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MuhammedGoldstein
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 Posted - 06/12/2008 : 21:31:16 [Permalink]
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The term (& idea of) "phenotype" was developed by a botanist in 1911, to describe his observation of the size distribution among genetically identical beans. While the definitions we've come up with don't spell out the connection with genetics, this connection is definitely there. As an example, Wikipedia's page on Genotype-phenotype distinction says (in part; bolding added by me):
[quote]The genotype-phenotype distinction is drawn in genetics.
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An organism's genotype is a major (the largest by far for morphology) influencing factor in the development of its phenotype, but it is not the only one. Even two organisms with identical genotypes normally differ in their phenotypes. One experiences this in everyday life with monozygous (i.e. identical) twins. Identical twins share the same genotype, since their genomes are identical; but they never have the same phenotype, although their phenotypes may be very similar. This is apparent in the fact that their mothers and close friends can always tell them apart, even though others might not be able to see the subtle differences. Further, identical twins can be distinguished by their fingerprints, which are never completely identical. |
this is talking about the phenotype of an individual.As you can see, they say the twins are never the same phenotype. Correct, in the view of phenotype as the individual as a whole. . they WILL have, will share millions of phenotypes, such as same hair colour, in the "particular phenotype" sense, of characters, not the whole organism, not the group.
fit this truth into your definition, and see why you are talking about a different phenotype. We know twins share many phenotypes !
this is the sense in which phenotypic differences are easily seen with no genetic cause for change involved.
The truth that twins share many phenotypes - and this does not fit your definition - shows there is a problem with your take on this. |
It does mention phenotype, just without using the word "phenotype."... DAVEW |
| Edited by - MuhammedGoldstein on 06/12/2008 21:35:47 |
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Dave W.
Info Junkie
USA
26022 Posts |
Posted - 06/12/2008 : 21:37:35 [Permalink]
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Originally posted by MuhammedGoldstein
The truth that twins share many phenotypes , and this does not fit your definition, shows there is a problem with your take on this. |
Still backwards. Twins share many characteristics, and at birth their phenotypes will be nearly identical (like their genotypes are), because most of their characteristics will be identical. As twins age, as described in that Tyson video you linked to, their phenotypes become different, because they can't possibly share the exact same environment 100% of the time, and (again as that video described), their environment feeds back on their genetics through epigenetics (which are a part of their phenotypes). |
- Dave W. (Private Msg, EMail)
Evidently, I rock!
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MuhammedGoldstein
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201 Posts |
Posted - 06/12/2008 : 21:41:08 [Permalink]
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Originally posted by Dave W.
Originally posted by MuhammedGoldstein
The truth that twins share many phenotypes , and this does not fit your definition, shows there is a problem with your take on this. |
Still backwards. Twins share many characteristics, and at birth their phenotypes will be nearly identical (like their genotypes are), because most of their characteristics will be identical. As twins age, as described in that Tyson video you linked to, their phenotypes become different, because they can't possibly share the exact same environment 100% of the time, and (again as that video described), their environment feeds back on their genetics through epigenetics (which are a part of their phenotypes).
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yes, the whole organism's phenotype. You seem blissfully unaware that with the flamingos, we weren't talking about the whole bird changing it's phenotype.
we saw an example of phenotypic difference in one particular...colour, due solely to diet change.
much like the twins are never the same "collection" of phenotypes, but in particulars, they can have the same phenotype, and do. |
It does mention phenotype, just without using the word "phenotype."... DAVEW |
| Edited by - MuhammedGoldstein on 06/12/2008 21:44:19 |
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Dave W.
Info Junkie
USA
26022 Posts |
Posted - 06/12/2008 : 21:57:17 [Permalink]
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Originally posted by MuhammedGoldstein
yes, the whole organism's phenotype. You seem blissfully unaware that with the flamingos, we weren't talking about the whole bird changing it's phenotype. |
But it does. The whole bird's phenotype does change. The phenotype is the complete set of observable characteristics due to the interaction of genotype and environment. An old person has a different phenotype than when that same person was young due to changes in individual characteristics like graying hair and wrinkling skin.| we saw an example of phenotypic difference in one particular...colour, due solely to diet change. |
If it was solely due to diet change, then you should be able to turn a raven from black to red by feeding it lots of beta carotene.| much like the twins are never the same collection , but in particulars, they can have the same phenotype, and do. |
Well sure, once you start ignoring the details, a knife and a quarter are the same because they're both made of metal. The whole "collection" is the phenotype. Individual observable characteristics are just characteristics. |
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MuhammedGoldstein
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201 Posts |
Posted - 06/12/2008 : 22:04:16 [Permalink]
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ABO blood type of someone who has had a bone marrow transplant is phenotypic the way that wings transplanted from a mutant fruit fly onto a wild type fruit fly are phenotypic...they aren't. It doesn't count, it isn't natural, it's just an example of humans mucking with one organism (OK, two).
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I don't see where it says man's actions are not natural, and I don't see where it says unnatural things are excluded.
So you are using the "natural" clause....defining that brings a slew of problems and...
consitutional clausitis |
It does mention phenotype, just without using the word "phenotype."... DAVEW |
| Edited by - MuhammedGoldstein on 06/12/2008 22:06:37 |
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Dave W.
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MuhammedGoldstein
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Posted - 06/12/2008 : 22:15:07 [Permalink]
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Originally posted by Dave W.
Quick quiz, Muhammed: what are the two main phenotypes that all species of flamingo fall into?
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let me see now... "who cares" and "somebody has a bruised ego" ?
[I apologize for the inadvertent edit; I hit the edit button when I mean to hit the reply button. Nevertheless, this post appears with none of the original wording, etc., edited in any way. I apologize for the mistake] --Cune |
It does mention phenotype, just without using the word "phenotype."... DAVEW |
| Edited by - Cuneiformist on 06/12/2008 22:40:01 |
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Cuneiformist
The Imperfectionist
USA
4955 Posts |
Posted - 06/12/2008 : 22:18:02 [Permalink]
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Originally posted by MuhammedGoldstein
Originally posted by Dave W.
Quick quiz, Muhammed: what are the two main phenotypes that all species of flamingo fall into?
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let me see now... "who cares" and "somebody has a bruised ego" ?
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Zebra
Skeptic Friend
USA
354 Posts |
Posted - 06/12/2008 : 22:24:17 [Permalink]
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*Sigh* Phenotype gets used in alot of ways. It's a biological term, used in biology when looking at groups in which there's a variation in one feature...trait...characteristic...and is really only useful, & used, when there may be a genetic basis for the difference. Example being, "wild-type" Drosophila versus Drosophila with a mutant phenotype [insert description of observed mutation here]. Sure, you could USE "phenotype" when referring to docked tails on dogs, but that use is not in the biological context in which "phenotype" is a meaningful term.
OK, so people (biologists, even) look at a bunch of flamingos in different settings. Most are pink. Some are white. Bingo, there are pink and white phenotypes of "flamingo"! But it's a trivial example, IMO, because the change ends up being solely dietary, not genetic (at least not as far as I have been able to determine), is fairly quickly reversible, and can be exploited willy nilly by humans who feed flamingos in captivity.
It's like saying that some people have garlic breath as a phenotype. Maybe it meets a literal definition, but it's not very useful, & doesn't fit with the usage of the word in its native environment (biological study, esp genetic study, of organisms & species).
It's also interesting that VERY few sites use "phenotype" to describe pink v. white flamingo. Try this. Do a Google search of "flamingo" and "phenotype" and "pink" (in any order):
Note that the Berkeley Evolution 101 site and the 2 discussions here at SFN come up. And a number of sites which use Flamingo but aren't referring to birds (some plants, and genes, have been named Flamingo). And the Scottish Terrier Club of America site, which goes into some very basic genetics including a familiar sentence, "A change in the environment also can affect the phenotype. Most people think of flamingos as being long legged, pink birds. But pinkness is not encoded into their genotype! It is actually the food they eat that makes their phenotype either white or pink."
And an article by S.P.R. Rose from the Journal of Molecular Biology in 2002, which I accessed through a subscription held by my workplace, & which says in part:
| Finally, not all phenotypic characters are adaptive. A core assumption of ultra-Darwinism is that observed characters must be adaptive, so as to provide the phenotypic material upon which natural selection can act. However, what constitutes a character—and what constitutes an adaptation—is as much in the eye of the beholder as in the organism to which the “character” belongs. The problem lies in part in the ambiguity of the term phenotype which can refer to anything from a piece of DNA (strictly the gene's phenotype) through the cellular expression of a protein to a property of the organism as a whole, like height, or “behaviour” such as gait. At which level of phenotype a character is “adaptive”, if at all, and at which its properties are epiphenomenal is always going to be a matter for debate. A not entirely apocryphal example is provided by the American artist Thayer, who suggested, early in this century, that the flamingo's pink coloration is an adaptation to make them less visible to predators against the pink evening sky. But the coloration is a consequence of the flamingo's shrimp diet and fades if the diet changes. Thus even if we were to assume that the coloration was indeed protective, it is an epiphenomenal consequence of a physiological—dietary—adaptation, rather than a selected property in its own right. |
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Dave W.
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USA
26022 Posts |
Posted - 06/12/2008 : 22:43:24 [Permalink]
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Originally posted by MuhammedGoldstein
Originally posted by Dave W.
Quick quiz, Muhammed: what are the two main phenotypes that all species of flamingo fall into?
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let me see now... "who cares" and "somebody has a bruised ego" ? |
Okay, I understand you completely, now. |
- Dave W. (Private Msg, EMail)
Evidently, I rock!
Why not question something for a change?
Visit Dave's Psoriasis Info, too. |
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MuhammedGoldstein
BANNED
201 Posts |
Posted - 06/13/2008 : 03:36:11 [Permalink]
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Originally posted by Zebra
*Sigh* Phenotype gets used in alot of ways. It's a biological term, used in biology when looking at groups in which there's a variation in one feature...trait...characteristic...and is really only useful, & used, when there may be a genetic basis for the difference. Example being, "wild-type" Drosophila versus Drosophila with a mutant phenotype [insert description of observed mutation here]. Sure, you could USE "phenotype" when referring to docked tails on dogs, but that use is not in the biological context in which "phenotype" is a meaningful term.
OK, so people (biologists, even) look at a bunch of flamingos in different settings. Most are pink. Some are white. Bingo, there are pink and white phenotypes of "flamingo"! But it's a trivial example, IMO, because the change ends up being solely dietary, not genetic (at least not as far as I have been able to determine), is fairly quickly reversible, and can be exploited willy nilly by humans who feed flamingos in captivity.
It's like saying that some people have garlic breath as a phenotype. Maybe it meets a literal definition, but it's not very useful, & doesn't fit with the usage of the word in its native environment (biological study, esp genetic study, of organisms & species).
It's also interesting that VERY few sites use "phenotype" to describe pink v. white flamingo. Try this. Do a Google search of "flamingo" and "phenotype" and "pink" (in any order):
Note that the Berkeley Evolution 101 site and the 2 discussions here at SFN come up. And a number of sites which use Flamingo but aren't referring to birds (some plants, and genes, have been named Flamingo). And the Scottish Terrier Club of America site, which goes into some very basic genetics including a familiar sentence, "A change in the environment also can affect the phenotype. Most people think of flamingos as being long legged, pink birds. But pinkness is not encoded into their genotype! It is actually the food they eat that makes their phenotype either white or pink."
And an article by S.P.R. Rose from the Journal of Molecular Biology in 2002, which I accessed through a subscription held by my workplace, & which says in part:
| Finally, not all phenotypic characters are adaptive. A core assumption of ultra-Darwinism is that observed characters must be adaptive, so as to provide the phenotypic material upon which natural selection can act. However, what constitutes a character—and what constitutes an adaptation—is as much in the eye of the beholder as in the organism to which the “character” belongs. The problem lies in part in the ambiguity of the term phenotype which can refer to anything from a piece of DNA (strictly the gene's phenotype) through the cellular expression of a protein to a property of the organism as a whole, like height, or “behaviour” such as gait. At which level of phenotype a character is “adaptive”, if at all, and at which its properties are epiphenomenal is always going to be a matter for debate. A not entirely apocryphal example is provided by the American artist Thayer, who suggested, early in this century, that the flamingo's pink coloration is an adaptation to make them less visible to predators against the pink evening sky. But the coloration is a consequence of the flamingo's shrimp diet and fades if the diet changes. Thus even if we were to assume that the coloration was indeed protective, it is an epiphenomenal consequence of a physiological—dietary—adaptation, rather than a selected property in its own right. |
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intersting post, Zebra. great digging. serious conflicts exist within this post and some of your position so far, though, IMO.
let's discuss this one some more. re: arbitrary choices, contradictions, circular reasonings, redefinitions
You're starting to take the "Berkeley is wrong" approach. I like your honest approach
Most of the others tried to say it's only me who sees Berkeley as saying what they say.
I take it you agree that Berkeley says diet is solely responsible for the DIFFERENCE ? You say it too ?
So you and I are now the only ones here saying that, I think.
Have you noticed some of the commentary directed to this idea ? They claim, basically, that diet CHANGE is never just environmental after all ! hehehe
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It does mention phenotype, just without using the word "phenotype."... DAVEW |
| Edited by - MuhammedGoldstein on 06/13/2008 04:35:50 |
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MuhammedGoldstein
BANNED
201 Posts |
Posted - 06/13/2008 : 04:01:46 [Permalink]
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Zebra, perhaps we should list the ways in which "phenotype" is used. The different things ( a single character, a specimen of a species, or organism, a group of the organism ) it can apply to, in regard to studies it can be used in.
For instance, let's look at the cats with the deformed ears from the Berkeley site. If we look at a roomful of them, we name the phenotype of the "funny ear" (vs "regular ear"}, as a group phenotype.
Let's say this was the first time seeing it appear in cats.
We know nothing of the cause as yet.
We want to determine the cause...is it caused by a poisoning of the mother ? a certain cat food or human food ? A medicine ? Was it caused by some environmental factor or genetics ? We don't know. But we can find out if it is genetically related, *****BECAUSE****** we can test and study, controlling the variables. This is the essence of science in this instance.
so we want to STUDY this using "phenotype and genotype".
so we attempt to label the ear difference as phenotypes, and do the breedings.
But NO ! Since we do not yet KNOW that the funny ears are genetically caused, are heritable , we CANNOT call them a phenotype yet !
Please tell me of what investigative use "phenotype" can ever be, if we must use
a priori knowledge of the cause in order to study the cause ???
Thus we KNOW that Berkeley is very precise, very correct, as are most sites put up by scientific groups.
Every definition so far, I have accepted, carte blanche, and yet you cannot make any definition work the way you want it to, without adding clauses...or using strained logic.
occam it. |
It does mention phenotype, just without using the word "phenotype."... DAVEW |
| Edited by - MuhammedGoldstein on 06/13/2008 04:52:18 |
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MuhammedGoldstein
BANNED
201 Posts |
Posted - 06/13/2008 : 04:46:24 [Permalink]
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Originally posted by Dave W.
Originally posted by MuhammedGoldstein
Originally posted by Dave W.
Quick quiz, Muhammed: what are the two main phenotypes that all species of flamingo fall into?
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let me see now... "who cares" and "somebody has a bruised ego" ? |
Okay, I understand you completely, now.
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then start polishing the Pope's Crown - there's a good lad !  |
It does mention phenotype, just without using the word "phenotype."... DAVEW |
| Edited by - MuhammedGoldstein on 06/13/2008 04:54:05 |
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bngbuck
SFN Addict
USA
2437 Posts |
Posted - 06/13/2008 : 10:02:18 [Permalink]
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Mishugunah Goldstein.....
About that circumcism.......!
Seriously, MG, where in dshehenna are you going with this endlessly circular chase around the definition of "phenotype"? I am not a biologist and am not competent to parse the finer points of taxonomic definition in the discipline, but many here obviously are; and all I can glean from reading some twenty-odd pages is that you are concerned that there is an inherent ambiguity in the word "phenotype"! Is this correct?
If not, can you state in one simple sentence, what you are trying to state? Or question?
I'm not trying to rattle your cage, insult you or ridicule you. I truly don't understand what point you are trying to make! I am a reasonably well-educated layman with respect to the biological sciences, and I don't understand what it is that you are trying to say!
Everytime it starts to clear up, you say something that further convolutes the intent of your original OP. I think! Perhaps it's just my lack of advanced training in Biology, but there are folks here with extensive academic backgrounds in that science that don't seem to understand either!
Please explain to me, as you might to a reasonably intelligent child, what it is that you are trying to say!
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Zebra
Skeptic Friend
USA
354 Posts |
Posted - 06/13/2008 : 10:05:14 [Permalink]
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I DO recognize the contradictions, or apparent contradictions, in the material I've presented.
"Phenotype" is a biological term. Biologists are not linguists.
"Phenotype" was coined by a botanist who was one of the first geneticists, almost 100 yrs ago, because he needed a word to describe the variety in appearance (size) that he saw when he looked at beans, because the variations were not fully explained by genetics, so he recognized that there had to be other factors in play which determined the appearance...the physical development...the formation of the members of the group. He needed a word to describe the fact that there were observed differences in the group of beans.
Yes, the definition you read for "phenotype" leaves open the possibility that it can be used for features which have nothing to do with genotype, but that is not how biologists use the word. If anything, it gets extended the other way, to describe behaviors or appearances of a group which may have basis in genetics (the "extended phenotype" of beaver dams, & of Dawkins' book). It's used to described an observed difference between groups within a species, & may be the starting point for investigations into cause, e.g. genetic vs. environmental.
You could publish a book called "Human Phenotypes" & have photos of 200 different haircuts. Biologists would look at you funny (if they looked at you at all). That's not what they mean when they use their word "phenotype".
"Evolution 101" is an attempt at entry-level, simplified explanation, for non-biologists. As has been said before, it's not the inerrant word of Biology-Definition God.
I've been trying to think of analogy in another field. Here's as close as I've been able to come. Some people get all excited, thinking that the Second Law of Thermodynamics PROVES that evolution can't be possible, because you can't move from a state of high entropy to a state of low entropy? Right?? That's what the Second Law of Thermodynamics says, so there, ha ha! But their understanding is based on a simplified statement of the Second Law of Thermodynamics, one which is incomplete, because it didn't include the qualifier "In a closed system..." (which those who are familiar with, & use, the Second Law of Thermodynamics essentially don't need to have stated, because it's so clearly a basic assumption).
End of responses from me. I have to get some work done.
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I think, you know, freedom means freedom for everyone* -Dick Cheney
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If I get a haircut 2
