Inheritance In Seeds Question

[guineapig]

I remember looking up a bunch of articles on sex determination in corn plants and it still
was not completely settled, but they thought 12-20 different genes played a role and really nobody really knew for certain.

I assume there would be different genes for seed coating, seed oil production, seed embryo size, the thickness of cell walls, and on and on.

Yes mofeta we could have a discussion about molecular techniques, but it might not make
for the most exciting thread, especially given scientists' penchant for cryptic vocabulary.

Science once believed in one single light receptor, phytochrome, which only absorbs red-light. Then another scientist came along and had evidence for a blue-light receptor. It took a long battle with the other scientists before the blue-light receptor, called cryptochrome, was accepted. So even within the scientific community is there ignorance and rejection of new ideas in favor of the old dogma.

Plant genetics are more complicated than animal genetics, much more complicated. I
never forgot that once I heard it.

I am guessing, somewhere between the two parents? Between two ferns?

kind regards from guineapig

 

[Tom Hill]

Sam's original poll question could have been worded a bit better as it confused many, myself included..

"If a small seeded variety and a large seeded variety are crossed what will the progeny seeds look like?

#1 Somewhere between the two."

ok as of this point we could certainly be talking about large population eg open pollination or certainly many individuals in many type of breeding schemes over perhaps more than one generation .... but then

"#2 Just like the Mom.
#3 Just like the Dad.
#4 Like none of the above."

now we have seemingly shifted to speaking of individuals and a single occurrence of mating- so the answer would be #2 just like the mom..

However,

if speaking of larger mating than 2 individuals more particularly more than a singular mating/generation, as some interpreted the question, and are speaking in a broader sense of inheritance,, the answer is certainly all #1 through #4 because we need to make room for transgressive segregation and accept #4 into the mix as well. That is to say,, at some point, there would be progeny seed size (etc) lying outside both of the extremes small and large (etc) that either original parental line has exhibited previously.

i believe that/those are the correct answer/s however one chose to interpret the question.

 

[J man]

Nukber 2 bwlecayse ir taies severap back ceosses ro regains inthee small swed oe clcise veesa

 

[mofeta]

Hi guys

I don't have a bunch of time to talk right now, but I wanted to recognize the excellence of discussion in this thread from everyone.

I would also like to complement Sativied on the quality of his (her?) comments. I somehow missed a whole page in which Sativied and others made a number of really good comments. I just saw them and repped as many of them as I could before vBulletin limited me. I will give more rep later when it will let me.

If I had seen those comments, I wouldn't have engaged Tom on the dominance thing, as I ended up just echoing what Sativied had already said. Sorry!

Hey Tom-

Check this out, the weed gods must be on your side:

Even though I wouldn't have stepped on Sativied's comments before, your persistance in being wrong is motivating me to continue! (stoops to retrieve guantlet)

To be serious for a moment, there is a lot of potential for deeper discussion here on the very nature of , and mechanisms of dominance in relation to fitness and selection. I am sure you are aware that this is one of the oldest and most hotly contested bones of contention in the modern era of the study of inheritance. I can't think of a better guy to discuss it with.

OK, the serious moment is over. I will now return to a adversarial tone because I like to fuck with people that can take it!

Now, ignoring your wrongness for now, what came first, the dominance or the fitness? In other words, is it fit because it is dominant, or dominant because it is fit?

 

[Tom Hill]

Even though I wouldn't have stepped on Sativied's comments before, your persistance in being wrong is motivating me to continue! (stoops to retrieve guantlet)

Good, I have been saddled with somewhat of an underdog position and though quite comfortable there, i am secretly rooting for you too. It may however require more than the typical parochial student type regurgitations,,,, that is so boring. I only give out brownie points for pure thought.

To be serious for a moment, there is a lot of potential for deeper discussion here on the very nature of , and mechanisms of dominance in relation to fitness and selection. I am sure you are aware that this is one of the oldest and most hotly contested bones of contention in the modern era of the study of inheritance. I can't think of a better guy to discuss it with.

Yes i am aware. In the beginning dominance was king, then some wisenheimer came along and proved otherwise - fitness reigns. What we have now if you'd care to take a gander at the web is a bunch of over zealous types as previously mentioned eager to share with the world what they think they have learned. Memorizing the answers for the big test coming on friday seems to be their strong suit, pure thought not so much. There is still value in dominance, as is most often the case, older suppositions were not completely without merit.

Now, ignoring your wrongness for now, what came first, the dominance or the fitness? In other words, is it fit because it is dominant, or dominant because it is fit?

I'd say the relation is not causal in either direction (i can't make it so easy for you ), it does however provide a hell of a double whammy in the case of the wild-type ascent.

Carry-on sir, if and when you dare

 

[mofeta]

It may however require more than the typical parochial student type regurgitations,,,, that is so boring. I only give out brownie points for pure thought.

....


What we have now if you'd care to take a gander at the web is a bunch of over zealous types as previously mentioned eager to share with the world what they think they have learned. Memorizing the answers for the big test coming on friday seems to be their strong suit, pure thought not so much.

I hear you Tom, but I am old-school when it comes to pedagogy. I firmly believe in rote learning. The abandonment of this time-tested method (new math anyone?) is why students from Europe and Asia spank the US in STEM stuff. Rote and rigor go hand in hand. Preparing the soil of the mind with lots of nutritious facts allows for the growth of deeper understanding, especially with complex, non-intuitive subject matter. Recent studies have shown this very clearly, and I hope it doesn't take long for our teachers to come to their senses.

 

[Tom Hill]

I knew it would not be lost on you, even though i also know you are teetering on the verge of taking us into a world of defective proteins and the like with this mention of a deeper discussion. I tend to side with guineapig on that (as a poor sap who often gets stuck with translation duty), bonus points for keeping in the most lay of tongue so as to not alienate those who would otherwise participate.

Suffice it to say that dominance and fitness are separate entities, that fitness > dominance, that they each can be assigned values, and when coupled together (as is often the case eg often the wild-type allele) they become a more powerful force within a genepool than either could have been on their own.

 

[mofeta]

OK, your thesis appears to be pretty clear:

However, answer this, does a recessive allele ever hold the same advantage over a dominant allele as is true in the reverse? No sir, no sir it does not.. Now carry those maths as far as you need to to realize that any advantage small as it may be,, wins in the end.. It's why we named it dominant. Once it is fixed and in place,, there is not the same threat to it's existence as holds true for more vulnerable conditions of genes.

i am not saying it is advantageous to the organism as a whole i am saying it is advantageous to the allele itself.

.....

....it does not require more than a third grade education to understand which form of gene has the advantage over the other..

But that the dominant allele prevails in the often instance of complete dominance, well, that is some serious friggin genetic mathematical judo over the long term. And that is a thing a mutant recessive hiding in corners and dark alleys simply can not lay claim to.

Simply put:

"Dominance in an allele is advantageous in and of itself." - Tom Hill

Is that correct?

 

[mofeta]

... i also know you are teetering on the verge of taking us into a world of defective proteins and the like with this mention of a deeper discussion.

No, that is not necessary or fruitful at this stage. I intend to stick to the classical paradigm you have laid out,

is enough to deal with this to begin with. Once that is dealt with we can go on to deeper stuff.

Suffice it to say that dominance and fitness are separate entities, that fitness > dominance

That is correct. That's all there is to it, really. This doesn't harmonize with the thesis you were stating before, though?

 

[Sativied]

Simply put:

"Dominance in an allele is advantageous in and of itself." - Tom Hill

Is that correct?

No that's not correct. Dominance does not give an advantage and means nothing for an allele "of itself", only to the relationship. Again, the same allele can be dominant to one but recessive to another.

If in a heterozygous combination one is complete dominant and the other is recessive they still have equal chances of being passed on to the next generation. It's as simple as that... It does not affect gene frequency unless you select for/against it.

"Dominance is not inherent to an allele meaning that there is nothing special about any allele that determines whether it is dominant or recessive. Rather it's the relationship between alleles because in some cases the phenotype of one allele "overrides" that of the other."
Src: one of thousands that stresses this to avoid the common misconception of attaching more value to the word than one should.

The fact that many deleterious traits are recessive does not automatically mean that dominance is advantagous. Nor that the resulting trait dominates in nature as in the underlying genes will dominate the genepool because a supposed advantage. It's the usefulness that matters. When a deleterious recessive is bred out in the wild it's because it's deleterious, and not an result inherit to it being recessive.

*****************************
Consider several student misconceptions about genetics, familiar to anyone who teaches introductory genetics (Donovan 1997; Allchin 2000):
A dominant trait is ‘stronger’ and ‘overpowers’ the recessive trait. A dominant trait is more likely to be inherited.
A dominant trait is more ‘fit’ in terms of natural selection.
A dominant trait is more prevalent in the population.
‘Wild type’ traits are inherently dominant, while mutants are recessive. Male or masculine traits are dominant.
Any well trained biologist knows better, of course. However, the errors themselves are not relevant here. Rather, why do these conceptions emerge at all?2 No one teaches these concepts. They emerge spontaneously and with stunning consistency (regardless of the teacher’s skill.3) What is the archaeology of the concepts (Foucault 1972), or the nature of the conceptual framework whereby these ideas can arise? In this case, all these misconceptions embody the metaphor of dominance.

The dilemma of dominance.
http://www.tc.umn.edu/~allch001/papers/dilemma.pdf

 

[mofeta]

Hi Sativied

Yeah, I was asking Tom if it was correct that that was his assertion, not whether the statement was correct.

Did you see my post above? This one? I felt bad that I had missed your excellent contributions, and wanted to make sure to acknowledge them, and apologize for seeming to ignore them. Sorry about that! You did a good job of correcting Tom. I think he is coming around now. Then we can move on to more interesting stuff.

 

[mofeta]

The dilemma of dominance.
http://www.tc.umn.edu/~allch001/papers/dilemma.pdf

Hey that looks good. I will read it when I get a chance.

Have you read Gilham's treatment of Galton's work and influence it had on Bateson and Pearson and Weldon? It is very good.

A Life of Sir Francis Galton: From African Exploration to the Birth of Eugenics

 

[Tom Hill]

Hi Sativied

Yeah, I was asking Tom if it was correct that that was his assertion, not whether the statement was correct.

I think he is coming around now.

don't worry there was no chance of me answering that in the affirmative either as too many set and understood parameters within the context of the discussion were conveniently absent.

gotta go water, be back soon, no sir not ready to come around yet you should know me better by now lol.

 

[Tom Hill]

Mofeta it's all fine to poke and jab it's all in good fun and humor brother but you now stand accused of the most horrendous case of cherry picking this side of western sunset climate zone 15 and tsk tsk tsk,, i'm telling on you to the school principal

If it was not clear to you before then please let it be now. This sidebar conversation began in the context of the wild type. It is from that point and all that goes with it (natural selection etc) that these comments were born out of.

You see i already knew that wild-type are generally dominant (did you catch that Sativied, generally, not inherently?) as well as of high fitness value - it's just how it is.

However, if you have some alternative theory of how the above came to be aside from being generally advantageous I am all ears. And I certainly do hope it is something better than chance occurrence or God playing dice with the universe or some crap like that?

 

[Tom Hill]

Dominance does not give an advantage and means nothing for an allele "of itself", only to the relationship. Again, the same allele can be dominant to one but recessive to another.

You speak of the relationship as if it were nothing, when it is damn near everything. Yes yes, the same allele can be dominant in one case and recessive in another but let's continue shall we? The same allele can be dominant in a great many cases too, is this not correct? And if so,, how can we sit here with a straight face and say that is of no advantage to that entity?

If in a heterozygous combination one is complete dominant and the other is recessive they still have equal chances of being passed on to the next generation. It's as simple as that... It does not affect gene frequency unless you select for/against it.

ah but you see, nature does select for it apparently.

The fact that many deleterious traits are recessive does not automatically mean that dominance is advantagous. Nor that the resulting trait dominates in nature as in the underlying genes will dominate the genepool because a supposed advantage. It's the usefulness that matters. When a deleterious recessive is bred out in the wild it's because it's deleterious, and not an result inherit to it being recessive

now let us compare that to how a deleterious dominant gets bred out, i think a healthy genepool would prefer all deleterious genes be dominant, i know i would,, it would be,,,, advantageous

I quickly browsed through the paper you posted, i missed it, did the author have an opinion as to an alternative?

I concur with the opinion of "it is 150 years too late". I do not feel i fall into the category of being unable to use the classical paradigm/nomenclature at the same time as making way for more modern enlightenments. But apparently you feel i do

 

[mofeta]

If it was not clear to you before then please let it be now. This sidebar conversation began in the context of the wild type. It is from that point and all that goes with it (natural selection etc) that these comments were born out of.

You see i already knew that wild-type are generally dominant (did you catch that Sativied, generally, not inherently?) as well as of high fitness value - it's just how it is.

However, if you have some alternative theory of how the above came to be aside from being generally advantageous I am all ears. And I certainly do hope it is something better than chance occurrence or God playing dice with the universe or some crap like that?

Hi Tom

Hmmm, this is not playing out like I thought it would.

All joking aside, is your comment I quoted above serious, or are you playing devil's advocate so a point can be illustrated? Have you been serious this whole time?

 

[Tom Hill]

Hi Mofeta, all joking aside?

Yes, that comment was quite serious. That wild-type are generally dominant is one of the few truths that has stood the test of time among all modern learning advance in regards to genetics.

It's why folk such as (Donovan 1997; Allchin 2000) must use words like "inherently" when saying "‘Wild type’ traits are inherently dominant" when referencing student misconceptions.... it's why he must omit using "wild-type" when going on to include the misconception "A dominant trait is more prevalent in the population"..

Yes i have mostly been playing devils advocate and yes the deck was stacked from the git. I am not however guilty of concealing anything, rather my learned colleagues in their eagerness to flex have not bothered to view all the cards that nature has been so kind to place on the table - pure thought?

We can say many things about dominance all of them revolving around the fact that dominance is not all we once thought it was cracked up to be..

However, i do not believe we can say it is worthless, as many of us have come dangerously close to doing in this sidebar. As nature has already decided that is simply not the case.

I suppose that is the point i am attempting to illustrate.

.... at the end of the day... Dominant > Recessive,,,,,, deal with it..

 

[Tom Hill]

Dominance does not give an advantage

no holds barred and cherry picking is all fine and dandy?

That comment is blasphemy and patently false and every bit as damaging as the wrong you are attempting to right.

 

[Tom Hill]

"Dominance in an allele is advantageous in and of itself." - Tom Hill

i beg of you, do not forge my signature again, for it is the greatest of sins and the very height of chumpness. I am here to attempt to further our collective knowledge, i did not have that shit coming man,, nobody does.

But, now that i have more completely stated my case i will say yes,, your quote is correct, for no other reason than i am curious as to where you may have taken it from there..

again,, i am hoping to see some pure thought here,, you have all of you,, let yourselves down so far in my opinion.. show me something now your opinion not "his" (he is always full of shit) and let's make it interesting ha?.

i do not give a flying rats ass of a fuck about what you read if you can't remove your friggin eyes from the book long enough to realize what is,,, is..what is wrong with you guys? Why do you not see the same things in Allchin's (wimpy-ass) observations as i do? Are you all fucking handicapped? Wise up!...

uhhmm,, excuse me sir,, but some of the ladies do not like the term dominant as it seems a bit sexist,, can we please change it? lol,, you have got to be kidding me! Apologies ma'am,, but nature has already spoken quite clearly on the subject.. - best of luck to your long and prosperous career mr Allchin,, in philosophy! lol

Hey that looks good.

try reading it again,, this time from a geneticists point of view, not that of a whore..

swwwwissshhhhhh!!!!

 

[mofeta]

Hi Tom

Hey I had planned on going back and forth with you for a while, like I said I like to fuck with guys that can take it. It is a fun way to transmit info to the people spectating. It looks like I'll have to cut it short though. I got in some trouble last night and need to devote most of my time to fixing it now. I'll be back sometime (hopefully soon) though.

It seems like you are actually upset? I hope not, that wasn't my intent. You are a very bright guy, and I like you.

I do think you have a problem with clear exposition, though. That's the only conclusion I can draw after you kept not giving a concise, easy to understand explanation of your point. You were given numerous chances to, but you just wouldn't do it. That's why I made my "This is not playing out the way I thought it would." comment. (I actually still kinda think you are just fucking with everyone)

So, I gotta go now and probably won't comment on these boards for a while, just won't have the time. As a parting gift though, here is this (these are my own words, so it may be different than what you see if you Google it, but the idea is the same. As a note, there is a good pop gen blog named after this principle, check it out):

Haldane's Seive:

In outcrossing diploid organisms, adaptation favors new mutations with a higher coefficient of dominance.

This is because this equation:

shows that at very low initial frequency, alleles that don't express in the heterozygote (recessive), lag behind those that do (dominant) to such a degree that stochastic processes like drift tend to eliminate them before they can be fixed, even if the recessive allele is more fit (as the homozygote, of course).

I have to point out that this is only true with very low initial frequency, and that when you said this:

Recessive traits fixed or not within loci or multiple loci, are at risk of being altered within any given population - by outside influence, traits controlled by fixed dominant loci are not.

You were quite incorrect. Once the frequency of the allele rises above a very low frequency, the only thing that mode of inheritance influences is the speed of change in frequency due to selective pressures.

When I come back we should discuss some new stuff, eh? HapMap for weed? Linkange disequilibrium? Compressed sensing for massively polygenic traits of fine kind? Maybe read this if you haven't yet:

Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index

It's about humans, but it is also about strawberries if you read it right.