Category Archives: preadaptation

The eukaryotic cell: Preadapted for multicellular existence

First, a review.

We’re looking at two different eukaryotic proteins: beta catenin and alpha importin. Beta catenin plays two different crucial roles in metazoan life: 1) It is a key component of the adherens junction which connects cells together and 2) it is involved in the transcription of genes that play an important role in the development of the embryo and the maintenance of organs. This is a neat example of one protein playing two important roles in metazoan life. A simplified figure is shown below, where the beta catenin is represented by the pink circle:

Next are the alpha importins. They transport proteins into the nucleus through the nuclear pore complex. The figure below shows the basic mechanism involved:

The alpha importin is shown in blue. It recognizes and binds the nuclear localization signal (NLS) on a protein that is destined for the nucleus (in the above figure, it is the experimentally designed radioactive protein) and then binds with another protein, beta importin, to be transported into the nucleus.

It is my hypothesis that the alpha importins imposed a form of guidance to evolution by front-loading the eventual emergence of the beta catenins which would, in turn, facilitate the evolution of metazoa. The first line of support for this hypothesis would be to show a homologous relationship between these two different proteins (and as far as I have been able to tell, no one has seriously proposed this). So allow me to make that case.

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Told ya so

The hypothesis of front-loading (or nudging) evolution is both reasonable and plausible and no one has shown otherwise.  In fact, it has become more reasonable and plausible as we have learned more about evolution over the years.  Doubt da bunny?  Consider the abstract for a paper that was published just this year:

Evolution. 2010 May;64(5):1189-201.
The importance of preadapted genomes in the origin of the animal bodyplans and the Cambrian explosion.
Marshall CR, Valentine JW.

The genomes of taxa whose stem lineages branched early in metazoan history, and of allied protistan groups, provide a tantalizing outline of the morphological and genomic changes that accompanied the origin and early diversifications of animals. Genome comparisons show that the early clades increasingly contain genes that mediate development of complex features only seen in later metazoan branches. Peak additions of protein-coding regulatory genes occurred deep in the metazoan tree, evidently within stem groups of metazoans and eumetazoans. However, the bodyplans of these early-branching clades are relatively simple. The existence of major elements of the bilaterian developmental toolkit in these simpler organisms implies that these components evolved for functions other than the production of complex morphology, preadapting the genome for the morphological differentiation that occurred higher in metazoan phylogeny. Stem lineages of the bilaterian phyla apparently required few additional genes beyond their diploblastic ancestors. As disparate bodyplans appeared and diversified during the Cambrian explosion, increasing complexity was accommodated largely through changes in cis-regulatory networks, accompanied by some additional gene novelties. Subsequently, protein-coding genic richness appears to have essentially plateaued. Some genomic evidence suggests that similar stages of genomic evolution may have accompanied the rise of land plants.

Front-loading and preadaptations

Cooption, the process by which traits switch function, is something we predict to be important from the hypothesis of front-loading evolution. The Design Matrix lays out a step-by-step case for the logic of front-loading that leads to the realization that cooption is entailed by front-loading. Functional shifts are the very strategy that would work in an attempt to design the future through the present. This is a subtle, but important, point to grasp. Cooption is not some add-on to the front-loading perspective. Cooption is a prediction given that front-loading would not work without it.

Yet there is a simpler way to help people understand that cooption is, at the very least, a process that fits very comfortably within a teleological framework. It is the simple fact that cooption is tightly linked to preadaptation. Stephen Jay Gould sought to replace the word ‘preadaptation’ with the word ‘exaptation,’ where an exaptation is a character that retains its ancestral form while taking on a new function. And the process by which the trait switches function is called cooption.

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RPB4 and Preadaptation

The front-loading hypothesis, under the guidance of PREPA, allows us to formulate a testable hypothesis – the “bells and whistles” of the archaeal RNAP – Rpb 4, 5, 7, 10, 11, and 12 – will play crucial roles in the emergence of a) the eukaryotic cell and/or b) complex, metazoan life.

To test this hypothesis, let’s go back to that assembly map.  The first thing that stood out to me was Rbp4 and 7 (which is E and F in archaea).  These two look like they interact with the core machine as a dimer (a combination of both proteins) and in cell biology, dimerization is a useful regulatory node.  In other words, the bells and whistles of the archaeal RNAP might represent preadaptations that would nudge the ability to regulate the RNAP in ways that would assist the emerging complexity entailed in the appearance of eukarya, then metazoa. So the telic perspective would allow us to predict these two proteins play some form of regulatory role.  With this hypothesis in hand, it was once again time to probe the literature.  Over the next few days, let me share some of the things I found.

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Convergence as a Function of Preadaptation

Let’s build on the convergence between vertebrates and cephalopods.  This time, let me quote some excerpts from the following article: Squid vascular endothelial growth factor receptor: a shared molecular signature in the convergent evolution of closed circulatory systems by Masa-aki Yoshida, Shuichi Shigeno, Kazuhiko Tsuneki, and Hidetaka Furuyaa (in EVOLUTION & DEVELOPMENT 12:1, 25–33 (2010)).

First, the researchers lay the groundwork for the convergence of these two systems:

Metazoan animals have evolved an incredible diversity of hearts and heart-like structures. The most elaborate case in invertebrates is observed in coleoid cephalopods: they exhibit an elaborate closed circulatory system (Schipp 1987; Budelmann et al. 1997). Their heart possesses a kind of advanced output structure similar to that of the human heart, which differs largely from molluscan typical nonendothelium primitive chambered hearts (see Kling and Schipp 1987; Schipp 1987). Neither morphological nor molecular data give strong support to a close phylogenetic relationship between vertebrates and cephalopods, suggesting that the closed circulatory systems and complicated hearts were formed independently in each lineage, and have converged during their evolution.


Their cardiovascular system is considerably similar to vertebrates in several respects such as high oxygen binding capacity, high concentrations of proteins, and short circulation time (Schipp 1987). Each vessel in the cephalopod is constructed similarly to vertebrate vessels, with an endothelial lining on a basement membrane (Budelmann et al. 1997), although the cephalopod blood vessel lining does not have the cellular junction typical among vertebrate species. Most invertebrates have no endothelium in their vascular walls so the cephalopods are unusual in that they are invertebrates with vertebrate type blood vessels. As the other molluscs have open vascular system, the peculiar blood vessel configuration in the cephalopods is in all probability secondarily developed similarly to the vertebrate among chordates (Ruppert and Carle 1983).

Then, they find something really cool.

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Driving biology to more and more complex forms

As I explained before, “The hypothesis of front-loading evolution would thus predict that significant transitions in evolution would depend on preadaptation.”

Recently, I discussed one such candidate – the origin of mitochondria.

A new paper has come out that strengthens this case for preadaptation:

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We need to blow it off its feet

Biologist PZ Myers sets out to prove that there is no purpose associated with evolution.

He writes:

I decided that what I wanted to make clear is that the origin of many fundamental traits of the nervous system is by way of chance and historical constraints


The word “purpose” is entirely inappropriate. Richard Dawkins has tried to deal with it by inventing a new term for the kind of purpose you’re talking about, but I think we’re better served by trying to cut that misconception off at the knees. No, ankles. No…we need to blow it off its feet and scour the footprints from the floorboards.

So how does Myers take teleology and “blow it off its feet and scour the footprints from the floorboards?”

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The Distant Potential of Front-loading

The reach of the Alu domain may have extended much further into the future that the evolution of eukaryotes.  Shortly after the dawn of the primate lineage, the gene for the SRP RNA was duplicated and the Alu domain was freed of its SRP function.  A second round of duplication occurred and the two Alu domains were merged to form what is now known as the Alu element [55].

The Alu elements have played an important role in the evolution of the primate genome.  Since escaping from its SRP function, the number of Alu elements has expanded to 1.1 million copies in the human genome, making up 11% of human DNA [56].  Since Alu elements do not code for any protein, they were once considered a classic example of “junk DNA.”  In reality, they are retrotransposons.  A retrotransposon is a gene that is transcribed into RNA and an enzyme known as reverse transcriptase uses it to make a DNA copy that can be inserted some other place in the genome.  Since the Alu element does not code for reverse transcriptase, where does the enzyme come from?  When the Alu elements were born early in the primate lineages, they commandeered the reverse transcriptase from an older retransposon in the genome known as L1.

What is the purpose of spreading all these Alu elements around during the dawn of human evolution?

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Connecting the Pieces

I really wish I had the time to write more detailed postings for y’all.  For example, last night I drew attention to some recent findings that further support the plausibility of front-loading and seamlessly connect with other proposals on this blog.  But I didn’t get a chance to flesh it out.  So let me add a little more flesh to those front-loaded bones and show specific points where this ties in to my views.

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More ‘Evidence’ of Front-loading Mitochondria

I have previously shared some evidence for the front-loading of mitochondria, along with an emerging picture where symbiogenesis is merged with front-loading. Now there is yet some more evidence in support of the plausibility of front-loading mitochondria.  Those who follow this blog, or have read The Design Matrix, will note how seamlessly this all fits in with my hypothesis of life’s design:

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