"Genes" a misnomer

[bweir123]

Hi to all here.

Just lately I have taken to correcting people on their use of the word "Gene". "DNA code you mean, a section/sequence of the DNA code" I tell them that DNA codes for body tissue only, therefore when someone says we have found the gay gene, an alcoholic or antisocial gene etc; we have a right to ask for what particular body tissue that DNA sequence codes for. Do scientists actually understand the DNA code well enough to be able to say exactly: that bit's for hair, that for bone and so?

[hypervalent_iodine]

I think you are misusing the word, 'tissue.' My understanding is that tissue is used to describe a set of cells of one particular type (muscle, liver, etc.). Genes code for proteins. You are probably right to question terminology such as, 'the gay gene,' etc., but I these are not phrases that scientists familiar with the area would use, IMO. You should also recognize that we are able to make associations between certain genes / mutations and various behavioural phenotypes. I don't think we have a complete picture for how exactly genes influence behaviour, but that is not the same as knowing whether or not they have an influence at all.

[bweir123]

There is no doubt that the DNA Code is responsible for constructing body tissue in all it's manifestations. How else is body tissue constructed? DNA is the blueprint for the construction of the Human body is it not? It's a glorified recipe book for body tissue and nothing more.

 

Have scientists reached the stage where they can take any section of the DNA code and say definitely what type of body tissue that section codes for, or are they still largely ignorant of what much of the DNA code is for? Because they cannot say that a particular sequence is responsible for intelligence, for instance, if they cannot say what physical attribute it is also responsible for.

[hypervalent_iodine]

Again, you are misuing the term tissue. DNA is responsible for the synthesis of tissue somewhat indirectly, which is to say that the proteins they actually code for (in addition to other pieces) are what build and make up the cells that comprise a given tissue. My point was that tissue is a term used to describe a given cell type and I think it is a mistake to say that "DNA codes for tissue", particularly since:

 

a.). Tissues are built up of things that DNA doesn't code for at all, but which come from the environment or that are synthesised by the proteins it does code for from things obtained through diet, etc.

 

And,

 

b.) DNA codes for genes that do other things besides make up the structural components of a cell (let alone a piece of tissue). Transcription factors, for instance.

 

Have scientists reached the stage where they can take any section of the DNA code and say definitely what type of body tissue that section codes for, or are they still largely ignorant of what much of the DNA code is for? Because they cannot say that a particular sequence is responsible for intelligence, for instance, if they cannot say what physical attribute it is also responsible for.

I think you are confusing laymen with actual scientists, here. As I said, we can (through the power of good experimental design and statistics) make associations between genes and mutations and certain phenotypes without knowing the physical mechanism that links the two together. No credible scientist would ever say that we know everything about how DNA works and no scientist would be able to tell you what every single gene did in order to create a certain line of tissue.

[bweir123]

My definition of tissue and DNA is perfectly all right.

The answer to my question is: Scientists have no idea what 98% of the Human Genome is for. They think that 20% is definitely junk, "pseudogenes" and most of the rest has no discernible purpose. But my guess is the bulk of the Human genome does have a purpose and their ignorance of its function merely reflects their general ignorance of the workings of the Human organism, particularly the brain and nervous system. What a shame it is they just can't say "We don't know" instead of "it's all a load of rubbish, there's nothing to know". So when they use matching DNA sequences to justify the inheritability of psychological traits, they may not be able to link those sequences to physical attributes, but you could ask, is that Junk DNA or what is it?

[hypervalent_iodine]

1. It definitely is not correct. Google is your friend.

 

http://en.wikipedia.org/wiki/Tissue_(biology)

http://www.merriam-webster.com/medical/tissue

http://www.biology-online.org/dictionary/Tissue

 

And something you desperately need to read:

http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology

 

2. Scientists do say, "we don't know," all the time. They especially say it in relation to DNA and genetics in general. If we did know it all or even claim to, then it would hardly be the active area of research it is, would it?

 

Edit: you might also want to look up what Junk DNA actually is while you're busy reading.

[Greg H.]

bweir, I'm going to stop you and offer you some friendly advice. There are a number of startlingly intelligent people who actively work in the field of science (in various disciplines) that are active posters on this site. If you stray down the path of spouting nonsense that contradicts established science, they will take you to task about it. It's fine if you want to propose new or alternative theories (though you should do that in the Speculations section) but you should be able to offer concrete evidence (or math) that backs up your side of the argument - without simply hand waving away decades of already established and validated research.

 

The simple fact of the matter is that the genes do not directly code tissues. They code and manage protiens - those proteins do most of the heavy lifting in building tissue, but they also do a good deal more including managing hormones, carrying oxygen in our blood, and developing neural pathways. There is no liver gene or muscle gene or skin gene. There are a variety of genes that contribute protein based instructions that determine these things,

[Ophiolite]

bweir, I urge you to read, re-read and then think carefully about the advice from Greg H. I see you have already attracted two negative reputation marks: that is quite an achievement after only three posts.

 

I would add a little further advice that I hope may be of service to you. Your comments on junk DNA suggest that you are gaining your information from pop-science sources: Discovery Channel documentaries, articles in newspapers, science magazines, general biology books. If these are your sources it is not surprising you have such flawed ideas. Concepts in these sources are typically dumbed down, simplified and dramatised.

 

Get a hold of some good textbooks and, as you study these, start to read relevant research papers. Or ask questions here, but please avoid arrogantly talking with confidence what you are obviously ill-informed about. Follow this approach and - as a side effect - that neg rep will quickly tun into a positive one.

[Arete]

My definition of tissue and DNA is perfectly all right.

The answer to my question is: Scientists have no idea what 98% of the Human Genome is for. They think that 20% is definitely junk, "pseudogenes" and most of the rest has no discernible purpose. But my guess is the bulk of the Human genome does have a purpose and their ignorance of its function merely reflects their general ignorance of the workings of the Human organism, particularly the brain and nervous system. What a shame it is they just can't say "We don't know" instead of "it's all a load of rubbish, there's nothing to know". So when they use matching DNA sequences to justify the inheritability of psychological traits, they may not be able to link those sequences to physical attributes, but you could ask, is that Junk DNA or what is it?

 

1. Non-coding DNA is not synonymous with "junk" DNA. We actually know a significant amount about the functions that non-coding DNA performs, including protection from frameshift mutations, regulatory functions, transcription factor sites, telomeres, etc. http://en.wikipedia.org/wiki/Noncoding_DNA#Functions_of_noncoding_DNA To say that " Scientists have no idea what 98% of the Human Genome is for." is plainly false. There's plenty of the genome that we don't know what does, but to say that everything non-coding is a mystery is just wrong.

 

2. Pseudogenes can perform evolutionary functions. For example I worked on Trypanosoma brucei for a while. 40% of the T. brucei genome is made up of pseudogene archives which encode a surface glycoprotein gene. Being non-expressed allows theses gene archives to mutate into novel forms, and about once every 100 clonal generations, the trypanosome will swap out the coding gene for a pseudogene via ectopic recombination, thus presenting the immune system of the host it's infecting with a new surface, and evading the host's immune response. http://en.wikipedia.org/wiki/Antigenic_variation Thus at least in this organism, pseduogenes perform a critical biological function. It's not inconceivable that for e.g. MHC pseudogenes in humans may play a similar role.

 

3. Coding genes encode proteins. A single cell is made up of many different proteins. A "tissue" in an organism is usually made up of a number of different cell types. Therefore, to say that genes encode tissues would be somewhat false. Multiple genes encode the proteins which make up each cell, their expression is controlled by other, regulatory genes, and tissues are made up of many such cells. We know which proteins a lot of genes encode, but there's a lot of genes which we don't. These are generally genomically annotated as hypothetical proteins. http://en.wikipedia.org/wiki/Hypothetical_protein

 

4. Scientists say they don't know stuff all the time. Even the example above - "hypothetical protein" implicitly suggests that we think there's a protein encoded by the gene, but there might not be and we sure as hell don't know what it is. Again, I've never even heard another geneticist use the term "junk DNA". That particular term is only really used in pop sci.

Edited June 12, 2014 by Arete

[bweir123]

Well if that's your attitude I'll post no more on this site.

[chadn737]

The word "gene" was originally coined long before we even knew that DNA existed and even longer before we knew DNA was the molecular basis of heredity. Originally, it was simply a term for a "unit of heredity". Because no known physical basis of heredity was known at the time, "genes" were abstract concepts and not referring to an actual physical stretch of DNA. The first geneticists would look at how traits, whether physical or behavioral, segregated and estimate the number of genes, the dominance/recessiveness of alleles, and the linkage of genes. This was all done in abstract, so at the time, it was valid to say that there is a "gene for X".

 

After the discovery of DNA as the basis of heredity, after it was known that proteins were encoded in the DNA, there was added a molecular definition of the word "gene" to mean a stretch of DNA that encoded a protein. What is interesting is that these two definitions coexisted and continue to coexist....in no small part depending upon the specialty of the scientist. Population geneticists, theoretical geneticists, quantitative geneticists still tend to think of genes somewhat in the abstract as "units of heredity" and not necessarily as protein coding sequences. Molecular biologists and biochemists think almost exclusively of "genes" as protein-coding.

With the discovery of non-coding RNAs with biological functions, the definition of a "gene" has been expanded somewhat to include those segments of DNA that code for non-coding RNAs.

 

So if you want to get anal about the definition of a gene, learn some history of genetics first.

 

4. Scientists say they don't know stuff all the time. Even the example above - "hypothetical protein" implicitly suggests that we think there's a protein encoded by the gene, but there might not be and we sure as hell don't know what it is. Again, I've never even heard another geneticist use the term "junk DNA". That particular term is only really used in pop sci.

 

Dan Graur....although he is more of an evolutionary biologist than a geneticist. Some great essays last couple of years attacking ENCODE. He makes a distinction between "junk" and "garbage" which has made me rather fond of the term "junk DNA".

 

The way he and others describe it, junk is stuff you have lying around that may someday be of use, while garbage is...well...garbage. Its a very long term evolutionary view, where the "junk DNA" lying around right now may not have a function, someday through evolution it may obtain a function.

Edited June 12, 2014 by chadn737

[Ophiolite]

Well if that's your attitude I'll post no more on this site.

What? I am not sure who that is directed to, but your response is disappointing.

 

In the posts of Greg H. and myself we both took time to offer you advice. That is not done lightly. Our attitude was one of wishing to guide you towards more productive posts, help you avoid negative rep and enhance your experience on this site. Do you seriously feel that is a bad, unacceptable, unwelcome attitude?

 

If you were targeting Arete, he didn't even have an attitude, just some concise, accurate facts.

 

No one likes to be corrected, but if you choose to bury your head in the sand when you are mistaken you have many disappointments ahead.

[Greg H.]

Well if that's your attitude I'll post no more on this site.

That escalated quickly.

 

It's certainly your choice (at this point) to remain a member of this community, but I doubt you'll get a much better response from any other serious science discussion board, if you refuse to at least hold a discussion rather than simply stating your ideas as if they were facts, regardless of their veracity or legitimacy.