is Phenotype All ?

Definitions of "phenotype" are usually shown in contrast to "genotype".
Most often some kind of equation is given, showing phenotype resulting from genotype and environment, and perhaps, "random variation".

The definition given almost always says phenotype is the observable trait(s) of an organism.
My question is this; as we are able to observe more, we are able to observe the genes.
So how is it that the genotype is never thought of as part of a possible phenotype ?

Thanks !

Because the phenotype of an organism is a consequence of the particular genotype the organism has (and in some regards environmental and developmental conditions). It seems circular to consider genotype as part of the overall phenotype of an organism.

This is my puzzle.
It seems not the case, that phenotype is necessarily a consequence of genetics. If proceeding in enquiry rather than asserting knowledge, one can find, for instance, that adult humans may have a "tanned" or "untanned" phenotype...under the bikini line.
The difference between phenotype "tanned" and phenotype "untanned", is due solely to an environmental influence, namely UV exposure.
To argue that we need the genetics to produce melanin produces no helpful results of investigation. We would need to assume, or we need to know the genetics, before we can investigate.

If, for instance, we observe that in areas that receive no sun, there is no tan, one might experiment, and add sunlight...and then see a phenotypic change as a result. Voila, the difference between phenotype "tanned" and phenotype "untanned", is due solely to an environmental influence, namely UV exposure.

To argue that we need the ability to produce melanin in the first place leads nowhere. cancels out any possible gain from enquiry, and replaces it with "knowledge" that is not true.

If we were to look at a population , some of which had only 4 digits on the hand, we could assume the difference is a consequence of genetics, but it may be a consequence of injury...so assumption that genetics is the cause of the difference is not helpful.

It brings us to asserting that the phenotypic difference between "tanned" and "untanned" is a consequence of "genetics".
Whereas, the phenotypic difference is solely due to environmental difference.
Phenotype "tanned" is not encoded for.


So that's where I'm stuck; although phenotype may be - but is not always - a consequence of genotype, genotype must always be a possible phenotype.
Therefore, Phenotype can be Phenotype plus environmental influence.


It seems as though the above statement must be wrong. But why is it wrong ?
What I am guessing at is that the first "Phenotype" ( tanned) is not the same as the second "Phenotype" ( tan-able ).

Help ! :bigsmile:
When it comes to people with Phenotype "4 digits per hand", (after having a finger cut off both hands ), is the second kind of Phenotype, "Phenotype 'fingers cut off-able' " ?

Because the phenotype of an organism is a consequence of the particular genotype the organism has (and in some regards environmental and developmental conditions). It seems circular to consider genotype as part of the overall phenotype of an organism.

Phenotype is still a consequence of genetics.

A phenotype is not necessarily observable to ordinary human senses. The effect of a gene may only be molecular, but it should still (and is) considered to be a phenotype.

Also, I'm not sure that I would call tanning a phenotype, as it would be similar to calling something like a hair style a phenotype.

Certainly I would call natural skin pigmentation a phenotype, but that's not the same thing as tanning and certainly isn't due solely to environmental conditions.

Indeed, although gene regulation is a phenotype unto itself, and it determines how your genes are actually expressed. So the distinction is blurrier.

Phenotype is still a consequence of genetics.

Indeed, although gene regulation is a phenotype unto itself, and it determines how your genes are actually expressed. So the distinction is blurrier.

exactly.If I dye my hair blue, it's a phenotype..and the investigator does not need to know before investigating whether I dyed my hair or if it's a genetic trait or a result of a peculiar disease. He only has to identify the phenotypic difference in order to start investigating the cause. So Phenotype "blue hair" is legit. Of course, I need to have hair, and it needs to be able to hold dye... just as the dye needs to have certain attributes...but those aren't particulars that the investigation needs to know aforehand.

right, it's not due solely to environmental influence on that individual. It's a genetic trait; encoded for.

If you think "tanned" is not a phenotype, why not? Isn't phenotype "pink" in pink flamingos ( solely a result of pigment in feed) a phenotype..although it's not encoded for ?


'Epigenetics' Means What We Eat, How We Live And Love, Alters How Our Genes Behave

research into epigenetics
NOVA | scienceNOW | Epigenetics | PBS

These days regulation is included in "genetics", I'd say.

The connection between a flamingo's pigment and a hairstyle is a stretch, as one is a conscious choice and the other is not.

Regardless, I would argue that a flamingo's genetic make-up does have an effective on their color, albeit an indirect one. It is the inability to metabolize the molecule that causes their pigmentation that leads to the observed phenotype.

If you do insist on calling "tan" a phenotype, then it is still a consequence of genetics, as the skin cells produce melanin to protect themselves from UV radiation.
I am well aware of epigenetics. You're going to be hard-pressed to find a phenotype that isn't influenced by genetics in some way. I never meant to imply that genetics was the sole-contributor to an observed phenotype, as any student who has taken introductory biology can (hopefully (!)) tell you. The point that I was trying to make was that phenotype is connected to genetics in very complex ways. Even when environmental factors influence genes (not necessarily by mutation, but via other mechanisms), genetics plays a role in the expressed phenotype.

Yes, but genotype and genetics are different concepts.

Ones genotype is generally defined as one's DNA sequence. The regulation of a given gene, however, is likely to be highly polygenic

Yes - to some, but not to others. To those who use the term "Gene" in a functional way, rather than a moleclular way, or developmental way, they're one and the same.

Not if we use the term in an evolutionary biologist's way, a functional way, rather than the molecular biologist's way; in the "functional gene" way, we include junk DNA , RNA, and more - not just DNA sequences

OK, it seems like we need to make three separate distinctions here. Phenotype can depend on genetics, environment and a combination of the two.

I disagree that my statement regarding genetics influencing flamingo pigmentation leads to an infinite regress because it does.

If you want to say it does, then the assertion that an organism's genotype is in and of itself a phenotype

must also lead to an infinite regression because it is unclear where the distinction of phenotype would stop.

Not the molecular level, what about the atomic or the subatomic?

To be clear, I don't want to say that your claim does lead to an infinite regression, but if you reason that mine does, then using similar reasoning, yours must as well.

The genotype-phenotype distinction is goes something like this: heredity produces, or at least leads to, certain effects. Some of these effects may be induced by environmental conditions, but heredity plays a factor nonetheless.

It is dangerous to try to consider genotype a particular phenotype because the distinction is a very important one when studying the evolution of a species.

That is, it would be impossible to adequately understand things like evolution without recognizing that the physical properties of an organism (the properties that are actually acted on during natural selection) are ultimately determined by what an organism's genotype is.

That isn't to say that we are able to predict an organisms phenotype based solely on genetics in most instances.

It can be done for certain genetic diseases such as CF, but in regards to the system as a whole, it is unlikely that the majority of characteristics can be predicted.

There is a reason why the terms genotype and phenotype were coined.
I'm not sure I follow. Molecular biologists talk about genes in a "functional way" all of the time.

There is a distinction between genetics and genotype. Genetics is a word pertaining to the study of heredity, whereas a genotype is the complete genetic makeup of an individual.

Junk DNA is part of an organism's genotype. Genotype does not refer to activated genes, but all of an organism's DNA sequence.

To those who use the term "Gene" in a functional way, rather than a moleclular way, or developmental way, they're one and the same.

Not if we use the term in an evolutionary biologist's way, a functional way, rather than the molecular biologist's way; in the "functional gene" way, we include junk DNA , RNA, and more - not just DNA sequences

No they're not. That's like saying that walking is synonymous with leg.

The function of a gene is called "gene expression". They are not the same terms. The product of gene expression is an RNA transcript that has a sequence complementary to the gene. The regulation of gene expression involves different actors. The gene cannot be synonymized with its function.

Evolutionary biology at the level of a gene is just applied molecular biology, so it's a semantic difference.

Evolutionary biologists study things like haplotype maps, SNPs, etc, so they need this lexicon every bit as much as a molecular biologist.

There are no RNA genes except in RNA-based viruses like HIV and influenza. There are DNA sequences that are non-coding sequences, like promoters and telomeres and introns. There are further distinctions, however. The coding sequences following a promoter that specify the mRNA are the gene. The entirety of the DNA sequence downstream from the promoter, including non-coding sequences like introns, is an open reading frame, not a gene. The site on a chromosome where a gene exists is a locus, not a gene.

It's like saying walking is synonymours with "balancing while putting one LEG in front of the other LEG and moving forward".

but in fact it is done, legitimately, buy scientists.

A gene is a thing, not a process.

I don't know, I've spent a long time in science and I've never heard that. My fellowship research, at a somewhat well known institution of higher learning, was in this very field (specifically the molecular evolution of the malaria parasite), and not in a single meeting, conference, conversation, or article in the years I spent there did I hear this claim.

I don't see where he and I disagree, except that he's lamenting the "traditional" use of the word gene that I share. He has not made any kind of case about acceptable uses of the word "gene" in scientific parlance, though, and his objections to the traditional use do NOT have to do with regulation of gene expression but rather the source of coding material to produce a transcript.

The concept of a gene is a fundamental part of the fields of genetics, molecular biology, evolution and all the rest of biology. Gene concepts can be divided into two main categories: abstract and physical. Abstract genes are the kind we refer to when we talk about genes "for" a certain trait, including many genetic diseases. Most geneticists and many evolutionary biologists use an abstract gene concept.

Philosophers have coined the term "Gene-P" for the abstract gene concept. The "P" stands for "phenotype" indicating that this gene concept defines a gene by it's phenotypic effects and not its physical structure.

Physical genes consist of stretches of DNA with a beginning and an end. These are molecular genes that can be cloned and sequenced. Philosophers call them "Gene-D" where "D" stands for "development"-a very unfortunate choice.

you don't see where he talks about different definitions being used in different science fields, for specific reason relating to type of work ? abstract( functional) vs. developmental (physical) gene, Gene-P ( phenotype) vs. Gene-D (develpmental) ?

The genotype is one of the causes, though. It seems you're trying to distinctly separate two things that, for all intents and purposes cannot be separated. I never once said that a person's genotype is the sole cause of that person's phenotype.

is ultimately the way to environmental influence and the person's genotype (via other genetic products) interact that give a particular phenotype. You're also incorrectly, as Aedes has pointed out, attributing the meaning of "gene" with its function. Like Aedes, in all of my time spent around scientists and doing scientific work, never once have I heard "gene" used in a sense that would imply genetic modification or gene function.