J. Eukaryot. Microbiol., 57(1), 2010 pp. 1–2r 2009 The Author(s)Journal compilation r 2009 by the International Society of ProtistologistsDOI: 10.1111/j.1550-7408.2009.00459.x Introduction: Protistan Biology, Horizontal Gene Transfer, and Common Descent Uncover Faulty Logic in Intelligent Design1 Department of Biology, Roger Williams University, Bristol, Rhode Island 02809 THE International Society of Protistologists (ISOP) organized a randomly and that the emergence of biological diversity could not pre-meeting workshop entitled ‘‘Horizontal Gene Transfer and have happened since the formation of planet Earth, simply because Phylogenetic Evolution Debunk Intelligent Design,’’ as part of the fortuitous evolution would have taken longer to generate current 1st North American Section meeting held June 11–13, 2009, at biological complexity than the age of the Earth itself (problems with Roger Williams University, Bristol, RI, USA. This workshop fo- this logic are examined by Paz-y-Min˜o C. and Espinosa, 2009).
cused on the acceptance of Darwinian evolution in the United States Farmer and Habura (2009) challenge these ID premises by dissect- and the role of intelligent design (ID) in the ongoing controversy ing one of ID’s ‘‘Trojan Horses’’ (see Forrest and Gross 2004), the between scientific knowledge and popular belief. Intelligent design, a evolution of chloroquine resistance in the protistan pathogen Plasm- doctrine born in the 1980s, proposes that a ‘‘Designer’’ is responsible odium falciparum, which causes malaria. Studies have shown that in for the complexity in biological systems and that Darwinism cannot P. falciparum, two amino acid substitutions in a plasma membrane explain holistically the origin and evolution of the natural world, nor protein are implicated in the resistance to the antimalarial drug the intricate chemical assemblage of most organic structures (Forrest chloroquine (Martin and Kirk 2004). A prominent figure of ID, Dr.
and Gross 2007; Padian and Matzke 2009). The workshop empha- Michael Behe (2007), has compared and contrasted the evolution of sized how to communicate evolutionary principles to student and resistance to chloroquine by P. falciparum to the incapacity of hu- public audiences by using examples of protistan evolution.
mans to have developed resistance to P. falciparum. Behe (2007) Dr. Guillermo Paz-y-Min˜o C., University of Massachusetts- has arrived at the conclusion that, based on the time required for two Dartmouth, talked about the essence of science, evolution, and the interacting mutations to originate at random, ‘‘. . . no mutation that struggle with belief; Dr. Avelina Espinosa, Roger Williams Uni- is of the same complexity as chloroquine resistance in malaria arose versity, discussed how horizontal gene transfer (HGT) and eu- [has arisen] by Darwinian evolution in the line leading to humans in karyote metabolic pathways can be used to challenge ID; Dr.
the past ten million years.’’ Behe (2007) asserts that ‘‘. . . on aver- Mark Farmer, University of Georgia, analyzed how protistan cell age, for humans to achieve a mutation like this [ 5 analogous to biology and genetics provide examples to dismiss ID arguments; chloroquine resistance by P. falciparum] by chance, we would need and Dr. Andrea Habura, Wadsworth Center, highlighted strategies to wait a hundred million times ten million years. Since that is many to communicate evolutionary theory to skeptical audiences. In this times the age of the universe, it’s reasonable to conclude the fol- issue, the four participants summarize their presentations in two lowing: No mutation that is of the same complexity as chloroquine papers. In the first article, Using Protistan Examples to Dispel the resistance in malaria arose by Darwinian evolution in the line lead- Myths of Intelligent Design, Farmer and Habura offer a broad ing to humans in the past ten million years [the amount of time at- analysis of ID. In the second article, Integrating Horizontal Gene tributed to Hominid evolution, the taxonomic human family].’’ Transfer and Common Descent to Depict Evolution and Contrast According to Farmer and Habura (2009) and others (e.g. Miller it with ‘‘Common Design,’’ Paz-y-Min˜o C. and Espinosa discuss 2007, see also Paz-y-Min˜o C. and Espinosa, 2009) there is faulty a case study of protistan protein evolution.
logic in Behe’s (2007) view; he diminishes the editing role of natural Farmer and Habura (2009) describe the philosophical roots of ID selection over mutation rate, a process that expedites molecular and link it to creationist beginnings. They examine influential ID evolution, and which is responsible for the origin and emergence of literature, including Darwin’s Black Box (Behe 1996) and The Edge further biological complexity (Paz-y-Min˜o C. and Espinosa, 2009).
of Evolution (Behe 2007), to highlight three ID proposals. (1) Irre- Behe (2007) rejects naturalistic causation, or the interaction between ducible complexity, or the premise that biological systems are too mutation rate and natural selection, which is responsible for the complex to have evolved, via natural selection, from simpler to evolution of drug resistance in P. falciparum (Miller 2007), and he more complex forms (Forrest and Gross 2007; Padian and Matzke also invokes ‘‘design creationism’’ to account for significant mo- 2009); according to ID, a ‘‘Designer’’ must have designed funda- lecular change which, in his view, is statistically unlikely to reach mental biological processes based on irreducibly complex building high levels of complexity via Darwinian mechanisms. Interestingly, blocks (Behe 1996). (2) Undocumented biological speciation, or the Farmer and Habura (2009) counter the claim of irreducible com- assumption that speciation events have never been observed directly plexity by referring to evidence from two studies which demonstrate by scientists, nor could speciation have occurred purely by means of that a single amino acid substitution suffices to confer resistance to natural laws (Meyer 2004); the latter is based on the supposition that chloroquine in P. falciparum (Jiang et al. 2008; Lakshmanan et al.
evolution via natural selection is a ‘‘random’’ phenomenon and, 2005), implying that, in the natural world, there is room for ‘‘re- therefore, an ‘‘accidental’’ outcome. (3) Impossibility of evolution, ducible simplicity’’ ( 5 a single mutation can work and provide re- or the lack of geological time for complex evolution to occur (Behe sistance), the opposite of Behe’s conceptualization of nature. Farmer 2007), which also relies on the belief that natural selection operates and Habura’s article is also illustrative of how the malaria examplefits the process of speciation and the possibility of evolution (points2 and 3 above). Various pathogens cause human malaria, for ex- 1Introduction to the workshop: Horizontal Gene Transfer and Phylo- ample, P. falciparum and Plasmodium vivax, two separate and dis- genetic Evolution Debunk Intelligent Design, 1st International Society tinctive species of protists that cause different host responses due to of Protistologists—North American Section Meeting, June 11–13, 2009, their diverse virulence (Mu¨ller et al. 2009). Moreover, the occur- Roger Williams University, Bristol, RI, USA.
rence of specific types of malaria, not only in humans, but in other Corresponding Author: A. Espinosa, Department of Biology, Roger animals, including mammals and birds, suggests a broad adaptive Williams University, One Old Ferry Road, Bristol, Rhode Island02809—Telephone number: 1401 254 3137; FAX number: 1401 254 radiation pattern of Plasmodium species, which now parasitize hosts of distant phylogenetic backgrounds, a remarkable example of J. EUKARYOT. MICROBIOL., 57, NO. 1, JANUARY– FEBRUARY 2010 speciation and, therefore, classical Darwinian evolution (Roy and Andersson, J. O. 2009. Horizontal gene transfer between microbial Irimia 2008; Janssen et al. 2002; Ricklefs and Fallon 2002).
eukaryotes. In: Boekels Gogarten, M., Gogarten, J. P. & Olendzenski, Paz-y-Min˜o C. and Espinosa (2009) take this idea of common L. (ed.), Horizontal Gene Transfer: Genomes in Flux. Humana Press, descent further in their article on the interaction between HGT and common descent. These authors discuss how continuous lateral ex- Bapteste, E. & Boucher, Y. 2009. Epistemological impacts of horizontal gene transfer on classification in microbiology. In: Gogarten, M. B., change of genes, or HGT, in bacteria, Archaea, and Eukarya com- Gogarten, J. P. & Olendzenski, L. (ed.), Horizontal Gene Transfer: Ge- plicate the identification of a single origin and/or dichotomous nomes in Flux. Humana Press, New York. p. 55–72.
branching pattern during the evolution of unicellular life. These Behe, M. J. 1996. Darwin’s Black Box. Free Press, New York, 307pp.
authors indicate that phylogenies rarely include in their vertical Behe, M. J. 2007. The Edge of Evolution. Free Press, New York, 336 p.
representations of evolutionary history the significance of the lat- Doolittle, W. F. 1999. Phylogenetic classification and the universal tree.
eral acquisition of genetic material by organisms, a problem widely discussed in the recent literature (Andersson 2009; Bapteste and Doolittle, W. F. & Bapteste, E. 2007. Pattern pluralism and the tree of life Boucher 2009; Gogarten, Gogarten, and Olendzenski 2009). Var- hypothesis. Proc. Natl. Acad. Sci. USA, 104:2043–2049.
ious models have been suggested to account for the contribution of Farmer, M. A. & Habura, A. 2009. Using protistan examples to dispel the myths of intelligent design. J. Eukaryot. Microbiol., HGT to vertical evolution, including a ‘‘reticulated tree’’ or ‘‘net’’ (Doolittle 1999), which represents interconnected earliest stages of Forrest, B. & Gross, P. R. 2004. Creationism’s Trojan Horse: the wedge of life’s history; the ‘‘ring of life’’ (Rivera and Lake 2004), where a intelligent design. Oxford University Press, New York, 432 p.
‘‘ring’’ connects the origin of eukaryotes to a dual genetic merging, Forrest, B. C. & Gross, P. R. 2007. Biochemistry by design. Trends Bioc- via endosymbiosis, of eubacterial and archaebacterial genomes; the ‘‘symbiogenetic whole-organism model’’ (Margulis 2009; Mar- Gogarten, M. B., Gogarten, J. P. & Olendzenski, L. (ed.), 2009. Horizontal gulis et al. 2006), which posits that entire genomes of ‘‘partner or- Gene Transfer: Genomes in Flux. Humana Press, New York, 500 p.
ganisms’’ became integrated and that a serial symbiotic fusion of Janssen, C. S., Barrett, M. P., Turner, C. M. & Phillips, R. S. 2002. A large ancestral lineages gave rise to eukaryotic cells; and the ‘‘pattern gene family for putative variant antigens shared by human and rodentmalaria parasites. Proc. Biol. Sci., 269:431–436.
pluralism scheme’’ (Bapteste and Boucher 2009; Doolittle and Jiang, H., Patel, J. J., Yi, M., Mu, J., Ding, J., Stephens, R., Coopers, R. A., Bapteste 2007), which considers that organisms can overlap in var- Ferdig, M. T. & Su, X-Z. 2008. Genome-wide compensatory changes ious natural and non-exclusive taxonomic units, making vertical accompany drug-selected mutations in the Plasmodium falciparum crt inheritance part of the conceptual understanding of evolution, but not the end. Paz-y-Min˜o C. and Espinosa (2009) highlight that a Keeling, P. J. & Palmer, J. D. 2008. Horizontal gene transfer in eukaryotic bifurcated tree-like representation of evolutionary relations, linked evolution. Nat. Rev. Gen., 9:605–618.
by common ancestry—an idea conceptualized by Charles Darwin Lakshmanan, V., Bray, P. G., Verdier-Pinard, D., Johnson, D. J., Horrocks, in The Origin of the Species of 1859, seems better suited for mul- P., Muhle, R. A., Alakpa, G. E., Hughes, R. H., Ward, S. A., Krogstad, ticellular organisms, where vertical inheritance of genomes is of D. J., Sidhu, A. B. S. & Fidock, D. A. 2005. A critical role for PfCRTK76T in Plasmodium falciparum verapamil-reversible chloroquine re- larger magnitude than horizontally acquired genetic traits (Anders- son 2008; Keeling and Palmer 2008; Lopez and Bapteste 2009).
Lopez, P. & Bapteste, E. 2009. Molecular phylogeny: reconstructing the Paz-y-Min˜o C. and Espinosa (2009) merge the reticulated pattern and tree phylogenies with the ring of life, symbiogenetic whole- Margulis, L. 2009. Genome acquisition in horizontal gene transfer: organism model, and pattern pluralism schemes to propose an ‘‘in- symbiogenesis and macromolecular sequence analysis. In: Gogarten, tegrative model of lateral and vertical evolution,’’ where both HGT M. B., Gogarten, J. P. & Olendzenski, L. (ed.), Horizontal Gene Trans- and common descent are graphically depicted and combined. These fer: Genomes in Flux. Humana Press, New York. p. 181–191.
authors use Entamoeba histolytica alcohol dehydrogenase 2 (Eh- Margulis, L., Chapman, M., Guerrero, R. & Hall, J. 2006. The last ADH2), a bifunctional enzyme in the glycolytic pathway of eukaryotic common ancestor (LECA): acquisition of cytoskeletal mo-tility from aerotolerant spirochetes in the proterozoic eon. Proc. Natl.
amoeba, to illustrate how EhADH2 could be the product of both horizontally acquired features from ancestral prokaryotes (i.e. alde- Martin, R. E. & Kirk, K. 2004. The malaria parasite’s chloroquine resis- hyde dehydrogenase [ALDH] and alcohol dehydrogenase [ADH]), tance transporter is a member of the drug/metabolite transporter super- and subsequent functional integration of these enzymes into Eh- family. Mol. Biol. Evol., 21:1938–1949.
ADH2, which is now inherited by amoeba via common descent.
Meyer, S. C. 2004. The origin of biological information and the higher Paz-y-Min˜o C. and Espinosa (2009) discuss how mutation rate taxonomic categories. Proc. Biol. Soc. Washington, 117:213–239.
coupled with natural selection and HGT coupled with common de- Miller, K. R. 2007. Falling over the edge. Nature, 447:1055–1056.
scent drove the evolution of EhADH2, and perhaps of most alcohol Mu¨ller, I., Genton, B., Rare, L., Kiniboro, B., Kastens, W., Zimmerman, dehydrogenases (ADHE), and contrast this analysis with proposals P., Kazura, J., Alpers, M. & Smith, T. A. 2009. Three different Plasm-odium species show similar patterns of clinical tolerance of malaria in- invoking ‘‘common design’’ (i.e. the independent emergence of major taxa with no common ancestry) to explain the interaction Padian, K. & Matzke, N. 2009. Darwin, Dover, ‘Intelligent Design’ and between horizontal and vertical evolution. Paz-y-Min˜o C. and Esp- textbooks. Biochem. J., 417:29–42.
inosa (2009) remark that the case study of lateral and vertical evo- Paz-y-Min˜o C., G. & Espinosa, A. 2009. Integrating horizontal gene trans- lution of EhADH2 is didactic in the context of the Darwinian fer and common descent to depict evolution and contrast it with ‘com- perspective, and that selection has acted continuously and cumula- tively on ancestors and intermediates of EhADH2. Therefore, a single or multiple emergence of EhADH2 arising from an ‘‘intel- Ricklefs, R. E. & Fallon, S. M. 2002. Diversification and host switching in ligent design’’ followed by adaptive change is improbable.
avian malaria parasites. Proc. R. Soc. Lond. B., 269:885–892.
Rivera, M. C. & Lake, J. A. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature, 431:152–155.
Roy, S. W. & Irimia, M. 2008. Origins of human malaria: rare genomic changes and full mitochondrial genomes confirm the relationship of Andersson, J. O. 2008. Eukaryotic gene transfer: adaptation and replace- Plasmodium falciparum to other mammalian parasites but complicate ments. In: Hensel, M. & Schmidt, H. (ed.), Horizontal Gene Transfer in the origins of Plasmodium vivax. Mol. Biol. Evol., 25:1192–1198.
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Source: http://faculty.rwu.edu/aespinosa/aespinosa/Publications_files/Espinosa_Intro_HGT_ID_JEM_2010.pdf

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Thursday, September 13 Registration 8:45-9:00 Opening Address (Main Hall) 9:00-10:45 Oral Session-1 (Main Hall) Intan Safinar Ismail, Universiti Putra Malaysia, Malaysia Constituents of selected Meliaceae species Wei-Lie Xiao, Kunming Institute of Botany, P. R. China Chemical and biological studies of Schisandra chinensis Li-Ming Sun, Dalian Polytechnic University

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