Icons of ID: Deinococcus, ID’s appeal to ignorance

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Another example of a system that could not have evolved via Darwinian pathways is discussed at ISCID.

It is hard to imagine how such a character could have evolved by a Darwinian mechanism. Darwinism requires an environment wherein an organism gradually evolves. For organism to evolve they require some sort of selective constraint. Darwinian theory explains traits according to the best adapted in a particular environment, but a highly radioactive environment has simpley never been present on earth. This must certainly mystified Darwinists.

Luckily science is not constrained by one’s lack in imagination and has found some interesting clues as to plausible scenarios.

Lets first introduce this remarkable organism: Deinococcus radiodurans, also known as Conan the bacterium, is a unique bacterium which can survive extremely high radiation dosages. The question thus becomes, how could a bacterium develop such high tolerances to radiation, when such sources are absent in nature? Such is the argument which leads some to argue that Deinococcus could not have evolved via Darwinian pathways.

D. radiodurans was discovered in 1956 by A.W. Anderson at the Oregon Agricultural Experiment Station in Corvallis, Oregon. Experiments were being performed to determine if canned food could be sterilized using high doses of gamma radiation. A tin of meat was exposed to a dose of radiation that was thought to kill all known forms of life, but the meat subsequently spoiled. D. radiodurans was isolated from the meat.

Source

But such an argument overlooks a ‘minor detail’, namely that the ability to rebuild one’s genome originated from dealing with another challenge such as dehydration?

Thus, selective pressures for the evolution of the radiation-resistant phenotype must have come from other sources. Clues to the answer come from studies demonstrating that in addition to radiation-resistance, D. radiodurans is also resistant to damage from UV, oxidizing agents, electrophilic mutagens, nitrous acid and other chemicals, and desiccation 5,7,11,16. No thorough study has ever been conducted to locate the natural ecology of the bacteria; however, cultures have been isolated from granite outcrops in Antarctica to elephant trunks6,16. It is now thought that desiccation was the phenotype to which D. radiodurans evolved, as it causes very similar DNA damage to ionizing radiation6,18. This, the bacterium may have evolved such extraordinary properties serendipitously as a result of desiccation-resistance genes, which repair similar DNA damage caused by the two environmental agents. In addition, freezing or desiccating D. radiodurans cultures increases their radioactivity-resistance phenotype, providing further evidence for this hypothesis 19.

Deinococcus radiodurans: Does this Bug Wear a Lead Vest or what? by Robyn Seipp Microbiology and Immunology, University of British Columbia Submitted November 2002

Here we read that

With the above serving as informative background reference, one may now examine the intriguing array of captivating features that D. radiodurans have to offer. Among the many characteristics of D. radiodurans, a few of the most noteworthy include an extreme resistance to genotoxic chemicals, oxidative damage, high levels of ionizing and ultraviolet radiation, and dehydration. The ability to survive such extreme environments is attributed to D. radiodurans ability to repair damaged chromosomes. It is known that heat, dehydration and radiation causes double-strand breaks in chromosomal DNA. D. radiodurans will repair these chromosome fragments, usually within 12-24 hours, using a two-system process with the latter being the most crucial method. Initially, D. radiodurans use a process called single-strand annealing to reconnect some chromosome fragments.

and

Radioresistance of Deinococcus radiodurans: functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation. Mattimore V, Battista JR. J Bacteriol. 1996 Feb;178(3):633-7.

Forty-one ionizing radiation-sensitive strains of Deinococcus radiodurans were evaluated for their ability to survive 6 weeks of desiccation. All exhibited a substantial loss of viability upon rehydration compared with wild-type D. radiodurans. Examination of chromosomal DNA from desiccated cultures revealed a time-dependent increase in DNA damage, as measured by an increase in DNA double-strand breaks. The evidence presented suggests that D. radiodurans’ ionizing radiation resistance is incidental, a consequence of this organism’s adaptation to a common physiological stress, dehydration.

Just for Charlie this reference

xperiments in Digital Evolution by Christoph Adami and Claus O. Wilke

Some Relevant resources

Physiologic Determinants of Radiation Resistance in Deinococcus radiodurans, Amudhan Venkateswaran, Sara C. McFarlan, Debabrota Ghosal, Kenneth W. Minton, Alexander Vasilenko, Kira Makarova,Lawrence P. Wackett, and Michael J. Daly Applied and Environmental Microbiology, June 2000, p. 2620-2626, Vol. 66, No. 6

Genome of the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans Viewed from the Perspective of Comparative Genomics Kira S. Makarova, L. Aravind, Yuri I. Wolf, Roman L. Tatusov, Kenneth W. Minton, Eugene V. Koonin, and Michael J. Daly, Microbiology and Molecular Biology Reviews, March 2001, p. 44-79, Vol. 65, No. 1

Meet Conan the Bacterium Humble microbe could become “The Accidental (Space) Tourist”

World’s Toughest Bacterium Has a Taste for Waste

Deinococcus radiodurans

Witches’ Brew of Weird Bugs

Proteome analysis of Deinococcus radiodurans

Unlocking radiation resistance mechanisms: still a long way to go Narumi I TRENDS IN MICROBIOLOGY 11 (9): 422-425 SEP 2003

S. Levin-Zaidman, J. Englander, E. Shimoni, AK. Sharma, KW. Minton, Minsky A. Ringlike structure of the Deinococcus radiodurans genome: A key to radioresistance?. SCIENCE 299 (5604): 254-256 JAN 10 2003

Robyn Seipp, Deinococcus radiodurans: Does this Bug Wear a Lead Vest or what? BioTeach Journal Vol. 1 Fall 2003

Levin-Zaidman S, Englander J, Shimoni E, Sharma AK, Minton KW, Minsky A. Ringlike structure of the Deinococcus radiodurans genome: a key to radioresistance? Science. 2003 Jan 10;299(5604):254-6.

The bacterium Deinococcus radiodurans survives ionizing irradiation and other DNA-damaging assaults at doses that are lethal to all other organisms. How D. radiodurans accurately reconstructs its genome from hundreds of radiation-generated fragments in the absence of an intact template is unknown. Here we show that the D. radiodurans genome assumes an unusual toroidal morphology that may contribute to its radioresistance. We propose that, because of restricted diffusion within the tightly packed and laterally ordered DNA toroids, radiation-generated free DNA ends are held together, which may facilitate template-independent yet error-free joining of DNA breaks.

Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev. 2001 Mar;65(1):44-79.

The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other bacteria, the D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats. In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism.

Griffiths, E., Gupta, R. S. (2004). Distinctive Protein Signatures Provide Molecular Markers and Evidence for the Monophyletic Nature of the Deinococcus-Thermus Phylum. J. Bacteriol. 186: 3097-3107

The Deinococcus-Thermus group of species is currently recognized as a distinct phylum solely on the basis of their branching in 16S rRNA trees. No unique biochemical or molecular characteristics that can distinguish this group from all other bacteria are known at present. In this work, we describe eight conserved indels (viz., inserts or deletions) in seven widely distributed proteins that are distinctive characteristics of the Deinococcus-Thermus phylum but are not found in any other group of bacteria. The identified signatures include a 7-amino-acid (aa) insert in threonyl-tRNA synthetase, 1- and 3-aa inserts in the RNA polymerase ß’ subunit, a 5-aa deletion in signal recognition particle (Ffh/SR54), a 2-aa insert in major sigma factor 70 (70), a 2-aa insert in seryl-tRNA synthetase (SerRS), a 1-aa insert in ribosomal protein L1, and a 2-aa insert in UvrA homologs. By using PCR primers for conserved regions, fragments of these genes were amplified from a number of Deinococcus-Thermus species, and all such fragments (except SerRS in Deinococcus proteolyticus) were found to contain the indicated signatures. The presence of these signatures in various species from all three known genera within this phylum, viz., Deinococcus, Thermus, and Meiothermus, provide evidence that they are likely distinctive characteristics of the entire phylum which were introduced in a common ancestor of this group. The signature in SerRS, which is absent in D. proteolyticus, was likely introduced after the branching of this species. Phylogenetic studies as well as the nature of the inserts in some of these proteins (viz., 70 and SerRS) also support a sister group relationship between the Thermus and the Meiothermus genera. The identified signatures provide strong evidence for the monophyletic nature of the Deinococcus-Thermus phylum. These molecular markers should prove very useful in the identification of new species related to this group.

Samuel Karlin and Jan Mrázek Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implications for resistance to ionizing radiation damage PNAS April 24, 2001 vol. 98 no. 9 5240-5245

Gupta RS, Johari V. Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-thermus group and cyanobacteria. J Mol Evol. 1998 Jun;46(6):716-20.

A number of proteins have been identified that contain prominent sequence signatures that are uniquely shared by the members of the Deinococcus-Thermus genera and the cyanobacterial species but which are not found in any of the other eubacterial or archaebacterial homologs. The proteins containing such sequence signatures include (1) the DnaJ/Hsp40 family of proteins, (2) DNA polymerase I, (3) the protein synthesis elongation factor EF-Tu, and (4) the elongation factor EF-Ts. A strong affinity of the Deinococcus-Thermus species to cyanobacteria is also seen in the phylogenetic trees based on Hsp70 and DnaJ sequences. These results provide strong evidence of a close and specific evolutionary relationship between species belonging to these two eubacterial divisions.

8 Comments

Excellent article. This just goes to show, yet again, how evolution is far more clever and subtle than the creationists who make hand-waving appeals to incredulity and assume that their personal ignorance defines the limit of what nature can do. It further goes to show, I think, how creationism is a sterile methodology, a scientific dead-end, while evolutionary biology is alive and vibrant: while creationists seemingly have nothing better to do than sit around thinking of problems, real scientists are hard at work every day solving them. Evolution is science because it works: it really does explain things, in a consistent, comprehensive and testable fashion. It yields knowledge we did not previously possess. Creationism, whether the young-earth variety or the ID variety (though those two seem to be blending into each other lately), does not.

What the article tries to show is that ID proponents often have too narrow a view of evolutionary pathways. If the function itself is not under direct control of natural selection then it cannot have arisen via Darwinian pathways. What at first may appear to be simple processes (variation and selection) can have a lot of interesting possibilities, making the outcome far more interesting than when viewed from a simplistic interpretation.

A great response that illustrates the dangers of using “an inability to imagine’ as the basis of a scientific argument. One can be forgiven in thinking that the “researchers” at ISCID never actually looked at the available literature (much less used their own imagination).

ID creationists have lost faith in the scientific method (for whatever reason); sadly they attempt to replace it with an ideology that is demonstrably less fruitful in terms of promoting understanding or human well being.

ID creationists have lost faith in the scientific method

Assuming they ever had such faith. In general, they tend to place faith in select books written by anonymous primitives, not knowledge produced by modern exceptionally well-trained scientists.

I’d say that in some ironic way Creationists are reinventing the scientific method under the name ID. Since ID is nothing more than finding falsifications, it is very similar to the scientific method. Of course some ID proponents seem to go too far in confusing evidence against as evidence in favor of ID.

ID certainly appeals to ignorants.

Creationists (including ID types) don’t lack imagination. They simply “backend load” it. Science “fontend loads” the imagination (finding all the possiblities). Creationists begin with a conclusion and imagine all the ways to defend it.

Adam Marczyk Wrote:

Evolution is science because it works: it really does explain things, in a consistent, comprehensive and testable fashion. It yields knowledge we did not previously possess. Creationism, whether the young-earth variety or the ID variety (though those two seem to be blending into each other lately), does not.

I detect 3 trends: Classic YECs are borrowing some ID-speak, abandoning some of their more absurd YE arguments, yet are less critical of OECs.” “Hard” IDers are less critical and condescending toward YECs than before. And a hybrid that I call “postmodern synthesis” seems to be “evolving” at least among Talk Origins posters and amateur websites.

Les Lane Wrote:

Creationists (including ID types) don’t lack imagination. They simply “backend load” it. Science “frontend loads” the imagination (finding all the possiblities). Creationists begin with a conclusion and imagine all the ways to defend it.

Classic creationists begin with a conclusion, but IDers are much more slippery. Their own default conclusion is simply “anything but ‘Darwinism’.” Since evolution is not their caricature of “Darwinism,” they don’t really dispute it at all. But they certainly make it easy for the audience to gravitate to the conclusion it wants, be it YEC, one of the OECs, panspermia, etc. And for all their pretense of “critical analysis,” ID promoters do nothing to encourage debate among the mutually contradictory alternative “theories,” even though they seem to know that they have all failed.

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This page contains a single entry by PvM published on July 11, 2004 2:05 PM.

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