For those wondering what "macroevolution" actually is...

[Speedwell]

Thanks for the detailed response- I think we agree on a lot here (but what fun is that!? )

except I think on the processes driving change, to the question in the OP, I'm not a biologist either, but many do make a fundamental distinction between the natural and superficial variation we see within a species, between dogs, sheep, our own family.. and the more fundamental changes and new developments in body plans- we cant necessary extrapolate one smoothly into the other-

Those traits can evolve which exhibit randomly distributed variation. The existing body plans were established when the number of limb-like extremities a creature possessed still varied from individual to individual. Once a few locally optimum body plans were arrived at, variation in the number of limbs was no longer a survival advantage and so it ceased. Consequently, if a modern creature would be advantaged by a limb with a different function, it must evolve from an existing limb by means of those traits of the limb which still exhibit randomly distributed variation--relative size of the parts primarily, as in a bat's wing which has all of the same structure as any mammalian forelimb, merely in different proportions.

 

[Guy Threepwood]

DNA is not computer code; it's bio-chemistry. Often times analogies are used for the purpose of explaining concepts, but it doesn't mean they are the same thing.

That was a quote from Dawkins- I should have credited him for it. Of course they are not the same thing; we use binary code and electronics, DNA uses primarily quaternary (base 4) code and chemistry- but as Dawkins recognized, they operate on uncannily similar architecture & design principles, whether or not that is by accident.. you have the same inherent limitations on what different parts of the hierarchical system can and cannot do. The information is organized in layers- just as this software-
we can randomly mutate superficial parameters like font size here, and get superficial changes. But we can't randomize information in the browser software or operating system- same thing in DNA, from control genes to regulatory networks- changes are required at different layers to achieve different degrees of change

At any rate, you still haven't explained what the barriers are for evolution in biology. That was the whole start of this discussion, but it seems it's drifting away with no resolution to that.

I was trying to explain the principle, - but the barriers are not necessarily for 'evolution' but for what can be achieved by random mutation and variation of the gene sequence-- i.e. micro to macro evolution by Darwinian mechanisms. It's getting pretty well established that something else at least is going on beyond that- e.g. epigenetics

I don't know what "Darwinism" is supposed to mean; regardless, eugenics as tied to misguided notions of racial supremacy is not an application of evolution.

Darwinism - Wikipedia
is a theory of biological evolution developed by the English naturalist Charles Darwin (1809–1882)
https://en.wikipedia.org/wiki/Darwinism
I'm just using that to distinguish from other theories of evolution- but some explicitly saw engineering racial supremacy as a direct application of the theory yes- very unfortunate of course

Regardless, that's not all what I am referring to. I am talking about things like pathogen tracking, identification and annotation of functional regions of genomes, etc. Things where evolution has direct, real-world application and those applications are a positive thing.

Do you have to be a Darwinist to apply these things though? Correct me if I am wrong, but was it not Darwinists who long maintained that 'JUNK DNA' served no purpose, where skeptics long suspected it did?

 

[Guy Threepwood]

You are taking your analogy to truly absurd levels. Can you give an example of how you can translate a computer -engineering article into a molecular biology article? I would suggest that you can't learn anything at all about living organisms by reading computer engineering articles.

Sorry- I should have credited that quote- it's a fairly well known one so people often get the reference

"we know that genes themselves, within their minute internal structure, are long strings of pure digital information. What is more, they are truly digital, in the full and strong sense of computers and compact disks, not in the weak sense of the nervous system. The genetic code is not a binary code as in computers, nor an eight-level code as in some telephone systems, but a quaternary code, with four symbols. The machine code of the genes is uncannily computerlike. Apart from differences in jargon, the pages of a molecular-biology journal might be interchanged with those of a computer-engineering journal. . . ."

Richard Dawkins, River out of Eden, 16-19

I don't think he was being absurd, and neither do many programmers-

the hardware may be different, but many similarities in design are striking yes.

 

[Speedwell]

I was trying to explain the principle, - but the barriers are not necessarily for 'evolution' but for what can be achieved by random mutation and variation of the gene sequence-- i.e. micro to macro evolution by Darwinian mechanisms. It's getting pretty well established that something else at least is going on beyond that- e.g. epigenetics




Darwinism - Wikipedia
is a theory of biological evolution developed by the English naturalist Charles Darwin (1809–1882)

So you're using the term because you want to knock down a straw man.

 

[Guy Threepwood]

What "either way?" If you think the evidence is pointing away from the theory of evolution, what's it pointing toward? Right now the TOE is the only credible explanation for the biological diversity we see around us. If you dismiss it as being only weakly supported you are left with no explanation at all.

I think the evidence is pointing away from ToE in very much the same way as it pointed away from classical physics.

Darwinism came out of a Victorian age reductionist model of reality, where a handful of simple 'immutable' laws + lots of time and space to randomly bump around in, were all you needed to account for all the wonders of physical reality, right? So it was a perfectly logical extension of this model at the time. While the belief that deeper, more sophisticated, mysterious, unpredictable guiding forces were required- was still for the 'ignorant superstitious masses', all before quantum mechanics of course

The simplest explanation may often be the most tempting, but how much regard does nature really show for Okhams razor?

Apples still fall from trees yes, and we see genetic apples fall not far from their 'evolutionary' trees..
but we can't automatically extrapolate superficial observations into comprehensive explanations

Because scales matter, things do work very differently at different scales, and that's inherent in any hierarchical system like physics, biology, or this software

 

[Speedwell]

I think the evidence is pointing away from ToE in very much the same way as it pointed away from classical physics.

Darwinism came out of a Victorian age reductionist model of reality, where a handful of simple 'immutable' laws + lots of time and space to randomly bump around in, were all you needed to account for all the wonders of physical reality, right? So it was a perfectly logical extension of this model at the time. While the belief that deeper, more sophisticated, mysterious, unpredictable guiding forces were required- was still for the 'ignorant superstitious masses', all before quantum mechanics of course

The simplest explanation may often be the most tempting, but how much regard does nature really show for Okhams razor?

Apples still fall from trees yes, and we see genetic apples fall not far from their 'evolutionary' trees..
but we can't automatically extrapolate superficial observations into comprehensive explanations

Because scales matter, things do work very differently at different scales, and that's inherent in any hierarchical system like physics, biology, or this software

Not only does that not make any sense, it doesn't even appear to be an attempt to answer my question.

 

[sesquiterpene]

Sorry- I should have credited that quote- it's a fairly well known one so people often get the reference

"we know that genes themselves, within their minute internal structure, are long strings of pure digital information. What is more, they are truly digital, in the full and strong sense of computers and compact disks, not in the weak sense of the nervous system. The genetic code is not a binary code as in computers, nor an eight-level code as in some telephone systems, but a quaternary code, with four symbols. The machine code of the genes is uncannily computerlike. Apart from differences in jargon, the pages of a molecular-biology journal might be interchanged with those of a computer-engineering journal. . . ."

Richard Dawkins, River out of Eden, 16-19

I don't think he was being absurd, and neither do many programmers-

the hardware may be different, but many similarities in design are striking yes.

I would hope that the part I quoted would be recognised by most molecular biologists as absurd hyperbole on the part of Dawkins,who was neither a molecular biologist nor a computer scientist (he was a zoologist) I don't know about computer scientists...for my part I am a mere chemist (retired).

 

[FrumiousBandersnatch]

... entirely new functions emerging spontaneously is probably beyond biological possibility. So it's variation from here on out - we're not going to be sprouting extra pairs of arms or anything.

The broad point is correct - you're right about entirely new functions, but polymelia (supernumerary limbs) is a thing, and can be a result of abnormal genes. In the case of minor inconveniences, such as extra digits, they can be inherited and run in families. Whole extra limbs tend to be a significant disadvantage, so those abnormal genes are unlikely to persist in a population.

 

[FrumiousBandersnatch]

I would hope that the part I quoted would be recognised by most molecular biologists as absurd hyperbole on the part of Dawkins,who was neither a molecular biologist nor a computer scientist (he was a zoologist) I don't know about computer scientists...for my part I am a mere chemist (retired).

As an ex-software developer, I would agree. Genes and computer code have some attributes in common, e.g. sequential digital encoding, transcription, partial modularity, etc., but they're very different in other respects, as one might expect. It's rather like comparing the brain to a digital computer.

 

[Guy Threepwood]

I would hope that the part I quoted would be recognised by most molecular biologists as absurd hyperbole on the part of Dawkins,who was neither a molecular biologist nor a computer scientist (he was a zoologist) I don't know about computer scientists...for my part I am a mere chemist (retired).

quite likely so I think, if they are not programmers..

Which gets to the heart of the issue- life runs on DNA, a hierarchical digital information system, that's where the answers to these questions lie- the biology represents the hardware the code runs on, but a biologist or zoologist trying to solve the mysteries of life in this sense, is perhaps a little like trying to fix a bug in windows 10 with a soldering iron!

 

[Guy Threepwood]

Not only does that not make any sense, it doesn't even appear to be an attempt to answer my question.

to simplify:

The evidence is pointing more towards predetermination, information, instructions specifying how life develops - as opposed to a simple algorithm + random interaction. Just as with physics.

So I agree with Darwin's original premise- that we might expect life to develop by the same general mechanisms as physics and chemistry before it- only that means something quite different today.

 

[xianghua]

Who asked you?

this guy

 

[sesquiterpene]

quite likely so I think, if they are not programmers..

Which gets to the heart of the issue- life runs on DNA, a hierarchical digital information system, that's where the answers to these questions lie- the biology represents the hardware the code runs on, but a biologist or zoologist trying to solve the mysteries of life in this sense, is perhaps a little like trying to fix a bug in windows 10 with a soldering iron!

This is your brain on analogies. It is not a pretty sight.

 

[xianghua]

we cant necessary extrapolate one smoothly into the other-

we can think about this analogy: say that we had a self replicating car (even with DNA). can such a car will evolve into an airplane? if not it cant happen among creatures too. so why variations over time will not give us a new organs\complex structures? because some traits need at least several parts for their minimal function. thus variation+time will not give us complex structures like eyes or ears.

another problem is that it seems that there is no real correlation between complexity and natural selection. bacteria has the largest population (about 10^30) and yet its very simple organism. so even if it was possible to change one into another its seems to be not very likely.

 

[Guy Threepwood]

we can think about this analogy: say that we had a self replicating car (even with DNA). can such a car will evolve into an airplane? if not it cant happen among creatures too. so why variations over time will not give us a new organs\complex structures? because some traits need at least several parts for their minimal function. thus variation+time will not give us complex structures like eyes or ears.

right, & cars of course do come with pre-defined variations which allow them to be better adapted to different and changing environments- just as we see in life, that's just a logical and useful design feature. Essential in fact for a rich diverse environment.

This capacity in itself suggests nothing about the spontaneous design of this very same capacity!- quite the contrary if anything

another problem is that it seems that there is no real correlation between complexity and natural selection. bacteria has the largest population (about 10^30) and yet its very simple organism. so even if it was possible to change one into another its seems to be not very likely.

'evolving bacteria' is often used as a very misleading 'evidence' for Darwinian evolution- I don't think it's usually intentionally misleading-

but when populations of bacteria 'evolve' we are generally just looking at a change in distribution of already existing variations. Another classic example being the peppered moth. There were already dark moths, the white ones were just reduced in number- no new design evolved here

 

[Lobster Johnson]

The broad point is correct - you're right about entirely new functions, but polymelia (supernumerary limbs) is a thing, and can be a result of abnormal genes. In the case of minor inconveniences, such as extra digits, they can be inherited and run in families. Whole extra limbs tend to be a significant disadvantage, so those abnormal genes are unlikely to persist in a population.

Yeah, but that's a case where genes for an already existing limb get duped out in irregular ways so you get extra limbs in awkward spots. I was talking about an entirely new type of limb developing from scratch - like, say, a pair of wings sprouting from our shoulders. Our ancient ancestors were generalized enough that they could accept the gradual growth of new pseudopods and have it be advantageous, and overtime they would be developed and refined further by mutation and natural selection. But we're too specialized to begin the slow generational development of complex new limbs that our ancestors underwent.

The only way we could realistically develop wings would be something like what Speedwell mentioned earlier - adapting our arms and hands into some kind of bat-like membrane wing structure. And I mean... hands are probably better, so odds of that are low.

we can think about this analogy: say that we had a self replicating car (even with DNA). can such a car will evolve into an airplane?

Yes, for a given value of 'plane'

so why variations over time will not give us a new organs\complex structures? because some traits need at least several parts for their minimal function. thus variation+time will not give us complex structures like eyes or ears.

It will if you start simple enough.

another problem is that it seems that there is no real correlation between complexity and natural selection. bacteria has the largest population (about 10^30) and yet its very simple organism. so even if it was possible to change one into another its seems to be not very likely.

How complex are modern bacteria compared to, let's say, bacteria from 2 billion years ago?

Also, if bacteria are (comparatively) simple and yet still have the largest population, it seems as if they're doing just fine. Not really any pressure on them to change, is there?

 

[FrumiousBandersnatch]

we can think about this analogy: say that we had a self replicating car (even with DNA). can such a car will evolve into an airplane? if not it cant happen among creatures too.

Analogies with imaginary objects are useless in this context.

However, non-flying dinosaurs evolved into flying dinosaurs, non-flying mammals evolved into flying mammals, etc.

 

[FrumiousBandersnatch]

Yeah, but that's a case where genes for an already existing limb get duped out in irregular ways so you get extra limbs in awkward spots. I was talking about an entirely new type of limb developing from scratch - like, say, a pair of wings sprouting from our shoulders. Our ancient ancestors were generalized enough that they could accept the gradual growth of new pseudopods and have it be advantageous, and overtime they would be developed and refined further by mutation and natural selection. But we're too specialized to begin the slow generational development of complex new limbs that our ancestors underwent.

Yes, agreed; and we're arguably too technologically developed for that kind of natural selection to have traction.

... bacteria are (comparatively) simple and yet still have the largest population, it seems as if they're doing just fine. Not really any pressure on them to change, is there?

Exactly.

 

[Guy Threepwood]

Analogies with imaginary objects are useless in this context.

However, non-flying dinosaurs evolved into flying dinosaurs, non-flying mammals evolved into flying mammals, etc.

debatable..

Scientists: Bird's Ancestors Likely Not Dinosaurs

 

[Speedwell]

another problem is that it seems that there is no real correlation between complexity and natural selection.

Why is that a problem? The theory of evolution neither predicts nor requires that there should be.