Category Archives: evolution

Is evolution predictable? To a surprising extent the answer is yes.

In chapter 7 of The Design Matrix, I have a section entitled, “Unpredictably Predictable.”  The basic argument is summarized in the last sentence of that chapter:

Even though evolution is supposed to be inherently unpredictable, as we can see, it has occurred within a very predictable biological matrix.

Evolution is not some random “free-for-all” where anything that just happens to work will eventually be selected for.  Evolution is a biological process that is constrained and thus channeled by the composition and arrangement of life’s machinery.

I then spell out one aspect of this evolution in a section entitled, “Designed to Redesign.”  Here I talk about the essential role that gene duplication plays in the function we call “evolution”:

It is a beautiful solution for a front-loading designer. In one process, we both propagate the original design and set things up to unpack secondary designs without erasing the original design. Stability and change, all in one package. As an added bonus, the infl uence of contingency is dampened. It does not matter if some or many gene duplication events drift off in unintended fashion (most will merely tweak the original function or decay away). Th e beauty of gene duplication is that it explores sequence space while retaining and propagating the original sequence. As long as the original sequence is essentially retained somewhere, someplace, evolution gets to “try again” over and over and over in its rigged search for some future design. In other words, if a designer wanted a secondary design to unpack itself in an animal cell, duplication of the original sequence is bound to happen in all cells, including animal cells. When it eventually occurs in an animal cell, the stage is set to unpack the secondary design. If it fails, we need only wait until the next round of duplication and mutation occurs. It is the intelligent use of chance.

Over five years later, a paper has appeared in the journal Science that adds even more plausibility to my perspective.  Enjoy:

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A humbling reversal?

I have long noted that the case for non-teleological evolution was stronger in the past than it is in the present.  Consider this tiny example.

Below is a figure from Eukaryotic Evolution: Getting to the Root of the Problem (Simpson and Roger, Current Biology, Vol. 12, R691–R693, October 15, 2002).

The figure on the left is the eukaryotic phylogenetic tree from 1993 and before.  Simpson and Roger explain it as follows:

A decade ago, phylogenies based on small subunit ribosomal (r)RNA sequences provided an intuitively appealing evolutionary tree of eukaryotes. Complex eukaryotes, including animals, fungi, plants and most algae, emerged as a broad radiation usually called the ‘eukaryotic crown’ [1]. Below this ‘crown’, more bizarre, and generally simpler, organisms diverged in a ladder-like succession. The small subunit rRNA tree was ‘rooted’ with mitochondrion-lacking unicellular eukaryotes such as diplomonads, parabasalids and microsporidia forming the basal branches (Figure 1a).

Yes, this was intuitively appealing from a non-teleological, neo-darwinian viewpoint.

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Evolution Follows the Path of Least Resistance

Over at Jerry Coyne’s blog, biologist Greg Mayer wrote:

One of the most important lessons of comparative anatomy is that evolution usually proceeds by the modification of pre-existing structures (or, stated more precisely, the modification of the pre-existing developmental programs that produce those structures). Certain changes are easier to evolve because the developmental system can be modified to produce them—evolution follows the developmental path of least resistance. In terms of the skeleton of vertebrates, this means that most evolutionary changes are reduction, fusion, loss, lengthening, shortening, thickening,  and narrowing of bones. Evolution uses what’s already there, and rarely do wholly new structures arise.  (from “Tinkering with elephants’ feet”)

All of this is true, yet we can proceed beyond this conventional thinking and ask a couple of questions:

WHY does evolution follow the developmental path of least resistance?

WHAT are the implications of evolution following the developmental path of least resistance?

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Evolutionary Thought Experiment

Let me provide you with a little evolutionary thought experiment.  Stephen J. Gould once noted that “evolution is a bush, not a ladder.”  Quite true.  Consider the following representation:

 

Notice that the evolution of mammals does not entail a straight shot from some ancestral chordate to mammal.  On the contrary, the evolution of mammals also involves the evolution of sharks, bony fish, frogs, snakes, and birds along the way.  What’s more, the bush shows a nesting pattern, where the tetrapods, for example, nest together to the exclusion of all other chordates.  This is because the tetrapods derive from an ancestral tetrapod state that was not shared by the other chordates.  In fact, the following arrangement makes this more clear.

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Genetic Switch for Limbs and Digits Found in Primitive Fish

From here:

Genetic instructions for developing limbs and digits were present in primitive fish millions of years before their descendants first crawled on to land, researchers have discovered.

Genetic switches control the timing and location of gene activity. When a particular switch taken from fish DNA is placed into mouse embryos, the segment can activate genes in the developing limb region of embryos, University of Chicago researchers report in Proceedings of the National Academy of Sciences. The successful swap suggests that the recipe for limb development is conserved in species separated by 400 million years of evolution.

“The genetic switches that drive the expression of genes in the digits of mice are not only present in fish, but the fish sequence can actually activate the expression in mice,” said Igor Schneider, PhD, postdoctoral researcher in the Department of Organismal Biology and Anatomy at the University of Chicago and lead author on the paper.

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Scientific discovery, not tautology

I previously showed that the scientific discovery of a complex LECA was not a tautology.  DrREC replied:

Mike Gene, do you recognize the difference between FIRST and LAST?

L as in LUCA or LECA is LAST-The Last Eukaryotic Common Ancestor, the most RECENT (not oldest) organism from which all organisms/all Eukaryotic organisms (respectively) living on Earth descend.

Not the First! Do you understand LECA isn’t the first Eukaryote?

This is a very strange line of questioning given that nowhere did I argue that the last eukaryotic common ancestor was the first Eukaryote.  Nor do I think so.  Thus, DrREC’s first objection amounts to shadow boxing with the straw man he invented.

But it gets worse.

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Complex LECA is no tautology

Someone with the moniker DrREC replied to my posting about the complexity of the last eukaryotic ancestor as follows:

This is almost a tautology. The last Eukaryotic common ancestor had the defining features of a Eukaryote….which happen to be more complex than prokaryotic life.

There is no tautology at work here.  Not even close.  We can appreciate this by simply recognizing that scientists could very well have discovered that LECA was remarkably simple.  For example, it could have been a cell with a nucleus, but lacking protein-coding introns, mitochondria, golgi bodies, ubiquitin, and flagella.  And its nuclear pore complex, cytoskeleton, and endomembranous system could have been rather simple.  But as it turned out, LECA had a level of complexity that rivals modern day cells.

Of course, we don’t need to be hypothetical about this.  Back in the 1980s, biologists expected LECA to have been rather simple.  Consider the simplest of eukaryotic cells – microsporidia.

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Koonin and LECA

Below the fold you will find some excerpts from Eugene Koonin’s article, The origin and early evolution of eukaryotes in the light of phylogenomics.

 

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Front-loading just became even more plausible

A recent research article nicely illustrates how front-loading is an increasingly plausible perspective on evolution.  The article is Protein Evolution by Molecular Tinkering: Diversification of the Nuclear Receptor Superfamily from a Ligand-Dependent Ancestorby Bridgham et al.

The researchers analyzed the superfamily of nuclear receptor transcription factors.  As they note, these proteins represent “a diverse superfamily of transcriptional regulators that play key roles in animal development, physiology, and reproduction.”  I briefly described one such receptor earlier – the retinoic acid receptor – as it appears the Alu elements are front-loaded to generate DNA binding sites for these proteins.

This class of receptors share common features:

a modular domain structure, including a highly conserved DNA-binding domain (DBD) and a moderately conserved ligand-binding domain (LBD)—which in most receptors contains a ligand-regulated transcriptional activation function—along with extremely variable hinge and N-terminal domains.

To recognize why this study is relevant to front-loading, pay close attention to this paragraph.

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When is a Flaw not a Flaw?

As you know, I have often pointed to the proteins as an incredible design material, raising the question as to just how much the blind watchmaker is dependent and indebted to protein biochemistry.  A recent study highlights yet another way in which protein biochemistry may be an essential prerequisite for the evolution of complex life.

First, you can read the summary of this research by Ariel Fernández and Michael Lynch here.  Then, come back and I will help you detect the teleological echo of this work.

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