Nothing in Microbiology makes Sense except in the Light of Evolution

2,857 views

Published on

Professor Mark Pallen's Inaugural Lecture at Warwick Medical School, University of Warwick, April 15th 2014.
Storified version of lecture: https://storify.com/mjpallen/palleninaugural

Published in: Education, Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
2,857
On SlideShare
0
From Embeds
0
Number of Embeds
624
Actions
Shares
0
Downloads
19
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Nothing in Microbiology makes Sense except in the Light of Evolution

  1. 1. Nothing in Microbiology makes Sense except in the Light of Evolution Professor Mark Pallen
  2. 2. Online extras  Live tweet #palleninaugural  Slides available at http://www.slideshare.net/mpallen/pallen- inaugural-warwickfinal  Online guide  https://blogs.warwick.ac.uk/microbialun derground  https://storify.com/mjpallen/palleninaug ural  YouTube  https://www.youtube.com/user/Warwick MedicalSchool  https://www.youtube.com/user/pallenm Unofficial after- lecture drinks at The Varsity pub, CV4 7AJ
  3. 3. In Memoriam Fred Sanger 13 Aug 1918 – 19 Nov 2013 Carl Woese Jul 15, 1928 – Dec 30, 2012 Steve Jobs Feb 24, 1955 – Oct 5, 2011 Si monumentum requiris, circumspice
  4. 4. Acknowledgements ―We were united by a common love of Science, which we thought sufficient to bring together persons of all distinctions, Christians, Jews, Muslims and Heathens, Monarchists and Republicans.‖ Joseph Priestley on the Birmingham Lunar Society, 1793
  5. 5. Acknowledgements ―We were united by a common love of Science, which we thought sufficient to bring together persons of all distinctions, Christians, Jews, Muslims and Heathens, Monarchists and Republicans.‖ Joseph Priestley on the Birmingham Lunar Society, 1793
  6. 6. I am not obsessed with Darwin…  ...despite quoting him at my wedding, calling my first two children Emma and Charles, being on first name terms with two of his descendants, writing scholarly works about his views on religion!  John van Wyhe, Alison Pearn, Randal Keynes are all obsessed with Darwin…  …I just have a passing interest  But I don‘t want to let my audience down…
  7. 7. What is to be covered…  History of life  History of science  History of me and my science  Century by century,  Decade by decade…
  8. 8. The Origin: November 24th 1859 1859-1959 1960s 1970s 1980s 1990s 2000s 2010s
  9. 9. From 1859 to 1959 Darwin's Influence on Modern Thought  notion of branching evolution  common descent of all living things from a single origin  the mechanism of evolution is (largely) natural selection  evolution gradual  no major discontinuities  evolutionary biology, by contrast with physics and chemistry, is a historical science  evolutionist attempts to explain events/processes that have already taken place  feeds on variation and randomness  banishing typology and determinism Ernst Mayr Jul 5, 1904 – Feb 3, 2005
  10. 10. Tools to think with… Darwin’s Notebooks If we choose to let conjecture run wild, then animals our fellow brethren in pain, disease, death and suffering, and famine, our slaves in the most laborious works, our companions in our amusements; they may partake from our origin in one common ancestor; we may be all netted together
  11. 11. From 1859 to 1959: Genetics  1860s  Mendel‘s experiments on peas  1900s onwards  Rediscovery of Mendel (de Vries, Correns, Bateson)  Soma/germ-line distinction (Weismann)  Chromosomes; mutations (Morgan)  1940s  ―Modern Synthesis‖ of Evolution and Genetics (Fisher, Haldane, Wright, Dodzhansky, Mayr)
  12. 12. From 1830s to 1959: Computing  1837  Analytical Engine: Babbage  1842  Ada Lovelace: first program  1854  Boolean algebra  1936  Turing machines  1950s  First transisterized computers
  13. 13. From 1859 to 1959: Germ Theory  1860s  Pasteur demolishes spontaneous generation  1870s  Koch links anthrax to bacteria  Cohn founds bacterial taxonomy  Cohn and Darwin correspond  1880s  TB; cholera; diphtheria; antiserum
  14. 14. From 1859 to 1959 1942: Bacteria don’t have genetics… ―[bacteria] have no genes in the sense of accurately quantized portions of hereditary substance; and therefore they have no need for the accurate division of the genetic system which is accomplished by mitosis‖ Julian Huxley, 1942
  15. 15. From 1859 to 1959 1951: Bacteria do have genetics Chapter on‗Mutation and selection in microorganisms‘ in Dobzhansky‘s 1951 Genetics and the Origin of Species ―Demerec (1945) and Luria (1946) showed that penicillin-resistant strains of Staphylococcus aureus arise by mutations which survive in the presence of enough penicillin in the medium to kill most individuals of the parental strain.‖
  16. 16. From 1859 to 1959 1953: from Darwin to DNA Darwin, Nature April 1882 “through the kindness of Mr W. D. Crick of Northampton…” Crick and Watson, Nature, April 1953 beetle bivalve
  17. 17. 1960: I am born!
  18. 18. 1964: Dobzhansky’s dictum
  19. 19. Sidestep: Sequences Genes: DNA Proteins Information Storage Genes consist of sequences of characters from 4-base alphabet ACTG Information into Action Proteins consist of sequences of characters from 20-amino-acid alphabet encode All the genes, all the DNA in a bacterium = its Genome Sequence its complete “genetic blueprint”
  20. 20. 1965: Zuckerkandl and Pauling sequence homology and molecular phylogenetics
  21. 21. Sidestep: Sequence homology  Languages and informational macromolecules consist of sequences of characters that show ―descent with modification‖  Similarity due to descent from common ancestor (homology) can be used to infer function or meaning  one, two, three  eins, zwei, drei  un, deux, troi Hittite (20-13th C BCE) nu NINDA-n ezzateni
watar-ma ekutteni Now you will eat BREAD, And you will drink water Hrozný, Bedřich (1917) nu BREAD-n ezzateni
watar-ma ekutteni
  22. 22. 1970s: Sanger invents DNA sequencing
  23. 23. 1970s: me  Wallington High School  ―Must learn to control his grasshopper mind!‖  ―The primary purpose of a liberal education is to make one's mind a pleasant place in which to spend one's time” Sydney J. Harris  DNA is not in the textbooks!  But Cambridge entrance exam asks for protein sequence assembly!
  24. 24. 1980s: me  Fitzwilliam College, Cambridge  ―How much genome is there in a pork pie?‖  Final year project on Leprosy  London Hospital  Royal Free  Barts “I know that I ought to feel ashamed of days and evenings thus spent, but as some of my friends were very pleasant and we were all in the highest spirits, I cannot help looking back to these times with much pleasure.” “During the three years which I spent at Cambridge my time was wasted, as far as the academical studies were concerned…”
  25. 25. 1987: Bacteria join Darwin’s tree of life Eucarya Archaea Bacteria
  26. 26. As the 1980s turned into the 1990s  Exploiting computers to find sequence homology  Helicobacter pylori  A bacterial urease shows homology to a plant urease!  Clostridium difficile  Butanol fermentation genes  (same pathway that earned Chaim Weizmann the Balfour Declaration)  Reverse transcriptase and a group II intron
  27. 27. From 1990s: Proteins and domains The search for distant homologies Signal Peptide A B Coiled coil domain C D Transitivity of Homology Proteins consist of domains Distant Homology Signal Peptide ―Let two forms have not a single character in common, yet if these extreme forms are connected together by a chain of intermediate groups, we may at once infer their community of descent, and we put them all into the same class.‖ Origin of Species CHAPTER 14
  28. 28. From 1990s: Stress!  The lab-cultured bacterium is an artifact  ―Life...in a state of nature is solitary, poor, nasty, brutish and short‖ Thomas Hobbes  In the wild, bacteria face stressful feast fast or famine lifestyle  During infection, host responses cause stress  WT-funded PhD on starvation stress in Salmonella  BBSRC grant to use microarrays in follow-up study
  29. 29. From 1990s: Stress! Emma Nov 5th 1995 Charlie Mar10th 1997 Natasha Aug 3rd 1999 Tom Jan 7th 2002 Final Late October 1995
  30. 30. From 1990s: Bacterial Pathogenomics Discovered Biology Undiscovered Biology
  31. 31. From 1990s: Bacterial Pathogenomics
  32. 32. From 1990s: Tools to think with… Internet Databases
  33. 33. 1999-2001 From Barts to Belfast to Birmingham
  34. 34. 2000s E. coli: avoiding typological thinking And God created E. coli K-12 MG1655…?
  35. 35. 2000s: Evolution in E. coli Genome Degeneration and convergent evolution
  36. 36. 2000s: Evolution in E. coli Virulence Effectors
  37. 37. 2000s: Evolution in E. coli and beyond The Evolution of Complexity
  38. 38. 2000s: Darwin Days Evolution as obsession… …and reward
  39. 39. 2008: Genomes as documents of evolutionary history
  40. 40. Sequencing singularity From 2008: High-throughput sequencing brings genomes for the masses
  41. 41. 2010s: Bacterial evolution within outbreaks
  42. 42. 2011-2012 Acinetobacter Outbreak  First reported case July 2011 (military patient)  Outbreak lasted 80 weeks and involved 60 patients, including military and civilian patients  >90 isolates from patients and environment genome-sequenced on Illumina MiSeq, including multiples from same patient (different time and body sites)  Reconstructed phylogenetic tree and potential transmission chains, focussing infection control efforts on an operating theatre
  43. 43. 2010s: Darwin in the drug store  Genomes of two Acinetobacter baumannii isolates from single patient sequenced  before tigecycline therapy (susceptible) and after therapy (resistant)  Eighteen changes detected between AB210 and AB211  nine non-synonymous, including mutation in adeS which accounts for resistance  Three sections of early genome missing in late genome,  loss of DNA repair gene, causing increase in mutation rate?  Planned work on MDR TB  Madikay Senghore, Martin Antonio
  44. 44. 2011: Social Evolution Open-Source Genomics
  45. 45. 2013 onwards: genome to metagenome Challenging Gram and Koch
  46. 46. 2013 onwards: ancient DNA Genomes as documents of human history
  47. 47. 2013 onwards: Negativicutes when Gram stain and genealogy conflict
  48. 48. 2014 onwards : Tools to think with CLIMB consortium
  49. 49. 2014 onwards: Tools to think with… Enterobase  "More individuals are born than can possibly survive. A grain in the balance will determine which individual shall live and which shall die—which variety or species shall increase in number, and which shall decrease, or finally become extinct...‖  ―The slightest advantage in one being, at any age or during any season, over those with which it comes into competition, or better adaptation in however slight a degree to the surrounding physical conditions, will turn the balance.‖  Origin of Species, 1859, Charles Darwin  "More proposals are submitted than can possibly be funded. A grain in the balance will determine which proposal shall be funded and which shall die— which research group or institution shall increase in number, and which shall decrease, or finally become extinct…‖  ―The slightest advantage in one proposal, at any stage or during any meeting, over those with which it comes into competition, or better adaptation in however slight a degree to the surrounding political conditions, will turn the balance.‖  Origin of Research Projects, 2014
  50. 50. There is grandeur in this view of life, with its several powers having been originally breathed into a few forms or into one; and that whilst this planet has been cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved. Back to 1859: Darwin’s grandeur

×