[asking]

Ordinaryguy asked:

I would like to hear your take on how the rapid increase in understanding of genetics and developmental biology is influencing evolutionary theory

[asking]

I think it's been wonderful for evolutionary biology. To my mind, the fusion between evolutionary biology, developmental biology (evo devo) and now ecology (eco devo) has produced new ways of understanding evolution that are on an intellectual scale comparable to the New Synthesis of the 1930s (which combined what was known about evolution with the new field of genetics). Got to go now. But will come back and see if ordinaryguy posted.

[ordinaryguy]

Yes, tell me more.

I read something not long ago where biologists were asked what they thought the most exciting and significant advances were in genetics in the last five years. I may not get it quite right, since I'm working from memory, but what I took away was the idea that it used to be thought that a particular gene was just a pattern for making a particular protein, or at most a set of a very few very similar proteins. But what's new is the realization that a sizeable minority--20-some percent maybe?--of the DNA strand actually functions to regulate the sequence and timing of the (more numerous) protein-making genes, and that's where the real action is.

For example, the difference between a wing and a front leg isn't a whole bunch of different genes, it's just a relatively few, relatively straightforward differences in the way the same genes are activated and regulated during embryonic development. This would seem to make adaptation and evolution a much "easier" process than previously thought.

Am I close at all?

[templelane]

Ordinaryguy you are spot on!
The difference between us and say chimps is not the genes but the timing. The interactions in a cell are all relays of signals carried by proteins in a sort of tag team of on/off signals. Proteins are coded by genes and the expression of genes is controlled by proteins.

The interesting parts of cells and what makes creatures different is the order the genes are transcribed and translated (made) into proteins and then for how long.

Some genes are controlled by the protein they express- the expressed protein can act in a feedback loop suppressing expression when levels are high enough. Other genes can be expressed when a metabolite or substrate for the gene's protein reaches a critical level.

This a very interesting area of science (of course I would say that being a biochemist) I'll be back later and find some cool examples.

[templelane]

In the second pargraph I think you are referring to Hox genes- the genes which control the order of what is express and therefore what grows where

"The key determining factors are (1) concentration ; (2) location ; (3) timing ; and (4) target gene specificity [of the hox gene's products]." Hox genes descovery in fruit flys

Hox genes were descovered in fruit flys (fast breeding, short lived, you can do what yuou like to them= excellent for genetic studies) from examining natural mutant that have legs in the place of antenna - Antennapedia

You can replace fly Hox genes with human Hox genes and still have a normal fly they are that conserved. Obviously you're not allowed to do the experiement the other way round...

If you actually want an easy read on this subject Matt Ridley has written an excellent book called Genome which I would recommend. It is 'pop science' so it is written ina scholarly yet not academic way- it assumes you are smart but you don't have to know any backgroud to understand it. It is also quiet humerous- well if you are geeky like me anyway...
The Great Debate Contributors: Matt Ridley
His book the Red Queen deals with the original posted question.

My own opinion on the original question is evolutionary theory has ben proven time and time again by increased understanding of genetics and developmental biology. You only have to compare foetus of animals to 'see' evolution. I have attatched a pic- I will only give out the link if I have to as the site it is off will probably send this discussion way off!

You can also map evolution in our mitochondrian DNA and trace back common ancestors- it can even be used as a molecular clock to determine when something changed.

Recently we have seen evolution in our very own DNA against the AIDs virus as we are fighting an arms race against it- in areas of high infection rates people are increasing the copies of a protective gene. Interestingly chimps who carry but are mostly immune to AIDs have multiply copies of this gene already- it seems we need to get to their level in order to be protected as well. This evolution is happening in front of our eyes!
These are the receptors I am referring to - they are involved in the immune system Sorry it's a journal :o

There are tons of examples where evolution has been traced via genes or actively watched. I think this is much more interesting than the old is evolution real question! :D

[asking]

Yes. You are both right, absolutely. Sorry I was slow to get back. One of my kids has finals and needed some organizing and tutoring yesterday...

But absolutely, I agree with both of you. The human genome project revealed that there are far fewer genes than most people expected (and also that a huge fraction of them are regulatory). Lots of consequences to this paucity of genes. One is that we don't have MORE genes/more complexity than "less complex" organisms.

Another consequence is that there isn't necessarily a gene for each protein that we make, or two or three genes if we need more of that same protein. When a protein is express (childhood, adulthood, 7 am or 5 pm), where its expressed (brain cells, skin cells, heart cells), and how much of each protein are virtually all controlled by regulatory genes or molecules.

Also, cells can often make more than one protein from the same gene, by cutting and splicing in different places. (Just as you could take a sentence and use the words in it to make one or more other sentences, by leaving out different words each time.) And a given gene can influence not just one trait but ten or 100. So the "gene for a growth factor" might influence cell division, hair length, longevity, and skin color--AND it might affect all these things differently under different circumstances. So the same gene might cause you to have really long hair if you were exposed to lots of light or eating a certain nutrient or no hair in a different environment.

I'm making up this example, unfortunately. But the idea is right. In fact, there is a case of a researcher creating a mouse that lacked an important gene for a growth factor. That's a gene "knockout." They thought the mice lacking the gene would probably all die. Instead the mice ended up with really long hair, down to their little paws.

Another example of how genes operate: small amounts of a hormone can cause bone cells to accelerate bone growth, while large amounts of the same hormone can cause bone loss (by changing gene expression in bone cells). In other words, hormones and other signaling molecules are rheostatic, and not necessarily linearly either.

Lastly, and this is the area that I think is most cool, the regulation doesn't just take place during early development (in embryos). It goes on throughout the life of the organism. There are species of fish that in one social situation are female, but if the dominant male is eaten or otherwise disappears, one adult female will respond by turning into a male within about 4 days! This is not an isolated example of major changes occurring in response to social or other environmental changes. It's common, although obviously a natural sex change is a cool example.

Even in humans, gene regulation changes according to our behavior and our environment. So, in a sense, you can think of the genes as less like a blueprint (which is a poor analogy) and more like a keyboard, like you are typing at now. And it's the enviromnent that is typing, inputting information to the genes in each cell by way of communication molecules such as hormones, pheromones, paracrine signals, prostaglandins, and neurotransmitters. We think of most of these signalling molecules as operating inside the body, but ultimately they are influenced by things that occur outside the body or in response to the body's two-way interactions with the outside world, what you eat, who you talk to (and what they say to you!), who your relatives are, and how they behave towards you. And so on.

It used to be thought that the bones were like steel girders, strong and immutable, but not only do they heal when they break, but they change shape in response to different uses. So if you take up badminton at age 45, the exercise will reshape your muscles and exert forces on the bones in your arms that subtley reshape and strengthen different parts of your bones. The same thing happens to the brain. It can reshape itself in response to changes in use.

One thing this means is that when researchers find "differences in brain structure" between two group of people, you don't know if it's caused by genetic differences or by differences that developed in the womb in response to differences in exposure to hormones, stress, and nutrition, or by differences that developed during childhood (in response to same), or by differences that developed last year... To say that differences are "biological" means only that you can see the difference. And, thanks to more and more powerful imaging technology for looking at the brain, we can see more and more differences.

I read about some researchers who were using MRI studies of the brain to look for differences in brain structure between "good" mothers and "bad" mothers, so they could (eventually) decide whose kids should be allowed to stay with their mothers and whose should be taken away and put in foster care, based on an MRI. I found this really creepy... especially knowing that brain structure can change in adults. But many medical researchers and psychologists still live in the past, when everyone assumed that "biological" differences meant innate, genetic, and immutable. I think the interface between environment and gene expression is probably THE hottest area of research in biology right now.
End of soapbox.
Good morning! I just have my coffee...
Asking

[asking]

I think this is much more interesting than the old is evolution real question! :D

Me, too! Thanks for all this interesting stuff!

I really should get Ridley's book, haven't read any of his books...

[templelane]

Genetic and protein interactions, signalling and regulation really is 'where it's at' it's a shame it takes quiet a bit of wading through a dry subject to get to it. I'm finding that genetics has become more of a tool for working out systems than the actual 'science' these days. Cloning has become so routine we have a service for it, although when the grant money runs out we have to do it ourselves :(.

I really like how you mentioned how one gene can control many phenotypes- it is something many people don't realise they think of genes as being very gene X makes me tall, gene Y makes me blonde. We are very beautiful systems.

Ridley's great- it was his books that got me into biochemistry.

[ordinaryguy]

This is SO COOL. Thank you both for responding in such careful and thoughtful detail. I have a more than passing interest in the subject, since I raise beef cattle breeding stock for a living, and the interaction between husbandry practices and genetic potential is, I believe, a hugely important and widely misunderstood subject.

But many medical researchers and psychologists still live in the past, when everyone assumed that "biological" differences meant innate, genetic, and immutable.

Likewise for many animal scientists, unfortunately.

I'll give you an example. For at least the last 30 years cattle breeders have been selecting for growth, and closely related factors such as milk production. As a result, cattle have been getting larger and larger and raising bigger and bigger calves. That's fine, except that they forgot that growth and reproduction are fairly antagonistic traits, so now the industry is trapped in this spiral of having to supply more and more expensive feed just to get these big, heavy milking cows to breed on time. A cow that doesn't breed back is a financial failure, no matter how big her last calf was.

Also, the common practice is to raise young breeding stock with access to as much high-energy feed as they can possibly eat, thinking that this is how to tell which individuals have the most "genetic potential" for growth. But all it REALLY tells you is which ones grow fastest under conditions of no nutritional stress at all. Guess what happens to these pampered and overfed young animals when they are kicked out in a range or pasture situation where either the quality or quantity of forage resources is limited, as it certainly will be in some years, and at some times of every year. That's right, too often they fall apart because they never had to develop the ability to adapt to nutritional stress, even though cattle and most other ruminants are admirably equipped and quite capable of doing exactly that.

As I see it, the new realization that the genome and the environment are involved in a lifelong interactive dance is very good news, because it means that fixing our past breeding mistakes will be easier. All we have to do is apply the right kind of selection pressure and husbandry practices to reactivate the latent ability to adapt to real-world, i.e. economically realistic, conditions. Only a tiny minority of breeders has grasped this so far, but I'm absolutely convinced that it's the wave of the future.

Thanks again for the great discussion. Keep it coming.

[asking]

You only have to compare foetus of animals to 'see' evolution. I have attatched a pic- I will only give out the link if I have to as the site it is off will probably send this discussion way off!

Aaagh!

Hi Templelane, I didn't actually see the picture you posted the first time. I just saw it and wanted to tell you that this particular image has been debunked. I think it comes from Haeckel. I assume this is either the original from the 19th century, or a redrawing. Anyway, it turns out to be inaccurate--although I don't know in what specific ways. Only that it supposedly exaggerates similarities among embryos.

Creationists have made hay with this 150-year-old error. It IS true that there are correlations among different kinds of vertebrate embryos. For example, all you have to do is look at the photo of the dolphin embryo in wikipedia's article on dolphins to see how much more similar early embryos are to one another than the corresponding adults are. I.e. the dolphin embryo looks like a human embryo. Mouse embryos look like human embryos.

BUT it's also not true that "ontogeny recapitulates phylogeny" exactly. People tend to go all one way or the other with this, when the truth is somewhere in between. But those of faith get pretty worked up over this supposed attempt to deceive people So I wanted to warn you that that image in not quite right. Better to stick with photos of embryos. Mammal embryos are of course even more similar to one another than if you go to birds or (other) reptiles.
Best,
Asking

[templelane]

Sorry I was being lazy and used the picture I could find- I've seen the actual (pickled) embryos of different species. My bad! I do have to be more careful, I know exctly what you mean you can get something slightly wrong and people will hold it against you for years. Did you watch the programme on the development of the dog, dolphin and elephant embyos? It was in the UK so you might not have seen it, it was very cool though. They used ultrasound to reconstruct CGI picture if I remember correctly.

[asking]

Sorry I was being lazy and used the picture I could find- I've seen the actual (pickled) embryos of different species. My bad! I do have to be more careful, I know exctly what you mean you can get something slightly wrong and people will hold it against you for years. Did you watch the programme on the developement of the dog, dolphin and elephant embyos? It was in the UK so you might not have seen it, it was very cool though. They used ultrasound to reconstruct CGI picture if I remember correctly.

Not your bad. It's a lovely image. But I just wanted to warn you so wouldn't draw fire for a relatively trivial reason. I have not seen the dog, dolphin, elephant embryos. I would love to see them. I worked in an embryology lab for a couple of years and became really enamored of development...

[asking]

OG, Your account of what's happening in the cattle breeding industry is fascinating and your analysis makes perfect sense to me. I’m a bit diffident about even offering an opinion, since you are the expert, but I see what you mean about there being two different approaches to solving the problem, the genetic and the developmental. I agree it's totally solvable.

I guess in terms of applying selective pressure, my first question would be how much genetic variation is left? Are the animals highly inbred? Or is there still a lot of heterogeneity left? If more, that’s great. If less, you might find it harder to select for the kind of robustness you want unless you outbreed. Or is out-breeding acceptable? I don’t know what kinds of constraints you are operating under.

As for phenotypic plasticity—the ability of the animal to develop depending on conditions—that’s something you could work with immediately if they are capable of a plastic response. Or at least look for it. Is there any sign of that? Do some cattle do much better than others? I am assuming you would be looking for husbandry techniques, for both the mothers and the calves, that would produce adults better able to live on lower-quality feed. Is that right?

As for your not knowing much, you have totally misrepresented yourself... as I suspected. You might recall that when Darwin was trying to figure out how selection could work to produce evolution, it was to animal breeders that he turned for information and ideas. They educated him.

[ordinaryguy]

I guess in terms of applying selective pressure, my first question would be how much genetic variation is left? Are the animals highly inbred? Or is there still a lot of heterogeneity left? If more, that’s great. If less, you might find it harder to select for the kind of robustness you want unless you outbreed. Or is out-breeding acceptable? I don’t know what kinds of constraints you are operating under.

Generally speaking there is a lot of genetic heterogeneity in cattle, some people would say too much. In the commercial segment of the industry, there has been a lot of crossbreeding, but the seedstock segment is still pretty much built around established breeds. There are a few seedstock producers who develop "composite" cattle for breeding purposes, which is what we're doing, but it's very much a niche market. Our cattle are a four-breed composite--Hereford x Barzona x Senepol x Red Angus. Our primary selection focus is on fertility, longevity, and low maintenance costs.

What I'm coming to realize is that better outcomes depend at least as much on how animals are raised and fed, especially when they're young, as on their genetic endowment. What I'm not sure about is how much has been truly lost by the several generations of excessive selection for growth under conditions of nutritional surplus. Hopefully, many of these capabilities are still there, latent, waiting for the right kind of husbandry and selection to reveal which individuals still have it and which don't.

]As for phenotypic plasticity—the ability of the animal to develop depending on conditions—that’s something you could work with immediately if they are capable of a plastic response. Or at least look for it. Is there any sign of that? Do some cattle do much better than others? I am assuming you would be looking for husbandry techniques, for both the mothers and the calves, that would produce adults better able to live on lower-quality feed. Is that right?

Yes, that's exactly right. And the only way to find out who can do it and who can't is to raise them under conditions that challenge them a little instead of giving them everything they can possibly want every day of their lives. I'm not talking about starvation, of course, but I am talking about applying enough selection pressure to reveal differences in adaptability and efficiency.

The urge that has to be resisted is to make their lives so easy that everyone succeeds. Perversely, this urge is strongest in the seedstock business where each animal tends to be worth a lot more money than in commercial herds, so it's more costly to let them fail. Yet commercial producers simply can't afford to feed their cattle that much high-cost feed. They have to get by on low-cost, sometimes low-quality, and often limited quantity of forages. So there's a real mismatch between the way most seedstock producers raise their cattle and the way their customers (commercial producers) are financially obliged to raise theirs. Given this mismatch, it should surprise no one that many of these fancy registered cattle fail miserably under commercial conditions.

As for your not knowing much, you have totally misrepresented yourself...as I suspected. You might recall that when Darwin was trying to figure out how selection could work to produce evolution, it was to animal breeders that he turned for information and ideas. They educated him.

Well, I'm learning. My formal education is in economics, not genetics, so I'm definitely playing catch-up there.

[asking]

My formal education is in economics, not genetics, so I'm definitely playing catch-up there.

Economics and ecology use many of the same concepts, just different language and culture, so it should be a comparatively short learning curve. The currency in ecology is (of course) energy. It's not for nothing they both start with "eco"...

[ordinaryguy]

Economics and ecology use many of the same concepts, just different language and culture, so it should be a comparatively short learning curve. The currency in ecology is (of course) energy. It's not for nothing they both start with "eco"...

Yes, there is a lot of really interesting research and innovation going on in rangeland ecology these days. In the past, too many "environmentalists" had a shallow and dangerously naïve view of semi-desert rangeland ecosystems. They saw most problems as the result of "overgrazing" and their solution was to remove all grazing animals. Much like foresters who advocated total fire suppression. The point they missed is that both grazing and fire were and are and must remain critical formative processes in that ecosystem. If you completely remove either or both of them, what you get is not in any sense of the word, "natural".

The key ingredient that makes both fire and grazing constructive and health-promoting processes is that they happen intermittently. The alternation between relatively brief episodes of radical disturbance, followed by relatively long periods of rest and recovery is the fundamental rhythm that promotes diversity, vitality, and resilience in these ecosystems. While there is no doubt at all that continuous grazing is harmful to ecosystem health, it is equally certain that continuous fire suppression or total cessation of grazing is just as harmful, and for the same reason.

The link to animal husbandry and genetic selection seems clear to me. EVERY biological system--from a cell, to an organ, to an organism, to a herd, to an ecosystem--NEEDS alternation between times of ease and plenty and times of stress and shortage to keep the adaptive capabilities sharp and functioning. An industrial model that seeks to reduce all variation, prevent all stress, and provide ideal conditions at all times is simply not the right tool for the job. It's a great model for manufacturing interchangeable machine parts, but not for producing healthy herds or healthy ecosystems.

OK, now I need to get off my soapbox. Great discussion. Keep it going.

[asking]

The key ingredient that makes both fire and grazing constructive and health-promoting processes is that they happen intermittently. The alternation between relatively brief episodes of radical disturbance, followed by relatively long periods of rest and recovery is the fundamental rhythm that promotes diversity, vitality, and resilience in these ecosystems.

This reminds me of an ecological concept that I learned in college--which is "patchiness" in both space and time. In those days, patchy environments were associated with lots of diversity and a fair amount of ecosystem stability, but I don't think they completely understood why patchiness was good. Nowadays, the view is that --if you view an area as having good habitat and marginal habitat--populations can live in both during good times. The good habitat is operating as "sources" and the marginal habitat as "sinks." When populations in the sinks go extinct, they can be repopulated by individuals from the sources. You can make this idea more sophisticated by considering that what's a source in this 1000 year period my turn out to be a sink in another. So you can think of patchiness or environmental heterogeneity as happening in both time and space.

Just the other day, I was reading about the ecology of diet (in a book) and the writer was arguing that actual selection pressure occurs not in the sources, where organisms reproduce with little adversity, but in the sinks, where, of course, conditions are harsh and not everyone survives. The result is that over time the population becomes increasingly adapted to the marginal habitat. I'm still struggling with these ideas, so it's probably not very clear... But I think it relates to what you are talking about.

One example, I read somewhere else, was that gorillas mostly eat fruit, but they are adapted to eating bamboo and other plants (tough, fibrous shoots and leaves) because that's what they have to eat when they can't get fruit. Fruit doesn't require specialized adaptations particularly because it's relatively easy to process and high in calories and nutrients. But even though gorillas are restricted to bamboo and other grasses and leaves at only a limited number of days per year, THAT's where the selection pressure comes from. So their adaptations to eating bamboo don't interfere with their ability to eat fruit when it's available. That seems like a good model for you to consider.

Anyway, to get back to sinks and sources, intermittent grazing is a kind of sink in time (from the perspective of the forage/grass), where adapation to grazing takes place. It also of course changes the vegetation, preventing succession, which is good for grazers. Allowing the forage to recover is an obvious good for the grazers. And I suppose there must be 10 other things I haven't thought of...

Total cessation of grazing is just as harmful, and for the same reason.

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? I don't doubt it, but I'm interested in hearing your (10) reasons.

And I haven't forgotten that we were talking about what some might view as Lamarckism, possibly even Lamarck might think so...

ASIDE: Also, after reading one of your posts, it crossed my mind that some might consider this discussion as sounding like Lysenkoism, and might therefore dismiss it. Do you know Lysenko (1898-1976)? He believed, for example, that Soviet wheat could be made to grow in cold Siberia just by stressing it. He didn't believe in genetics at all and he and his political mentor Stalin basically killed off an entire generation of Soviet geneticists, including some very good ones (not to mention some excellent strains of wheat!). So in the west, biologists have a very strong reaction against any hint of his ideas. It's more than a reaction to a bad idea... Good to avoid sounding like Lysenko. He was also wrong.

The link to animal husbandry and genetic selection seems clear to me. EVERY biological system--from a cell, to an organ, to an organism, to a herd, to an ecosystem--NEEDS alternation between times of ease and plenty and times of stress and shortage to keep the adaptive capabilities sharp and functioning.

If you have a particular environment that you want a population to be adapted TO, I guess that would be true. But I tend to view the environment as constantly changing in time and space and at different levels of scale. So in Time, you see changes from hour to hour, over days, and seasons, but also over periods of thousands or tens of thousands etc, millions of years. Same for geographic patchiness--this creek bed, vs that hill top, this Mississippi Valley drainage vs that Continental Divide. And then time and space can interact with one another, too. In that view, alternation between times of ease and plenty and harsh selection just IS, it's not something that organisms "need." Selection is an inevitable consequence of the tendency of organisms to breed beyond the carrying capacity of ANY environment. (No exceptions.)

But if you want something very specific--cattle adapted to a particular habitat--then I suppose that argument would make sense. So I guess that in ecological terms, your business would be considered a source and your customers would be sinks, where the actual selection occurs. The problem is that no cattle are coming back to you carrying the right genes for surviving in the marginal sink habitat. I'm probably not helping... Sorry. But it's interesting to think about.

I asked earlier if you see any sign of a plastic response in your animals and I'm not sure I understood your answer. Have you actually tried raising calves on some proportion of lower quality food to see if they can grow up to be able to digest lower quality food than calves raised on "the best" food? I know that'd be an expensive experiment. Really, your customers are doing the experiment for you. It seems like that's where you'd find your answers, by talking to them...

Because, there's no way to know in advance if it's possible to raise the same cattle (genotypically) to do better on worse food. Also, you can't know Which intervention would produce that hypothetical result. Would it be feeding worse food to mothers and calves? Or would it be something completely unexpected, like a cortisol spike on a certain day of development? This isn't something that's necessarily going to be intuitively obvious (although you might get lucky).

Ok. Off MY soapbox...

[ordinaryguy]

This is getting really good, because it's making me think, and read, and question some things that I thought I understood. I love it.

I checked out Ridley and some of his reviewers. Here's an interview Edge: A TALK WITH MATT RIDLEY that might interest you if you haven't already seen it. He's plugging his new book Nature Via Nurture: Genes, Experience, and What Makes Us Human. Have you read it?

The most interesting thing I've found googling around the web is K.Kull - Outlines for a post-Darwinian biology. I'm only about halfway through it, and finding it pretty tough slogging in places since I'm not that familiar with some of the terms, and mostly ignorant of the history, but it's fascinating. I'd be most interested in your take on it. Here's a little sample to whet your appetite:

Evolution as led by organism's search

New evolutionary findings could be rapid since these are primarily a result of the functioning of organisms, a new or changed way of using the ROM [the genome] by organisms. Corresponding genetic changes could be treated as after-effects of the morphological and behavioural change.

Rapid morphological changes in speciation, as described by punctualists, and gradual genetic changes, as described by molecular evolutionists, are thus found to be in correspondence, since the latter follow the former.

In the existing models of Darwinian theory of evolution (synthetic theory of evolution), the organism is not considered to have a multi-level structure with independent activity and a possibility to use its genome in various ways. Assuming the organisms to have activity, we find the autogenetic theory of evolution work. Darwinian theory of evolution happens to be a special case of the autogenetic theory of evolution, assuming the organism to be very simple and passive.

The main material for evolution is phenotypic variability. If phenotype and genotype are strongly connected (i.e. the phenotypic variability corresponds to the genotypic one), then evolution is Darwinian. If phenotype and genotype are more or less uncoupled due to plasticity, then the directional changes are phenotypic, and genetic variability is of minor importance.

An evolutionary change is like finding of a new melody by a player - the organism. It has a number of ways to keep this melody so long that it could be fixed by the stochastic changes of the genome.

So, asking, your question about plasticity is exactly the right one, I think, and the answer is yes, there is a great deal of plasticity in the way different animals respond to selection pressure.

I asked earlier if you see any sign of a plastic response in your animals and I'm not sure I understood your answer. Have you actually tried raising calves on some proportion of lower quality food to see if they can grow up to be able to digest lower quality food than calves raised on "the best" food? I know that'd be an expensive experiment.

Well, not prohibitively expensive, actually. Of course, what we're doing isn't quite a scientific experiment, since we don't have a "true" control group, but the prevalence of the idea that "nutritional stress is always bad and must be avoided at all costs" among our competitors in the seedstock business does provide a basis for making some comparisons.

For example, we develop our calves on a relatively low-energy diet over their first winter of life (8-12 months of age), during which time they gain only about a pound a day, sometimes less. Common practice is to feed weaned calves for a gain of 2-2.5 lb/day. However, by the time our heifers are exposed to the bull for the first time at 15 months of age, they have been on lush spring grass for at least two months, during which time they typically gain 2.5-3 lb/day. We calve in April and May (which means breed in July and August), which also diverges from the more typical practice of calving in February and March. Under that scenario, when breeding begins in May, they haven't had much time to benefit from the spring flush of forage growth, which in most years doesn't really come until May and June.

Our first-service conception rate is usually between 70% and 80%, whereas for heifers developed on a higher-energy diet 80% to 90% is probably more typical. We feel this is quite acceptable, because our feed cost per pregnancy is probably less than half what it would be for a high-gain scenario. Even more important though, to get that extra 10% bred, we'd have to feed all of them, including the 75% that don't need it, and still wouldn't know which were the less-efficient ones--at least not until they fail to breed back as 3- or 4-year-olds. The basic strategy is to set the bar pretty high at the beginning, believing that those that manage to clear it have a much better chance of being reproductively successful for a long time.

Really, your customers are doing the experiment for you. It seems like that's where you'd find your answers, by talking to them...

Well, not entirely, because we keep all our heifers and give them a chance to breed, and the female progeny (we suppose) have a lot more influence on reproductive success than the male side. Only about a third of the bull calves make it through the selection process and get offered for sale as breeding bulls.

Not that the male side is completely out of the loop when it comes to reproductive success, of course. One reason our customers choose our bulls rather than more conventionally-raised ones is that they think their daughters are more likely to make efficient, fertile cows. Another is that our bulls have more stamina, durability, heat tolerance, libido, and other strengths that make them able to breed more cows in a shorter period.

There are several other things you both have mentioned that I hope to respond to, but haven't had the time yet. Having to do some reading, and actually think about it means it takes longer, but I guess it's worth it. Thanks so much for taking the trouble to do this discussion. I'm finding it exceedingly useful and interesting.

[asking]

granmaboat agrees: Is this from that book? Is this the best book of the LAY or laim person like myself. It sounds so hopeful. How does it relate to alztimers.

Um no. It's just me spouting off. But I know what I'm talking about (sometimes), and I sometimes write books. Maybe I should write one about this? :)

I don't know much about alzheimers. I assume though that if it's not a straight genetic disease (like Huntington's, where you get one gene and you can be almost certain of getting the disease), then environment would affect things like when you get it and how seriously. I keep reading that people who live certain life styles are more or less likely to get alzheimers. That suggests that environment plays a role in alzheimers.

By the way, you will often see magazines and newspapers say something like, this disease (whatever disease) "runs in families, so we know it's genetic." But that's illogical. Just because a parent and child have the same problem doesn't mean it's genetic. Obesity is a good example. It also runs in families because of life style choices. Culture runs in families too, whether religion or eating habits. So knowing that a disease runs in families actually tells you nothing.

Asking

[templelane]

granmaboat can we synthesize this protective gene. or in someway encourage it's development. and whoe's children is it showing up

What you are asking about is gene therapy where a piece of foreign DNA is inserted into cells in order to be expressed. We are a long way away from this currently.

Most research into this area is being done with very simple genetic disorders for example Cystic Fibrosis . It is caused (in most cases) by a single amino acid mutation in an ion channel. Amino acids are the building blocks of proteins like ion channels- you get an important block wrong and it doesn't form properly or behave properly.

If you just have to replace one gene it should be easy. We do it in simple organisms like yeast and e. coli all the time turning them into mini factories to make what we want. However because people are large multicellular creatures it can be very difficult.

The main problems are:
Targeting- how to get the gene into the cell?
Rejection- the body is designed to get rid of foreign DNA most of which comes from viruses.
Overexpression- sometimes you can get over the first two problems and then have too much DNA in the cell, which can cause it to make too much protein.
Retention- sometimes everything goes well but after a few days the DNA just gets degraded or the cells are short lived and die. This seems to be the main problem with CF at the moment.
Cancers and immune responses

Developing gene therapies is a very complex business- I have no doubt that one day it will be used to treat diseases. However due to multiple problems that can happen and the fact patients treated by it at the moment have suffered from vast immune responses, organ failure and death, I think it will be a long time before such treatment is widely available.

Don't despair at the HIV front though there is some brilliant research going into preventing it and minimising its effects.