is Phenotype All ?

@memester,

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then may I suggest we cooperatievely avoid that stench, by having you stick by your words !

Fair enough. I will try my best to be as clear as possible from now on. See my edit on my previous post for clarification.

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do you now have a problem with "gene expression"?

Sort of. If anything, I would prefer "gene regulation" for what we are talking about. Gene regulation, as defined in Genetics: A Conceptual Approach, 3rd edition is the "mechanisms and processes that control the phenotypic expression of genes." Gene expression is defined to be the "production of an observable molecular product (RNA or protein) by a gene" (The Molecular Biology of the Cell, 5th edition).

It seems that gene regulation, as defined above, is more representative to what this discussion is actually about than gene expression is, as we are less concerned with the actual product of the gene than we are with what causes a gene to be expressed (specifically direct environmental influences).

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@gregulus,

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To be more clear about epigenetics, the environmental impact doesn't directly effect the expression of genes.

Please make your changes in this. Smile

I think it would be this part you'd want to change ?

taken from this, which is "Gene regulation"

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Edit: To be more clear about epigenetics, the environmental impact doesn't directly effect the expression of genes. Rather, the environmental stimulation influences other cellular mechanisms that then regulate the gene.

You see, going "Abstact Gene concept", you get that "bundled in" with your monthly bill at no extra cost.

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@memester,

My edit would be as follows:

To be more clear about epigenetics, the environmental impact doesn't directly* effect the regulation of gene expression. Rather, the environmental stimulation influences other cellular mechanisms that then regulate the expression of the gene.

* "directly" should be taken to mean what it does here, http://www.philosophyforum.com/forum/philosophy-forums/branches-philosophy/philosophy-science/4781-phenotype-all-6.html#post70528

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@gregulus,

gregulus;70534 wrote:

My edit would be as follows:

To be more clear about epigenetics, the environmental impact doesn't directly* effect the regulation of gene expression. Rather, the environmental stimulation influences other cellular mechanisms that then regulate the expression of the gene.

* "directly" should be taken to mean what it does here, http://www.philosophyforum.com/forum/philosophy-forums/branches-philosophy/philosophy-science/4781-phenotype-all-6.html#post70528

Are you sure that's what you're trying to say ? it looks like you defined the definition as the definition.

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the environmental impact doesn't directly* (sp. ? [a]) [e]ffect the regulation of gene expression.

"regulation of gene expression" is "gene regulation", to many.

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Rather, the environmental stimulation[< substituted for "impact"] influences[<substituted for "affects"]

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other cellular mechanisms that then regulate the expression of the gene.

or, to put them back together, in plain and unshifting english.

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the environmental impact doesn't directly* affect gene regulation . Rather, the environmental impact affects gene regulation

1 Reply

@memester,

memester;70536 wrote:

Are you sure that's what you're trying to say ? it looks like you defined the definition as the definition.

I was just trying to be as clear as possible. If you know what directly means, then yes, that's what I am trying to say. My argument is that the environment doesn't directly regulate the expression of genes. Instead, it stimulates other cellular responses that then act to regulate the expression of genes.

I continued to use "regulation of gene expression" instead of "gene regulation" because I wasn't sure you had read the part where I defined gene regulation. They are being used as synonyms.

Out of curiosity, am I being trolled?

For an idea of how regulation and expression are being used,

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If anything, I would prefer "gene regulation" for what we are talking about. Gene regulation, as defined in Genetics: A Conceptual Approach, 3rd edition is the "mechanisms and processes that control the phenotypic expression of genes." Gene expression is defined to be the "production of an observable molecular product (RNA or protein) by a gene" (The Molecular Biology of the Cell, 5th edition).

It seems that gene regulation, as defined above, is more representative to what this discussion is actually about than gene expression is, as we are less concerned with the actual product of the gene than we are with what causes a gene to be expressed (specifically direct environmental influences).

(This was an edit to a previous post).

1 Reply

@gregulus,

gregulus;70541 wrote:

I was just trying to be as clear as possible. If you know what directly means, then yes, that's what I am trying to say. My argument is that the environment doesn't directly regulate the expression of genes. Instead, it stimulates other cellular responses that then act to regulate the expression of genes.

Out of curiosity, am I being trolled?

For an idea of how regulation and expression are being used,

(This was an edit to a previous post).

being trolled..let's just say that you equivocate a lot. it's normal. it's hard to avoid because we've been taught through the means of equivocation, to accept what is being forwarded.
but it can easily be avoided by sticking with terms used.

1 Reply

@memester,

memester;70542 wrote:

being trolled..let's just say that you equivocate a lot. it's normal.

Ha. You're probably right about that. At least I finally caught on.

Is it clear now what I mean?

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@gregulus,

sorry that I have to edit and edit..my pc shuts down and wipes out my post, so I post fragments, and edit if i get time.

it's clear as mud.

you probaby misssed my post #64 above, as I was editing as you were posting. It's more explanatory now.

recheck now again. it's finished . at the bottom of post 64

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@memester,

The environmental influence doesn't directly effect gene regulation. Rather, the environmental influence stimulates other cellular mechanisms that then affect gene regulation.

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@gregulus,

gregulus;70547 wrote:

The environmental influence doesn't directly effect gene regulation. Rather, the environmental influence stimulates other cellular mechanisms that then affect gene regulation.

why are you changing words from phrase to phrase ? we have to literally control your variables in speech at this point, as in an experiment where it's necessary to control the variables, in order to get anywhere.

so let's take it as you have it here then.

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Environmental influence doesn't directly affect gene regulation.

Is that the challenge ? to show that it does ? Further back you already show that you know it does. When you were talking to Paul, about the fact that he was showing some of the example of that. So I don't think that's the challenge.

There is a reason people like the abstract concept.

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@memester,

memester;70548 wrote:

why are you changing words from phrase to phrase ? we have to literally control your variables in speech at this point, as in an experiment where it's necessary to control the variables, in order to get anywhere.

so let's take it as you have it here then.

environmental influence doesn't directly affect gene regulation

This is what I've been arguing all along. All of this because I used "effect" instead of "affect" and "regulation of gene expression" instead of "gene regulation?"

This whole semantics thing was just a giant red herring, btw.

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@gregulus,

i don't object to you using "effect" for "affect', I merely try to use them properly myself.
I need to mention it to show why I was not accepting your word - as I think it's the wrong word.

I had thought it was a spelling error, but you're using the wrong word, and I tried to use the right word in my explanations.

I'll just leave it as is, even though I changed your word for my explanations.

Please accept my apologies for changing your word, I did it for expediency.

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@memester,

It honestly was a spelling error at first. I just kept inadvertantly glancing over it during my revisions.

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@gregulus,

so we're all good on that.
now what are we to do with this to make it mean something ?

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the environmental impact doesn't directly* affect gene regulation . Rather, the environmental impact affects gene regulation

Paul and you have already shown that environment directly influences OR directly affects ( whichever you like) gene regulation - as opposed to showing it directly affects DNA sequence ( classical gene)

I think my challenge may in fact be to show that environmental influence causes change in gene expression that is not from change to the DNA sequence, the classical gene, and not even from change to the classical units of gene regulation..right ?
Might be fun to check for that under the bikini line again. I'll google about under "suntan", maybe "agouti". :a-thought: I'm sure they haven't done enough research on phenotype "blue" for hair, or phenotype "crew cut", so I have to think tangentially.

I wonder if you consider "gene expression" to be "the phenotype" ? I think most do.

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@memester,

memester;70527 wrote:

The challenge is to show change in gene expression without change in DNA sequence, was it not ?

That's a very easy thing to show in the lab. You can do quantitative RNA reverse PCR to quantify the amount of transcript. You can do Western blots to quantify the amount of the protein gene product. And you can sequence the protein, sequence the RNA, or sequence the genome of the cell to ascertain that the sequence has not changed.

The hard part is elucidating the mechanisms that regulate expression.

memester;70552 wrote:

I think my challenge may in fact be to show that environmental influence causes change in gene expression that is not from change to the DNA sequence, the classical gene, and not even from change to the classical units of gene regulation..right ?

Again, that's easy to show. Do some reading into gene expression during mosquito diapause. When the number of daylight hours drops below a certain number, there are marked changes in gene expression, and this induces a sort of hibernation called diapause. Or look at gene expression during sporulation under stress conditions in bacilli.

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@Aedes,

Aedes;70581 wrote:

The hard part is elucidating the mechanisms that regulate expression.

Not a problem for the "Abstract Gene Concept" users. an not a problem for me, because for now I am holding to the classical physical "gene" concept, as is gregulus. Classical physical "regulatory mechanisms", too.

It wouldn't make consistent sense. to go classical physical for "gene" and then abstract for "regulator"

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@memester,

The concept isn't the problem. Having an "abstract gene concept" doesn't make biology benchwork any easier or harder.

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@Aedes,

Aedes;70602 wrote:

The concept isn't the problem. Having an "abstract gene concept" doesn't make biology benchwork any easier or harder.

No, but it makes getting out of a sandtrap easier. Otherwise we have to stay consistent, with physical entities being "gene" and "regulator".

The question can still be answered, either way, by showing an environmental influence that changes phenotype without having to change the classical physical gene or change it's physical regulators in order to do so.

What I'm being cautious of is gregulus going Ultra Dawkins Abstract and could therefore legitimately claim that ANY influence that affects gene expression is, by definition, a "regulator".

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@memester,

The concept doesn't matter. Honestly, just spend 5 minutes in a lab and it will be obvious. Biological research is about surmounting technical problems to get information. It's technically easy to sequence genes, technically easy to measure gene activity (as evinced by the quantity of gene transcripts), and it's easy to measure these things under different environmental conditions. The hard part is fishing for the intermediate elements that regulate the gene's activity.

But it's all the same technicalities whatever your gene concept.

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@Aedes,

Aedes;70614 wrote:

The concept doesn't matter. Honestly, just spend 5 minutes in a lab and it will be obvious. Biological research is about surmounting technical problems to get information.

Fortunately, that's where abstract thinking comes in, unfortunately.
Biology can also be about finding new or different ways to look at things.
Users of the abstract concept can show where users of the physical concept have holes to fix, and vice versa.

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It's technically easy to sequence genes, technically easy to measure gene activity (as evinced by the quantity of gene transcripts), and it's easy to measure these things under different environmental conditions. The hard part is fishing for the intermediate elements that regulate the gene's activity.

But it's all the same technicalities whatever your gene concept.

You don't need to know those, if you claim you're using an abstract concept. that's the whole point, Paul. Abstracters can assume all those things are included, gratis, whether it's a classical physical regulator, transcription or translation mechanisms, sunlight, moon phase, presence of pheromone...it's an "Understood", that the all the necessary elements ARE in operation, and they go from there, to prove a point about evolution.
They just need to insist that gene expression IS regulated, whether by internal or external factors, and be done with it.
And that takes us right back to the equation, Square One:
Phenotype is Genotype and Environmental Influence. Sometimes now seen with "plus 'random' variation".( likely somatic variation as a cherry )

By going "abstract" you get to say more but have less chance of being wrong as a result of saying more. Through equivocation, and sliding between abstract and physical, a Dawkins can say that chemical reactions show Selfish Nature, as electrons are being selfishly taken.
If someone claims it's altruism or selflessness, when giving, he then claims it's selfishly motivated altruism.

It's astounding, to me, the various people who buy this, whilst showing no other obvious signs of impairment.

But there are real uses, as well as Dawkins' uses, for abstraction.

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