The Fossil Record Proves Speciation, Not Evolution of Lifeforms Observed

[Ophiolite]

The point is that tiny steps of improvement are statistical advantages.

Indeed. The odds in roulette are only marginally in favour of the house, yet casinos rarely go bust.

 

[Justatruthseeker]

Gills don't turn into lungs. However there are many animals with both.

The point is that tiny steps of improvement are statistical advantages.

Since land life developed from sea life, gills sure did turn into lungs, or did you forget that part of the story?

Name one statistical advantage of gills turning into lungs that won’t detract from the usefulness of gills, but add to the eventual functionality of lungs? What are these improvements?

Or is this where we just ignore the details and revert to imagination and because we want it to be that way?

 

[Speedwell]

Since land life developed from sea life, gills sure did turn into lungs, or did you forget that part of the story?

Name one statistical advantage of gills turning into lungs that won’t detract from the usefulness of gills, but add to the eventual functionality of lungs? What are these improvements?

Or is this where we just ignore the details and revert to imagination and because we want it to be that way?

I didn't forget it, just never heard it before. The story I heard was that lungs (and swim bladders) developed from pouches in the gut.

https://www.quora.com/How-did-fish-evolve-lungs

 

[PsychoSarah]

Since land life developed from sea life, gills sure did turn into lungs, or did you forget that part of the story?

-_- the only time I hear that is with oversimplifications on the level of 13 year olds. Not my problem unscientific sources tend to botch science.

Name one statistical advantage of gills turning into lungs that won’t detract from the usefulness of gills, but add to the eventual functionality of lungs? What are these improvements?

Or is this where we just ignore the details and revert to imagination and because we want it to be that way?

Fyi, lungs can become better at their function without gills missing out whatsoever, they aren't even competing physically for space. Gills are far closer to the head than lungs, in case you haven't noticed.

 

[Shemjaza]

Since land life developed from sea life, gills sure did turn into lungs, or did you forget that part of the story?

Name one statistical advantage of gills turning into lungs that won’t detract from the usefulness of gills, but add to the eventual functionality of lungs? What are these improvements?

Or is this where we just ignore the details and revert to imagination and because we want it to be that way?

It isn't true. The evidence points to creatures who used gills developing an additional capacity to also breath air... then sine of them shredding the gills. Just because two systems serve a similar purpose, didn't mean they are the same system.

 

[Kylie]

But a single mutation won’t change gills into lungs. It would take thousands over millions of years.

So despite what you said you want us to believe that useless mutations are kept until they can all add up together to create a lung.

Why if I didn’t know better I would think you were implying intelligence working behind the scene, keeping mutations that do nothing yet until one has a fully functional lung from a gill.

First, I'm not aware of any reputable scientist who says that lungs came from gills. "...lungs, which likely arose from gas-filled bladders functioning for gas exchange and/or buoyancy control in primitive air-breathing fish prior to the radiation of ray-finned (Actinopterygi) and lobe-finned (Sarcopterygi) fishes." Evolution of lung breathing from a lungless primitive vertebrate

Secondly, no one is saying that it had to be done with only a single mutation. It would have been many mutations, each one improving the function a little. Seriously, why is it that creationists always have the ridiculous idea that things had to pop into existence complete?

Thirdly, what calculations have you done to show that the evolutionary process for the development of lungs would take thousands of millions of years? It has been calculated that the evolution of the eye would have taken only 364,000 years or so. Evolution: Library: Evolution of the Eye

 

[stevevw]

You have mentioned this on several occasions, but always - as far as I have read - in a very general way. Can you flesh this out with some specifics, ideally in your own words, but supported by relevant citations to peer reviewed research? This would facilitate a meaningful discussion about your views on this. On a related matter, but distinct from the foregoing point, would you agree that your view necessarily includes an implicit measure of teleology?

I posted the papers on this earlier and gave a brief description of how I understand these influences. Basically, living things can affect each other and be affected by their environment or can control change themselves which influences the outcomes of change. Living things are not seen in isolation but in cohabitations in a changing ecosystem. This takes a more holistic and interactive view where living things have inbuilt processes that produce suitable change are capable of controlling things rather than the narrow gene-centric and adaptive view of Neo-Darwinism.

Development biology involves how physical development influences the generation of variation (developmental bias). All living things have similar forms and basically the same development programs for producing certain forms rather than any possible form. Changes to existing forms are more to do with switching on or alterations existing genetic info rather than evolving through Darwinian evolution. The environmental pressures that living things experience may trigger processes that bring certain changes that help living things fit into environments.

Much variation is not random because developmental processes generate certain forms more readily than others3. developmental bias and natural selection work together4, 5. Rather than selection being free to traverse across any physical possibility, it is guided along specific routes opened up by the processes of development5, 6.
Does evolutionary theory need a rethink?

Plasticity also allows living things to change form and fit into their environments. Living things can change form without genes changing as well. Here there can be several different variations of the same creature in the same environment which would normally be attributed to different species. Yet the change in form has not been generated through evolution.

Plasticity not only allows organisms to cope in new environmental conditions but to generate traits that are well-suited to them.
Does evolutionary theory need a rethink?

This is also related to what is called Inclusive inheritance which covers epigenetics. Environmental influences such as stress can have an effect on gene expression and this can be passed down through generations. This takes a Lamarckian view of where how a creature lives and experiences things can have an influence on how genes are expressed in the next generation.
http://extendedevolutionarysynthesi.../Muller-GB_Interface-Focus_2017_corrected.pdf

Niche Construction allows living things to change their environment to help them survive rather than being subject to having to adapt to certain environments through evolution. This will also affect the surrounding life and therefore ecosystems are affected and changed as well. This puts the control for the change in the hands of living things rather than being subject to the fit in or perish view of evolution.
http://extendedevolutionarysynthesi.../Muller-GB_Interface-Focus_2017_corrected.pdf

There is some research which shows that cells can be affected and react to the pressures that living things are subjected to and this may also influence change that can help creatures adjust to changing situations. This points to living things having some ability to self-organise and construct change like self-regulated biological engineering.
https://www.quora.com/Whats-wrong-w...ion-by-natural-selection/answer/David-Kincade

This is also covered in this article
Do the mutations “lead” evolutionary change… mutations create the variation (modern synthesis = via random mutation)? Or are mutations a reflection of the organism shuffling its own genome (natural genetic engineering: Shapiro, or Barbara McClintock: genome shock)??? Or do mutations simply represent changes needed by the organism for information storage related to new information collected when environments change (“intended evolution”), not necessarily entirely different than the other two, or Lamarck. just broader?
https://www.quora.com/How-are-mutations-important-to-the-process-of-evolution

And this paper about
Natural genetic engineering

Life has an inbuilt capacity to survive regardless of whether it is well adapted and will naturally work towards what is best i.e. bacteria will move away from poison and will move towards nutrients, cells have the ability to rebuild DNA if broken. Cells can generate unlimited sets of DNA sequences similar to a Lego set or computer programming and are not random but produce specific outcomes. This may help understand the sudden appearance of well-defined life forms through the production of novel proteins by reorganising existing material to generate new combinations of biochemical activities.

Just as cells are smart and have an inbuilt capacity to survive and restructure DNA this may support the idea that all pressures and life experience from their environments and other living things have an effect on their system and can influence change.
What Natural Genetic Engineering Does and Does Not Mean | HuffPost

<< ‘It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works. All careful studies of mutagenesis find statistically significant non-random patterns of change, and genome sequence studies confirm distinct biases in location of different mobile genetic elements’ (Shapiro, 2011, p.82).>> >>

Also
Genome shock

McClintock’s challenge in the 21st century
McClintock’s challenge in the 21st century

 

[Ophiolite]

I posted the papers on this earlier and gave a brief description of how I understand these influences. Basically, living things can affect each other and be affected by their environment or can control change themselves which influences the outcomes of change. Living things are not seen in isolation but in cohabitations in a changing ecosystem. This takes a more holistic and interactive view where living things have inbuilt processes that produce suitable change are capable of controlling things rather than the narrow gene-centric and adaptive view of Neo-Darwinism.

Development biology involves how physical development influences the generation of variation (developmental bias). All living things have similar forms and basically the same development programs for producing certain forms rather than any possible form. Changes to existing forms are more to do with switching on or alterations existing genetic info rather than evolving through Darwinian evolution. The environmental pressures that living things experience may trigger processes that bring certain changes that help living things fit into environments.

Much variation is not random because developmental processes generate certain forms more readily than others3. developmental bias and natural selection work together4, 5. Rather than selection being free to traverse across any physical possibility, it is guided along specific routes opened up by the processes of development5, 6.
Does evolutionary theory need a rethink?

Plasticity also allows living things to change form and fit into their environments. Living things can change form without genes changing as well. Here there can be several different variations of the same creature in the same environment which would normally be attributed to different species. Yet the change in form has not been generated through evolution.

Plasticity not only allows organisms to cope in new environmental conditions but to generate traits that are well-suited to them.
Does evolutionary theory need a rethink?

This is also related to what is called Inclusive inheritance which covers epigenetics. Environmental influences such as stress can have an effect on gene expression and this can be passed down through generations. This takes a Lamarckian view of where how a creature lives and experiences things can have an influence on how genes are expressed in the next generation.
http://extendedevolutionarysynthesi.../Muller-GB_Interface-Focus_2017_corrected.pdf

Niche Construction allows living things to change their environment to help them survive rather than being subject to having to adapt to certain environments through evolution. This will also affect the surrounding life and therefore ecosystems are affected and changed as well. This puts the control for the change in the hands of living things rather than being subject to the fit in or perish view of evolution.
http://extendedevolutionarysynthesi.../Muller-GB_Interface-Focus_2017_corrected.pdf

There is some research which shows that cells can be affected and react to the pressures that living things are subjected to and this may also influence change that can help creatures adjust to changing situations. This points to living things having some ability to self-organise and construct change like self-regulated biological engineering.
https://www.quora.com/Whats-wrong-w...ion-by-natural-selection/answer/David-Kincade

This is also covered in this article
Do the mutations “lead” evolutionary change… mutations create the variation (modern synthesis = via random mutation)? Or are mutations a reflection of the organism shuffling its own genome (natural genetic engineering: Shapiro, or Barbara McClintock: genome shock)??? Or do mutations simply represent changes needed by the organism for information storage related to new information collected when environments change (“intended evolution”), not necessarily entirely different than the other two, or Lamarck. just broader?
https://www.quora.com/How-are-mutations-important-to-the-process-of-evolution

And this paper about
Natural genetic engineering

Life has an inbuilt capacity to survive regardless of whether it is well adapted and will naturally work towards what is best i.e. bacteria will move away from poison and will move towards nutrients, cells have the ability to rebuild DNA if broken. Cells can generate unlimited sets of DNA sequences similar to a Lego set or computer programming and are not random but produce specific outcomes. This may help understand the sudden appearance of well-defined life forms through the production of novel proteins by reorganising existing material to generate new combinations of biochemical activities.

Just as cells are smart and have an inbuilt capacity to survive and restructure DNA this may support the idea that all pressures and life experience from their environments and other living things have an effect on their system and can influence change.
What Natural Genetic Engineering Does and Does Not Mean | HuffPost

<< ‘It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works. All careful studies of mutagenesis find statistically significant non-random patterns of change, and genome sequence studies confirm distinct biases in location of different mobile genetic elements’ (Shapiro, 2011, p.82).>> >>

Also
Genome shock

McClintock’s challenge in the 21st century
McClintock’s challenge in the 21st century

Thank you for your detailed reply. I shall take some time to digest this. If I think it appropriate I may open a new thread to develop a discussion on your points.

 

[stevevw]

Yes, the mutations are random, but which mutations are passed on to offspring are NOT random.

The mutation is still random. It is said that it is Natural selection that will select the random mutation that best provides a selective advantage for survival. But this is opposed to other specific variation that may be well suited for a creature to fit into their environment and therefore is not random and does not need to be selected. Or for how a creature may manipulate their situation/environment themselves and therefore control their own destiny as far as survival.

Any mutations which convey some difficulty to the organism will likely result in that organism NOT reaching maturity and producing offspring, hence the mutations will not get past on.
Any mutations that convey some benefit will make it more likely that the organism will reach maturity, and so beneficial mutations are more likely to be passed on.

Some mutations have a small harmful effect and are passed on. That is why we are seeing more and more harmful mutations in humans. Mutation is not the best way to generate change and can be damage to what is already good. When more than one mutation is needed to produce a feature it is very unlikely that this will happen as it needs to be very specific but the possible likelihood of harmful mutations undermining the entire structure is more likely.

That is why it makes more sense that new variation may stem from processes that produce specific change that is well suited in the first place which is biased towards certain forms over others from pre-existing genetic info.

Natural selection is blind in the sense that it won't try to keep the gills of an animal in case they could be useful in 100,000 years if getting rid of the gills produces a benefit in the here and now.

It is blind in that if there are several components to making a feature it cannot know which components are needed ahead of time.

 

[VirOptimus]

The mutation is still random. It is said that it is Natural selection that will select the random mutation that best provides a selective advantage for survival. But this is opposed to other specific variation that may be well suited for a creature to fit into their environment and therefore is not random and does not need to be selected. Or for how a creature may manipulate their situation/environment themselves and therefore control their own destiny as far as survival.


Some mutations have a small harmful effect and are passed on. That is why we are seeing more and more harmful mutations in humans. Mutation is not the best way to generate change and can be damage to what is already good. When more than one mutation is needed to produce a feature it is very unlikely that this will happen as it needs to be very specific but the possible likelihood of harmful mutations undermining the entire structure is more likely.

That is why it makes more sense that new variation may stem from processes that produce specific change that is well suited in the first place which is biased towards certain forms over others from pre-existing genetic info.

It is blind in that if there are several components to making a feature it cannot know which components are needed ahead of time.

This is all very very wrong and have no scientific support.

 

[PsychoSarah]

The mutation is still random. It is said that it is Natural selection that will select the random mutation that best provides a selective advantage for survival. But this is opposed to other specific variation that may be well suited for a creature to fit into their environment and therefore is not random and does not need to be selected. Or for how a creature may manipulate their situation/environment themselves and therefore control their own destiny as far as survival.

-_- organisms have multiple adaptations that benefit survival, and there is no reason for natural selection to inherently result in one benign adaptation being promoted at the expense of another.

As for creatures manipulating their environment, the only ones that actually have the capacity to shape their own evolution willfully are humans, and that's a pretty recent development.

Some mutations have a small harmful effect and are passed on.

Sure, as long as they aren't so detrimental as to prevent survival and reproduction, detrimental mutations are not weeded out by natural selection.

That is why we are seeing more and more harmful mutations in humans.

Not really. Rather, harmful mutations that used to be a death sentence no longer necessarily are thanks to medical intervention. As a result, people that normally wouldn't have been able to survive long enough to have children now are, and thus the detrimental mutation becomes more frequent in the population.

Mutation is not the best way to generate change and can be damage to what is already good.

We deal with what we are dealt or we die. No one claimed this was an ideal system, it's just what we have ended up with.

When more than one mutation is needed to produce a feature it is very unlikely that this will happen as it needs to be very specific but the possible likelihood of harmful mutations undermining the entire structure is more likely.

It's like the dealer with the very large deck again. Just because any given 5 cards are unlikely doesn't mean the dealer isn't going to deal a 5 card hand. There are so many organisms and so many instances of mutation that novel benign mutations are an inevitability, so many hands being dealt that a winning one is an inevitability.

Also, in case you haven't noticed, most species that have ever existed are extinct. Extinction happens all of the time because a population just never got the traits necessary to continue on. It is the most common outcome, some might say even an inevitable outcome.

That is why it makes more sense that new variation may stem from processes that produce specific change that is well suited in the first place which is biased towards certain forms over others from pre-existing genetic info.

If that were the case, then why do so many organisms end up going extinct, even before humans existed? Why didn't this process ensure that they would get the benign mutations necessary to persist. Not every extinct organism has a modern descendant, in fact, the majority don't. Which is what one would expect of a system that doesn't grant traits in a targeted fashion.

It is blind in that if there are several components to making a feature it cannot know which components are needed ahead of time.

Which is why most things go extinct.

 

[Kylie]

The mutation is still random. It is said that it is Natural selection that will select the random mutation that best provides a selective advantage for survival. But this is opposed to other specific variation that may be well suited for a creature to fit into their environment and therefore is not random and does not need to be selected. Or for how a creature may manipulate their situation/environment themselves and therefore control their own destiny as far as survival.

Care to give any SPECIFIC examples of this?

If there is another variation that also leads to an individual being well suited for their environment, then natural selection will select for that as well. Do you really think that natural selection only works on one trait at a time?

And natural selection will select for the traits that give an individual an advantage in whatever environment they happen to exist in - whether the animals in question have manipulated that environment themselves or not.

Why is this a difficult concept for you?

Some mutations have a small harmful effect and are passed on. That is why we are seeing more and more harmful mutations in humans. Mutation is not the best way to generate change and can be damage to what is already good. When more than one mutation is needed to produce a feature it is very unlikely that this will happen as it needs to be very specific but the possible likelihood of harmful mutations undermining the entire structure is more likely.

Again, please provide a SPECIFIC example of such a mutation.

That is why it makes more sense that new variation may stem from processes that produce specific change that is well suited in the first place which is biased towards certain forms over others from pre-existing genetic info.

Lamarckianism has been well and truly discredited.

It is blind in that if there are several components to making a feature it cannot know which components are needed ahead of time.

Exactly right.

Which is why I can predict that if there are any traits that require several mutations, then the mutations that come first have some benefit OTHER than the final trait that they affect.

Congratulations of disproving irreducible complexity.

 

[stevevw]

Care to give any SPECIFIC examples of this?

I thought I already did. They are covered in the papers I posted.

phenotypic variation can be biased by the processes of development, with some forms more probable than others [12,17,25–28]. Bias is manifest, for example, in the non-random numbers of limbs, digits, segments and vertebrae across a variety of taxa [25,26,29,30], correlated responses to artificial selection resulting from shared developmental regulation [31], and in the repeated, differential re-use of developmental modules, which enables novel phenotypes to arise by developmental rearrangements of ancestral elements, as in the parallel evolution of animal eyes [32].

Some work on developmental bias suggests that phenotypic variation can be channelled and directed towards functional types by the processes of development [27,28].
The extended evolutionary synthesis: its structure, assumptions and predictions

So, if developmental bias channels or directs changes to produce certain functional types of features through development then where is the need for natural selection. The feature is already functional and suitable for the creature and does not need to be selected. These changes are produced as a result of the interactions a creature has with its environment and with other living things. These interactions will affect development and what variation/change is produced often resulting in well suited outcomes becuase of the feedback the creature experienced.

Natural selection may consolidate and refine things but the feature is basically well suited already. It seems that any new forms of variation stem from the re-arrangement of pre-existing body plans through the development process. There is a bias towards certain forms rather than evolution being open to any form i.e. 4 limbs as opposed to 6 or 10, 3 sectioned body forms as opposed to 2 or 4 in complex animals regardless of what natural selection does and these forms are well suited for animals and their environments.

Most creatures follow these body plans regardless of species, differential environments and they seem to have suddenly appeared already formed without any trace of transition from simpler forms. This also gives a better explanation for similar features in different or unrelated creatures which is often attributed to convergent evolution. As we are seeing more and more of this even right down to the genetic info development bias makes much more sense rather than appealing to more and more coincidences of convergence.

SET explains such parallels as convergent evolution: similar environmental conditions select for random genetic variation with equivalent results. This account requires extraordinary coincidence to explain the multiple parallel forms that evolved independently in each lake. A more succinct hypothesis is that developmental bias and natural selection work together4, 5. Rather than selection being free to traverse across any physical possibility, it is guided along specific routes opened up by the processes of development5, 6.
Does evolutionary theory need a rethink?

This makes more sense then claiming evolution through random mutations and selection will filter through 1000's of possible mutated variation which include harmful ones to find a specific type that will prove not only beneficial but functional and well integrated. Developmental bias throws up already functional and well integrated variation for which selection may then refine and consolidate.

So rather than different creatures coincidently evolving the exact same features right down to the molecular level there are certain basic development programs like laws in nature that produce these features no matter what environment or condition. The difference is a particular feature is due to certain addtional genetic switches being turned on or off in pre-existing programs.

Another example is developmental, or phenotypic, plasticity

Developmental, or phenotypic, plasticity is the capacity of an organism to change its phenotype in response to the environment.

Particularly contentious is the contribution of plasticity to evolution through phenotypic and genetic accommodation [27,48,49]. Phenotypic accommodation refers to the mutual and often functional adjustment of parts of an organism during development that typically does not involve genetic mutation [27].
The extended evolutionary synthesis: its structure, assumptions and predictions

So, it seems organisms can change forms without gene mutation. It is mutual in that creatures can get feedback from their environments which and affect their form without gene change which is the central mechanism of Darwinian evolution. So, this would mean that some changes in body shape which are being interpreted as coming from evolution ie random mutations and natural selection is coming from plasticity and therefore wrongly assumed. What may be interpreted as a new species is, in fact, a form changes of the same species. This can explain the anomalies we see in the same species which cannot be explained through the standard theory i.e. a wide variety of different forms for the same species in the same environments.

Another influence is Niche construction.

‘Niche construction’ refers to the process whereby the metabolism, activities and choices of organisms modify or stabilize environmental states, and thereby affect selection acting on themselves and other species [71–73]. For example, many species of animals manufacture nests, burrows, webs and pupal cases; algae and plants change atmospheric redox states and modify nutrient cycles; fungi and bacteria decompose organic matter and may fix nutrients and excrete compounds that alter environments. Niche construction frequently scales up, across individuals in a population, and over time, to generate stable and directional changes in environmental conditions [73,74].
The extended evolutionary synthesis: its structure, assumptions and predictions

So, creatures can change their environments to make them more suitable for how they live rather than having to be adapted to their environment. In this way, they determine the direction of evolution rather than it being something open to a hit and miss process that will eventually find beneficial and suitable adaptations.

Once again in some cases, natural selection will work with these other processes to cement the new features/forms in place but in some cases, it is bypassed altogether. Primarily these changes are more or less being dictated by the creatures experiences and behaviour. The pressures from the environment and the relationships creatures have with other living things affect the development process and therefore their phenotypes. In this sense, evolution takes a holistic view where creatures are affected by several influences and whole ecosystems change rather than just having a gene-centric and adaptive view with Neo-Darwinism.

 

[Kylie]

I thought I already did. They are covered in the papers I posted.

phenotypic variation can be biased by the processes of development, with some forms more probable than others [12,17,25–28]. Bias is manifest, for example, in the non-random numbers of limbs, digits, segments and vertebrae across a variety of taxa [25,26,29,30], correlated responses to artificial selection resulting from shared developmental regulation [31], and in the repeated, differential re-use of developmental modules, which enables novel phenotypes to arise by developmental rearrangements of ancestral elements, as in the parallel evolution of animal eyes [32].

Some work on developmental bias suggests that phenotypic variation can be channelled and directed towards functional types by the processes of development [27,28].
The extended evolutionary synthesis: its structure, assumptions and predictions.

I'll just point out here that eyes have evolved several times, and very different kinds of eyes can be found in different kinds of animals, so the claim of parallel development doesn't really strike me as very accurate.

So, if developmental bias channels or directs changes to produce certain functional types of features through development then where is the need for natural selection. The feature is already functional and suitable for the creature and does not need to be selected. These changes are produced as a result of the interactions a creature has with its environment and with other living things. These interactions will affect development and what variation/change is produced often resulting in well suited outcomes becuase of the feedback the creature experienced.

What's to stop a harmful trait appearing? Say, a trait that causes brittle bones? Why don't we see that trait?

Natural selection may consolidate and refine things but the feature is basically well suited already. It seems that any new forms of variation stem from the re-arrangement of pre-existing body plans through the development process.

Why do you think that natural selection can only do the fine tuning? It seems obvious to me that natural selection can also to the big stuff as well.

There is a bias towards certain forms rather than evolution being open to any form i.e. 4 limbs as opposed to 5 or 6, 3 sectioned body forms as opposed to 2 or 4 in complex animals regardless of what natural selection does and these forms are well suited for animals and their environments.

Most creatures follow these body plans regardless of species, differential environments and they seem to have suddenly appeared already formed without any trace of transition from simpler forms. This also gives a better explanation for similar features in different or unrelated creatures which is often attributed to convergent evolution. As we are seeing more and more of this even right down to the genetic info development bias makes much more sense rather than appealing to more and more coincidences of convergence.

You also mention that animals have four limbs (I'll assume you meant vertebrates, since invertebrates can have a great many more. From the six found in insects to dozens of pairs in millipedes.) That's simply because the common ancestor had four limbs, and it worked, and producing variations of those limbs is a lot easier, evolutionarily speaking, than creating extra limbs.

SET explains such parallels as convergent evolution: similar environmental conditions select for random genetic variation with equivalent results. This account requires extraordinary coincidence to explain the multiple parallel forms that evolved independently in each lake. A more succinct hypothesis is that developmental bias and natural selection work together4, 5. Rather than selection being free to traverse across any physical possibility, it is guided along specific routes opened up by the processes of development5, 6.
Does evolutionary theory need a rethink?

You speak of Selection! What kind of selection is this? Is it nature that does the selecting?

This makes more sense then claiming evolution through random mutations and selection will filter through 1000's of possible mutated variation which include harmful ones to find a specific type that will prove not only beneficial but functional and well integrated. Developmental bias throws up already functional and well integrated variation for which selection may then refine and consolidate.

This shows a pretty big misunderstanding of what natural selection is.

Natural selection takes an organism that works, makes a whole bunch of copies of it, each one slightly different. It then gets rid of the ones that don't work as well as the original and favours the ones that work better than the original.

How do you think this is incapable of producing large changes over many generations?

Another example is developmental, or phenotypic, plasticity

Developmental, or phenotypic, plasticity is the capacity of an organism to change its phenotype in response to the environment.


Particularly contentious is the contribution of plasticity to evolution through phenotypic and genetic accommodation [27,48,49]. Phenotypic accommodation refers to the mutual and often functional adjustment of parts of an organism during development that typically does not involve genetic mutation [27].
The extended evolutionary synthesis: its structure, assumptions and predictions

So, it seems organisms can change forms without gene mutation. It is mutual in that creatures can get feedback from their environments which and affect their form without gene change which is the central mechanism of Darwinian evolution. So, this would mean that some changes in body shape which are being interpreted as coming from evolution ie random mutations and natural selection is coming from plasticity and therefore wrongly assumed. What may be interpreted as a new species is, in fact, a form changes of the same species. This can explain the anomalies we see in the same species which cannot be explained through the standard theory i.e. a wide variety of different forms for the same species in the same environments.

Give a specific example of this.

And by what mechanism do you propose that creatures can get feedback from their environment?

And if this is true, why do we see any animals at all being born with harmful traits, like deformed legs? Why do these individuals not take the feedback from the environment and simply not change their form in that way?

Another influence is Niche construction.

‘Niche construction’ refers to the process whereby the metabolism, activities and choices of organisms modify or stabilize environmental states, and thereby affect selection acting on themselves and other species [71–73]. For example, many species of animals manufacture nests, burrows, webs and pupal cases; algae and plants change atmospheric redox states and modify nutrient cycles; fungi and bacteria decompose organic matter and may fix nutrients and excrete compounds that alter environments. Niche construction frequently scales up, across individuals in a population, and over time, to generate stable and directional changes in environmental conditions [73,74].
The extended evolutionary synthesis: its structure, assumptions and predictions

So, creatures can change their environments to make them more suitable for how they live rather than having to be adapted to their environment. In this way, they determine the direction of evolution rather than it being something open to a hit and miss process that will eventually find beneficial and suitable adaptations.

Once again in some cases, natural selection will work with these other processes to cement the new features/forms in place but in some cases, it is bypassed altogether. Primarily these changes are more or less being dictated by the creatures experiences and behaviour. The pressures from the environment and the relationships creatures have with other living things affect the development process and therefore their phenotypes. In this sense, evolution takes a holistic view where creatures are affected by several influences and whole ecosystems change rather than just having a gene-centric and adaptive view with Neo-Darwinism.

This can happen, but not to the extent that it can override the natural environment. Even we Humans are still at the mercy of the natural world - we still have to deal with floods and storms and fires, despite all the advancements we have made to control our environment. And in some of the examples you mention, the organisms causing the changes are not doing so because they benefit from the end result. The change comes about purely as a byproduct of them doing something else.

 

[stevevw]

If there is another variation that also leads to an individual being well suited for their environment, then natural selection will select for that as well. Do you really think that natural selection only works on one trait at a time?

And natural selection will select for the traits that give an individual an advantage in whatever environment they happen to exist in - whether the animals in question have manipulated that environment themselves or not.

Why is this a difficult concept for you?

The problem is the forms produced by these other processes can already be well suited and therefore Natural selection has little if not no work to do in some cases by selecting those forms. Not all change is subject to adaptations through Neo-Darwinism.

This is where the idea of living things being more interactive with their environments come in. So, the pressures and experiences creatures have with their environments or lifestyles has an effect on them and this can influence the way they develop and how genes can be expressed. Plasticity has shown that for example a plant that is placed in a new environment will change form and will change to fit into that new environment being affected by its surroundings. The genes to cement these changes will come later.
Does evolutionary theory need a rethink?

I’m not disputing that Natural selection if a force in evolution. I am saying that it is attributed to things that it is not involved with and some variation/change is not associated with natural selection or random mutations. The assumption is all change is because of random mutations and natural selection when it may be that natural selection is only one small part of many influences and in some cases not prominent at all.

Again, please provide a SPECIFIC example of such a mutation.

Genome sequencing studies indicate that all humans carry many genetic variants predicted to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy in the human genome.
A systematic survey of loss-of-function variants in human protein-coding genes

Stability effects of mutations and protein evolvability. October 2009
Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,
Stability effects of mutations and protein evolvability. - PubMed - NCBI

The waiting time problem in a model hominin population
We show that the waiting time problem becomes very severe when more than one mutation is required to establish a new function. On a practical level, the waiting time problem greatly inhibits the establishment of any new function that requires any string or set of specific linked co-dependent mutations. For nucleotide strings of moderate length (eight or above), waiting times will typically exceed the estimated age of the universe – even when using highly favourable settings.
The waiting time problem in a model hominin population

Simulating evolution by gene duplication of protein features that require multiple amino acid residues.
We conclude that, in general, to be fixed in 10(8) generations, the production of novel protein features that require the participation of two or more amino acid residues simply by multiple point mutations in duplicated genes would entail population sizes of no less than 10(9).
Simulating evolution by gene duplication of protein features that require multiple amino acid residues. - PubMed - NCBI

Lamarckianism has been well and truly discredited.

This is incorrect. Recent research has shown especially through epigenetics that there is ample support for Lamerack type influences. How a creature lives, the pressures they are under can affect how genes are expressed, ie turned on and off for future generations. This can even go down to the cell and tissue level where they are affected and can have an effect on the development process and how it will determine phenotypic change. This is explained under the name inclusive inheritance in the EES. I have already provided support for this above.

The pathways of inheritance that derive from a parental phenotype (‘parental effects’) have a number of evolutionary consequences similar to those of plasticity, cultural inheritance and niche construction [67]. For example, non-genetic inheritance can bias the expression and retention of environmentally induced phenotypes, thereby influencing the rate and direction of evolution [68]. There is also increasing evidence for more stable transgenerational epigenetic inheritance, or the transmission across generations of cellular states without modification of the DNA sequence, which demonstrates that adaptive evolution may proceed by selection on epigenetic variants as well as variation in DNA sequence [60,69,70].
The extended evolutionary synthesis: its structure, assumptions and predictions

Darwin’s theory that natural selection drives evolution is incomplete without input from evolution’s anti-hero: Lamarck
On epigenetics: we need both Darwin’s and Lamarck’s theories | Aeon Essays

 

[Kylie]

The problem is the forms produced by these other processes can already be well suited and therefore Natural selection has little if not no work to do in some cases by selecting those forms. Not all change is subject to adaptations through Neo-Darwinism.

You have not yet come anywhere near close to explaining how any process other than natural selection has the power to create new traits.

This is where the idea of living things being more interactive with their environments come in. So, the pressures and experiences creatures have with their environments or lifestyles has an effect on them and this can influence the way they develop and how genes can be expressed. Plasticity has shown that for example a plant that is placed in a new environment will change form and will change to fit into that new environment being affected by its surroundings. The genes to cement these changes will come later.
Does evolutionary theory need a rethink?

Give specific examples. You are very bad at providing examples. Why is this?

I’m not disputing that Natural selection if a force in evolution. I am saying that it is attributed to things that it is not involved with and some variation/change is not associated with natural selection or random mutations. The assumption is all change is because of random mutations and natural selection when it may be that natural selection is only one small part of many influences and in some cases not prominent at all.

You have not shown how natural selection does not work. All you've done is claim it doesn't, then claimed that some alternate idea is much better and been vague about the details.

Genome sequencing studies indicate that all humans carry many genetic variants predicted to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy in the human genome.
A systematic survey of loss-of-function variants in human protein-coding genes

Be specific. What genes? And how does redundancy in the genome mean natural selection doesn't have a part to play?

Stability effects of mutations and protein evolvability. October 2009
Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,
Stability effects of mutations and protein evolvability. - PubMed - NCBI

Be specific. What proteins? And how does the fact that proteins can't tolerate a huge variety of amino acid substitutions invalidate natural selection?

The waiting time problem in a model hominin population
We show that the waiting time problem becomes very severe when more than one mutation is required to establish a new function. On a practical level, the waiting time problem greatly inhibits the establishment of any new function that requires any string or set of specific linked co-dependent mutations. For nucleotide strings of moderate length (eight or above), waiting times will typically exceed the estimated age of the universe – even when using highly favourable settings.
The waiting time problem in a model hominin population

Is this taking into account the fact that such mutations are being tried throughout the entire population? A population that may number in the BILLIONS?

Also, again, be specific. What kind of new functions? How many mutations are required?

Simulating evolution by gene duplication of protein features that require multiple amino acid residues.
We conclude that, in general, to be fixed in 10(8) generations, the production of novel protein features that require the participation of two or more amino acid residues simply by multiple point mutations in duplicated genes would entail population sizes of no less than 10(9).
Simulating evolution by gene duplication of protein features that require multiple amino acid residues. - PubMed - NCBI

Is only one possible combination of amino acids suitable? Because my understanding is that there are many varieties - different "spellings" if you will - that work equally well.

This is incorrect. Recent research has shown especially through epigenetics that there is ample support for Lamerack type influences. How a creature lives, the pressures they are under can affect how genes are expressed, ie turned on and off for future generations. This can even go down to the cell and tissue level where they are affected and can have an effect on the development process and how it will determine phenotypic change. This is explained under the name inclusive inheritance in the EES. I have already provided support for this above.

The pathways of inheritance that derive from a parental phenotype (‘parental effects’) have a number of evolutionary consequences similar to those of plasticity, cultural inheritance and niche construction [67]. For example, non-genetic inheritance can bias the expression and retention of environmentally induced phenotypes, thereby influencing the rate and direction of evolution [68]. There is also increasing evidence for more stable transgenerational epigenetic inheritance, or the transmission across generations of cellular states without modification of the DNA sequence, which demonstrates that adaptive evolution may proceed by selection on epigenetic variants as well as variation in DNA sequence [60,69,70].
The extended evolutionary synthesis: its structure, assumptions and predictions

Darwin’s theory that natural selection drives evolution is incomplete without input from evolution’s anti-hero: Lamarck
On epigenetics: we need both Darwin’s and Lamarck’s theories | Aeon Essays

Yes, I know that there is some research which suggests that SOME kinds of experiences that happen in an organism's life can alter their seed cells (be they sperm or egg) and thus pass on traits to offspring that way.

But I have not seen any evidence that such a mechanism is more powerful than natural selection. If you have a source that claims Lamarckian style evolution is more responsible for variation among organisms than natural selection, please provide it.

 

[VirOptimus]

You have not yet come anywhere near close to explaining how any process other than natural selection has the power to create new traits.



Give specific examples. You are very bad at providing examples. Why is this?



You have not shown how natural selection does not work. All you've done is claim it doesn't, then claimed that some alternate idea is much better and been vague about the details.



Be specific. What genes? And how does redundancy in the genome mean natural selection doesn't have a part to play?



Be specific. What proteins? And how does the fact that proteins can't tolerate a huge variety of amino acid substitutions invalidate natural selection?



Is this taking into account the fact that such mutations are being tried throughout the entire population? A population that may number in the BILLIONS?

Also, again, be specific. What kind of new functions? How many mutations are required?



Is only one possible combination of amino acids suitable? Because my understanding is that there are many varieties - different "spellings" if you will - that work equally well.



Yes, I know that there is some research which suggests that SOME kinds of experiences that happen in an organism's life can alter their seed cells (be they sperm or egg) and thus pass on traits to offspring that way.

But I have not seen any evidence that such a mechanism is more powerful than natural selection. If you have a source that claims Lamarckian style evolution is more responsible for variation among organisms than natural selection, please provide it.

You will only get the same old links.

 

[Kylie]

You will only get the same old links.

I know.

So many people post articles without thinking critically about what the articles are.

 

[stevevw]

You have not yet come anywhere near close to explaining how any process other than natural selection has the power to create new traits.

That’s because Natural selection has no power to create new traits. I am not sure what you mean. If you mean there are other forces besides random mutations that produce variations this is a well-known fact.

Give specific examples. You are very bad at providing examples. Why is this?

I have already done this several times now. I just gave you an example in the last post regarding development plasticity. A plant can change form when placed in a different environment without any gene changes. The environment such as the soil composition its nutrients and the surrounding organisms all contribute to helping the plant fit into its new environment. This is a well suited and integrated change. Therefore, natural selection plays a minor part because the changes have already been determined as a good fit before selection gets the chance to do anything. Selection is more about weeding out the weak and sick lifeforms so if the changes are already well suited and integrated then there's no need for selection. If you want to know more then read the paper.

I have also given the example of how development bias can produce certain phenotypic variation over others such as the number of limbs in land-dwelling complex creatures being 4 as opposed to 5 or 6 or 8 regardless of the environmental pressures or species. If evolution is open to any possibility, then why not 6 legs so creatures can run faster and get away from prey. Why not several eyes or eyes in the back of the head to be able to see predators more easily. Why are there certain forms repeated over and over again rather than any other forms regardless of environment and the individual circumstances of the different creatures?

The standard theory says these similar forms are the result of a massive coincident from convergent evolution. But evidence shows it is more because of the development process being biased to produce certain forms. The example is given by the paper

For example, cichlid fishes from Lakes Malawi and Tanganyika exhibit striking similarities in body shape, despite being more closely related to species from their own lake than to those from the other lake [17,33]. Such repeated parallel evolution is generally attributed to convergent selection. However, inherent features of development may have channelled morphology along specific pathways, thereby facilitating the evolution of parallel forms in the two lakes [17,33]. If so, then the diversity of organismal form is only partly a consequence of natural selection—the particular evolutionary trajectories taken also depend on features of development.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632619/

So it is not a case of mutations throwing up any possible variation and selection weeding out the bad and finding the best in a blind process like the watch maker Dawkins describes but that the development process drives change and throws up only certain forms which selection may then refine. Primarily the variation has already been decided before natural selection comes into the picture.

Here are some examples for niche construction
‘Niche construction’ refers to the process whereby the metabolism, activities and choices of organisms modify or stabilize environmental states, and thereby affect selection acting on themselves and other species [71–73]. For example, many species of animals manufacture nests, burrows, webs and pupal cases; algae and plants change atmospheric redox states and modify nutrient cycles; fungi and bacteria decompose organic matter and may fix nutrients and excrete compounds that alter environments. Niche construction frequently scales up, across individuals in a population, and over time, to generate stable and directional changes in environmental conditions [73,74].
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632619/

So creatures can alter their environments and those changed environments alter creatures including those around them and visa versa. Therefore entire ecosystems change as well. If creatures can change environments so that they are well suited and accommodating for them then why would they need natural selection as much. Living things change the environment rather than having to be adapted to the environment through selection and random mutations.

You have not shown how natural selection does not work. All you've done is claim it doesn't, then claimed that some alternate idea is much better and been vague about the details.

I haven't made any personal claims but have repeated what the scientific articles have said. If you want further info on this then you will have to read the papers. They clearly state that natural selection is only one influence on evolution and there are many other influences of variation and, in some cases, natural selection is not needed at all. IE,

What is in question is whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms.
http://www.pnas.org/content/104/suppl_1/8597.full

Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651812/

As for the difference between the Extended Evolutionary Synthesis (EES) and the Standard Evolution Theory (Modern Synthesis)

The Modern Synthesis
adaptive variants are propagated through selection
The EES
In addition to selection, adaptive variants are propagated through repeated environmental induction, non-genetic inheritance, learning and cultural transmission
The Modern Synthesis
rapid phenotypic evolution requires strong selection on abundant genetic variation
The EES

rapid phenotypic evolution can be frequent and can result from the simultaneous induction and selection of functional variants

Developmental processes play important evolutionary roles as causes of novel, potentially beneficial, phenotypic variants, the differential fitness of those variants, and/or their inheritance (i.e. all three of Lewontin's [98] conditions for evolution by natural selection). Thus, the burden of creativity in evolution (i.e. the generation of adaptation) does not rest on selection alone [12,19,25,27,60,64,73,99–101].

It can be summed up by the following statement

The extended evolutionary synthesis perspective
From this standpoint, too much causal significance is afforded to genes and selection, and not enough to the developmental processes that create novel variants, contribute to heredity, generate adaptive fit, and thereby direct the course of evolution.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632619/

 

[stevevw]

Be specific. What genes? And how does redundancy in the genome mean natural selection doesn't have a part to play?

I wasn’t referring to natural selection but rather random mutations.

Be specific. What proteins? And how does the fact that proteins can't tolerate a huge variety of amino acid substitutions invalidate natural selection?

The paper states that they were looking at any functional protein and how a single mutation may have a small effect which can be tolerated but as mutations increase the effects of negative epistasis will take a toll. But once again this is to do with mutation rather than natural selection.

Is this taking into account the fact that such mutations are being tried throughout the entire population? A population that may number in the BILLIONS?

Also, again, be specific. What kind of new functions? How many mutations are required?

The paper is looking at any new function from replacing the original nucleotides with new ones that are functional. The study was on hominin populations from 10,000 to 100,000. But they also found there were big time problems in larger populations as well. They found that the time problem for humans were far beyond the 6 million years it is supposed to have taken apes to evolve into humans.

They calculated the waiting time for a single fixed-point mutation at 1.5 to 15.9 million years with a generous fitness benefit for mutations. When this is adjusted to the more realistic fitness rate the time increases 10-fold to 15.9 million years. Add to this that the waiting time for a particular string of mutations to be fixed will be even longer. Considering that humans evolved from apes in 6 million years it brings up a major problem for evolution. If an 8-string nucleotide is needed the time factor goes beyond the age of the universe.

They also found in lager populations there was a mutation density problem. Single point mutations will still arise somewhere in larger population every generation. But when specific sets of mutations are needed these are still very rare. A bigger population increases the number of mutations per generation but doesn’t increase the number of mutations per short DNA strand (mutation density).

It is when linked mutations are needed that the time is still a factor and becomes a problem regardless of population size. To create a string of 5 nucleotides 5 specific mutations are needed on the same short stretch of that specific DNA molecule. It is easier to get a single point mutation in larger populations but regardless of population size it still takes a very long time to create specific strings of more than 3 nucleotides.

Furthermore, even with a population size of one million, waiting time was 500 million years – which is still extremely prohibitive. This amount of time approximates the estimated time required for the evolution of worm-like creatures into people.


In a very large population it can take almost no time to get any particular point mutation, but regardless of population size it still takes a very long time to create specific strings of more than three nucleotides.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573302/#CR15

Is only one possible combination of amino acids suitable? Because my understanding is that there are many varieties - different "spellings" if you will - that work equally well.

This is similar to the above paper. When nucleotide sequence strings are required to make a functional change, they need to be specific and the mutations need to happen in the right place at the right time and be significant enough to be selected and fixed.

This combination is rare and as the paper states to establish 2 strings will take on average 84 million years. To establish a string of five nucleotides required on average 2 billion years. When there were as many as six nucleotides in the string, the average waiting time (4.24 billion years) approached the estimated age of the earth. When there were eight nucleotides in the string, the average waiting time (18.5 billion years), exceeded the estimated age of the universe.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573302/#CR15

Yes, I know that there is some research which suggests that SOME kinds of experiences that happen in an organism's life can alter their seed cells (be they sperm or egg) and thus pass on traits to offspring that way.

But I have not seen any evidence that such a mechanism is more powerful than natural selection. If you have a source that claims Lamarckian style evolution is more responsible for variation among organisms than natural selection, please provide it.

Lamarck type evolution covers a broad set of influences and come under the headings of Inclusive inheritance, develoment biology and plasticity in the EES. There is scientific evidence for these influences.

Since variations in DNA methylation pattern can be sensitive to the environmental conditions and may lead to heritable variations in gene expression, there is a potential for soft inheritance here, for Lamarckian inheritance.
http://extendedevolutionarysynthesis.com/epigenetic-inheritance-evolution-interview-eva-jablonka/

Developmental plasticity, the capacity of a single genotype to give rise to different phenotypes, affects evolutionary dynamics by influencing the rate and direction of phenotypic change. It is based on regulatory changes in gene expression and gene products, which are partially controlled by epigenetic mechanisms. Plasticity involves not just epigenetic changes in somatic cells and tissues; it can also involve changes in germline cells. Germline epigenetic plasticity increases evolvability, the capacity to generate heritable, selectable, phenotypic variations, including variations that lead to novel functions.
https://www.sciencedirect.com/science/article/pii/S0079610712000818