Gene is a fragment of DNA which can be transcribed into functional RNA or translated into functional protein

Gene is a fragment of DNA which can be transcribed into functional RNA or translated into functional protein

From a reductionist point of view Siva´s answer sounds logical but exhaustively it does not cover all bases because if that were the case the UTR´s which are´nt by themselves transcribed but are key to transcription would not be part of the Gene. If I had to look at it simplistically gene is primarily DNA which is/or has the functional capacity as a combined unit in the presence of key enzymatic components to get transcibed/translated. The gene might infact have cis(continous) or trans(discontinous) components all of which at any point of time maybe apparent or not.

Arijit's definition might be more accurate in a sense, but it's so complex that it makes the term "gene" pretty useless. Anyone who is trying to understand "gene" would probably also fail to understand that definition. Siva's answer could be considered oversimplified by some, but it concisely expresses the meaning of "gene" as it's normally used by the informed public and by experts.

I work on the complex regulatory elements that Arijit is talking about, so I definitely appreciate their importance. A gene without its associated regulatory sequences (promoters, enhancers, insulators, silencers, etc.) wouldn't function. But I'm happy to let a gene be defined simply as a segment of the genome that makes a functional transcript, as Siva suggests. If you have to count everything that regulates a gene as part of the gene itself, then ultimately the whole genome would have to be defined as one massively complex gene, rendering the term meaningless.

Scott, maybe my definition is more philosophical..:)

Exactly Arijit! Your answer is for getting deep with your colleagues over drinks, and Siva's answer is for describing your work to your friends in the humanities. I'm sorry to criticize your answer, which is a very good one, but I worry that people sometimes get very complicated answers on this forum that could leave them more confused than before. People need to start simply and then add the interesting complexities as they go forward.

The way genes were discovered and first described calls for the involvement of phenotype in the definition. I'd say a gene is a (the minimal?) hereditary unit capable of causing some phenotype. Nowadays we could add that it is a certain part of the DNA molecule, not as a definition, but rather a better specification of what we just defined above. Given what we already know about life, any attempt to specify the gene physically is probably doomed to end in some level of fuzziness. For example if a nucleotide at certain position could have any of the four bases without affecting the phenotype, should it be considered part of the gene or not?

Are you familiar with Cold Spring Harbor Laboratory - Dynamic gene site? http://dynamicgene.dnalc.org/

looking through genetics history from Mendel we learn the gene concept is dynamic: it evolves. The was the gone gene dogma, DNA - RNA - protein. We can look from function view point, the sequences, etc... to answer this question and explain particular phenomena.

To be simple, gene is such a reservoir that contains all the information that all living creatures need to function properly.

Why is it so difficult for biologists to openly admit that they don't know if the "gene" is an adequate concept for addressing the originally intended issues?

@Lev you are right...but as Scott put it in an early comment you have got to start someplace.

There is this article written by a philosopher of science and a biologist about the uses of the concept of gene. I hope it helps:

http://paul.representinggenes.org/webpdfs/Griff.Stotz.06.Postgenomic.pdf

Thank you Jesus, it's useful!

Arijit: ". . .but as Scott put it in an early comment you have got to start someplace."

The very big problem with such oversimplified "starts" is that, after a while, one is confusing (him/her)self and everyone else. In general, I find that biologists are quite inadequately educated/prepared for dealing with the 'abstractions' involved, which are supposed to guide them in their mainly experimental work. In particular, they are dealing with the 'hardware' (DNA) and are not really prepared to accept that, most likely, there is a much less visible 'software'.

Well you have the reductionist approach which is more suitable for a layman and you have the exhaustive approach which is suitable for someone working on minute details but yes the definition is by nature abstract and perhaps to encapsulate this idea into one constrictive definition would never be possible..its a matter of perspective.

Arijit: "perhaps to encapsulate this idea into one constrictive definition would never be possible."

I am much more optimistic: just because we live during an almost pre-scientific stage of biology, doesn't mean that it will last forever. ;--)

When we don't know a thing, we add a new name to it, whatever a thunder, a gene, gravity or mass... It is a philosophical discussion dealing with what is real or virtual, as Plato and Aristotle begun arguing long time back...

Lev,

when you say "Why is it so difficult for biologists to openly admit that they don't know if the "gene" is an adequate concept for addressing the originally intended issues?" what do you exactly mean with "originally intended issue"? Also, what makes you think that biology is in an almost pre-scientific stage?

Thanks All !!!

Markus: "what do you exactly mean with "originally intended issue"? "

How did the idea of "gene" appeared?

From http://en.wikipedia.org/wiki/Gene#History:

"The notion of a gene[11] is evolving with the science of genetics, which began when Gregor Mendel noticed that biological variations are inherited from parent organisms as specific, discrete traits. The biological entity responsible for defining traits was later termed a gene, but the biological basis for inheritance remained unknown until DNA was identified as the genetic material in the 1940s. "

Obviously, this is a very mechanistic, or simplistic, approach to the idea of "traits". These cannot be properly approached without a much better---than we currently have---understanding of, for example, developmental processes, or more specifically, of the nature of developmental "program". The latter, most likely, cannot be properly approached relying mainly on "genes".

Lev,

i see nothing wrong with the concept of genotype and phenotype and with the original and still to my opinion very correct use of the term gene. There are plenty of cases where traits have been successfully described, in fact so successfully that probably no one sees a need for changing this concept. Sure, there is plenty of refinement and certainly some traits are rather difficult to describe and in fact for many we dont yet know enough of the details. But i cant see why this would not be possible or why this cannot be properly approached. Its a matter of figuring out the details not changing the conecpts.

OK, Markus. Then, where and how is the complete developmental process/program is encoded?

its in the cell, which means DNA and cell machinery (without it the cell wouldnt be able to access the program). And as all cell components are phenotypes expressed through their genes, its in the genome. As you refer to development process/program it probably means that you'd need to extend this to the germ cells (in case of sexual reproduction) / the omnipotent stem cell / the mother cell.

What about the interaction of the developmental process with the "environment"?

By the way, your answer "its in the cell, which means DNA and cell machinery" is not really a concrete scientific answer to my question.

agreed, there are some interactions but i would say by and large they are not so important, evolution has consistently favoured solutions for shutting off the environment during ontogenesis. Environmental interactions / stimuli are of course important for development of sensory systems etc... but nevertheless, this doesnt disclassify the stndard definition of a gene. A "word" is also not an insufficient concept just because someone needs to read it ´.

Have you heard, for example, of the "bioelectric code"?

http://www.whatayear.org/06_13.php

and

http://sites.tufts.edu/biip2012/files/2012/05/Levin2012.pdf

I still would go with gene as a DNA sequence that codes for a functional RNA or protein which is controlled by several regulatory elements which is not of our concern when we define a gene in simple terms

Siva: "I still would go with gene as a DNA sequence that codes for a functional RNA or protein "

But if we don't know the *structure* of the overall process 'running', among other things, genes, how can we be sure about their 'true' role?

Let me give you a simplified analogy. Take a person from, let's say, 5th century B.C., and show him/her *only* the changing states of the RAM (random-access memory) as they are observed when some program is running. How would that person be able to get an adequate understanding of what is going on?

Lev: I agree with you that it is important to know the structure of the gene to understand the function but that is more than what you are asking for in a simple difinition

Lev,

the bioelectric code and morphogenetic fields would again be a conseqeunce of the genes and their regulation, i cant see in how far this would necessitate a new definition of the gene. Also, your example supports my point. You dont need to change the defintition of "Bit". Surely you do need additional (auxiliary) levels of understanding (programming language, software in your example) but in the end everything can be reduced to the bit state (physiological state of the cell) and processor architecture (genome).

You say: "But if we don't know the *structure* of the overall process 'running', among other things, genes, how can we be sure about their 'true' role?".

We cant, and we never can. There is no absolute certainty. As scientist we have to constantly test our theories against reality, refine and improve them and sometimes completely reject them. The key here is not to claim that a theory/model/hypothesis is insufficient but to point out exactly where it fails and then provide an alternative hypothesis, that can be tested. For this discussion, can you provide "A Case", an example that clearly shows that our common definition of a gene is insufficient? I am not refering to abstract cases of the type " we havent understood at all how this and that works" (as the reason for this is likely that we havent spend enough time yet to work it out), i am refering to a detailed case.

I guess, similar to my simplified analogy with RAM, everything comes to the following choice:

Has the emergence and evolution of DNA (RNA) been 'guided' by the structure of some generalized 'developmental' process, which is probably of informational nature, or has it been the other way around?

gene is a specifi DNA sequence and structure which carry a genetic informations

Shinedalgarno sequence, start codon, endcodon. And?

One cannot generalize on S-D seq while defining a gene for obvious reasons

"When people say Gene, they have no idea what was the gene was. It's just a name for whatever it was."

Quote from Prof Eric Lander.

So, Anthony; this throw us back at the beginning of the discussion...

Again, given the educational background of almost all biologists, I believe that this discussion is not productive: presently, gene is viewed as a part of the 'hardware'---the only presently accessible part of the the corresponding informational system---and hence its true function/meaning cannot now be adequately perceived, or assessed.

Gene as an "unit on expression". Give to expression anything you want...