W. Ford Doolittle

Education

• PhD, Stanford University
• FRSC
  

Academic Positions

• Department member since 1971
• Cross-appointed with Department of Philosophy in 2020
• Member, U.S. National Academy of Sciences

Research Topics

Genomics, Molecular Phylogeny, Gene Transfer

Research

I examine prevailing concepts in genomics, molecular biology and microbial ecology, most often as these reflect understandings of evolution by natural selection. Particular concerns are multilevel selection theory, selection for differential persistence (instead of differential reproduction), holobiosis and selection on cycles and interactions, microbiology and the Modern Synthesis, origin of eukaryotes and cellular complexity, lateral gene transfer and the Tree of Life, and the meaning of “function”.

Current Lab Members

Publications

1. Inkpen, S.A. and Doolittle, W.F. (2021) Adaptive regeneration across scales: Replicators and interactors from limbs to forests. Philosophy, Theory and Practice in Biology, in press.
2. Novick, A. and Doolittle, W.F. (2020) ’Species’ without species. Studies in History and Philosophy of Science, in press.
3. Brunet, T.D.P., Doolittle, W.F., and Bielawski, J.P. (2020) The role of purifying selection in the origin and maintenance of complex function. Studies in History and Philosophy of Science, in press.
4. Novick, A. and Doolittle, W.F. (2020) Horizontal persistence and the complexity hypothesis. Biology & Philosophy 35: 2
5. Doolittle, W.F. (2020) Two domains or three: What’s at stake? Curr. Biol. 30: R177-R179.
6. Linquist, S., Doolittle, W.F., and Palazzo, A.F. (2020) Getting clear about the F-word in genomics. PloS Genetics 16: e1008702
7. Doolittle, W.F. (2020) Could this pandemic usher in evolution’s next major transition?. Curr Biol. 30: R846-R848.
8. Doolittle, W.F. (2020) Is the Earth an Organism? Aeon. Published 3 December.
9. Doolittle, W.F. (2019) Making evolutionary sense of Gaia. Trends Ecol. Evol. 34: 889-894 [Article]
10. Wideman, J.G., Novick, A., Munoz-Gomez, S., Doolittle, W.F. (2019). Neutral evolution of cellular phenotypes. Curr. Op. Gen. Dev. 56-59: 87-94. [Article]
11. Doolittle, W.F. (2018) We simply cannot go on being so vague about “function”. Genome Biology 19: 223 [Article]
12. Mariscal, C. and Doolittle, W.F. (2018) Life and Life only: a radical alternative to life definitionism. Synthese 197: 2975-2989 [Article]
13. Doolittle, W.F, and Inkpen, S.A. (2018) Processes and patterns of interaction as units of selection: an introduction to ITSNTS thinking. Proc. Natl. Acad. Sci. U.S.A. 115: 4006-4014. [PubMed]
14. Booth, A. and Doolittle, W.F. (2015) Eukaryogenesis, how special really? Proc. Natl. Acad. Sci. U.S.A. 112: 10278-85. [PubMed]
15. Doolittle, W.F. (2013) Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. U.S.A, 110: 5294-5300. [PubMed]
16. Doolittle, W.F. and Zhaxybazyeva, O. (2009) On the origin of prokaryotic species. Genome Research 19: 744-756.
17. Doolittle, W.F. and Bapteste, E. (2007) Pattern pluralism and the Tree of Life hypothesis. Proc. Natl. Acad.Sci. U.S.A. 104: 2043-2049.
18. Papke, R.T., Koenig, J.E., Rodriguez-Valera, F. and Doolittle, W.F. (2004) Frequent recombination in a saltern population of Halorubrum. Science 306: 1928-1929.
19. Doolittle, W.F. (1999) Phylogenetic classification and the universal tree. Science 284: 2124-2128.
20. Archibald, J.M., Logsdon, J.M., Jr. and Doolittle, W.F. (1999) Recurrent paralogy in the evolution of archaeal chaperonins. Current Biology 9: 1053-1056.
21. Doolittle, W.F. (1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet. 14: 307-311.
22. Brown, J.R. and Doolittle, W.F. (1997) Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 61: 456-502.
23. Stoltzfus, A., Spencer, D., Zuker, M., Logsdon, J.M., Jr., and Doolittle, W.F. (1994) Testing the exon theory of genes: the evidence from protein structure. Science 265: 202-207.
24. Lam, W. and Doolittle, W.F. (1989) Shuttle vectors for the archaebacterium Halobacterium volcanii. Proc. Natl. Acad. Sci. U.S.A. 86:5478-5482.
25. Darnell, J.E. and Doolittle, W.F. (1986) Speculations on the early course of evolution. Proc. Natl. Acad. Sci. U.S.A. 83:1271-1275.
26. Gray, M.W. and Doolittle, W.F. (1982) Has the endosymbiont hypothesis been proven? Microbiol. Rev. 46:1-42.
27. Doolittle, W.F. (1981) Is nature really motherly? (A critique of J.E. Lovelock's Gaia: A New Look at Life on Earth). CoEvolution Quarterly 29:58-63
28. Doolittle, W.F. (1978) Genes in pieces, were they ever together? Nature 272:581-582.
29. Bonen, L. and Doolittle, W.F. (1975) On the prokaryotic nature of red algal chloroplasts. Proc. Natl. Acad. Sci. U.S.A. 72:2310-2314.
30. Doolittle, W.F. and Pace, N.R. (1971) Transcriptional organization of the ribosomal RNA cistrons in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 68:1786-1790.