Biology 9214

Teach the Controversy

An intelligently designed graduate course on current attacks on biological evolution

Instructor: André Lachance - 2036 BGS

The course will be offered in 2016 if there are at least six registrants

Course outline, fall 2016



Mental health

Controversy in the News
Texas State Board of Education again (September 2016)
New: A Vice-Presidential Candidate's explanation of evolution
(October 2016)

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In another (unpublished) paper, Dembski concludes that "there might be good reasons for thinking" that humans were designed "from the ground up" and not as a modification of an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

DiscoveryU - online course

Logic 101

 Institute for Creation Research

Old Earth Ministries

   Evolution on Conservapedia

Designed DNA

The True Origin

Pro Science


National Center for Science Education

Panda's Thumb


Talk Reason



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


Creation Research Quarterly

Answers Research Journal

ICR Acts and Facts

Journal of Creation (formerly TJ)

Is there enough time for evolution?

Ewert et al 2012 BioComplexity 2012(4)1-7

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


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


Wood  2006  Creation Science Quarterly 43:149-158

Hominid classification

Wood  2010  Answers Research Journal 3:71-90


Peer-reviewed literature

Intelligent Design, etc

Evolution references

Peer reviewed ID - part 1

"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

Mitochondria, endosymbiosis, and the soul

Warda & Han 2008 Proteomics 8

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


Science in the Scriptures

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


I'm fine with microevolution, but...

Padian  2010  Evo Edu Outreach  3:206-214


Relevance of evolution
in medical education

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


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

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

Filling the gaps in the fossil record

Ngaps = Nfossils – 1


 Evolution of whales

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

Transitional fossils for whales

Thewissen 2007 Nature 450:1190-1194

New: Keratin evolution links birds to crocodilians

Greenwold & Sawyer 2013 Journal of Experimental Zoology 320:393-405

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


Daeschler et al 2006 Nature 440:757-763

Shubin et al 2006 Nature 440:764-771

volution of new functions, beneficial mutations


New: New ways of making cafeine from old genes

Huang et al  2016  PNAS 113:10613-10618

Origin of new genes

Ding et al. 2012 Annual Reviews of Ecology, Evolution and Systematics 43:345

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 489:513–518

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

Ancient DNA Research


Centre for Genenetics, Denmark

Svante Pääbo's laboratory - Max Planck Insitute

Human Nature


New: CHRM2, a gene with a Drosophila homolog, influences success in life

Dick et al 2011 Psychol Sci 22:481

Fairness as a uniquely human trait

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?

New: Genomics of human evolution

Science News May 17 2016

Human genes under positive selection due to agriculture

Mathieson et al  2015  Nature doi:10.1038/nature16152

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

Origin of life: abiogenesis

Evolution of homochirality by autocatalysis

Blackmond 2004  PNAS 101:5732-5736

 RNA, protein, and lipids appeared at the same time

Patel et al  2015  Nature Chemistry 7:301

Origin of cellular life

Koonin 2014 Antonie van Leeuwenoek 106:27

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

History of the RNA world theory

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

Natural selection in action

Majerus's last experiment: Kettlewell rules!

Cook et al   2012  Biology Letters doi:10.1098/rsbl.2011.1136

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 mothzard horns

Majerus  2008  Ecological entomology 33:679-683

Evolution of belief


God as inclusive fitness

Crespi & Summers 2014 Animal Behaviour 92:313-323

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

Kapogiannis et al 2009 cgi doi 10.1073 pnas.0811717106

Handedness and acceptance of creationism

Niebauer et al  2004  Laterality  9:433-447 

Is religion an evolutionary adaptation?

PyysiäinenHauseriebauer  2010  Trends in Cognitive Sciences 14:104-109

Evolution in action


Selection of butterfly colour

Wasik et al. 2014  PNAS

Adaptive radiation in bacteria

Rainey & Travisano 1998 Nature 394:69-72

Human adaptation to high altitude

Simonson et al  2010  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



Speciation in spite of gene flow
Martin et al  2013  Genome Research  23:1817

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

Cunha et al 2008 Phil Trans Royal 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

Synthetic life


Synthetic yeast 2.0

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

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:

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

Evolution of altruism



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


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

Evolution of flightlessness


Phylogenetics of flightlessness

Cubo & Arthur  2001  Evolutionary Ecology 14:693-702

Are phylogenetic trees real?


Different genes, different trees

Nosenko et al 2013 Molecular Phylogenetics and Evolution 67:223

The protostome/deuterostome furcation

Martín-Durán et al  2012  Current Biology

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?

PCanfield 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



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


Fernald  2000  Current Opinion in Neurobiology

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

Dinosaurs-bird sisterhood


Brachylophosaurus canadensis protein sequences

Schweitzer  2009  Science  324:626-631

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

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


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 -

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



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

Background on ID

The Controversy in Society

The Evolution of Antievolution

Matzke  2016  Science 4351 (6268):28

Response by Discovery Institute

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


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 excerpt

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


Updated September 22 2016