ERIC LANDER: Good morning.
Good morning.
So last time, we ran
into a problem.
We had Mendel, my hero Mendel,
this MIT-like mathematical,
physical monk, had developed
this gorgeous theory of
particles of inheritance.
He didn't use the
word "gene" yet.
Gene doesn't get invented
for much longer.
For every trait, you had
two such particles.
You gave one to your
offspring.
Each of the parents gave
one to their offspring.
And that's how each offspring
gets two of them.
That choice of which of the
two alleles to transmit to
your offspring is
a random draw.
And that explains beautifully,
for example, the 3-to-1
segregation pattern
that Mendel saw--
gorgeous.
We put that model, which was
an ex post facto model, a
model made after the data were
available, to a test.
You guys insisted we had to
test it before you would
publish it.
And it holds up pretty well,
making pretty surprising
predictions that you
would otherwise
not have ever expected.
Like amongst that 3 to 1, the
threes are not all the same.
Some of those round peas
were homozygous
for the big-R allele.
And in selfing, they'll never
produce wrinkled peas.
But 2/3 of those round peas
were heterozygous.
And when you self them, you
get 1/4 wrinkled peas.
So the wacky prediction that
1/3 of the rounds will give
rise to no wrinkleds, and 2/3
of the rounds will give rise
to 1/4 wrinkleds is a surprising
prediction and,
therefore, something that bears
stating as a scientific
prediction.
And so all those kind of
predictions can emerge.
Then we turned to the question
of two factors.
I'm practicing using
our words here--
homozygous, heterozygous,
alleles, et cetera.
We now turn to two traits,
two phenotypes.
We have two phenotypes
segregating.
We had round and wrinkled, and
we had green and yellow.
And Mendel determined, rather
brilliantly, that they
segregated, were transmitted
independently of each other.
There was no correlation between
which alleles you got
at round and which alleles
you got at wrinkled.
That was pretty cool.
Let's just go over that, because
there's a real tension
to be resolved because we have
Mendel's second law versus the
chromosome theory.
So Mendel's second law--
let's just go back to it-- in
the F0 generation, we had our
round green peas, genotype big
R, big R, big G, big G. We had
our wrinkled yellow peas,
genotype little r, little r,
little g, little g.
We cross them together, we get
F1 double heterozygotes, big
R, little r, big G, little g.
We then perform a back cross
or test cross to the doubly
homozygous parent with the two
recessive phenotypes--
we're practicing
our words here.
And what do we get?
Well, we get certain options.
As we said, the gametes that
emerge from this parent on the
left could be of the
following types.
The gametes from the
parent on the right
are all those alleles--
Are those the recessive
alleles?
No.
You'll forget this over time,
but just to make me
comfortable--
they're actually the alleles
associated with the recessive
phenotype that we're
talking about.
Because you know-- but will
forget, I assure you, because
all my colleagues in the
biology department have
forgotten--
that they could also control
multiple other phenotypes,
some of which could
be dominant.
But that's OK.
I forgive you in advance
that you'll call
them recessive alleles.
Anyway, you get this.
And then these should occur at
equal frequency of one to one
to one to one.
All right.
Now, we had the chromosome
theory.
The chromosome theory, the
observation of the
choreography of chromosomes
during meiosis--
chromosomes in meiosis--
looks like this.
We have chromosomes lining
up in pairs.
Now, I'm not drawing
it terribly well.
But the two members of each
pair are of the same size.
But this pair could be
bigger, and this
pair could be smaller.
It looks like they're really
finding each other.
These chromosomes are visibly
different in shape.
And so maybe I'll make this guy
a little longer, just to
indicate that, that
it actually knows.
Now an explanation, we said, for
how Mendel's second law of
independent assortment of two
different phenotypes could
occur is that, for
example - round.
It could be that the gene for
roundness is located on
chromosome number one.
These are two copies of
chromosome one that have been
duplicated, each of which
has the big-R allele.
Next to it, two copies of
chromosome one that have been
duplicated, each of them having
the little-r allele.
Over here on chromosome
number two.
let's say, lies the gene
for green or yellow.
And in this picture here, the
big G's are on the two copies
of this chromosome number
two that are here.
The little g's are on the two
copies of chromosome number
two that are here.
When the cell undergoes meiosis
one, we get to the
situation where we have big G,
big G; little g, little g.
We've got big R, big R;
little r, little r.
Could it have been the case
that the big G was on the
right and the little
g was on the left?
Yeah, of course.
It's totally independent
which way.
I happened to draw
it this way.
But with probability 50%,
it's the other way.
That's why they're independent
of each other.
And then when it undergoes
meiosis two that looks just
like mitosis, we end up with
our four gametes here.
Sorry, our four gametes with big
G, big G; little g, little
g; big R, big R; little
r, little r.
And that accounts for the big G,
big G; big R, big G; little
r, little g gametes.
And then when they went the
other way, the organism would
make a set of gametes that had
the other combination of big
R's with little g's.
So that's perfectly fine.
And because the second
chromosome is independently
ordered compared to the first
chromosome-- when they line up
at the midline, they
don't really care
which way they are--
that'll account for one
to one to one to one.
It's so straightforward.
But what happens if, instead,
both the roundness gene and
the greenness gene live on
the same chromosome?
We'll have little r,
little r there.
We'll have big G, big G here;
little g, little g.
And then when they split,
we'll end up with--
now, chromosome two has
nothing that we
care about on it.
It has a lot of genes.
In fact, there could be
chromosomes three, four, five.
I'm just not drawing them.
But we're really going
to focus on
chromosome number one here.
And you'll notice that here on
chromosome one, the big G's or
the little g's are coupled,
physically coupled to each
other, the bigs with
the bigs and the
smalls with the smalls.
So now the kind of gametes that
can emerge from this will
only be big R, big G type or--
big G type--
or they'll be little
r, little g type.
We can't get the reverse
combination.
We can't get bigs and littles.
So this, because these are
independent of each other,
will get us one to one
to one to one.
These are the big, little,
and then these other
combinations like that.
This will get us only, if we
look at the big R, big G;
little r, little g; big R,
little g; little r, big G;
will get us one to one
to zero to zero.
Let's give a name to this type,
the big R's and the
little g's.
Let's call that a recombinant
type, OK?
I'm just going to use that
word for the moment.
The recombinant types-- the
bigs and the littles, and
littles and the bigs--
we're not going to
see any of them.
This is a very strong difference
between Mendel's
second law and the chromosome
theory.
If the chromosome theory is
right, and these chromosomes
are physical entities that have
integrity, they can't
both be right.
So that's a great thing in
science, when you have two
different models and they can't
both be right, because
you learn things then.
You can test them.
Now, Mendel tested this without
actually knowing the
chromosome theory.
And he always got one to one
to one to one for the seven
traits he looked at.
Was he just lucky that they
happened to lie on the seven
different chromosomes?
Or is there some problem
with this
chromosome theory, or what?
It took a while.
And then, of course, everybody
forgot about Mendel from 1865
until the year 1900.
In the year 1900, people begin
to rediscover Mendel.
Cytology has come along.
In January of the year 1900,
plant breeders start
rediscovering Mendel.
Sorry.
Thank you.
I see already.
Thank you.
I could tell by the look on your
face that something must
be wrong there.
Good.
Plant breeders start
rediscovering Mendel.
And in January of 1900, three
different groups say, you
know, we found these laws.
And they're just like
Mendel's laws--
which now everybody starts
paying attention to.
But plant breeding-- and people
tried to do mice, and
people tried to do rats.
What turned out to be the
winner, the place to really
study genetics, was
the fruit fly.
Thomas Hunt Morgan at Columbia
University decided, after he
was really frustrated wasting
years breeding mice and rats
that just took too long, around,
oh, I don't know, 1906
or something like that, began to
start breeding fruit flies.
Fruit flies are the teeny little
flies that when you
open a banana or fruits
or other kinds of
things, you'll see them.
And studying Drosophila gave us
the answer to this question
of what the problem is, how
can it be that either it's
independent or totally
dependent?
So we're going to talk about
Drosophila melanogaster, the
fruit fly, and the discovery
of recombination.
So now, Morgan--
I'm going to now start using
fruit fly notation to give you
some practice with fruit
fly notation.
We're not going to use big
G's and little g's.
They like to refer to
the normal allele
and the mutant allele.
The normally allele is plus.
The mutant allele gets
some kind of a name.
And so he had a female fly that
was normal and normal at
two different loci, two
different genes.
I haven't told you what
the genes are.
And the male fly had a
black-colored body-- black
across its whole body--
and its wings were
shriveled and,
therefore, called vestigial.
So the phenotype here is black
and vestigial, black body and
vestigial wings.
And this wasn't the normal
appearance of a fly.
So he took these females by
these males, and he crossed
them together.
And he got an F1.
And the F1 was black over
vestigial, plus over plus.
And what was their phenotype?
Were they normal appearance,
which is kind of a
sandy-colored body
and normal wings?
Or were they this all black
body and vestigial wings?
Turns out they were normal.
From that, what do we infer
about these two traits, black
body and vestigial wings?
They're recessive traits.
So here, the phenotype was
normal appearance.
So then he crosses them back,
doing a test cross.
Let's say he'll take males here
and females here, but it
actually works either way.
And what he does is just
like we did there.
He could get gametes that
were black, vestigial.
He could get gametes that were
black, plus; plus, vestigial;
or plus, plus.
Those are the four possibilities
that come out.
So when he does it--
let's keep score.
I'm going to write them now--
plus, plus; black, vestigial.
And from the other parent,
you got this--
black, plus; black,
vestigial; plus,
vestigial; black, vestigial.
Those are the four
possibilities.
And if this was just like
Mendel's traits, it would be
one to one to one to one.
These were the parental
types that went in.
Plus, plus went in.
And black, vestigial went in.
Those were the combinations
of traits here.
These were new combinations.
What he observed--
Let's see.
If Mendel's right, it'll be
one to one to one to one .
If the chromosome theory's
right, it'll be one to one to
zero to zero.
And who was right?
STUDENT: No one.
ERIC LANDER: No one.
The answer was 965 to
944 to 206 to 185.
Neither model was right.
Neither model's right.
The new combinations, the
recombinant combinations, the
non-parental combinations--
we can call these recombinant
combinations.
These were recombinant.
They recombined in some way.
They were a new combination,
or they were the
non-parental types.
We use both of those
words frequently--
were neither equal nor were
they completely absent.
They occurred, but at
a lower frequency.
What was the frequency?
Well, we could just add it up.
The frequency of recombinant
types, of new types of were
different than the
parents', is 17%.
What's going on?
Now, maybe this is some magic
number like the 3-to-1 ratio.
And you should look at that 17%
and say, ah, this is some
constant of the universe, that
when you put in traits you get
17% percent of recombinant
types.
But it takes a little judgment
to say, I don't think so.
And he actually tried
other traits.
And sometimes he got one
to one to one to one.
But very often he got
some funny number--
6%, 28%, 1%.
There was some funny
business going on.
What's going on?
Recombination.
That's what's going
on is there is
recombination occurring.
What do we mean by
recombination?
Recombination is very important
stuff, by the way.
At some point, I will tell
you that understanding
recombination was actually
the origin of the
Human Genome Project.
And it traces back to
a good MIT story.
But that will be for a little
later in the semester.
So what do we think's
happening here?
I'm now going to draw a close-up
of that chromosome.
And here's another chromosome,
the other pair.
And what we think here might be
happening is that you might
have plus and black;
black and plus--
oh, sorry.
Black, right?
Black, black; plus, plus.
This would be plus.
This would be plus.
This is the normal chromosome.
This is plus.
So this chromosome here
carries the pluses.
This guy here carries those
alleles black and vestigial.
Well, what happens, the idea
was that somehow these
chromosomes exchanged
material here.
And the chromosome that was
plus, plus; plus, plus now
somehow acquires that bit,
and this chromosome
somehow gets that bit.
And we end up instead with a
picture like this, where some
of this came from here.
And those two loci, black and
vestigial, were separated from
each other such that the black
allele moves over to that
chromosome.
Is that clear?
That's the notion.
Why did they think
this was true?
Well, it turns out that in fruit
flies, you can actually
look at eggs under
the microscope.
And you can look at
the chromosomes.
And if you take if you take
the cells, and you take a
cover slip, and you squash it
down with your finger, you can
actually see chromosomes lying
right over each other, making
little crosses like I drew
there, up there, called
chiasmata, which
means crosses.
And so people said, see, in the
microscope, you can see
they're lying on top
of each other.
Are you impressed by that
piece of evidence?
No.
You took the cover slip,
you squished it
down with your fingers.
So they're lying on
top of each other?
Big deal.
I'm not going to be impressed.
And calling it chiasmata doesn't
make me any more
impressed, right?
Although it's always good to
call things Greek names,
because people think they're
more sophisticated if you call
them Greek names.
But this was the notion
people had.
And the frequency 17% would
indicate how often these
crossovers occur.
But if I were in the situation
we talked about with Mendel,
and I wrote this up, and I said,
see, it's 17% sometimes,
6% sometimes, 28% sometimes;
and when I look in the
microscope, they lie on top of
each other; therefore, it's
recombination--
There were actually other ideas
floating around too.
Maybe it has something to do
with developmental biology.
It was a puzzle.
When you have a really deep
puzzle, the most important
thing in science is to
find a young person.
Because young people come
without prejudice.
They say, let me just
look at all of this.
Stand back.
I don't come with
any prejudice.
So at MIT, what is the solution
when you have a
problem like this?
A UROP.
You want a UROP.
So even 1911, that was the
solution at Columbia.
Thomas Hunt Morgan got a UROP.
I'm serious.
He was called Alfred
Sturtevant.
Alfred Sturtevant was a
sophomore at Columbia.
Everybody else was busy finding
this recombination
data, how often this recombined
with this, this
with this, this with this.
Sturtevant--
he's a sophomore--
he says, god, this stuff's
interesting!
Professor Morgan, could I
have all the data and
try to look at it?
Sturtevant took it home
and actually pulled an
all-nighter, blew off
his homework--
it actually says so in
his autobiography.
He says, I blew off my homework
and pulled an
all-nighter--
essentially in those words, he
says. "To the detriment of my
undergraduate homework"
is the way he puts it.
But in any case, genetic maps
and Sturtevant's all-nighter.
What Sturtevant did
was the following.
He said, how are we going to
prove the chromosome theory?
I like this idea that
recombination is about
distance on the chromosomes.
I like the concept that
maybe 17% is how often
these things recombine.
Why would things only recombine
1% of the time?
What would that mean?
They've got to be pretty close
together so that a crossover
between them happens
not so often.
And what if things
were far apart?
Well, it could be more likely.
So he likes the idea
that recombination
frequency means distance.
But how are you going
to prove that?
It could mean a zillion
other things.
It could mean biochemical
pathways,
developmental biology.
How are you going to prove that
recombination frequency
means distance?
You've got to make predictions,
right?
The only to do it would be
to make predictions.
So Sturtevant takes the data,
and he starts making
predictions.
I think, says Sturtevant,
these things are alleles
living at genes with locations
on the chromosome--
black, vestigial.
How often do black
and vestigial
recombine with each other?
What is the frequency
of recombinant
non-parental types?
17%.
So Sturtevant goes through the
data and he says, what about
other crosses people
did in the lab?
Well, it turns out people did
crosses with another mutant
that produces a funny eye color
called cinnabar, Cn.
So cinnabar.
It turns out that the
recombination frequency
between cinnabar to
vestigial was 8%.
Vestigial, cinnabar,
8% recombination.
If this chromosome business
is right, where
should I put cinnabar?
Sorry?
Where do you want it?
STUDENT: [INAUDIBLE].
ERIC LANDER: Somewhere
in between.
You'd like me to
put that there.
STUDENT: On the other side.
ERIC LANDER: Oh, OK.
Wait a second.
On the other side.
OK, which is it?
How many vote for the left?
How many vote for the right?
How many conscientious
abstainers are there?
Do we know?
STUDENT: No.
ERIC LANDER: No.
There are two possibilities.
It could be 8% this way, or
it could be 8% that way.
How are we going to know?
Yes?
STUDENT: [INAUDIBLE].
ERIC LANDER: Black.
What if we knew the answer
between cinnabar and black?
That would constrain
the problem.
Can you give me two predictions
for what the
answer might be?
STUDENT: Either 9% or--
ERIC LANDER: Either 9% or 25%.
So now we have a prediction.
We don't know where
cinnabar is.
But the answer could be that
black to vestigial should
either be about 9%--
that's what that
would be here--
or about 25%.
The answer?
About 9%.
That's what Sturtevant found.
That's a prediction
and kind of cool.
And you can imagine taking the
data home and it's probably 9
o'clock, and you've
now realized, wow,
freaky, it's 9%.
So then he looked at the
mutation "lobe." Lobe was
another mutation.
The lobe mutation showed 5%
recombination from vestigial.
Where should we put it?
Left or right, well, let's
make some predictions.
Suppose it's over here.
Will it be very close
to cinnabar?
Will it be closer to black?
But what if it was over here?
Well, it would be further.
So let's put lobe in.
And suppose we know
that lob is 5%.
Then what's the prediction
for black to lobe?
22%.
Answer, according to the
notebooks, 21%, pretty close.
You'd like it to
be exactly 22.
But life doesn't always
turn out that way.
21's pretty close to 22.
What other predictions
could we make?
If this is cinnabar here, could
you give me a prediction
for cinnabar to lobe?
13%.
Yep, that works.
Curved wing.
Recombination distance
from lobed, 3%.
So now you have some
predictions.
You have this prediction here.
You predict 8%.
Answer, about 8%.
Over here you predict 16%.
Answer, about 16%.
Bingo.
Sturtivant says, if
these genes--
we call them loci, often.
I'll use the word locus
synonymous with gene.
Locus means a place.
And geneticists think about
genes as a place on a
chromosome.
If these loci--
the plural of locus-- if these
loci were really arrayed along
a linear structure, then it
would have to be the case that
they would have certain
additive
relationships between them.
And the chance that they would
have these additive
relationships if they weren't
part of a line is pretty
implausible.
That's a real prediction, a very
remarkable prediction.
And it holds up with the data.
Sturtivant pulls the
all-nighter.
By the time the sun comes up at
Columbia University-- this
is Morningside Heights--
he's got the whole
thing worked out.
Yes, this chromosome theory
must be right.
It fits beautifully
all of these data.
Pretty cool.
You are all authorized to blow
off your homework anytime you
make a discovery like that.
[LAUGHTER]
That's a course rule.
Any homework will
be forgiven for
discoveries of that magnitude.
All right.
Tell your TAs.
So now, what does it
really tell us?
It tells us that if genes are
very close together, the
recombination frequency, R
recombination frequency, or
RF, might be very little.
They could be as low as almost
zero, which means you never
see a recombinant because
they're right
next to each other.
Or it could be that they're
further apart.
It might be 1%.
It might be 10%.
It could keep growing.
It might be 30%.
Suppose it's way, way, way,
way, way far away.
What's the largest it
ever gets to be?
Well, if they were on different
chromosomes--
suppose there were totally
independent segregation,
different chromosomes--
what would they be?
STUDENT: [INAUDIBLE]
ERIC LANDER: No, it's 50%
because remember, one to one
to one to one says that
the recombinant--
well, actually, this is an
interesting question.
Let's come to that 100.
On different chromosomes, one
to one to one to one means
that it's 50%, half of them
are recombinant types.
It turns out on the same
chromosome, as you get farther
and farther and farther, you
might say there's going to be
100% chance of a crossover.
And you might say the
recombination frequency could
keep growing past 50%.
It turns out it doesn't.
The reason is that multiple
crossovers can happen.
So mathematical interjection
here, if here's my gene and
here's my gene, there could
be one crossover.
There could be two crossovers.
There could be three
crossovers.
And so in fact, it turns out, as
you get very far away, you
have to start paying attention
to the probabilities of double
crossovers and triple
crossovers.
And so it turns out that it's
a Poisson process of the
number of crossovers that
occurs, give or take.
And you see a recombination
if there's an odd number.
And for that reason, it
never gets above 50%.
So as the distance gets further
and further and
further, it goes from zero to
50, which is the same number
you get for separate
chromosomes.
Otherwise, you might think that
if there was just one
crossover, it gets to 100%
probability of recombination.
But it never does, because
there are doubles.
And you can actually observe,
if you make a cross that has
three different genes
segregating in it, you can
actually see the double
crossover type.
So you can see very nicely
that if you make a cross
involving black, cinnabar, and
vestigial over plus, plus,
plus, you can see that cinnabar
is right in the
middle because this
recombination happens at a
pretty good frequency.
This recombination happens at
a good frequency, giving you
plus, cinnabar, vestigial
or black, plus, plus.
Sometimes you will get
that recombination.
You'll get out gametes that are
black, plus, vestigial,
but at a much lower frequency
because they take two
crossovers.
What will be the probability
of seeing a
black, cinnabar, vestigial?
Well, we said that this
one was about 9%, this
one was about 8%.
What's the product of a 9%
chance and an 8% chance?
It's about a 1% chance, a little
less than a 1% chance.
That how frequently you see
black, plus, vestigial.
You can even predict the
probability of a double
crossover event by multiplying
the two events
that have to happen.
So your bottom-line rules here
is that because of these
double crossovers our
recombination frequency can go
from zero to about 50%.
This is independent
assortment.
And it either occurs if you're
on different chromosomes or,
if you're very far away on the
same chromosome, they behave
as if they're independent
of each other.
Any questions about
any of that?
Yes?
STUDENT: Why didn't Mendel
ever see recombination?
ERIC LANDER: Why didn't Mendel
ever see recombination?
It turns out that with seven
chromosomes, and they're
biggish in length, he never
actually ran into two loci
that were close enough,
to notice it.
That's why.
Flies actually only have three
major chromosomes.
There's a fourth, but it's
a puny little thing.
And because they were much more
intensively collecting
mutations in Morgan's fly room,
they began having a lot
of them, and they
had to bump into
recombination pretty early.
Mendel simply didn't have enough
that were close enough.
Think about what would have
happened if just by chance,
somebody were selling a strain
of peas in the market which
had a mutation in a locus that
had 10% recombination
distance, and it screwed up
Mendel's law of independent
assortment of two loci?
Mendel might not have
published the paper.
Sometimes in science it's
actually valuable to first get
the oversimplification out ,
like his second law, and then
deal with the complexity
that sits on top of the
oversimplification.
It's kind of lucky that Mendel
didn't have enough of them to
be bothered, in the
first paper.
So in fact, all of Mendel's
seven loci
have now been mapped.
Most have been cloned
molecularly.
And so we actually know where
they are, et cetera.
It's a really good question.
That's sort of why he didn't.
