26 September 2007
The genomes of 17 species of fungi have been analysed to reconstruct gene duplication that took place during approximately 300 million years of evolution. Using a specialized computer program, four analysist probed 121,050 predicted protein-coding genes for evidence of duplication. They classified these into 30,110 orthogroups, of which, 11,103 had multiple members.

(1) One question was, "What innovations typically arise from gene duplication events?" In answer, they observed, "Gene duplication results in limited biochemical divergence.... Surprisingly, our analysis shows that paralogous pairs rarely migrate between functional gene ontology categories.... This highlights inherent limitations of gene duplication in accomplishing molecular innovation." Instead, "Gene duplication innovates through regulatory divergence." Finally they suppose, "Increasing gene copy number may eventually simplify a system rather than making it more complex."

Distribution of orthogroup volatility scores (colored and grey bars). The black line shows the expected random distribution.

(2) They also noticed, "The observed variation in copy number changes ['volatility'] among orthogroups is inconsistent with random expectation." Some categories of genes are much likelier than others to be duplicated or lost. Likely ones include those that encode "peripheral transporters, receptors and cell wall proteins, and genes that participate in stress responses." Unlikely ones include "genes involved in essential growth processes, genes residing in the nucleus, nucleolus, mitochondrion, endoplasmic reticulum and Golgi apparatus, and genes essential for viability. ...Evolutionary forces have acted very differently on these two classes...."

(3) Early in the analysis they deduced that members of just over half of the multigene orthogroups had been present in the last common ancestor; they defined these as "ancestral." In the well-studied S. cerevisiae, for example, "1,008 of 1,047 genes essential for growth in rich medium are ancestral... as are 668 of 730 genes essential only for growth in other conditions.... Nevertheless, 36 essential genes are not ancestral... suggesting that new essential functions can arise, albeit rarely."

Although the researchers interpret the results under a strictly darwinian paradigm, we think the data support strong panspermia, because: (1) Gene duplicates normally keep close to their original functions; (2) The duplications are not random, but are apparently under the control of a software management system; (3) If the S. cerevisiae example is typical, genes are either very similar to their predecessors, or they "seem to have come from nowhere." The latter ones, we think, were likely acquired by gene transfer, a phenomenon apparently ignored in the new analysis.

As our regular readers know, we think that reconstructing the past from today's genomes is a poor third-best as a method for probing the power and range of Darwinian evolution. But more data, by far, are available for this method of analysis than are produced by the closed system tests that we prefer.

20 September 2007
A meteorite caused illness in Peru? A "bright streak of light and loud bangs" were reported by locals before a crater appeared near Carancas in the Peruvian Andes, 15 September. Soon thereafter, ~200 people reported headaches, nausea and breathing problems caused by sulfurous-smelling fumes emanating from the crater (right), which may have boiled briefly. One correspondent wonders if the fumes contained hydrogen sulfide gas produced by bacteria in the meteorite. But was the crater even caused by a meteorite? So far, little about the phenomenon is certain.

14 September 2007

Nicolle Rager Fuller, National Science

Lateral gene transfer... may happen much more frequently between bacteria and multicellular organisms than scientists previously believed, posing dramatic implications for evolution — The University of Rochester

A new study by a 20-member interrnational team has confrmed that heritable lateral gene transfer "occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions."

W. Ford Doolittle, Canada Research Chair in Comparative Microbial Genomics at Dalhousie University, comments, "This study establishes the widespread occurrence and high frequency of a process that we would have dismissed as science fiction until just a few years ago. This is stunning evidence for increased frequency of gene transfer."

Another development in the ongoing paradigm shift for evolution.

28 August 2007
Varying environments can speed up evolution according to a team at Israel's Weizmann Institute. In computer simulations Kashtan et al. used four "network" models and one model representing RNA secondary structure. Each model was given one or several goals to attain. The team found that when goals [or environments?] were switched, populations were released from confinement on fitness plateaus or local maxima. "Over many goal switches a 'ramp' is formed," they report. They believe that these findings have implications for biology, because "Natural evolution usually occurs in temporally and spatially changing environments."

Commenting on prior research, they confess, "Current computer simulations of evolution are well known to have difficulty in scaling to high complexity." Right, but the simulations from Weizmann look no better in that respect. The noticed "ramps" are very short optimization paths that never lead to new inventions. In fact, the Weizmann team has no intention of simulating new inventions, because their evolution "proceeds toward a defined goal: producing a specified output based on inputs." Of course, survival is the only goal allowed in darwinian evolutionary theory. Anything else amounts to teleology.

We still believe that the range of darwinian evolution in closed systems is strictly limited. The virtue of this study may be that it finds a quicker route to the limit.

27 August 2007
When I repeated the Viking experiments, I was surprised to see that despite the huge amount of organic matter present [at Rio Tinto] , there was virtually no detection of organics in the sediments. This was quite strange. — Rafael Navaro-González

This month, another mass spectrometer is on its way to Mars. The Thermal and Evolved Gas Analyzer (TEGA) heats soil samples at a constant rate, measuring changes in the rate of warming so as to detect phase changes. It includes a small mass spectrometer which will be used on the output from samples heated as high as 1,000°C — 500C° hotter than Viking's ovens, and hot enough to decompose the most refractory compounds. NASA's Phoenix mission, carrying TEGA, was launched on 4 August, and is scheduled to touch down 1,200 kilometres from the north pole of Mars on 28 May 2008.

26 August 2007
The first analysis of the genome of the sea anemone shows it to be nearly as complex as the human genome — UC Berkeley News

...The [animal] ancestral genome... contained nearly complete toolkits for animal biochemistry and development, write geneticists at Berkeley. This evidence adds to the list of examples of genetic programming that was apparently available and installed before it could be shaped by natural selection. This order of events is inexplicable in standard darwinism, but is expected in cosmic ancestry.

...But many animal-specific genes contain sequences with no readily recognizable counterparts outside of animals. As eminent geneticist W. Ford Doolittle once wrote, they "seem to have come from nowhere." DNA sequences lacking apparent predecessors are also troubling for darwinism and expected in cosmic ancestry.

25 August 2007
The great obstacle to discovering the shape of the Earth, the continents and the oceans was not ignorance but the illusion of knowledge — Daniel Boorstin, historian of science

      "The currently fashionable concordance model of cosmology... has 18 parameters, 17 of which are independent. Thirteen of these parameters are well fitted to the observational data; the other four remain floating. This situation is very far from healthy....
      "Any theory with more free parameters than relevant observations has little to recommend it. Cosmology has always had such a negative significance, in the sense that it has always had fewer observations than free parameters... though cosmologists are strangely reluctant to admit it. While it is true that we presently have no alternative to the Big Bang in sight, that is no reason to accept it....
      "The three successful predictions of the concordance model... are overwhelmed by at least half a dozen unpredicted surprises, including dark matter and dark energy. Worse still, there is no sign of a systematic improvement in the net significance of cosmological theories over time....
      "A skeptic is entitled to feel that a negative significance, after so much time, effort and trimming, is nothing more than one would expect of a folktale constantly re-edited to fit inconvenient new observations....
      "Acceptance of the current myth, if myth it is, could... hold up progress in cosmology for generations to come."

20 August 2007
Comets are much more likely than Earth to have hosted the origin of life, simply because the combined volume of their life-friendly, potentially prebiotic environment is greater by some 24 to 25 powers of ten. So write Bill Napier and Janaki and Chandra Wickramasinghe of the Cardiff Centre for Astrobiology in an article forthcoming in the International Journal of Astrobiology. The claim has already created a stir. NASA senior astrobiologist David Morrison says their theory is "built on air, not solidly grounded in scientific facts." Linked below from this website are the original article, Morrrison's critique, and today's reply from Napier and the Wickramasinghes. Our own estimates of the actual probabilities aside, we think Cardiff has the relative probabilities right. We will post followups as they become available.

29 July 2007
The Limits of Organic Life in Planetary Systems is the title of new report by a distinguished interdisciplinary committee named by the National Research Council. This study aims to inform research pro­gram managers, policymakers, and mission designers about the possibilities for life on other solar system bodies, with special attention to biochemistries that may be different from ours. It also includes some helpful, basic instruction on earthlike biochemistry. And we are pleased that the report gives adequate consideration to panspermia.

It is clear that panspermia is possible and even probable if bacterial spores become embedded in rocks that are ejected from one planet and eventually enter the atmosphere of another (p 37). However, Amino acids are found in natural specimens, including meteorites, that are almost certainly not influenced by biological processes (p 55). Oh well. At least the committee is not entirely certain.

The section titled "Origin of Life" (p 53-68) contains plenty of speculations pertaining to old and new theories. Not hiding the difficulties, it is a fair status report on this research topic. And while almost any approach to the hardware aspect of the problem is allowed, the software problem, as usual, is ignored.

But the software problem does not go away after life emerges; it pertains to the scientific account of new genetic programs throughout evolution. On this score, the report, in its Introduction, endorses a profound, quiet, ongoing paradigm shift (p 7-8):

• It is understood that lateral gene transfer is one of the most important and one of the earliest mechanisms for creating diversity and possibly for building genomes with the requisite information to result in free-living cells.
• Lateral gene transfer is an ancient and efficient mechanism for rapidly creating diversity and complexity.
• Lateral gene transfer is also an efficient mechanism for selecting the genes that are most "fit" for specific proteins and transferring them into diverse groups of organisms.
• Natural selection based solely on mutation is probably not an adequate mechanism for evolving complexity.
• Lateral gene transfer is also one of the mechanisms to align genes from different sources into complex functional activities.

A frequent objection to panspermia is that it simply moves the origin-of-life problem elsewhere. Logically, the same objection could be made about lateral or horizontal gene transfer — new genetic programs were composed elsewhere? Yet we never hear that objection. Evidence for L/HGT is too strong, apparently. But the phenomenon challenges the standard darwinian account of new genetic programs, especially if transferred genes come from species with no use for them, as more and more examples seem to indicate.

We want scientists to question the assumption that virtually open-ended evolutionary progress, including the orign of life, is possible in a genetically closed system. The authors of this report do not go that far. But their respect for panspermia and their acceptance of lateral gene transfer gratify us.

5 July 2007 | 10:30 AM PDT
The transfer to our new web host is complete.