Welcome back to the deep dive. Today, we're going
to look at a picture. Just one picture. Just
one. Yeah. But it's an image you have absolutely
seen a thousand times. It's on the walls of biology
classrooms. It's, you know, in textbooks, probably
on a few t -shirts. We call it the tree of life.
Oh, right. It's totally iconic. And usually when
we see it, we just think, ah. OK, pretty picture.
Roots at the bottom, branches, monkeys, and then
us sitting right at the top. It feels very intuitive.
Exactly. I mean, we could completely take it
for granted. But the stack of sources we're diving
into today, which spans from French priests in
1801 all the way to modern genetic databases,
it suggests that this image is actually one of
the most controversial, difficult, and misunderstood
models in the history of science. It really is.
It functions as a metaphor, a conceptual model,
and a research tool all at the same time. And
the really fascinating thing we're going to uncover
is that the tree isn't just a drawing of nature.
It's actually a drawing of how humans think about
nature. And that thinking has changed so radically
over time. So our mission today, for everyone
listening, is to trace that evolution. We're
going to find out why the first tree of life
had absolutely nothing to do with evolution,
how Darwin turned a drawing into a mathematical
calculation, and why modern genetics is currently
threatening to just chop the whole tree down.
Yeah, it's basically a journey from perfect order
to absolute chaos. So let's start at the beginning,
or I guess the pre -beginning, because before
we had evolutionary trees, we had, well, regular
family trees. Right, if you go back to medieval
times, tree diagrams were everywhere, but they
were strictly for human genealogy. Oh, like for
royalty. Exactly. If you were a king or a duke,
you had a family tree to show your pedigree.
You showed how noble blood flowed down to you.
So as a status symbol, look at my mighty roots.
Yeah, pretty much. Yeah. But nobody applied that
visual to nature. Nature was usually viewed as
a ladder, the skull and atre. Right, the great
chain of being. Mm -hmm. A fixed hierarchy with
rocks at the bottom. than plants, animals, humans,
angels, and God at the very top. You don't climb
the ladder, you just stay exactly where you're
put. It seems so obvious to us now to use a tree
for species, but back then, the ladder was the
dominant mental model. So when does the tree
metaphor actually jump the fence from human families
over to biology? The sources point us to 1801,
and this is our first big surprise. The man who
draws the first real botanical tree, isn't a
radical scientist. He's a French Catholic priest.
Augustin Agier. That's the one. Which is so ironic,
right? You'd think a priest would stick to the
latter idea, given the theology of the time.
You really would. But Agier was looking at plants,
and he saw relationships that a latter just couldn't
capture. So he published this work called the
arbre botanique, the botanical tree. And if you
look at the image in the sources, it looks remarkably
like a modern evolutionary tree. Yeah, it has
a trunk, branches, leaves representing different
plant families. And here's the key distinction
we need to make. This wasn't about time or change.
Not at all. No. Auggie wasn't saying this plant
evolved from that plant. He was saying this is
the perfect order of nature as instituted by
God at the moment of creation. So it's basically
a static map. Precisely. It's a timeless snapshot.
He believed God created everything in perfect
order, and the tree shape just happened to be
the best way to draw that order on a piece of
paper. It's so interesting that the visual came
before the theory. He had the shape, but he didn't
have the mechanism for evolution. Right. The
mechanism. The idea that things actually do change.
That starts creeping in a few years later with
Jean -Baptiste Lamarck. Ah, Lamarck. I feel like
he always gets a bad rap in high school biology.
Oh, definitely. He's just the guy who thought
giraffes have long necks because they stretch
them. That is the caricature, yes. Yeah. But
Lamarck was a heavyweight. In 1809, he published
his tableau, and he was one of the first to strongly
argue for transmutation. Meaning he believed
species weren't fixed. They changed. Yes. And
he drew a branching diagram for animals. But,
and this is a really subtle detail in the research,
he absolutely refused to call it a tree or a
genealogy. Why the hesitation? If he believed
things changed, why not call it a family tree?
Because he didn't believe in common descent.
Wait, help me parse that. He thought animals
changed into new forms, but he didn't think they
were related. Correct. Lamarck's view was wild
by modern standards. He believed in constant
spontaneous generation. Meaning life just popping
into existence. Yes. He thought simple life forms
were constantly generating from mud or matter
in parallel lines and then moving from simple
to complex over time. So instead of one big tree
where we all come from one root, it's like a
thousand parallel escalators. Exactly. Nature
had this drive toward perfection. So a simple
worm today is just on the bottom step and given
enough time its descendants will become complex.
But that worm isn't related to us. It's just
riding a newer escalator. That is such a distinct
way of seeing the world. It's about parallel
progress, not shared history. Right. It explains
why a single tree metaphor didn't fit his math.
Exactly. Which brings us to 1840 and an American
paleontologist named Edward Hitchcock. He's the
next major stop in our deep dive. He draws these
two really fascinating charts, one for plants,
one for animals. You're looking at the notes
here. The visual details are spectacular, but
they seem really well regal. They are. Hitchcock
wasn't subtle at all. He literally crowned his
trees graphically. The plant tree has palms right
at the very top. And the animal tree. Let me
guess. Humans? You got it. A big crown labeled
man. It reflects this lingering worldview of
the time that the tree has a destination. It's
growing toward something. It's the ego again.
The universe exists to produce me. It's a very
hard habit to break. The idea that we are the
final product is comforting. But then... We hit
1859. The year everything changes. Yes. Charles
Darwin publishes on the origin of species. And
this is a piece of trivia I absolutely love.
The most famous book in the history of biology
has exactly one illustration in it. Just one.
And it's not a picture of animals. It's an abstract
chart. Yeah. Unlike the lush botanical trees
we just talked about, this thing looks like a
subway map. It does. And that abstraction is
its genius. Darwin labels horizontal lines with
distinct species. just hypothetical letters,
A through L. And the vertical lines represent
time. Specifically, thousands of generations,
right? Yes. So this is technically the very first
time tree. Because it combines phylogeny, the
relationships with time. Exactly. Before this,
maps were about how things looked. Darwin made
it a mathematical process showing branching descent
over time. Walk us through the mechanics of the
diagram. What happens to species A through L?
Well, look at species A. Over 10 ,000 generations,
it produces multiple distinct varieties. The
lines split and branch out, but then look at
species E, F, and G. Their lines just stop. Right.
They go extinct. Previous thinkers saw extinction
as a mistake. Darwin baked it into the very mechanics
of life. Some lines branch out and diversify.
Others stop. That brings up the specific text
Darwin used, which really contrasts with how
we usually think of the tree of life. We often
think of it as this peaceful Kumbaya family tree.
Right. Very harmonious. But Barwin's metaphor
is actually incredibly violent. It really is.
I have the quote right here. He writes, at each
period of growth, all the growing twigs have
tried to branch out on all sides and to overtop
and kill the surrounding twigs. Overtop and kill.
That is definitely not a family reunion. No,
it represents a great battle for life. He says
the crust of the earth is filled with dead and
broken branches, which are the fossils. So it's
a graveyard of what didn't make it. But Darwin
kept it abstract with the letters. He didn't
write human or monkey on that chart. He left
the labeling to Ernst Hackel. Who coined the
term phylogeny? He did. And in 1866, Hackel decides
to take Darwin's abstract lines and turn them
into literal trees. And these contrast so sharply
with Darwin. Hackel has these three kingdoms,
Plantae and Amalia, and Partista. Yes, the 1866
model. Partista was a big deal, acknowledging
microscopic life. But the real showstopper is
his 1879 pedigree of man. Pedigree? That's a
loaded word. It traces all life. Tumonia at the
very bottom, and places mention man explicitly
at the very top of the highest branch. So even
after Darwin showed that evolution is this sprawling
competitive bush where every surviving twig is
technically equal, Haeckel just puts us right
back on the pinnacle. It's that intense anthropocentrism.
Putting humans at the top is just so visually
compelling to people. OK, so when does that image
finally break? When do we realize we aren't the
top of the tree? It takes until the 1990s. This
is the molecular turn. Right, because before
that, everyone is grouping things based on morphology,
how they look. Exactly. But in 1990, Carl Woese,
Otto Kandler, and Mark Willis propose an entirely
new tree based on molecular phylogenetics. Genetics,
not just how things look. Because you can't really
tell bacteria apart just by looking at them.
No, they just look like tiny rods or dots. So
these researchers looked at the genetic code,
and they proposed the three domains of life.
Bacteria, archaea, and eukarya. Right, and this
is a big shift. The tree gets divided into those
three. And recent studies, like a major one in
2016, show that the tree of life is mainly composed
of bacteria. Meaning we, the eukaryotes, are
just a tiny, tiny little branch. A hidden majority
of life is microscopic. The tools we have now,
like the time tree database and the open tree
of life, operate on a massive scale. The 2022
time tree includes nearly 150 ,000 species. I've
seen the visuals for these modern trees. They're
often spiral or circular. They have to be just
to fit all that genetic data on a screen. So
we finally mapped the tree using math and genetics.
We figured it out. This is where the plot twist
comes in. Right. The tree is broken. It's broken.
The whole tree metaphor actually fails for prokaryotes,
which are the bacteria and archaea. Because of
horizontal gene transfer, HGT. Let's dig into
that. What exactly is the mechanism here? Think
about a regular tree. A branch splits, and those
two new branches never touch again. They just
grow apart. That's vertical descent, parent to
child. Right. But organisms like bacteria, and
even some animals like these tiny creatures called
boletiloid rotifers, they don't just pass genes
vertically. They can freely pass genetic info
horizontally to completely unrelated neighbors.
So if genes are moving sideways between different
branches, the lines of descent cross over each
other. It's no longer a bifurcating tree where
branches just split. It becomes a web, a network.
And it gets even wilder when we look at our own
deep roots. There's this consensus now about
the fusion at the root of the tree. Yes. Eukaryotes,
which includes us, plants, animals, we arose
from the fusion between bacteria and archaea.
So the very trunk of our part of the tree is
actually two branches merging together. Exactly.
It means the tree cannot be fully bifurcating
at this crucial node. Branches came together.
Which completely shatters the tree metaphor.
Trees don't do that. They really don't. Because
of this complexity, some scientists are now arguing
that unrooted phylogenetic networks are much
more accurate than a single tree. Unrooted phylogenetic
networks. It doesn't have quite the same poetic
ring to it as the tree of life. No, it doesn't
look as nice on a t -shirt. But it's closer to
the reality of the data. It's incredible to look
back at this journey. We started with Augier's
God -ordered static chart. Then Darwin's violent
battle of twigs. Right, and Heckel's pedigree
putting us right at the top. And now we're looking
at a messy modern genetic web. It completely
changes how we see ourselves. We aren't the lonely
figure standing at the pinnacle of a pine tree.
We are just a small part of a massive tangled
web dominated by microscopic life. And it's a
web that is constantly sharing and swapping information,
which brings up a really provocative thought
for you to mull over after listening. If the
very roots of this structure, the bacteria and
archaea, are constantly swapping genes sideways,
and our own branch comes from a fusion of those
organisms, maybe the Tree of Life is just the
wrong metaphor entirely. It certainly seems that
way. Perhaps we need a new image for the history
of life that allows for branches to fuse back
together. Something like a massive river delta
where streams endlessly split off, cross over,
and merge back into one another. It really makes
you wonder if life is just an endless tangled
network of shared code. Is the concept of a totally
distinct separate species just a convenient human
illusion? That's a deep one to end on. It really
is something to think about next time you see
that classic tree diagram. Thanks for joining
us on this deep dive. It was a pleasure. We'll
see you next time