As the sequence of the the unicellular choanoflagellate Monosiga brevicollis continues to be analyzed, it is now clear this “simple” creature is loaded with all kinds of animal genes. Today, let us consider the research of Xinjiang Ca, from Duke University Medical Center. Cai’s paper is entitled “Unicellular Ca2+ Signaling ‘Toolkit’ at the Origin of Metazoa” (Mol. Biol. Evol. 25(7):1357–1361. 2008).
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From here:

Most biochemists traditionally believe proteins have many random, uncontrolled movements.

Research conducted by Jernigan, director of the L.H. Baker Center for Bioinformatics and Biological Statistics together with Guang Song, an assistant professor in computer science and graduate student Lei Yang, over a 10-year period shows that not only are protein motions more restricted, but also that these restricted, controlled motions are part of the function of the proteins.

From here:

They were seeking examples along the tree where animals evolved that were simpler than their ancestors.

Instead they found organisms with increasingly more complex structures and features, suggesting that there is some mechanism driving change in this direction.

“If you start with the simplest possible animal body, then there’s only one direction to evolve in – you have to become more complex,” said Dr Matthew Wills from the Department of Biology & Biochemistry at the University of Bath who worked with colleagues Sarah Adamowicz from from the University of Waterloo (Canada) and Andy Purvis from Imperial College London.

“Sooner or later, however, you reach a level of complexity where it’s possible to go backwards and become simpler again.

“What’s astonishing is that hardly any crustaceans have taken this backwards route. Instead, almost all branches have evolved in the same direction, becoming more complex in parallel.

“This is the nearest thing to a pervasive evolutionary rule that’s been found.

But don’t forget -

“Our results apply to a group of animals with bodies made of repeated units. We must not forget that bacteria – very simple organisms – are among the most successful living things. Therefore, the trend towards complexity is compelling but does not describe the history of all life.”

Indeed.

There is another very significant implication from the sequenced genome of Trichoplax adhaerens:

“Our whole genome analysis supports placing the placozoans after the sponge lineage branched from other animals,” said Daniel Rokhsar, the publication’s senior author, DOE JGI’s head of Computational Genomics Program, and Professor of Genetics, Genomics and Development at the University of California, Berkeley.

“Trichoplax has had just as much time to evolve as humans, but because of its morphological simplicity, it is tempting to think of it as a surrogate for an early animal,” said Mansi Srivastava, the study’s first author, a graduate student under the direction of Rokhsar, at the Center for Integrative Genomics, U.C. Berkeley.

Earlier mitochondrial DNA studies suggested that this “mother of all metazoans,” Trichoplax, was the earliest branch, before sponges diverged, but this remains debatable—even among collaborators.

“The latest and most complex analysis again suggests that placozoans populated the oceans long before sponges evolved,” said Bernd Schierwater, director of the Institute of Animal Ecology & Cell Biology and head of the Center for Biodiversity at TiHo Hannover, Germany.

So why is such an ancient origin for the placozoans significant from the front-loading perspective? Let me simply provide a quote from another paper:

The amount of gene loss in sponges may be partly determined by the phylogenetic position of placozoans. If they are at the base of the metazoan tree (as hypothesized in Dellaporta et al. 2006), it is likely that the genome of the LCA to placozoans, sponges, and eumetazoans was markedly more complex than observed in either extant sponge or placozoan genomes, given the lack of overlap in the constituencies of specific gene families in these animals. (emphasis added)

From Larroux et al. 2008. Genesis and Expansion of Metazoan Transcription Factor Gene Classes. Molecular Biology and Evolution 25:980-996.

Thus, the sequenced genome of Trichoplax is telling us that the last common ancestor of all metazoans was more genetically complex than modern day sponges or placozoans.

Another genome is sequenced and the hypothesis of front-loading evolution continues to grow stronger. This time it is the genome of Trichoplax adhaerens, the sole member of the placozoan phylum. The genome analysis “supports placing the placozoans after the sponge lineage branched from other animals.”

Although I have yet read the paper, sample these tasty morsels:

Trichoplax is a two-millimeter flat disk containing fluid sandwiched between two cell layers. It lacks organs and only has four or five cell types. Yet, despite its apparent simplicity, its genome encodes a panoply of signaling genes and transcription factors usually associated with more complex animals.

Trichoplax has no neurons, but has many genes that are associated with neural function in more complex animals. “It lacks a nervous system, but it still is able to respond to environmental stimuli. “It has genes, such as ion channels and receptors, that we associate with neuronal functions, but no neurons have ever been reported,” explained Rokhsar.

Of the 11,514 genes identified in the six chromosomes of Trichoplax, 80 percent are shared with cnidarians and bilaterians. Trichoplax also shares over 80 percent of its introns—the regions within genes that are not translated into proteins—with humans. Even the arrangement of genes is conserved between the Trichoplax and human genomes. This stands in contrast to other model systems such as fruit flies and soil nematodes that have experienced a paring down of non-coding regions and a loss of the ancestral genome organizations.

Apart from the growing evidence that preadaptation played a huge role in the evolution of neurons (yet another topic I need to discuss), I’m starting to notice a common theme – compared to the genomes of flies and worms, the human genome is looking much more like the ancient metazoan genome.

More

If you wanted to channel a single-celled organism toward the evolution of a metazoan state, various themes would have to emerge, including the ability of cells to connect to each other, communicate to each other from a distance, and the ability to recognize self. In the past, I have been filling in some of the details to front-load cell connections (see here and here) and signaling (the tyrosine kinases, which we’ll be getting back to). Today, let me touch on another neat example of intercellular communication.

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Earlier, I cited one example of a tyrosine kinase found in the protozoan Tetrahymena. Let me provide another one.

GTP avoidance in Tetrahymena thermophila requires tyrosine kinase activity, intracellular calcium, NOS, and guanylyl cyclase.

Bartholomew J, Reichart J, Mundy R, Recktenwald J, Keyser S, Riddle M, Kuruvilla H.
Purinergic Signal. 2008 4:171-81.

Guanosine 5′-triphosphate (GTP) is a chemorepellent in Tetrahymena thermophila that has been shown to stimulate cell division as well as ciliary reversal. Previous studies have proposed that GTP avoidance is linked to a receptor-mediated, calcium-based depolarization. However, the intracellular mechanisms involved in GTP avoidance have not been previously documented. In this study, we examine the hypothesis that GTP signals through a tyrosine kinase pathway in T. thermophila. Using behavioral assays, enzyme immunosorbent assays, Western blotting, and immunofluorescence, we present data that implicate a tyrosine kinase, phospholipase C, intracellular calcium, nitric oxide synthase (NOS) and guanylyl cyclase in GTP signaling. The tyrosine kinase inhibitor genistein eliminates GTP avoidance in Tetrahymena in behavioral assays. Similarly, pharmacological inhibitors of phospholipase C, NOS, and guanylyl cyclase all eliminated Tetrahymena avoidance to GTP. Immunofluorescence data shows evidence of tyrosine kinase activity in the cilia, suggesting that this enzyme activity could be directly involved in ciliary reversal.

And I also found this study, providing evidence of TK activity in yet another protozoan:

Evidence of tyrosine kinase activity in the protozoan parasite Trypanosoma brucei.
Wheeler-Alm E, Shapiro SZ.
J Protozool. 1992 39:413-6

Phosphorylation of proteins at tyrosine is an important mechanism for regulating cell growth and proliferation in metazoan organisms. In this report, we have demonstrated that Trypanosoma brucei, a protozoan parasite, possesses a tyrosine kinase that plays a role in regulation of proliferation of this protozoan. Genistein, a tyrosine kinase inhibitor, prevented multiplication of the parasite. An in vitro kinase assay demonstrated the presence of a kinase capable of phosphorylating an exogenous substrate at tyrosine, and genistein was able to reduce trypanosome-mediated phosphorylation of this substrate. An alkali digestion of 32P-labeled trypanosome proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated several proteins phosphorylated at tyrosine. These results indicate that T. brucei has a tyrosine kinase that is involved in proliferation or growth regulation of the parasite and provide further evidence for the possibility of growth factor regulation and signal transduction in trypanosomes.

The relevance of all this will become clear shortly.

In light of my third clarification about front-loading, I should probably address one aspect of Michael Sherman’s paper (Universal Genome in the Origin of Metazoa) that is being discussed on Telic Thoughts.

Sherman proposes his model and outlines its predictions:

According to this model, (a) the Universal Genome that encodes all major developmental programs essential for various phyla of Metazoa emerged in a unicellular or a primitive multicellular organism shortly before the Cambrian period; (b) The Metazoan phyla, all having similar genomes, are nonetheless so distinct because they utilize specific combinations of developmental programs. This model has two major predictions, first that a significant fraction of genetic information in lower taxons must be functionally useless but becomes useful in higher taxons, and second that one should be able to turn on in lower taxons some of the complex latent developmental programs, e.g., a program of eye development or antibody synthesis in sea urchin.

As I see it, chapter 6 from The Design Matrix once again becomes important if one desires to extrapolate Sherman’s model/predictions to a case for teleological evolution/design. With such an extrapolation, the predictions that Sherman makes are more relevant to the realm of epistemological evidence than ontological evidence. Put simply, these predictions, if verified, would be revolutionary and might indeed convince hardcore skeptics of teleological evolution, but I don’t think that we should expect such things from the hypothesis of design through front-loading itself.

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Another installment in my series of essays that correct common misunderstandings about the hypothesis of front-loaded evolution as laid out in The Design Matrix.

Today, we’ll deal with a question that was posed to me back in 2001 on the ARN Forum:

Isn’t the prediction of “front-loading” that we should find genes that serve no apparent purpose until the new function (in this case multicellularity) arise?

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Another installment in my series of essays that correct common misunderstandings about the hypothesis of front-loaded evolution as laid out in The Design Matrix.

Today, we’ll deal with the following erroneous belief:

Claim #2: Front-loading assumes that life began with a super-cell that contained all the genes needed to build complex multicellular life, including humans beings.

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