part where he documents defects in DNA in four of the populations.  Not all the resulting Lenski populations had DNA defects.  More from AIG

Lenski states (based on calculated mutation rates in E. coli), “It is clearly very difficult for E. coli to evolve this function. In fact, the mutation rate of the ancestral strain from Cit- to Cit+ is immeasurably low . . . .”¹ If developing the ability to utilize citrate under certain conditions using random mutations of a pre-existing citrate utilization system is so rare, then how even more improbable is it to believe that these same random mutations can lead to completely new information and functional systems

Yes, but as Lenski points out in an exasperated response to Andrew Layton Schlafly

Did you know that your own bowels harbor something like a billion (1,000,000,000) E. coli at this very moment? So remember to wash your hands after going to the toilet, as I hope your mother taught you. Simple calculations imply that there are something like 10²⁰ = 100,000,000,000,000,000,000 E. coli alive on our planet at any moment. Even if they divide just once per day, and given a typical mutation rate of 10^-9 or 10^-10 per base-pair per generation, then pretty much every possible double mutation would occur every day or so. That’s a lot of opportunity for evolution.

Indeed there continue to be publications and journal articles written that continue to confirm and reconfirm the results of Lenski's work.  Along with providing specific genomic evidences for the mutations involved the results demonstrate the specific chain of mutations.  Studies of Lenski's E. coli strains continue to provide insight into evolution of new traits.

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.

Evolutionary Origin of Morality: A Rebuttal to Callie Joubert

This is a response to the article in Answers in Genesis, Can Theistic Evolutionism Explain the Origin of Morality?  Based on the source, I think it seems clear from the outset that the author, Callie Joubert, doesn't think so.  

Firstly I want to note this article probably isn't directed at me, since I reject the term theistic evolutionist to describe me.  I am a person that believes in a Christian God and evolutionary theory at the same time.  But I ask anyone that wishes to label me a theistic evolutionist, to think about why they don't feel the need to label me a theistic gravitationalist, nor a theistic electromagnetist since I agree with those scientific descriptions of reality (or theories) as well.

And the rebuttal.  This might be a long one and it might get philosophical.  So I don't know if this blog is the place for it, since it's a science blog.

If we accept that morality and ethics are about good and evil, right and wrong, and the truth and falsehood of moral beliefs (Holmes 1984), then it is only consistent with being a biblical Christian to exhibit thought and modes of moral reasoning that are consonant with God’s nature...

I would explain morality a little simpler.  My view of morality is actually rather simple.  Good actions are those that seek to minimize suffering.  Evil actions are those that tend to cause suffering.  Just because an action is evil, doesn't mean that it isn't unjustifiable, and there is a spectrum of good and bad actions.  The reason I define morality in this way is because justification is not quantifiable and subject to opinion.  Suffering, though not measurable precisely at the moment, can be quantified eventually because human neural responses to stimulus are phenomenon that involve measurable quantities.  I would classify an action that causes suffering to another is always immoral, although in certain circumstances it can be justifiable.

When it comes to the evolution of morality we need to start at something more rudimentary. Altruism or cooperation is observed among animal species. Indeed one can observe these behaviours among animals. What we observe as human morality is simply a very complex set of altruistic behaviours developed through social interaction. Some of these memes are useful and so they stick around, while others don't.  The end result of this being what we call a moral code or behaviour.

Elsewhere Scripture refers to, for example, “the falcon after its kind,” “every raven after its kind,” “the ostrich, the short-eared owl, the sea gull, and the hawk after its kind,” “the heron after its kind,” “the locust, cricket, and grasshopper after its kind,” and the mole, mouse, lizard...

...First, the created kinds were created in mature form and completely functional. Second, each of the created kinds can be called a “natural kind”,⁴ for each was endowed by the Creator with the ability to naturally reproduce...

I skipped quoting a bit of material. It seems to be a review of scripture.  But what does a review of Genesis have to do with an evolutionary origin of morality?  It now seems that Ms. Joubert is simply trying to show that scripture is incompatible with evolution.

What do we normally do when scripture comes into conflict with modern observations and refinements?  We have encountered situations like this before where modern information conflicts with scripture, the same way evolution conflicts with it.  Take 1 Kings 7:23

²³And he made a molten sea, ten cubits from the one brim to the other: it was round all about, and his height was five cubits: and a line of thirty cubits did compass it round about. 

In this passage we are given a definition for π which is clearly inaccurate for modern calculation.  These are examples where the Bible produces suboptimal answers in a modern context.  A modern school child knows π to at least two digits, 3.14, or maybe even to a few more 3.141592.  We are now aware that π is an irrational transcendental number, which means it can't be computed from basic operations like addition, subtraction, multiplications, roots, etc.  Without disregarding the Biblical answer in contexts like engineering, we would not be able to build working electric or mechanical devices.  In short, when the Bible and well established scientific fact come into conflict, the appropriate resolution is to go with what is observed.  Of course Ms. Joubert hasn't presented any attempt to demonstrate incompatibility, so I digress.  Back to my response.

Joubert's review of Genesis continues, and then

The facts of the biblical record of creation put theistic evolutionists under huge pressure to explain to us how human nature and the moral sense, as part of that nature, can “emerge” from ape-like ancestors (so-called hominids) over millions of years, when they entirely lacked these properties.

To say that ape-like ancestors entirely lacked moral sense is quite an astounding thing to say considering what we know about the mammalian brain.  Moral sense is observable even in non-human animals.  A rather marvelous example is one of not just empathy, but cross species empathy observed in elephants for example

South African conservationists are baffled by the behaviour of a herd of elephants which appeared to raid an enclosure on a private game reserve "deliberately" to release a group of antelope captured by rangers as part of a relocation and breeding programme. 

"The herd circled the fence and then the matriarch moved to the gate and very carefully and deliberately undid all the gate's metal latches with her trunk and pushed it open."

Of course, they aren't even close to being human, so we would expect something closer to human to have an even more developed sense of social context and morality.  It would have been a necessary adaptation for humans living in large groups together.  Indeed, non-human apes like Bonobos display these rudimentary traits of morality and social structure.  Though far different than what we are accustomed to as humans, there is a set of social customs that are followed.  It is possible to realistically map great ape behaviour to at least some of the rudimentary social and sexual behaviours of human beings.

In contrast to theistic evolutionists, biblical creationists are under no such pressure. We have seen that God not only created kinds of things and equipped them with abilities appropriate to and natural for them to exercise, but also that the Creator made the first humans in His image. This means that creationists already have a first instance of a maximally moral Person;

She seems to imply that her position is superior because she is not under any pressure to explain anything, because she can simply defer it to a Creator.  I don't know when that became the deciding factor in determining whether a position fits the description of reality or not.  But I still haven't heard her explain why she feels it's not possible, for someone that finds evolution the most compelling description of what we observe, to meaningfully explain morality.

Elsewhere Murphy (1998) concluded that there is a “massive amount of evidence” which suggests that we no longer “need to postulate the existence of a soul or mind in order to explain life and consciousness” (Brown, Murphy, and Malony 1998, p. 17).¹¹ The real reason why she and fellow theistic evolutionists found such “evidence” in the neuro-sciences is very simple...

...We can summarize. Murphy and fellow theistic evolutionists make it difficult for us to believe that methodological reductionism can be embraced by a Christian and continue to maintain Christian faith...

Joubert's seems to be reading too much from Murphy's words.  I believe what they are saying is that based on the evidence there is no need to postulate a soul or mind.  Murphy is not saying that one must accept there is no soul.

Is it really true that it is the brain or size of the brain that makes us human? And if it is true, can evolutionists explain this, as opposed to merely asserting it as a fact of evolution? Eminent neuroscientist Professor Joseph LeDoux (1997), who adheres to the view that it is the brain that makes us human, admitted that he and his fellow neuroscientists are unable to explain...

Brain size alone doesn't make us human but it goes a long way.  It's true we don't understand exactly why humans got to be so intelligent compared to other animals and even to other primates.  But we didn't understand exactly what the value of π was either and we figured that out.  The Bible continues to give us the same answer.  This is why we must actively seek the truth, and test results which is what the search for scientific truth is about.

While I commend her on her knowledge of scripture, Ms. Joubert seems to make many philosophic assertions.  Sadly she also seems to use the argument from ignorance fallacy continuously when speaking of human consciousness.  Of course the argument from ignorance fallacy has nothing to do with calling anyone ignorant; simply that she seems to imply because it cannot be explained at the moment it must be false.  Because it is fruitless to continue providing a response to these types of claims, I shall sum up my position at this point.

When scripture and well established scientific principle come into conflict, I reject scripture on that topic.   Take Galileo and his conflict with the early church over heliocentricism, for example.  The reason is that on every issue where scripture and scientific fact have come into conflict through the ages, it has been shown repeatedly that science gives the best answers.

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.

Fetal Semi-Allograft: The Danger of Politicizing Medical Models

I am interested in the ability to transplant fetuses from one mother to another in order to resolve the current issue we have with abortion.  It is my belief that by doing this, we can give both parties a solution to the problem that we all could live with.  During my research I came across a seemingly knowledgeable person who educated me about the biological model of the maternal-fetal interface.  Despite the differences between the fetal tissue and maternal tissue, the fetus manages to attach itself and not be rejected by the mother.  We now understand immunology to understand why site rejection doesn't occur, though we do not understand the mechanism completely.  This is called the fetal semi-allograft theory.

There is a hormonal exchange that occurs between the new cells and the maternal cells at the attachment point that prevent rejection by the host (mother.)  This series of exchanges sets up a cross immunity between mother and unborn child.  Over time, and the exchange of hormonal messengers, the attachment point develops into an umbilical system that taps into the mother's blood supply to provide her child with nutrients.  Without this cross immunity, both would die in the resulting systemic histamine reactions.  Leukocytes from both mother and child would relentlessly attack each other until both would perish.  It is impossible to be nothing less than awed by the delicate ballet of chemical interactions and the beauty of the result of reproduction.

It is useful at times to look at the combination of fetus and mother as one organism, for the purposes of doing medicine and diagnosing conditions.  Just as sometimes it is handy to look at a given system in different ways in order to derive solutions to different problems.  It might be useful to look at conjoined twins as a single organism for the purposes of diagnosis since they might share organs for example.  That does not mean that they are not two separate individuals.

Which brings me back to the individual that educated me about this theory, Eileen E.  She apparently has a website where she tries to draw consequences for the individuality for the fetus from a medical model.  Eileen states,

With this concept the woman and her fetus are represented as a single organism which could be referred to as the "Pregnancy Unit" as the textbook Williams Obstetrics does...

I find it very hard for this person to derive a concept of what constitutes an individual from a medical model for practicing obstetrics.  Just as very few people would consider conjoined twins to be a single individual, it might be useful to treat them as one when practicing medicine.  I'm sure for obstetrics purposes treating the fetal-allograft as a single pregnancy unit might be useful, since mother and child would act as one unit.  This is not a justification for politicizing a medical model to justify abortion as this author apparently does.

No evidence based practitioner nor scientist wants a medical model used for pushing a particular agenda out of context.  In this case, I'm afraid this is what Eileen is doing.  What's worse is this is exactly what the Nazi scientists did as well.  When individuals do this, they truly do a disservice by delegitimizing the research and models for practicing medicine.  It simply makes it harder for practitioners to do their job.

Cytochrome c and Evolution

One of the most powerful evidences for evolution is some of the details of the protein cytochrome c on Talk Origins.  This is their baby, it's original research.  This protein is present in all living things.  An interesting property common to all amino acids, is that mutations have little effect on function.  Indeed, even within species, most amino acid mutations do nothing.  This is called protein functional redundancy (PFR) and is present in all known proteins and genes.  What that means when we are talking about protein cytochrome c, is that no matter what the specific configurations or mutations are present they all work the same, with minor differences in electron transport ability.

Cytochrome c doesn't just work in a wide variety of configurations, it also is essential for life.  Remarkably, experiments have shown that if you knock out the cytochrome c gene of a yeast, and replace it with human cytochrome c it works the same.  If that wasn't stunning enough, yeast cytochrome c differs from human cytochrome c over 40% of the protein.  This is an incredible testament to its redundancy; a consequence being there is no particular reason for any given configuration to have any advantages over another.  If evolution is false, we would not expect to see any correlation between species and cytochrome c, or all species would have the same cytochrome c.  Furthermore, we observe that only about 30 of the 100 amino acids are even required for the protein to function.  If that wasn't enough, any number of the amino acids can be replaced by many other functionally equivalent ones.

So evolution is very vulnerable here.  It would be remarkably easy to fail this delicate test.  There are a total of 2.3×10⁹³ possible functional cytochrome c sequences.  There are more functional cytochrome c sequences than there are atoms in the universe.  Yet chimpanzees and humans have the same cytochrome c sequences.  The chance of this happening outside of a hereditary process is 10^-93 probability (that's 1 one over a number starting with one that has 93 zero's behind it--tiny number.)  It doesn't stop there; when we compare protein sequences with other species, we find that the cytochrome c sequences match the phylogenetic tree arranged by morphological and physiological characteristics.  This provides an independent confirmation of the validity of the phylogenetic and hereditary tree of life.  A back of the napkin calculation (multiplying the probability 10^-93 by some geometrically shrinking number times the number of species, accounting for broader genetic drift across more distantly related species) of the probability of this occurrence by random chance, absent a ancestral relationship, I find is no better than 10^-100.