Not your mom and dad’s evolution: the failure of natural selection

If I asked you what drives evolution, what are the first things that come to mind? If you are like me, it is mutation and natural selection. That is what we are taught in school and that is what we read about on the popular level and hear in most popular-level discussions. Now, what if I told you that prominent evolutionary biologists dissent from this view, or at least significantly modify it. We will explore a case of this dissent in this blog post.

A while back I was interested to revisit the arguments for Intelligent Design (ID) and was led down an alternate path. Out of all the ID arguments out there, one that strikes me as particularly difficult and nagging is the problem of generating new biological information. This can be stated as: natural selection tells us how genes survive, but not how they arrive. How do genes and phenotypes arrive on the scene? Again, if you are anything like me, you’ve heard it so many times that it is the mantra we all adhere to: microevolution working on an epochal timescale equals macroevolution. That’s it. But, this time I began wondering if this assertion is really plausible. We now have tools to examine the plausibility thanks to the molecular revolution.

From my own searches I could find virtually nothing that directly addresses this question, so I decided to seek out the most qualified scientists and read their material on the subject. That is when I learned about Michael Lynch, an emeritus professor, member of the Academy, and author of a textbook on population genetics. We will be examining select arguments from Lynch’s paper, “The Frailty of Adaptive Hypotheses for the Origins of Organismal Complexity”. (1) From the outset Lynch sets up the problem that at its core is ID’s nagging question, where does new genetic information come from? This is considered in terms of genomic complexity and finally organismal complexity as the title states. Early on in a moment of polemical gold he states:

It has long been known that natural selection is just one of several mechanisms of evolutionary change, but the myth that all of evolution can be explained by adaptation continues to be perpetuated by our continued homage to [Charles] Darwin’s treatise in the popular literature. For example, [Richard] Dawkin’s agenda to spread the word on the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms. . .

He goes on to explain that there are four primary forces of evolution: natural selection, mutation, genetic drift, and recombination. Only the first is adaptive, therefore the remaining forces are nonadaptive.

Lynch frequently utilizes differences between prokaryotes and eukaryotes to understand the origin of complexity, so we will review these briefly. Let’s start with morphologic differences. Prokaryotes are unicellular organisms that are relatively small, lack a nuclear membrane, have a capsule, and flagellum for motility. Think bacteria. Next, eukaryotes can be unicellular (yeast) or multicellular (animals) and have relatively larger cells, nuclear membrane present, usually no capsule, and no flagellum. In multicellular organisms, cells differentiate to take on specific functions such as nervous tissue, muscle, connective tissue, absorptive epithelium in the gut, endocrine cells, and so on. Notice that morphologically eukaryotes can be vastly more complex. Prokaryotes represent an earlier phase in evolutionary history compared to eukaryotes, thus complexity developed over evolutionary history leading to our modern biosphere. This complexity is mirrored on the genomic level. Eukaryotic genomes contain an abundance of mobile elements, genes with multiple introns, multiple transcription-factor binding sites, preservation of gene duplications, and genes which are transcribed into units with untranslated flank sequences (i.e., poly A tail). Prokaryotic genomes do not contain any of these thus are streamlined by comparison, and this is main point you should get from this.

Recall the Central Dogma of Biology: biological information flows from gene to phenotype and the starting point is the gene. This means that if we understand the origins of genomic complexity (i.e. from prokaryotes to eukaryotes), we understand the origins of complexity on other levels of biological organization such as morphology, multicellularity, size, function, and so on. This is what the molecular revolution affords us. So, the central question is, what evolutionary forces are primarily responsible for producing complexity?

Lynch argues for the “passive emergence of genome complexity by nonadaptive processes”. That is a mouthful, so take a minute to digest each term. Passive meaning no one is tampering with it (i.e., no intelligent agent). Nonadaptive processes meaning mutation, genetic drift, and recombination as opposed to the adaptive process of natural selection. Alright folks, here is the bad news. The bad news is Lynch’s argument hinges on population genetic theory which is a bit technical. I am not going to derive population genetic theory here, however suffice it to say that nonadaptive processes predominate (over natural selection) when 2Ngs << 1 where Ng is the effective population size and s is the fractional selection advantage. This is also called the “criterion for effective neutrality” with neutrality referring to nonadaptive and non-deleterious. Further substituting in the equation, s = nu where n is number of nucleotides to be conserved for proper gene function and u is the mutation rate per nucleotide site. Notice that as s increases so does (they are directly proportional), which means that each adaptive embellishment comes with the cost of maintaining the fidelity of more nucleotides. This is called mutation hazard. Using population genetic data to calculate real numbers for the criterion for effective neutrality, we find that:

. . . an embellishment that increases the mutational target size of a vertebrate by n<250 will be largely immune from selection, and hence free to drift to fixation, whereas the critical value of n for a prokaryote is << 10.

In simplified terms, vertebrates have a markedly easier time increasing the complexity of their genome without mutational hazard whereas prokaryotes have a difficult time. Recall the differences in complexity between prokaryote and eukaryote genomes. The criterion of neutrality provides a powerful explanation for the observed differences. The differences are explained by neutral or nonadaptive increases in complexity. This, in a nutshell, is Lynch’s argument for the passive emergence of genome complexity by nonadaptive processes.

Lynch points out that even if one was not convinced that complexity primarily emerges from nonadaptive processes, these provide the null hypothesis. I find this interesting, and wonder how to go about establishing this from a philosophy of science point of view. Should the null hypothesis be totally random nonadaptive evolution and the adaptationists shoulder the burden of proof, or something else? (If anyone has an insight or has studied the philosophy of science, please indulge us). Lynch also points out frequently that there is no direct evidence for adaptive hypotheses. This makes his case stronger.

Lynch’s paper has a frustrated tone that suggests a broad failure of engagement with data and arguments for nonadaptive evolution. For example:

Most biologists are so convinced that all aspects of biodiversity arise from adaptive processes that virtually no attention is given to. . . neutral evolution, despite the availability of methods to do so. Such religious adherence to the adaptationist paradigm has been criticized as being devoid of intellectual merit [citing a paper by Stephen Jay Gould and Richard Lewontin].

And poignantly,

The hypothesis that expansions in the complexity of the genomic architecture are largely driven by nonadaptive evolutionary forces is capable of explaining a wide range of previously disconnected observations. . . This theory may be viewed as overly simplistic. However, simply making the counterclaim that natural selection is all-powerful (without any direct evidence) is not much different from invoking an intelligent designer (without any direct evidence).

There are likely to be scientists who understand these arguments and know the data yet disagree. However, there are also probably scientists who simply avoid mathematical theories, as biologists are infamous for. And, there are also scientists whose careers or reputations hang on the power of natural selection, so they have motivations to dismiss or sidestep engagement. What Lynch seems to press in this paper is more serious and objective engagement.

Let us revisit ID’s nagging question: how is new biological information introduced? Is this plausible? It seems the answer is, complexity accrues primarily through nonadaptive forces which is also called neutral evolution. When neutral evolution was first worked out in the 80’s Kimura coined the term “survival of the luckiest” to counter adaptationist’s term “survival of the fittest”. (2) And, this is where I ask my dear readers:

How lucky are we?

Sources

1) Lynch M. “The frailty of adaptive hypotheses for the origins of organismal complexity.” Proc Natl Acad Sci USA. 2007 May 17;104 Suppl 1:8597-604. Free full text.

2) Kimura M. “The neutral theory of molecular evolution and the world view of the neutralists.” Genome. 1989;31(1):24-31. PMID: 2687096.

The Gaia Hypothesis and Extraterrestrial Life

We are now in the Golden Age of exoplanet science. The Kepler Space Telescope has tantalized us with data showing a rich diversity of exoplanets including the discovery of Kepler-186f which orbits in the habitable zone of its sun and has a radius comparable to the Earth. Kepler-186f is the best Earth-analog we have discovered as of September 2014, and probably just the tip of the iceberg of what is out there. Does life exist outside of our solar system? This blog post examines the possibility of intelligent life existing outside of our solar system focusing on the factor of climate stability. It was first inspired when I read the book Lucky Planet by David Waltham which I would recommend for anyone interested in this subject.

Defining the problem

According to the Solar Standard Model, the sun has dramatically evolved over the course of its lifetime. If we could measure the solar output 4 billion years ago, we would find the output to be about 30% less than today. Around this time liquid water emerged on the surface of the Earth. We have evidence of liquid water on Earth as early as 3.8 billion years ago and hints of life date to as early as 3.5 billion years ago. The question is: how could a 30% dimmer sun coincide with an ocean on the Earth? This question was first asked by astronomers Carl Sagan and George Mullen in 1972 and has been dubbed the “faint young sun paradox”. Before addressing this let’s dig a bit deeper.

Since life began billions of years ago we know that liquid water had to exist on Earth. In fact, the Earth has enjoyed a remarkably stable climate to have continuous liquid water and complex life. The geological temperature record shows the global temperature has remained at 15 plus or minus 10 degrees C over the past 500 million years and with an overall cooling trend. The general explanation given by scientists is that the Earth started with a stronger greenhouse effect which compensated for a dimmer sun. Over time the sun became brighter (following the main sequence for stars) and geological and/or biological processes decreased the greenhouse effect and this cancellation led to a relatively stable climate. But, why did it happen this way?

When thinking about an explanation of the Earth’s remarkable climate stability, there seems to be only two games in town: the Gaia hypothesis or blind luck. We will try to differentiate between these possibilities. The Gaia hypothesis was first proposed by James Lovelock and has been debated by the scientific community ever since. Heavyweights like Richard Dawkins and Stephen J Gould have argued against Gaia. We are left with a nuanced discussion. For our purposes the Gaia hypothesis will be stated as: the biosphere interacts with the environment in such a way to promote a stable climate. This is accomplished unconsciously by climate sensing and feedback systems that exist within the biosphere. There are many criticisms of Gaia, but I want to focus on one that I find particularly convincing.

The Great Oxygenation Event is evidence against Gaia

Several billion years ago the Earth’s atmosphere was largely composed of nitrogen, carbon dioxide, and methane. Then, life evolved photosynthesis which introduced oxygen into the environment. It is thought that oxygen initially reacted with minerals which prevented it from building up significantly in the atmosphere for several million years. Eventually oxygen levels built up in the atmosphere which is called the Great Oxygenation Event. What was the consequence of this atmospheric change? Oxygen chemically reacts with methane and eliminates it. Methane’s greenhouse effect is 30X as potent as carbon dioxide. Since photosynthesis both removed carbon dioxide and eliminated methane, it greatly reduced the greenhouse effect and led to global cooling. Eventually ice at the poles advanced toward the equator and a period of global glatiation began, the Huronian glatiation. We have evidence that the entire Earth was frozen in what is called the Snowball Earth! Almost all life became extinct, but some pockets of life survived. Photosynthetic organisms could have survived under several meters of transparent ice at the equator. Also, ecosystems relying on volcanic vents in the ocean could have survived. What seems to have rescued the Earth from the snowball conditions is volcanism and possibly asteroid impacts which reintroduced greenhouse gases into the atmosphere eventually warming the Earth and melting the snowball.

Now, if we look at the advent of photosynthesis that led to a Snowball Earth episode that wiped out almost all life, we can infer that there was certainly no biological foresight. But, more importantly there seems to be no evidence of a biological climate sensor. If there was a biological climate sensor, it was totally powerless to provide adequate feedback to prevent the cooling. From this we can also infer that there were not significant Gaian mechanisms at work at this point in evolution. Life was lucky that nonbiological forces happened to rescue the Earth from this deep freeze. There are two criticisms to anticipate. First, perhaps the biosphere had simply not yet evolved strong Gaian mechanisms. The problem with this idea is that the biosphere itself cannot be considered life because it does not self-replicate. This is not a matter of semantics, self-replication is required for evolution to occur through natural selection, therefore Gaia will not emerge from evolution. Second, perhaps Gaian mechanisms became stronger by chance after this Snowball Earth episode. The problem with this idea is that it does not help Gaia triumph over blind luck. Lucky-Gaia is just blind luck.

Conclusion: how this alters the likelihood of finding complex or intelligent life

To recap, the Earth has enjoyed billions of years of climate stability, of course with a few blips like the Snowball Earth episode. The sun’s initially lower but steadily increasing output was counterbalanced by a decreasing greenhouse effect, and this was not an inevitable consequence of the biosphere. It seems to be just blind luck. How does this alter the likelihood of finding complex or intelligent life? The probability of complex or intelligent extraterrestrial life is severely diminished in this way because it increases reliance on the universal lottery. Of course, that doesn’t mean it doesn’t exist or that we shouldn’t look for it.

How I became an Atheist – part 2

At the end of part 1 things weren’t too bad. I was probably around 17 years old and was mostly just becoming angry at church feeling like it was anti-intellectual regarding Deep Time and evolution. But, something inside me also wanted me to show them. I thought if only I could show them (i.e., as Bill Nye did in a debate this year), then they would understand.

The remainder of my high school days I went from church to church. But, the religion thing had little to do with it. The main reason me and my best friend would go was for sociality and meeting girls. Of course taking communion made me feel absolved, but I think I barely listened to a single word blasting out of the pulpit. My thinking was if these teachers can’t get something as simple as Big Time, how can they possibly provide an adequate interpretation of a 2000 year old text that was not written to modern people?

Then, came university. I approached church the exact same way. I was just there to say “Sup, yall” and meet hot chicks and take communion to make myself right with God. It’s the developing skeptic’s triad of church activities.

Then, I met my future wife. She had an eyebrow ring, tattoos on her feet, and was into traveling. I had long dirty hair, looked like a grunge rock star, and had a mysterious personality. Match made in heaven, I know. But, remember in my triad, one of the factors that kept me going to church was to meet girls. Once we got married after university, I lost a major reason to go to church.

After university my first job was in basic science, specifically the study of protein structure-function relationship. As I got more and more into the scientific literature I actually became addicted to science. I would work so many hours making hypotheses, performing experiments, and read every article I could find relevant to my field. This is when I really developed an appreciation for scientific method and skepticism. One of my first projects was to verify work from a Japanese group of scientists. It’s nothing against their credibility, rather this is how science works. If you publish something, be prepared to have it scrutinized and possibly even retested if it’s important enough to another research group.

This is when skipping church actually became just not going at all. Sundays were for sleeping in.

Fast forward about one year. I was skating by the beach with an atheist friend when he asked me a question that hit like a baseball bat to the head, “How can God send people to hell for an infinite period of time for committing finite crimes?” It didn’t matter that I could argue against this notion of hell, what this question did was send me on a journey to figure if this whole religion had any truth whatsoever.

I dove into the debate headfirst and made a commitment to seek out anything, I would not hide my eyes from anything anyone was saying about God and religion. This is exactly what I did! I really liked Hitchens and Harris, they were particularly eloquent, even able to criticize atheism which to me gave them credibility. These are some of the things that I concluded:

(1) Every single argument for God’s existence can be refuted.
(2) The whole Christian narrative of God saving the world 250,000 years after humans evolved is absurd.
(3) The idea of Jesus absorbing God’s wrath is absurd.
(4) The Mosaic Law and the Canaanite genocide are immoral.
(5) The bible is misogynistic through and through.
(6) There is no evidence for a worldwide flood.
(7) Organized religion is tyrannical and people that fall into it simply have not studied science and reason or have not taken it seriously enough.
(8) I see no evidence for an all-good God in a world plagued with pain and suffering, particularly the innocents, the infants and children.

Needless to say, I quickly graduated to agnosticism.

I need to admit something. I never “came out” as an agnostic or atheist to my family or even my wife. I feared the consequence, but I have a feeling they suspected it after all the heated discussions. I recently asked my wife what she thought all those years and she said she basically knew it the whole time. She’s smart. 🙂

How I became an Atheist

Although I have been doing philosophical blogging as of late, I thought I would interject a personal story. Sometimes, perhaps often, a person is easier to appreciate than an idea.

This is part 1.

My journey to atheism began as a child. I grew up in the northern Texas which is renowned for its religiosity. We had a church on every street corner and every denomination (or non-denomination) from A to Z was listed in the phone book.

My family for at least two generations had been committed Christians. My grandfather was a benevolence minister; he literally had a job finding poor families and taking them groceries and supplies. I love and miss him dearly. My parents were fundamentalist Christians. They belonged to a denomination that believed they were right, so naturally everyone else was wrong. In addition to black and white thinking and their sense of doctrinal superiority, they held to a strict literal interpretation of the creation story in Genesis.

This is where it all began. As a child I was obsessed with dinosaurs. (Velociraptor was my favorite. The dinosaur skeleton shown above is a Velociraptor 😀 ). But I wondered, why are dinosaurs not in the bible? After all, the bible was supposed to contain all of world history since the creation. It vexed my poor little brain. Somehow I learned that dinosaurs might have been mentioned in the book of Job chapter 41 as the Leviathan. This was wonderful news to my ears, I had my answer: dinosaurs were in the bible! They must have gone extinct within biblical times.

Fast forward about five or so years to a thing called Youth Group, a sort of mini-church meeting for teenagers. There we were taught that evolution was evil and completely false. Also, I remember at a large church service (>1000 people) the preacher argued that evolution was statistically as impossible as a monkey randomly typing a Shakespeare sonnet. They successfully convinced me that evolution was untenable and that the bible was right all along.

As I was developing my beliefs at this particular church, the overall experience was fraught with negativity. There was excessive petty infighting and a good dose of hypocrisy that even a kid could see. [Insert examples here]. I thought maybe this is not God’s fault, but this reasoning did not make it easier to continue going to church.

Even though I was a Christian one of my best friends in high school was an atheist. We would play chess, video games, debate, play guitar, and create untold mischief. What was interesting is that we had such different beliefs and different consciences, yet we had a strong friendship. I actually had trouble making Christian friends. Most of my real friends seemed religiously ambivalent. I find it a great irony that God would make me such a conscientious Christian teenager yet only fit in with the ambivalent and the atheist. It didn’t seem ironical at the time, it was frustrating to feel like an outsider. Was this teen angst or did it source from a deeper religious frustration? Maybe a little of both.

One day I bought a book about science and religion, my first real exposure to the subject. I had to read it slowly because it was so dense, but I devoured that book like a Velociraptor (had to get that one in). The book was sympathetic to evolution. When I could see the evidence for evolution clearly laid out before me and how the creation story does not have to be read with literal days in mind, my world was suddenly turned upside down. Cognitive dissonance, a very uncomfortable state, ensued. When the calamity began to settle, I decided I could no longer reject evolution. I did not know what to do with religion anymore. . . I would have to try to make evolution and religion work together. . .

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Do you have a similar experience? Do you know someone with a similar experience? Feel free to comment or question about anything.