>> From the Library of
Congress in Washington DC. >> Dan Turello: Good afternoon,
welcome to our program, the origins of the RNA world:
a collective oral history. We're glad you're here, we're
glad the Metro shutdown yesterday and not today. This is a good thing. I'm Dan Turello, I'm on staff of the
Kluge Center and before we begin, I want to remind you
of a couple of items, we 're recording today's
conversation for future placement on the library's YouTube
and iTunes channels and also please turn off any
cell phones or any other devices that might interfere
with the conversation. This afternoon's conversation
is being moderated by Nathaniel Comfort. He is the Blumberg NASA Library
of Congress chair in astrobiology. I'm going to introduce him in just
a few moments, but first a few words about the Kluge Center and about
the Blumberg program as a whole. The Kluge Center was created 16
years ago thanks to a generous gift by philanthropist John W. Kluge. We have two primary roles, the first
is to create a scholarly community of approximately a hundred
scholars every year. These are senior scholars,
postdoctoral fellows, pre-doctoral fellows,
all of whom contribute to a vibrant community here on
Capitol Hill and in the library. The second function is to
administer the Kluge prize. This is awarded by the
librarian of Congress, it's a one million dollar award
that recognizes lifetime achievement in the study of humanity. It was last awarded to
philosophers Jürgen Habermas and Charles Taylor this past summer. So within the Kluge
Center, the Blumberg chair in astrobiology is the result
of what has been a unique and rewarding collaboration between
NASA and the Library of Congress. The chair takes its name from
Nobel Prize winner Barry Blumberg, he was the founder of the
NASA Astrobiology Institute and also a founding
member of the Library of Congress Scholars Counsel. Blumberg envisioned the creation
of a chair in the Kluge Center that would focus on the humanistic and societal impacts
of astrobiology. The idea was to connect
scientific discoveries in the field of astrobiology with
the best thinking in the humanities and
social sciences. And astrobiology is a field
of inquiry, in particular, is one that allows
for the big questions. Things like investigations
on the origins of life about which we are going to
hear more about this afternoon. So placing scientific knowledge
within the context of historical and philosophical thinking gives
us the chance to consider questions of meaning and of value that are
important to us as human beings. Nathaniel was the third
chair to be in residence. Our first chair was David Grinspoon,
who I see sitting here in the back. He researched a book
on the Anthropocene. We then had historian
of science Steven Dick, who wrote about the potential
societal impact of the discovery of microbial or complex
life beyond earth, and this year we've been thrilled to
have Nathaniel with us since October and he is looking at the
history of the genomic revolution in origin of life research. In addition to holding the Blumberg
chair here at the Kluge Center, Nathaniel is professor in
the department of the history of medicine at the Johns
Hopkins University. He has published scores of
articles and several books, I mentioned just a few
of the more salient ones. "The Science of Human Perfection:
How Genes Became the Heart of American Medicine" published by
Yale in 2012, "The Tangled Field: Barbara McClintock's
Search for the Patterns of Genetic Control" published by
Harvard in 2001, he' also the editor of the volume "The
Panda's Black Box: Opening Up the Intelligent
Design Debate" published by Hopkins in 2007. He writes extensively for
the Atlantic, the Nation, the New York Times book
review, and other outlets. He also blogs and so
you can look this up. His blog is
genotopia.scienceblog.com. So we've been thrilled to
have him with us this year and we' re grateful to him for
bringing such a distinguished group of panelists to the library
today and we look forward to a fascinating program. >> Nathaniel Comfort:
Well thank you Dan. It's a real pleasure to be here
and I would just like to begin by, with a word of thanks
to the Kluge Center. This is an absolutely marvelous
and a unique place to be, just tell you how great it is
when I got my acceptance letter, it had a line in it saying that
we expect you to protect your time for research and scholarship
and reflection . Now how rare is that,
I mean in these days, so this is a wonderful place
and I'm delighted to be here. And I'm particularly thrilled
to have this distinguished panel of guests with me today to
talk about the RNA world, which is an important aspect of
research on the origin of life. And I'm just going to introduce
them briefly in alphabetical order, first W. Ford Doolittle, who's from Dalhousie University
in Halifax, Nova Scotia. He got a PhD in, his PhD in
biological sciences from Stanford, he then did postdoctoral work with the distinguished scientists
Sol Spiegelman and Norm Pace. He then joined the department of
biochemistry and molecular biology at Dalhousie in 1971 and
he's been there ever since. He has won a Guggenheim Fellowship,
he's a member of the fellow, a fellow of the Royal
Society of Canada, a member of the National Academy
of Sciences, and on and on, many distinguished honors. And his research is on, has been on
the molecular genetics of microbes and things like lateral
gene transfer instead of hereditary transfer of
genetic material across species, selfish DNA, gene structure,
particularly introns about which I'm going
to say a little bit in a moment, and the tree of life. And one thing that's really quite
distinctive about this scientist is that he, right now, has
two postdoctoral fellows who are philosophers of science,
so he really bridges the sciences and humanities which is something
that I find really appealing. George Fox is the Moores professor
of biochemistry and biology at the University of Houston, he
got his PhD in chemical engineering from Syracuse, he's the
co-discoverer with Carl Woese, of the archaea, one of the three
fundamental domains of life which really overturned the way
people thought life evolved. He is a fellow of the International
Astrobiological Society, member of the American
Academy of Microbiology, fellow of the American Academy
of the Association of Science, and his research has been on
the evolution of the machinery of genetic translation, how
information moves from nucleic acids into amino acids and forming
proteins that form the enzymes and interesting structures
in the body. Ray Gesteland is the
emeritus professor of biology and the former vice president of
research at the University of Utah, he 's a Howard Hughes
Medical Institute investigator, his PhD was from Harvard where
he studied with James Watson. He did postdoctoral work
in Geneva, Switzerland and joined Cold Spring
Harbor Laboratory in 1967, staying there until 1978 when he
joined the University of Utah. With Ray White, he began a new and
now very distinguished Institute for Human Genetics, and since 1972,
he has collaborated with John Atkins on the phenomenon of
genetic recoding. He is the editor of the volume
"RNA World" so he wrote the book, or at least edited it, and, which
is now in its fourth edition so it's really the sort
of Bible of this field, so it 's really a
delight to have him. And Walter Gilbert is the Carl
Loeb emeritus professor at Harvard, he has a doctorate in physics
from the University of Cambridge, and was appointed to the Harvard
physics department in 1959, he then switched from physics to
biology and he ran a lab jointly with James D. Watson of
the double helix fame. He won a Nobel Prize in chemistry in
1980 for the invention of a method of DNA sequencing, and he's
a pioneer in biotechnology, he founded Biogen, one of the first
biotech companies, if not the first, he oversaw the development of a
number of groundbreaking products, including alpha interferon
and hepatitis B vaccine, and he also cofounded the
large biotechnology company, Myriad Genetics. Other honors besides the Nobel Prize
include Louisa Gross Horwitz prize, the Gairdner award from Canada, the
Lasker award, the National Academy of Sciences, he is a foreign
member of the Royal Society, British Royal Society,
and on and on. His research has included the
identification of messenger RNA, the lac repressor, a fundamental
component of the lactose gene in bacteria model system,
pioneering work in recombinant DNA, the first genetic engineering,
including the expression of insulin in bacteria, he is a
founding, a pioneer member of the human genome project, and
he coined the term RNA world. So, it is an absolute thrill to have
these gentlemen here with me today and to get into a conversation
with them. And before we start that, I just
want to give a few remarks just to make sure we're all on the same
page, just introduce you to the idea of the RNA world, alright? So I can't see, oh here we are. So what is the RNA world? Well beginning in 1953,
James Watson, Francis Crick, aided by Maurice Wilkins and
Rosalind Franklin, of course, solved the double helical
structure of DNA. Now the double helix, the shape of the molecule usually
gets all the credit, but the really interesting
thing about it is those bars on the ladder crossing the spiral
staircase because those are, those symbolize the
nucleotide bases that pair up, so it's really two half
spiral staircases, right, each specifying another
nucleic acid and they realized that in the sequence of those bases
was genetic information, okay? So it was in the DNA that
the information was held for making proteins. DNA information goes to
protein the A s, C s, G s, and T s of DNA turns
into the amino acids that are strung together
to form proteins. Proteins are crucial molecules in
the cell, they do all sorts of work, they are enzymes most importantly,
but they're also structural and the basis of neuronal
transmission and structural elements in the cell, and so forth, crucial,
crucial components of the cell. And in 1956, three years
after the double helix, Francis Crick coined what he
whimsically called the central dogma of molecular biology and Watson
drew it out in this cartoon, which says a number of things about
the flow of genetic information. This is really the first
time people began to think about genetic information,
and the important thing that most people remember of the central dogma is this
simple phrase DNA makes RNA, makes proteins, okay, so
what's DNA versus RNA? They're very similar molecules, there are really only two
differences between them, one of the four bases is different,
RNA uses Uracil instead of Thymine, and you'll see that there's on
the ring, there's one difference, an OH instead of an H, those
are the only differences between the two molecules but those
two slight differences make huge differences in the chemistry, and DNA of course forms a
double-stranded molecule. RNA is usually single-stranded,
and that means it can bend around and form into all kinds of
different shapes, alright? It's also much more
reactive than DNA, and those two facts become
important in the RNA world. Okay. So the DNA makes RNA, makes
protein through two processes, one called transcription where
an RNA molecule messenger RNA, which Dr. Gilbert was a
key figure in identifying, and then that messenger RNA
is translated into a sequence of amino acids that
makes a protein, okay? And as I said, proteins
are ubiquitous in the cell, they form hair, nails,
muscles, nerve cells, and most importantly enzymes. There are a couple of, and that
translation process is really sort of the heart of what we 're
going to be talking about today. Translation occurs in
structures called ribosomes, so the messenger RNA
is read off the DNA, and then it moves outside the
cell nucleus to the outer part of the cell and in the ribosome
it is pulled through like a tape through a tape recorder and it
is read off and the sequence of those nucleotides specifies
the sequence of amino acids so this building chain of amino
acids then forms the protein. Now you'll notice a
couple of things here, one is that there is an
awful lot of RNA here, you have the messenger
RNA, ribosomal RNA, the ribosome itself is made of RNA
mostly, and then, I've got one more, and then transfer RNA is the
molecule that actually attaches to the amino acid and brings
it to the building chain. So there's a lot of RNA in
this part of the cell, okay? People very quickly began to
notice this fact and in 1962 one of the pioneers of molecular biology
Alex Rich gave a paper on the origin of life so this was just nine
years after the double helix and in fact was the
year that Watson, Crick, and Wilkins won the Nobel Prize,
and he said the hypothetical stem or parent nucleotide molecule
was initially an RNA-like polymer which was able to convey
genetic information as well as organize the amino acids into a specific sequence
to make proteins, okay? So there's a, so RNA does most
of the work of that process. And in 1965, just 3 years later, two other scientists made
similar realizations. J. B. S. Haldane said that life, by which he meant indefinite
replication of patterns of large molecules, can be based on
RNA without DNA, and Fritz Lipmann at the same conference said that
DNA probably evolved later than RNA, so there was a time in which you had
RNA and proteins and not yet DNA. So back to this diagram here,
another thing that we can notice about this is that there are
enzymes or proteins involved in each of these processes, so none of this, although there are RNA molecules
involved, none of this can happen without enzymes, without
proteins, alright. So these things are
specifying proteins and you need proteins to do it. So that leads to a kind of
chicken and egg problem, alright, where you have genes that store
information, that encode proteins that make enzymes and
you need those enzymes to catalyze the reactions
to copy the genes. So how do you get out
of that problem? The RNA world is the way you
get out of that problem, okay? And several people noticed this in
a speculative way in the late 1960s. Carl Woese said that proto-RNA could
have been, the proto-ribosomal RNA, could have been the original genome,
and Francis Crick the next year said that possibly the first
enzyme was an RNA molecule with replicase properties, the
ability to copy other RNAs. Thus a system based mainly
on RNA is not impossible, and the same year his
colleague Leslie Orgel said, asked could polynucleotides of RNA with well-defined secondary
structures folding act as primitive enzymes? Could they be more than just
information storage molecules? Could they actually
catalyze reactions too? That would be a way out of
the chicken and egg problem. So the answer is yes! But hang on one second. First I want to tell you about
a couple things that are going to come up in the conversation. One is the, as I mentioned earlier,
the discovery of the archaea, this brand-new group of single
celled organisms that George and Carl Woese recognized through
sequencing RNA, ribosomal RNA, were different from the bacteria,
and so this created a lot of discussion about how, what was
the original branching structure in the tree of life. And the same year, 1977 was a big
year for origin of life research. Phil Sharp and his colleagues
at Yale and Rich Roberts at Cold Spring Harbor and his
colleagues independently discovered that genes come in pieces. In higher organisms, eukaryotes, organisms with a membrane-bound
nucleus that contains the chromosomes, have
genes that can be segmented, okay, they can, and when you go
through the transcription and translation process,
those middle bits between the segments get spliced out
and the segments join it together to form the final RNA that
gets read into the protein. So that's really odd,
genes come in these pieces. Walter Gilbert wrote an article the
next year called Genes in Pieces and in that paper he named those
segments exons, for the segments that are part of the genes,
and introns as the segments between the exons, so they're
inter, in between the exons, okay. And he and Ford Doolittle
over the next few years got in a lively discussion
about which came first, when introns were invented
evolutionarily. Were they part of the
very first organisms or did they get invented later
as the eukaryotes evolved? So this was a very
important discussion in origin of life research that I want
to talk about more later. And then finally, the
discovery of RNA enzymes. Crick and Orgel were right. RNA can act as an enzyme and that
was found first by Tom Cech and, in 1982, and then Sidney
Altman at Yale found that a molecule called RNase
P that he'd been working on for years also had, the RNA
also had catalytic properties. So RNA can act as both a catalyst
and an information molecule. So that breaks the chicken
and egg problem, alright? So this is kind of like the
old Saturday Night Live sketch where you have the, you know,
the shimmer which is a floor wax and a dessert topping
all in one, right? The next, just a couple
of years later, Walter Gilbert wrote an
article called The RNA World, and this was the coining of the
term and we're going to talk more about that I just want
put that up there so you have a sense
of the dates, okay. In 1987, Cold Spring Harbor
held a meeting on RNA catalysis that involved a lot of discussion
about the RNA world, and in 1993, Ray Gesteland and John
Atkins edited a volume of, a collection of papers called
the RNA world, and as I said, it went through multiple editions
I forgot to put up the fourth. What year did the fourth
edition come out? 2011, okay, so this is still a very
vital and ongoing project, alright? So that is a quick
introduction to the RNA world. Now I'm going to sit down, I'm going
to mostly turn it over to the them. Thank you. Okay just wave your
hands or something if you can't hear or can't see. I m trying to get out of the
way but I also want to make sure that I' m in conversation
with my guests here. So, with that, let 's
begin with evolution. Theodosius Dobzhansky
famously said that nothing in biology makes sense except
in the light of evolution, but the early generation of molecular biologists
were often criticized for not taking evolution
sufficiently seriously. One of those critics, at least
in my reading, was Carl Woese. What do you think? Is that criticism fair? To what extent did the RNA world
emerge from evolutionary thinking, I mean from thought based on serious
reading of evolutionary literature. >> Dr. Walter Gilbert:
I thought that, I think it 's an unfortunate
question. I do agree the early generation
of molecular biologists did not, most part didn't think of evolution. The discovery of the DNA sequencing
in 76, discovery of DNA sequencing in 76 suddenly made it possible to
look at the genes of many organisms and one of the first
things that happened as molecular biologists did this
was they discovered that the genes in [inaudible] were like the genes
in plants and stuff like that and suddenly evolution
swept the field. I remember going to a conference
in which in fact this sort of suddenly became a fantastic
element in people's thinking. Those of us who had a slightly
more genetic background were more conscious of evolution,
but the general field of molecular biology was not. I think the RNA world
image is deeply based in a notion of evolution. The point of the paper that
I wrote in 1986 was twofold. One, it picked up from
arguments that had been made, I would say picked up from the
discovery of the RNA enzymes that had been made and reiterated
just before that and had picked up from an older notion
from the biochemists that RNA was more primary than DNA,
and the biochemistry of that is that all of the DNA structures,
the DNA sugars and the DNA, of the DNA bases and nucleotides,
are made from RNA precursors. So if you look at the biochemistry,
you would not say DNA is separate in any way or primary in any
way, you would say, oh, the chemistry suggests
that RNA is the thing that you made biochemically and from
that you would later make DNA. People knowing that thought
of a RNA protein world. RNA is a genetic material,
machines in the organism, and that genetic material can
be used to dictate the sequence of amino acids and amino acids were
thought of as the interesting things in the world, the enzymes. And the protein chemists ignored
the nucleic acids intensely, they thought everything interesting
in the world was in the proteins. It makes very interesting meetings in which the protein
chemists meet separately and the nucleic acid chemists
meet separately and they never like to talk to each other or the protein chemists
totally ignore nucleic acids. >> Nathaniel Comfort: Nobody could
translate between the two languages. >> Dr. Walter Gilbert: But the
discovery of the enzymatic activity of RNA made me think that
maybe RNA could be entirely, play the role of all of the
enzymes and so the paper I wrote in 86 makes actually two statements. One, it suggests maybe RNA
enzymes could in fact do all of the necessary activities for a
cell to exist, including the copying of RNA itself, and therefore you
could imagine evolution is beginning with a small RNA molecule that
develops by random structures, random association of bases,
the ability to copy itself, and once it can copy itself, it
can make more, makes more copies, but in fact since it' s a
biological process, it makes copies which would also have
errors and so it can evolve. It can make random changes and those
random changes can be acted upon by natural selection to eventually
produce better molecules. Second part of that essay,
however, points out that because one of the RNA enzymes that was then
known at that time was an intron, the region inside an RNA molecule,
it could splice itself out. I could make the argument that that
activity clearly could be used, not only to splice introns out
of the RNA, but by combining two of those structures, develop a
structure that can move an RNA piece around from one molecule
to the other, inserting it like a transposon,
splicing out the rest, and creating a novel
RNA combination, and that's a very powerful
evolutionary tool, we call it recombination
when it occurs at DNA level, but in fact here was a model
that clearly could happen at the RNA level, and
so I could immediately in that paper suggest two things. Maybe there could be RNA-based
organism, completely using RNA as enzymes, and the evolutionary
processes would be able to shuffle the pieces of RNA
around to make novel pieces again. The original intron, exon idea you
alluded to, the critical element of that idea was an
evolutionary argument, it was not just the
biochemical argument that you had on the DNA long regions that we
call introns that are spliced out of the RNA molecule
to produce small pieces, together they code
for pieces of protein. But the evolutionary argument is that by spreading those
regions apart from the DNA, you would increase the recombination
rates between those regions and hence you could more
rapidly create protein structures and evolve them to better
function by recombination and by shuffling the
pieces of the protein. So in fact both the intron, exon
idea is conditioned by a vision of evolution and the RNA
world idea is also conditioned by that vision of evolution. That paper in fact finally includes
that sort of a hidden definition of life as that thing which
can by replication, mutation, and recombination as by changing
random changes can evolve and thus can be operated
upon by natural selection to reduce ever better functioning. >> Nathaniel Comfort:
Okay, thank you. I think that was a very
fortunate question in that case. I can now throw away
half of my questions but [laughter] Ford I think you
might have something to say on this. >> Dr. W. Ford Doolittle: Yeah well, I think your initial question
involved the phrase serious reading of the evolutionary
literature or something like that and I think most molecular
biologists did not seriously read the evolutionary literature,
probably still don t. Mostly evolution is something you
talk about in the last paragraph of the paper and I think, and
over a few beers kind of thing because I think there was a general
feeling amongst the molecular biological community that
evolution obviously was important but also there is nothing
you can really say about it so you could just say
whatever you wanted and everybody would
accept that politely. >> Nathaniel Comfort:
I think that s right. >> Dr. W. Ford Doolittle:
I think you were right that 1977 was a very important
year for some of us and I want to go back a little bit about the
intron relationship to the RNA world because I wasn't always lab
on sabbatical at that time and [inaudible] came back
from Switzerland, I think, having heard for the first
time about the introns in the immunoglobulin
genes, I believe, and gave, there were live meetings
once a week in all these labs with very strong tea as I recall. >> Nathaniel Comfort: Why tea
and not something stronger? >> Dr. W. Ford Doolittle: And while
we presented the exon shuffling idea, which I thought was
a brilliant way for things to evolve more rapidly in the
way that he just described, but I had one concern about that
which was I believe thinking the way that most of people, for most
people thought in those days, we imagined that higher
cells, eukaryotes, animals and plants evolved from bacteria
and bacteria don't have introns and eukaryotes, higher cells do have
introns and so that sort of implied that these relative event
cells would suddenly take on these interruptions in all
their genes just so that they can in the future do a better job
of evolving and which seem, not something could, anybody who
have done any serious reading on evolutionary literature would
be willing to accept is possible. >> Nathaniel Comfort:
You're not quite fair. >> Dr. W. Ford Doolittle:
I'm not blaming you for that. >> Dr. Walter Gilbert: I was going
at large, at that moment we knew of introns only in more complicated
genes, and so the first suggestion, I learned about the introns
and exons from the people who discovered the splicing in
the Cold Spring Harbor meeting in probably May or June that year and in my laboratory we had a
sequence of an immunoglobulin gene which actually had an intron
and we just sequenced it. We didn't actually know what
that was, but it was an intron. So when I came back from Switzerland
having thought about these ideas, I suggested that eukaryotes uniquely
use the greater evolutionary speed of recombination within introns
to reduce the great explosion, pre-cambrian explosion
of the eukaryotic genes, and that' s the background. >> Dr. W. Ford Doolittle: And
that s what I objected to. >> Nathaniel Comfort: Right. >> Dr. W. Ford Doolittle:
Because of, if we believe, which I think 99 percent of the
people believed at that time that eukaryotes came
from prokaryotes, then they would have had to
take on the burden of introns and ten introns on average
on every gene in order that several million years
down the road they 'd be able to do these wonderful
evolutionary things which seem kind of anticipatory and
not the kind of thing, evolution really can't look ahead
so that was my reaction to what you, and I don't think you
actually implied that but that' s my reaction. And I also happen to be privileged
because I had worked on [inaudible] and I knew Carl Woese and
I knew George and I knew about this almost simultaneous
publication of the three the main
view of life that George and Carl Woese had been working
on that, in their view, eukaryotes and prokaryotes were not
evolved, I mean it wasn't that eukaryotes evolved
from within the prokaryotes, they evolved separately from some
more primitive ancestral form, so then I thought, well actually
went home and had a bottle of scotch and wrote overnight that piece
and I thought that, you know, it'd make more sense if
introns were actually present from the very beginning. And then as evolution proceeded,
prokaryotes lost all the introns but eukaryotes retained them and this gave them the evolutionary
ability to become complex organisms like ourselves and
prokaryotes have'n t done that although they've done a
lot of other wonderful things and they've gotten much more
streamlined, we use the word. >> Nathaniel Comfort:
Streamlining, yes. >> Dr. W. Ford Doolittle:
