Giant viruses join as another ancestral superkingdom

Mimivirus in amoeba. Credit: Professor Didier Raoult, Rickettsia Laboratory, La Timone, Marseille, France

A study of the proteins of giant viruses adds them to the list of primitive life forms that have existed since the dawn of life.  They seem to constitute a fourth superkingdom. Professor Gustavo Caetano-Anollés led the analysis.

Scientists found ancient structural patterns in the folds of the virus proteins, which are virtually molecular fossils. Folds that are common to all organisms studied are the oldest. Less common folds are, literally, new wrinkles.

The researchers looked at archaea, bacteria, eukaryotes, and both kinds of viruses. The giant viruses have  biochemistry for making proteins, which small viruses have lost.

Modern viruses have lost much of their biochemical machinery and become obligate parasites of an extreme kind.

Giant Viruses Coexisted With the Cellular Ancestors and Represent a Distinct Supergroup Along With Superkingdoms Archaea, Bacteria and Eukarya

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Evolution of complexity in molecular “machines”

V-ATPase proton pump and evolutionary pathway

A proton pump is a ring of proteins embedded in a cell wall, which moves molecules, atoms, or ions through the wall in a preferred direction. Research into the V-ATPase proton pump in eukaryotes has a ring of  six linked protein molecules in the membrane wall and a ring of eight inside the cell. As its name implies, it moves hydrogen ions (protons), through the cell wall. Research into its history shows that greater complexity can evolve without a change in function. The “V” indicates a plant vacuolar pump. They are found not in the external cell wall but in the walls of vacuoles, or liquid-filled spaces, within the cell.

…the complexity of an essential molecular machine—the hexameric transmembrane ring of the eukaryotic V-ATPase proton pump—increased hundreds of millions of years ago. We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. Reintroducing a single historical mutation from each paralogue lineage into the resurrected ancestral proteins is sufficient to recapitulate their asymmetric degeneration and trigger the requirement for the more elaborate three-component ring. Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.

“Evolution of increased complexity in a molecular machine,” Gregory C. Finnigan, Victor Hanson-Smith, Tom H. Stevens & Joseph W. Thornton. Nature (2012). doi:10.1038/nature10724.

I won’t be able to give a detailed explanation until the description comes out from behind a paywall. There’s an explanation at Nature blog and one at  Kurzweil.

Look here for a diagram of V-ATPase. This diagram shows the ancestral molecule, in green, and its more specialized descendents, which need their increased complexity to properly assemble and function. The ancestor is on the left.

Evolution of V-ATPase protein chains

Evolution of the bacterial flagellum

Dr. Ian Musgrave

Pace Michael Behe and William Dembski, bacterial flagella are not irreducibly complex. Here is Ian Musgrave’s clear explanation, “Evolution of the Bacterial Flagellum.”

Dr. Musgrave points out, “The specification of “ an outboard motor,” which provided the IC [irreducibly complex] system description of motor, shaft, and propeller, is a flawed human analogy to the actual flagellar system.” He also points out that Behe’s own definition of irreducibly complex systems excludes flagella, whose original function was not motility but secretion. Dembski, by building on Behe’s flawed description, in my opinion goes further astray into “Why bumblebees can’t fly” territory.

There’s much more! Read the article.

Why trust the theory of evolution?

Science is about what you can test and not disprove. Three hundred years ago European scientists started with the assumption that the Bible was a historical record and that the biblical flood was a real event. It took about one hundred years of gathering evidence to prove that one single flood could not be the explanation and that glaciers had caused many of the features formerly ascribed to a giant flood and another hundred to correlate geographical features into a coherent history.

It took about two hundred years, from the 1600s to the 1800s, to demonstrate that animal species had died out or changed over time. At this point, it was a historic discipline, like political history, studying what had occurred in the past by the evidence that remained. Darwin’s and Wallace’s brilliant suggestion as to how that happened, in general, was rapidly accepted. As Darwin pointed out, if cave critters had been specially designed for caves, you’d expect to find the same perfect cave critters everywhere. Instead, cave critters in each ecosystem are modified versions of the organisms that live above the ground in that area, just as if they had descended from something that fell or wandered into the cave.

However, at that time genes and chromosomes were unknown. Neither Darwin nor his colleagues knew how a special trait could become more common and not blend back into the average. About that time, Gregor Mendel, breeding peas for years and recording the results, worked out the math of simple dominant inheritance with one gene or two genes; but he published in an obscure Austrian journal. His work did not reach the larger scientific community until almost one hundred years later. In the 1930s, when the genetic theory was added to the theories of natural and sexual selection, the theory of evolution became robust.

Quite a bit of mathematical analysis and prediction, by R.A. Fisher and others, made testable cases for evolution, and evolution passed them. For example, why do most species have equal numbers of both sexes? What should the ratio be when resources are temporarily plentiful? What if resources are restricted but it’s easy to find a mate?  But what carried the genetic information was still a mystery. Was it DNA or a protein, perhaps albumin? In the late 1930s, DNA was proven to be the key to inheritance.

The giant chromosomes in the salivary glands of fruit flies let us see something of their structure. Since then, we have learned to trace the evolution and ancestry of individual genes and chromosomes. For example, chimpanzees have one more chromosome than we do: but one of our chromosomes matches up with two of theirs; and there’s even an extra centromere in our chromosome, vestige of its former existence as a separate unit. It’s pretty obvious that we diverged from chimpanzees before the chromosomes fused.

Molecular evolution was developed in the 1960s; that’s where we trace the changes in a single important molocule through various species, noting the changes along the way. It’s the equivalent of literary research, where a single change in a manuscript of the Bible, e.g. the change from “young woman” to “virgin,” is used to track what further manuscripts were copied from the new error clarification.

The “family trees” made from comparing organisms agree with the evidence of fossils. Hypotheses about the environments and conditions where significant evolution might have occurred suggest places for scientists to look for fossils. That’s how the famous Tiktaalik transitional fossil was found in the sediments of Devonian freshwater swamps. And new discoveries occur all the time. Surely you know of the complete set of transitional mammals, discovered in the 1990s, from a hoofed land-dweller to a swimmer to whales.

In the past decade, evolution has been observed in the laboratory with the development of completely novel traits in bacteria. Evolution has been observed in the wild with two new species of flower developing in the U.S. Northwest in the 1940s. It has been observed in the development of a new species of mosquito that inhabits the London subway system, in a mere 150 years. On a similar time scale, the hawthorn gall midge produced a variety that prefers apples and does not mate with its ancestral strain. Other examples abound.

It only strengthens the case for evolution when the family trees drawn by research into molecular evolution match those drawn on the basis of physiology and fossils.

Then look into ERVs: endogenous retroviruses. Viruses can and do read themselves into our genes. Those, too, are inherited and can also be traced in family trees. Many of them are inactive; however, mutations sometimes reactivate them by chance. For example, the ERV for mouse mammary tumor gives women a higher chance of developing breast cancer.

With evolution, with science, it’s all about the facts.

Microbiology and immunology research at Western

The University of Western Ontario has more than thirty researchers working on the molecular and cellular biology of microorganisms or the immune system. Here’s an index to them and their research projects. Several of the researchers are accepting graduate students. Have a look and see if anything strikes your fancy.

Evolution of complex systems

Nick Matzke rounds up the arguments and evidence, beginning with Darwin’s work, that explains how complex systems needing multiple parts can evolve:

The standard answer to this question was put forward by Darwin. Mivart (1871) argued that the “incipient stages of useful structures” could not have evolved gradually by variation and natural selection, because the intermediate stages of complex systems would have been nonfunctional. Darwin replied in the 6th edition of Origin of Species (Darwin, 1872) by emphasizing the importance of change of function in evolution. Although Darwin’s most famous discussion of the evolution of a complex system, the eye, was an example of massive improvement of function from a rudimentary ancestor (Salvini-Plawen and Mayr, 1977; Nilsson and Pelger, 1994), Darwin gave equal weight to examples of functional shift in evolution. These included the complex reproductive devices of orchids and barnacles, groups with which he was particularly familiar (Darwin, 1851, 1854, 1862). Intricate multi-component systems such as these could not have originated by gradual improvement of a single function, but if systems and components underwent functional shift, then selection could have preserved intermediates for a function different from the final one. The equal importance of improvement of function and change of function for understanding the evolutionary origin of novel complex systems has been similarly emphasized by later workers (Maynard Smith, 1975; Mayr, 1976). Recent studies give cooption of structures a key role in the origin of feathers (Prum and Brush, 2002), and novel organs (Pellmyr and Krenn, 2002); Mayr (1976) gives many other examples. Computer simulations also show the importance of cooption for the origin of complex systems with multiple required parts (Lenski et al., 2003).

Do these common insights from classical, organismal evolutionary biology help us to understand the solution to the puzzle Macnab put forward regarding the origin of flagellum? Cooption at the molecular level is in fact as well-documented at it is at the macroscopic level (Ganfornina and Sanchez, 1999; Thornhill and Ussery, 2000; True and Carroll, 2002). It has been implicated in origin of ancient multi-component molecular systems such as the Krebs cycle (Melendez-Hevia et al., 1996) as well as the rapid origin of multi-component catabolic pathways for abiotic toxins that humans have recently introduced into the environment, such as pentachlorophenol (Anandarajah et al., 2000; Copley, 2000), atrazine (de Souza et al., 1998; Sadowsky et al., 1998; Seffernick and Wackett, 2001), and 2,4-dinitrotoluene (Johnson et al., 2002); many other cases of catabolic pathway evolution exist (Mortlock, 1992). All of these systems absolutely require multiple protein species for proper function. Even for some molecular systems equaling the flagellum in complexity, reasonably detailed reconstructions of evolutionary origins exist. Generally these are available for systems which originated relatively recently in geological history, which are well-studied due to medical importance, and where phylogeny is relatively well resolved; examples include the vertebrate blood-clotting cascade (Doolittle and Feng, 1987; Hanumanthaiah et al., 2002; Jiang and Doolittle, 2003) and the vertebrate immune system (Muller et al., 1999; Pasquier and Litman, 2000).

Evolutionary and phylogenetic trees

Casey Luskin seems to be stepping into Michael Behe’s clown shoes to perpetrate another round of “scientific analysis” based on inaccuracies. The Non-discovery blog analyzes why Luskin is wrong: Molecular evolution, retroviral evolution, and standard phylogeny give similar trees: “Why we know the tree is real.”

Hat tip to ERV: “Bort grows ERV and CytB trees!

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