1
   

is Phenotype All ?

 
 
Aedes
 
  1  
Reply Tue 16 Jun, 2009 03:24 pm
@memester,
memester;69710 wrote:
Esteemed scientists say it is so - it's so regardless of your experiences.
Esteemed scientists aren't what matter. It's usage that matters. But since you bring them up I've worked with a lot of esteemed scientists in this field and while I won't speak for them they all have a consistent use of a basic word like "gene". And Dawkins esteem isn't as a scientist, by the way. He's a writer with popular appeal to atheists who feel affronted. I'm an atheist who has no need for his point of view.
0 Replies
 
memester
 
  1  
Reply Tue 16 Jun, 2009 03:30 pm
@Aedes,
Aedes;69703 wrote:
No, I don't see that, am I just missing it? He talks about philosophers' coinage of different terms, and he talks about the so-called gene-p as an abstraction of the genetic determinant of a phenotype, but he to my reading doesn't talk about differential usage in different fields of science.


I'm quoting here;
Quote:
Most geneticists and many evolutionary biologists use an abstract gene concept.


---------- Post added at 05:33 PM ---------- Previous post was at 05:30 PM ----------

Aedes;69712 wrote:
Esteemed scientists aren't what matter. It's usage that matters. But since you bring them up I've worked with a lot of esteemed scientists in this field and while I won't speak for them they all have a consistent use of a basic word like "gene". And Dawkins esteem isn't as a scientist, by the way. He's a writer with popular appeal to atheists who feel affronted. I'm an atheist who has no need for his point of view.

they are what matters for our discussion, as I'm knitting together what esteemed scientists say !
As for Dawkins, he is the Chair of Public Understanding of Science, a position of esteem. I think he's the worst thing since the Pinto. But no matter, that.

I want to stress that in no way do I reject your preferences, or experience per se, but for this discussion I am looking to what various authorities say, to make the point in the first post. I do acknowledge that many will not have heard that there are several meanings to the words "gene" , "genetics", "phenotype", and so on.
Know what I mean ? I'm not asking "What decade did you go to school for this ?" or "When was the last time you had a paper on this published ?" :flowers:

as for me, I'm an outsider, and would have to answer "never".:bigsmile:
Aedes
 
  1  
Reply Tue 16 Jun, 2009 08:28 pm
@memester,
memester;69714 wrote:
I'm quoting here...
That's a very vague statement and I don't agree that what he's communicating is the presence of some sort of lexical division within the biological sciences.

memester wrote:
they are what matters for our discussion, as I'm knitting together what esteemed scientists say !
Well, it may be interesting to see, but unless you get them all in a room and ask them all the exact same question, then their musings on the subject aren't going to shed light on the functional use of a word like "gene" in science. They may alternatively define it, but then again 100 esteemed sciences may also alternatively define "dog" or "amoeba".

If you really want to answer this question, just go into medline or some other scientific journal search engine and type in "gene" as a search term. Then go through articles and determine whether there is a consistent difference in its use between medical scientists / physicians, evolutionary biologists, developmental biologists, molecular biologists, etc.
memester
 
  1  
Reply Tue 16 Jun, 2009 09:04 pm
@Aedes,
Aedes;69786 wrote:
That's a very vague statement and I don't agree that what he's communicating is the presence of some sort of lexical division within the biological sciences.
What is he communicating, then? To me, it seems very clear and concise. He talks of the two general classifications that are used, and tendency to use them by which kind of scientist. I was challenged to show that what I claimed was supported by evidence, and I have just done so; a first deposit. Scientists, not just a philosopher, do use the abstract concept, and others use the physical entity concept.
Quote:
Most geneticists and many evolutionary biologists use an abstract gene concept.
Quote:


Well, it may be interesting to see, but unless you get them all in a room and ask them all the exact same question, then their musings on the subject aren't going to shed light on the functional use of a word like "gene" in science. They may alternatively define it, but then again 100 esteemed sciences may also alternatively define "dog" or "amoeba".
they may, and if it turns out that "dog" can be considered to be "amoeba", through equating, then I want to point that out. And figure out where the weakness lies.

Quote:
If you really want to answer this question, just go into medline or some other scientific journal search engine and type in "gene" as a search term. Then go through articles and determine whether there is a consistent difference in its use between medical scientists / physicians, evolutionary biologists, developmental biologists, molecular biologists, etc.
that's what prompted this thread.
Aedes
 
  1  
Reply Tue 16 Jun, 2009 09:09 pm
@memester,
memester;69794 wrote:
What is he communicating, then? To me, it seems very clear and concise. He talks of the two general classifications that are used, and tendency to use them by which kind of scientist.
He's generalizing without any detail at all, and his only elaboration is in philosophers' uses of the term. The 'abstract gene' concept is often in my readings not really talked about as a 'gene' unless a trait is known to be monogenic, or if it is a specific gene product under discussion. Otherwise, if we have a complex phenotype that is presumed to be genetic but the gene(s) is/are not known, we refer to "genetic determinants". For instance if we agree that schizophrenia runs in families and we don't know the responsible gene(s), we may speak abstractly as the genetic determinant of schizophrenia. The other gene concept he talks about is not at all mutually exclusive with this -- it just gets down to the nitty gritty of what's on the chromosome that gives us a gene transcript.
memester
 
  1  
Reply Tue 16 Jun, 2009 09:15 pm
@Aedes,
and for that, I'll find at least one paper written on the subject by an expert. Larry has some other pages that go into more detail, as well.
Quote:
his only elaboration is in philosophers' uses of the term.
I don't think so. He mentions that philosophers have distinguished the two, but he then says that scientists use that abstract concept.. why would he need to re-iterate ?

I don't think it's necessary to show that either of the two general kinds have definitions that would be considered exclusive of one another. No reason to assume they are, no reason for them to be.
Just as the very many "species" concepts are used, for differing purposes..a hammer doesn't have to exclude a trowel as a tool.
0 Replies
 
Aedes
 
  1  
Reply Tue 16 Jun, 2009 09:26 pm
@memester,
Either way, this is not even his point -- his point that which follows, i.e. the source of a gene transcript can be a number of complex variants. His (very!) brief statement about the semantics of a gene is just a prelude.

But again, the way to prove this one way or another is to study it. Study usage of the word in practice by looking at the actual literature. If that's even important enough a question to demand the effort...
memester
 
  1  
Reply Tue 16 Jun, 2009 09:40 pm
@Aedes,
Aedes;69799 wrote:
Either way, this is not even his point -- his point that which follows, i.e. the source of a gene transcript can be a number of complex variants. His (very!) brief statement about the semantics of a gene is just a prelude.

But again, the way to prove this one way or another is to study it. Study usage of the word in practice by looking at the actual literature. If that's even important enough a question to demand the effort...
His "point" is not important to this discussion. His point is about his use. His preamble tells you that I was correct; that evolutionary biologists and geneticists often use the abstract concept.

I have been searching and searching through papers...you can tell, that for an uneducated person, I have the on-topic links to show that I have been searching...you noted the blogger on "Heritable vs. Genetic Traits" was good...you don't find that kind of thing without searching, and learning which is good and which is pap.
memester
 
  1  
Reply Wed 17 Jun, 2009 04:45 am
@Aedes,
Aedes;69665 wrote:


There are no RNA genes except in RNA-based viruses like HIV and influenza.
Hi Paul. There are many arguments that are quite interesting on why "gene" can be said to include RNA.


RNA genes - Google Search

but again, I think that it's all part of showing why a dog is an amoeba

Here's Paul Griffiths, who helps explain why there is disagreement and even more confusion about the word "gene", and it may help fit together a better overall appreciation of how people can think so differently about the same word, and why some scientists vascillate or conflate. Noted that now we are into 3 concepts Smile

http://philsci-archive.pitt.edu/archive/00002641/01/Genes_postgenomic_era.pdf


0 Replies
 
Aedes
 
  1  
Reply Wed 17 Jun, 2009 08:37 am
@memester,
memester;69801 wrote:
His "point" is not important to this discussion. His point is about his use. His preamble tells you that I was correct; that evolutionary biologists and geneticists often use the abstract concept.
Again, all he offers is a vague generalization about evolutionary biologists and geneticists (even though those two terms are FAR more vague than the term "gene"). I am asking you for a systematic demonstration that the word "gene" and the idea of "gene expression" are synonymous, which is what launched this discussion.

memester;69801 wrote:
I have been searching and searching through papers...you can tell, that for an uneducated person, I have the on-topic links to show that I have been searching...
I believe you, but you're not going to get a credible answer by searching through blogs, simply because this is not a method of science communication that has any sort of checks or balances. Anyone can write a blog. Not anyone can pass editorial muster to write a journal article. People have been talking about the scientific lexicon for generations, and they've been talking about genetics since Mendel, so we can do better than blogs.
memester
 
  1  
Reply Wed 17 Jun, 2009 09:24 am
@Aedes,
Aedes;69884 wrote:
Again, all he offers is a vague generalization about evolutionary biologists and geneticists (even though those two terms are FAR more vague than the term "gene"). I am asking you for a systematic demonstration that the word "gene" and the idea of "gene expression" are synonymous, which is what launched this discussion.
But that is not what was needed previously. This is changing the goalposts. And as well, I did provide the abstract of the paper that shows such a division. Now you claim that what was asked for was more vague than the word "gene". You didn't claim that earlier. Soon I'll have to prove what "biology" means, or what "life" means - it's all so vague. Is all that really my problem ?

Quote:

I believe you, but you're not going to get a credible answer by searching through blogs
the blog I mentioned was only a sample showing that I'm not looking at pap. Blogs by scientists can show that what I claimed is not my imagination working overtime, as seemed to be suggested. I have been reading PAPERS, was what I said. Not just blogs. I don't have much access to all the papers in full though. Mostly I can get abstracts only.

Quote:
simply because this is not a method of science communication that has any sort of checks or balances. Anyone can write a blog. Not anyone can pass editorial muster to write a journal article. People have been talking about the scientific lexicon for generations, and they've been talking about genetics since Mendel, so we can do better than blogs.
anyone can claim that a scientist who writes peer reviewed literature blogs not believable evidence, too ! I haven't been shown to be wrong here, from what I can tell. Where have I been shown to be in error ? I'm not finished with investigating, but my question is what was wrong with my opening posts ?

Passing muster, as you call it, can be a very internecine thing. Sometimes all involved are intimately related, all had the same teacher, or the teacher of the teacher...all work together, all have similar views.

I was talking to one person for a while, and only when I disclosed that I had access to biologist-collected samples of what they were supposed to be studying, did he tell me that he was judging on the board for the upcoming paper I was questioning for method.

He had the same teacher as the student's teacher. Long-time friends of the prof and of the prof's prof. Everyone in a small enough field is intimately connected

and the in the study, they didn't actually use proper specimens from the locale in question...just any old sample collected from varous locales that had been labeled as such..where the top biologist/collector in the world insists it is not the same organism.

The prof in charge responded that it would indeed be interesting to get a hold of the real thing from the holotype collection locale..but no follow up, the paper was a week or so from being submitted.
and this is from the prof who is considered the the leading scientist in that area of cladistic research.
the excuse given me by an associate is that there is no money to go get proper samples..even though they were all somewhat surprised to find NO suitable holotype or related specimens of the genus in institutions, just as most really interested parties had insisted for years..

so peer review might be what you think it is, or it might not be.

right now I'm investigating ideas, not compiling extensive lists of peer reviewed papers in a mountain of evidence showing what I said , to be true.
As if there are extensive lists of papers showing it to be true.

what you're saying is that I need to build a case that's strong, to show that my whimsical proposition can be backed with solid research.
but I only only asked where my proposition was obviously wrong.
I have a shown that some esteemed scientists use the word in the way I said they did, and I have shown that it is not at all uncommon.

I don't need to show percentages of use, within differing scientific fields. That's merely setting up roadblocks instead of commenting on where I am wrong.
Now, if you are a prof that will get me an honorary degree in one of those vaguely defined scientific areas from a respected university if I do so, it might be different. :poke-eye:

It seems to me to be more a philosophical question than a scientific one.
Aedes
 
  1  
Reply Wed 17 Jun, 2009 11:57 am
@memester,
memester;69891 wrote:
Blogs by scientists can show that what I claimed is not my imagination working overtime, as seemed to be suggested. I have been reading PAPERS, was what I said.
Well, if there is semantic disagreement about whether a gene is a thing (or group of related things) as opposed to a process that concerns this thing, then it will only be revealed through this search of papers. And I think you'll find that processes concerning a gene are referred to by the name of the process, be it gene expression or gene silencing or whatever.

memester;69891 wrote:
anyone can claim that a scientist who writes peer reviewed literature blogs not believable evidence, too
But the blog is not peer reviewed.

memester;69891 wrote:
so peer review might be what you think it is, or it might not be.
I know what it is, having peer-reviewed grants and peer-reviewed papers of my own. The world is sometimes small and rarified in science, and people know each other, it is true. And peer-review is not failsafe. But at least it upholds a certain quality threshold that does not exist in journalism, in blogs, in opinion pieces, etc.

memester;69891 wrote:
what you're saying is that I need to build a case that's strong, to show that my whimsical proposition can be backed with solid research. but I only only asked where my proposition was obviously wrong.
You propose something that is unorthodox, so shouldn't you own the responsibility of supporting it?

But it wasn't in your first post that I had any disagreement. Here is your first post:

memester wrote:
Definitions of "phenotype" are usually shown in contrast to "genotype"...
So how is it that the genotype is never thought of as part of a possible phenotype ?
I don't have a problem with this. My response was more or less that regulation of gene expression is a phenotype unto itself. If I could elaborate, what I mean is that the most fundamental manifestation of phenotype is indeed the control of gene expression.

Why would I not include gene expression under the conceptual umbrella of a "gene"? Simply because the gene is what is inherited, and it's fundamentally what specifies all phenotypes including its own regulation.

I have a shown that some esteemed scientists use the word in the way I said they did, and I have shown that it is not at all uncommon.

memester wrote:
Now, if you are a prof that will get me an honorary degree in one of those vaguely defined scientific areas from a respected university if I do so, it might be different.
I am a prof, and from a quite well respected university, but regrettably I don't have influence over honorary degrees Very Happy
memester
 
  1  
Reply Wed 17 Jun, 2009 02:41 pm
@Aedes,
Aedes;69906 wrote:
Well, if there is semantic disagreement about whether a gene is a thing (or group of related things) as opposed to a process that concerns this thing, then it will only be revealed through this search of papers.
Incorrect. What would be revealed is ( in peer reviewed papers) which scientist used it which way, and when, and then numbers put to it.

Quote:
[And I think you'll find that processes concerning a gene are referred to by the name of the process, be it gene expression or gene silencing or whatever.
Sure, they use those terms to talk about the different processes, but that does not mean that they don't also refer to the group of processes or things as a "gene", as already shown.

Quote:
But the blog is not peer reviewed.
Sure they can be and sometimes are reviewed and commented upon by peers with names. It's just not the kind of peer review you would demand. Whether or not you give credence to books, articles, blogs, or lectures is your decision.
Quote:


I know what it is, having peer-reviewed grants and peer-reviewed papers of my own. The world is sometimes small and rarified in science, and people know each other, it is true. And peer-review is not failsafe. But at least it upholds a certain quality threshold that does not exist in journalism, in blogs, in opinion pieces, etc.
the superior quality assurance is existent only as far as the single item is concerned, whereas a more comprehensive understanding of what goes on comes through looking into lectures, books, blogs, relplies, articles.
Quote:

You propose something that is unorthodox, so shouldn't you own the responsibility of supporting it?
I have supported it, but now you require more than is necesary for supporting it.
Quote:


But it wasn't in your first post that I had any disagreement. Here is your first post:

I don't have a problem with this. My response was more or less that regulation of gene expression is a phenotype unto itself. If I could elaborate, what I mean is that the most fundamental manifestation of phenotype is indeed the control of gene expression.

Why would I not include gene expression under the conceptual umbrella of a "gene"? Simply because the gene is what is inherited, and it's fundamentally what specifies all phenotypes including its own regulation.
that doesn't mean that many scientists don't do so, as I have shown evidence for.

I have a shown that some esteemed scientists use the word in the way I said they did, and I have shown that it is not at all uncommon.
Quote:
I am a prof, and from a quite well respected university, but regrettably I don't have influence over honorary degrees Very Happy
then why should I be concerned with finding, analysing, and supplying the result of that in order to satisfy an uneccessary, onerous demand ?
Aedes
 
  1  
Reply Wed 17 Jun, 2009 02:54 pm
@memester,
memester;69925 wrote:
Incorrect. What would be revealed is ( in peer reviewed papers) which scientist used it which way, and when, and then numbers put to it.
We're not concerned with "which scientist". Many scientists do a combination of things in their research. Furthermore, nearly all papers have multiple authors and numerous collaborations. What we're concerned with is the domain-specific use of the term. So you'd need to categorize papers based on the type of scientific question being asked.

memester;69925 wrote:
Sure, they use those terms to talk about the different processes, but that doesn ot mean that they don't also refer to the group of processes or things as a "gene", as already shown.
Shown where?? All you've shown me is one guy who claims that this is true in philosophical terms, and then makes an unsupported vague statement that you have yet to demonstrate with any specific corroboration.

memester wrote:
It's just not the kind of peer review you would demand. Whether or not you give credence to books, articles, blogs, or lectures is your decision.
Was the blog in question peer-reviewed?

---------- Post added at 04:56 PM ---------- Previous post was at 04:54 PM ----------

memester;69925 wrote:
then why should I be concerned with finding, analysing, and supplying the result of order to satisfy an uneccessary, onerous demand ?
It should be an enobling challenge if you are actually interested in asking this question. It is only onerous if you're satisfied with a half-assed generalization (and no offense is intended by that -- but you're standing quite firm for something you've made little effort to support).
memester
 
  1  
Reply Wed 17 Jun, 2009 03:06 pm
@Aedes,
Aedes;69927 wrote:
We're not concerned with "which scientist". Many scientists do a combination of things in their research. Furthermore, nearly all papers have multiple authors and numerous collaborations. What we're concerned with is the domain-specific use of the term. So you'd need to categorize papers based on the type of scientific question being asked.
another change. what you said one post back was this
Quote:
Well, if there is semantic disagreement... then it will only be revealed through this search of papers.
It seems that you need me to show that one specific field uses one kind, and another field uses the other kind; that's not what I claim. It could potentially be a mix, too, with conflation happening. I'm not at all interested in showing that "this guy is in this branch of evolutionary biology or genetics or paleontology" when he uses "gene" this way or that.



please bear with me, my pc is shutting down every few minutes.Perhaps I will have to go point by point , then answer the reply to each.

why would I need to delineate the differences between various kinds of "vaguely described' evolutionary biologists or geneticists in order to show that the different meanings ARE employed ?

---------- Post added at 05:17 PM ---------- Previous post was at 05:06 PM ----------

Aedes;69927 wrote:


Shown where?? All you've shown me is one guy who claims that this is true in philosophical terms, and then makes an unsupported vague statement that you have yet to demonstrate with any specific corroboration.
Paul Griffith's article, for one. He describes who, where, when, and why. I can fetch more articles by different people, book reviews and replies to criticism and so on, too.


Quote:
It should be an enobling challenge if you are actually interested in asking this question. It is only onerous if you're satisfied with a half-assed generalization (and no offense is intended by that -- but you're standing quite firm for something you've made little effort to support).
"enobling gas" ? :bigsmile:

It doesn't take much effort to support, as it's fairly obvious. why spend more than it takes to prove a point, if half my ass can do the trick ?

Effort expended is not the measure of success that I use.

Of course I stand firm. Why wobble ?
Aedes
 
  1  
Reply Wed 17 Jun, 2009 07:47 pm
@memester,
memester;69932 wrote:
Of course I stand firm. Why wobble ?
Because those who are wise know that they forever might be wrong Smile
memester
 
  1  
Reply Wed 17 Jun, 2009 09:43 pm
@Aedes,
Aedes;69989 wrote:
Because those who are wise know that they forever might be wrong Smile
oh, I'm always wrong, to some extent, but I'm so often right, that I don't wobble. Wobbling MAKES you more wrong.No need to feed that.
When I admitted I was deluded, I wasn't, you see.
0 Replies
 
Aedes
 
  1  
Reply Wed 17 Jun, 2009 09:46 pm
@memester,
When I'm wrong I'm wrong.

When I'm right, I reserve the privilege to be wrong at a later date.

If that's not a wobble, I don't know what is!
memester
 
  1  
Reply Wed 17 Jun, 2009 09:47 pm
@Aedes,
When you're hot, you're hot - and when you're not, you're not.

You could send my degree in a plain brown wrapper...I don't want anyone to know I indulge in that stuff.
0 Replies
 
Aedes
 
  1  
Reply Wed 17 Jun, 2009 09:57 pm
@memester,
If I hope to keep my job, that's the only kind of degree I'll be sending you. Don't spend too much time near the mailbox quite yet, i'm collecting pennies for postage.
 

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