Evolvability

[Sriram]

Hi everyone,

People here have been arguing for years about random gene variation and Natural Selection...while I have been trying to argue for some kind of a direction and progress in evolution.

Here is an article about evolvability or the increasing ability to evolve in a particular way.

http://www.bbc.com/earth/story/20170301-life-may-actually-be-getting-better-at-evolving

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Creatures do not seem to be merely at the mercy of random changes, or mutations, in their genes over time. Instead, they actually seem to "improve" their ability to adapt. It seemed this ability was not explained solely by the process of natural selection, in which the best traits are passed on by the most successful organisms.

His ideas could help explain why animals are so good at evolving: a trait called their "evolvability".

Many people will be familiar with the idea that genes are passed from parent to offspring, and those genes that help their hosts survive and reproduce have a better chance of getting passed on. This is the essence of evolution and natural selection.

But there is more to it, because genes often work together. They form "gene networks", and those gene networks can also sometimes be passed intact down the generations.

His contribution is largely to do with the way natural selection acts on those networks.

He believes it does not just act like a partial barrier, letting some adaptations through over others. Instead, the impact of this filtering allows gene networks in animals to actually "learn" what works and what does not over time. This way, they can improve their performance – in much the same way that the artificial neural networks used by computer scientists can "learn" to solve problems.

"Gene networks evolve like neural networks learn," he says. "That's the thing that's novel."

Watson's basis for this claim is the idea that the connections between genes can be strengthened or weakened as a species evolves and changes – and it is the strength of those connections in gene networks that allow organisms to adapt.

This process is similar to how human-made artificial neural networks on computers work.

the connections between adjacent neurons that have similar outputs are strengthened over time. In short: "neurons that fire together, wire together". The network "learns" by creating strong links within itself.

If an organism has certain genes firing together in this way, and that organism proves successful enough to reproduce, then its offspring will not simply inherit its beneficial genes, argues Watson. They will also inherit the connectivity between those genes.

To begin with, this process of trial-and-error updating might work reasonably well. But over time, updating the code this way would become ever more cumbersome. The code would begin to look messy, making it difficult to work out what impact a particular addition might have.

If organisms actually evolved this way, says Watson, "their evolvability – their ability to adapt to new stresses or environments – would be rubbish." But in fact, "the ability of natural organisms to evolve to new selective environments or challenges is awesome."

Watson has also suggested that gene networks can contain "memories" of past adaptations, which can be expressed when required by the environment.

Watson's idea means that organisms would be imbued with multiple options for adapting.

It also implies that gene networks have evolved – in all animals – to be adaptable to Earth's natural world. That is why organisms are so good at responding to the environment: the stresses and strains of living in Earth's environments have been imprinted in the regulatory connections between genes, over the course of millions of years.

The gene networks, he argues, have gradually learned to respond in similar ways in similar situations. Those modular features, such as a butterfly's wing pattern, might be more likely solutions for the learning system than others.

In other words, when given a few necessary conditions, evolution will perform the same tricks again and again.

All of this raises some rather philosophical questions. For one thing, is evolution functioning like a big, natural computer? And does "evolvability" suggest that life is in some sense programmed to improve – at the genetic level at least?

Some biologists flinch at the idea, but if the capacity of organisms to adapt is getting better and better over time, if evolution is learning as it goes, then might it just as well be described this way?

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He doesn't seem to talk of epigenetics specifically which is funny. But the idea that organisms are learning to evolve in certain ways to improve their adaptability, seems to indicate a built in 'Intelligence' and ability to evolve in certain ways. 

Cheers.

Sriram

[Stranger]

What the hell has this got to do with "Ethics and Freethought"?

People here have been arguing for years about random gene variation and Natural Selection...while I have been trying to argue for some kind of a direction and progress in evolution.

Well you and your fellow religiously motivated fantasists may have been arguing but, out in the real world, random variation and natural selection has been well established science for some considerable time.

Here is an article about evolvability or the increasing ability to evolve in a particular way.

http://www.bbc.com/earth/story/20170301-life-may-actually-be-getting-better-at-evolving

Okay, what actually do we have here? This seems to be based on an opinion paper (full pdf) and the BBC article itself says that he has no evidence that supports his ideas:-

However, the big challenge for Watson's hypothesis is whether any empirical evidence for it can be found in nature.

Oddly, you missed that bit out of your quote. As an aside, if you are going to quote big chunks of an article, it is usual to indicate where you have omitted sections.

Anyway - what we have here is basically speculation. There is nothing wrong with that but as I said elsewhere, it is important to know what you are actually looking at.

He doesn't seem to talk of epigenetics specifically which is funny.

Why? The idea doesn't appear to have anything at all to do with it.

But the idea that organisms are learning to evolve in certain ways to improve their adaptability, seems to indicate a built in 'Intelligence' and ability to evolve in certain ways. 

I don't think you've understood. The speculation is about gene networks "learning" over evolutionary time - not about organisms learning during their individual lifetimes. He doesn't appear to be suggesting any literal intelligence.

For example (in another bit you cut out):-

For instance, perhaps certain groups of organisms could rapidly evolve to eat a food that is harmful to other members of the same species – because their ancestors had already endured such a diet.  In the past, the gene-regulatory structure would have been changed, making some gene-expression patterns easier to trigger than others. This "bias" would ultimately help their descendants to digest a tricky meal.

And here, where it talks about how the ideas could be tested:-

Watson suggests analysing how gene networks change in microbes that evolve in the lab. Because microbes like bacteria reproduce so quickly, it is possible to observe several generations of adaptation in a matter of days.

I haven't read the whole paper yet but from the BBC article, it seems we basically have a speculation that a process somewhat like neural network learning may be happening to networks of genes over evoutionary time due to the way random variation and selection acts on said networks.

[Maeght]

But the idea that organisms are learning to evolve in certain ways to improve their adaptability, seems to indicate a built in 'Intelligence' and ability to evolve in certain ways.

A big conclusion to draw when you consider 'the big challenge for Watson's hypothesis is whether any empirical evidence for it can be found in nature.'

[Stranger]

A big conclusion to draw when you consider 'the big challenge for Watson's hypothesis is whether any empirical evidence for it can be found in nature.'

It's actually worse than that. Even if Watson's ideas are 100% correct, it wouldn't mean what Sriram wants it to mean.

It's a proposal about mathematical equivalences between types of machine learning and the processes of variation, selection and inheritance. For example, he points out that genotype-phenotype maps are themselves the products of evolution, so, in a sense, the processes of variation are evolving.

It remains to be seen to what extent these ideas are useful but it doesn't question the fact that it is all built on random variation, selection and inheritance. There is nothing here that would give evolution the "direction" Sriram is so keen on - nor does it propose anything like a controlling intelligence.

[Sriram]

Hi everyone,

I am not trying to read any elaborate spiritual details into the new finding.  I am not talking of God or after-life or any thing like that.

The dice is obviously loaded in favor of complexity and this implies a direction. Whether a God has decided this or whatever, is irrelevant. We don't know that.

Many people here have however argued that there is no direction at all and that given enough time, humans will automatically arise merely through random genetic various and NS.

The above article clearly states ......

'Creatures do not seem to be merely at the mercy of random changes, or mutations, in their genes over time. Instead, they actually seem to "improve" their ability to adapt. It seemed this ability was not explained solely by the process of natural selection, in which the best traits are passed on by the most successful organisms.'

'And does "evolvability" suggest that life is in some sense programmed to improve – at the genetic level at least?' '.. if the capacity of organisms to adapt is getting better and better over time, if evolution is learning as it goes, then might it just as well be described this way'


This means that probably there is a mechanism through which this kind of 'learning' can be enabled and organisms can adapt 'better and better' over time.

[wigginhall]

How does complexity imply a direction?   If a star is formed from a mass of dust and gas, this can be explained in part by the effects of gravity.   So does gravity imply a direction? 

'Direction' to me suggests intelligence also.   So stars are formed by an unseen hand?

[Maeght]

I for one wasn't suggesting you were trying to include a God but rather that you were reading far too much into this hypothesis for which there is currentl no evidence in nature as it stated.

[wigginhall]

Do organisms evolve 'better and better'?  An awful lot of them have become extinct, and a lot of them are becoming extinct right now.   I don't see how evolution itself is 'improving'. 

[Stranger]

I am not trying to read any elaborate spiritual details into the new finding.

It isn't a "finding", it's a speculative hypothesis for which there is, as yet, no supporting evidence.

The dice is obviously loaded in favor of complexity and this implies a direction.

Where did you get the idea that complexity is favoured? Even if it was, that is hardly a specific direction.

Many people here have however argued that there is no direction at all and that given enough time, humans will automatically arise merely through random genetic various and NS.

I know of absolutely nobody who has argued that "humans will automatically arise" from random variation and natural selection - what a silly idea! All the evidence is that humans are a random product of undirected evolutionary change. There was never anything "automatic" or inevitable about it.

There is nothing in the article, or the paper it's based on, that would affect that conclusion.

This means that probably there is a mechanism through which this kind of 'learning' can be enabled and organisms can adapt 'better and better' over time.

The hypothesis suggests that there are processes that have evolved "on top of" the basic random variation of genes, their direct expression in organisms and subsequent selection. The upshot of which would be "better" adaptation to whatever environment a population found itself in (within the limits of previous "experience" or "learning"). There is no magic change in direction - it's basically an increase in the efficiency.

The example I quoted before illustrates the sort of thing being proposed:-

For instance, perhaps certain groups of organisms could rapidly evolve to eat a food that is harmful to other members of the same species – because their ancestors had already endured such a diet.  In the past, the gene-regulatory structure would have been changed, making some gene-expression patterns easier to trigger than others. This "bias" would ultimately help their descendants to digest a tricky meal.

[wigginhall]

Yes, if humans arise automatically, that would favour the idea of a direction and a plan.  The people who advocate that are people  like Simon Conway Morris, a paleontologist who is a Christian.   I haven't seen it expressed on this forum. 

[Stranger]

Yes, if humans arise automatically, that would favour the idea of a direction and a plan.  The people who advocate that are people  like Simon Conway Morris, a paleontologist who is a Christian.   I haven't seen it expressed on this forum.

Yes, if there is a direction/plan then we might expect humans to be inevitable but I totally fail to see how anybody could argue that "there is no direction at all and that given enough time, humans will automatically arise merely through random genetic various and NS" - it makes no sense.

[Sriram]

Yes, if there is a direction/plan then we might expect humans to be inevitable but I totally fail to see how anybody could argue that "there is no direction at all and that given enough time, humans will automatically arise merely through random genetic various and NS" - it makes no sense.

You are arguing this in reverse. 

If  complex and intelligent humans have arisen from simpler organisms....the usual argument given by spiritualists and others   is that there must be a direction and some superior Intelligence must be wanting humans to arise....or Consciousness must be driving evolution in specific directions (I like that!). 

Humans cannot possibly arise just by chance. To illustrate this point, usually the old monkey and the typewriter analogy is used. A monkey playing around with a typewriter cannot by chance produce the entire works of Shakepeare. Or a 747 cannot get assembled by chance ...and so on.

The counter argument to this by atheists and scientists is that, given enough time, merely through random variation and NS, humans could be produced. Selection works over long periods of time and will eventually produce complex beings like humans. There is therefore no need to resort to any direction or superior Intelligence to explain the origin of humans! This is what I meant by saying that humans will arise just by random variation and NS, given enough time. This has been argued on here many times (though I can't now produce those threads).

Now ..... according to the above article, evolution does not work entirely by chance. There is a learning process that influences adaptation and evolution (programmed to improve).

I quote once again from the article.....

'Creatures do not seem to be merely at the mercy of random changes, or mutations, in their genes over time. Instead, they actually seem to "improve" their ability to adapt. It seemed this ability was not explained solely by the process of natural selection, in which the best traits are passed on by the most successful organisms.'

'And does "evolvability" suggest that life is in some sense programmed to improve – at the genetic level at least?' '.. if the capacity of organisms to adapt is getting better and better over time, if evolution is learning as it goes, then might it just as well be described this way'

[Maeght]

That article is someones hypothesis Sriram with no supporting evidence. A thought experiment, nothing more. You do get that don't you?

[Sriram]

That article is someones hypothesis Sriram with no supporting evidence. A thought experiment, nothing more. You do get that don't you?

Lots of things are hypothesis (Dark Energy, Dark Matter, Parallel Universes, String). But they are taken seriously and could turn out to be true.  You can't cherry pick your hypothesis. 

[Maeght]

Lots of things are hypothesis (Dark Energy, Dark Matter, Parallel Universes, String). But they are taken seriously and could turn out to be true.  You can't cherry pick your hypothesis.

I'm not, but you are quoting an hypothesis as if it is something supported by evidence. I asked if you recognised that is what you are doing. Do you?

[Stranger]

You are arguing this in reverse. 

- sigh -    No Sriram, that would be you.

If  complex and intelligent humans have arisen from simpler organisms....the usual argument given by spiritualists and others   is that there must be a direction and some superior Intelligence must be wanting humans to arise....or Consciousness must be driving evolution in specific directions (I like that!). 

That would be because "spiritualists and others" don't actually understand evolution.

Humans cannot possibly arise just by chance. To illustrate this point, usually the old monkey and the typewriter analogy is used. A monkey playing around with a typewriter cannot by chance produce the entire works of Shakepeare. Or a 747 cannot get assembled by chance ...and so on.

All of which demonstrates the point that you don't understand evolution.

The counter argument to this by atheists and scientists is that, given enough time, merely through random variation and NS, humans could be produced. Selection works over long periods of time and will eventually produce complex beings like humans. There is therefore no need to resort to any direction or superior Intelligence to explain the origin of humans! This is what I meant by saying that humans will arise just by random variation and NS, given enough time. This has been argued on here many times (though I can't now produce those threads).

Misunderstanding piled on misunderstanding. Do you ever pay any attention at all to what is actually said in the posts you don't agree with?

Firstly, the process of natural selection means that the typewriting monkeys and 747 analogies are totally wrong (just how many time does this need repeating!?). Evolution is a process of random variation and (crucially) filtration. Random changes that increase the chances of survival and reproduction, in the context of the environment, are preserved and those that work against it are discarded. There is no need to produce a complex result all at once. In effect, it is an algorithmic "design" process that produces organisms (complex or simple) that are suited to their environments. Producing improbable results (if you tried to generate them all at once, from nothing) is what it does.

Secondly, you using the lottery fallacy in assuming that the improbability of the particular result is significant in itself. Each time lottery numbers are drawn, a very improbable selection of numbers is inevitably produced. If humans were never the target, the improbability of humans in particular, isn't significant. Every organism is very improbable and so is every organism that didn't evolve but could have.

Now ..... according to the above article, evolution does not work entirely by chance. There is a learning process that influences adaptation and evolution (programmed to improve).

Well to be fair, the article, and even the paper, seem a little sensationalized. The point is that there is nothing being proposed that really changes things as fundamentally as you seem to think.

We already know that organisms evolve to deal competently with their environments without any need for an intelligent input or direction. What is being proposed is that it is not only organisms that have evolved but that there are processes, to do with things like the genotype-phenotype maps, that also evolve and do so in a way that compares to machine learning algorithms.

Nowhere is there a suggestion that there is any other input to the overall process other than random variation and selection. It's just making the algorithmic "design" process at bit more complicated. The paper itself has a lot to say about mathematically equivalent processes and nothing to say about new inputs.

You need to read and understand what is being said - it's silly just to jump on single words or phrases ("programmed to improve" - wow - programmed! - that must mean by some programmer! - that's like direction and intelligent design!).

And, yet again - this is nothing more than a speculative hypothesis for which there is no evidence...

[Sriram]

I'm not, but you are quoting an hypothesis as if it is something supported by evidence. I asked if you recognised that is what you are doing. Do you?

Maeght,

As I said...a hypothesis is usually good enough to explain most phenomena.  You will not find hard evidence for everything. Even Relativity was a hypothesis for many decades. Nothing wrong with that.

As I understand the article in the OP, we can perhaps think of it in terms of the ...'Monkey and the typewriter' analogy.

Though many scientists claim that  a monkey typing randomly on a typewriter (computer) will eventually, given enough time, produce meaningful essays....this is clearly nonsense!!  Nothing of that kind will ever happen.

However, if the computer is programmed to isolate and store separately in its memory, every word that is meaningful...then such words could form a  large word bank.   If these words are thrown up every time the monkey types, then in course of time meaningful sentences could get produced. Such sentences would again get isolated and stored, to be thrown up every time the monkey types. If this process continues, it is indeed possible (given enough time) that some meaningful essay is produced by the monkey even though it is typing at random.

In other words, the programming of the computer to isolate meaningful words and sentences, could give a direction to a random event.

This is what I find quite interesting about the article.

Obviously, the question would arise as to how and why the computer is programmed and who decides which words and sentences are meaningful. But that is a premature discussion currently.

Cheers.

Sriram


 

[Stranger]

As I said...a hypothesis is usually good enough to explain most phenomena.

No they aren't. A hypothesis is essentially a detailed guess. They cannot be considered as explanations until there is evidence.

You will not find hard evidence for everything. Even Relativity was a hypothesis for many decades. Nothing wrong with that.

You are right that hypotheses are a necessary part of the scientific method and that a few of them go on to become established theories.

Though many scientists claim that  a monkey typing randomly on a typewriter (computer) will eventually, given enough time, produce meaningful essays....this is clearly nonsense!!  Nothing of that kind will ever happen.

This is not a claim that is made by scientists in order to explain evolution. I challenge you to cite a single instance in which this argument has been used by a scientist as an explanation of how evolution works.

It's actually a rather pitiful straw man fallacy used by dishonest creationists and proponents of intelligent design.

However, as an aside, it is actually true that if you generate random characters for long enough, then any desired string will eventually be produced. It's just not how evolution works.

However, if the computer is programmed to isolate and store separately in its memory, every word that is meaningful...then such words could form a  large word bank.   If these words are thrown up every time the monkey types, then in course of time meaningful sentences could get produced. Such sentences would again get isolated and stored, to be thrown up every time the monkey types. If this process continues, it is indeed possible (given enough time) that some meaningful essay is produced by the monkey even though it is typing at random.

In other words, the programming of the computer to isolate meaningful words and sentences, could give a direction to a random event.

Yes, except of course there is already a known process that isolates and preserves "meaningful" information from random variation - it's called "natural selection" - you may have heard of it.

This is what I find quite interesting about the article.

Obviously, the question would arise as to how and why the computer is programmed and who decides which words and sentences are meaningful. But that is a premature discussion currently.

Again, you've totally misunderstood. There isn't "a computer" in the hypothesis - just (many) systems that are responding to natural selection in ways that resemble machine learning algorithms.

[Maeght]

Maeght,

As I said...a hypothesis is usually good enough to explain most phenomena.

Absolutely not.

[Sriram]

Again, you've totally misunderstood. There isn't "a computer" in the hypothesis - just (many) systems that are responding to natural selection in ways that resemble machine learning algorithms.

No...you don't understand. Natural Selection acts on all organisms equally in any specific environment. Worms, spiders, lizards, birds, lions, elephants and ...humans. It doesn't explain diversity or complexity or emergent properties.

[Gordon]

No...you don't understand. Natural Selection acts on all organisms equally in any specific environment. Worms, spiders, lizards, birds, lions, elephants and ...humans. It doesn't explain diversity or complexity or emergent properties.

Wrong.

[Stranger]

No...you don't understand. Natural Selection acts on all organisms equally in any specific environment. Worms, spiders, lizards, birds, lions, elephants and ...humans. It doesn't explain diversity or complexity or emergent properties.

As Gordon succinctly put it, this is just wrong. For one thing, if two different species are in the "same environment" then the environment of one species includes the other - so they don't have the same environment at all. If they are predator and prey you can get an "evolutionary arms race".

You clearly don't have the first clue about evolution and natural selection; if you're going to talk about it - learn about it!
Evolution 101.

[Sriram]

I  don't agree that random genetic variation and Natural Selection explain evolution as we see it. This, to me, is common sense.

'Natural Selection' is just a metaphor and not a specific process at all! 

Cheers.

[Maeght]

I  don't agree that random genetic variation and Natural Selection explain evolution as we see it. This, to me, is common sense.

'Natural Selection' is just a metaphor and not a specific process at all! 

Cheers.

Common sense?! Blimey - lets rip up all the scientific papers, text books and learned journals and replace them with Sriram's common sense conclusions.

[Stranger]

I  don't agree that random genetic variation and Natural Selection explain evolution as we see it. This, to me, is common sense.

So, Sriram thinks that the vast majority of scientists that study evolution are idiots who can't see "common sense".

'Natural Selection' is just a metaphor and not a specific process at all! 

No Sriram, it can't possibly be a metaphor because it's a term that was coined specifically to denote the process in question. It's even defined by the process in the dictionary...

Biology

The process whereby organisms better adapted to their environment tend to survive and produce more offspring. The theory of its action was first fully expounded by Charles Darwin, and it is now regarded as be the main process that brings about evolution.