20 July 2008
The number of cases of HGT involving eukaryotes is now so great that it no longer makes sense to attempt to comprehensively compile individual cases — Patrick Keeling and Jeffrey Palmer

Analysed in isolation, a gene transferred between distant species [or into both!] will make the species seem closely related.

In a broad new survey, Keeling and Palmer discuss gene transfers to eukaryotes from organellar genomes, symbiotic prokaryotes, nonsymbiotic prokaryotes, and other eukaryotes. One transfer between fungal species apparently occurred only 70 years ago. In another instance, a species of green algae apparently acquired a whole chromosome by transfer. In yet another, the entire genome of a common intracellular bacterial endosymbiont, Wolbachia is found in the genome of a fruitfly. But Keeling and Palmer are actually quite conservative in estimating the importance of horizontal gene transfer in eukaryotes, for several reasons. They write —

• The gold standard for identifying HGT with confidence is …strong conflict between the phylogenies of the gene and of the organism. [So HGT between related species will be overlooked.]
• To confidently detect phylogenetic incongruence requires a level of taxonomic sampling for the gene in question that is often lacking at present…. [So many HGTs between unrelated species will be overlooked.]
• The more ancient a transfer, the harder it is to detect. [So ancient ones will likely be overlooked.]
• An organism with traits that seem to discourage HGT today might have evolved from ancestors with traits that encouraged it, and it might still harbour many genes acquired by that ancestor. [More ancient transfers will go unnoticed.]
• Eukaryote–eukaryote transfer of nuclear genes is underestimated for a number of reasons.... Given all this, it is noteworthy how many gene phylogenies have led to the conclusion that genes are in fact transferred between eukaryotes.
• Most described cases of HGT in eukaryotes involve bacterial genes.
• ...Looking forward from the many transfers that are already known to be a source of new functions, it is clear that HGT should feature prominently in future studies on the comparative genomics of eukaryotes.
• The ecological advantages that HGT might confer during a period of adaptation, such as becoming anaerobic or parasitic, are obvious (and this is not restricted to bacterial genes), but this is not to imply that HGT is only associated with extreme adaptations.

7 July 2008
The Design Matrix: A Consilience of Clues, by someone writing as Mike Gene, was recently sent to us. We occasionally read tracts by proponents of Intelligent Design (ID) because our questions about darwinism are often the same as theirs. This book promotes a four-criteria scoring system for deciding whether something was designed "by a mind" or not. Ultimately it gives high probability scores to books, cars, and the genetic code. Surprisingly, the writer never overtly attempts to overturn the scientific approach, and never even mentions the big bang. His brief in support of Michael Behe's irreducible complexity is strictly logical and thought provoking. The text is more informative and less assertive than many others we have seen in support of ID.

The writer argues that ID and darwinian natural selection are not mutually exclusive. Introducing the concept of "Original Mature Design," he explains how the genetic programs for highly-evolved life could be carried forward by more primitive life from the deep past. In support of this concept he cites, as we do, the presence of genes for complex features in primitive organisms without those features. And he mentions several examples of "moonlighting proteins," a phenomenon we knew, but a term we didn't. The hypothesis that very old genetic programs can be activated by darwinian tinkering, also mentioned by Behe, is actually quite close to principles of our own cosmic ancestry. This is interesting. But panspermia is never mentioned.

We wonder where the writer goes as he probes the past more deeply. Is supernatural intervention required? How does it work? And we are suspicious if someone uses a pseudonym — what is his real ID! Aware of such questions, the writer has a blog wherein he discusses his refusal to answer. "The silence is part of a political strategy itself. This, at least, is how many critics of Intelligent Design think." Right.

We have long complained about the false dichotomy of choices for explaining evolution and the origin-of-life, namely darwinism or creationism/ID. Both camps, comprising 99% of people who discuss the subject, believe that we must explain how life and the genetic programs for higher life forms originated. But if they can originate, there should be credible direct evidence of such processes. Until there is, virtually everyone is trying to explain never-observed phenomena. Without evidence, both camps rely heavily on faith (in the big bang!) to mandate that these origins must occur. And to explain them, both resort to miracles — either incredible unlikelihoods or supernatural intervention.

Cosmic ancestry is a third alternative. It offers a plausible way to explain what we observe, scepticism about what we don't observe, and no need for ongoing miracles. We think it deserves a role in the discussion. Meanwhile, we welcome support for the hypothesis that very old genetic programs are available in Earth's biosphere and can be activated by darwinian tinkering. Panspermia, anyone?

5 July 2008
Current methods of gene sequence alignment are error-prone, according to a pair of molecular biologists from the European Bioinformatics Institute in Hinxton, UK. Current methods default to the assumption that similar sequences in the same place are inherited from a common ancestor. This and related assumptions are often wrong and lead to incorrect reconstructions of evolutionary history.

The pair from EBI have devised a "phylogeny-aware" method that is better able to recognize multiple separate insertions at the same location or nearby. For example, in a sequence of amino acid positions in 23 strains of HIV and SIV, older methods find multiple point substitutions and eight independent deletions. In the same sequence, the phylogeny-aware method (illustrated) detects instead seven insertions, two deletions, and fewer point substitutions.

Targetted insertions are essential for evolutionary progress in cosmic ancestry. We welcome this clue that they are more common than previously thought.

4 July 2008
Multicelled animals use a three-part molecular toolkit to mediate phospho-tyrosine signaling. This toolkit enables animals to conduct a number of important communications between their cells, including immune system responses, hormone system stimulation and other crucial functions. "Without these three molecules to help our cells 'write,' 'read' and 'erase' chemical messages between them, our bodies would never be able to conduct the complex tasks needed to survive, such as reproduction, digesting food or even breathing." An international team studied 41 eukaryotic genomes, asking, "How did this system of three components evolve, given their interdependent function?"

They found that a handful of single-celled eukaryotic species have genes for two of the enzymatic functions, writing and erasing. "This makes sense considering these organisms don't need the tools to communicate between cells since they are made up of only one cell." But why would they need any of them? Well, maybe this incomplete set confers a previously unsuspected benefit, "most likely to deal with limited tyrosine phosphorylation cross-catalyzed by promiscuous Ser/Thr kinases."

One single-celled species, the choanoflagellate Monosiga brevicollis (illustrated, left), has genes for all three functions. "The researchers conclude that the presence of the full three-component signaling system may have played a role in the development of metazoan organisms.... Probably there was an ancestor to these organisms that first developed these chemicals." But what use are they to one-celled choanoflagellates? "[They] may potentially give cells a wide range of communication possibilities, including uses within single cells. ...There's a certain amount of signaling you can do, and you allocate that apparently for whatever function you want."

We commend this analysis of phospho-tyrosine signaling in metazoa. But please notice that it does not even claim to account for the origin of the three-part toolkit. The parts are only observed to exist already in single-celled eukaryotes with no obvious use for them. Actually, finding genes with unexplained origins and no plausible initial purpose is the usual result in studies seeking the origins of genes. Under these circumstances one might expect darwinists to step back and reconsider some of their assumptions. Not yet, apparently.

25 June 2008
Vertebrate and jellyfish eyes use similar genes. Both lineages probably recruited them independently. An international research team writes: Combined, the available data favor the possibility that vertebrate and cubozoan eyes arose by independent recruitment of orthologous genes during evolution. Otherwise, if they were inherited from a common ancestor (the default assumption), many other lineages apparently lost them. This loss would violate the principle that evolution preserves advantageous features.

Actually, neither scenario supports the darwinian paradigm of gradual program composition. If the genes were independently recruited, their ultimate source is not accounted for in either vertebrate or jellyfish lineages. But if they come from common ancestry, the genes appear to wholly precede the first appearance of the features they encode.

For other possibilities, could convergent darwinian evolution produce the same genes multiple times? The similarities of the subject genes, apparently, make this implausible. Or, could the genes have evolved in the vertebrate lineage according to darwin, and then been acquired by jellyfish? After all, we are looking at today's jellyfish. The genomic-historical-reconstruction method suffers from this ambiguity.

The research team further notes that recruitment of genes by widely diverse species is not uncommon: …Entire regulatory circuits can be co-opted for development of different cell types, tissues, or organs. For example, the Pax–Six–Eya–Dach gene regulatory network has a fundamental role in Drosophila visual system development but is also used for specification of muscle cells or placodes in vertebrates. This is how evolution is expected to work in cosmic ancestry — genetic programs are not gradually composed, but acquired. If regulatory genes are included in the acquisitions, we are not surprised.

14 June 2008
Organic compounds were present in the early solar system, according to an international collaboration studying the Murchison meteorite. Nine astrobiologists from the The Netherlands, UK and USA used isotopic analysis to determine that uracil and xanthine in the meteorite are not Earthly contaminants. Uracil is a component of RNA, and xanthine (shown in diagram) is an intermediate in the synthesis of other biological molecules. The study suggests that these and other similar products, delivered by meteorites, "would have enriched the prebiotic organic inventory necessary for life to assemble on the early Earth." Could they even be the remnants of prior life?

11 June 2008
We will see organics, for sure, because we're bringing them, says Aaron Zent of NASA's Ames Research Center, talking about the organics detector that the Phoenix lander just delivered to the surface of Mars. TEGA, the Thermal and Evolved Gas Analyzer, can detect much lower concentrations of organics than the instruments sent to Mars with the Viking missions that landed in 1976 and 1977, which detected no organics. However, apparently, TEGA is so sensitive that it may end up sensing only contamination from Earth.

Of course the Phoenix team would dispute the suggestion that TEGA is unreliable. But in general, biological contamination is pervasive and extremely difficult to prevent. Only lately has the true magnitude of this problem been recognized. Even when non-contamination is the first priority in controlled laboratory experiments, contamination still happens. To achieve reliable results in biology, foolproof protocols are needed. Can such protocols be designed? In a related issue, for testing the range of evolution in closed systems, would nonbiological media such as computer models be preferable?

5 June 2008
Cloned bacteria evolved an unexpected feature in a long-running experiment led by Richard Lenski at Michigan State University. After some 31,500 generations, a population of E. coli suddenly began to metabolize citrate aerobically. The inability to do so is a defining characteristic of this species, and this rare adaptation looks like a significant innovation.

The Long-Term Evolution Experiment (LTEE), started in 1988, has now run for more than 44,000 generations. The observed mutation rate is apparently sufficient to have supplied for testing, many times, every typical one-step mutation available to the 4.6 million base-pair genome. And frozen samples that remain viable are taken every 500 generations, so it is possible to reanalyze prior stages of the process. The system is uniquely useful for studying evolution.

The research team was especially interested to know whether the latest adaptation "required an unusually rare mutation or, alternatively, was historically contingent and depended on the prior evolution of a certain genetic background." Using the frozen samples, they decided that historical contingency was the answer.

They then ask, "What is the genetic basis of this evolutionary innovation?" And they acknowledge, "We anticipate that identifying the potentiating mutation will be especially challenging, however, because its only known phenotype is to increase the rate of production of certain mutants that are themselves extremely rare." While there are difficulties, we feel that closed-system research like this is exactly what is needed for truly understanding how evolution works. We are pleased that MSU is doing it.

Of course, understanding how evolution works is a primary concern of our own as well. Specifically, we want to know if mutations in closed systems like this one can write new genetic programs or not. If so, as mainstream science assumes, the darwinian paradigm would be sufficient to explain the evolution of life on Earth, with no need for input from elsewhere. If not, as we suspect, darwinian evolution would be limited to exploring the capabilities of the programs that are provided, initially or eventually. We believe ours is a more conservative position, and that the mainstream proposition amounts to an extraordinary claim. Therefore we view the evidence with unusual scrutiny.

The MSU researchers acknowledge the possibility that "some complex mutation, or multiple mutations, activated cryptic genes that jointly expressed a citrate transporter." They also mention that contamination occasionally happens in the experiment, although the strain which underwent the studied adaptation is not a contaminant. However, E. coli "from agricultural and clinical settings ...harbor plasmids, presumably acquired from other species, that encode citrate transporters." Could a non-surviving contaminant have introduced similar plasmids in this case? These possibilities — cryptic genes and contamination — undermine the argument that mutations wrote a new program this time.

Perhaps more experiments and analysis will uphold the darwinian position. If so, we think Richard Lenski's approach will be the one that succeeds. Meanwhile, the capability of darwinian evolution to write new programs in a closed system has not been clearly demonstrated.

4 June 2008
Prokaryotic life in Earth's deep dark ocean, subsisting on rock, has been observed to be far more abundant and diverse than expected. "We now know that this remote region is teeming with microbes, more so than anyone had guessed," said David Garrison, director of the National Science Foundation's Biological Oceanography Program.

Would similar life be able to to subsist on the bottom of deep dark oceans on other moons or planets such as, possibly, Ganymende, Enceladus, Europa, or Callisto? Why not?