Epigenetic Factors as 'Creative' influence in Evolution

I have recently tried to understand epigenetics beyond simply the idea that nature and nurture form a constant feedback for development of an organism. There is an emergence now of literature that says that epigenetic factors are the primary source of novel adaptations to the environment. It seems to suggest that genetic mutation does not play that much of a role in developing new variation but rather changes in development of the organism.Assuming the accuracy of these claims bears fruit how significant of a change in evolutionary theory do you think this? The idea that a population has mechanisms to proactively respond to its environment seems to me to alter significantly at least the 'chance' debate of creationist. It seems analogous to the idea that amino acids preference for certain forms alters any of the probability equations for arriving at life significant chains.Was hoping someone more familiar with these ideas might have some time to kill between real life and ramming the creationist. This place seems an awesome resource.

Initially this is how I thought epigenetics functioned. Essentially that it was expression of genotypes being turned on or off by cues from the environment or development. It reminded me of work that I was doing with trying to model cellular differentiation as a giant complex of genes turning each other on and off.But the epigenetic literature seems to be making a much larger claim. Essentially that changes in developmental-behavior can produce novel effects without any prior genetic tendency, and that over time natural selection operates in these new environments and genes are selected for the environment. It seems to be saying that changes to the genome occur because of developmental changes due to environmental changes.Or slightly differently, that novel behavior or adaptation can occur not because of a genetic mutation or other genetic alteration but a behavioral/developmental change outside of the genome, which can then cause changes in the genome as the organism optimizes to the new environment. It seems to be a proactive change, and separates the genes from the behavior. It certainly respects genes as a powerful force but instead of a one-way arrow from genes to environment it’s placing a two-way arrow.

Genes turning each other on or off, or external proteins triggered by environmental factors regulating binary gene networks is I believe pretty well established. This is still an "in the genes" view of an organisms morphology and behavior and from what I understand would not really be considered an epigenetic factor.I am not sure I really understand your question though, how would environmental selection NOT reflect developmental selection or vice-versa? I agree with this statement but I think epigenetics also talks about more than just regulation directly under control of genes. I think development can be viewed as a sliding scale between factors that are completely under genetic control towards factors that are a mix of the environment and genetics and then factors that are completely under environmental control.The fact that certain aspects of an organism are totally controlled by genes has been shown, but I would believe most of these are fairly simple process since the more complex a process is the more it needs some level of regulatory control from the environment. A feedback system is defiantly necessary for most "adaptive functions."The other end of the scale is less researched. Clearly the environment can exact a change on an organism that is not coded at all in its genome but whether the environment can trigger an adaptive reaction that can be selected for with out genes coding for most of the behavior is what I believe is open to debate.Certain heritable phenomenons that have nothing to do with genes have been produced in fairly simple organisms. Forgive my lack of specifics it’s been a while since I read the study, if necessary I can dig it up again. But essentially researchers grafted the membrane from one single celled organism on to the membrane of a different organism but the same species. The number of cilia on the membrane is usually genetically controlled but in this case the section that was grafted was replicated such that the offspring had the grafted number of cilia and not the genetic number.This is a basic example and does not generalize well and other examples seem to start bringing up problems of confounding variables. Mice that are handled while young will have grand children that have a higher fear response regardless of rearing. Is this some sort of non-gene passage of behavior or is there a genetic control over the delivery of predation cues to offspring? There are many other similar examples of this behavior both in labs and in the wild.I think the jury is still out on whether the environment can create these sort of adaptive changes in organisms without a genetic predisposition to the change given the circumstances. But there are a lot of die hard supporters of the idea starting to emerge.Environment can clearly alter an organism’s development but can this alteration serve as a 'creative' medium for developing adaptive functions? I think this has large ramifications for evolutionary theory since organisms can have some level of proactive adaptation and don't simply have to have a genetic mutation develop to create a new behavior.My main area of study is biological psychology and evolutionary psychology and many examples that are emerging in this field seem bring up these kinds of questions of development. Several researchers showed that people will often alter the priority they give to physical attractiveness in mate selection in relation to the parasite load of the group they are in. In a somewhat gene dominated view this would be selection between a genetic system that didn’t recognize health cues, a system that recognized health cues regardless of the environment, or a system the recognized health cues in relation to an environmental feedback system. Selection would probably favor the latter and that’s why modern man functions in this way. A more epigenetic view might describe this as people using a genetic predisposition to certain health cues and consciously increasing or decreasing its priority based on what one sees in the group. Instead of genes being responsible for creating the regulation people were able to actively co-opt the process for changing environments.

I think the classification of memes as epigenetic is rooted in how accurate the concepts in epigenetics are. I think the door is still wide open on how much of a role genes can play in thought, behavior and adaptivness of an organism.From what I understand of memes they are "thought units" that easily gain prominence and have a high likelihood of being "passed on" to other people because they involve concepts that have high adaptive benefit to pay attention too. Mating behaviors and histories, food selection and availability, survival risks whether predatory or pathonogenic, ect. Most modern memes take advantage of these ancestral cues and spread accordingly.So if this definition is an honest portrayal you are left with the question of whether there is a set of genes that have activated the mind to pay attention to these concepts or if the importance of these concepts was heritable through means other than genes. The proximate cause is almost always going to be environmental, even with a very gene dominated view. The question is, what is the ultimate causation? Was it natural selection acting on genes that regulated thoughts, or was it a non-genetic regulation of thoughts that was beneficial and thus spread. If the former then I think memes are genetic consequences and probably not "epigenetic" if the latter you could even make the case the memes are a form in which epigenetic factors are transmitted across generations or "inherited."The mice question faces this same dilemma. If there is some gene in the mice that receives a stress hormone from the mother and then stays "on" producing a heightened fear response and as such a stress hormone that activates the genes in their offspring you have a very strongly genetic determinate of behavior and its not really "epigenetic." But if this fear response is passed on without change in the regulation of genes than you have an epigenetic factor. Whether this could be called memetics or not I am not sure, the fear response is not dependent on the rearing environment so it’s not a "cultural" transmission but something involved in embryonic development. In a sense though it could be considered perhaps a more primitive form of the concepts.I think in general the whole thing is a slight twist on the nature vs. nurture debate. How much of ones behavior do genes really control? But I think what epigenetics brings to the discussion is the idea that even things that exist outside of the genes can be heritable and as such be selected for from evolutionary pressures.

Yes, some behavior is certainly caused primarily by genetics. Others are caused by a mixture between genetic and environmental factors. This is probably the vast majority of behavior. Finally, some behavior maybe caused by environmental effects, I have a hard to time seeing much behavior at all that is caused solely by factors outside the individual. There is behavior in novel environments that appears to be novel behavior, but is probably just some application of a behavior defined in the Environment of Evolutionary Adaptiveness (EEA, which is probably Pleistocene African Savannah for humans).The question I have is about what defined these EEA behaviors. Is it primarily genetically based and developed through population variation and mutation? Or is there ability for an organism to pass on adaptive strategies to offspring in ways that go beyond genes. At this point I should probably mention that this really isn't a neo-Lamarckian idea. There isn't a transfer of morphology changes due to stressors from parent to fetus. While some information about the environment a fetus is being born into is transferred this is only a small portion. It’s more the idea that behaviors and adaptations in one area could be co-opted in new areas to create new adaptive behaviors without having to wait for genetics to change. Many pathologies are probably failures of development or genetics. Huntington's chorea is an obvious psychosis caused by genetics. Development and genetics probably mix to create more common problems. The brain, especially during development, is very sensitive to negative influences. It is VERY VERY hard to get the brain to grow right, and any significant deviation from the mean will cause serious issues. Hormonal regulation is probably similar, for example Grave's Disease dumps tons of thyroid into the system and causes all kinds of pathologies. So there is defiantly a genetic factor and environmental factor in most pathologies/psychosis.What’s interesting is that it is hypothesized that some pathologies have adaptive benefits under some circumstances. For example, psychopaths could have an advantage in social arrangements as long as they are a small portion of the population. Rape is another hot button issue. One of my undergraduate advisors, Dr. Randy Thornhill, hypotheses a rape adaptation in men. It says that under certain circumstances in the EEA men who used sexual coercion for sexual access would have more reproductive success than those who did not. Rape probably dates pretty far back, since most of the great ape family shows a propensity for it. Its most likely a homologous behavior for the hominidaes and dates at least to the ape common ancestor.Edit: I forgot to add (and couldn't resist) that human pathologies could also be caused by demonic possession, but these are easily cured by consuming mass quantities of beans.[This message has been edited by Parsimonious_Razor, 03-03-2004]

Maybe it’s an issue with loose terminology in my main field of study. Most of the work that I have run into (which is admittedly heavily biased towards evolutionary psychology/evolutionary developmental psychology) has defined epigenetic much more broadly. It seems to suggest that an organism can make proactive changes to its environment and that these changes can be heritable to offspring and grandchildren. It suggest that these heritable changes do not require any alteration in the genes of the organism, though genetic alteration may occur over time. Maybe its better to dump the term epigenetic if it has a more specific meaning in microbiology. It wouldn't be the first time EvoPsych has co-opted a term rather loosely.Examples of what I mean are:
Mice ability to pass information about environments they were reared in to offspring and grandchildren regardless of rearing environment for the offspring (heightened fear response from grandchildren of handled rats)A single celled organism grafted with a portion of membrane from a different organism will pass on the grafted portion not what is "genetically" programmed.A species of fruit fly that started laying its eggs in old world apple tree when they were brought over despite no genetic propensity for the type of fruit, the difference in seasonal variance eventually lead to enough of a pre-zygotic barrier that the species diverged genetically as well as behaviorally.Humans changing priority of health markers in mate selection depending on parasite load in the environment.The question I have is: Do these phenomenon have a mostly genetic basis, just representing genetic networks programmed in the species responding to stimuli? Or are they examples of a form of proactive adaptive behavior that goes beyond genes?I think the answer to this question has ramification for what the 'creative' force is in natural selection and evolution.

I am going to take a step back for a moment and try and link all this into a broader idea. I think the main question I am interested in on this topic is how much control DNA has on morphology and behavior. If DNA is the primary source for both than new behaviors or new morphologies have to await mutation and other alterations to the DNA strand to develop. If on the other hand DNA plays only one part in a much larger picture a whole range of alterations can take place at different levels that create new potential adaptations.I think it’s worth separating the difference between the concept of DNA and the concept of a gene. If you define gene as a heritable unit it can encompass many levels other than just the DNA strand. Such as areas of the molecule that regulate the expression of the strand, the various mechanisms that alter and recode the mRNA in the nucleus, hormone interactions, feedback mechanisms, ect. I think this complex of interactions is the primary source of heritable information, and the actual DNA codes play only a part in the overall picture. This heritable unit can go beyond just the DNA molecules, histone proteins, and transcription factors. It can include hormones, temperature, population dynamics, cultural standards, and feedback mechanisms (like how bones grow into joints).In addition to my Evo-Psych studies I am working on models of pathways of cellular differentiation. The main working model is that different cell types represent different systems of "genes" turning each other on and off. The model assigns either an 'on' state or ‘off’ state to each gene and then randomly assigns various Boolean functions between the genes. For example: If X is on then Y is off. If Y and X is on Z is off. If Z or Y are on X is off. The more genes you have the more hideously complex the Boolean network becomes. Dr. Stuart Kaufmann originally set up these kinds of networks in the 70’s and discovered that there are many states that get locked into repeating cycles so that you may go through 20 different on/off states and then go back to where you started. He hypothesized that these cycles were different cell types. I have been working with Dr. Kaufmann on several models for how a cell moves from one state to another. The next question about these pathways is how do they evolve. The evolution of these pathways is starting to be modeled now (assuming NIH comes through with some money!) but the actual content of the DNA plays only a minor role. The evolvability of these mechanisms requires a very large holistic model of all the interactions of the genes and regulators, and also the systems that create noise in the process along with a host of other factors. There are million pieces to this puzzle that could be altered and have drastic effects. I think this starts to bring up the question that the DNA is USED by the heritable system and is not THE heritable system.In evolutionary psychology there is a core set of basic behavioral and mental faculties that have been brought to humans through the evolutionary chain. Some more recent than others. What you find is that these various basic functions get constantly co-opted and changed and prioritized depending on a whole host of environmental cues. I have already talked about the example of parasite load changing priority of health cues. Status seeking behavior in males is another big one. Culturally what gives one male more status than another is fairly arbitrary and highly variable, males will pursue these status indicators to their near demise no matter what they are. And on top of that they will not even know why they are doing it, they just know they want whatever it is. Money is an example. Most men who pursue money see it was an end in itself not simply as a mate value thing. Increasing relative mate value has a genetic basis far in the past, while pursuit of money is a culturally transmitted. So the proximate cause and the ultimate cause are separate but similar, if the results of the proximate cause last a long time and are selected for I think they can become ultimate causations for behavior in future generations.
I guess more succinctly the idea I am trying to put forth is that an ultimate cause can produce highly variable responses depending on the proximate causations. If these proximate causes create enough variation in responses and some of the responses are better than others the proximate cause can be selected for even though it may lie in cultural or hormonal or cytoplasm events.I think my example of the maggot flies was shown to be a poor example of this behavior so I will go ahead and withdraw it as an example. But let me try describing another example and how it represents why I wonder if DNA is not the CAUSE of a change but is a tool being used in an adaptive behavior.Tiger salamanders have a cannibal morphology that has a low but significant occurrence in nature. Several studies have examined what causes the morphology to come into being. There has to be three environmental influences present, if any one of them is missing the morph never shows up. First there must be a large number of chorus frog larvae present (or other larvae similar to the tiger salamander larvae), second there must be a large number of tiger salamanders in the area and three there must be a shortage of zooplankton the preferred prey for the salamander. If all three of these are present SOME salamander larvae grow into the cannibal morph. The salamanders are genetically as identical as any species is, all receiving the same environmental influences. Obviously this is a very tightly balanced interaction between environmental influences and genetics. The salamander activates a series of developmental genes to create the cannibal morph. Is the propensity to activate these genes a DNA code in and of itself? I am not convinced. The percentage of morphs even in environments that should trigger it is extremely rare. And the ability to develop the morph stays in the populations even after multiple generations with no morphs appearing. Its staying active with out any selection, which makes me think its present in most if not all salamanders. Even given all the right conditions there seems to be some level of choice in development that goes beyond any deterministic process. This third factor could potential be selected for or against, and if heritable could produce changes in the frequency of a behavior with out the need to invoke DNA mutation.That’s the main point I am trying to make here. If the genetic unit is a complex area of cultural, hormonal, regulatory, stochastic, and DNA interactions significant changes to the development, morphology and behavior of an organism could be achieved without a change in the DNA structure. This offers a different force in generating ‘creative’ adaptations in evolution. If a change is made in a regulatory system or regulatory systems for the regulatory systems, ect. You could see much more significant changes in organisms even in only a hand full of generations.

I am not sure the full significance of the Escherichia coli study. It seems to point to a particular area where increased mutation rates could create a beneficial adaptation in species that produces many generations in consistently harsh environment. But species with a much larger generation time and/or more variable environment would still have a tendency to limit mutations. To me this suggests that there is power to be found in adaptive changes that lie outside of DNA changes.

I guess I am not convinced that DNA is a controlling mechanism. Certainly the instructions present in the DNA molecule are necessary to for the creation of all the regulatory and structural properties of the organism. But that doesn't mean its the deterministic part of the system. The examples I have given certainly have a genetic basis, exemplify classic genetic/environmental interaction but more than that I don't think you can explain what happens by an appeal to the genes. Genes seem to be activated or not activated by forces that lay outside of the genes.For example, the Boolean network model does not have any "control" genes in that they regulate the various expressions of all the possible regulators. Instead it is a giant spider web of rules, the cell differentiate in this model either through noise or some form of random fluxuations. Therefor, this initial developmental step is in the genes in that certain sets of genes code for certain cell types but the ability to achieve differentiation is not in the genes. The evolvability of the mechanism to me has to lie in the environment that then acts on the genes. The genes are a tool in this sense not managers. I am not sure I actually agree with this. It depends on what you mean by culture or biology. I think every culture while distinct in many arbitrary ways basically falls under the same fundamental model. This model was defined in the human EEA (Environment of Evolutionary Adaptiveness). My point is that the behavioral aspects of humans are an inheritable chunk that can under go selection and have just as much staying power as any DNA based behavior. Other organism probably wouldn't have anything approaching the variability of human behavior but I think you can find simpler examples that begin to foreshadow what you find in primates and specifically humans. I agree exactly. My point is that since the genetic propensity is being based down even in the absence of any possible selection (it is not expressed for multiple generations) probably MOST salamanders have the gene. But even when all the right trigger events are present only a small fraction form the morphology. There does not seem to be any deterministic part in this equation. If it was only gene/environment interaction I would expect to see a much higher percentage of the morph emerging in laboratory conditions.