Biology 9214

Teach the Controversy

An intelligently designed graduate course on current attacks on biological evolution

Instructor: André Lachance - 2036 BGS

 


 

Another outstanding year comes to an end.

We covered fascinating topics including evolution of gene duplication, kin selection, the eye, the origin of birds, the problem of conflicting phylogenies, evolving algorithms, junk DNA, the origin of plants, the evolution of spirituality, the 'creation' of artificial microbes, speciation in butterflies and in fruit flies, the Cambrian explosion, the evolution of viruses, bottlenecks and Noah's ark, and the evolution of homosexuality.

Thank you, class of 2013, for such a wonderful series.

 


Course outline 2013


 

Controversy People

Controversy Web Sites

M J Behe

Irreducible complexity

W A Dembski

 Dr Dembski's web site contains links to his many publications.  See in particular:

The Logical Underpinnings of Intelligent Design.

In another (unpublished) paper, Dembski concludes that "there might be good reasons for thinking" that humans were designed "from the ground up" and not as a modification of an ape-like ancestor:

Reflections on Human Origins.

Papers that supposedly address intelligent design and natural selection but never mention any of these words.  Lots of math,though.

Co-authored with RJ Marks II.

The search for a search

2010  Journal of Advanced Computational Intelligence and Intelligent Informatics 14:475-486

Conservation of information

2009  IEEE Transactions on Systems, Man, and Cybernetics  39:1051-1061
Dr Dembski has been referred to as
the Issac Newton of Information Theory

S C Meyer

Dr Meyer's Discovery Institute website contains a list of his publications, including his controversial paper in Proceedings of the Biological Society of Washington (2004 117:213-239).

R Steinberg's website provides an analysis of the controversy surrounding the peer review process in this case.

Dr Meyer is an expert in media relations.

See for example this press release regarding Dawkins's 2009 book tour.  See also what Dr. Meyer did to celebrate Charles Darwin's 200th birthday in his very home town.
Dr. Meyer's latest book,
Darwin's Doubt, once again makes the unending case for a too short Cambrian explosion.  Here is a critique from the journal Science.

J C Wells

Dr Wells is best known for his book Icons of Evolution.  His background within the Unification Church is fascinating.

R Steinberg

Biologic Institute

A link connecting Dr Steinberg to Baraminology
no longer works...

Good science will come out of ID

Axe et al 2007 New Scientist 193(2586):18

Biologic Institute

S C Burgess

Prof Burgess has two versions of his article on the peacock's tail.  The peer-reviewed version is listed below under "Past presentations".

Article on Peacock's tail in Answers in Genesis

J D Morris

In the following article, Dr Morris concludes:

"Evolution tales are pseudo-scientific stories about an imaginary history. Evolution is best understood as an anti-God origins myth, attempting to explain man's existence without a Creator. We can do better."

Why do we still have apes?

J Bergman

One of Dr Bergman’s claim to fame is that he holds nine academic degrees.

Pro Creationist

Answers in Genesis

Discovery Institute

Center for the Renewal of Science and Culture

 Institute for Creation Research

   Evolution on Conservapedia

Designed DNA

The True Origin

Pro Science

TalkOrigins

National Center for Science

Education

 

Panda's Thumb

 Antievolution

  Talk Reason

Resources

TalkOrigins

Index to Creationist claims

(by M Isaak)

 

The Geological Time Scale

Using dice to demonstrate how selection makes the impossible inevitable

Nature's 15 gems of evolution

Creationist journals

Bio-Complexity

Creation Research Quarterly

Answers Research Journal

ICR Acts and Facts

Journal of Creation (formerly TJ)

Gaps in the fossil record

Garner 2003 Journal of Creation 17:111-117

Navigating through sequence space

Truman 2006 Journal of Creation 20:90-99


Origin of Protein Folds
Axe 2010 Bio-Complexity 1:1-12


Reductive Evolution
Gauger 2010 Bio-Complexity 2:1-9

Design of the eye

The backward human retina

Bergman & Calkins 2005 Impact #388

Bergman 2011 Answers Research Journal 4:75-80

Gurney 1999 Journal of Creation 13(1):37-44

Lumsden  1994  Creation Research Quarterly 31:13-22

Flightlessness

Dawkins's straw-men and flightless birds

Sarfati 2010  Journal of Creation. 24[1]:43-47

The Giraffe's neck

An icon to creation

Bergman  2002  Journal of Creation 16:120-127


The laryngeal nerve
Bergman  2011  Journal of Creation 25(1):63-68

Baraminology

Wood  2006  Creation Science Quarterly 43:149-158

Hominid classification

Wood  2010  Answers Research Journal 3:71-90

 

Peer-reviewed literature

Peer reviewed ID - part 1

Evolution references

"Behe's first rule"

Behe  2010  Quarterly Review in Biology  85:419-445


Gene duplication and point mutation hardly account for new functions

Behe & Snoke  2001  Protein Science 13:2651-2664


Repetitive DNA is not junk

Shapiro & Sternberg  2005  Biological Reviews  80:227-250


There is more to genotype than just DNA

Sternberg  2000  Annals of the New York Academy of Science  901:224-236


Navigating through neutral space

Axe 2000 Journal of Molecular Biology 301:585-595 


The peacock's feather

Burgess et al 2006 Optics and Laser Technology 38:329-3

 

Speciation

 

Speciation in spite of gene flow

Martin et al  2013  Genome Research

doi: 10.1101/gr.159426.113


Speciation in the subway

Byrne & Nichols  1999  Heredity  82:7-15


Darwin's finches: speciation in action

Grant & Grant  2009  PNAS  106:20141–20148


Rapid speciation in the apple maggot fly

Jiggins & Bridle  2004  Trends in Ecology and Evolution  19:111-113


Speciation by homoploid hybridization in butterflies

Jiggins et al  2008  Mallet  2008  Philosophical Transactions of the Royal Society B  363: 3047–3054 


Ecological speciation in butterflies

 Chamberlain et al  2009  Science 326:847-850


Speciation by domestication: the fox

Trut et al  2009  BioEssays  31:349-360


Reverse speciation in yeast

Delneri et al 2003 Nature 422:68-72


Rapid speciation by sensory drive on cichlids

Seehausen 2008 Nature 455:620-626


Colour-driven speciation in fish

Puebla et al  2007  Proceedings of the Royal Society B  274:1265-1271


Continuity between species

Mallet  2008  Phylosophical Transactions of the Royal Society B  363:2971-2986


Speciation and chemical communication in moth

Zhu et al  1997  Journal on Insect Behaviour  10:805-817

Evenden et al  2002  Chemoecology  12:53-59


Ring species

Irwin et al  2001  Nature 409:333-337


Tetraploidization

Cunha et al 2008 Phil Trans R. Soc B 363:2921–2929

How long was the Cambrian explosion?

 

Evolutionary rates during the Cambrian were consistent with other rates

Lee et al  2013  Current Biology 23, 1889–1895


What exactly is the Cambrian explosion?
Smith & Harper  2013  Science 341:1355-1356


Not really an explosion

Lieberman  2001 Proceeding of the Royal Society of London B  268:1707-1714


Ediacaran fossils were terrestrial

Retallak  2013  Nature 493:89-92


The molecular clock

Blair & Hedges 2005 Molecular Biology and Evolution 22:387-390


Morphological disparity vs. cladogenesis

Fortey et al  1996  Biological Journal of the Linnean Society 57:13-33


Cambrian fossils in the Ordovician
Van Roy et al  2010  Nature 465:215-218

Evolution of belief

 

Not one, but many God spots

Johnstone et al  2012  International Journal for the Psychology of Religion  22:267-284


Minimally counterintuitive concepts

Fondevila et al  2012 Social Neuroscience 7:445-457


Biology of spirituality

Urgesi et al  2010  Neuron 65:309–319


Belief and creation-evolution perspectives

Evans  2001  Cognitive Pschology 42:217-266


Existential anxiety affects ID-evolution acceptance

Tracy et al  2011  PLoS One 6(3):e17349


Religion as a brain by-product

Boyer  2003  Trends in Cognitive Sciences 7:119-124  


Neurology of religious belief and morality

Young et al  2010  PNAS www.pnas.org/cgi/doi/10.1073/pnas.0914826107

Kapogiannis et al 2009

www.pnas.org cgi doi 10.1073 pnas.0811717106


Handedness and acceptance of creationism

Niebauer et al  2004  Laterality  9:433-447 


Is religion an evolutionary adaptation?

Pyysiäinen & Hauseriebauer  2010  Trends in Cognitive Sciences 14:104-109

Synthetic life

 

A synthetic Genome

Smith et al  2003  PNAS 100:15440-15445


Creation of a bacterial cell

Gibson et al  2010 Science 329:52-56

Junk DNA

 

The Encode Project: there is no junk!
Nature website
Well, may be there is...
Graur et al  2013 Genome Biology and Evolution 5, 578-590
Doolittle 2013  PNAS 110:5294–530


Rapid evolution of bladderwort, a plant with nearly no junk DNA

Ibarra-Laclette et al  2011  BMC Plant Biology  11:101

 

Humans among the apes

 

Ardipithecus ramidus

Special Issue of Science


The human chromosome 2 junction

IJdo et al 1991 PNAS 88:9051-9055

Fan et al 2002 Genome Research 12: 1651-1662


Hominine karyotypes

Yunis & Prakash 1982 Science 215:1525-1530

Jstor recommended


Human and chimp Y chromosomes are so different

Hughes et al  2010  Nature  doi:10.1038/nature08700


Hominid morphometrics

Lockwood 2004 PNAS 101:4356-4360


Why are monkeys still around?

Rightmire 2008 Evolutionary Anthropology 17:8–21


Is "Mitochondrial Eve" only 6500 years old?

Parsons et al 1997 Nature 15:363-368

Ingman et al 2000 Nature 408:708-713


The evolution of brain size
Dumas et al  2012 American Journal of Human Genetics 91:
http://dx.doi.org/10.1016/j.ajhg.2012.07.016

 

Conflicting ape phylogenies

 

Humans are the second orangutans

Grehan & Schwartz  2009  Journal of Biogeography 36:1823-1844


Chimps are the sister species

Scally et al  2012  Nature 483:169-175

Perelman et al  2011  PLoS Genetics 7(3):e1001342

Hobolth et al  2011  Genome Research 21:349-356

Gagneux 1999 PNAS 96:5077–5082

Salem 2003 PNAS 2003 100:12787–12791

Uddin et al  2004  PNAS 101:2957–2962

Ebersberger 2007 Molecular Biology and Evolution 24:2266–2276


Morphological and molecular phylogenies agree
Bjarnason et al  2010  Journal of Human Evolution 60:47-57


Dating the chimp-human split

Kumar et al  2005  PNAS 102:18842–18847

Human Nature

 

Is laughter uniquely human?

Ross et al  2009  Current Biology  19:1106-1111


Is empathy uniquely human?

Chen et al. 2009 PLoS ONE 4(2): e4387


Have humans stopped evolving?

Sabeti et al 2006 Science 312:1614-1620

Hawks et al 2007 PNAS 104:20753–20758

Stock 2008 EMBO reports 9(Special Issue):S51-S54

Evans et al 2008 Science 309:1717-1720


Are humans a uniquely different species?

Christiansen & Kirby  2003 Trends in Cognitive Sciences 7:300-307

Osvath &Osvath  2008  Animal Cognition 11:661–674


Genes that are unique to humans

Knowles & McLysaght  2009  Genome Research  19:1752-1759

Evolution of new functions, beneficial mutations

 

The Innovation-Amplification-Divergence model in Salmonella

Näsvall et al  2012  Science  338:384-387


Evolution of citrate utilization in E. coli
Blount et al  2012 Nature
doi:10.1038/nature11514


Orphan genes
Tautz & Domazet-Lošo  2011 Nature Reviews Genetics 12:692-702


Overlapping genes
Sanna et al  2008  BMC Genomics 9:169


Genetic mechanisms of adaptation in yeast

Hansche  1975  Genetics 79:661-674

and references therein


A new gene from a non-coding sequence

Cai et al  2008 Genetics 179:487–496


Evolution of feathers by co-optation

Perrichot et al 2008 Proceedings of the Royal Society of London Series B 275:1197-1202

Prum & Brush 2002 Quarterly Review of biology 77:261-295

Prum 2005 Journal of Experimental Zoology 304B:570-579


Gene duplication and new functions

Hugues  1994  Proceedings: Biological Sciences  256:119-124


Death and resurrection of a human gene

Bekpen et al  2009  PLoS Genetics 5:e1000403


On the origin of nori genes in humans
Hehermann  2010  Nature 464:908-914

From fin to fish

Zhang et al  2010  Nature 466:234-238


Duplication and the domestication of sunflower

Blackman et al  2010  Curr Biol  20:629-635


Genetics of tooth loss of teeth in whales
Meredith et al  2010  PRSB  doi:10.1098/rspb.2010.1280

Filling the gaps in the fossil record

 

Evolution of whales


Ngaps = Nfossils - 1

Gatesy et al  2013  Molecular Phylogenetics & Evoluiton 66:479-506


Transitional fossils for whales

Thewissen 2007 Nature 450:1190-1194


Evolution of birds


Limb-body size ratio and the origin of birds

Dececchi & Larsson  2013  Evolution  67-9:2741-2752


The wings of Archaeopteryx are different from those of birds

Longrich et al  2012  22:2262-2267


From dinosaurs to birds

Hu et al  2009  Nature 461:640-643


Pushing back the link to birds

Choinière et al  2010  Science 327:571-574

 

Baraminology of the gaps

Senter  2010  Journal of Evolutionary Biology 23:1732-1743


Creationist critique
Wood  2011  Journal of Evolutionary Biology 24:914-918


More baraminology of the gaps
Senter  2011  Journal of Evolutionary Biology 24:2197-2216


Horses as icons of evolution

Orlando et al  2009  PNAS 106:21754–21759


A missing link to the pinnipeds?

Rybczynski et al 2009 Nature 458(April):1021


Gradual evolution of flatfish eyes

Friedman 2008 Nature 454(July):209-212


Tiktaalik roseae

Website

Daeschler et al 2006 Nature 440:757-763

Shubin et al 2006 Nature 440:764-771

Evolution of altruism

 

Insects


Extreme eusociality

Ratnieks & Helantera  2009  PTRSB 364:3169-3179


A proximate mechanism: ovary suppression

Cardoen et al  2012  Journal of Proteome Research  11:2838-2850


Birds

Krams et al  2008  Behav Ecol Sociobiol  62:599-605


Hamilton's rule in humans

Borgerhoff Mulder  2007  Evolution and Human Behavior  28:299-312


Is altruistic behaviour uniquely human?

Gomes et al  2009  Proceedings of the Royal Society B  276:699-706


An altruism gene in yeast

Smukalla et al 2008 Cell 135:726-737


Limiting clutch size as a survival strategy

Lack 1947 Ibis. 87:302-362

Styrsky et al 2005 Ecology. 86:3238-3244


Altruism in microorganisms
West et al  2010  Nature Reviews 4:597-607

Symbioses, chimeras, hybridization

 

Dating the primary endosymbiosis event

Shih & Matzke  2013  doi: 10.1073/pnas.1305813110


The onychophoran saga: science or folly?

Williamson  2009 PNAS 106:19901-19905

Giribet  2009  PNAS 106:E131

Williamson 2009 PNAS 106:E132


Origin of Gram-negative bacteria by endosymbiosis

Lake  2009  Nature  460: 967-970

Origin of life: abiogenesis

 

Urzymes are more likely than ribozymes

Li et al  2013  Journal of Biological Chemistry 288:26856-26863


Did peptide nucleic acids come first?

Banack et al  2012 PLoS One 7(11):e49043


Long RNAs in water

Costanzo et al.  2009  Journal of Biological Chemistry 48:33206–33216


Ribonucleotides from scratch

Powner et al  2009  Nature  459:239-242

See also the supplement


The multiverse and the origin of life

Koonin 2007 Biology Direct 2:15


History of the RNA world theory

Snakaran  2012  Studies in History and Philosophy of Science C  43:741-750

Evolution of homosexuality

 

Reciprocal altruism

Kirkpatrick  2000 Current Antropology 41:385-413


Higher female fertility

Camperio-Ciani 2004 Proceedings of the Royal Society of London, Series B 271:2217–2221


Epigenetic basis for homosexuality

Rice et al  2012  Quarterly Review of Biology 87(4)


A review in non-human animals

Bailey & Zuk  2009  Trends in Ecology & Evolution 24:439-446

Extreme adaptation
 

Bird-eating fish
Cucherousset et al.  2012  PLoS One 7(12): e50840. doi:10.1371

Evolution of flightlessness

 

Phylogenetics of flightlessness

Cubo & Arthur  2001  Evolutionary Ecology 14:693-702


Wing length

McCall et al  1998  Evolutionary Ecology  12:569-580


Energy conservation hypothesis

McNab  1994  The American Naturalist  144:628-642

Are phylogenetic trees real?

 

The protostome/deuterostome furcation

Martín-Durán et al  2012  Current Biology 

doi.org/10.1016/j.cub.2012.09.037


Is common descent falsifiable?

Sober & Steel 2002  Journal of Theoretical Biology 218:395-408

Penny et al 2003 Journal of Theoretical Biology 223:377-385


Is there really a tree of life?

Daubin et al  2003 Science 301:829-832


The tree is not a tree but a bush
Boto  2010  PRSB 277:819–827


Is there a single common ancestor (LUCA)?
Theobald  2010  Nature 465:219–222

Early earth and the Miller-Urey experiment(s)
 

When did oxygen appear?

Canfield  2005  Annual Reviews of Earth & Planetary Sciences 33:1-36

Sexual selection
 

Sexual selection in yeast

Rogers & Greig  2009  Proceedings of the Royal Society B  276:543-549


Sexual selection in Humans

Penton-Voak & Perrett  2000  Evolution and Human Behavior 21:39–48


Synergy of natural and sexual selection

van Doorn  2009  Science  326:1704-1017


Intralocus sexual conflict

Bonduriansky & Chenoweth  2009  Trends in Ecology and Evolution  24:280-288

Foerster et al  2008  Nature  447:1107-1110

Evolution of (irreducible) complexity

 

Irreducible equivocation
Boudry et al  2010  Quarterly Review of Biology  85:473-492


An essay by a co-founder of molecular evolution

Zuckerkandl  2006  Gene 385:2-18


Mitochondrial engines

Clements et al  2009  PNAS 106:15791-15795

Behe's rebuttal


Evolution of synapses by co-optation

Sakarya et al 2007 PLOS One June 2007 e506: 1-9


A hormone receptor

Bridgham et al 2006 Science 312(April):97-101


Blood clotting

Xu & Doolittle 1990 PNAS 87:2097-2101


The bacterial flagellum

Pallen & Matzke 2006 Nature Reviews Microbiology  4:784-790

Liu & Ochman 2007 PNAS 104:7116–7121


A critique of Liu and Ochman's paper

Doolittle & Zhaxybayeva 2007 Current Biology  17:R510-R512


Evolution of immunity

Travis  2009  Science  324:580-582


Viruses as a source of genetic complexity

in mammals

Freshotte  2010  Nature 463:39-40

Horie et al  2010  Nature 463:84-88

Plant evolution

 

Lignin

Martone  et al  2009  Current Biology 19:169-175
Vanholme et al  2010  Plant Physiology 153:895-905

Zhanyou  2009  BMC Bioinformatics  10(Suppl 11):S3


Emergence of land plants
Ligrone  2012  Annals of Botany  109:851-871
Qiu & Palmer  1999  Trends in Plant Science – reviews 4:26-30

Evolution of the eye

 

On the origin of opsins

Feuda et al  2012  PNAS  doi: 10.1073/pnas.1204609109


Reviews

Fernald  2000  Current Opinion in Neurobiology
10(4):444–450

Lamb et al 2007 Nature Reviews Neuroscience 8:960-975


Blood vessel shadows

Adams & Horton  2002  Science 298:572-576


The retina of cephalopods

Talbot & Marshall  2011  Philosophical Transactions of the Royal Society B  366:724-733


Co-optation of enzymes in the crystallin

Piatigorsky 2003 Integrative and Comparative Biology 43:492-499


Genetic control of different eye types

Gehring 2001 Zoology 104:171–183

Gehring 2002 International Journal of Developmental Biology 46:65-73


A new eye type involving reflection

Wagner et al 2009 Current Biology - doi:10.1016/j.cub.2008.11.061


The time for an eye to evolve

Nilsson & Pelger 1994 Proceedings of the Royal Society of London Series B 256:53-58


A thematic issue of

Evolution: Education and Outreach

on the evolution of the eye (2008 vol 1 no 4)


Evolution of colour vision

Yokoyama & Radlwimmer  1998  Mol Biol Evol. 15:560–567

Ödeen & Håstad  2003  Mol Biol Evol 20:855–861

Navigating through sequence space

 

Protein evolution by tinkering

Bridgham et al  2010  PLoS Biology 8(10):e1000497

Povolotskaya and Kondrashov  2010  Nature 465:922-927
Dryden et al  2008  J. R. Soc.
Interface 5:953–956

Evidence for design

 

Are humans intelligently designed?

Avise  2010 PNAS 107 (suppl. 2):8969–8976

Natural selection in action

 

Human personality and fitness

Alverge et al  2010  PNAS Science 107:11745–11750


Darwin's finches

Grant & Grant 2006  Science  313:224-226


An adaptive coloration gene in deer mice

Linnen et al  2009  Science 325:1095-1098


Lizard horns

Young et al 2008 Science 304:65


The truth about the peppered moth

Majerus  2008  Ecological entomology 33:679-683

Dinosaurs-bird sisterhood

 

Brachylophosaurus canadensis protein sequences

Schweitzer  2009  Science  324:626-631


A Jurassic Alvarezsauroid
Choinière et al  2010  Science 327:571-574

Evolution in action

 

Adaptive radiation in bacteria

Rainey & Travisano  1998  Nature 394:69-72


Human adaptation to high altitude

Simonson et al  Science 329:72-75


Evolution in vitro

Buckling et al  2009  Nature 457:824-829


In silico evolution of complexity by selection

Lenski et al 2003 Nature 423:139-144


Why seahorses stood up

Teske & Beheregaray  2009  Biology Letters 5:521-523

Vestigial organs

 

Was Darwin wrong about the appendix?

Smith et al  2009  Journal of Evolutionary Biology  22:1984-1999

Bat Evolution

 

Primitive Bat

Simmons et al 2008 Nature 451(February):818-822


Evolution of bat echolocation

Neuweiler 2003 Journal of Comparative Physiology A 189:245-256

Speakman  2001  Mammal Reviews 31:111–130


Evolution of bat flight

Sears et al 2006 PNAS 103:6581-6586


Evolution of vampire anticoagulants

Tellgren-Roth  2008  Naturwissenschaften

DOI - 10.1007/s00114-008-0446-0

Fossils and molecular phylogenies

 

Horse ancient DNA phylogeny

MacFadden  on et al 2005  Science  307:1728-1729


Dolphins

Hamilton et al. 2001 Proceeding of the Royal Society of London Series B 268:549-558


Cave bears

Bon et al 2008 PNAS doi 10.1073 pnas.0806143105

The evolution of sex

 

Sex change by a single point mutation

Airoldi et al - www.pnas.org/cgi/doi/10.1073/pnas.1009050107


Killer sex

Hosken & Price  2009  Current Biology  19:R519-R521


Sex as a major evolutionary force

West et al 1999 Journal of Evolutionary Biology 12:1003-1012


Origin of spermatogenesis

Shah et al  2010  PLoS Genetics 6(7):e1001022


Origin of sex

Cavalier Smith  2002  Heredity  88:125–141

Fossil hypes and self-correction in science

 

Missing link to anthropoid primates?

Franzen et al  2009 PLoS ONE 4:e5723 doi:10.1371/journal.pone.0005723


Not really, but cool nonetheless

Seiffert et al  2009  Nature  461:1118-1122

Evolution of the ear

 

The middle ear of mesozoic mammals

Ji et al  2009  Science  326:278-281


Background on mammalian ear

Martin & Ruf  2009  Science  326:243-244

Origin of the genetic system

 

Early evolution of the ribosome

Bokov & Steinberg 2009 Nature 457:977-980


Is the current genetic code the best that could possibly be?

Lui et al  2008 PNAS 105:17688-17693

Probability, information theory

 

The peacock and runaway 

sexual selection

Petrie and Roberts 2007 Heredity 98:198–205


Dembski's explanatory filter

Olofsson  2008  Biology & Philosophy 23:545–553


Dembski's specified information

Elsberry & Shallit  2009  Synthese  DOI 10.1007/s11229-009-9542-8

Adaptive mutations

 

Bacteria

Perfeito 2007 Science 317:813-815

Blount et al 2008 PNAS 105:7899–7906

Imhof & Schlotterer 2001 PNAS 98:1113-1117

Orr 2006 Journal of Theoretical Biology 238:279-285

Stanek 2009  BMC Evolutionary Biology 9:302


Adaptive walks in Fungi

Schoustra 2009 PLoS Biology 7:e1000250


Mutation and selection in prions

Li et al 2009 Sciencexpress Dec 31 2009:1-5


Mutator genes, mutation, coevolution & adaptation

Pal et al 2008 Nature 450:1079-1081

Neutral mutations

 

Documenting the accumulation of

neutral mutations in a plant

Ossowski 2010 Science 327:92-94

Living fossils

 

Sequence of a dinosaur protein

Schweitzer  2009  Science  324:626-631

The geological time scale
 

Noah's flood

Aksu et al 2002 GSA Today - May 2002 4-10

Evolution of language
 

Proto-syntax in monkeys

Ouattara  2009  PNAS 106:22026–22031


Monkeys as taxonomists
 Zuberbühler et al  1997  Animal Behaviour 53:589-604

Protists and ID

 

Espinosa 2010 Journal of Eukaryotic Microbiology 57:1-2 

Farmer & Habura 2010 Journal of Eukaryotic Microbiology 57:3-10

Paz y Miño & Espinisa 2010 Journal of Eukaryotic Microbiology 57:11-18

The Haeckel affair

 

Pickett 2005 The American Biology Teacher 67:275-282
Richardson and Keuck  2002  Biological Research  77:496-528
Richarson et al 1997  Anatomy & Embryology 196:91-106

Peer reviewed ID - part 2

ID in nematodes

Greeley 2008 Endocrinology 149:3184–3186 


ID of Interleukin-7 receptor expression

Mazzucchelli and Durum 2007 Nature Reviews Immunology 7:144-154


Evolution through ID

Karlan 2006 Gynecologic Oncology 102:1–4


Laparoscopy and ID

Peters 2006 Journal of Urology 175:1993-1994


Protein interactions, the internet, and ID
Yang et al 2006 Computational systems bioinformatics 299-309

Theology

 

Science in the scriptures

Loukas et al  2009  doi:10.1016/j.ijcard.2009.05.011

 

Education

 

I'm fine with microevolution, but...

Padian  2010  Evo Edu Outreach  3:206-214

 

Relevance of evolution
Evolution in medical education

Nesse et al  2010  PNAS  107 (suppl.):1800-1807

Philosophy

Can evolution (science) and theology get along?

 

Critique of Plantinga
Ruse 2012 The Philosophical Quaterly 62(248):620-625

Intelligent design as science?

 

Methodological and metaphysical naturalism
are the same thing
Boudry et al  2010 Foundations of Science 15:227-244


ID as a controversial discovery claim

Grinnell 2006 The FASEB Journal 20:410-411


Is intelligent design falsifiable?

Miller  2009  Cold Spring Harbor Symposia on Quantitative Biology 74:1-6


Why Darwin rejected design

Sulloway  2009  Journal of Bioscience  34:173-183


Evolution is in fact intelligent design

Costanza  2009  Trends in Ecology and Evolution  24:414-415


Is Evolution a religion?

Ruse  2003  Science 299:1523-1524

Reiss  2009  Evolution 63:1934–1941

Science in the media
 

Science Spin

Spin PLoS Medicine 2012 9 (9)

Occam's razor, parsimony, and evolution

 

The principle of minimum evolution

Edwards  1996  Systematic Biology  45:79-91

Hoffmann et al  1997  International Journal for Philosophy of Chemistry  3:3-28

Evolution as a source of immorality

 

Does evolution beget eugenics?

Cebrat & Pekalski 1999 European Physical Journal B 11:687-690 
Pekalski 2000 European Physical Journal B 17:329-332.


Beliefs and social dysfunction

Paul  2009  Evolutionary Psychology  7:398-441


Bats do it too

Tan et al  2009  PLoS One  4:e7595

 

Background on ID

The Controversy in Society

Darwin, ID, and the Dover Trial

Padian & Matzke  2009  Biochemical Journal 417:29–42

Transcript of the Dover Trial Judgment

ID as the latest version of Creationism

Forrest 2008 Integrative and Comparative Biology 48:189–201

A taxonomy of Creationists

Scott 2000 NCSE Resources

A history of American Creationism

Matzke  2010  Evolution Education & Outreach  3:145-162

From Creationism to ID
Scott & Matzke  2007  PNAS  104 (suppl.1):8669-8676

The Wedge Document

Canada - Angus Reid Poll

The rest of the World

Miller et al 2006 Science 313:765-766

Science and science literacy in the US

PEW survey

Of Penguins and People

Wexler 2008 Studies in History and Philosophy of Biological and Biomedical Sciences 39:273–279

Larry Moran (U of T) on

"Teaching the Controversy"

ID/Creationism books

Movies

Behe - Darwin's Black Box

"Overthrows Darwin at the end of the 20th century in the same way that quantum theory overthrew Newton at the beginning."


Davis & Kenyon - Of Pandas and People

"An outstanding supplement to standard high school biology textbook."


Dembski & Ruse - Debating Design

PDF version


Dembski & Wells - The Design of Life

"When future historians list the books that toppled Darwin's theory, The Design of Life will be at the top."

Flock of Dodos
Discovery Institute's critique (notice anonymity)


Expelled - No Intelligence Allowed
NCSE's critique


 

Evolution vs. God

Shaking the  Foundations of Faith

 

Biology 3466b Website  ●   Biology 4289 Website  ●   André Lachance's UWO-Biology Website   ●   Yeast Newsletter Website

 

Updated December 4 2013