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.
the Evolution of Pathogenesis. Cambridge University Press, Cam-bridge. p. 293–315.
COLORADO DEPARTMENT OF HUMAN SERVICES NUMBER: LEAP 07-02-A 1575 SHERMAN ST., DENVER, COLORADO 80203-1714 CROSS REFERENCE AGENCY LETTER DIVISION OR OFFICE: Food and Energy Assistance DATE: .April 26, 2007 PROGRAM AREA: LEAP – LEAP DIVISION DIRECTOR: TITLE: LEAP OUTREACH INCENTIVE PROGRAM - 2007-08 MANAGER: TYPE: A – Action Purpose: The p
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