What'sNEW April–June 2009
27 June 2009
More than 20% of diatom genes were apparently recruited from red and green algae. The process probably began with endosymbiosis, when the algae were engulfed as organelles within cells ancestral to diatoms, but the recruited genes are now incorporated into the diatoms' nuclear genomes. Endosymbiosis is horizontal gene transfer (HGT) in wholesale form, and the subsequent migration of organellar genes into the eukaryotic nucleus is a well known phenomenon. However, other more piecemeal forms of HGT might also account for some of the transferred genes, according to an international research team. Examples of HGT in any form are consistent with evolution by cosmic ancestry.
Ahmed Moustafa, Bánk Beszteri et al., "Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms" [abstract], doi:10.1126/science.1172983, p 1724-1726 v 324, Science, 26 Jun 2009.
20 June 2009
...Some microbes thrive at ...10 times the salinity of seawater.
Antje Boetius and Samantha Joye, "Thriving in Salt" [summary], doi:10.1126/science.1172979, p 1523-1525 v 324, Science, 19 Jun 2009.
20 June 2009
The tree of life was always a net. Nature was always a genetic engineer.
Stefan Helmreich, Alien Ocean: anthropological voyages on microbial seas, ISBN-10: 0520250613, University of California Press, 5 Jan 2009. (p 103)
The Tree of Life is a related webpage.
15 June 2009
A novel bacterium that has been trapped more than three kilometres under glacial ice in Greenland for over 120,000 years, may hold clues as to what life forms might exist on other planets. This is what astrobiologists are saying about Herminiimonas glaciei, recently found and cultured by a team at Penn State. The bacteria are small enough to pass through a normal sterilizing filter, and culturing them was tedious. But could their hardiness enable them to survive on a place like Europa? These extremely cold environments are the best analogues of possible extraterrestrial habitats, said team leader Jennifer Loveland-Curtze.
Jennifer Loveland-Curtze et al., "Herminiimonas glaciei sp. nov., a novel ultramicrobacterium from 3042 m deep Greenland glacial ice" [abstract], doi:10.1099/ijs.0.001685-0, p 1272-1277 v 59, International Journal of Systematic and Evolutionary Microbiology, Jun 2009.
10 June 2009
...Metabolically active microbes were reported in 111-million-year-old sediments buried as deep as 1.6 kilometres below the seabed. This is among the surprises in a recent article about prokaryotes that can survive in harsh deep environments. Some of them may reproduce only once per thousand years. Some can persist solely on energy that comes from radioactivity. Astrobiologists are wondering why they couldn't live on other planets. We think they probably could.
9 June 2009
Formic acid ...has been found at record levels on a meteorite that fell onto a frozen Canadian lake in 2000. The University of Alberta's meteorite curator Chris Herd (pictured with sample) reported this finding to the American Geophysical Union in Toronto in May. The Tagish Lake meteorite is an especially pristine one; organic compounds in it are unlikely to be earthly contaminants. Organics from space are usually called "prebiotic", but we think they could as well be "postbiotic".
Space rock yields answers about origins of life on Earth by Wanda Vivequin, University of Alberta, 2 Jun 2009.
6 June 2009
Astrobiologist Richard Hoover discusses his work in a new short video. In five minutes he describes extremophiles that could apparently survive in ice on Mars or Europa, and microfossils that resemble microbial life, found inside carbonaceous meteorites (see example). One microfossil in the Murchison meteorite was seen for the first time as the video was being filmed.
Extremophile Hunter, narrated by Bruce Burkhardt, produced by Kate Tobin for the National Science Foundation's online magazine Science Nation, 1 Jun 2009.
5 June 2009
The enemy has become more diverse, says anthropologist Eugenie Scott, executive director of the National Center for Science Education. "Darwin's golden retriever," as she likes to be known, Scott was recently interviewed for Science magazine. In the quoted phrase she may be acknowledging the fact that some who see problems with the mainstream theory of evolution have no agenda beyond science. But she categorizes them all as "the enemy," keeping the discussion strongly polarized and superficial. This tactic impedes scientific progress.
The mainstream theory of evolution has no credible acount of the origin of life, certainly. Acknowledging this, Scott stubbornly says, "Not yet." Alchemists trying to turn lead into gold said the same thing.
Also unexplained are the genetic programs contained within DNA. Darwinan mutation-and-natural-selection is supposed to compose them, but direct evidence for this composing is lacking. Instead, darwinan mutation-and-natural-selection can be seen only to toggle, shuffle and optimize programs that are already present in a given genome. New genetic programs often appear suddenly during evolution; many are known to arrive by gene transfer (HGT). But Scott would minimize the importance of HGT and assert that evidence for the mainstream account of new genetic programs is abundant. In a similar manner, Galileo's opponents held that Ptolemaic astronomy was perfectly adequate.
Given the described shortcomings, it is no surprise that a majority of Americans are not satisfied with the mainstream theory of evolution. Apparently, the National Center for Science Education sees a majority of Americans as "the enemy." Such animosity from the science establishment is unwarranted and, to our knowledge, unprecedented.
Yudhijit Bhattacharjee, "Eugenie Scott Toils in Defense of Evolution" [html], doi:10.1126/science.324_1250b, p 1250-1251 v 324, Science, 5 Jun 2009. 30 May 2009 28 May 2009
Yudhijit Bhattacharjee, "Eugenie Scott Toils in Defense of Evolution" [html], doi:10.1126/science.324_1250b, p 1250-1251 v 324, Science, 5 Jun 2009.
30 May 2009
28 May 2009
...In 1995, Craig Thompson, then at the University of Chicago in Illinois, formally proposed that the DNA now encoding RAG1 and RAG2 was once a mobile genetic element called a transposon.
...In 2006, a team led by Jonathan Rast of the University of Toronto in Canada and Sebastian Fugmann of the National Institute on Aging in Bethesda, Maryland, analyzed the genome of the purple sea urchin and found genes that closely resemble RAG1 and RAG2, the first time they've been uncovered in invertebrates.
In cosmic ancestry, evolutionary innovations depend on genetic programs acquired by various means of horizontal gene transfer (HGT). These programs must necessarily reside silently somewhere before they arrive in species that can use them. The programs would need a means of transfer such as viral or bacterial infection. And they would need tools and systems within the acquiring genome to place and assemble them correctly. Of course, every element of this scenario is already well observed. If evolutionary innovations emerge as cosmic ancestry predicts, the immune system of jawed vertebrates makes a striking example.
22 May 2009
22 May 2009
And an international team proposes that dissolved minerals can explain saline liquid water activity on the surface of Mars at mean global temperatures well below 273 K. 18 May 2009 13 May 2009
J. L. Dickson et al., "Amazonian-aged fluvial valley systems in a climatic microenvironment on Mars: Melting of ice deposits on the interior of Lyot Crater" [abstract], doi:10.1029/2009GL037472, L08201 v 36, Geophysical Research Letters, 17 Apr 2009. 6 May 2009
Xiao C, Kuznetsov YG, Sun S, Hafenstein SL, Kostyuchenko VA, et al., "Structural Studies of the Giant Mimivirus" [article], doi:10.1371/journal.pbio.1000092, v7 n4 e92, PLoS Biology, 28 Apr 2009. 6 May 2009
18 May 2009
13 May 2009
J. L. Dickson et al., "Amazonian-aged fluvial valley systems in a climatic microenvironment on Mars: Melting of ice deposits on the interior of Lyot Crater" [abstract], doi:10.1029/2009GL037472, L08201 v 36, Geophysical Research Letters, 17 Apr 2009.
6 May 2009
Xiao C, Kuznetsov YG, Sun S, Hafenstein SL, Kostyuchenko VA, et al., "Structural Studies of the Giant Mimivirus" [article], doi:10.1371/journal.pbio.1000092, v7 n4 e92, PLoS Biology, 28 Apr 2009.
6 May 2009
A renowned physicist, Dyson was among nine distnguished scientists who spoke at a two-day public symposium sponsored by The Harvard-Smithsonian Center for Astrophysics and The Harvard Origins of Life Initiative, held during the Cambridge Science Festival. Others speakers included Harvard Astronomy Professor David Charbonneau (left), and University of Washington paleontologist Peter Ward (right). Panspermia was favorably mentioned by several of the speakers, including Dimitar Sasselov, who heads the Harvard Origins Initiative. Because impacts can launch life-bearing material into space, he said, "Panspermia is the future of the galaxy."
Crossroads: The Future of Human Life In The Universe Conference moderated by David Aguilar, 30 Apr - 2 May 2009. 28 April 2009
Crossroads: The Future of Human Life In The Universe Conference moderated by David Aguilar, 30 Apr - 2 May 2009.
28 April 2009
Inserting RNA molecules into an RNA First scenario without explaining how they got there seems to us an inadequate foundation for an origin theory. The RNA molecule is too complex, requiring assembly first of the monomeric constituents of RNA, then assembly of strings of monomers into polymers. As a random event without a highly structured chemical context, this sequence has a forbiddingly low probability and the process lacks a plausible chemical explanation, despite considerable effort to supply one.
In their Metabolism-First scenario a simplified version of the Krebs cycle originally ran backward, using carbon dioxide and hydrogen to produce water and acetate (right). They believe that this cycle could arise naturally, and could acquire "further elaborations" enabling it to produce more complex organic molecules. Hopefully, a way to exclude the harmful byproducts will become apparent, they note. Later the system could come under the control of RNA molecules and begin to resemble life as we know it. They suggest that, this way, "the early stages in the emergence of life are no more surprising, no more accidental, than water flowing downhill."
The hope is that when a full theory is available, we will see the formation of life as an inevitable outcome of basic thermodynamics, like the freezing of ice cubes or the formation of magnets.
We admire the optimism and imagination of origin-of-life theorists, but we have questions:
What Is Life? is a related local webpage.
The RNA World is our main webpage about origin-of-life theories.
The Second Law of Thermodynamics is a related local webpage.
Thanks, Stan Franklin.
23 April 2009
It's hard to imagine a planet's surface exhibiting handedness without the presence of self assembly, which is an essential component of life — Thom Germer, physicist, the National Institute of Standards and Technology. A team at NIST is working on a system for detecting life on other planets by looking at the light reflected from their surfaces. If the light exhibits a biased circular polarity, it is probably coming from living surfaces, they believe. They think this signal would be present even if the life there is chemically unlike Earthly life.
Chirality has already been studied in carbonaceous meteorites. In a recent study of six of them, all six contained amino acids that were predominantly left-handed, like Earthly life. We think NIST's logic for planets should apply to meteorites as well. The chiralty observed in them is easily understood if their parent bodies once harbored Earth-like life whose amino acid remnants still bear traces of left-handedness.
William Sparks et al., "Detection of circular polarization in light scattered from photosynthetic microbes" [Open Access abstract], doi:10.1073/pnas.0810215106, Proc. Natl Acad. Sci. USA, online 28 Apr 2009. 22 April 2009 22 April 2009
William Sparks et al., "Detection of circular polarization in light scattered from photosynthetic microbes" [Open Access abstract], doi:10.1073/pnas.0810215106, Proc. Natl Acad. Sci. USA, online 28 Apr 2009.
22 April 2009
22 April 2009
Complex organic molecules were once thought to come from only biological processes, so finding them in space, beginning in the 1960s, was a surprise. Now more than a hundred different ones have been observed, and nonbiological processes to explain them are being proposed. We think biological processes should be considered. Life is far more efficient than nonlife at making organic molecules.
R. Garrod et al., "First Detections of Interstellar Ethyl Formate and NPropyl Cyanide: Dust-Grain Chemistry Strikes Again," presented at The European Week of Astronomy & Space Science, University of Hertfordshire, UK, 21 Apr 2009. 17 April 2009
R. Garrod et al., "First Detections of Interstellar Ethyl Formate and NPropyl Cyanide: Dust-Grain Chemistry Strikes Again," presented at The European Week of Astronomy & Space Science, University of Hertfordshire, UK, 21 Apr 2009.
17 April 2009
DNA analysis reveals that the pool contains species similar to known marine microorganisms, but they must be ones that can survive "without the food and light sources available in the open ocean." By logic, the genetic programs enabling the necessary new metabolic processes must have become effective promptly when food and light were sealed out by the glacier. Otherwise — even if the various species could remain viable by going dormant — metabolism and evolution would cease. Their prompt availability suggests to us that the programs were pre-existing.
The research team wonders if similar life could survive, "perhaps even on other icy planets in the solar system such as below the Martian ice caps or in the ice-covered oceans of Jupiter's moon Europa." Why not?
Jill A. Mikucki et al., "A Contemporary Microbially Maintained Subglacial Ferrous 'Ocean'", doi:10.1126/science.1167350, p 397-400 v 324, Science, 17 Apr 2009. 12 April 2009
Jill A. Mikucki et al., "A Contemporary Microbially Maintained Subglacial Ferrous 'Ocean'", doi:10.1126/science.1167350, p 397-400 v 324, Science, 17 Apr 2009.
12 April 2009
Still, darwinists maintain that HGT is of minor importance among eukaryotes. But important examples have now been documented too often to keep count. The studied marine algae simply add to the evidence that HGT is crucial for eukaryotic evolution as well.
As genomic databases grow, darwinists expect the number of genes without known orthologs to decrease. This is not happening. Also, darwinists expect genes for given features to be found only in organisms that exhibit those features. Otherwise, the unnecessary genes would lack the pressure of natural selection and degrade. Moreover, they would never have had the benefit of natural selection to help them form in the first place. Yet many examples of such unnecessary genes have been documented. The recent analysis adds to that list.
In cosmic ancestry, all genes are very old. They would naturally be sometimes found in species that don't use them. Among eukaryotes, processes like gene conversion may help to preserve the silent genes from degradation. By HGT, species that can use them may eventually acquire the genes, and an evolutionary advance may ensue. We think the evidence supports this scenario. The recent analysis of marine algae does not surprise us.
Alexandra Z. Worden et al., "Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas" [abstract], doi:10.1126/science.1167222, p 268-272 v 324, Science, 10 Apr 2009. 7 April 2009
Alexandra Z. Worden et al., "Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas" [abstract], doi:10.1126/science.1167222, p 268-272 v 324, Science, 10 Apr 2009.
7 April 2009