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Something to Scratch Your Head About

At PhysOrg they have a blurb about a paper showing that an organism that is 99.99% (!!) identical has, nevertheless, found a way of dealing with the presence of Uranium in completely different ways. Absolutely fascinating!

Obviously we’re dealing with two very different environments—one is in a volcanic spring, and the other is atop a pile of uranium waste apparently. One is liquid-based, the other land-based.

What I suspect has happened—keeping Behe’s Edge of Evolution in mind—is that two different parts of the genome have had to make their own respective a.a. substitutions (2? 3?), since the ‘solution’ in water most likely has different constraints than the ‘solution’ for an atmosphere-based form of the same organism.

Only detailed whole-genome analysis will uncover this. It should be interesting to see how well Behe’s EoE results hold up (i.e., 2-4 a.a.s) against such a detailed analysis. If they do, maybe even evolutionary biologists (otherwise known as “Darwinists”) will start paying attention.

In the meantime, that’s my best guess. Anyone else have some hypotheses?

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12 Responses to Something to Scratch Your Head About

  1. evolutionary biologists (otherwise known as “Darwinists”)

    Now now, there’s always Todd Wood and perhaps Richard Sternberg (not sure where he falls). I expect that if the field ever embraced design wholeheartedly, evolutionary biology would become a much more useful science by understanding the limits of what evolution can and cannot accomplish. The problem comes when it’s shoe-horned into a biological theory-of-everything.

  2. Well, although I don’t know much about Archaea in particular, I do know that this detoxification of poisonous heavy metals and acids from the earth falls in line with the evidence for bacteria ‘terra-forming’ the primeval earth from a toxic wasteland into a place suitable to host advanced life.

    Notes:

    The Microbial Engines That Drive Earth’s Biogeochemical Cycles – Falkowski 2008
    Excerpt: Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides. –
    Paul G. Falkowski – Professor Geological Sciences – Rutgers

    evidence for ancient ‘sulfate reducing’ bacteria has been discovered alongside the evidence for ancient photosynthetic bacteria in the oldest sedimentary rocks, (rocks formed underwater), ever found on earth:

    When Did Life First Appear on Earth? – Fazale Rana – December 2010
    Excerpt: The primary evidence for 3.8 billion-year-old life consists of carbonaceous deposits, such as graphite, found in rock formations in western Greenland. These deposits display an enrichment of the carbon-12 isotope. Other chemical signatures from these formations that have been interpreted as biological remnants include uranium/thorium fractionation and banded iron formations. Recently, a team from Australia argued that the dolomite in these formations also reflects biological activity, specifically that of sulfate-reducing bacteria.
    http://www.reasons.org/when-di.....pear-earth

    On the third page of this following site there is a illustration that shows some of the necessary, interdependent, ‘biogeochemical web’ of the different types of bacterial life on the early Earth.,,,

    Microbial Mat Ecology – Image on page 92 (third page down)
    http://www.dsls.usra.edu/biolo.....nit2.2.pdf

    Sulfate-reducing bacteria helped prepare the earth for advanced life by detoxifying the primeval earth and oceans of poisonous levels of heavy metals while depositing them as relatively inert metal ores. Metal ores which are very useful for modern man, as well as fairly easy for man to extract today (mercury, cadmium, zinc, cobalt, arsenic, chromate, tellurium and copper to name a few). To this day, sulfate-reducing bacteria maintain an essential minimal level of these heavy metals in the ecosystem which are high enough so as to be available to the biological systems of the higher life forms that need them yet low enough so as not to be poisonous to those very same higher life forms.

    Bacterial Heavy Metal Detoxification and Resistance Systems:
    Excerpt: Bacterial plasmids contain genetic determinants for resistance systems for Hg2+ (and organomercurials), Cd2+, AsO2, AsO43-, CrO4 2-, TeO3 2-, Cu2+, Ag+, Co2+, Pb2+, and other metals of environmental concern.,, Recombinant DNA analysis has been applied to mercury, cadmium, zinc, cobalt, arsenic, chromate, tellurium and copper resistance systems.
    http://www.int-res.com/article.....26p203.pdf

    The role of bacteria in hydrogeochemistry, metal cycling and ore deposit formation:
    Textures of sulfide minerals formed by SRB (sulfate-reducing bacteria) during bioremediation (most notably pyrite and sphalerite) have textures reminiscent of those in certain sediment-hosted ores, supporting the concept that SRB may have been directly involved in forming ore minerals.
    http://www.goldschmidt2009.org...../A1161.pdf

    Researchers Identify Mysterious Life Forms in the Extreme Deep Sea
    Excerpt: Xenophyophores are noteworthy for their size, with individual cells often exceeding 10 centimeters (4 inches), their extreme abundance on the seafloor and their role as hosts for a variety of organisms.,,, The researchers spotted the life forms at depths up to 10,641 meters (6.6 miles) within the Sirena Deep of the Mariana Trench.,,, Scientists say xenophyophores are the largest individual cells in existence. Recent studies indicate that by trapping particles from the water, xenophyophores can concentrate high levels of lead, uranium and mercury,,,
    http://www.sciencedaily.com/re.....165037.htm

    Man has only recently caught on about this ancient detoxification ability of bacteria:

    What is Bioremediation? – video
    http://www.youtube.com/watch?v=pSpjRPWYJPg

    Metal-mining bacteria are green chemists – Sept. 2010
    Excerpt: Microbes could soon be used to convert metallic wastes into high-value catalysts for generating clean energy, say scientists writing in the September issue of Microbiology.
    http://www.physorg.com/news202618665.html

    At Least 200,000 Tons of Oil and Gas from Deepwater Horizon Spill Consumed by Gulf Bacteria – Sept. 11, 2012
    Excerpt: Researchers from the University of Rochester and Texas A&M University have found that, over a period of five months following the disastrous 2010
    Deepwater Horizon explosion and oil spill, naturally-occurring bacteria that exist in the Gulf of Mexico consumed and removed at least 200,000 tons of oil and natural gas that spewed into the deep Gulf from the ruptured well head.
    http://www.sciencedaily.com/re.....125315.htm

  3. It is simply incredible how fined tuned some of these detoxification bacteria are

    Planet’s Nitrogen Cycle Overturned – Oct. 2009
    Excerpt: “Ammonia is a waste product that can be toxic to animals.,,, archaea can scavenge nitrogen-containing ammonia in the most barren environments of the deep sea, solving a long-running mystery of how the microorganisms can survive in that environment. Archaea therefore not only play a role, but are central to the planetary nitrogen cycles on which all life depends.,,,the organism can survive on a mere whiff of ammonia – 10 nanomolar concentration, equivalent to a teaspoon of ammonia salt in 10 million gallons of water.”
    http://www.sciencedaily.com/re.....132656.htm

    Engineering and Science Magazine – Caltech – March 2010
    Excerpt: “Without these microbes, the planet would run out of biologically available nitrogen in less than a month,” Realizations like this are stimulating a flourishing field of “geobiology” – the study of relationships between life and the earth. One member of the Caltech team commented, “If all bacteria and archaea just stopped functioning, life on Earth would come to an abrupt halt.” Microbes are key players in earth’s nutrient cycles. Dr. Orphan added, “…every fifth breath you take, thank a microbe.”
    http://www.creationsafaris.com.....#20100316a

    As well, in conjunction with bacteria, geological processes helped detoxify the earth of dangerous levels of metal and depositing them as useful ores:

    The Concentration of Metals for Humanity’s Benefit:
    Excerpt: They demonstrated that hydrothermal fluid flow could enrich the concentration of metals like zinc, lead, and copper by at least a factor of a thousand. They also showed that ore deposits formed by hydrothermal fluid flows at or above these concentration levels exist throughout Earth’s crust. The necessary just-right precipitation conditions needed to yield such high concentrations demand extraordinary fine-tuning. That such ore deposits are common in Earth’s crust strongly suggests supernatural design.
    http://www.reasons.org/TheConc.....tysBenefit

    And on top of the fact that poisonous heavy metals on the primordial earth were brought into ‘life-enabling’ balance by complex biogeochemical processes, there was also an explosion of minerals on earth which were a result of that first life, as well as being a result of each subsequent ‘Big Bang of life’ there afterwards.

    Newly Discovered Bacterium Forms Intracellular Minerals – May 11, 2012
    Excerpt: A new species of photosynthetic bacterium has come to light: it is able to control the formation of minerals (calcium, magnesium, barium and strontium carbonates) within its own organism. ,, carbonate rocks that date back some 3.5 billion years and are among the earliest traces of life on Earth.
    (Calcium carbonate, of which chalk, limestone and marble are made, also makes up corals, shells of snails and other animals, and stromatolites. Strontium Carbonate is used in Ceramics, Pyrotechnics, Electronics and metallurgy. Barium carbonate is widely used in the ceramics industry as an ingredient in glazes. It acts as a flux, a matting and crystallizing agent and combines with certain colouring oxides to produce unique colours not easily attainable by other means. In the brick, tile, earthenware and pottery industries barium carbonate is added to clays to precipitate soluble salts. Magnesium carbonate also has several important uses for man.)
    http://www.sciencedaily.com/re.....101352.htm

    The Creation of Minerals:
    Excerpt: Thanks to the way life was introduced on Earth, the early 250 mineral species have exploded to the present 4,300 known mineral species. And because of this abundance, humans possessed all the necessary mineral resources to easily launch and sustain global, high-technology civilization.
    http://www.reasons.org/The-Creation-of-Minerals

    “Today there are about 4,400 known minerals – more than two-thirds of which came into being only because of the way life changed the planet. Some of them were created exclusively by living organisms” – Bob Hazen – Smithsonian – Oct. 2010, pg. 54

    To put it mildly, this minimization of poisonous elements, and ‘explosion’ of useful minerals, and deposits of useful ores, is strong evidence for Intelligently Designed terra-forming of the earth that ‘just so happens’ to be of great benefit to modern man.

    Verse and music:

    Isaiah 45:18-19
    For thus says the Lord, who created the heavens, who is God, who formed the earth and made it, who established it, who did not create it in vain, who formed it to be inhabited: “I am the Lord, and there is no other. I have not spoken in secret, in a dark place of the earth; I did not say to the seed of Jacob, ‘seek me in vain’; I, the Lord speak righteousness, I declare things that are right.”

    Casting Crowns – Until The Whole World Hears W/Lyrics
    http://www.youtube.com/watch?v=C9jVK9cZ2aw

  4. PaV, of related interest to Behe’s ‘EoE’:

    Innovation or Renovation? By Ann Gauger – Sept. 24, 2012
    Excerpt: But how significant was this innovation (citrate; Lenski) ? In his paper in Quarterly Review of Biology, Dr. Michael Behe pointed out that E. coli was already capable of using citrate for anaerobic growth (when no oxygen was available). He postulated that a change in gene regulation could turn on citrate transport and permit growth on citrate under aerobic conditions.
    After an enormous amount of work, having sequenced the genomes of many clones along the lineages that led to the ability to use citrate, as well as lineages that never did, and testing the phenotypes of identified mutations, Blount et al. have now reported that Behe was largely right. The key innovation was a shift in regulation of the citrate operon, caused by a rearrangement that brought it close to a new promoter.
    The new trait additionally required one or two pre-adaptive steps that could not be definitively identified, perhaps because of variable or weak phenotypic effects, perhaps because of epistatic interactions. Once in place though, those mutations enabled the next step, a duplication of the citrate operon that moved it next to another promoter, enabling the aerobic transport of citrate and its metabolism.
    The total number of mutations postulated for this adaptation is two or three, within the limits proposed for complex adaptations by Axe [2010] and Behe in Edge of Evolution. Because the enabling pre-adaptive mutations could not be identified, though, we don’t know whether this was one mutation, a simple step-wise series of adaptive mutations, or a complex adaptation requiring one or two pre-adaptations before the big event.
    But does this adaptation constitute a genuine innovation? That depends on the definition of innovation you use. It certainly is an example of reusing existing information in a new context, thus producing a new niche for E coli in lab cultures. But if the definition of innovation is something genuinely new, such as a new transport molecule or a new enzyme, then no, this adaptation falls short as an innovation. And no one should be surprised.
    http://www.biologicinstitute.o.....ation?og=1

  5. BA77

    If I’m reading the paper right, it took 30,000 generations to evolve one adaptive mutation to nylonase for the E.Coli. Considering the amount of differences between humans and chimpanzees, how many generations would it take to evolve them? Also taking into account the time span of 6,000,000 years, when humans and chimps diverged, to 150,000 years when homo sapiens appeared. Wouldn’t there have to be at least one adaptive mutation every generation that would work itself into the population? What would the odds of that be considering that neutral and harmful mutations would also take place? Of course humans could also evolve differently than E. Coli.

  6. JLAfan2001, though I am not to adept at figuring those rates out from population genetics, Dr. Gauger has another paper along the same lines that may be exactly what you are looking for to answer your question:

    More from Ann Gauger on why humans didn’t happen the way Darwin said – July 2012
    Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population.
    You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect.
    Facing Facts
    But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes.
    http://www.uncommondescent.com.....rwin-said/

  7. OT: Dr. Wells gives some historical background as to why some neo-Darwinists are doing everything they can to discredit the recent ENCODE findings:

    Why All the Fuss Over Some Junk? – Jonathan Wells – September 25, 2012
    Excerpt: Some historical context might help. After James Watson and Francis Crick discovered the molecular structure of DNA in 1953, Crick announced that they had found “the secret of life,” a popular formulation of which became “DNA makes RNA makes protein makes us.” But biologists discovered that about 98% of our DNA does not code for protein, and in 1972 Susumu Ohno and David Comings independently used the term “junk” to refer to non-protein-coding DNA (though neither man excluded the possibility that some of it might turn out to be functional).
    Why didn’t biologists simply call non-protein-coding sequences “DNA of unknown function” rather than “junk DNA?” For some, it was because “junk DNA” seemed more suited to the defense of Darwinism and survival of the fittest. In 1976, Richard Dawkins wrote in The Selfish Gene that “the true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus [i.e., non-protein-coding] DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.”
    In 1980, W. Ford Doolittle and Carmen Sapienza wrote in Nature (284:601) that many organisms contain “DNAs whose only ‘function’ is survival within genomes,” and that “the search for other explanations may prove, if not intellectually sterile, ultimately futile.” In the same issue of Nature (284:604), Leslie Orgel and Francis Crick wrote that “much DNA in higher organisms is little better than junk,” and its accumulation in the course of evolution “can be compared to the spread of a not-too-harmful parasite within its host.” Since it is unlikely that such DNA has a function, Orgel and Crick concluded, “it would be folly in such cases to hunt obsessively for one.”
    Two biologists then wrote to Nature (285:617,618) expressing their disagreement. Thomas Cavalier-Smith considered it “premature” to dismiss non-protein-coding DNA as junk, and Gabriel Dover wrote that “we should not abandon all hope of arriving at an understanding of the manner in which some sequences might affect the biology of organisms in completely novel and somewhat unconventional ways.” Cavalier-Smith and Dover were not criticizing evolutionary theory; they were merely questioning the claim that non-protein-coding DNA is non-functional.
    After the rise of intelligent design (ID) in the 1990s, “junk DNA” became a favorite weapon against ID in the hands of some Darwinists, including Richard Dawkins and the four bloggers mentioned above. According to ID, it is possible to infer from evidence in nature that some features of the world, including some features of living things, are explained better by an intelligent cause than by unguided natural processes. The Darwinists’ argument was that an intelligent designer would not have filled our genomes with so much junk, but that it could have accumulated as an accidental by-product of unguided evolution. In 2004, Dawkins wrote in A Devil’s Chaplain that much of our genome “consists of multiple copies of junk, ‘tandem repeats,’ and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.” Dawkins suggested that creationists (among whom he included ID advocates) “might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.”
    Dawkins continued to rely on junk DNA in his 2009 book The Greatest Show on Earth: The Evidence for Evolution. “It is a remarkable fact,” he wrote, “that the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes.” In particular, pseudogenes “are genes that once did something useful but have now been sidelined and are never transcribed or translated.” Dawkins concluded: “What pseudogenes are useful for is embarrassing creationists. It stretches even their creative ingenuity to make up a convincing reason why an intelligent designer should have created a pseudogene… unless he was deliberately setting out to fool us.”
    But if most of our DNA is functional, as the ENCODE results suggest, then the “junk DNA” argument against ID collapses.
    So the four bloggers listed above are doing everything they can to discredit the ENCODE project’s estimate of functional DNA. Yet whatever the estimate may currently be, it is certain to increase with further research. In 2007, the ENCODE pilot project reported on the basis of about 200 datasets that our DNA is “pervasively transcribed,” suggesting functionality. The 2012 results, based on 1,640 datasets, documented that “the vast majority (80.4%) of the human genome” is biochemically functional in at least one cell type. But ENCODE has so far sampled only a fraction of the cell types in the human body.
    Clearly, we have a lot more to learn about our genome — but not if we start by assuming that most of it is junk.
    http://www.evolutionnews.org/2.....64721.html

  8. …unless he was deliberately setting out to fool us.

    Maybe he was deliberately setting out to let you fool yourself.

  9. OT:

    Cambrian Soft Animal Survived Unchanged 200 Million Years – Sept. 2012
    Excerpt: the fossil shows virtually no evolution for 200 million years: the authors said, “the morphology has not changed in any significant aspect.” If living tardigrades and velvet worms represent modern counterparts of lobopodia, then evolution within this phylum has been scant or non-existent for the whole duration of the fossil record from the lower Cambrian onward.
    http://crev.info/2012/09/cambr.....ion-years/

    This following video is interesting for it shows that some paleontologists have been less than forthright (misleading) in clearly naming fossils so as to reflect the stasis observed in the fossil record:

    Living Fossils, Evolution: The Grand Experiment, Episode 2
    http://www.youtube.com/watch?v=q7PdH3rwIL4

    Supplemental videos that may be of interest to some readers:

    Cambrian and Ediacara Biota – Animated Video Snapshot
    http://www.metacafe.com/w/8554429

    Exotic Cambrian Animals and Plants and Ediacaran biota- Animated videos
    http://www.lightproductionsvid.....imals.html

    Fossil Gallery – images of species from Cambrian period – Main Gallery
    The Main Gallery is a comprehensive source of information based on the latest scientific research covering the majority of species so far described from the Burgess Shale. It contains a growing collection of over 500 high resolution images representing 184 species in 135 genera. In addition, dozens of scientifically accurate drawings and breathtaking digital animations will allow you to visualize these organisms in three dimensions and see how they lived.
    http://burgess-shale.rom.on.ca.....pecies.php

    Anomalocaris – The largest predator of the Cambrian (3D Animation)
    http://burgess-shale.rom.on.ca.....ntro_1.php

    Virtual Sea Odyssey; Observe the creatures who lived in the Burgess Shale community from a “virtual submarine”. – video
    http://burgess-shale.rom.on.ca/en/sea-odyssey/

  10. BA:

    Thank you for the very interesting quotes of Gauger! They are absolutely pertinent, I believe, to the long discussion on the other thread with the TSZ field. And Behe, as usual, had seen it all in advance.

    There is another point that it is interesting to stress: bacteria are not only extremely numerous and fast replicatiing (they are indeed the most successful replicators on our planer, neo darwinian evolution could really stop at them instead of taking the pain of “evolving” big, slow, frail and inefficient replicators like us!); they are also extremely adaptive, much more probably that more complex being.

    Bacteria seem to act like a collective entity, spread on all our planet (see Shapiro). And hey have specific systems, like the plasmid system, that sepcifically add very high HGT efficiency to the process. It’s not a case, for instance, that thewhole nylonase process took place at plasmid level.

    Adaptation by existing intelligent algorithms needs to be studied better. We know how powerful it can be. We have the wonderful example of antybody maturation for that, perhaps the best example of bottom up protein engineering in natural biology. But even that cannot certainly create a new protein domain or function: it needs an existing starting point that already has the function (the initial antibody with weak affinity for the pertinent epitope, which was part of the existing low affinity repertoire). Through very organized and intelligent algorithms of targeted mutation and (indirect) intelligent selection, the process achieves in a few months a small engineering miracle: high affinity antibodies for the epitope.

    But, even in its brilliancy, this is a tweaking too: the structure of the molecule remains the same, only a few useful mutations are added to the active size to tweak its biochemical affinity to the target epitope, and the function remains the same (binding to that epitope).

  11. gpuccio, you may be very interested in this following video:

    the ‘social networks’ of bacteria are very sophisticated and certainly defy any coherent explanation from the simplistic reductive (i.e. bottom up) materialistic narrative of neo-Darwinism:

    Learning from Bacteria about Social Networks – video
    Description: Bacteria do not store genetically all the information required to respond efficiently to all possible environmental conditions. Instead, to solve new encountered problems (challenges) posed by the environment, they first assess the problem via collective sensing, then recall stored information of past experience and finally execute distributed information processing of the 109-12 bacteria in the colony,,, I will show illuminating movies of swarming intelligence of live bacteria in which they solve optimization problems for collective decision making that are beyond what we, human beings, can solve with our most powerful computers.
    http://www.youtube.com/watch?v=yJpi8SnFXHs

  12. I was hoping for something to scratch my behind about.

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