
Evolution’s Random Paths Lead to One Place - digital55
http://www.simonsfoundation.org/quanta/20140911-evolutions-random-paths-all-lead-to-the-same-place/
======
skywhopper
There's an oversimplification going on here, I think (in the article I mean--
the experiment is simplified for a good reason). The "one place" that all of
these strains reach is that they are more fit for the environment than the
starting point of each. This is not a new idea. This was the thesis of "On the
Origin of Species".

As for the level of fitness of each strain... after sufficient generations,
basic statistics would tell tell us to expect this result. The combination of
random mutations influenced by one constant factor (natural selection in a
fixed environment) over a large number of generations _implies_ this result.

But the article appears to assert that this means that evolution's course is
predictable. But what's not addressed is _how_ each strain is succeeding. They
know that the variations in the genes from strain to strain vary quite a bit.
Yes, the result measured from one statistic (growth rate) is the same, but
future evolution and other traits of the yeast will be influenced by the
particular paths taken.

Finally, once you put this mechanism in an environment filled with millions of
other competing gene pools and a varying environment not bound by natural
selection which means there's an actual threat of extinction, then that's
where the true variability of the process emerges.

~~~
Houshalter
The "one place" that they reach is the same level of fitness. This is
surprising because they expected some strains to take different evolutionary
paths and evolve different traits, and therefore have different levels of
fitness in the end. Some would be better than others just by chance. The
probability of the same mutations happening in all the samples is very small.

Instead they all seem to converge on the same fitness. Even though they have
different mutations.

------
aethertap
In Per Bak's "How Nature Works" [1] he describes an simulation he did in which
he tried to replicate the series of evolutionary discontinuities and mass
extinctions we see in Earth's history. The reason this article brought that to
mind was that Bak was not able to get the complex behavior by selecting only
the fittest to survive. Instead, he ended up having to kill off the _least_
fit of the species and leave the rest to proliferate and develop
interdependencies.

His result doing that was some very interesting behavior in which extinctions
of all sizes happened in the population of species in a way evocative of
natural history on Earth. His idea was that in order for an evolutionary
system to reach the self-organized critical state in which big changes happen,
the species had to develop interdependencies so that the success or failure of
one could affect that of the others.

It would probably be a much more difficult experimental procedure because he
would have to keep the yeast strains in a community and somehow eliminate
rather than select a variety, but it would be really interesting to see if the
result of a common convergence point would survive with the model of "death of
the least-fit" rather than survival of the fittest.

1\. [http://amzn.com/038798738X](http://amzn.com/038798738X)

~~~
icefox
> ...not able to get the complex behavior by selecting only the fittest to
> survive. Instead, he ended up having to kill off the least fit of the
> species and leave the rest to proliferate and develop interdependencies.

How is "selecting only the fittest to survive" aka killing the least fit
different from "kill off the least fit of the species" aka selecting only the
fittest to survive they sound like exactly the same thing thing.

~~~
aethertap
I probably could have stated it more clearly like this: "selecting only the
fittest ONE to survive," and "killing off the least fit ONE."

The difference was in what the composition of the surviving population was -
in the extreme case where only the fittest one survives, there's only one
species that makes it to the next round. In the case where the least fit one
is killed off, there are n-1 species still in the mix with their relationships
intact. You can of course extend it to keeping more than one of the fittest,
or killing more than one of the least fit.

I was just re-reading that section of the book to try to give you a better
answer and I think I must have mis-remembered his original experiment a bit
(sorry about that). The original evolution model that failed to exhibit the
behavior was more complex than just a survival of the fittest (he was playing
with mutations and connections between species in a kind of complicated way).
The part about killing off the least-fit species really was the key to getting
complex behavior though, so at least that part of my original comment was
right.

The eventual solution was to simplify the model so that the least-fit single
species would go extinct and be replaced by a new randomly generated one each
round. The fitness of a species was related to its connections, so if one
species was to go extinct it could trigger others to cross the fitness
threshold and go extinct as well. This led to cascades of extinctions with a
power law distribution (like the pattern observed in real extinctions on
Earth). The mass extinctions would eventually stabilize at a point where all
species were above the fitness threshold, but the "gene pool" had been seeded
with lots of new randomly generated species at that time, so there were
periods of rapid mutation punctuating long stable periods where not much
changed.

His book is pretty interesting, although it's sometimes a little over the top
with self-congratulation. I'm reading another one now called "Self-Organized
Criticality"[1] which is a much more rigorous treatment of the idea that I
think will be a bit less sensational and more applicable to real problems.
Bak's book is excellent if you want to get excited about making simple models
do complex things though.

1\. [http://amzn.com/0521483719](http://amzn.com/0521483719)

------
tendeer
Very well written article that allowed a non-biologist but engineer like me to
follow. Systems Biology is quickly becoming one of the most interesting
fields, IMO.

The observations about organisms catching up and slowing down is consistent
with (the regression to the
mean)[[http://en.wikipedia.org/wiki/Regression_toward_the_mean](http://en.wikipedia.org/wiki/Regression_toward_the_mean)].
Although it's something I only recently read about in Daniel Kahnemnan's
Thinking Fast and Slow, it's applicability is widespread; so much so that I
was not surprised seeing it in action here.

One thing that I do not fully agree with (or maybe that I do not fully
understand) is the final evolutionary endpoint was measured simply by it's
ability to grow in specific lab conditions. While this is a necessary
condition for equality of endpoints, it is in no way a sufficient one. It is
very possible, and even highly likely that while that goal of fitness is
optimized for, evolution changes the final organism's way of reacting to other
phenomena. I'm not sure if there is a better way to quantify equality (or some
notion of edit distance) though.

------
api
I'm a fan of the view that evolution should be viewed as an information
transfer process. It transfers information about the fitness landscape into
the genome.

Similar environments will give rise then to similar information. There will be
variance, of course, but it's going to be a lot narrower than the random walk
interpretation of evolution would predict.

There is evidence for this from several places:

* Convergent evolution on Earth at many scales

* Digital evolution experiments showing similar endpoints in similar environments and against similar fitness landscapes

* ... and now this series of experiments showing convergent evolution in the lab even down to the genetic level

There's a lot of interesting implications here. For example: can we really say
that another planet very similar to Earth that is of similar age might not
harbor another bipedal warm blooded sentient species physically similar to
ourselves? I'd be really surprised if we found Star Trek levels of similarity
(e.g. biological and sexual compatibility), but some level of similarity in
areas like basic anatomical structure would not shock me. Perhaps the
anthropomorphic alien depictions in sci-fi (Giger's alien, the "greys," etc.)
are not terribly implausible.

Of course a radically different world harboring life might yield something
radically different for similar reasons.

~~~
djokkataja
I think a lot of it boils down to what the evolutionary pressures (defn: [1])
on another planet might look like. If we discover life on another planet, it
wouldn't surprise me if some of the organisms we find resemble organisms in
some branches of the "tree of life" on Earth, but I think it would be unlikely
that there would be so many similar evolutionary pressures that we would see
something particularly similar to ourselves.

For example, life has been around for at least 3.5 billion years on this
planet[2]. At this point in time, there is no evidence that any other species
on this planet has ever had a technological civilization that would be of
particular interest to us in the way that is often envisioned for hypothetical
alien visitors. This isn't for lack of different species[3] or for
insufficient genomic complexity[4] in other species. In other words, there's
nothing about the human genome that represents a "pinnacle" of evolution, as
much as we tend to hold ourselves in pretty high regard among other species.

As another example, let's walk the tree of life
([http://tolweb.org/Life_on_Earth/1](http://tolweb.org/Life_on_Earth/1)) to
get a ballpark idea of how many different features we run into before
encountering homo sapiens:

1\. Eukaryotes (organisms with nucleated cells)
[http://tolweb.org/Eukaryotes/3](http://tolweb.org/Eukaryotes/3)

2\. Animals (multicellular, heterotrophic, lack rigid cell walls, motile, most
have embryonic blastula stage)
[http://tolweb.org/Animals/2374](http://tolweb.org/Animals/2374)

3\. Bilateria (bilateral symmetry with three germ layers)
[http://tolweb.org/Bilateria/2459](http://tolweb.org/Bilateria/2459)

4\. Deuterostomes (blastopore becomes the anus during development)
[http://tolweb.org/Deuterostomia/2466](http://tolweb.org/Deuterostomia/2466)

5\. Chordates (animals possessing a notochord, a hollow dorsal nerve cord,
pharyngeal slits, an endostyle, and a post-anal tail for at least some period
of their life cycles)
[http://tolweb.org/Chordata/2499](http://tolweb.org/Chordata/2499)

6\. Craniata (have hard bone or cartilage skull)
[http://tolweb.org/Craniata/14826](http://tolweb.org/Craniata/14826)

7\. Vertebrata (have backbones)
[http://tolweb.org/Vertebrata/14829](http://tolweb.org/Vertebrata/14829)

8\. Gnathostomata (have jaws)
[http://tolweb.org/Gnathostomata/14843](http://tolweb.org/Gnathostomata/14843)

9\. Sarcopterygii (lobe-finned fish & terrestrial vertebrates. I am not an
evolutionary biologist but it seems like this roughly corresponds to the
evolution of limb-like structures)
[http://tolweb.org/Sarcopterygii/14922](http://tolweb.org/Sarcopterygii/14922)

10\. Tetrapods (more properly terrestrial vertebrates, but to simplify things
a little. Basically 4 limbs)
[http://tolweb.org/Terrestrial_Vertebrates/14952](http://tolweb.org/Terrestrial_Vertebrates/14952)

11\. Amniota (have eggs equipped with an amnios)
[http://tolweb.org/Amniota/14990](http://tolweb.org/Amniota/14990)

12\. Synapsids (have a temporal fenestra)
[http://tolweb.org/Synapsida/14845](http://tolweb.org/Synapsida/14845)

13\. Therapsids (have particular skeletal and muscular structures)
[http://tolweb.org/Therapsida/14973](http://tolweb.org/Therapsida/14973)

14\. Mammals (hair, three middle ear bones, mammary glands, and a neocortex)
[http://tolweb.org/Mammalia/15040](http://tolweb.org/Mammalia/15040)

15\. Eutheria (have particular skeletal structures--not strictly placental)
[http://tolweb.org/Eutheria/15997](http://tolweb.org/Eutheria/15997)

16\. Primates
[http://tolweb.org/Primates/15963](http://tolweb.org/Primates/15963)

There are several more branches before getting to homo sapiens.

I think the big remaining questions are:

1\. What features of an organism are necessary for that species to develop a
technological spacefaring civilization?

2\. Are evolutionary pressures that support the development of those features
likely to appear eventually on life-bearing planets similar to Earth? (I think
this assumes that abiogenesis on other planets would be likely to produce
simple cellular structures with similar capacities for evolution.)

3\. Are we in a simulation created by another species in a "real" universe to
answer similar questions? :)

I'd guess...

1\. Limbs (and the supporting underlying physical structures) with significant
capacity for manipulating objects, terrestrial-dwelling (as opposed to living
in the sea), a advanced neocortex, and way too much free time, along with very
difficult-to-impress mating prospects.

2\. Depends on how similar to earth (a waterworld would be unlikely to have
any species developing advanced technology, I think... maybe I'm not being
imaginative enough). Also depends on how many of the evolutionary pressures
that got us to this point were more or less inevitable as opposed to random.
It seems that even if it's relatively likely that a species similar to humans
will evolve on planets similar to Earth, there are still numerous additional
hurdles in the development of different kinds of societies that could make or
break the whole spacefaring thing. Even now, humans are not a spacefaring
species, and the odds that we nuke ourselves out of existence or create a
genetically engineered superbug that wipes us all out are relatively high
considering we have absolutely no backup plan as a species for either of those
events (or any number of other catastrophic global events). So maybe my answer
to #1 is insufficient because we're not really a spacefaring species yet.

3\. If they have that kind of computing power, I would've expected something
more interesting. Maybe they're trying to predict the odds of encountering
other species like themselves during a galactic collision? :)
[https://en.wikipedia.org/wiki/Andromeda%E2%80%93Milky_Way_co...](https://en.wikipedia.org/wiki/Andromeda%E2%80%93Milky_Way_collision)

[1]:
[https://en.wikipedia.org/wiki/Evolutionary_pressure](https://en.wikipedia.org/wiki/Evolutionary_pressure)

[2]:
[https://en.wikipedia.org/wiki/Abiogenesis](https://en.wikipedia.org/wiki/Abiogenesis)

[3]: There are approximately 10 million species currently alive on Earth (more
or less a minimum bound, the actual number may be much higher).
[http://www.nytimes.com/2011/08/30/science/30species.html?_r=...](http://www.nytimes.com/2011/08/30/science/30species.html?_r=0)
At least 99% of all species to have ever lived are extinct now:
[http://www.physicalgeography.net/fundamentals/9h.html](http://www.physicalgeography.net/fundamentals/9h.html)

[4]:
[http://en.wikipedia.org/wiki/Genome#Genome_size](http://en.wikipedia.org/wiki/Genome#Genome_size)

------
lutusp
The article's "one place" claim will confuse those who don't understand
evolution. It's like saying that all algebraic equations are the same because
they all have equals signs. It's true, but it misses the point that the
equations surrounding the equals signs are all different.

The "one place" being described is "fitness", but to any number of
environments in constant change. It's like saying that all women are alike --
they aren't men. It's a meaningless claim masquerading as meaningful.

------
tokenadult
This is an interesting, readable report on an automated procedure for
experimenting on evolution of microorganisms that will be good to try out with
microorganisms other than yeast. Figuring out the different gene interactions
over many generations of random mutations will eventually develop a deeper
understanding of how these one-celled organisms work. And that, as an expert
interviewed for the article suggested, will help deepen understanding of
evolution as a process. "'I think many people think about one gene for one
trait, a deterministic way of evolution solving problems,' said David Reznick,
a biologist at the University of California, Riverside. 'This says that’s not
true; you can evolve to be better suited to the environment in many ways.'"

Scaling up this approach to study multicellular organisms with longer
generation times than yeast will of course take a lot of time and effort.
Sometimes (as here) experiments on simple model organisms produce surprising
findings. There will be even more surprising findings, I think, as evolution
is studied in more detail in multicellular organisms at the molecular genetic
level with strict experimental controls of developmental environments.

EDIT TO REPLY TO ANOTHER COMMENT:

Another participant asked,

 _I feel like a CS education should prepare one for this kind of field. What
's a good way to get started learning more about evolution?_

It will indeed take a lot of hard work by experienced computer scientists to
solve some problems in evolutionary theory. A quite good way to start learning
about evolution is to read the book _Why Evolution Is True_ , which talks not
only about evidence for evolution but also about implications of the theory.
Then read the book's website[1] frequently for the latest news.

Other good things to read are the books by biologist Sean Carroll (not to be
confused with physicist Sean Carroll) such as _Endless Forms Most Beautiful._
[2]

[1]
[http://whyevolutionistrue.wordpress.com/](http://whyevolutionistrue.wordpress.com/)

[2] [http://www.amazon.com/Endless-Forms-Most-Beautiful-
Science/d...](http://www.amazon.com/Endless-Forms-Most-Beautiful-
Science/dp/0393327795)

~~~
lumpypua
The public perception of evolution misses out on the depth of scientific work
being done these days. Two more books that make modern evolutionary research
accessible to the public:

1\. Nick Lane's Power, Sex, Suicide: Mitochondria and the Meaning of Life -
Covers the evolution of the eukaryotic cell, why it's such insanely chance
event, why multicellular life depends on it, almost as an aside making a great
argument that complex multicellular life is extremely rare in the universe.
Also has a couple of fascinating chapters on how the interaction of the
mitochondrial genome with the nuclear genome influenced development of sexes
and sex.

[http://amzn.com/0199205647](http://amzn.com/0199205647)

2\. Nick Lane's Life Ascending: The Ten Great Inventions of Evolution - Covers
very different material and again all fucking fascinating. It's amazing to see
how things like sight have evolved over and over and over because they're so
fucking useful, and the genetic analysis that allows us to pick out each
separate emergence of a feature.

[http://amzn.com/0393338665](http://amzn.com/0393338665)

------
icegreentea
This is pretty cool! One thing to think about (and its raised in the last two
paragraphs of the article) is how this might change in a dynamic environment,
and with the addition of other simultaneously evolving agents.

I think its pretty clear that given some static environment, there will be
some maxima of fitness - everything is limited by physics and thermodynamics
at some point. Aside from the question of 'how close can we get to this
maxima', another question is, if we have a bunch of different sets of
mutations that together generate an organism that is at or near the current
environmental maxima, what happens as the environment changes?

By the way, here's a preprint of the paper in question:
[http://sergeykryazhimskiy.webs.com/1519.full.pdf](http://sergeykryazhimskiy.webs.com/1519.full.pdf)

The e. coli studies cited can be found:
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3461117/](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3461117/)
and
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430337/](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430337/)

------
vinceguidry
Biological evolution isn't the only kind of evolution that can be dreamed up.
"Self-arised change over time" can be applied to all sorts of domains, it
would be interesting to have a mathematical definition of evolution that can
handle all the things. This appears to be a step in that direction.

------
washedup
It would be interesting to know if inventing an internet is a natural outcome
of evolving life on a somewhat-stable planet. Regardless of the aesthetic
differences among life forms developing from different initial conditions,
will a planetary ecosystem arrive at similar milestones along the way?
Mobility, eyesight, language, society, etc.

I think this research is very exciting because it actually is narrowing in on
the limitations of evolution, or the "search-space" of possible life forms.
This points to the idea that life on other planets may be similar to us, if
not only in milestones, but possibly aesthetics as well. Maybe we can even get
to the point where if we know the current and past environmental conditions of
a planet, we can make educated guesses as to what life would look like on its
surface.

~~~
tjradcliffe
Specifically human intelligence of the kind that builds internets and
spaceships has evolved exactly once on all of Earth's history, in contrast to
things like eyes and wings, which have evolved dozens of times. And it evolved
very recently, and appears to be due to run-away sexual selection of the kind
that produced the peacock's tail.

All of this suggests that specifically human intelligence--not dolphin or bird
or any other kind of intelligence that does not build internets and spaceships
--has an unusually narrow bottleneck to get through compared to most other
capabilities, despite the ridiculous benefits available once a species gets
through it.

As such, I'm betting that we'll find life pretty much everywhere in the
universe, and intelligence almost no-where. When intelligence does arise, it
will likely be wildly different from us due to the essentially random nature
of the sexual selection process that takes it through the bottleneck. The
precursor species will almost certainly be tool-using and social, but tool use
and social behaviour are both extremely common, so we could find anything from
intelligent birds to octopuses.

With regard to the "surprise" that evolution can produce convergent
morphology, this isn't really that surprising: genetic studies have shown that
such things occur in nature. For example there are two species of coastal
lizard in the Yucatan both of which have evolved an extra vertebra in their
neck which were thought to come from a common ancestral population, but thanks
to genetic analysis in the '90's were found to be due to convergent
adaptations to coastal conditions by different inland species. Furthermore,
while gene selection does occur, the basic unit of selection is the whole
organism, which in most cases either reproduces, or does not.

Evolution happens at multiple levels (a topic it is fun to speculate on:
[http://www.amazon.com/Darwins-Theorem-TJ-Radcliffe-
ebook/dp/...](http://www.amazon.com/Darwins-Theorem-TJ-Radcliffe-
ebook/dp/B00KBH5O8K/ref=sr_1_1?ie=UTF8&qid=1410468328&sr=8-1&keywords=darwin%27s+theorem))
and the competition between them is likely to be a focus of increasing study
in coming years.

~~~
jquery
> despite the ridiculous benefits available once a species gets through it

From an evolutionary perspective, the benefits are far from proven. On an
evolutionary timescale, civilization hasn't been around that long and has had
a disproportionate number of existential risks over its timescale. In the
nearer term, there is also evidence for large scale dysgenetic fertility in
many countries with respect to genotypic IQ.
[http://en.wikipedia.org/wiki/Fertility_and_intelligence](http://en.wikipedia.org/wiki/Fertility_and_intelligence)

------
otakucode
"Under identical conditions."

In other words - not in reality.

------
obblekk
I feel like a CS education should prepare one for this kind of field. What's a
good way to get started learning more about evolution?

~~~
kartman
The Selfish Gene is a great and insightful book that I would recommend.

~~~
stan_rogers
Great book, yes, but don't stop there. There is a lot more to evolution than
Dawkins suggests; selection, no matter the mechanism, is, after all,
determined by phenotype (the "realised organism", if you will) rather than
genotype. And there are a lot of models of selection (and of modification)
that make accurate predictions but don't have the Dawkins seal of approval.
You'd be missing a lot if you allow yourself to become stuck in the notions of
1976, no matter what their merits at the time.

