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.

We are alone in the universe (part 1)

Suppose there are many different ways for the universe or multiverse to evolve intelligent life. There will be easy ways to evolve intelligence and difficult ways, and these ways will fall on a spectrum as such. In fact, it is reasonable to suppose that this spectrum can be plotted as a frequency distribution and will be a bell-shaped curve. Where would humans fall on this curve?

Before answering this let’s pay homage to the debate of the Anthropic Principle. This principle states that the universe is geared towards producing us. It is derided by modern scientists because it seems like cosmic hubris. Since the time of Copernicus, we have been moving away from this thinking starting with the heliocentric model of the solar system. In keeping with this trend the latest proposal is the multiverse which solves the problem of fine-tuning of physical constants. This change in thinking is called the Copernican Principle, or Principle of Mediocrity, and would suggest that we are most likely an average way to make intelligent life. We are not found at the tail ends of the bell curve, rather smack in the middle. Earth-like biology is probably a rather easy way to make intelligent life in this universe/multiverse. Applying the Principle of Mediocrity, the frequency of earth-like complex life, is a surrogate marker for the frequency of intelligent life in the universe. That is very important because we can actually say something about the possibility of earth-like life out there. What does science say? How difficult is it to make earth-like life?

If you think we are in an infinite multiverse where all possibilities become actualities, then this question might be of less importance to you. Because even if it’s one in a zillion zillion, there ought to be an infinite number of earths out there in the multiverse. This is theoretical physicist Brian Green’s take on the matter. There is another Naïve Thinker out there but who is actually the President of Mars, but this doppelganger must be almost infinitely far away. If you are going to be this generous with reality, you will run into a problem. If absolutely everything possible is actualized, then God must exist. And, an all-powerful being would also be God of the whole multiverse. Also, the Flying Spagetti Monster would exist, but God would eat it for lunch. Alright, alright come back down to reality now! This escapade proves the point that we should not be too generous. Such bizarre notions of the possible do not respect the elegant universe we can actually observe, and it’s not a multiverse. . . yet. And, if we eventually find we are in a multiverse, it will not necessarily be infinite. How could we even prove that it is infinite?

Barring an infinite multiverse which I think is reasonable, how difficult is it to make earth-like complex life? We will address this in more detail in part 2.

What are dreams?

I woke up and walked into the kitchen. Peering through the window I could see an orange tree in the backyard. The tree was tall and had produced many fruit. I stood in the kitchen gazing at the tree’s beauty and success; and during this hypnosis time itself became impatient and rushed forward. The fruit grew larger. Oranges became like basketballs. The branches began to bend at the weight of the fruit. Suddenly a sense of urgency overcame me. I needed to harvest the fruit before it all detached and burst on the ground. I was panicking but stood there frozen. I could see the roots popping out of the ground. Finally, the tree collapsed to the earth with its fruit gone forever. The fruit was gone forever, and I had only watched.

. . . I awoke from my dream. (This was written in first person, but this dream was actually not mine).

What is a dream?

It seems that waking reality imposes a stringent world on us with its natural law. Natural law seems to be unbreakable. Err, natural law is unbreakable by definition. But, while asleep our minds can create reality, albeit not with total freedom. Our memories and emotions and other deep parts of us seem to restrict the dream’s content and meaning.

In the second century AD Artemidorus wrote the Oneirocritica, a treatise on dreams which ultimately influenced thinkers like Freud and Foucault. Two things make Artemidorus stand out IMHO. First, he attempted to be empirical before theorizing about dreams by interviewing many people and gathering data. Second, he concluded that dreams were unique to the individual and was symbolic of something within their waking lives. Therefore, he concluded that dream interpretation requires intense knowledge of the dreamer. Even with this very naturalistic understanding of dreams, Artemidorus left room for prophetic dreams.

This should not be a huge surprise given the religions of ancient Greece. Classics scholar, Verity Platt, provides evidence that dreams were important for epiphanies about Pagan deities, their image, and related sacred knowledge:

“ While the coalescence of god and statue in Aristides’ dreams draws upon public representations in order to authenticate and reify his private experiences, we can trace an inverse relationship in Pausanias’ Description of Greece, which repeatedly draws upon the epiphanic quality of personal dream-visions in order to confirm the sanctity of objects and locations within the public realm. In particular, Pausanias accounts for the creation and appearance of cult images through tales of oneiric inspiration, whereby artists claim legitimacy for their descriptions of deities through narratives of epiphanic autopsy. In this sense his use of the mutually reinforcing relationship between dream vision and sacred object reflects the aetiological function of mantic dreams. . .” (emphasis added)

Prophetic dreams are also found in Hebrew scripture. One great example is the story of Joseph interpreting Pharaoh’s dream (Genesis 41). Pharaoh had two dreams which were similar. In the first he was standing on the bank of the Nile when seven healthy cows came out of the water and began feeding. Then, seven emaciated cows came out of the Nile and swallowed the healthy ones. In the second there were seven healthy heads of grain and seven withered heads of grain. The withered heads of grain swallowed the healthy ones. Joseph interpreted Pharaoh’s dreams as predicting seven years of plenty followed by seven years of famine, and the fact of two dreams was interpreted as God having fixed this for the future. Accordingly the monarch built storehouses for food during the years of plenty in order to avert the upcoming crisis.

To conclude, no matter what worldview one espouses, dreams can be an interesting subject. What are they? What can they be? How can they give meaning to us? How should they give meaning to us? These are just some of the interesting questions we can ask.

Source
Platt, V. “Facing the Gods: Epiphany and Representation in Graeco-Roman Art, Literature and Religion.” Cambridge University Press. Page 266. Accessed on Google eBooks 5-25-2014.