The Frailty of the Darwinian Hypothesis (Part 1 and 2)

Editor's Note: Ann Gauger is a senior research scientist at Biologic Institute. Her work uses molecular genetics and genomic engineering to study the origin, organization and operation of metabolic pathways. She received a BS in biology from MIT, and a PhD in developmental biology from the University of Washington, where she studied cell adhesion molecules involved in Drosophila embryogenesis. As a post-doctoral fellow in the Department of Molecular and Cellular Biology at Harvard, she cloned and characterized the Drosophila kinesin light chain. Her research has been published in Nature, Development, and the Journal of Biological Chemistry. Her awards include a National Science Foundation pre-doctoral fellowship and an American Cancer Society post-doctoral fellowship.

A long-standing controversy exists among evolutionary biologists that is little known outside of professional journals. This controversy is significant because it deals directly with the question of how evolutionary processes produce functional changes in organisms —- whether or not the changes we observe are due to adaptive processes guided by natural selection.

Why such a controversy? In his landmark book On the Origin of Species, Darwin proposed natural selection as a force sufficient to account for the organismal complexity and diversity we see around us today. But Darwin knew nothing about genetics or molecular biology. He knew nothing about how variation among organisms was produced or inherited, or what the limits of variation might be. He knew nothing about population dynamics or how difficult it might be for a slightly advantageous trait to spread throughout a population.

In the many years since Darwin wrote his book, scientists have learned much about these topics, and as a result, they have identified four forces driving evolution, not just the one known to Darwin. The four forces are natural selection, mutation, recombination, and genetic drift, and when taken together they affect evolving populations of organisms in sometimes surprising ways. This has led to the controversy I outlined above concerning the efficacy of natural selection to drive evolution in adaptive directions.

Let me explain what the four forces are, and then I will describe the problem they pose.

Natural selection is the evolutionary force with which most people are familiar, and can be simply stated as follows: organisms better adapted to their environment tend to survive and have more offspring than other less fit counterparts, all other things being equal. Mutation and recombination act as the engine of organismal variation: mutations change an organism’s DNA (by substitution, insertion or deletion of particular bases, or modification of the DNA), while recombination shuffles the DNA into new combinations, thus producing further variation. This means that each individual has a unique genome. Differences in each individual’s DNA can produce differences in how well the organism functions in its environment. Finally, genetic drift causes particular variations to be lost from small populations at random, simply because individuals may die or fail to reproduce for reasons unrelated to their fitness for their environment.

It is important to note that three of these four evolutionary forces are non-adaptive and stochastic. An evolutionary force is considered non-adaptive when the change it produces is independent of whether it confers a benefit. It is stochastic when its occurrence is randomly distributed, and cannot be precisely predicted. We can say something about how frequently a stochastic event is likely to occur, but we cannot say what specific changes will occur.

With regard to the above evolutionary forces, this means that mutations occur at random, independent of whether they help or harm, and recombination occurs at random, whether or not it produces helpful or harmful new combinations of genes.[1] Similarly, genetic drift increases the likelihood that a potentially beneficial mutation will be lost before it becomes widespread in the population. This is particularly true for organisms with small effective population sizes, such as vertebrates. The net effect of genetic drift in such populations is “to encourage the fixation of mildly deleterious mutations and discourage the promotion of beneficial mutations,”, in the words of one evolutionary biologist.[2] Only natural selection is adaptive, that is to say, working to ensure that beneficial changes are preserved in the population, and harmful changes are eliminated.

This may seem counter-intuitive, so let me reiterate this point. Because of the accidental effects of genetic drift in small populations, natural selection is not strong enough to guarantee that beneficial mutations will eventually become fixed (universal) in a population or that weakly harmful mutations will be eliminated. Thus, in organisms with small effective population size (e.g. all vertebrates, which includes us humans), the stochastic and non-adaptive forces of mutation, recombination, and drift will tend to drive evolution in non-adaptive directions.

We see the powerlessness of natural selection to eliminate harmful mutations quite clearly, with the variety of hereditary diseases that exist in human populations today. Extremely harmful dominant mutations that cause death immediately, or prevent reproduction, do not spread in the population. However, less immediately harmful dominant mutations, such as those that cause Huntington’s Chorea, permit survival into and past the reproductive years and so are not eliminated. Recessive mutations, like those causing sickle cell anemia or cystic fibrosis, can be present at substantial levels in the population, because having one mutated gene copy has little or no effect on an individual. Only when someone inherits a bad copy from both mother and father do they develop the disease.

And new mutations happen all the time, most of which are either neutral (having no effect), or harmful (causing varying amounts of damage or disease).

What about the rare beneficial mutations? Once again, unless the benefit is very strong, and confers a very large advantage to the individual carrying the mutation, it may never spread through the population. An example here might be the ability of Northern Europeans to digest milk as adults. This ability arose when a mutation allowed an enzyme that digests milk to be produced in adults, and not just in infants. This is a simple advantageous mutation for milk drinkers, but it is not universal among humans, as any one with lactose intolerance can tell you. And it may never be universal, because the selective advantage of being able to eat dairy products is not large unless your diet depends exclusively on milk products for most of the year.

This picture of evolution is strikingly in contrast to the stories told by biologists who believe in the adaptive power of natural selection to generate whole new cellular systems, behaviors, and body plans (see for example Endless Forms Most Beautiful by Sean Carroll [3] or most evolutionary psychology arguments [4]). If three out of the four forces driving evolution are non-adaptive, then perhaps most evolutionary change is also non-adaptive, and not due to the power of natural selection. Hence the controversy.

In the next post I will consider some of the implications of this controversy for intelligent design theory.

The Frailty of the Darwinian Hypothesis, Part 2 In the previous post I described the debate among evolutionary biologists over the so-called adaptive hypothesis. Some biologists believe that natural selection has the power to drive evolution in adaptive directions, and that most changes that we observe in organisms are there because they confer some adaptive benefit. Other biologists believe that most of the changes we see in organisms over time are due to neutral, non-adaptive processes.

You don’t need to take my word for the existence of this debate. Michael Lynch, an eminent evolutionary biologist, lays out the case against the power of natural selection in a paper called “The Frailty of the Adaptive Hypothesis,” [1] published a few years ago for an evolutionary symposium. In it he argues that natural selection is neither a necessary or sufficient explanation for organismal complexity. Rather, he contends that many of the genomic complexities of multicellular organisms are the result of the passive non-adaptive forces that I outlined in my previous post.

For example, mobile genetic elements tend to proliferate, inserting themselves more or less at random into new chromosomal positions, leading to what Lynch calls genomic bloat. In bacterial species with large populations and rapid generation time, this excess baggage is rapidly purified by natural selection. In contrast, among multicellular organisms, with their small effective population sizes and longer generation times, natural selection is usually not strong enough to prevent the accumulation of neutral or weakly harmful insertional mutations.

However, when it comes to answering how organisms deal with the continual genetic disruption such insertional mutagenesis would produce, Lynch has no answers. He offers no explanation of how non-adaptive forces can produce the functional genomic and organismal complexity we observe in modern species.

Lynch believes that evolution is the result of the four forces he lists, mutation, recombination, drift, and natural selection, with the first three non-adaptive forces having a major shaping role. He must accept that natural selection is enough to generate coordinated functional complexity, even in the face of these non-adaptive processes, because after all, what else is there?

Yet it’s clear that other evolutionary biologists are beginning to recognize that the problem is larger than Lynch realizes.[2] They understand they are up against some hard limits — everything from how many mutations can be required before a new selectable function is achieved [3,4], to how much time is available to produce the highly divergent body plans of the Cambrian explosion [5,6]. They continue to come forward with new proposals for how to generate innovation by purely naturalistic means [7]. But all these new ideas suffer from the same flaw — they are undirected, stochastic processes themselves, and likely to suffer from the same failings as the four forces of Michael Lynch.

The problem is clear when we consider the limit mentioned above — how many independent mutations are within reach of an evolutionary search. Recent papers have suggested that anything beyond two mutations may be impossible unless special scenarios are introduced [3,4]. Yet a single enzymatic innovation can require many changes and still result in a very poorly functioning enzyme 8. So how do we account for the huge diversity of proteins existing in nature — over a thousand distinct protein folds that can be subdivided into more than 3400 distinct families of similar proteins, according to the most recent count [9]?

The problem just keeps growing exponentially the higher up the scale of biological complexity you go. Consider the information in a single cell. Even the simplest minimal cell needs to be able to reproduce itself, use and store energy, and make new cellular components not available in its environment, all of which require the complex cellular systems of replication, transcription, translation and metabolism. To organize and control such systems requires an enormous amount of information.

The only source that is able to generate this level of specified, complex information [10] is intelligence. We know from our own experience that intelligent agents can develop systems to store information and recall it when needed. Intelligent agents can reconfigure non-living things (and to a limited extent, living things) in purposeful ways, to modify or produce new functions as desired and to coordinate those functions into a working whole.

Obviously, biologists recognize the information storing and processing capacity of cells. What they are now realizing is how much information is needed to produce living systems. This is knowledge Darwin didn’t have. We need to begin to take account of it in any theory of life’s origin and change over time.

1 This is the standard story. Some scientists are now proposing that mechanisms exist to promote targeted mutations when organisms are stressed [see for example Rosenberg SM (2001) Evolving responsively: adaptive mutation. Nat Rev Genet 2:504-15]. This idea remains highly controversial. If true, the resulting mutations would occur at a higher frequency in the targeted gene(s), but should still be stochastic in nature, and without regard to adaptive benefit. 2 Lynch, Michael (2007) The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci USA 104:8597-8604. 3 Sean Carroll (2005) Endless Forms Most Beautiful. WW Norton and Company, New York. 4 See for example: http://www.epjournal.net

1 Lynch M (2007). The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci USA 104:8597-8604. 2 http://www.scoop.co.nz/stories/HL0803/S00051.htm 3 Durrett R and D Schmidt (2008). Waiting for two mutations: with applications to regulatory sequence evolution and the limits of Darwinian evolution. Genetics 180:1501-1509. 4 http://www.biology-direct.com/content/3/1/18 5 Morris SC (2006). Darwin’s dilemma. Phil. Trans. R. Soc. B 361:1069-1083. 6 Meyer S (2004). The origin of biological information and the higher taxonomic categories. Proc Biol Soc Washington 117:213-239. 7 Koonin EV (2007). The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life. Biology Direct 2:15. doi:10.1186/1745-6150-2-15. 8 Graber R et al. (1999) Conversion of aspartate aminotransferase into an L-aspartate β-decarboxylase by a triple active-site mutation. J Biol Chem 274: 31203-31208. 9 http://scop.berkeley.edu/ 10 Dembski W (1998) The Design Inference: Eliminating Chance through Small Probabilities. Cambridge University Press, ed. B Skyrms.

Ping.

Darwin was already dead at the discovery of the DNA molecular structure and the complexities of the cell.....his believers are too afraid of the scientific evidence that leads to anything remotely to the conclusion that the universe had a creator. I suspect the Darwinist will come up with some theory plausible or not for the above inconsistencies.

Some excerpts from the article ...

Lynch believes that evolution is the result of the four forces he lists, mutation, recombination, drift, and natural selection,

Some biologists believe that natural selection has the power to drive evolution in adaptive directions, and that most changes that we observe in organisms are there because they confer some adaptive benefit. Other biologists believe that most of the changes we see in organisms over time are due to neutral, non-adaptive processes.

Actually, have you noticed that they braying chorus keeps getting smaller and smaller. I looked up the usual suspects to see if they’re still here, and besides Coyoteman and JS1138 (of the ones I am familiar with), they are all still in good standing. What do you supposed happened. Did we defeat them? Did they get tired and give up? Did they lose interest? Either way, its good to see the active members of their posse shrink on an almost daily basis :o)

All the best—GGG

I think one of my favorite evolution stories is "The Tale of the Whale".

As the story goes many, many years ago a fish crawled out of the water and became a mammal.

Then, some years later, a mammal crawled back into the ocean and became a whale.

Now that is one whale of a tale!

I’m still here GGG. (Hugs :))

I can’t speak for anyone else, but in my case I’ve found that trying to have intelligent conversations with creationists regarding science is much like beating one’s head with a hammer – it feels so good when you stop. And it’s just as pointless BTW.

All the best—Caramelgal

The theory of evolution is evolving as more facts about biology are uncovered. These hypothesis will be tested and added to the growing knowledge of the fact of evolution.

It’s easy to say, “God did it.” which may be true, but the facts are interesting to read about.

Thanks for the post

It is entirely compatible with Christianity.

I would argue that it is not....in fact it is complete opposites. Darwin tried to explain our development is part of a natural process...we weren't really "designed" we just came into existance randomly. However, this random occurrence can not account for the utmost complexity of our universe and how finely tuned it is, from cosmology to biochemistry...if life occurred 'randomly' the universe simply isn't OLD ENOUGH to handle that level of probability. Also, out of the thousands and thousands of fossils that have been found in the last few decades where are the fossils demonstrating, not microevalution, but macroevolution, changes from one species to the next. There is no fossil of any kind showing one animal turning into another.

Also, Christianity teaches that death happened as a result of sin, not age. For a Christian to believe in millions of years is a direct contradiction to what the bible actually teaches. If we can not trust that the bible is true to say the universe was created within 7 days, how can we say that the bible is true when it says a man named Jesus came back from the dead?

I say the bible is true on all accounts. In my view, it has stood the test of doubt for thousands of years. Science, on the other hand seems to change from one generation to the next.

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