Landrace/adaptive breeding discussion

[Ridgerunner]

I found (again) most hens lay any of their eggs in a human provided nest box, move to another location for egg laying if enough options are available.

I've seen some hens, not most but some, move to a hidden (feral) nest before they go broody. Not all hens that hide a nest go broody but some do. I generally retrain them to lay in a coop nest when they try to hide one so it's not a perfect test. Some of the hens I retrain to lay in the coop do go broody within a month, I have noticed a correlation, but certainly not all of them do. I'd say most do not.

is it possible to be at the cusp of going broody, but some factor being off, and thus never committing?

I strongly believe that. I've had hens act broody during the day with all the different signs. Spending time on the nest, walk around puffed up and pucking, avoiding the main flock, whatever. Some for a day or two, some for as much as two weeks. Some of these finally commit to being broody, some never do. This is why I never give eggs to a hen until she spends two consecutive nights on the nest. So far that two consecutive night test has worked but since you are dealing with living animals it will probably fail me one day.

RSLs are tricky indeed.

Maybe off topic a bit but maybe not. There are two types of red sex links sold. Some are the commercial egg laying hybrids like the ISA Browns that have been bred to be egg laying machines and to not go broody.

The other type is when you cross a rooster with the gold genetics with a hen with the silver genetics so you can tell sex at hatch by down color. Say a Rhode Island Red or Buff Orpington rooster over a Light Sussex or Delaware hen. These are going to inherit their traits or behaviors on broodiness or anything else from their parents. All red Sex Link has to do with is down color at hatch. Them being a red sex link had nothing to do with egg laying ability or anything else. It depends on what chickens were their parents.

I've never had a male, don't know if they're even sold.

I get my new breeds from hatcheries. One time I wanted a new breed to play with genetics so I got a half dozen. To fill out my order I got 20 Red Sex Link males of the type that had dual purpose parents (Rhode Island Red rooster on a Rhode Island White hen) to butcher. Those grew to a size like Rhode Island Reds, not the size of an ISA Brown.

 

[U_Stormcrow]

OK, don't worry, the thrust of the book is that biology has changed its thinking a lot in the last couple of decades but no-one's really bothered to explain the changes to the general public, so we're all really behind the curve now and need to get up to speed.

There's a lot to take in so let's do it in stages.

So the first point to grasp, and grasp firmly, is that the genome is no longer thought of as a blueprint, or the genes as instructions to build an organism, or proteins as sort of organic machines, or the body working like some sort of organic machine or computer programme. The problem of how genotype (the genes) becomes phenotype (the observable traits) has not really been cracked despite all the work on the human genome project since the 1960s.

The second point is our desire to map things 1 to 1: we want to see 1 allele 1 trait, different allele different trait etc. but it does not fit well with the evidence. Lots of alleles may contribute to a trait, and in very messy ways. Shank colour in chickens' legs springs to mind.

The third point is that the conventional narrative is all about coding proteins, but only 2% of the genome codes proteins. What on earth is the other 98% doing then? It can't all be junk in the evolutionary attic! This was sort of rubbed in when the human genome project discovered that the final tally of protein-coding genes is a little over 20,000; apparently most biologists don't believe that is anything like enough to make a human. Surely there must be more instructions needed to make something as complex as a person?

Then, what is passed on to the next generations is not genes, it's the whole genome. Natural selection works on the organisms that carry the genes, not on the genes directly, and it's the phenotype, not the genotype, that determines fitness. (Indeed, some argue that natural selection works on the group, not even the individual, but let's park that for the time being.)

And a genome can't build a cell. Rather, the cell is a precondition for anything the genome can do (p. 94). An organism won't spontaneously form, so "a genome sequence can never fully specify an organism: how it will grow, how it will look, how it will behave - in short, how it works." (idem) Ball reasserts the role of the cell as a key functional living unit, at least as far as I've got into his book.

A big problem is that the gene is not alive. How something not alive turns into something alive is still a mystery. The gene has been too atomised to actually explain how life works. "Genes do not produce life, but on the contrary depend on it." (p.104)

So how does this impact so far on the mutation that stopped a hen sensing that her clutch was complete so she should stop laying and start incubating, with the result that she didn't go broody and just kept laying till her body was spent? In short, it's probably not 1 mutation in 1 hen; it's lots of mutations in lots of hens, randomly caused in different places and times, some of which have the same effect, albeit by a variety of different routes, with one last little change or other that in combination with what went before was 'the straw that broke the camel's back'. Many people here have hens that never go broody and lay all season long, that are not production hens; I have some, you have some. Commerce took the 'best' of these types and honed them into birds that, with artificial light and food, lay for about a year and are then discarded as waste, because they are unfit for continued commercial production. They did not do rocket science. They just exaggerated traits that nature created.

"Its complicated". Heh.

As a further note, research has pretty conclusively demonstrated that the protein producing segments aren't really "switches", either, with an "on or off" position. They are more like dials, variable rheostats, or the like whose expression ranges from off to cranking out proteins full time, and everywhere in between.

I've read some poultry research on protein expression changing due to dietary and other environmental factors in addition to previously accepted factors like age and stage of ovulation.

Like working a sound board with at least 20,000 sliders constantly in potential motion...

 

[LaurenRitz]

OK, don't worry, the thrust of the book is that biology has changed its thinking a lot in the last couple of decades but no-one's really bothered to explain the changes to the general public, so we're all really behind the curve now and need to get up to speed.

There's a lot to take in so let's do it in stages.

So the first point to grasp, and grasp firmly, is that the genome is no longer thought of as a blueprint, or the genes as instructions to build an organism, or proteins as sort of organic machines, or the body working like some sort of organic machine or computer programme. The problem of how genotype (the genes) becomes phenotype (the observable traits) has not really been cracked despite all the work on the human genome project since the 1960s.

The second point is our desire to map things 1 to 1: we want to see 1 allele 1 trait, different allele different trait etc. but it does not fit well with the evidence. Lots of alleles may contribute to a trait, and in very messy ways. Shank colour in chickens' legs springs to mind.

The third point is that the conventional narrative is all about coding proteins, but only 2% of the genome codes proteins. What on earth is the other 98% doing then? It can't all be junk in the evolutionary attic! This was sort of rubbed in when the human genome project discovered that the final tally of protein-coding genes is a little over 20,000; apparently most biologists don't believe that is anything like enough to make a human. Surely there must be more instructions needed to make something as complex as a person?

Then, what is passed on to the next generations is not genes, it's the whole genome. Natural selection works on the organisms that carry the genes, not on the genes directly, and it's the phenotype, not the genotype, that determines fitness. (Indeed, some argue that natural selection works on the group, not even the individual, but let's park that for the time being.)

And a genome can't build a cell. Rather, the cell is a precondition for anything the genome can do (p. 94). An organism won't spontaneously form, so "a genome sequence can never fully specify an organism: how it will grow, how it will look, how it will behave - in short, how it works." (idem) Ball reasserts the role of the cell as a key functional living unit, at least as far as I've got into his book.

A big problem is that the gene is not alive. How something not alive turns into something alive is still a mystery. The gene has been too atomised to actually explain how life works. "Genes do not produce life, but on the contrary depend on it." (p.104)

So how does this impact so far on the mutation that stopped a hen sensing that her clutch was complete so she should stop laying and start incubating, with the result that she didn't go broody and just kept laying till her body was spent? In short, it's probably not 1 mutation in 1 hen; it's lots of mutations in lots of hens, randomly caused in different places and times, some of which have the same effect, albeit by a variety of different routes, with one last little change or other that in combination with what went before was 'the straw that broke the camel's back'. Many people here have hens that never go broody and lay all season long, that are not production hens; I have some, you have some. Commerce took the 'best' of these types and honed them into birds that, with artificial light and food, lay for about a year and are then discarded as waste, because they are unfit for continued commercial production. They did not do rocket science. They just exaggerated traits that nature created.

I'm not going to go over every point because it would be tldr. Suffice it to say this is what I've been trying to tell people most of my life--junk dna is not a thing!

Problem is that most people have been taught exactly as I was--that even our DNA is top down, centralized, mass produced. I had no idea that the field had changed so much.

I would be curious to know what they're saying about epigenetics. They used to say that was just junk as well. Now they know it holds a sort of short-term racial memory that might or might not create long term effects...

Anyway, what you're saying makes a lot more sense than one random mutation somehow spontaneously spreading to millions of birds. We need a better word than mutation, though. I would be interested to know when he thinks this mass change took place. With the magnetic field of Earth reducing so quickly, the timing of such a major change might be significant.

 

[LaurenRitz]

Basically, the genes are a card catalog to a microfiche library the size of Texas. (Old fashioned analogy, I know, but I don’t think there's a computer corollary that fits)

 

[Perris]

I would be curious to know what they're saying about epigenetics. They used to say that was just junk as well. Now they know it holds a sort of short-term racial memory that might or might not create long term effects...

In a nutshell, "there is no good reason to believe that inherited epigenetic marks on the genome can last for more than a generation or two before they are washed away" [by the mechanisms that clean the gametes as they mature into primordial germ cells for reproduction] p.134.

 

[Perris]

"Its complicated". Heh.

As a further note, research has pretty conclusively demonstrated that the protein producing segments aren't really "switches", either, with an "on or off" position. They are more like dials, variable rheostats, or the like whose expression ranges from off to cranking out proteins full time, and everywhere in between.

I've read some poultry research on protein expression changing due to dietary and other environmental factors in addition to previously accepted factors like age and stage of ovulation.

Like working a sound board with at least 20,000 sliders constantly in potential motion...

yes they are much better analogies than 'switches'.

 

[Perris]

We need a better word than mutation, though. I would be interested to know when he thinks this mass change took place.

yes we do.
I'll let you know as soon as I refind it!

 

[NatJ]

You're talking about probably millions of unrelated birds at the point where they say the mutation occurred. But mutation does not "spread" except to progeny. If a mutation occurred, how did it "infect" birds on the other side of the world to the point that the mutation is in nearly (?) all populations?

This has already been addressed in several better ways, but I can tell how a mutation would spread to millions of chickens all over the world: people deliberately breed it into them.

If there was a single mutation that had major commercial value, I could believe it being bred into all the commercial flocks worldwide in a timespan of about 10 to 20 years.

Chickens reproduce very fast.

Assuming you can get 300 eggs from a hen in one year, hatch 2/3 of them, and have half of those be females, a single hen would produce 100 daughters in a year. The next year her daughters could produce 10,000 daughters, and the year after that there could be one million daughters of them. Another year gives you one hundred million.

A rooster can produce about 10 times that many offspring in a given year, assuming he is mating with about 10 hens who each lay at about that rate. That would give him about 1000 daughters and 1000 sons in one year, and his sons could sire a million sons and a million daughters the next year.

People usually do not want to have chickens multiply that fast, but it would definitely be possible to get a given gene into millions and billions of chickens within just a few years' time, if it was considered important enough (making a big profit is the kind of "important" that would be most likely to motivate the big producers to do it.)

 

[fluffycrow]

I've seen some hens, not most but some, move to a hidden (feral) nest before they go broody. Not all hens that hide a nest go broody but some do. I generally retrain them to lay in a coop nest when they try to hide one so it's not a perfect test. Some of the hens I retrain to lay in the coop do go broody within a month, I have noticed a correlation, but certainly not all of them do. I'd say most do not.


I strongly believe that. I've had hens act broody during the day with all the different signs. Spending time on the nest, walk around puffed up and pucking, avoiding the main flock, whatever. Some for a day or two, some for as much as two weeks. Some of these finally commit to being broody, some never do. This is why I never give eggs to a hen until she spends two consecutive nights on the nest. So far that two consecutive night test has worked but since you are dealing with living animals it will probably fail me one day.


Maybe off topic a bit but maybe not. There are two types of red sex links sold. Some are the commercial egg laying hybrids like the ISA Browns that have been bred to be egg laying machines and to not go broody.

The other type is when you cross a rooster with the gold genetics with a hen with the silver genetics so you can tell sex at hatch by down color. Say a Rhode Island Red or Buff Orpington rooster over a Light Sussex or Delaware hen. These are going to inherit their traits or behaviors on broodiness or anything else from their parents. All red Sex Link has to do with is down color at hatch. Them being a red sex link had nothing to do with egg laying ability or anything else. It depends on what chickens were their parents.


I get my new breeds from hatcheries. One time I wanted a new breed to play with genetics so I got a half dozen. To fill out my order I got 20 Red Sex Link males of the type that had dual purpose parents (Rhode Island Red rooster on a Rhode Island White hen) to butcher. Those grew to a size like Rhode Island Reds, not the size of an ISA Brown.

Interesting. I'm talking about the ISA brown kind of sex link. Don't know if the other one's sold over here. Generally, the pure breed market is very lacking here. You need to know where to look for to find pure breeds, and have connections with chicken peeps. Up until this September, my free ranging birds have always had the lead hen be an ISA brown. The last one was a particularly good lead hen. She was never too fond of the rooster, but respected him for his work. She was one that had attempted a feral nest, but never fully committed

 

[LaurenRitz]

Is there a standard for identifying mixed breeds? One cross is Biel x JG, but how to identify his children? Biel x JG x BA? If you're dealing with only two or three breeds that's workable, but anything more starts to look like an algebra problem.

[(Biel x JG) x BA] x (RIR x JG)