Phenotypic Plasticity & Polyphenism

[Sriram]

Hi everyone,

I was just reading up on Phenotypic Plasticity which is an interesting aspect of evolution but which no one generally talks about.

https://en.wikipedia.org/wiki/Phenotypic_plasticity

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Phenotypic plasticity is the ability of one genotype to produce more than one phenotype when exposed to different environments.

Phenotypic plasticity refers to some of the changes in an organism's behavior, morphology and physiology in response to a unique environment.[1] Fundamental to the way in which organisms cope with environmental variation, phenotypic plasticity encompasses all types of environmentally induced changes (e.g. morphological, physiological, behavioural, phenological) that may or may not be permanent throughout an individual's lifespan. The term was originally used to describe developmental effects on morphological characters, but is now more broadly used to describe all phenotypic responses to environmental change, such as acclimation (acclimatization), as well as learning.[2] The special case when differences in environment induce discrete phenotypes is termed polyphenism.

Plasticity is usually thought to be an evolutionary adaptation to environmental variation that is reasonably predictable and occurs within the lifespan of an individual organism, as it allows individuals to 'fit' their phenotype to different environments.

Phenotypic plasticity is a key mechanism with which organisms can cope with a changing climate, as it allows individuals to respond to change within their lifetime.[61] This is thought to be particularly important for species with long generation times, as evolutionary responses via natural selection may not produce change fast enough to mitigate the effects of a warmer climate.

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Quite clearly there is lot more adaptation and active response to environmental changes taking place in nature than the standard 'random variation and Natural Selection' explanations suggest. 

Cheers.

Sriram

[ProfessorDavey]

Hi everyone,

I was just reading up on Phenotypic Plasticity which is an interesting aspect of evolution but which no one generally talks about.

https://en.wikipedia.org/wiki/Phenotypic_plasticity

***********

Phenotypic plasticity is the ability of one genotype to produce more than one phenotype when exposed to different environments.

Phenotypic plasticity refers to some of the changes in an organism's behavior, morphology and physiology in response to a unique environment.[1] Fundamental to the way in which organisms cope with environmental variation, phenotypic plasticity encompasses all types of environmentally induced changes (e.g. morphological, physiological, behavioural, phenological) that may or may not be permanent throughout an individual's lifespan. The term was originally used to describe developmental effects on morphological characters, but is now more broadly used to describe all phenotypic responses to environmental change, such as acclimation (acclimatization), as well as learning.[2] The special case when differences in environment induce discrete phenotypes is termed polyphenism.

Plasticity is usually thought to be an evolutionary adaptation to environmental variation that is reasonably predictable and occurs within the lifespan of an individual organism, as it allows individuals to 'fit' their phenotype to different environments.

Phenotypic plasticity is a key mechanism with which organisms can cope with a changing climate, as it allows individuals to respond to change within their lifetime.[61] This is thought to be particularly important for species with long generation times, as evolutionary responses via natural selection may not produce change fast enough to mitigate the effects of a warmer climate.

************

Quite clearly there is lot more adaptation and active response to environmental changes taking place in nature than the standard 'random variation and Natural Selection' explanations suggest. 

Cheers.

Sriram

Yes it is an interesting subject, but it does largely boil down to the fundamental genetics and epigenetic - effectively those genotypes that support environmental adaptability may confer evolutionary advantage and therefore be more likely to be retained through generations.

However I have no idea why you may posted this in the 'Philosophy, in all its guises' section - this has nothing to do with philosophy - suggest the mods move this to 'Science & technology'.

[Enki]

Indeed, it is a fascinating subject. However please don't think that 'random variation and Natural Selection' are regarded as the only processes aiding evolution, even if they are regarded as the most important. It might be worthwhile looking up 'gene flow' and 'genetic drift' as they are generally accepted adjuncts to evolution also.  Phenotypic plasticity is still debated as to its importance in evolutionary terms as to whether it is an evolutionary trait of adaptability in species and as to whether its effects are longer lasting than on individual organisms.

[Owlswing]

Hi everyone,

I was just reading up on Phenotypic Plasticity which is an interesting aspect of evolution but which no one generally talks about.

https://en.wikipedia.org/wiki/Phenotypic_plasticity

***********

Phenotypic plasticity is the ability of one genotype to produce more than one phenotype when exposed to different environments.

Phenotypic plasticity refers to some of the changes in an organism's behavior, morphology and physiology in response to a unique environment.[1] Fundamental to the way in which organisms cope with environmental variation, phenotypic plasticity encompasses all types of environmentally induced changes (e.g. morphological, physiological, behavioural, phenological) that may or may not be permanent throughout an individual's lifespan. The term was originally used to describe developmental effects on morphological characters, but is now more broadly used to describe all phenotypic responses to environmental change, such as acclimation (acclimatization), as well as learning.[2] The special case when differences in environment induce discrete phenotypes is termed polyphenism.

Plasticity is usually thought to be an evolutionary adaptation to environmental variation that is reasonably predictable and occurs within the lifespan of an individual organism, as it allows individuals to 'fit' their phenotype to different environments.

Phenotypic plasticity is a key mechanism with which organisms can cope with a changing climate, as it allows individuals to respond to change within their lifetime.[61] This is thought to be particularly important for species with long generation times, as evolutionary responses via natural selection may not produce change fast enough to mitigate the effects of a warmer climate.

************

Quite clearly there is lot more adaptation and active response to environmental changes taking place in nature than the standard 'random variation and Natural Selection' explanations suggest. 

Cheers.

Sriram

Oh dear! This would be so much more interesting if I understood more than about half-a-dozen words of it!

[Stranger]

Quite clearly there is lot more adaptation and active response to environmental changes taking place in nature than the standard 'random variation and Natural Selection' explanations suggest. 

You do get that phenotypic plasticity is itself a trait that originates in random variation and can be selected for? From wiki article you quoted: "If the optimal phenotype in a given environment changes with environmental conditions, then the ability of individuals to express different traits should be advantageous and thus selected for. Hence, phenotypic plasticity can evolve if Darwinian fitness is increased by changing phenotype" [my emphasis].

[SusanDoris]

Oh dear! This would be so much more interesting if I understood more than about half-a-dozen words of it!

Seems to me, having listened through without pausing to take it in, that since the human species evidently already has whatever adaptations are necessary for survival, they are probably and quite naturally taking advantage of them!

[Owlswing]

Seems to me, having listened through without pausing to take it in, that since the human species evidently already has whatever adaptations are necessary for survival, they are probably and quite naturally taking advantage of them!

Thank you. Ma'am!

[Sriram]

You do get that phenotypic plasticity is itself a trait that originates in random variation and can be selected for? From wiki article you quoted: "If the optimal phenotype in a given environment changes with environmental conditions, then the ability of individuals to express different traits should be advantageous and thus selected for. Hence, phenotypic plasticity can evolve if Darwinian fitness is increased by changing phenotype" [my emphasis].

You are saying that plasticity arose for some random reason...and after that, since it is advantageous, it has continued to be 'selected'.    You really have an emotional connect with Natural Selection, don't you?! Won't let it down...

IMO, phenotypic plasticity is obvious and does not require any 'process' such as natural selection to keep it going. It is the only way evolution can possibly happen. The point is that, phenotypic plasticity has arisen, which is itself something to think about.

As I see it, in the years to come, it will become clear that plasticity is the single process by which evolution happens in all organisms. Natural Selection, at least in the manner in which it is currently defined, will be discarded.     

Secondly, plasticity clearly highlights how 'intelligent' natural processes are.  The above article says  '.... occurs within the lifespan of an individual organism, as it allows individuals to 'fit' their phenotype to different environments'.  Organisms actually 'fit' their phenotypes to specific environments!

How with a single genotype several phenotypes can be generated to 'fit' into specific environmental requirements....is something scientists are going to find very awkward to unravel.....!   

Cheers.

Sriram

[ProfessorDavey]

You are saying that plasticity arose for some random reason...and after that, since it is advantageous, it has continued to be 'selected'.    You really have an emotional connect with Natural Selection, don't you?! Won't let it down...

No - it is simple evolution by natural selection theory and has been demonstrated time and again. Indeed it is really easy to reproduce in the lab and is used as a routine tool when genetic modification is being used in a range of techniques. Typically an antibiotic resistance is 'knocked-in' along with the gene of interest - you then 'select' for the cells (usually bacteria or yeast) that have been modified by adding the antibiotic to the environment and guess what, only the modified cells survive and divide. Simple.

IMO, phenotypic plasticity is obvious and does not require any 'process' such as natural selection to keep it going. It is the only way evolution can possibly happen. The point is that, phenotypic plasticity has arisen, which is itself something to think about.

If it didn't convey evolutionary advantage it would not be selected for and would not be transmitted from generation to generation. So there will be, no doubt, countless examples where phenotypic plasticity has arisen which is either neutral in terms of evolutionary advantage, or even negative - those traits will fail to survive. Only those that are advantageous, or co-arisen with an advantageous trait survive.

As I see it, in the years to come, it will become clear that plasticity is the single process by which evolution happens in all organisms. Natural Selection, at least in the manner in which it is currently defined, will be discarded.

But phenotypic plasticity is merely one of countless traits that can arise through the normal evolutionary process - it isn't distinct from evolution by natural selection - it is part of it. 

Secondly, plasticity clearly highlights how 'intelligent' natural processes are.  The above article says  '.... occurs within the lifespan of an individual organism, as it allows individuals to 'fit' their phenotype to different environments'.  Organisms actually 'fit' their phenotypes to specific environments!

How with a single genotype several phenotypes can be generated to 'fit' into specific environmental requirements....is something scientists are going to find very awkward to unravel.....!

Not really - scientist have been studying this for decades and understand it very well, although of course there is always more detail to uncover. So don't forget that the genotype merely reflects the genetic code in our DNA - phenotype is driven by the patterns of genes that are turned on and turned off in various parts of the organism and across time. It is pretty easy to see phenotypic change in a single organism through its lifespan - just look at the phenotypic changes that occur from a new born baby to an adult - throughout this period the genotype is, effectively, unaltered but there are immense phenotypic changes as different sets of genes are turned on and off.

The control of the turning on an off of genes and the ensuing activity of the proteins they code for (and therefore phenotype) involves a range of mechanisms, and many of them are environmental. Interestingly some are heritable - so called epigenetic traits, and again some environmentally control alterations are epigenetic.

So Sriram - I know you want to try to turn this into some kind of great mystery that is perplexing to science and challenges traditional thinking on evolution. But it doesn't - ask any credible biologist and they'll shrug their shoulders and go 'sure, yes we've know this sort of thing happens for decades - still plenty to uncover about the mechanisms, but they'll be more about that in the articles in next week's edition of Nature and I've got a grant proposal being submitted to find out a little more myself'.

[Sriram]

The point is...Prof D that, evolution does not happen just by random variations and NS....which are chance factors. Evolution happens through deliberate adaptation suited to specific environments. 

There is a clear objective of survival and a clear process of responding intelligently to the environment. Now...please don't say we knew this all along...!

[ProfessorDavey]

The point is...Prof D that, evolution does not happen just by random variations and NS....which are chance factors. Evolution happens through deliberate adaptation suited to specific environments. 

There is a clear objective of survival and a clear process of responding intelligently to the environment. Now...please don't say we knew this all along...!

You are missing the point Sriram - random variation lead to all sorts of traits - many are entirely neutral in survival terms, others are negative - some are positive. Those that are positive are likely to be selected for - in other words increase the likelihood of survival of that individual organism and its ability to pass on that trait to offspring - in other words evolution by natural selection.

One of the traits that may arise via random variations is the adaptability of gene expressions, epi-genetics and protein activities to environmental factors. In other word the randomly generated trait confers environmental adaption. If that environmental adaptation confers evolutionary advantage (not all will) it will be selected for and be more likely to be passed on to offspring.

[Stranger]

The point is...Prof D that, evolution does not happen just by random variations and NS....which are chance factors.

Natural selection isn't a chance factor, that's kind of the point.

Evolution happens through deliberate adaptation suited to specific environments. 

There is no evidence of this. The ability of individual organisms to adapt to an environment (including phenotypic plasticity) is something that evolves in the normal way.

There is a clear objective of survival and a clear process of responding intelligently to the environment.

If you bothered to find out how natural selection works, and tried to understand it rather than dismiss it, you'd know why it looks like that.

"Natural selection is not some desperate last resort of a theory. It is an idea whose plausibility and power hit you between the eyes with stunning force, once you understand it in all its elegant simplicity. Well might T. H. Huxley cry out, 'How extremely stupid of me not to have thought of that!'" -- Richard Dawkins

Now...please don't say we knew this all along...!

You do realise that phenotypic plasticity is not something that has only just been discovered and that people are struggling to explain, yes?

[ProfessorDavey]

You do realise that phenotypic plasticity is not something that has only just been discovered and that people are struggling to explain, yes?

As a mechanobiologist such of my career's research has been involved in understanding phenotypic plasticity - in my case how our tissues adapt phenotypically to alterations in the mechanical environment they find themselves in. So I do understand rather a lot about it.

And I'll introduce you to this chap:

https://en.wikipedia.org/wiki/Julius_Wolff_(surgeon)

Julius Wolff was a Prussian surgeon and he studied the phenotypic adaptation of bone to the altered mechanical environment that occurs when a leg it amputated. The bone he studied was from from soldiers in the Franco-Prussian war of 1870. He understood that bone adapted itself to an altered mechanical environment. He didn't understand how, but we know have huge amounts of evidence on the mechanism and its underlying molecular components.

Bone isn't my main interest (I mainly study other tissues in the musculoskeletal system) but I know most of the key players in the bone mechanobiology field. Obviously I didn't know Wolff (he died in 1902) but I did know Harold Frost (mentioned in the article) - he was one tough cookie.

[Owlswing]

The point is...Prof D that, evolution does not happen just by random variations and NS....which are chance factors. Evolution happens through deliberate adaptation suited to specific environments. 

There is a clear objective of survival and a clear process of responding intelligently to the environment. Now...please don't say we knew this all along...!

Prove it! To someone who doesn't have a clue what all the long scientific terms mean - explain it in words of not more than two sylables an old man who never had that much intelligence even when he was young!

PLEASE!

[Sriram]

Prove it! To someone who doesn't have a clue what all the long scientific terms mean - explain it in words of not more than two sylables an old man who never had that much intelligence even when he was young!

PLEASE!

Well...never mind Owlswing...    Just know that Intelligence is built into natural processes. Evolution is not random or chance driven.  That's all I am talking about.

Cheers.

[ProfessorDavey]

Well...never mind Owlswing...    Just know that Intelligence is built into natural processes. Evolution is not random or chance driven.  That's all I am talking about.

Cheers.

You can say that all you like Sriram - but you are wrong.

The development of mechanisms that allow adaption of an individual phenotype to environmental variations arise through random variation/mutations etc in the genome and epidemic-genome. Where those randomly generated traits confer evolutionary advantage (for example better tolerance to extreme conditions) they will be more likely to be passed on to future offspring and therefore retained. We are able then to witness this by observation as phenotypic plasticity. However, of course, we never see the countless other mutations/random variation that do not confer evolutionary advantage and/or confer evolutionary disadvantage as these die out.

There is no intelligence involved, except perhaps the intelligence to understand that this process does not require intelligence.

[Enki]

You come over as knowing very little about evolutionary processes, Sriram. All you seem to focus on is your favourite idea, that there is some sort of intelligence behind evolution. Unfortunately(for you, that is) you don't seem prepared to learn, preferring to try to fit selective bits of science to your ill informed views, rather than change your views to fit the science. Perhaps if you got rid of your tunnel vision and took a more telescopic view of evolution that might help, but I suspect your reaction will be that you have the truth and  those replying to you here are just incapable of seeing it.

[Sriram]

Natural selection isn't a chance factor, that's kind of the point.

There is no evidence of this. The ability of individual organisms to adapt to an environment (including phenotypic plasticity) is something that evolves in the normal way.

If you bothered to find out how natural selection works, and tried to understand it rather than dismiss it, you'd know why it looks like that.

"Natural selection is not some desperate last resort of a theory. It is an idea whose plausibility and power hit you between the eyes with stunning force, once you understand it in all its elegant simplicity. Well might T. H. Huxley cry out, 'How extremely stupid of me not to have thought of that!'" -- Richard Dawkins

You do realise that phenotypic plasticity is not something that has only just been discovered and that people are struggling to explain, yes?

Natural Selection has to be chance.  If random variation is chance and environmental changes are chance...NS has to be chance.  In one end of a forest a particular moth may survive and the same moth may perish at the other end of the forest 100 miles away.

There is no evidence that Phenotypic plasticity has arisen due to RV and NS.  It is too complex a mechanism and requires different processes in different species (plants and animals)....and is unlikely to have arisen by chance. 

PP is present in a variety of organisms and probably arose as a part of the evolutionary mechanism ab initio.  Very early people like Lamarck noticed  intelligent responses to the environment by organisms but later scientists dismissed it as hocus pocus.

Secondly...in whatever way PP may have arisen....once an organism has the internal intelligence to adapt and respond suitably to a specific environment and it is able to 'fit' its phenotype to that environment....the concepts of RV and NS are redundant. Evolution can be explained entirely through this mechanism. 

Chance survivals and deaths due to sudden changes in the environment will of course be there every now and then. I agree. This can be considered as also contributing to evolution...but only as a relatively sudden and unpredictable factor.

[ProfessorDavey]

There is no evidence that Phenotypic plasticity has arisen due to RV and NS.  It is too complex a mechanism and requires different processes in different species (plants and animals)....and is unlikely to have arisen by chance.

Rubbish - all it requires is for the control of genomic transcription of protein function to be linked to some feature of the environment - perhaps the most obvious examples being temperature, light and the osmotic environment. There are countless examples of proteins whose function is controlled in that way and likewise DNA conformation.

Let me give an example - linked to environmental drought - when water is scarce many plants sag, they lose turgor. What that means is that the water content in the plant is reduced than that increases the osmolarity in the cells. The conformation or shape of many proteins is altered by the osmotic environment and this often makes the protein (e.g. an enzyme) more or less active. So change the osmotic environment and you change the function (i.e. the phenotype).

So, you may ask how could this arise by random variation or chance - easy. A mutation in the gene encoding that protein will subtly change its primary structure (the amino acid chain) which may then become more susceptible to change in shape (and function) under altered osmotic conditions. Bingo - simple and random gene mutation results in phenotypic adaptation to the environment. If this has evolutionary benefit that mutation will be selected for and retained in future generations.

It works at the level of DNA too. DNA isn't just a long strand - it is tightly coiled and how tightly it is coiled affects whether genes are turned on or off (silenced). And guess what, the osmotic environment affects the degree of packing. There are some regions of the genome that are generally quite loose (so typically active) others very tight (silenced) and other regions where active/inactive state can be controlled osmotically. So those genes will be active or inactive on the basis of the environment.

Again, you may ask - how can this occur by random variation and chance - again easy. One of the major drivers of evolution are gene translocations - this is where an error is made during cell division (often meiosis) and a region of the genome ends up in a different place. So that may result in a gene moving into a location which is highly susceptible to osmotic change. Bingo - simple and random gene translocation results in phenotypic adaptation to the environment. If this has evolutionary benefit that mutation will be selected for and retained in future generations.

And if these genes now under osmotic control and kind of master genes - e.g. hormones that control a whole range of other processes, you end up with major phenotypic adaptation to the environment, purely driven by random variation.

[ProfessorDavey]

PP is present in a variety of organisms and probably arose as a part of the evolutionary mechanism ab initio.  Very early people like Lamarck noticed  intelligent responses to the environment by organisms but later scientists dismissed it as hocus pocus.

While for the uninitiated this may all sound rather Lamarckian - it isn't. This is classic Darwinian evolution working on the basis of randomly generated adaption to environmental conditions that may be evolutionarily advantageous or not and then being susceptible to natural selection.

[ProfessorDavey]

Secondly...in whatever way PP may have arisen....once an organism has the internal intelligence to adapt and respond suitably to a specific environment and it is able to 'fit' its phenotype to that environment....the concepts of RV and NS are redundant. Evolution can be explained entirely through this mechanism.

Again you are wrong.

Typically this process will result in adaptation within a range of environmental conditions and therefore if the environment drift further any benefit is lost.

Secondly the random variations don't stop. So new random variations may arise that provide greater evolutionary advantage and or may be more energetically efficient which become dominant. A good example would be temperature variation - cold blooded animals use ambient temperature as a key component for thermal regulation. This is very energy efficient but limits their phenotypic adaptation to extreme environments - effectively they cannot live in cold places. The evolution of warm blooded animals via random variants to temperature control mechanism has produced species that demonstrate phenotypic adaptability to much more extreme temperature ranges. And a cold blooded animal cannot simply will itself into developing the features of a warm-blooded one (in a kind of Lamarckian neck stretch). No, it requires the variation to arise via random variation which imbues evolutionary advantage.

[Stranger]

Natural Selection has to be chance.  If random variation is chance and environmental changes are chance...NS has to be chance.  In one end of a forest a particular moth may survive and the same moth may perish at the other end of the forest 100 miles away.

If the environment is different 100 miles away, yes. Natural selection not chance exactly because it depends on the environment. That's why you get adaptation to the population's current environment.

I see the Prof has comprehensively answered the rest.

[Sriram]

Prof D

You are going on and on about mechanisms.... I am talking of causes. 

You are still banking on 'random variations' to enable an organism to develop suitable phenotypes to match the environment.....in every single instance of  plasticity in every organism, in every situation in the world. This is what I am saying is impossible.

PP happens within the lifetime of an organism, perhaps many times.....and the organism develops phenotypes to fit the environment.  This simply cannot be random.

Random variations are genetic. Phenotype changes are not necessarily genetic. Genotype remains the same in most cases. That is what PP is all about. There has to be an inner process by which the organism detects the environmental conditions and changes its phenotype while the genotype remains the same.

There is an active process of adaptation.....nothing random about it.   Call it by whatever name you want.

[ProfessorDavey]

Prof D

You are going on and on about mechanisms.... I am talking of causes.

Same thing in evolutionary terms.

Random variations are genetic. Phenotype changes are not necessarily genetic. Genotype remains the same in most cases. That is what PP is all about. There has to be an inner process by which the organism detects the environmental conditions and changes its phenotype while the genotype remains the same.

You do understand that phenotype is related to genomic function not just genomic structure (i.e. genotype) per se - in other words which genes are active, which are not, which resultant RNA is translated, which is not, which proteins are produced, how those proteins are modified to control function and the whole variety of cues and signals (the environment) which controls the overall function.

I'm sorry Sriram - you really do not have a clue what you are talking about, and I don't want to 'pull rank' so to speak - but I do. I am a professional scientist who has spent my whole career understanding the relationship between environmental cues (yet I've studies osmotic, thermal, chemical, mechanical cues impact on phenotype and the underlying mechanisms involved.

[Sriram]

Same thing in evolutionary terms.
You do understand that phenotype is related to genomic function not just genomic structure (i.e. genotype) per se - in other words which genes are active, which are not, which resultant RNA is translated, which is not, which proteins are produced, how those proteins are modified to control function and the whole variety of cues and signals (the environment) which controls the overall function.

I'm sorry Sriram - you really do not have a clue what you are talking about, and I don't want to 'pull rank' so to speak - but I do. I am a professional scientist who has spent my whole career understanding the relationship between environmental cues (yet I've studies osmotic, thermal, chemical, mechanical cues impact on phenotype and the underlying mechanisms involved.

With all due respect for your professional knowledge....the fact that you are a professional scientist is probably the problem. The mind is too caught up in details to understand the broader point I am making.

Phenotype changes that are generated to fit the environment ...cannot be based on random variations. There has to be an intelligent (responsive) cause for them.

That's all I have to say...

Cheers.

Sriram