Ben Stein Exposes Richard Dawkins (Dawkins admits possibility of ID, Just Not God).

In Ben Stein's new film "Expelled," there is a great scene where Richard Dawkins is going on about how evolution explains everything. This is part of Dawkins' grand claim, which echoes through several of his books, that evolution by itself has refuted the argument from design. The argument from design hold that the design of the universe and of life are most likely the product of an intelligent designer. Dawkins thinks that Darwin has disproven this argument.

So Stein puts to Dawkins a simple question, "How did life begin?" One would think that this is a question that could be easily answered. Dawkins, however, frankly admits that he has no idea. One might expect Dawkins to invoke evolution as the all-purpose explanation. Evolution, however, only explains transitions from one life form to another. Evolution has no explanation for how life got started in the first place. Darwin was very clear about this.

In order for evolution to take place, there had to be a living cell. The difficulty for atheists is that even this original cell is a work of labyrinthine complexity. Franklin Harold writes in The Way of the Cell that even the simplest cells are more ingeniously complicated than man's most elaborate inventions: the factory system or the computer. Moreover, Harold writes that the various components of the cell do not function like random widgets; rather, they work purposefully together, as if cooperating in a planned organized venture. Dawkins himself has described the cell as the kind of supercomputer, noting that it functions through an information system that resembles the software code.

Is it possible that living cells somehow assembled themselves from nonliving things by chance? The probabilities here are so infinitesimal that they approach zero. Moreover, the earth has been around for some 4.5 billion years and the first traces of life have already been found at some 3.5 billion years ago. This is just what we have discovered: it's quite possible that life existed on earth even earlier. What this means is that, within the scope of evolutionary time, life appeared on earth very quickly after the earth itself was formed. Is it reasonable to posit that a chance combination of atoms and molecules, under those conditions, somehow generated a living thing? Could the random collision of molecules somehow produce a computer?

It is ridiculously implausible to think so. And the absurdity was recognized more than a decade ago by Francis Crick, co-discoverer of the DNA double helix. Yet Crick is a committed atheist. Unwilling to consider the possibility of divine or supernatural creation, Crick suggested that maybe aliens brought life to earth from another planet. And this is precisely the suggestion that Richard Dawkins makes in his response to Ben Stein. Perhaps, he notes, life was delivered to our planet by highly-evolved aliens. Let's call this the "ET" explanation.

Stein brilliantly responds that he had no idea Richard Dawkins believes in intelligent design! And indeed Dawkins does seem to be saying that alien intelligence is responsible for life arriving on earth. What are we to make of this? Basically Dawkins is surrendering on the claim that evolution can account for the origins of life. It can't. The issue now is simply whether a natural intelligence (ET) or a supernatural intelligence (God) created life. Dawkins can't bear the supernatural explanation and so he opts for ET. But doesn't it take as much, or more, faith to believe in extraterrestrial biology majors depositing life on earth than it does to believe in a transcendent creator?

But you’re already drawing conclusions about the results before the process is finished.

No, I am not. The researcher drew the valid implication. I explained what the implication meant.

Yes, there are "ifs" involved. However, the "if" presented by the researcher is supported by evidence. Your "ifs" are nothing but speculation. And the comment by the researcher indicates that Darwinism is controversial.

I think Lynch has been peer-reviewed.




Publications: 




Lynch, M. 1974. The phytoplankton of the Allegheny Reservoir from May 1972 to 
September 1973. Science Studies (St. Bonaventure University) 30: 5-29. 




Shapiro, J., V. Lamarra, and Lynch, M. 1975. Biomanipulation: An ecosystem 
approach to lake restoration, pp. 85-96. In P. L. Brezonik and J. L. Fox (eds.) 
Water Quality Management Through Biological Control. Proc. Symp. Univ. 
Florida.




Lynch, M. 1977. Zooplankton competition and plankton community structure. 
Limnology and Oceanography 22: 775-777. 




Lynch, M. 1977. Fitness and optimal body size in zooplankton populations. 
Ecology 58: 763-774. 




Lynch, M. 1978. Complex interactions between natural coexploiters - Daphnia 
and Ceriodaphnia. Ecology 59: 552-564. 




Lynch, M. 1979. Predation, competition, and zooplankton community structure: 
An experimental study. Limnology and Oceanography 24: 253-272. 




Lynch, M. 1980. The evolution of cladoceran life histories. Quarterly Review 
of Biology 55: 23-42. 




Lynch, M. 1980. Predation, enrichment, and the evolution of cladoceran life 
histories: A theoretical approach. In W. C. Kerfoot (ed.) The Evolution and 
Ecology of Zoplankton Communities. American Society of Limnology and 
Oceanography Special Symposium No. 3: 367-376. 




Lynch, M. 1980. Aphanizomenon blooms: Alternate control and cultivation by 
Daphnia pulex. In W.C. Kerfoot (ed.) The Evolution and Ecology of Zooplankton 
Communities. American Society of Limnology and Oceanography Special Symposium 
No. 3: 299-304. 




Lynch, M. 1981. Predation, enrichment, and phytoplankton community structure. 
Limnology and Oceanography 26: 86-102. 




Lynch, M., B. Monson, M. Sandheinrich, and L. Weider. 1981. Patterns of 
size-specific mortality in zooplankton populations. Verh. Internat. Verein. 
Limnol. 21: 363-368. 




Lynch, M. 1982. How well does the Edmondson-Paloheimo model approximate 
instantaneous birth rates? Ecology 63: 12-18. 




Lynch, M. 1983. Ecological genetics of Daphnia pulex. Evolution 37: 358-374. 





Weis, A., P. Price, and M. Lynch. 1983. Selection for clutch size in the 
gall-maker Asteromyia carbonifera. Ecology 64: 688-695.




Lynch, M. 1983. Estimation of size-specific mortality rates in zooplankton 
populations by periodic sampling. Limnology and Oceanography 28: 533-545. 




Lynch, M., and R. Ennis. 1983. Resource availability, maternal effects, and 
longevity. Exper. Gerontology 18: 147-165.




Lynch, M., and W. Gabriel. 1983. Phenotypic evolution and parthenogenesis. 
American Naturalist 122: 745-764.




Lynch, M. 1984. The genetic structure of a cyclical parthenogen. Evolution 
38: 186-203. 




Lynch, M. 1984. The limits to life history evolution in Daphnia. Evolution 
38: 465-482. 




Lynch, M. 1984. Destabilizing hybridization, general-purpose genotypes, and 
geographic parthenogenesis. Quarterly Review of Biology 59: 257-290. 




Lynch, M. 1984. The selective value of alleles underlying polygenic traits. 
Genetics 108: 1021-1033. 




Lynch, M. 1985. Elements of a mechanistic theory for the life history 
consequences of food limitation. Ergeb. Limnol. 21: 351-362. 




Lynch, M. 1985. Speciation in the Cladocera. Verh. Internat. Verein. Limnol. 
22: 3116-3123. 




Lynch, M. 1985. Spontaneous mutations for life history characters in an 
obligate parthenogen. Evolution 39: 804-818. 




Lynch, M., L. Weider, and W. Lampert. 1986. Measurement of the carbon balance 
in Daphnia. Limnology and Oceanography 31: 17-33.




Lynch, M. 1986. Random drift, uniform selection, and the degree of population 
differentiation. Evolution 40: 640-643. 




Lynch, M., and W. G. Hill. 1986. Phenotypic evolution by neutral mutation. 
Evolution 40: 915-935.




Lynch, M. 1987. The consequences of fluctuating selection for isozyme 
polymorphisms in Daphnia. Genetics 115: 657-669. 




Lynch, M., and W. Gabriel. 1987. Environmental tolerance. American Naturalist 
129: 283-303.




Lynch, M., and W. Gabriel. 1987. Evolution of breadth of biochemical 
adaptation, pp. 67-83. In P. Calow (ed.) Evolutionary Physiological Ecology. 
Cambridge Univ. Press, Cambridge, UK.




Kerfoot, W. C., and M. Lynch. 1987. Branchiopod communities: associations 
with planktivorous fish in space and time, pp. 367-378. In W.C. Kerfoot and A. 
Sih (eds.) Predation. Univ. Press New England, Hanover, NH.




Lynch, M. 1987. The evolution of intrafamilial interactions. Proc. Natl. 
Acad. Sci. USA 84: 8507-8511. 




Lynch, M. 1988. The rate of polygenic mutation. Genetical Research 51: 
137-148. 




Lynch, M. 1988. The divergence of neutral quantitative characters among 
partially isolated populations. Evolution 42: 455-466. 




Lynch, M. 1988. Path analysis of ontogenetic data, pp. 29-46. In L. Persson 
and B. Ebenman (eds.) The Dynamics of Size-structured Populations. 
Springer-Verlag. 




Lynch, M., and S. J. Arnold. 1988. Measurement of selection on size and 
growth, pp. 47-59 In L. Persson and B. Ebenman (eds.) The Dynamics of 
Size-structured Populations. Springer-Verlag.




Lynch, M. 1988. Estimation of relatedness by DNA fingerprinting. Mol. Biol. 
Evol. 5: 584-599. 




Lynch, M. 1988. Design and analysis of experiments on random drift and 
inbreeding. Genetics 120: 791-807. 




Lynch, M. 1989. Phylogenetic hypotheses under the assumption of neutral 
quantitative genetic variation. Evolution 43: 1-17. 




Lynch, M., K. Spitze, and T. Crease. 1989. The distribution of life history 
variation in Daphnia pulex. Evolution 43: 1724-1736.




Lynch, M. 1989. The life history consequences of resource depression in 
Daphnia pulex. Ecology 70: 246-256. 




Lynch, M. 1990. The rate of morphological evolution in mammals from the 
standpoint of the neutral expectation. American Naturalist 136: 727-741. 




Lynch, M., and T. Crease. 1990. The analysis of population survey data on DNA 
sequence variation. Mol. Biol. Evol. 7: 377-394.




Crease, T., M. Lynch, and K. Spitze. 1990. A hierarchical analysis of 
population genetic variation in nuclear and mitochondrial genes in Daphnia. Mol. 
Biol. Evol. 7: 444-458.




Lynch, M. 1990. The similarity index and DNA fingerprinting. Mol. Biol. Evol. 
7: 478-484. 




Lynch, M., and W. Gabriel. 1990. Mutation load and the survival of small 
populations. Evolution 44: 1725-1737.




Gabriel, W., R. Bürger, and M. Lynch. 1991. Population extinction by 
mutational load and demographic stochasticity, pp. 49-59. In A. Seitz, and V. 
Loeschcke (eds.) Species Conservation: a Population Biological Approach. 
Birkhäuser Verlag, Basel.




Lynch, M. 1991. Methods for the analysis of comparative data in evolutionary 
biology. Evolution 45: 1065-1080. 




Lynch, M. 1991. The genetic interpretation of inbreeding depression and 
outbreeding depression. Evolution 45: 622-629. 




Lynch, M. 1991. Analysis of population genetic structure by DNA 
fingerprinting, pp. 113-126. In T. Burke, G. Dolf, A. J. Jeffreys, and R. Wolff 
(eds.) DNA Fingerprinting: Approaches and Applications. Birkhäuser Verlag, 
Basel.




Crease, T. J., and M. Lynch. 1991. Ribosomal DNA variation in Daphnia pulex. 
Mol. Biol. Evol. 8: 620-640.




Spitze, K., J. Burnson, and M. Lynch. 1991. The covariance structure of life 
history characters in Daphnia pulex. Evolution 45: 1081-1090.




Lynch, M., W. Gabriel, and A. M. Wood. 1991. The adaptive and demographic 
response of plankton populations to environmental change. Limnol. Oceanogr. 36: 
1301-1312.




Cohen, J. E., M. Lynch, and C. E. Taylor. 1991. Forensic DNA tests and 
Hardy-Weinberg equilibrium. Science 253: 1037.




Lynch, M. 1992. The life history consequences of resource depression in 
Ceriodaphnia quadrangula and Daphnia ambigua. Ecology 73: 1620-1629.




Gabriel, W., and M. Lynch. 1992. The selective advantage of reaction norms 
for environmental tolerance. J. Evol. Biol. 5: 41-59.




Lynch, M., and R. Lande. 1993. Evolution and extinction in response to 
environmental change, pp. 234-250. In P. Kareiva, J. Kingsolver, and R. Huey 
(eds.) Biotic Interactions and Global Change. Sinauer Assocs., Inc. Sunderland, 
MA.




Lynch, R. Bürger, D. Butcher, and W. Gabriel. 1993. Mutational meltdowns in 
asexual populations. J. Heredity 84: 339-344.




Lynch, M., and P. Jerrol. 1993. A method for calibrating molecular clocks and 
its application to animal mitochondrial DNA. Genetics 135: 1197-1208.




Lynch, M., and K. Spitze. 1994. Evolutionary genetics of Daphnia, pp. 
109-128. In L. Real (ed.) Ecological Genetics. Princeton Univ. Press.




Lynch, M. 1994. The neutral theory of phenotypic evolution, pp. 86-108. In L. 
Real (ed.) Ecological Genetics. Princeton Univ. Press.




Gabriel, W., M. Lynch, and R. Bürger. 1994. Muller's ratchet and mutational 
meltdowns. Evolution 47: 1744-1757.




Lynch, M., and B. Milligan. 1994. Analysis of population-genetic structure 
using RAPD markers. Molecular Ecology 3: 91-99.




Bürger, R., and M. Lynch. 1994. Evolution and extinction in a changing 
environment: a quantitative-genetic analysis. Evolution 49: 151-163.




Lynch, M., and H. W. Deng. 1994. Genetic slippage in response to sex. 
American Naturalist 144: 242-261.




Toline, C. A., and M. Lynch. 1994. Mutational divergence of life-history 
traits in an obligate parthenogen. Genome 37: 33-35.




Avise, J. C., S. M. Haig, O. A. Ryder, M. Lynch, and C. J. Geyer. 1995. 
Descriptive genetic studies: applications in population management and 
conservation biology, pp. 183-244. In J. D. Ballou, M. Gilpin, and T. J. Foose 
(eds.) Population Management for Survival and Recovery. Columbia Univ. Press, 
New York.




Conery, J. S., M. Lynch, and T. Hovland. 1995. Irregular computations on SIMD 
machines: a case study. Proc. 5th Symp. Frontiers of Massively Parallel 
Computation: 222-230.




Lehman, N., M. E. Pfrender, P. A. Morin, T. J. Crease, and M. Lynch. 1995. A 
hierarchical molecular phylogeny of the genus Daphnia. Mol. Phylog. Evol. 4: 
395-407.




Lynch, M., J. Conery, and R. Bürger. 1995. Mutational meltdowns in sexual 
populations. Evolution 49: 1067-1080.




Lynch, M., J. Conery, and R. Bürger. 1995. Mutation accumulation and the 
extinction of small populations. American Naturalist 146: 489-518.




Lynch, M. 1996. A quantitative-genetic perspective on conservation issues, 
pp. 471-501. In J. Avise and J. Hamrick (eds.) Conservation Genetics: Case 
Histories from Nature. Chapman and Hall, New York.




Lynch, M. 1996. Mutation accumulation in transfer RNAs: molecular evidence 
for Muller's ratchet in mitochondrial genomes. Mol. Biol. Evol. 13: 209-220.




Deng, H.-W., and M. Lynch. 1996. Change of genetic architecture in response 
to sex. Genetics 143: 203-212.




Deng, H.-W., and M. Lynch. 1996. Estimation of deleterious-mutation 
parameters in natural populations. Genetics 144: 349-360.




Houle, D., R. Morikawa, and M. Lynch. 1996. Comparing mutational 
variabilities. Genetics 143: 1467-1483.




Kibota, T., and M. Lynch. 1996. Estimate of the genomic mutation rate 
deleterious to overall fitness in Escherichia coli. Nature 381: 694-696.




Crease, T., S. K. Sung, S. L. Sung, N. Lehman, K. Spitze, and M. Lynch. 1997. 
Allozyme and mitochondrial DNA variation in populations of the Daphnia pulex 
complex from both sides of the Rocky Mountains. Heredity 79: 242-251.




Deng, H.-W., and M. Lynch. 1997. Inbreeding depression and inferred 
deleterious mutation parameters in Daphnia. Genetics 147: 147-155.




Lynch, M. 1997. Mutation accumulation in nuclear, organelle, and prokaryotic 
genomes: transfer RNA genes. Mol. Biol. Evol. 14: 914-925.




Schultz, S. T., and M. Lynch. 1997. Deleterious mutation and extinction: 
effects of variable mutational effects, synergistic epistasis, beneficial 
mutations, and degree of outcrossing. Evolution 51: 1363-1371.




Bürger, R., and M. Lynch. 1997. Adaptation and extinction in changing 
environments, pp. 209-240. In R. Bijlsma and V. Loeschcke (eds.) Environmental 
Stress, Adaptation and Evolution. Birkhäuser Verlag, Basel.




Lynch, M., and J. Blanchard. 1998. Deleterious mutation accumulation in 
organelle genomes. Genetica 102/103: 29-39.




Deng, H.-W., Y.-X. Fu, and Lynch, M. 1998. Inferring the major genomic mode 
of dominance and overdominance. Genetica 102/103: 559-567.




Lynch, M., and R. Lande. 1998. The critical effective size for a genetically 
secure population. Anim. Cons. 1: 70-72.




Lynch, M., L. Latta, J. Hicks, and M. Giorgianni. 1998. Mutation, selection, 
and the maintenance of life-history variation in a natural population. Evolution 
52: 727-733.




Vassilieva, L., and M. Lynch. 1999. Accumulation of spontaneous mutations in 
Caenorhabditis elegans. Genetics 151: 119-129.




Lynch, M., M. Pfrender, K. Spitze, N. Lehman, D. Allen, J. Hicks, L. Latta, 
M. Ottene, F. Bogue, and J. Colbourne. 1999. The quantitative and molecular 
genetic architecture of subdivided species. Evolution 53: 100-110. 




Lynch, M., and K. Ritland. 1999. Estimation of relatedness with molecular 
markers. Genetics 152: 1753-1766.




Lynch, M. 1999. The age and relationships of the major animal phyla. 
Evolution 53: 319-325. 




Force, A., M. Lynch, B. Pickett, A. Amores, Y.-L. Yan, and J. Postlethwait. 
1999. Preservation of duplicate genes by complementary, degenerative mutations. 
Genetics 151: 1531-1545.




Lynch, M., J. Blanchard, D. Houle, T. Kibota, S. Schultz, L. Vassilieva, and 
J. Willis. 1999. Spontaneous deleterious mutation. Evolution 53: 645-663. 




Conery, J. S., and M. Lynch. 1999. Genetic simulation library. Bioinformatics 
15: 85-86.




Lynch, M. 1999. Estimation of genetic correlations in natural populations. 
Genetical Research 74: 255-264.




Schultz, S. T., M. Lynch, and J. H. Willis. 1999. Spontaneous deleterious 
mutation in Arabidopsis. Proc. Natl. Acad. Sci. USA 96: 11393-11398. 




Lynch, M., and A. Force. 2000. The probability of duplicate-gene preservation 
by subfunctionalization. Genetics 154: 459-473.




Vassilieva, L., A. M. Hook, and M. Lynch. 2000. The fitness effects of 
spontaneous mutations in Caenorhabditis elegans. Evolution 54: 1234-1246.




Blanchard, J., and M. Lynch. 2000. Why do mitochondrial genes end up in the 
nuclear genome? Trends in Genetics 16: 315-320. 




Denver, D., K. Morris, M. Lynch, L. L. Vassilieva, and W. K. Thomas. 2000. 
High direct estimate of the mutation rate in the mitochondrial genome of C. 
elegans. Science 289: 2342-2344. 




Pfrender, M. E., and M. Lynch. 2000. Quantitative genetic variation in 
Daphnia: temporal changes in genetic architecture. Evolution 54: 1502-1509.




Lynch, M., and A. Force. 2000. Gene duplication and the origin of 
interspecific genomic incompatibility. American Naturalist 156: 590-605.




Pfrender, M. E., K. Spitze, J. Hicks, K. Morgan, L. Latta, and M. Lynch. 
2000. Lack of concordance between genetic diversity estimates at the molecular 
and quantitative-trait levels. Conservation Genetics 1: 263-269. 




Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of 
duplicate genes. Science 290: 1151-1154. 




Lynch, M. 2000. The limits to knowledge in quantitative genetics. Evol. Biol. 
32: 225-237.




Lynch, M., and J. S. Conery. 2001. Gene duplication and evolution: response 
to Long and Thornton and Zhang et al. Science 293: 1551a.




Higgins, K., and M. Lynch. 2001. Metapopulation extinction due to mutation 
accumulation. Proc. Natl. Acad. Sci. USA 98: 2928-2933. 




Morgan, K. K., J. Hicks, K. Spitze, L. Latta, M. Pfrender, C. Ottone, and M. 
Lynch. 2001. Patterns of genetic architecture for life-history traits and 
molecular markers in a subdivided species. Evolution 55: 1753-1761. 




Lynch, M. 2001. The molecular natural history of the human genome. Trends in 
Ecology and Evolution 16: 420-422. 




Lynch, M., and M. O'Hely. 2001. Supplementation and the genetic fitness of 
natural populations. Conservation Genetics 2: 363-378.




Lynch, M., M. O'Hely, B. Walsh, and A. Force. 2001. The probability of 
fixation of a newly arisen gene duplicate. Genetics 159: 1789-1804. 




Lynch, M. 2002. Intron evolution as a population-genetic process. Proc. Natl. 
Acad. Sci. USA 99: 6118-6123.




Lynch, M., and A. Richardson. 2002. The evolution of spliceosomal introns. 
Curr. Opin. Gen. Devel. 12: 701-710.




Lynch, M. 2002. Chromosomal repatterning by gene duplication. Science 297: 
945-947.




Jackson, R. B., C. R. Linder, M. Lynch, M. Purugannan, and S. Somerville. 
2002. Linking molecular insights and ecological research. Trends in Ecology and 
Evolution 17: 409-414.




Azevedo, R. B. R., P. D. Keightley, C. Lauren-Maatta, L. L. Vassilieva, M. 
Lynch, and A. M. Leroi. 2002. Spontaneous mutational variation for body size in 
Caenorhabditis elegans. Genetics 162: 755-765.




Lynch, M., and J. S. Conery. 2003. The evolutionary demography of duplicate 
genes, pp. 35-44. In A. Meyer and Y. Van de Peer (eds.), Genome Evolution. 
Kluwer Academic Publishers, Dordrecht.




Keightley, P. D., and M. Lynch. 2003. Towards a realistic model of mutations 
affecting fitness. Evolution 57: 683-685.




Lynch, M., and A. Kewalramani. 2003. Messenger RNA processing and the 
evolutionary proliferation of introns. Mol. Biol. Evol. 20: 563-571.




Baer, C. F., and M. Lynch. 2003. Correlated evolution of life-history with 
size at maturity in Daphnia pulicaria: patterns within and between populations. 
Genetical Research 81: 123-132.




Estes, S., and M. Lynch. 2003. Rapid recovery of mutation-accumulation lines 
by compensatory mutation. Evolution 57: 1022-1030.




Housworth, E., E. Martins, and M. Lynch. 2003. The phylogenetic mixed model. 
American Naturalist 163: 84-96.




Lynch, M., and J. S. Conery. 2003. The origins of genome complexity. Science 
302: 1401-1404.




Katju, V., and M. Lynch. 2003. The structure and early evolution of recently 
arisen gene duplicates in the Caenorhabditis elegans genome. Genetics 165: 
1793-1803. 




Denver, D. R., S. L. Swenson, and M. Lynch. 2003. An evolutionary analysis of 
the helix-hairpin-helix superfamily of DNA repair glycosylases. Molecular 
Biology and Evolution 20: 1603-1611.




Lynch, M. 2004. Gene duplication and evolution, pp. 33-47. In A. Moya and E. 
Font (eds.), Evolution: From Molecules to Ecosystems. Oxford University Press, 
New York, NY.




Estes, S., P. C. Phillips, D. R. Denver, W. K. Thomas, and M. Lynch. 2004. 
Mutation accumulation in populations of varying size: The distribution of 
mutational effects for fitness correlates in Caenorhabditis elegans. Genetics 
166: 1269-1279.




Denver, D. R., K. Morris, M. Lynch, and W. K. Thomas. 2004. High mutation 
rate and predominance of insertions in the Caenorhabditis elegans nuclear 
genome. Nature 430: 679-682.




Lynch, M., and V. Katju. 2004. The altered evolutionary trajectories of gene 
duplicates. Trends in Genetics 20: 544-549.




Denver, D. R., K. Morris, A. Kewalramani, K. Harris, A. Chow, S. 
Randell-Estes, M. Lynch, and W. K. Thomas. 2004. Abundance, distribution and 
mutation rates of homopolymeric nucleotide runs in the genome of Caenorhabditis 
elegans. J. Mol. Evol. 58: 584-595. 




Pfrender, M. E., J. Hicks, and M. Lynch. 2004. Biogeographic patterns and 
current distribution of molecular-genetic variation among populations of 
speckled dace, Rhinichthys osculus (Girard). Mol. Phylogenet. Evol. 30: 
490-502.




Dudycha, J. L., and M. Lynch. 2005. Ontogeny and allometry of resource 
allocation in animals with indeterminate growth. Evolution 59: 565-576.




Lynch, M., D. G. Scofield, and X. Hong. 2005. The evolution of 
transcription-initiation sites. Mol. Biol. Evol. 22: 1137-1146.




Denver, D. R., K. Morris, J. T. Streelman, S. K. Kim, M. Lynch, and W. K. 
Thomas. 2005. The transcriptional consequences of mutation and natural selection 
in Caenorhabditis elegans. Nature Genetics 37: 544-548.




Denver, D. R., S. Feinberg, S. Estes, W. K. Thomas, and M. Lynch. 2005. 
Mutation rates, spectra and hotspots in mismatch repair-deficient Caenorhabditis 
elegans. Genetics 170: 107-113. 




Baer, C. F., F. Shaw, C. Steding, M. Baumgartner, A. Hawkins, A. Houppert, N. 
Mason, M. Reed, F. Shaw, K. Simonelic, W. Woodward, and M. Lynch. 2005. 
Comparative evolutionary genetics of spontaneous mutations affecting fitness in 
rhabditid nematodes. Proc. Natl. Acad. Sci. USA 102: 5785-5790.




Colbourne, J. K., B. Robison, K. Bogart, and M. Lynch. 2005. Five hundred and 
twenty eight microsatellite markers for ecological genomic investigations using 
Daphnia. Mol. Ecol. Notes 4: 485-490.




Force, A., W. Cresko, F. B. Pickett, S. Proulx, C. Amemiya, and M. Lynch. 
2005. The origin of gene subfunctions and modular gene regulation. Genetics 170: 
433-446.




Paland, S., J. K. Colbourne, and M. Lynch. 2005. Evolutionary history of 
contagious asexuality in Daphnia pulex. Evolution 59: 800-813.




Ajie, B. C., S. Estes, M. Lynch, and P. C. Phillips. 2005. Behavioral 
degradation under mutation accumulation. Genetics 170: 655-660. 




Estes, S., Ajie, B. C., M. Lynch, and P. C. Phillips. 2005. Spontaneous 
mutational correlations for life-history, morphological, and behavioral 
characters in Caenorhabditis elegans. Genetics 170: 645-653.




Lynch, M. 2005. Intelligent design vs. intelligent evolution. Nature 435: 
276.




Lynch, M. 2005. Simple evolutionary pathways to complex proteins. Protein 
Science 14: 2217-2225.




Lynch, M., X. Hong, and D. G. Scofield. 2006. Nonsense-mediated decay and the 
evolution of eukaryotic gene structure, pp. 197-211. In L. E. Maquat (ed.) 
Nonsense-mediated mRNA Decay. Landes Bioscience, Georgetown, TX.




Robinson, C. D., S. Lourido, S. P. Whelan, J. L. Dudycha, M. Lynch, and S. 
Isern. 2006. Viral transgenesis of embryonic cell cultures from the freshwater 
microcrustacean Daphnia. J. Exp. Zool. 305: 62-67.




Lynch, M. 2006. The origins of eukaryotic gene structure. Mol. Biol. Evol. 
23: 450-468.




Paland, S., and M. Lynch. 2006. Transitions to asexuality result in excess 
amino-acid substitutions. Science 311: 990-902.




Lynch, M., B. Koskella, and S. Schaack. 2006. Mutation pressure and the 
evolution of organelle genome architecture. Science 311: 1727-1730.




Katju, V., and M. Lynch. 2006. On the formation of novel genes by duplication 
in the Caenorhabditis elegans genome. Mol. Biol. Evol. 23: 1056-1067.




Cristescu, M. E., J. K. Colbourne, J. Radivojac, and M. Lynch. 2006. A 
microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: on the 
prospect of crustacean genomics. Genomics 88: 415-430.




Denver, D. R., S. Feinberg, C. Steding, M. Durbin, and M. Lynch. 2006. The 
relative roles of three DNA repair pathways in preventing Caenorhabditis elegans 
mutation accumulation. Genetics 174: 57-65.




Hong, X., D. G. Scofield, and M. Lynch. 2006. Intron size, abundance, and 
distribution within untranslated regions of genes. Mol. Biol. Evol. 23: 
2392-2404.




Snoke, M. S., T. U. Berendonk, D. Barth, and M. Lynch. 2006. Elevated 
effective population sizes in unicellular eukaryotes. Mol. Biol. Evol. 23: 
2474-2479.




Lynch, M. 2006. Streamlining and simplification of microbial genome 
architecture. Ann. Rev. Microbiol. 60:327-349.




Omilian, A. R., M. E. A. Cristescu, J. L. Dudycha, and M. Lynch. 2006. 
Ameiotic recombination in asexual lineages. Proc. Natl. Acad. Sci. USA 103: 
18638-18643.




Scofield, D. G., X. Hong, and M. Lynch. 2007. Position of the final intron in 
full-length transcripts: determined by NMD? Mol. Biol. Evol. 24: 896-899.




Lynch, M. 2007. The frailty of adaptive hypotheses for the origins of 
organismal complexity. Proc. Natl. Acad. Sci. USA 104 Suppl.: 8597-8604. 




Rho, M., J. H. Choi, S. Kim, M. Lynch, and H. Tang. 2007. De novo 
identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics 8: 
90.




Lynch, M. 2007. The evolution of genetic networks by nonadaptive processes. 
Nature Reviews Genetics (in press).

I'd like to see what he says in the last publication listed above.

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Analysis

The evolution of genetic networks by non-adaptive processes