'Junk DNA' Cell biology Ecology News

A new ocean mystery: Bacterium allegedly doesn’t make sense

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DNA of bacteria crucial to ecosystem defies explanation
Trichodesmium/John Waterbury,Woods Hole

Life forms always make sense. Some theories do not.

From Phys.org:

By sequencing multiple Trichodesmium genomes—and using a wide variety of samples to ensure that there was no error—researchers found that only about 63 percent of the bacteria’s genome is expressed as protein. That’s an incredibly low amount for a bacterium and unheard of for a free-living oligotroph.

(lives under very poor conditions, in this case it thrives massively in barren stretches of the ocean)

“The unique evolutionary path reflected in this genome contradicts nearly all accounts of free-living microbial genome architectures to date,” said lead author Nathan Walworth, a Ph.D. candidate at USC. “Different evolutionary paths are foundational to all arenas of biology, including biotechnology, so it is important for the field to be cognizant of different paths a living organism can take to achieve ecological success.”

More.

Most bacteria don’t have much non-coding DNA (called by Darwin’s followers “junk DNA”), the theory being

Oligotrophs, in particular, shun non-coding DNA, possibly because of the high energy-cost of living in a harsh environment. Cells need every ounce of energy simply to replicate and survive.

Apparently not. Or not necessarily.

The rest of the media release is a treat, as various Darwinians try their hand at explaining this according to their sacred knowledge. More.

13 Replies to “A new ocean mystery: Bacterium allegedly doesn’t make sense

  1. 1
    bornagain77 says:

    That’s almost as interesting as these bacteria:

    Extreme Genome Repair – 2009
    Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.,,,
    http://www.ncbi.nlm.nih.gov/pm.....MC3319128/

    In the lab, scientists coax E. coli to resist radiation damage – March 17, 2014
    Excerpt: ,,, John R. Battista, a professor of biological sciences at Louisiana State University, showed that E. coli could evolve to resist ionizing radiation by exposing cultures of the bacterium to the highly radioactive isotope cobalt-60. “We blasted the cultures until 99 percent of the bacteria were dead. Then we’d grow up the survivors and blast them again. We did that twenty times,” explains Cox.
    The result were E. coli capable of enduring as much as four orders of magnitude more ionizing radiation, making them similar to Deinococcus radiodurans, a desert-dwelling bacterium found in the 1950s to be remarkably resistant to radiation. That bacterium is capable of surviving more than one thousand times the radiation dose that would kill a human.
    http://www.news.wisc.edu/22641

    Pond scum smashes genome into over 225k parts, then rebuilds it – Sept. 9, 2014
    Excerpt: The pond-dwelling, single-celled organism Oxytricha trifallax has the remarkable ability to break its own DNA into nearly a quarter-million pieces and rapidly reassemble those pieces when it’s time to mate,
    http://www.uncommondescent.com.....builds-it/

    Imagine your computer breaking its hard drive into a quarter million pieces and then putting it back together again. That would be roughly similar to what is happening here (save for the fact that the computer cannot replicate itself. 🙂

    Of related interest to bacteria (and viruses) violating the supposed coding rules that are in evolutionary theory:

    A glimpse into nature’s looking glass — to find the genetic code is reassigned: Stop codon varies widely – May 22, 2014
    Excerpt: While a few examples of organisms deviating from this canonical code had been serendipitously discovered before, these were widely thought of as very rare evolutionary oddities, absent from most places on Earth and representing a tiny fraction of species. Now, this paradigm has been challenged by the discovery of large numbers of exceptions from the canonical genetic code,,,
    Approximately 99% of all microbial species on Earth fall in this category, defying culture in the laboratory but profoundly influencing the most significant environmental processes from plant growth and health, to the carbon and other nutrient cycles on land and sea, and even climate processes.,,,
    “We were surprised to find that an unprecedented number of bacteria in the wild possess these codon reassignments, from “stop” to amino-acid encoding “sense,” up to 10 percent of the time in some environments,” said Rubin.
    Another observation the researchers made was that beyond bacteria, these reassignments were also happening in phage, viruses that attack bacterial cells.,,,
    The punch line, Rubin said, is that the dogma is wrong.
    “Phage apparently don’t really ‘care’ about the codon usage of the host.
    http://www.sciencedaily.com/re.....141422.htm

    Oh well, evolution must just be smarter than we thought so as to be able to program multiple different codes like that. Or maybe,,,

    “Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source — from a mind or personal agent.”
    (Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).)

  2. 2
    bornagain77 says:

    OT:

    Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes
    Matilda S. Newton , Vickery L. Arcus , Wayne M. Patrick – April 2015
    http://rsif.royalsocietypublis.....7/20150036

    Research prompts rethink of enzyme evolution – April 28, 2015
    Excerpt: Biochemist Dr Wayne Patrick says that people tend to imagine evolution as a slow and steady march from barely functional life forms in the primordial soup, towards a modern-day pinnacle of near perfection.
    “When it comes to enzyme evolution, this is also the textbook version of the events occurring at the molecular level; a smooth and steady trajectory, from barely functional primordial catalysts to the highly active and specific enzymes that we observe today. However, upon closer examination, the reality appears quite different.”
    In an article appearing in the UK Journal of the Royal Society Interface, Dr Patrick, his PhD student Matilda Newton and their collaborator Professor Vic Arcus (Waikato), summarise experimental data that challenges the prevailing thinking.
    “We discuss examples in which enzymes have evolved with lightning speed—over years, rather than eons—and provide evidence that many enzymes were better catalysts in the ancient past than they are today.”
    One example of extraordinarily rapid evolution is the emergence of enzymes that modern-day bacteria use to break down human-made antibiotics and pesticides, he says.
    http://phys.org/news/2015-04-p.....ution.html

    One problem with their claim that antibiotics give proof for the rapid evolution of ‘new’ proteins/enzymes is that antibiotic resistance is ancient and is therefore not proof of anything ‘new’ being evolved within bacteria.
    Another problem with their antibiotic resistant example is that antibiotic resistant bacteria are ‘less fit’ than their unresistant counterparts when the antibiotic is removed from the environment.
    The same principle holds for pesticide resistant insects.
    Thus, minus their claimed evidence for ‘new’ proteins/enzymes evolving rapidly, all they have really established is that many enzymes were better catalysts in the ancient past than they are today. Which is a fact that even Young Earth Creationists would readily concede.
    Notes:

    (Ancient) Cave bacteria resistant to antibiotics – April 2012
    Excerpt: Antibiotic-resistant bacteria cut off from the outside world for more than four million years have been found in a deep cave. The discovery is surprising because drug resistance is widely believed to be the result of too much treatment.,,, “Our study shows that antibiotic resistance is hard-wired into bacteria. It could be billions of years old, but we have only been trying to understand it for the last 70 years,” said Dr Gerry Wright, from McMaster University in Canada, who has analysed the microbes.
    http://www.scotsman.com/news/h.....1-2229183#

    The Diseaseome Could Take Medicine Beyond the Genome By Cynthia Graber on Thu, 09 Oct 2014
    Excerpt: Today, antibiotic resistance is thought to emerge because, scientists have believed, there are a few bacteria in a given community that are naturally resistant to a drug, and they thrive after the drug kills off the bacteria’s brethren. But instead, as Collins’ research has demonstrated, antibiotics themselves induce mutations, leading to antibiotic-resistant bacteria.
    http://www.pbs.org/wgbh/nova/n.....-medicine/

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    https://www.youtube.com/watch?v=rYaU4moNEBU

    Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology
    Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution.
    http://www.evolutionnews.org/2.....s_wro.html

  3. 3
    bornagain77 says:

    OT: How Cells Keep Right-Handed Amino Acids Out – April 29, 2015
    Excerpt: One of the wonders of life at the molecular scale — a fact that defies chance — is the purity of left-handed amino acids in proteins. Without this “homochirality,” as it is known, proteins would never fold properly into the functional structures that make life possible.
    Theoretically, life could be built backwards, using only right-handed amino acids — as long as the mixture is pure. But the cell’s translation machinery (TM) would have to be redesigned to accommodate the change. (Note: left-handed amino acids are prefixed by L- and right-handed ones by D-).
    Whenever amino acids form naturally, they occur in “racemic” mixtures of L- and D- “isoforms.” It’s been a long-standing mystery in the origin-of-life community how cells first discriminated between them. The physical and thermodynamic properties of L- and D- forms are identical; the only way they can be discriminated in the lab is by seeing which way they rotate polarized light. How could a primordial soup lead to a homochiral protocell? Unless the TM already existed to discriminate between the isoforms, the probability of getting a usable protein of any functional length is vanishingly small.,,,
    ,,,(it is found that) the ribosome itself participates in the rejection of D-amino acids.,,,
    “Collectively, these methods have allowed us to conclusively demonstrate that the ribosome itself discriminates the chirality of the amino acid”,,,
    Natural selection could not have operated before the first accurately replicating system (i.e. ribosome) arose. But without this complex proofreading and error-correcting equipment (made up of proteins and RNA) already in operation, functional proteins would be impossible. So how did the first proteins (and nucleic acids, which are also homochiral) arise from a primordial soup of racemic ingredients? The short answer is, they didn’t. The improbability of that occurring exceeds the Universal Probability Bound. An inference to intelligent causation is thus warranted.
    http://www.evolutionnews.org/2.....95601.html

  4. 4
    drc466 says:

    BA77,
    Great links. I vote we rename D. Radiodurans “Deadpool”.

  5. 5
    bornagain77 says:

    drc466, I had to look up your “Deadpool” reference

    Deadpool is a disfigured and mentally unstable mercenary with the superhuman ability of an accelerated healing factor.,,,
    Created by artist Rob Liefeld and writer Fabian Nicieza, Deadpool made his first appearance in the pages of The New Mutants #98, cover dated February 1991.
    http://en.wikipedia.org/wiki/Deadpool

    Works for me,,, Perhaps a theme song to boot?

    lyric from madness

    “I, I can’t get these memories out of my mind
    And some kind of madness has started to evolve”

    Muse – Madness (HD) Lyrics
    https://www.youtube.com/watch?v=Ek0SgwWmF9w

  6. 6
    ppolish says:

    More non coding DNA = more complex, right? I bet this bacterium was designed with a more complex than average purpose.

  7. 7
    Querius says:

    All we really know about this mysterious bacterium and its large proportion of non-coding DNA is that it once again demonstrates exactly what was expected by evolutionists. 😉

    -Q

  8. 8
    groovamos says:

    hee hee good one. It doesn’t take much to know everything – would be the scientific takeaway. I guess.

  9. 9
    Silver Asiatic says:

    From BA77’s link to Radiodurans:

    After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.

    Follow-up quiz:
    Q. How does radiodurans reassemble its genome?
    A. Miraculously

    Scientific proof that miracles happen- right there in a peer-reviewed paper from NIH.

  10. 10
    velikovskys says:

    SA:

    Scientific proof that miracles happen- right there in a peer-reviewed paper from NIH.

    God so loved the little D.radiodurans that He miraculously healed their little genes, interesting choice of miraculous intervention.

  11. 11
    Querius says:

    Lol, velikovskys. Silver Asiatic simply was noting the irony in the published paper.

    The amazing thing is the *design* of the code to be able to reassemble itself. It is an indication for people who think for themselves rather than simply rage at God, that there must be another mechanism accessible to or in control of DNA itself.

    -Q

  12. 12
    Silver Asiatic says:

    Thumbs up, Querius – and thank you for explaining that. 🙂

  13. 13
    Silver Asiatic says:

    vel

    God so loved the little D.radiodurans that He miraculously healed their little genes, interesting choice of miraculous intervention.

    I forgot to add that your skepticism would be understandable if the intervention of God was a rare thing. Then, why waste a rare act on such a tiny event. But if the action of God in nature is like a continual presence — that life itself is an ‘energy’ of God, sustained constantly that way … then it makes sense when we say that “God so loves his creation”.

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