
Can Darwinian Evolution Explain Lamarckism? - Errorcod3
https://www.quantamagazine.org/can-darwinian-evolution-explain-lamarckism/
======
alexholehouse
This is oddly poignant to me. I just (literally a few hours ago) submitted my
PhD thesis on (broadly) the biophysics of emergent phenomena. People don't
usually read theses cover to cover, with good reason, but I included one short
paragraph in the preface to be the true "take home" message:

 _We wish to understand mechanism through the elucidation of design
principles, yet evolution does not select for principles, it selects for
fitness, an epistatic and emergent property. If similar outcomes can be
achieved in different but equivalently fit ways, then given the stochastic
nature of evolution this is almost guaranteed to happen. We have specific
examples where every statement in the preceding paragraph is true [ed: a
collection of proposed mechanisms]. We do not need one person to be right or
wrong; our nascent understanding of complex biological systems is that the
space of information-processing solutions is astronomical. Think of the
diversity observed in structural biology - the repertoire of tertiary
structures is enormous. There are countless examples of nearly identical
functions being performed by proteins with radically different structure.

This divergence, this variety in structure and function, is what makes
evolution robust. It is an inherent bet-hedging mechanism woven into the
fabric of statistical physics. On the contrary, the desire to categories and
abstract complexity into distinct groups is an inherently human endeavour.
Much as we may wish and as convenient as it would be, Nature does not have a
plan._

~~~
irickt
Is your work available to read?

~~~
dtornabene
+1 as well, very very interested. If you could post some resources that an
interested reader could educate themselves with in the meantime, it would be
deeply appreciated. Maybe a sample of the bibliography from your thesis?

~~~
alexholehouse
So for some context, my work is not directly about evolution, but about how
amino acid sequence determines function in the context of unfolded/disordered
proteins.

That said, here are several at least semi-relevant papers that have influenced
my thinking on a bunch of things (no particular order).

[1] Wheeler, L.C., Lim, S.A., Marqusee, S., and Harms, M.J. (2016). The
thermostability and specificity of ancient proteins. Curr. Opin. Struct. Biol.
38, 37–43. (Probably paywalled but available on the Harms' lab website -
[https://harmslab.uoregon.edu/publications/](https://harmslab.uoregon.edu/publications/).
Mike's work on thinking about the biophysics of evolution is in general super
cool. Similarly work by Adrian Serohijos is really interesting, although I am
in general less familiar with it
[http://www.serohijoslab.org/publications.html](http://www.serohijoslab.org/publications.html))

[2] Tikhonov, M. (2016). Community-level cohesion without cooperation. Elife
5. (Open Access, really cool, and publishing a single-author original paper in
a top journal in this day-and-age is incredibly impressive).

[3] Riback, J.A., Katanski, C.D., Kear-Scott, J.L., Pilipenko, E.V., Rojek,
A.E., Sosnick, T.R., and Drummond, D.A. (2017). Stress-Triggered Phase
Separation Is an Adaptive, Evolutionarily Tuned Response. Cell 168,
1028–1040.e19. (Paywalled, but IMO a HUGELY important study for thinking about
'aggregation' in the context of cellular fitness)

[4] Chakrabortee, S., Byers, J.S., Jones, S., Garcia, D.M., Bhullar, B.,
Chang, A., She, R., Lee, L., Fremin, B., Lindquist, S., et al. (2016).
Intrinsically Disordered Proteins Drive Emergence and Inheritance of
Biological Traits. Cell 167, 369–381.e12. (Paywalled, but _potentially_ one of
the most important discoveries in cellular adaptation in decades. More work to
be done though!)

[5] Halabi, N., Rivoire, O., Leibler, S., and Ranganathan, R. (2009). Protein
sectors: evolutionary units of three-dimensional structure. Cell 138, 774–786.
(Paywalled, but super important for thinking about the relationship between
local structural coupling and evolutionary behaviour. In general, everything
Rama puts out is just gold.)

------
SamBam
This is pretty straightforward. The existance of the epigenetic mechanism is,
itself, a result of Darwinian evolution.

Where epigenetics seems weird to people is simply that it goes beyond the
modern synthesis -- i.e. it's not just DNA base pairs. But plain-ol' Darwinian
evolution doesn't depend on genetics via DNA base-pairs, it depends simply on
inherited characteristics, however they are inherited.

------
jfaucett
I'm not a biologist. Can someone that knows more here help me out?

From the article it seems epigenetic mechanisms aren't inheritable i.e. they
do not change the DNA just how the DNA is interpreted and/or which genes are
activated. So even though epigenetic mechanisms might get passed on for
several generations once the environmental factor affecting the mechanisms is
removed the organisms would revert wouldn't they?

It seems all this does is allow some Lamarckian traits to act as a factors in
the natural selection process.

Also the two explanations for how Giraffes got their long necks seem pretty
ridiculous to me. Does anyone know of legit research into that topic?

~~~
SamBam
Epigenetic mechanisms _are_ heritable. Just via other methods than DNA base-
pair order. For example, through chromatin bookmarking, which effects the
_state_ of the DNA (which parts are tightly folded and which aren't), not the
code itself:

[https://en.wikipedia.org/wiki/Transgenerational_epigenetic_i...](https://en.wikipedia.org/wiki/Transgenerational_epigenetic_inheritance)

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

------
carapace
Gregory Bateson has a good piece in one of his books (it might have been
"Steps to an Ecology of Mind") where he derives from cybernetic principals the
result that Darwinian evolution _works better_ than Lamarckian.

The key insight is that we can think of meta-evolution driving the form of the
"first-order" evolution, meaning we evolved to evolve Darwinian-ly. (In
practice meta-evolution cannot be separated from evolution, there is only
one.)

This implies that we should _expect_ limited Lamarckian evolution anywhere it
leads to greater fitness than Darwinian.

From this POV epigenetic mechanisms are expected.

(I still look askance and the so-called "Central Dogma" of biology. Why on
Earth would you assume that genes can't be changed by soma? If there was
adaptive advantage to being able to edit DNA then it seems like cells and
viruses would have it. As I typed that my brain said: CRISPR stoopid. SO,
yeah, duh.)

~~~
rflrob
> This implies that we should expect limited Lamarckian evolution anywhere it
> leads to greater fitness than Darwinian.

Not necessarily... evolution is good at finding local maxima, but not
necessarily global ones if there's a deep valley in between. Transgenerational
epigenetic inheritance is hard to evolve (compared to more Darwinian/DNA
sequence-based evolution, it requires extra mechanistic steps and typically
the effect size is small), so most of the time it isn't employed. If you look
at enough cases where Lamarckian evolution might be advantageous, you'll find
a few where it's employed to a limited degree, but in any given situation, it
probably won't be.

------
fiatjaf
Since biologists and evolutionists are liken to gather here, I would like to
ask something that's been occurring to me lately: does evolution explain all
the things? For example, does it explain my personal musical taste? Or perhaps
the aesthetic tastes of those birds that mate based on aesthetic choices? If
evolution doesn't explain these and other factors that are involved in natural
selection, so we can say that external factors (explained by what?) are
involved in the process of evolution, so evolution may be being partially
caused by other, non-emergent, forces?

I don't know if this is clear or if it makes sense. Please feel free to say
I'm stupid.

~~~
Elrac
Sort of. Here's a sloppy analogy off the top of my head:

Evolution explains your musical taste in the same way that gravity explains
why much of the rainfall on the Alps ends up in Lake Constance. It's not a
detailed, step-by-step explanation, but it's an explanation at the level of
"duh, what else could it be?" Evolution, on a pretty fundamental level, is the
reason for every last difference in behavior (down to the chemical level)
between a bacterium and you, and no serious biologist doubts this.

Now, evolution is not an isolated process; it's exactly the connection between
real-world "external factors" as you say and the survival (or not) of our
ancestors. So sure, parts of your genome may have been shaped by the climate
in Ethopia or the prevalence of mammoths in Siberia. All those stories are
_part_ of "evolution."

I'm not a biologist but I can speculate on what one might say about your
musical tastes: Humans and other mammals enjoy rhythms of certain frequencies,
maybe because those are what you hear as a child nestled against your parent's
chest. Hearing that kind of noise usually meant you were safe. Music in
general is enjoyed as a form of social communication (which is a vital to
human survival), roughly along the same lines that howling together
strengthens the unity of a wolf pack. Beyond that, your individual music
tastes, i.e. the tempi, rhythms, tones and harmonies you like, are most likely
learned behaviors (and that's why they're often not inherited), influenced by
what you heard a lot of in a certain age range. On the other hand, the
learning capability itself, your acquisition of your surrounding culture and
its musical features, is almost certainly another survival-enhancing evolved
skill.

------
aaron695
I often thinks 'Evolution' is a shifting goal post.

They just keep redefining it to suit new information.

Given by mass the majority of mammals (ok pretty specific) have been designed.
I'm not sure it's currently true.

~~~
boomboomsubban
>They just keep redefining it to suit new information.

Also known as "the scientific method."

------
thriftwy
The nature is not set on supporting our positivist "yes or no" theories.

Which means, for every theory that says "A is causes by X and not by Y", there
will be a few cases where the inverse is true.

The solution is probably to stop making a religion out of knowing a few true
yes/no theories, and understand the why's.

