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Originally Posted by asking

I think the interface between environment and gene expression is probably THE hottest area of research in biology right now.

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Is there nothing new under the sun? Here's a reprint of an 1896 paper by J. M. Baldwin: A New Factor in Evolution.

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It seems proper, therefore, to call the influence of Organic Selection "a new factor;" for it gives a method of deriving the determinate gains of phylogeny from the adaptations of ontogeny without holding to either of the two current theories. The ontogenetic adaptations are really new, not preformed; and they are really reproduced in succeeding generations, although not physically inherited.

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This guy seems to be one of Baldwin's intellectual descendents/disciples:
Walter Fontana / Novelty in Evolution

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The overall theme is to explore notions of organization at vastly different levels of abstraction and to understand innovation for each organizational class in response to change ocurring at the level upon which that class is founded. The realm of molecular organization is the one where substantial theoretical progress is most likely to occur in this decade. Yet, the evolution (in some generalized sense) of functional, self-maintaining and homeostatic organizations is a central theme in many fields beyond biology proper, including many cognitive processes, as well as a diversity of human social and economic institutions. The origination and innovation of organization constitutes a ``vertical question'' cross-cutting chemistry, molecular biology, cognitive science, social science and economics. In all these disciplines the challenge is to (1) achieve a clear definition of organization as an autonomous individualized entity distinguished from mere aggregation, (2) understand how the robustness required for autonomy and individualization squares with evolvability, the capacity to be innovated, and plasticity, the capacity to be flexible and adaptive without losing identity, (3) understand the topology of the possible, that is, the routes by which organizations are transformed into new organizations, (4) understand what determines the possible.

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Are you familiar with this line of thought and research? What do you think?

I guess as I learn more about how genetics actually works, i.e. how organisms use the genome they were born with to cope with the environment they were born into, I'm becoming more convinced that my initial impression was basically correct, which is: At the practical level of animal husbandry and breeding, the importance of the particular genome that an animal is born with is generally overestimated as a determinant or predictor of its "success", and the importance of environmental factors (including husbandry practices), especially during developmental stages of maturation, is generally underestimated. In other words, bad management will almost certainly produce bad results, even from a "superior" genome, while good management, consistently applied, will likely produce good and continually improving results even from an "ordinary" genome. I'm even starting to wonder whether the notion of a "superior genome" has any practical relevance. This is a somewhat uncomfortable conclusion for a purveyor of "genetics" to come to. Do you think it's too extreme?

At the level of evolutionary theory, these ideas seem to me to diminish the role of "natural selection" as a guiding force. Natural selection is the definition of (penalty for?) failure, but offers little in the way of promoting success in varying degrees:

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Natural Selection is too often treated as a positive agency. It is not a positive agency; it is entirely negative. It is simply a statement of what occurs when an organism does not have the qualifications necessary to enable it to survive in given conditions of life; it does not in any way define positively the qualifications which do enable other organisms to survive. Assuming the principle of Natural Selection in any case, and saying that, according to it, if an organism do [sic] not have the necessary qualifications it will be killed off, it still remains in that instance to find what the qualifications are which this organism is to have if it is to be kept alive. So we may say that the means of survival is always an additional question to the negative statement of the operation of natural selection.

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(From Baldwin, op. cit.)

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Originally Posted by ordinaryguy

I'm even starting to wonder whether the notion of a "superior genome" has any practical relevance. This is a somewhat uncomfortable conclusion for a purveyor of "genetics" to come to. Do you think it's too extreme?

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I don't think that it is an extreme concept it is merely the old nature vs nurture debate. I still think that a small genetic change could still vastly improve your product (the cow). For instance supposing one cow had a gentic mutation which meant it could process rougage with increased effiency- for expample an extra efficient enzyme. I think that is more likely to happen with direct genetic intervention.

This is happing more in agriculture, cold resistant tomatoes being a famous example. Also 'functional foods' are a hot area of research, american scientist have just produced a carrot which has high levels of bioavailable calcium. I really don't think it will be too long before the same will start to happen in animal farming. However it may take longer to become socially acceptable.

Maybe one of the problems with breeding for success in farming is the animals have already been optimised in most ways? Perhaps there isn't much that can be done? I could be completely wrong though I know nothing about it!

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Originally Posted by templelane

I don't think that it is an extreme concept it is merely the old nature vs nurture debate. I still think that a small genetic change could still vastly improve your product (the cow). For instance supposing one cow had a gentic mutation which meant it could process rougage with increased effiency- for expample an extra efficient enzyme.

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I'm not sure I understand what you mean by "a genetic mutation...an extra efficient enzyme". Do you mean that this cow's genome includes a whole new gene (which other cows don't have) that is coded to produce this better-than-average enzyme? Or did this cow's regulator genes that already direct the production of the ordinarily-efficient enzyme somehow figure out how to build a slightly better version by using the same genes in a slightly different order or duration because she had nothing to eat but low-energy forage and therefore needed to squeeze more energy out of every pound?

If the latter, and this cow's regulator genes were able to improve on the standard enzyme production process, but her herd-mates' regulator genes weren't so creative, is she truly superior to them genetically? Almost certainly, a cow that has (and maintains) such an advantage throughout her productive life will have more offspring than her less-fortunate herd mates. But are her offspring more likely than theirs to have the ability to make the better enzyme, or does the search for an improved version begin anew with every generation (under the same low-energy dietary regime)?

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Originally Posted by templelane

I think that is more likely to happen with direct genetic intervention.

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If it's a matter of inserting a new gene or gene part, I imagine you're right. If it's an adaptive variation on the use of existing genes, I'm not so sure.

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Originally Posted by templelane

This is happing more in agriculture, cold resistant tomatoes being a famous example. Also 'functional foods' are a hot area of research, american scientist have just produced a carrot which has high levels of bioavailable calcium. I really don't think it will be too long before the same will start to happen in animal farming. However it may take longer to become socially acceptable.

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How much more complex is the structure and operation of animal (mammalian, specifically) genomes compared to plant genomes? Is animal life fundamentally more "plastic" than plant life, or are the differences relatively minor in terms of genetic processes?

This idea of plasticity leads me to wonder if it's really a good idea to go inserting genes into a genome that's as highly plastic as most mammals seem to be. It seems like the results could be quite unpredictable.

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Originally Posted by templelane

Maybe one of the problems with breeding for success in farming is the animals have already been optimised in most ways? Perhaps there isn't much that can be done? I could be completely wrong though I know nothing about it!

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The mainstream breeders, and to a lesser extent commercial producers, may have come close to optimizing the cattle population for an economic environment of cheap fossil fuels combined with government policies that keep high-energy starchy feed (corn) cheap. To the extent that this environment changes, these cattle will definitely be sub-optimal.

What I wonder is whether this adaptation involves fundamental changes to the genome, or whether it mostly involves changes in the use and expression of the (relatively stable) genome as appropriate under conditions of nutritional surplus.

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I'm not sure I understand what you mean by "a genetic mutation...an extra efficient enzyme". Do you mean that this cow's genome includes a whole new gene

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No just a slight alteration of an existing gene which provides the cow a competitive edge. The mutation would be random but if it gave the cow a competitive advantage it could be selected for. You would be surprised how even a small change in a proteins coding sequence can cause a dramatic effect. As the effect is in the protein's genome it will be inherited.

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How much more complex is the structure and operation of animal (mammalian, specifically) genomes compared to plant genomes? Is animal life fundamentally more "plastic" than plant life, or are the differences relatively minor in terms of genetic processes?

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The size of the genome tends to be really large in plants. However they can be easier to manipulate genetically but just because of technical reasons. It's not that hard to manipulate animal genomes, mice are a favourite lab play thing- they have been genetically manipulated loads- knocking out genes, putting genes in, changing genes slightly, putting other organisms genes in etc.
Most agricultural animals either have had their genomes sequenced or it is on it's way. It has just been legalised in the US to sell cloned and genetical manipulated animal meat and products.

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It seems like the results could be quite unpredictable.

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Not as much as you'd think if you know what you are doing. We are nowhere near knowing everything but the cell isn't the huge black box it once was.

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What I wonder is whether this adaptation involves fundamental changes to the genome, or whether it mostly involves changes in the use and expression of the (relatively stable) genome as appropriate under conditions of nutritional surplus.

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What it sounds like in your business is it is hard to tell if an improvement is a true adaptation caused by genetic mutation or just a temporary response to the environment. In this respect I think you are right that not giving the creatures an ideal environment to discover which animal is actually the genetically fitter.

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Originally Posted by templelane

No just a slight alteration of an existing gene which provides the cow a competitive edge. The mutation would be random but if it gave the cow a competitive advantage it could be selected for. You would be surprised how even a small change in a proteins coding sequence can cause a dramatic effect. As the effect is in the protein's genome it will be inherited.

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I've taken quite a bit of statistics, including stochastic processes, and I know what "random" means in that context, but what does it mean in reference to changes in the genome? Does it mean that the a priori probability of some kind of change is the same for every base pair in the DNA sequence? Is the probability that a "random" change in the genome will be advantageous to the organism equal to the probability that it will be detrimental, or are "bad" random changes more likely than "good" ones (which is what I would expect)?

In terms of the example you gave of a "better enzyme", I find it much more plausible to expect that such an outcome would be the result of variations in the cow's use of the existing genome rather than a result of a random change at an arbitrary position on the genome. Am I wrong to think that?

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Originally Posted by templelane

The size of the genome tends to be really large in plants. However they can be easier to manipulate genetically but just because of technical reasons.

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Any ideas why plant genomes are "larger" (meaning longer chains of base pairs?) than animal genomes? Is the proportion of regulator genes to protein-making genes lower in plants? Are plants less "plastic" than animals?

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Originally Posted by templelane

Not as much as you'd think if you know what you are doing. We are nowhere near knowing everything but the cell isn't the huge black box it once was.

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That's good, I guess, but for some reason I don't feel very reassured. It seems that most if not all major technological advances that have been adopted and applied widely have usually involved some spectacular failures and bad outcomes due to thinking we know more than we actually do, and I doubt that genetic engineering will be any different.

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Originally Posted by templelane

What it sounds like in your business is it is hard to tell if an improvement is a true adaption caused by genetic mutation or just a temporary response to the environment.

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I'm having trouble with the phrase "a true adaption caused by genetic mutation". I thought genetic mutations were random, not an "adaptation". To me the term adaptation implies some kind of responsive change by the organism (either behavioral or via genetic plasticity) that makes it more successful in a given environment. Am I missing something?

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Originally Posted by templelane

In this respect I think you are right that not giving the creatures an ideal environment to discover which animal is actually the genetically fitter.

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Well, see, that's what I don't quite get. If we apply selection pressure and some individuals adapt better than others, is it really proper to conclude that they are genetically superior, or may it just be that they are more adept (or luckier) at finding a novel way to use the existing genome to achieve a better outcome? Is it maybe fair to say that such adaptations are also "genetic" in the sense that the regulator genes work better, are more creative, or whatever? Something I've read recently seemed to suggest that the probability of realizing a mutation (a permanent, reproducible molecular change) at a particular site on the genome was higher if that site was more "actively used" or some such notion. Have you encountered such an idea? I'm not sure I could find it again.

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Originally Posted by asking

I know a fair amount about why fire suppression is bad. (I live in a tinder box canyon, among other things.) But why is total suppression of grazing bad?

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Both fire and grazing alter the terms of competition for sunlight, water, and soil nutrients between various plant species. Fire knocks back woody invaders, and grazing alters the balance between grasses, legumes, broadleaf plants and other forbs. Grazing without fire leads to encroachment of trees and shrubs. Fire without grazing leads to terminal mixtures that are less diverse, less productive, and less dynamic than intermittently grazed ranges. In addition to forage consumed by grazers, hoof action and trampling speeds up decomposition and nutrient recycling, especially in arid environments.

I said earlier that removing either fire or grazing leads to a system that is not "natural", but I suppose that overstates the case somewhat. I guess "nature" doesn't really care what the shaping and limiting forces are that play across the landscape, she'll adapt and change in some way in response to whatever happens.

What I really meant to say was something less general than that, which is just that the ecosystem that flourished on the semi-arid high plains of the American West at the time of Lewis and Clark was incredibly diverse and productive, and it got that way as a result of thousands of years of continuous interplay between the forces of large herds of grazing animals (not just ruminants--insects remove more herbage in many situations) fire, flood and drought. I think it's accurate to say that everything we've done since that time has reduced the aggregate energy capture and biological productivity of that system.

Sorry for the late reply I had a fall out with my competer over how often is an acceptle level of crashing, freezing, hanging and just generally being a little $%^&!

This wiki article on genetic mutations should answer a lot of your questions about what random means on this context, how mutations occur and what effect good, bad or indifferent they may have. Mutation - Wikipedia, the free encyclopedia It's more concise that I would probably be!
I don't know why plant genomes are larger. I'm not much of a plant geneticist so I don't know what the current theories explaining this phenomenon are. I do know that genome size has no relation to organism complexity – this is known as the C value enigma.
I've realised we are both using two different meanings if the term adaptation. You are using the physiologist definition whist I am using the genetic one. In genetics what you are talking about is called acclimatisation- the organism gets better at living in its environment by a series of physiological changes. Adaptation is when a genetic change allows the organism to live in its environment easier.

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Something I've read recently seemed to suggest that the probability of realizing a mutation (a permanent, reproducible molecular change) at a particular site on the genome was higher if that site was more "actively used" or some such notion. Have you encountered such an idea? I'm not sure I could find it again.

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I think I have but I can't remember everything about this so I'm going to go an ddo some more reading if I get time and come back to you on that! Perhaps asking might know..

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Originally Posted by ordinaryguy

Something I've read recently seemed to suggest that the probability of realizing a mutation (a permanent, reproducible molecular change) at a particular site on the genome was higher if that site was more "actively used" or some such notion. Have you encountered such an idea? I'm not sure I could find it again.

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I think "actively used" in this context refers to RNA transcription. High rates of transcription are associated with increased mutation rates in yeast and the phenomenon was termed “transcription-associated mutation (TAM)” in yeast [url=http://mcb.asm.org/cgi/content/abstract/24/11/4801]. It has also been described in bacteria. I have seen it written that “transcription is well known to be mutagenic to the gene being transcribed”, but I think it is more complicated in multicellular organisms where there are both germ cells & somatic cells.

templelane--
Thanks for the Wiki link about mutation. I spent several hours going from topic to topic, and down various side alleys of terminology and background. Had to stop to let it soak in awhile. I have so little background in genetics and biology that I spend a lot of time just figuring out what the words mean, before I can understand the ideas.

About randomness: Statisticians mean one thing, physicists mean another thing, biologists seem to mean something else again. The meaning also seems to vary depending whether we're talking about a sequential process in time, or a distribution of positions in space. The key concept seems to be a lack of "pattern", or to be more exact, if there IS a pattern, WE are unable to discern it.

It has always bothered me a little bit that such a fundamental concept would have to be defined on the basis of what it isn't--predictable, ordered, patterned--rather than in terms of what it is. If you are only able to make one observation, of a process or system, is there any way to tell whether what you observe is a "random" event or state? I don't see how, unless you already know how the system "works", i.e. what "pattern" is inherent in its structure and function.

Here's an interesting piece about mutations.

The Wild Side - Olivia Judson - Evolution - Opinion - New York Times Blog

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Mutations that alter proteins have been linked to specific changes in a huge number of traits in organisms from bacteria to humans. Yet the proportion of a genome that contains the instructions to make proteins is tiny; in humans, it may be less than 2 percent. So there’s a lot of other DNA that will experience mutations. The question is, what might such mutations do?

Here’s one possibility. We know that some of that 98 percent is involved not in making proteins, but in regulating where and when the genes they are made from will get switched on. The biology of this gets pretty complicated — but what it amounts to is that most genes have an elaborate control region — a set of on/off switches officially known as cis-regulatory elements. When the right switches are on, the protein gets made; when they are off, it doesn’t. So mutations to the switches can alter how the protein is deployed. Then, the protein stays the same shape as it was before, but instead of being made in, say, just the liver, it starts being made somewhere else as well.

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I’m betting that a substantial number of traits do evolve through this type of mutation. Altering the way a gene is turned on or off has the advantage of leaving the protein itself unaffected. Since many changes to a protein are deleterious — they interfere with the protein’s ability to do its job — it may sometimes be the case that tweaking how and where a protein is used results in less disruption to the organism. Moreover, with so little DNA given over to making proteins, and with long stretches of DNA given over to regulating them, it seems likely that mutations often happen in the regulatory regions, and that sometimes they will be naturally selected.

Another reason for my bet is that while the number of genes that different animals have does not vary nearly as widely as everyone expected, and does not seem to correlate closely with how complex organisms are, the complexity of gene regulation differs greatly from one group to the next. This allows the same basic set of proteins to be used in ever more elaborate ways.

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