Talk by Jonathan Eisen for #LAMG16

1. #LAMG16 @phylogenomics
Arrowhead and Microbial Genomes:
Update on the Tree of Life
September 18, 2016
Lake Arrowhead Microbial Genomes
#LAMG16
Jonathan A. Eisen
University of California, Davis
@phylogenomics

2. TWO KEY THINGS TO REMEMBER
#LAMG16 @phylogenomics
Arrowhead and Microbial Genomes:
Update on the Tree of Life
September 18, 2016
Lake Arrowhead Microbial Genomes
#LAMG16
Jonathan A. Eisen
University of California, Davis
@phylogenomics

3. TWO KEY THINGS TO REMEMBER
#LAMG16 @phylogenomics
Arrowhead and Microbial Genomes:
Update on the Tree of Life
September 18, 2016
Lake Arrowhead Microbial Genomes
#LAMG16
Jonathan A. Eisen
University of California, Davis
@phylogenomics

4. #LAMG16 @phylogenomics
Arrowhead and Microbial Genomes:
Update on the Tree of Life
September 18, 2016
Lake Arrowhead Microbial Genomes
#LAMG16
Jonathan A. Eisen
University of California, Davis
@phylogenomics

5. #LAMG16 @phylogenomics
Arrowhead and Microbial Genomes:
Update on the Tree of Life
September 18, 2016
Lake Arrowhead Microbial Genomes
#LAMG16
Jonathan A. Eisen
University of California, Davis
@phylogenomics

6. #LAMG16 @phylogenomics
The Tree of Life
http://phylogenomics.blogspot.com

7. #LAMG16 @phylogenomics
Arrowhead and Microbial Genomes:
Update on the Tree of Life
September 18, 2016
Lake Arrowhead Microbial Genomes
#LAMG16
Jonathan A. Eisen
University of California, Davis
@phylogenomics

8. Arrowhead and Microbial Genomes:
Update on the Tree of Life
September 18, 2016
Lake Arrowhead Microbial Genomes
#LAMG16
Jonathan A. Eisen
University of California, Davis
@phylogenomics
THREE KEY THINGS TO REMEMBER
#LAMG16 @phylogenomics

9. Origin of the Meeting
• Who knows how the meeting started?
#LAMG16 @phylogenomics

10. Origin of the Meeting
• Who knows how the meeting started?
• How could you find out?
#LAMG16 @phylogenomics

11. Origin of the Meeting
• Who knows how the meeting started?
• How could you find out?
• The Google …
#LAMG16 @phylogenomics

12. Using the Google
#LAMG16 @phylogenomics

13. Using the Google
#LAMG16 @phylogenomics

14. Using the Google
#LAMG16 @phylogenomics

15. Possible Source of Confusion
#LAMG16 @phylogenomics
Jeffrey van Leeuwenhoek Miller

16. History of the Meeting
• See http://
www.lamg.info/
history
#LAMG16 @phylogenomics
Jeffrey van Leeuwenhoek Miller

17. History of the Meeting
• And see http://microbe.net/lake-arrowhead-
microbial-genomes-history/ for 1998-2016 notes
• http://tinyurl.com/LAMG16
#LAMG16 @phylogenomics

18. Sampling from 1998-2014
#LAMG16 @phylogenomics

19. Sampling from 1998
#LAMG16 @phylogenomics

20. Sampling from 1998
#LAMG16 @phylogenomics

21. Sampling from 1998
#LAMG16 @phylogenomics

22. The Real Story of 1998?
#LAMG16 @phylogenomics

23. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

24. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

25. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

26. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

27. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

28. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

29. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

30. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

31. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

32. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

33. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

34. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

35. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

36. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

37. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

38. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

39. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

40. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

41. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

42. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

43. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

44. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

45. 1998 - Doodles Reveal All
#LAMG16 @phylogenomics

46. Real History of Arrowhead
QUOTES, QUOTES, QUOTES
#LAMG16 @phylogenomics

47. 2014 …
#LAMG16 @phylogenomics

48. 2014 …
• I am spending bioinformatic time up the
wazoo
#LAMG16 @phylogenomics

49. 2014 …
• I am spending bioinformatic time up the
wazoo
• It may be sh*t to you but it's my bread and
butter
#LAMG16 @phylogenomics

50. 2002
#LAMG16 @phylogenomics

51. 2002
• Leave it to Jeff Miller to take a shot at the
Gordon Conferences in his intro
#LAMG16 @phylogenomics

52. 2002
• Leave it to Jeff Miller to take a shot at the
Gordon Conferences in his intro
• It looks like someone with a bad cold
sneezed against the wall
#LAMG16 @phylogenomics

53. 2002
• Leave it to Jeff Miller to take a shot at the
Gordon Conferences in his intro
• It looks like someone with a bad cold
sneezed against the wall
• Wild mistakes - brilliant guesses
#LAMG16 @phylogenomics

54. 2002
• Leave it to Jeff Miller to take a shot at the
Gordon Conferences in his intro
• It looks like someone with a bad cold
sneezed against the wall
• Wild mistakes - brilliant guesses
• He lied about the size of anthrax
#LAMG16 @phylogenomics

55. 2002
• Leave it to Jeff Miller to take a shot at the
Gordon Conferences in his intro
• It looks like someone with a bad cold
sneezed against the wall
• Wild mistakes - brilliant guesses
• He lied about the size of anthrax
• If it grows you win, if it doesn’t you have
to give me your soul for all eternity
#LAMG16 @phylogenomics

56. 2002
• Leave it to Jeff Miller to take a shot at the
Gordon Conferences in his intro
• It looks like someone with a bad cold
sneezed against the wall
• Wild mistakes - brilliant guesses
• He lied about the size of anthrax
• If it grows you win, if it doesn’t you have
to give me your soul for all eternity
• That’s because she has the arrogance of
the aristocrats
#LAMG16 @phylogenomics

57. 2004
#LAMG16 @phylogenomics

58. 2004
• He wanted to keep his finger in the
Chlamydia stuff
#LAMG16 @phylogenomics

59. 2004
• He wanted to keep his finger in the
Chlamydia stuff
• Engineering other systems that don’t
suck
#LAMG16 @phylogenomics

60. 2004
• He wanted to keep his finger in the
Chlamydia stuff
• Engineering other systems that don’t
suck
• It’s like a tootsie pop
#LAMG16 @phylogenomics

61. 2004
• He wanted to keep his finger in the
Chlamydia stuff
• Engineering other systems that don’t
suck
• It’s like a tootsie pop
• Space time continuum of genes and
genomes
#LAMG16 @phylogenomics

62. 2004
• He wanted to keep his finger in the
Chlamydia stuff
• Engineering other systems that don’t
suck
• It’s like a tootsie pop
• Space time continuum of genes and
genomes
• The wormhole that allows us to tunnel
into today’s world
#LAMG16 @phylogenomics

63. Other years
• Space-time continuum of genes and
genomes
#LAMG16 @phylogenomics

64. Quotes
• Space-time continuum of genes and
genomes
• Microbes not only have a lot of sex, they
have a lot of weird sex
#LAMG16 @phylogenomics

65. Quotes
• Space-time continuum of genes and
genomes
• Microbes not only have a lot of sex, they
have a lot of weird sex
• Gene sequences are the wormhole that
allows one to tunnel into the past
#LAMG16 @phylogenomics

66. Quotes
• Space-time continuum of genes and
genomes
• Microbes not only have a lot of sex, they
have a lot of weird sex
• Gene sequences are the wormhole that
allows one to tunnel into the past
• This is how you do metagenomics on 50
dollars, and that’s Canadian dollars
#LAMG16 @phylogenomics

67. Quotes
• Space-time continuum of genes and
genomes
• Microbes not only have a lot of sex, they
have a lot of weird sex
• Gene sequences are the wormhole that
allows one to tunnel into the past
• This is how you do metagenomics on 50
dollars, and that’s Canadian dollars
• The human guts are a real milieu of stuff
#LAMG16 @phylogenomics

68. Quotes
• Space-time continuum of genes and
genomes
• Microbes not only have a lot of sex, they
have a lot of weird sex
• Gene sequences are the wormhole that
allows one to tunnel into the past
• This is how you do metagenomics on 50
dollars, and that’s Canadian dollars
• The human guts are a real milieu of stuff
• Antibiotics do not kill things, they corrupt
them #LAMG16 @phylogenomics

69. Quotes
• There comes a point in life when you have
to bring chemists into the picture
#LAMG16 @phylogenomics

70. Quotes
• There comes a point in life when you have
to bring chemists into the picture
• The rectal swabs are here in tan color
#LAMG16 @phylogenomics

71. Quotes
• There comes a point in life when you have
to bring chemists into the picture
• The rectal swabs are here in tan color
• If I have time I will tell you about a dream
#LAMG16 @phylogenomics

72. Quotes
• There comes a point in life when you have
to bring chemists into the picture
• The rectal swabs are here in tan color
• If I have time I will tell you about a dream
• Another thing you need to know" pause
"Actually you don't NEED to know any of
this
#LAMG16 @phylogenomics

73. Quotes
• There comes a point in life when you have
to bring chemists into the picture
• The rectal swabs are here in tan color
• If I have time I will tell you about a dream
• Another thing you need to know" pause
"Actually you don't NEED to know any of
this
• I have been influenced by Fisher Price
throughout my life
#LAMG16 @phylogenomics

74. Quotes
• There comes a point in life when you have
to bring chemists into the picture
• The rectal swabs are here in tan color
• If I have time I will tell you about a dream
• Another thing you need to know" pause
"Actually you don't NEED to know any of
this
• I have been influenced by Fisher Price
throughout my life
• This is going to be ironic coming from
someone who studies circumcision#LAMG16 @phylogenomics

75. Quotes
• And we will bring out the unused cheese
from yesterday
#LAMG16 @phylogenomics

76. Quotes
• And we will bring out the unused cheese
from yesterday
• A paper came out next year
#LAMG16 @phylogenomics

77. Quotes
• And we will bring out the unused cheese
from yesterday
• A paper came out next year
• It takes 1000 nanobiologists to make one
microbiologist
#LAMG16 @phylogenomics

78. Quotes
• And we will bring out the unused cheese
from yesterday
• A paper came out next year
• It takes 1000 nanobiologists to make one
microbiologist
• In an engineering sense, the vagina is a
simple plug flow reactor
#LAMG16 @phylogenomics

79. Quotes
• And we will bring out the unused cheese
from yesterday
• A paper came out next year
• It takes 1000 nanobiologists to make one
microbiologist
• In an engineering sense, the vagina is a
simple plug flow reactor
• The human mind can conceive of things
with no basis in physical reality
#LAMG16 @phylogenomics

80. Quotes
• And we will bring out the unused cheese
from yesterday
• A paper came out next year
• It takes 1000 nanobiologists to make one
microbiologist
• In an engineering sense, the vagina is a
simple plug flow reactor
• The human mind can conceive of things
with no basis in physical reality
• Thoughts can go faster than the speed of
light #LAMG16 @phylogenomics

81. Quotes
• We are the environment. We live the
phenotype.
#LAMG16 @phylogenomics

82. Quotes
• We are the environment. We live the
phenotype.
• We have been using this word for many
years without actually realizing it was
correct
#LAMG16 @phylogenomics

83. Quotes
• We are the environment. We live the
phenotype.
• We have been using this word for many
years without actually realizing it was
correct
• A little bit about time, but I am going to
spend a lot less time on time than on
space
#LAMG16 @phylogenomics

84. Quotes
• We are the environment. We live the
phenotype.
• We have been using this word for many
years without actually realizing it was
correct
• A little bit about time, but I am going to
spend a lot less time on time than on
space
• I am going to wrap up as I hear the
crickets chirping
#LAMG16 @phylogenomics

85. 2004
#LAMG16 @phylogenomics

86. Sampling from 2004
#LAMG16 @phylogenomics

87. Sampling from 2004
#LAMG16 @phylogenomics

88. Sampling from 2004
#LAMG16 @phylogenomics

89. Sampling from 2004
#LAMG16 @phylogenomics

90. Sampling from 2004
#LAMG16 @phylogenomics

91. Sampling from 2004
#LAMG16 @phylogenomics

92. Sampling from 2004
#LAMG16 @phylogenomics

93. Sampling from 2004
#LAMG16 @phylogenomics

94. Sampling from 2004
#LAMG16 @phylogenomics

95. Trends in Topics
#LAMG16 @phylogenomics

96. Topics Over Time
0
25
50
75
100
1998 2000 2002 2004 2006 2008 2010 2012 2014 2016
Genomes Communities
Metagenomes Microbiomes

97. Topics Over Time
0
25
50
75
100
1998 2000 2002 2004 2006 2008 2010 2012 2014 2016
Genomes Communities
Metagenomes Microbiomes

98. Topics Over Time
0
25
50
75
100
1998 2000 2002 2004 2006 2008 2010 2012 2014 2016
Genomes Communities
Metagenomes Microbiomes

99. Topics Over Time
0
25
50
75
100
1998 2000 2002 2004 2006 2008 2010 2012 2014 2016
Genomes Communities
Metagenomes Microbiomes

100. Topics Over Time
0
25
50
75
100
1998 2000 2002 2004 2006 2008 2010 2012 2014 2016
Genomes Communities
Metagenomes Microbiomes

101. Topics Over Time
0
25
50
75
100
1998 2000 2002 2004 2006 2008 2010 2012 2014 2016
Genomes Communities
Metagenomes Microbiomes

102. Topics Over Time
0
25
50
75
100
1998 2000 2002 2004 2006 2008 2010 2012 2014 2016
Genomes Communities
Metagenomes Microbiomes

103. Topics Over Time
0
25
50
75
100
1998 2000 2002 2004 2006 2008 2010 2012 2014 2016
Genomes Communities
Metagenomes Microbiomes

104. Topics Over Time
0
25
50
75
100
1998 2000 2002 2004 2006 2008 2010 2012 2014 2016
Genomes Communities
Metagenomes Microbiomes

105. Topics Over Time
0
25
50
75
100
1998 2000 2002 2004 2006 2008 2010 2012 2014 2016
Genomes Communities
Metagenomes Microbiomes

106. Possible Talks for 2016?
#LAMG16 @phylogenomics

107. Possible Talks for 2018?
#LAMG16 @phylogenomics

108. Microbiome Will GIVE The Talks
#LAMG16 @phylogenomics

109. #LAMG16 Speakers
#LAMG16 @phylogenomics