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.

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.