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[MOVED] The Extended Evolutionary Synthesis

Speedwell

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Every single paper I have posted is from mainstream science and the EES which is regarded as mainstream science though it differs and challenges the SET. Try and find one paper or source that is a creationist or ID source. I bet you cant. I specifically did not want to introduce that into this thread and on;y want to debate the science of the SET and the EES and I think that has been the case. You are desperate to turn it into the creationism v evolution debate so in fact, you have introduced creationism and ID into this thread more than anyone else which is really off-topic.
Oh, fiddle-faddle. You just cited for me a paper from an ID source--the Discovery Institute, no less..
https://www.researchgate.net/public...ciple_for_the_Extended_Evolutionary_Synthesis
 
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FrumiousBandersnatch

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Not according to the EES. For some variations, natural selection will be diminished, biased, and even replaced by the EES forces.
Citation?

Please explain in your own words how natural selection can be 'biased'? What can replace it, and how does that work?

For example under niche construction when an organism creates an environment like a nest it has created an enclosed environment that is cocooned from outside forces. It is disease-free and has all the precise conditions needed for the offspring to thrive and survive. The organism has this capacity to know how to create niche environments that are precisely what they need to adapt, survive and pass of their traits. Because these niche environments are conducive to thriving and surviving they are advantageous.
IOW, niche construction is a behavioural pattern that has a selective advantage.

JFYI - very few, if any, niche constructors are 'disease free' or have 'all the precise conditions needed for the offspring to thrive and survive'. That's ridiculous hyperbole.

ISTR suggesting that you focus less on those articles and more on thinking it through for yourself.

Consider - an evolutionary advantage means reproductive success; when a population evolves towards niche construction, what is the process that selects for the relevant behaviours? When a population of niche constructors reproduces, generating variant offspring, what is the process that selects for those variants that maintain or improve on those behaviours? IOW what is the process which establishes whether a certain pattern of behaviour is advantageous?

The same with inheritance beyond genes where certain behaviours are conducive for producing outcomes and conditions that help organism thrive and survive. These behaviours are intuitive but also learnt creatures know what is needed and best for thriving and surviving. So they will always produce advantageous results.
Which behaviours in which creatures, for example?

What, exactly, do you mean by learnt behaviour? Learnt how - by imitation? It can't be trial and error.

You say niche construction behaviours "always produce advantageous results", but it's common that the predictability of niche behaviours allows predators and parasites to specialise on them, and in the case of literal niches, for usurpers to requisition or 'cuckoo' the niche. When environmental conditions change, a niche may become uninhabitable, unconstructible, or may simply disappear, leaving the niche constructer specialised for a non-existent or unconstructible niche... In what sense are these 'advantageous results'?

Developmental processes are another source. The developmental system has the capacity to produce certain changes that help an organism adapts to environments. The specific variations develop has produced are precisely what is needed for those environments as opposed to all other variations and as opposed to random mutations that may produce disadvantageous changes.
Developmental plasticity only gives a limited range of adaptability; it will not always produce 'precisely what is needed' for an environment. Random mutations still occur, but they are relevant over multiple generations, whereas developmental plasticity is an individual response.

What is the process that selects for developmental plasticity over developmental fixity/rigidity? What is the process that selects for a particular type of developmental plasticity in a changing environment?

The SET treats the environment and living things as separate entities where a creature needs to be adapted to an environment by outside forces like random mutation and NS. Those random variations are not conducive for advantageous changes and therefore need to be tested and sifted by NS.
Good grief... that is 'not even wrong'. It reflects a fundamental lack of understanding or joined-up thinking about evolution.

BTW, when answering the questions I ask above, the key word is 'selects'...
 
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FrumiousBandersnatch

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Then what is meant by these quotes

heritable variation can only arise by mutation. Evolution is simply not possible without random genetic change for its raw material.
Mutations Are the Raw Materials of Evolution | Learn Science at Scitable

Mutations are essential to evolution. Every genetic feature in every organism was, initially, the result of a mutation.

Without variation (which arises from mutations of DNA molecules to produce new alleles) natural selection would have nothing on which to act.

All genetic variation in the population is generated by mutation.
Mutations Are the Raw Materials of Evolution | Learn Science at Scitable

Asexual organisms or organisms, such as bacteria, that very seldom undergo sexual recombination do not have this source of variation, so new mutations are the only way in which a change in gene combinations can be achieved.
Sources of variation - An Introduction to Genetic Analysis - NCBI Bookshelf.
What are the problems you see?

How does genetic drift and recombination generating information for new variations conflict with any of the quotes above?
 
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FrumiousBandersnatch

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Sorry with all the furor going on I must have missed this one. But I noticed VirOptimus couldn't wait to put the boot in as though I had not responded on purpose and that it would be optimistic that I did respond. Shows his low opinion of me and that before I even have a chance to reply I am condemned.
In the time it took to complain about mean old VirOptimus, you could have answered my question.

So why not do it now?
 
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FrumiousBandersnatch

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... when you take an overall view of variations that randomly distributed variation only falls within a certain set of variations of all possible variations that could have happened from a random process variations available to natural selection are not really randomly distributed and that is the important point as far as what is driving evolution. We only see certain variations and body plans out of all possibilities. Why is that.
I think I managed to translate some of that. I think you're asking why random mutations don't produce random results... It's because the genome is somewhat modular and hierarchical, and when mutations change some small part of it, or a regulator of the expression of a gene or genes in it, there's a limited number of ways function can change, and those ways are likely to be variations on the expression of existing gene networks (or 'toolkits'); that's why it's said that evolution proceeds by modification and repurposing of existing functionality.
 
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stevevw

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Oh, fiddle-faddle. You just cited for me a paper from an ID source--the Discovery Institute, no less..
https://www.researchgate.net/public...ciple_for_the_Extended_Evolutionary_Synthesis
Gee and I were doing so well, :doh:. I didn't realize this was an ID source. Anyway, it was still submitted for peer review which is the important thing. The point is I have tried to ensure that I am not using any ID or creationist sources and I think you will find apart from this that 99% are from mainstream sources. I have not mentioned God as the support for the EES but rather mainstream support and for this thread, I am not making out that the EES is a God of the gaps argument. My only intention is to support the EES view of evolution.
 
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stevevw

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That you dont see the problem is very telling.

The second quote has you saying that things are "designed" even.
Here we go again with the semantics and picking out single words to make some strawman argument that is not there. Are you seriously saying that because I used the word 'design in that quote that this shows I am bringing religious concepts into the thread. Look at the sentence it's used in IE

Steve said
You are engaging in a logical fallacy designed to try and undermine the content which has nothing to do with whether the content is correct or not.

Are you honestly saying that the above is a religious term when it was about how you are designing a logical fallacy. Besides the mainstream evolution literature uses the word design, code, language, etc when describing genetics or biology.

I think it is more telling that you sit there on the edge of this thread not engaging in anything and only jump in when you think you can turn the thread into a creation v evolution debate. You make an unsupported assertion that the info I have linked on the EES is creationist and ID and yet it clearly shows it is not. Maybe it is you who is the one seeing these things more than anyone and bring religion into the thread.

Here's a couple of the sources I have been using. Show me how it is a creationist or ID source.
The extended evolutionary synthesis: its structure, assumptions and predictions
https://royalsocietypublishing.org/doi/10.1098/rspb.2015.1019
What is the extended evolutionary synthesis?
About the EES – Extended Evolutionary Synthesis
 
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VirOptimus

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Here we go again with the semantics and picking out single words to make some strawman argument that is not there. Mainstream literature uses the word design, code, language, etc when describing genetics or biology.

I think it is more telling that you sit there on the edge of this thread not engaging in anything and only jump in when you think you can turn the thread into a creation v evolution debate. You make an unsupported assertion that the info I have linked on the EES is creationist and ID and yet it clearly shows it is not. Maybe it is you who is the one seeing these things more than anyone and bring religion into the thread.

Here's a couple of the sources I have been using. Show me how it is a creationist or ID source.
The extended evolutionary synthesis: its structure, assumptions and predictions
https://royalsocietypublishing.org/doi/10.1098/rspb.2015.1019
What is the extended evolutionary synthesis?
About the EES – Extended Evolutionary Synthesis
You dont understand my points.
 
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stevevw

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Yes, but the way you use them and try to argue is ID/creationist style so I'm sure you have gotten your arguments from an ID/creationist source which try to twist the science and as you don't really understand it you just parrot.
The only language I have used is based on the EES papers.
 
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stevevw

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You don't understand my points.
You said the EES is creationist and ID C*** when it is clearly not. I think it is easy to see the point. You made an unsupported claim. This shows the extent you want to stretch and twist things to make out that what is being said is not science but religious.
 
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VirOptimus

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You said the EES is creationist and ID C*** when it is clearly not. I think it is easy to see the point. You made an unsupported claim. This shows the extent you want to stretch and twist things to make out that what is being said is not science but religious.
No I have said your "arguments" are ID crap.

The EES is not.

But you dont argue the EES, you argue ID/creationist points.
 
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Speedwell

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Gee and I were doing so well, :doh:. I didn't realize this was an ID source. Anyway, it was still submitted for peer review which is the important thing.
No, it wasn't submitted to peer review. It was published in BIO-Complexity, a pseudo-science magazine put out by the Discovery Institute and reprinted in Researchgate, which is basically a social media site.
The point is I have tried to ensure that I am not using any ID or creationist sources and I think you will find apart from this that 99% are from mainstream sources. I have not mentioned God as the support for the EES but rather mainstream support and for this thread, I am not making out that the EES is a God of the gaps argument. My only intention is to support the EES view of evolution.
I don't care if you mention God or not. I think you are pushing EES because you are under the impression that SET can't work because it's "random" and needs EES because it's "non-random," which reveals an inadequate grasp of SET and puts more load on EES than even its creators intended.
"
 
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stevevw

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Citation?
In the EES, development assumes a constructive role, natural selection is not the only way that variation in populations can be modified, and causation does not run solely in one direction from the external environment to populations and, instead of a single inheritance mechanism, several modes of transmission exist between generations.

The evolutionary significance of niche construction stems from: (i) organisms modify environmental states in non-random ways, thereby imposing a systematic bias on the selection pressures they generate; In addition to accepted evolutionary processes that directly change gene frequencies, the EES recognizes processes that bias the outcome of natural selection, specifically developmental bias and niche construction. All processes that generate phenotypic variation, including developmental plasticity and some forms of inclusive inheritance are potential sources of bias.
Niche construction

Please explain in your own words how natural selection can be 'biased'? What can replace it, and how does that work?
Under the SET view the source of variation is random so natural selection is regarded as the all-important and only determining factor as to which variation are adaptive and heritable. Therefore NS is seen as the driving force of evolution. But the EES forces can produce nonrandom variations such as through development, niche construction or inheritance beyond genes where only certain variation are produced in line with an organisms needs. These variations can be adaptive and heritable before NS comes along.

Therefore the EES forces become the driving force of evolution and replace NS. They are both the source of variation and the determining factor of adaptive and heritable variations. In this way, NS is biased because the EES forces are now determining what is adaptive and heritable and not NS. NS only serves to release the variation produced by the EES forces.

IOW, niche construction is a behavioural pattern that has a selective advantage.
That maybe the case but it implies that NS is the only force doing the selecting. This is what the EES is challenging. Niche construction is now seen as a theory itself (NCT) like natural selection which can also select adaptive conditions and traits that is heritable and therefore drives evolution.
Niche construction

The standard theory views niche constructive behaviours as extended phenotypes which were only derived from previous NS. They dismiss niche construction as actual causes of evolution that are sometimes beyond genes. Under the EES the creature itself becomes the selecting force rather than NS by creating the condition that would usually be determined by natural selection before NS even comes along. Also, niches themselves are also passed on besides traits which also determine adaptive and survival conditions.
Niche construction is perceived to have no independent evolutionary significance because to the extent that it is evolutionarily consequential, it is regarded as fully explained by a preceding cause, natural selection (e.g. Dawkins 2004). Niche-construction effects are treated as ‘extended phenotypes’, whose sole evolutionary role is to affect the probability that gene variants underlying niche construction are passed on to the next generation. Similar reasoning underlies the treatment of niche construction as an indirect genetic effect, with, for example, a mother’s genes affecting her offspring’s phenotype by modifying its environment (Wolf et al. 1998).

There are two major problems with this line of reasoning:

First, as described above, the processes underlying variation, fitness and inheritance are causally intertwined. All organisms have always engaged in niche construction, going right back to the beginning of life. Hence there is no reason to assume that natural selection must be the first cause of any evolutionary episode. Causation in biological systems is reciprocal rather than linear, with natural selection and niche construction codirecting each other.


Second, not all evolutionarily consequential aspects of niche construction (nor all aspects of development, in general) are under genetic control. Niche-construction theorists, like many developmental biologists, regard organisms (and their environmental modification) as under-determined by genes. The changes that organisms bring about do not flow only from their adaptations, but also derive from plasticity, byproducts, and acquired characters.
Niche construction

Also, some of the changes from niche constructions would even be considered a disadvantage or deleterious under the SET requirements of NS. Yet these changes are preserved as they bring benefits overall for future generations. Niche construction helps creatures to survive in what would be deemed disadvantageous environments under the adaptive view. This is because the EES doesn’t just take the narrow view that all change is a matter of fittest landscapes and NS but also includes developmental processes and behaviours that apply to the organism and their specific situation.

Niche construction can fix genes or phenotypes that would, under standard evolutionary theory, be deleterious, create or eliminate equilibria, and affect evolutionary rates (Laland et al. 1999; Silver & Di Paolo 2006; Creanza & Feldman 2014, Tanaka et al. 2020), Niche constructive changes can be favoured, even when currently costly, because of the benefits that will accrue to distant descendants (Lehmann 2007, 2008). Niche construction can regulate environmental states, allowing persistence in otherwise inhospitable conditions, facilitating range expansion and affecting carrying capacities (Kylafis & Loreau 2008; Krakauer, Page & Erwin 2009) It can strongly affect heritability, and challenges how it is commonly defined and measured (Uller & Helanterä 2020
Niche construction

JFYI - very few, if any, niche constructors are 'disease free' or have 'all the precise conditions needed for the offspring to thrive and survive'. That's ridiculous hyperbole.
I don't think it's hyperbole. It may only seem that way because you don't appreciate the full implications. I think overall Niche construction is a benefit to the individual and the ecosystem. Creatures are equipped to provide a safe and healthy birthing and rearing environment through niche construction. They continue to create an environment that suits them and their offspring which helps them adapt and survive.

Offspring inherit not just genes but a ‘start-up niche’, comprising a specific parentally chosen location for birth and a transmitted package of resources (Odling-Smee 2010). Many organisms provide protective chemicals for their offspring in this start-up niche, including antibodies such that the young can survive before their immune systems mature (birds, mammals), compounds that are poisonous or distasteful to predators (moths) (Dussourd et al. 1988), or even sun-blocks that protect transparent embryos and larvae from the effects of solar radiation (Goldstone et al. 2006).

From the niche-construction perspective, the key task for any developing organism becomes the active regulation of its inherited ‘niche’, by responding to its environment, and by altering its environment, in ways that keep it's personal organism-environment relationship continuously adaptive, for the rest of its life.
https://nicheconstruction.com/

There are also many examples of how niche changes made by creatures have good effects on the surrounding environment and this benefits other creatures. For example, beaver dams create pooled water which allows other organisms to grow and improves the surrounding vegetation which provides more habitats. There are also examples of how creatures work together and use other creatures to create niches such as the dung beetle using other creatures dung to create a perfect environment for egg-laying. Or how bacteria live within a creature’s gut which provides a niche and benefit for both.

In this mutualistic arrangement, both organisms change their gene expression patterns, in a beneficial way. The bacteria get a niche, and the squid develops a light organ that allows it to swim at night.

The same holds for niche construction, which predictably generates environmental states that are coherent and integrated with the organism's phenotype and its developmental needs, as well as environmental states that are adaptive for the constructor, or its descendants.

Across scales that encompass both the presence and absence of ecosystem engineering/niche construction, the net effect should be to enhance species richness via a net increase in habitat diversity (Jones et al. 1997). Recent studies provide support for this hypothesis.
Niche construction
 
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stevevw

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Consider - an evolutionary advantage means reproductive success; when a population evolves towards niche construction, what is the process that selects for the relevant behaviors?
As I have already shown in the previous post that it is an assumption to say that natural selection alone is the process that selects for relevant behaviors. Even before natural selection comes along it is the creature that is selecting the healthy and positive conditions that will enhance their fitness and provide benefits for their offspring in future generations. So long as that niche is maintained it will provide heritable benefits.

When a population of niche constructors reproduces, generating variant offspring, what is the process that selects for those variants that maintain or improve on those behaviours? IOW what is the process which establishes whether a certain pattern of behaviour is advantageous?
The process that establishes whether a certain pattern of behavior or environment is advantageous is the creature itself through changing its environment, its developmental responses to its environment, and the back and forth feedback between these factors as well as NS. Natural selection is not the privileged or only force at play here and that is what the EES is trying to dispel. I think I have provided ample evidence for this in the other responses. The fact that you still want to emphasize selection over everything else shows even though you claim that the SET acknowledges the EES forces they don’t really recognize them as actual causes that direct evolution like NS.

Niche construction can be summed up here
However, niche construction is not restricted to the biological adaptations of organisms but also stems from their developmental plasticity, their by-products, and their acquired characters. Organisms are viewed as active agents that impose order on the conditions of their existence, and direction on their development and evolution.

Niche construction theory emphasizes how niche construction can scale-up across individuals in populations and overtime to generate a stable and directional modification of environmental components. As a result, niche construction generates consistent and sustained forms of natural selection and thereby impose biases on evolution (Laland et al, 2015).
Niche construction

As the article points out “niche construction generates consistent and sustained forms of natural selection”. Creatures have the ability to create conditions that provide well-integrated and suited changes that provide fitness and adaptive benefits just like NS can do and therefore is another source that determines the course of evolution and in doing so biases and diminishes NS.

Which behaviours in which creatures, for example?
As far as niche constructions many creatures such as insects, birds, and mammals, basically most creatures that produce offspring create conditions conducive for healthy birthing and rearing through a number of behaviors. These include creating protective birthing conditions with insects such as the Dung Beetle or with birds and mammals.

As far as inheritance beyond genes we now know through processes like epigenetics and direct interactions that whatever behaviors a creature has and teaches their offspring will affect and influence future generations. We know that social and cultural practices can help with evolvability and put creatures in better positions to thrive and survive. These forces are part of the EES and influence the course of evolution by helping creatures be in a more adaptive position.

What, exactly, do you mean by learnt behaviour? Learnt how - by imitation? It can't be trial and error.
Under inheritance beyond genes creatures' behaviors can be passed along and down to future generations through social and cultural practices which can be advantageous similar to niche construction in putting creatures in a better position to be fitter and adapt. These behaviors like niches can be passed on and provided the creatures maintains that behavior or niche and adjusts it accordingly when needed it will continue to provide benefits now and in the future. But behavior can also cause negative outcomes as we have seen with humans.

I think most animals have an inherent ability to work with nature and therefore their behaviour is more likely to provide benefits. But humans often work against nature as well. But we also have the ability to make a big difference in rectifying the harm done and counteracting those negative outcomes by reestablishing nature and creating artificial environments that help cultivate environments and niches. As we have seen humans are so good at mitigating natural consequences such as through medicine and technology that we are overriding NS influence altogether. To a lesser extent, all life has this ability but to a lesser extent as mentioned with niche construction and inheritance beyond genes.

You say niche construction behaviours "always produce advantageous results", but it's common that the predictability of niche behaviours allows predators and parasites to specialise on them, and in the case of literal niches, for usurpers to requisition or 'cuckoo' the niche. When environmental conditions change, a niche may become uninhabitable, unconstructible, or may simply disappear, leaving the niche constructer specialised for a non-existent or unconstructible niche... In what sense are these 'advantageous results'?
I am not sure it is common and the fact that this happens doesn’t negate the important role niche construction plays as a cause of evolutionary change. According to NCT creatures are not dumb passive creatures that cannot change with changing environments. They have a great capacity to adjust environments to suit. Living things seem to have a ready set of behaviors and tools available (hormonally, chemically, etc.) that help create the right environment. It seems inherent in them.

They are in tune with nature and their particular environment, what the dangers are, and how to set things up in the best possible way to grow, develop, and survive. That’s not to say that mistakes are not made and disasters don’t come along or that creatures are just as smart in getting around these niches. But these may be individual occurrences for both creatures and environments. Each will be different and are not the environment or species-wide events. If creatures are found out then they have the capacity to learn and try to create a better niche.

But this is different from the narrow view, SET takes that treats creatures as passive entities subject to predators and changing environments where they can only survive if they are adapted genetically through NS.

Developmental plasticity only gives a limited range of adaptability; it will not always produce 'precisely what is needed' for an environment. Random mutations still occur, but they are relevant over multiple generations, whereas developmental plasticity is an individual response.
As far as I understand there is a certain scope for plasticity through development just like there is a certain scope of variation developmentally in the first place. There is good reason for this as only certain variations work in environments so saying that random mutations are going to find a better solution that doesn’t seem to be supported.

Plasticity is often the first step in adapting to environments and usually produces well suited and integrated change that may be cemented later with NS. But it doesn’t take generations and can happen pretty quickly because there is only certain variations that can be produced and because taking the constructive and reciprocal view of the EES creatures are not separate to their environments and evolve with their environments. So variations are often developmental responses to the environments they are in.

What is the process that selects for developmental plasticity over developmental fixity/rigidity? What is the process that selects for a particular type of developmental plasticity in a changing environment?
When you consider that there are only certain variations that can be produced and only a certain scope within those variations, it seems to me that initially and primarily it is the development system that is responding to environments and producing the required changes as a result. As mentioned above this seems to be the main way that development works and NS is something that may come along later and refine and fix these plastic changes in.

But when you consider that these developmental changes are unlike the random ones from mutations but are nonrandom then they are more directed at achieving specific changes that have been determined to be most suitable. This would mean that it is not NS but developmental systems that are determining which variations work best and not NS or at least not NS on its own but both working together.

Good grief... that is 'not even wrong'. It reflects a fundamental lack of understanding or joined-up thinking about evolution.
Why I can support everything that is said here. I think I have already covered this above. For example, how the SET treats the environment and creatures as separate entities whereas the EES sees them intertwined and therefore affecting each other is supported here

Central to these debates are different assumptions concerning the independence or interdependence of the causes of phenotypic variation, differential fitness, and inheritance, which are Lewontin’s (1970) three conditions for evolution by natural selection (Walsh 2015; Uller & Helanterä 2019). Traditionally, evolutionary biologists have assumed these processes are quasi-independent, but in practice, they are often causally intertwined.
Niche construction

As far as showing that random mutations that produce random variations not being conducive for advantageous changes and therefore need to be tested and sifted by natural selection that's easy to explain without any references. As random mutations cannot be predetermined as to whether they provide a benefit for adaptations they need NS to determine their worth by testing each variation against the environment.
 
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