Tag Archives: Evolution

New study: evolutionary algorithms fail to produce meaningful change

Apologetics and the progress of science
Apologetics and the progress of science

Dr. Ann Gauger has a short post at Evolution News about a new paper in the peer-reviewed journal BIO-Complexity.

She writes:

Winston Ewert of Biologic Institute has just published a new article in the peer-reviewed journal BIO-Complexity (“Overabundant mutations help potentiate evolution: The effect of biologically realistic mutation rates on computer models of evolution”).

He and his colleagues have been engaged in a series of critiques of evolutionary algorithms for the last several years.

[…]The advantage of these computer simulations is that they can be run many, many times and thus approximate the long time necessary for biological evolution. The disadvantage is that they do not replicate true biological evolutionary processes, but use “analogous” algorithms. Typically these models, such as Ev and Avida, are purported to solve complex problems.

Yet Ewert and his colleagues have shown that in every case the necessary information for the models to find their targets was smuggled in, whether intentionally or not, by the respective programmers.

[…]Ewert shows that even taking the models as they are, when they are tested using realistic scenarios they fail to accomplish their goals. In fact, they accomplish little beyond their starting positions. He determines the reason for this failure — the models can only go as far as one step will take them. They can’t evolve anything that requires two or more mutations, unless mutation rates are unrealistically high.

Here’s the abstract of the new paper:

Various existing computer models of evolution attempt to demonstrate the efficacy of Darwinian evolution by solving simple problems. These typically use per-nucleotide (or nearest analogue) mutation rates orders of magnitude higher than biological rates. This paper compares models using typical rates for genetic algorithms with the same models using a realistic mutation rate. It finds that the models with the realistic mutation rates lose the ability to solve the simple problems. This is shown to be the result of the difficulty of evolving mutations that only provide a benefit in combination with other mutations.

This reminds me of William Dembski’s “No Free Lunch” theorems, which show that you can never get information for free, through simple mechanisms like genetic algorithms. The only proven source of functional information is an intelligent agent.

William Lane Craig debates Peter Atkins: Does God Exist?

Apologetics 315 posted the video of a debate from the Reasonable Faith speaking tour in the UK:

This is a must-see debate. It was extremely fun to watch.


On Wednesday 26th October 2011 William Lane Craig debated Peter Atkins on the topic: Does God Exist? This debate took place at the University of Manchester  as part of the UK Reasonable Faith Tour with William Lane Craig. The debate was chaired by Christopher Whitehead, Head of Chemistry School at the University. Post-debate discussion was moderated by Peter S Williams, Philosopher in Residence at the Damaris Trust, UK.

Dr. William Lane Craig:

William Lane Craig (born August 23, 1949) is an American analytic philosopher, philosophical theologian, and Christian apologist. He is known for his work on the philosophy of time and the philosophy of religion, specifically the existence of God and the defense of Christian theism. He has authored or edited over 30 books including The Kalam Cosmological Argument (1979), Theism, Atheism and Big Bang Cosmology(co-authored with Quentin Smith, 1993), Time and Eternity: Exploring God’s Relationship to Time (2001), and Einstein, Relativity and Absolute Simultaneity (co-edited with Quentin Smith, 2007).

Craig received a Bachelor of Arts degree in communications from Wheaton College, Illinois, in 1971 and two summa cum laudemaster’s degrees from Trinity Evangelical Divinity School in Deerfield, Illinois, in 1975, in philosophy of religion and ecclesiastical history. He earned a Ph.D. in philosophy under John Hick at the University of Birmingham, England in 1977 and a Th.D. underWolfhart Pannenberg at the University of Munich in 1984.

Dr. Peter Atkins:

Peter William Atkins (born 10 August 1940) is a British chemist and former Professor of Chemistry at the University of Oxford and a Fellow of Lincoln College. He is a prolific writer of popular chemistry textbooks, including Physical ChemistryInorganic Chemistry, and Molecular Quantum Mechanics. Atkins is also the author of a number of science books for the general public, including Atkins’ Molecules and Galileo’s Finger: The Ten Great Ideas of Science.

Atkins studied chemistry at the University of Leicester, obtaining a bachelor’s degree in chemistry, and – in 1964 – a PhD for research into electron spin resonance spectroscopy, and other aspects of theoretical chemistry. Atkins then took a postdoctoral position at the UCLA as aHarkness Fellow of the Commonwealth fund. He returned to Oxford in 1965 as fellow and tutor of Lincoln College, and lecturer in physical chemistry (later, professor of physical chemistry).

You can get the audio of the debate here, along with links to their previous debate from 1998. This debate is accessible and understandable to novice-level Christians.

I am happy when debates like this come out. I have friends who are Christians who doubt the importance of apologetics in evangelism, because they don’t think that apologists can prove anything or win arguments. I have friends who are skeptical of using arguments that assume a 14-billion year old universe, because they think that the Big Bang is compatible with atheism (!). I have friends who think that philosophical arguments have no persuasive force. I have friends who think that nothing can be proven from history, beyond a reasonable doubt. I have co-workers who ask me whether anyone wins these debates. I think that this debate answers all of those questions.

This debate clearly shows why Christians should not shy away from studying science, philosophy and history. We will not discover anything that harms Christian theism by thinking logically and by looking at the evidence. To the contrary, it is the atheist who makes war on the progress of science, and who is forced to resist the clear experimental evidence, and to resort to baseless speculations and blind faith. If you want to see a good debate with an intelligent atheist, I recommend watching the debate between William Lane Craig and Peter Millican instead. But if you want to see a really, really overwhelming defeat for atheism, watch this debate. It is very clear at the end of this debate why Richard Dawkins refused to debate William Lane Craig at Oxford.


I only had time to summarize the first two speeches. Keep in mind that Dr. Craig always shines in his rebuttals, and this debate is no different. So you’ll want to watch those rebuttals. Dr. Atkins literally says in this debate in his first rebuttal “There was nothing here originally. There is nothing here now. But it is an interesting form of nothing which seems to be something.” And the audience laughs nervously. This debate is like that. You will see a clear winner and clear loser in this debate. This fight is decided by knockout.

William Lane Craig opening speech:

1. the origin of the universe
2. the moral argument
3. the resurrection of Jesus

Peter Atkins opening speech:

1. Dr. Craig is stupid, lazy and evil:
– Dr. Craig’s arguments are old: from the 11th century! Old arguments can’t be true
– Dr. Craig is just asserting that “God did it” because he is lazy
– Dr. Craig feels pressured to agree with the theistic majority
– Dr. Craig needs a psychological crutch to comfort him
– Dr. Craig is fearful of death
– Dr. Craig is just wishing for an eternal life of bliss
– Dr. Craig is driven by his heart, and not by his head

2. Origin of the universe:
– Maybe the universe is eternal and has no beginning – we don’t know
– Maybe mommy universes can give birth to daughter universes
– It is naive to think that a cause is needed to cause the creation of the universe from nothing
– Science is just about to show how it is possible that something appears out of nothing without cause
– Some scientists have already begun to speculate about about how something can come into being out of nothing
– Maybe nothing is not really nothing, but it is actually something
– It would be admitting defeat to say that God created the universe out of nothing

3. Fine-Tuning:
– It could be the case that the fundamental constants are not variable
– It could be the case that the fine-tuning of the cosmic constants is a happy accident
– It could be the case that there are billions of billions of unobservable universes that are not fine tuned
– It could be the case that the cosmic constants in these billions and billions of unobservable universes are all random so that some are fine-tuned
– Anyone who infers that an intelligence is the best explanation of a finely-tuned set of life-permitting cosmic constants is lazy

4. Purpose:
– Philosophers and theologians are stupid
– I don’t think that there is purpose in the universe
– I think that the universe is more grand if there is no purpose, so there is no purpose

5. Miracles:
– I don’t think that miracles happen
– The resurrection is a fabrication
– It could be the case that Jesus didn’t exist
– It could be the case that Jesus wasn’t really crucified
– It could be the case that Jesus didn’t  really die after being crucified
– It could be the case that the disciples stole his body
– It could be the case that the women went to the wrong hole in the ground
– the gospels are political propaganda written long after the events they are reporting on

6. Theodicy:
– God has no morally sufficient reason for allowing humans to perform actions that result in suffering
– God has no morally sufficient reason for allowing nature to cause suffering

7. Morality:
–  customs and conventions emerges arbitrarily in different times and places based on an awareness of the consequences of actions, as well as various anecdotes and experiences
–  these customs and conventions are decided based on the goal for survival, in much the same way as politeness and manners emerge for decorum and to avoid offense
– it is childish to presume that there is an umpire God who decides moral values and duties

8. Religious believers are stupid, lazy and evil:
– the notion of God has arisen because people are stupid and want to be comforted
– there are no arguments or evidences for belief in God
– people who believe in God do not think, but instead take refuge in incomprehensible nonsense

Greg Koukl debates Michael Shermer on God, atheism, meaning and morality

The full transcript of a debate between Michael Shermer, editor of Skeptic magazine, and Greg Koukl, president of Stand to Reason. This debate occurred on Hugh Hewitt’s radio show, and was moderated by Hugh Hewitt.

HH = Hugh Hewitt
GK = Greg Koukl
MS = Michael Shermer

Here is a 32-page PDF with the full debate transcript.

And here’s an excerpt:

GK: Right. Actually, the big question here, Hugh, is whether it’s possible to be good without God. Now I’m not talking about whether it’s possible to be good without a belief in God. I certainly think that’s possible, but be good without God. And the answer to that question hinges entirely on precisely what you mean by good. And so I was going to give an illustration. So a man drags a young girl into the alley, he sexually abuses her, strangles here, and tosses her into the dustbin. Is that act wrong? Now I think everybody listening is going to admit it is wrong. But here is the real question. What do we mean when we say that that act of rape and abuse and murder is wrong? Are we describing the action itself, the object? Are we saying that the object, the rape, the murder, has a quality of being wrong, and therefore, wherever that rape goes, the wrongness follows it, just like your height, 6’ 2”, or whatever it is, is an objective quality of you. Wherever you go, your height follows you in the same way. Does the wrongness follow the rape? Well, if it’s a quality of the rape, if it’s an objective quality of the rape, then it does. And it doesn’t matter what people think about it, or what cultures decides, or what your evolutionary conditioning is. The rape is still wrong. The other alternative is that you’re not talking about the rape. You’re talking about yourself. You’re talking about your genetic conditioning. You’re talking about your culture’s decision about that kind of thing. And if that’s the case, then the truth of the wrongness of the rape is simply in the individual or the subject. And this is why philosophers distinguish between ethical objectivism and ethical subjectivism. Now there’s lots of different subjectivisms in ethics. But simply put, if you’re an ethical subjectivist, you’re a relativist. And actual ethics don’t exist. Ethics are an illusion. If you conclude that ethics are an illusion, there’s lots of different ways to explain it. Michael’s written a really great book, I think, called The Science Of Good And Evil. I’ve read most of it, and it’s well written, and it’s very compelling. But it’s a description about how the illusion of ethics has taken place. If you want to go that route, you’re welcome to go that route. But what you can’t do is you can’t then talk about morality as if it’s objective when your explanations are subjective. So this is a problem that I think all atheists, including Michael, have to solve. Are ethics objective or relative? And if they’re relative, then how can we make moral judgments that are meaningful on other people?

HH: Michael Shermer?

MS: Wow, let’s just get right into it. Well, I don’t think it’s quite so black and white. That is to say I think there are provisional moral truths that exist whether there’s a God or not. In other words, it’s wrong, morally, absolutely morally wrong to rape and murder. And that would be true whether there was a God or not. In other words, if…is God saying that it’s wrong because it’s really wrong, and He’s instructing us in his Holy Scripture that it’s wrong? Or is it only wrong because He said so? And if it turned out there wasn’t a God, would that make it okay? And my answer is no, it really is wrong, whether God says it’s wrong or not. That is to say I think it really exists, a real, moral standard like that. Why? Well, because first, you could ask the person who is being affected, we should always ask the moral recipient of the act, how do you feel about being raped or murdered or stolen from or lied to. And the moral actor will tell you, it doesn’t matter whether, if I could use a current example, I haven’t any idea if Tiger Woods and his wife are religious or not. But you can just ask his wife whether it was morally right or wrong, and she’ll tell you. It doesn’t matter whether there’s a God or not. It’s wrong. And so that’s the first principle. Just ask. Ask the moral recipient of whether it’s right or wrong. But I think Greg’s after something deeper, that is to say is there something even deeper still behind the moral actor’s feelings about how they’re treated. And the answer is yes, I think so. We’re a social species. We don’t live in isolation. We live as members of a group. And as such, there’s no possible way our group could survive, be cohesive, be a unit of any kind of solidarity against other groups, or against a harsh environment. If there were too much violations of social norms, that is if there were constant lying and cheating and raping and murdering, there’s no way a social group could hang together. And as such, as we all know, we’re very tribal. We’re tribal against other groups, but within our groups, we’re very pro-social, altruistic, cooperative. We have a good and evil in our nature. So to this extent, I find myself interesting often in agreement with my conservative friends on most of the things they consider morally, moral truths. That is, we share the same moral values, even though I come at it from a different perspective.

HH: Greg?

GK: Yeah, I’m actually not after something deeper here, Michael. At least to start out the discussion, I’m trying to be as simple and clear and precise as possible, because it’s very easy to weave together a bunch of things that sound persuasive, but turn out to be different things. Like for example, Darwinian evolution, which is a materialistic process, and here I mean the blind watchmaker thesis, the neo-Darwinian synthesis, natural selection working on mutations, and a kind of a cultural evolution that Michael has just referred to as we work together as a group to survive as a group. Those are two entirely different things. One is materialistic, Darwinian, the other one is intelligent design, quite frankly, where the group gets together and makes some determinations to encourage some behavior and discourage others. What I’m trying to do is to be able to answer the question that came up initially, is God necessary for morality, which Michael denies. It’s to say well, what is it that morality, that we’re trying to describe? It is either objective, and therefore an immaterial obligation that applies to certain behaviors, or it is subjective. The things that Michael described were variously subjective, evolutionary elements, subjective cultural elements, but then he affirmed that we all have good and evil in our nature, or an awareness of that. I agree with that entirely. We all are aware of those things. That’s why even if we don’t believe in God, we can still know morality and follow it. The question is what accounts for real, genuine objective morality?

HH: One minute to the break, Michael Shermer.

MS: I’m not arguing for cultural evolution. I’m actually arguing as part of our, what you described as materialistic, natural selection, Darwinian evolution, that it’s not enough to just pretend or fake being a good group member. You actually have to believe it, feel it, and live it. So what I’m arguing is that natural selected certain moral sentiments, as Adam Smith called them, moral feelings, an actual empathy, Adam Smith talked about, we actually empathize with somebody else, we can put ourselves into their shoes and feel their pain, I’m arguing that’s very real. It’s every bit as real a part of our evolutionary heritage as our eyes and our hands.

– – – –

HH: Michael Shermer, when we went to break, you were saying that evolutionary biology has produced a real morality.

MS: Yeah, I think really, Adam Smith had it right in his very first book, The Theory Of Moral Sentiments, long before Darwin, that we actually have in our biological nature, our human nature, the capacity to feel other people’s pain. He called it empathy, we think of it often either as empathy or sympathy. That is, we really do connect to other people. A lot of good research on this now, brain scans, you can show somebody a little video of somebody they know, or have feelings for, getting pricked with a pin, and the same areas of their brain light up, the pain receptors, as in the person getting the pin prick. In other words, we have an evolved tendency to really be deeply, emotionally connected to our fellow group members. And that’s why I say groups like World Vision, where you want to adopt a child, it doesn’t help to show a picture of 10,000 starving African kids. What does affect us is one child, a picture of one child with a little biography. That’s how you get people to adopt a child to donate. The reason for that is because essentially they’re tricking the brain, our brains into making that stranger an honorary family member, an honorary within group member, which is why I argue that free trade is one of the best ways of defusing normal tribal tensions between people. It makes them honorary friends, honorary members. Well, what’s going on there is we’re tricking the brain into sort of this evolutionary rule of thumb – be nice to people that are like you and that are related to you, and that you know, and that are fellow group members, and don’t do what our natural tendency is, is to be tribal and xenophobic against those other guys. And free trade is one of the best things you can do for that. So I’m arguing that’s actually tapping something deep within us.

HH: Greg Koukl?

GK: Yeah, basically, I agree with Mike completely here. We do have this tendency, and it seems to be universal among humankind. The question is, what is that tendency, actually? And what is the best way to explain it? And I see like a handful of significant problems with using evolution to explain morality. The first one is that evolution is a materialistic process. And here, I’m going back to an original point, and I don’t want people to lose it. There is no way that you can take molecules, and reorganize them in any fashion, over any length of time, and have pop out of the mixture an objective moral principle that’s immaterial, and that applies to human beings. All you’re going to get is a reorganization of the molecules. And what they can produce, and this is what Mike has done in his book, and he mentioned just s few moments ago, they can produce sentiments. They can produce feelings. They can produce behavior. But this leads us to the second problem of using evolution to explain morality, is that morality is more than sentiments, feelings and behavior. Morality entails things like motive and intention. I mean, you could have a guy walk into a garage, walk out with a hose, and is that wrong? Well, it depends. Is it his hose or somebody else’s hose? Did he intend to take the other person’s hose? Is he borrowing the hose? So we can see here are elements that are part of the moral thing that needs to be explained, that are immaterial, and therefore the Darwinian explanation can’t even in principle go there. It can’t do that job. But here’s the worst problem. Regardless of what our sentiments happen to be regarding moral actions, we can feel good or feel bad or whatever, the problem is that morality is prescriptive, not merely descriptive. That is it tells us not just what we did, but what we ought to have done in the past, and what we ought to do in the future. That is not something that any Darwinian mechanism can describe, because nothing about my biology can inveigh upon me to act a certain way for moral reasons in the future. It doesn’t tell me why I should be good tomorrow. This is a huge difference between these two views, the descriptive and the prescriptive. Prescriptive is part of morality, and can’t even, in principle, be explained by an evolutionary materialistic system.

HH: Michael Shermer, I’ll give you a start on that. We have about 45 seconds to the break, so you may want to…we’ll come back after the break and pick up. But what’s your start to that?

MS: Well, the start would be that again, let’s not think of evolution just as nature red and tooth and claw, and it’s nasty, brutish and short, but that in fact, we have this whole other social evolution. And I’m not talking about cultural evolution where we consciously make decisions, but subconsciously, because it’s in part of our nature to actually, seriously, deeply feel for other people and their actions, and the consequences of our actions, so that we actually have a sense of right and wrong that we’re born with, but then culture taps into and tweaks, one way or the other.

– – – –

HH: Michael Shermer, when we went to break, Greg had made the argument that the Darwinian model simply cannot explain immaterial concepts like morality, that there’s just no way you can rearrange the molecules to get there. You’re saying well, yes you can.

MS: Yeah, I think so, because if we think of morality as another suite of emotions that are involved with other people’s behaviors, the consequences of our actions, how we feel about them, how people feel about us when we do these things, that’s as every bit as important a biological part of our nature as anything else we talk about. So let’s take a real simple emotion. When you’re hungry, nobody does any calculations about the caloric input/output ratios of eating an apple versus an ice cream, although now it’s posted on the walls for us to see. But we just feel hungry, and we feel hungry for certain kinds of foods. The feeling of hunger is a proxy for something else. Evolution’s done the calculating for us. You need food, so we’re going to, your hypothalamus is going to secrete these certain chemicals that causes your stomach to rumble and so on. When you’re attracted to somebody else, a member of the opposite sex, nobody does the calculation by, let’s say, a man finds a woman attractive who has a .67 hip to waist ratio, and an hourglass figure, although that is pretty much universal. Nobody walks about with calipers taking measurements of who they’re going to want to date or ask out. You just look around, and you just go wow, I really find this woman attractive. It’s a feeling you have, okay? So those are kind of simple emotions, but sliding up the scale, the moral emotions are really no different. When I lie to somebody, I’ve violated a social norm, and they respond in a very angry, hostile way. So those emotions that we both share, guilt, shame, anger, disgust, involved a social relationship that whether it was a norm violation, those are the kinds of emotions that are just like hunger and sexual attraction that are built into us by nature, by evolution. Or, if you wish, this is how God created the moral sentiments, just like He created everything else in the universe, through a process of nature. I think that’s equally reasonable to argue. So I don’t see that it has to be an atheistic viewpoint versus a theistic viewpoint to get to our moral sentiments. Why couldn’t God have used evolution to create the moral sentiments as I’ve described them?

GK: Yeah, well, you don’t actually believe that, I know, Mike, so this is kind of like adding God to the soup, you know, if it makes people feel better. But the basic argument is that evolution all by itself can do the trick. And I think if your listeners are listening carefully, what they’re going to hear is Mike has just described, and if I’m being unfair to your assessment here, let me know, Mike, that moral feelings are simply that. They are sophisticated emotions that do some work for us for survival, and even on a group level. Now there’s a name for this. It’s called emotivism. A.J. Ayer, the famous atheist, offered this description of morality. It’s a relativistic scheme of morality. Morality doesn’t actually exist, Ayer argued. There is no objective right or wrong. Rape isn’t wrong itself. What happens is, we have feelings about it, and we express it in moral language, but rape isn’t really wrong. So your listeners are going to have to ask themselves the questions. When they just survey their own moral senses, and we all have access to this, do we want to believe that scientists have figured out that really what we’re doing is feeling sophisticated, complicated emotions, and that the emotions are in us, and we are not seeing anything about the action? Or does it seem like rape is wrong? Look, when I say rape is wrong, I’m talking about the rape. When I say liver is awful, I’m talking about me. I’m talking about my own tastes and preferences. It’s interesting, as Michael has given his explanation, though, that he’s doing, and I don’t know if you are aware of this, Michael, but you’re doing the very thing that I kind of warned against. You give a description of the foundations of morality that turn out to be relativistic, but then there’s a smuggling of a more objectivistic morality in the back door, like when Michael says you don’t have to do what your nature tells you to do, in other words, what you’ve been programmed by evolution to do. You can kind of rise above that. Well, now we’re talking about a morality that isn’t dictated by evolution, but a morality that we can employ through our acts of will, to rise above this kind of brutish evolutionary morality. And that sounds suspiciously like the very thing that I’m talking about here.

MS: But I don’t mean, there’s nothing to rise above by itself. Yes, we have to say rise above our tribal instincts to be xenophobic when we meet somebody who’s a stranger, who’s different from us. We all struggle against that, particularly in a black and white America, where there’s always been this underlying tension. Indeed, so culture helps us do that – education, travel, diversity of exposure to different people. That makes you a little more tolerant. Okay, but I’m not talking about that. What I’m talking about is tapping into the good part of our nature, the fact that in addition to that xenophobic tribalism we have, we also have this other side that almost never gets discussed in evolutionary…even in evolutionary circles, you’ll still hear evolutionary biologists talking about, in a way that Huxley did, and Herbert Spencer did in Darwin’s own time, that we have to somehow struggle mightily against our genes to overcome that nasty tendency we have to want to rape, kill, pillage and destroy. Well no, actually, we have this whole other side that’s just as genetically programmed into our nature. And the point of culture – education, politics, economics and so on, is to tap into the better angels of our nature as Lincoln said.

GK: Okay, here’s the question I have for you, Michael, then. You’ve identified that really, we have good and we have bad. That’s part of, under your terms, that’s part of our genetic nature, and we can choose to tap into what you call the good side. Why ever should we do such a thing if there is not a higher standard that directs our action to the better side, your words, than the bad side, your words, if really, ultimately, they are both the result of a genetic evolution, and from outside terms, neither is better than the other. Why should we do that, Michael?

MS: Yeah, well I don’t see how entering God into the equation changes that problem at all.

GK: Well, that’s the next step. What I’m trying to show is that the should comes from the outside, and if we can demonstrate that, then we can ask…

Read the rest by click here to get the PDF.

Peer-reviewed paper: Michael Behe’s “First Rule of Adaptive Evolution”

Apologetics and the progress of science
Apologetics and the progress of science

JoeCoder was writing some JavaScript code last night and he ran into a problem where a 3rd-party open source library was not performing as expected. So he got the non-minified version of the library and commented out two lines to get the behavior he wanted. He said this to me “Michael Behe’s first rule of adaptive evolution has been confirmed once again.” So, let’s take a look at Mike Behe’s first rule of adaptive evolution.

The paper was published in the Quarterly Review of Biology. I found it on PubMed.


Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

By far the most common adaptive changes in the examples we have are due to loss of function or modification of pre-existing function?

Evolution News has a post up about the paper.


After reviewing the effects of mutations upon Functional Coding ElemenTs (FCTs), Michael Behe’s recent review article in Quarterly Review of Biology, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” offers some conclusions. In particular, as the title suggests, Behe introduces a rule of thumb he calls the “The First Rule of Adaptive Evolution”: “Break or blunt any functional coded element whose loss would yield a net fitness gain.” In essence, what Behe means is that mutations that cause loss-of-FCT are going to be far more likely and thus far more common than those which gain a functional coding element. In fact, he writes: “the rate of appearance of an adaptive mutation that would arise from the diminishment or elimination of the activity of a protein is expected to be 100-1000 times the rate of appearance of an adaptive mutation that requires specific changes to a gene.” Since organisms will tend to evolve along the most likely pathway, they will tend to break or lose an FCT before gaining a new one. He explains:

It is called the “first” rule because the rate of mutations that diminish the function of a feature is expected to be much higher than the rate of appearance of a new feature, so adaptive loss-of-FCT or modification-of-function mutations that decrease activity are expected to appear first, by far, in a population under selective pressure.(Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).)

Behe argues that this point is empirically supported by the research reviews in the paper. He writes:

As seen in Tables 2 through 4, the large majority of experimental adaptive mutations are loss-of-FCT or modification-of-function mutations. In fact, leaving out those experiments with viruses in which specific genetic elements were intentionally deleted and then restored by subsequent evolution, only two gain-of-FCT events have been reported

After asking “Why is this the case?” Behe states, “One important factor is undoubtedly that the rate of appearance of loss-of-FCT mutations is much greater than the rate of construction of new functional coded elements.” He draws sound and defensible conclusions from the observed data:

Leaving aside gain-of-FCT for the moment, the work reviewed here shows that organisms do indeed adapt quickly in the laboratory–by loss-of-FCT and modification-of-function mutations. If such adaptive mutations also arrive first in the wild, as they of course would be expected to, then those will also be the kinds of mutations that are first available to selection in nature. … In general, if a sequence of genomic DNA is initially only one nucleotide removed from coding for an adaptive functional element, then a single simple point mutation could yield a gain-of-FCT. As seen in Table 5, several laboratory studies have achieved thousand to million-fold saturations of their test organisms with point mutations, and most of the studies reviewed here have at least single-fold saturation. Thus, one would expect to have observed simple gain-of-FCT adaptive mutations that had sufficient selective value to outcompete more numerous loss-of- FCT or modification-of-function mutations in most experimental evolutionary studies, if they had indeed been available.

But this stark lack of examples of gain-of-functional coding elements can have important implications:

A tentative conclusion suggested by these results is that the complex genetic systems that are cells will often be able to adapt to selective pressure by effectively removing or diminishing one or more of their many functional coded elements.

Behe doesn’t claim that gain-of-function mutations will never occur, but the clear implication is that neo-Darwinists cannot forever rely on examples of loss or modification-of-FCT mutations to explain molecular evolution. At some point, there must be gain of function.

Now, there was a response to this paper from Jerry Coyne on his blog, and then a rebuttal from Mike Behe in a separate article on Evolution News.

Convergence detected in the genetic structure of bats and dolphins

Apologetics and the progress of science
Apologetics and the progress of science

We have to start this post with the definition of convergence in biology.

In evolutionary biology, convergent evolution is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches.

It is the opposite of divergent evolution, where related species evolve different traits.

On a molecular level, this can happen due to random mutation unrelated to adaptive changes; see long branch attraction. In cultural evolution, convergent evolution is the development of similar cultural adaptations to similar environmental conditions by different peoples with different ancestral cultures. An example of convergent evolution is the similar nature of the flight/wings of insects, birds, pterosaurs, and bats.

All four serve the same function and are similar in structure, but each evolved independently.

Jonathan Wells explains the problem that convergence poses for naturalistic evolution:

Human designers reuse designs that work well. Life forms also reuse certain structures (the camera eye, for example, appears in humans and octopuses). How well does this evidence support Darwinian evolution? Does it support intelligent design more strongly?

Evolutionary biologists attribute similar biological structures to either common descent or convergence. Structures are said to result from convergence if they evolved independently from distinct lines of organisms. Darwinian explanations of convergence strain credulity because they must account for how trial-and-error tinkering (natural selection acting on random variations) could produce strikingly similar structures in widely different organisms and environments. It’s one thing for evolution to explain similarity by common descent—the same structure is then just carried along in different lineages. It’s another to explain it as the result of blind tinkering that happened to hit on the same structure multiple times. Design proponents attribute such similar structures to common design (just as an engineer may use the same parts in different machines). If human designers frequently reuse successful designs, the designer of nature can surely do the same.

I’m a software engineer, and we re-use components all the time for different programs that have no “common ancestor”. E.g. – I can develop my String function library and use it in my web application and my Eclipse IDE plug-in, and those two Java programs have nothing in common. So you find the same bits in two different programs because I am the developer of both programs. But the two programs don’t extend from a common program that was used for some other purpose – they have no “common ancestor” program.

Now with that in mind, take a look at this recent article from Science Daily, which Mysterious Micah sent me.


The evolution of similar traits in different species, a process known as convergent evolution, is widespread not only at the physical level, but also at the genetic level, according to new research led by scientists at Queen Mary University of London and published in Nature this week.

The scientists investigated the genomic basis for echolocation, one of the most well-known examples of convergent evolution to examine the frequency of the process at a genomic level.

Echolocation is a complex physical trait that involves the production, reception and auditory processing of ultrasonic pulses for detecting unseen obstacles or tracking down prey, and has evolved separately in different groups of bats and cetaceans (including dolphins).

The scientists carried out one of the largest genome-wide surveys of its type to discover the extent to which convergent evolution of a physical feature involves the same genes.

They compared genomic sequences of 22 mammals, including the genomes of bats and dolphins, which independently evolved echolocation, and found genetic signatures consistent with convergence in nearly 200 different genomic regions concentrated in several ‘hearing genes’.

[…]Consistent with an involvement in echolocation, signs of convergence among bats and the bottlenose dolphin were seen in many genes previously implicated in hearing or deafness.

“We had expected to find identical changes in maybe a dozen or so genes but to see nearly 200 is incredible,” explains Dr Joe Parker, from Queen Mary’s School of Biological and Chemical Sciences and first author on the paper.

“We know natural selection is a potent driver of gene sequence evolution, but identifying so many examples where it produces nearly identical results in the genetic sequences of totally unrelated animals is astonishing.”

Nature is the most prestigious peer-reviewed science journal. This is solid material.

There is an earlier article from 2010 in New Scientist that talked about one of the previous genes that matched for hearing capability.


Bats and dolphins trod an identical genetic path to evolve a vital component of the complex sonar systems they use to pursue and catch prey.

The finding is unusual, because although many creatures have independently evolved characteristics such as eyes, tusks or wings, they usually took diverse genetic routes to get there.

Analysis of a specific gene has now demonstrated that although bats live in air and dolphins in water, where sound travels five times faster, they independently evolved a near-identical gene that allows them to accept high-frequency sound in the ear – vital for sonar.

The gene makes prestin, a protein in hair cells of the cochlea, which is the organ in the inner ear where sonar signals are accepted and amplified. Prestin changes shape when exposed to high-frequency sound, and this in turn deforms the fine hair cells, setting off an electrical impulse to the brain. So the protein has the important jobs of detecting and selecting high-frequency sounds for amplification.

When researchers examined the molecular structure of the prestin gene from a range of animals, they found that the variants in echolocating bats and dolphins were virtually indistinguishable.

Indistinguishable genes in animals that don’t share a common ancestor? Maybe a better explanation for the evidence we have is – common designer.