Darwin re-visited

[Ben]

Originally Posted by Pyrotex

DNA does not code for body parts. There are no genes for a trunk.

Oh? Then the tendency for elephants to "have" trunks is not inherited? Inheritance is mediated by things that are abstractly referred to as genes. And it is now known that a gene is just a little piece of DNA.

Proteins have no relation to body parts or body plans.

Then what does have such a relation? God?

Along comes an amino acid and a specific protein will respond to its (and only its) electric field and will change shape and "grab" the amino acid.

Huh? Are you suggesting that proteins can grow without bounds?

proteins that are building a segment of RNA.

One assumes here you are referring to RNA polymerase (which is most decidedly a protein)

A free electron is pumped into Protein #1 and it releases its amino acid and reverts to its default shape.

This is gibberish - how can a protein "release its amino acid" in the way you claim?

and the amino acid is strung onto the end of the RNA strand.

Wow! So now RNA is a sequence of amino acids? I doubt this is true

The DNA creates proteins in a certain sequence.

A sequence of proteins? No, a gene "creates" (wrong term) a sequence of amino acids.

One patch of DNA generates the shape of a body segment.

Then you contradict yourself, unless you mean to imply that a "patch of DNA" with the property you ascribe can be anything other than a gene.

I couldn't read further.

[Larv]

Originally Posted by Ben

Oh? Then the tendency for elephants to "have" trunks is not inherited? Inheritance is mediated by things that are abstractly referred to as genes.And it is now known that a gene is just a little piece of DNA.

Then what does have such a relation? God?

Huh? Are you suggesting that proteins can grow without bounds? One assumes here you are referring to RNA polymerase (which is most decidedly a protein) This is gibberish - how can a protein "release its amino acid" in the way you claim? Wow! So now RNA is a sequence of amino acids? I doubt this is true

A sequence of proteins? No, a gene "creates" (wrong term) a sequence of amino acids.Then you contradict yourself, unless you mean to imply that a "patch of DNA" with the property you ascribe can be anything other than a gene.

I couldn't read further.

Ben, I, too, saw the mistakes Pyrotex was making. A lot of it was gibberish. But I hasten to point out that a gene is more than a piece of DNA. A gene is not the chemical material itself, but the coded information on that piece of DNA, which contains many superfluous nucleotides. This is not unlike a CD of a Beatles' album, which contains a lot of superfluous plastic.

[Pyrotex]

Originally Posted by Ben

Oh? Then the tendency for elephants to "have" trunks is not inherited?

[This post has been edited to correct a stupid mistake]

--- Ben, I believe you have misunderstood. Of course the tendency for elephants to "have" trunks IS inherited. That is obviously true. What is NOT obvious, and bears repeating, is that there is NO single part of the elephant's DNA that is responsible for the trunk. There is no segment of DNA that could be "clipped out" and would cause a trunk to grow if inserted into the DNA of another animal. Genes do not code for body parts. Now, what IS responsible for the "blueprint" or design or construction of the trunk? The correct answer is "genes"--but you will find them spread all over the DNA! Each gene that plays some role in the structure of the trunk does so ONLY by virtue of the fact that the gene codes for an amino acid, that becomes part of a protein, that plays some role in regulating cell growth (say), and this role of that protein, combined with other roles played by other proteins combine in a way that produces a trunk (in an elephant!), but might produce an entirely different facial feature in some other animal.

Huh? Are you suggesting that proteins can grow without bounds?

I fail to see how you drew that conclusion from my last post. I said the protein "grabbed" an amino acid nucleotide--not that it added the amino acid nucleotide to itself. If there was a chopped-off finger on the table, you could grab it with your hand. This would NOT mean your hand now "had 6 fingers".

One assumes here you are referring to RNA polymerase (which is most decidedly a protein) This is gibberish - how can a protein "release its amino acid nucleotide" in the way you claim? Wow! So now RNA is a sequence of amino acid nucleotides? ...

I didn't say the protein released one of its OWN amino acid nucleotides. I said that a certain protein could be capable of "grasping" an amino acid nucleotide(or any other bio-molecule), and then "releasing" it elsewhere. This indeed happens in the cell, though the details may differ from what I described.
DNA is a double strand of amino acid nucleotides attached to a pair of phosphylated sugar backbones.
RNA is a single strand of amino acid nucleotides attached to a single sugar backbone.

A sequence of proteins? No, a gene "creates" (wrong term) a sequence of amino acids. Then you contradict yourself....

What I said was, "DNA creates a sequence of proteins". A single gene codon encodes for a single amino acid--I think that's what you meant, and you're correct. A multitude of genes codons encode for a sequence of amino acids, which if properly assembled, constitute a protein of some kind. The DNA, considered globally as many multitudes of genes, creates (or encodes for) a sequence of many, many proteins. It takes many thousands of different proteins to make living cells.

Does this address your concerns?

[Ben]

Originally Posted by Pyrotex

--- Ben, I believe you have misunderstood. Of course the tendency for elephants to "have" trunks IS inherited. That is obviously true. What is NOT obvious, and bears repeating, is that there is NO single part of the elephant's DNA that is responsible for the trunk.

This is probably true, but not proven. What you loosely call "body parts" are likely determined by a family of genes - they are genes nonetheless.

Genes do not code for body parts.

From the above, this is a false statement

and this role of that protein, combined with other roles played by other proteins combine in a way that produces a trunk (in an elephant!), but might produce an entirely different facial feature in some other animal.

Ever hear of the "one gene one protein" paradigm? Same genes produce same phenotype (up to environmental influence). So this is a false statement

DNA is a double strand of amino acids attached to a pair of phosphylated sugar backbones.
RNA is a single strand of amino acids attached to a single sugar backbone.

Then this is your problem right here. DNA is NOT a strand of amino acids, it is a strand of nucleotides. Chemically they (amino acids and nucleotides) are quite distinct

A single gene encodes for a single amino acid--.......... A multitude of genes encode for a sequence of amino acids, which if properly assembled, constitute a protein of some kind.

Again, this is false - a gene codes for a protein, not an amino acid; one gene, one sequence of amino acids, i.e. a protein (as above). A multitude of genes codes for a multitude of proteins, it really is that simple

The DNA, considered globally as many multitudes of genes, creates (or encodes for) a sequence of many, many proteins.

No. Again, a gene codes for a sequence of amino acids, which, by convention, we call a protein. What is a "sequence of proteins"?

Does this address your concerns?

Not at all. I am sorry to be so abrupt in this and my previous, but molecular genetics was my PhD

[Pyrotex]

Originally Posted by Ben

This is probably true, but not proven. What you loosely call "body parts" are likely determined by a family of genes - they are genes nonetheless. ...Not at all. I am sorry to be so abrupt in this and my previous, but molecular genetics was my PhD

Ben,
with just a little research, I see I did indeed make an egregious error. DNA and RNA are constructed of nucleotides, not amino acids. Your "abruptness" was indeed justified, and I apologize for the confusion. I derive MY authority on this subject by having read three books on molecular genetics, and one of them hadn't even been colored in yet.

Now, I see another semantic problem between us, and that is the definition of "gene". I have always used the word in a general sense to indicate a contiguous segment of DNA that produces (encodes for) a protein. You seem to have a different definition. I would appreciate knowing how a PhD MolGen interprets and uses the word "gene".

To be precise, a codon (three contiguous nucleotides in DNA or RNA) encodes for an amino acid. A contiguous sequence of codons encode for a sequence of amino acids that constitute a protein. Is there any other "name" that specifically refers to this sequence of codons? If it's okay with you, I will call this sequence of codons a (singular) "gene".

Back to body parts. The statement that "genes do not encode for body parts" is indeed true and correct. The "proof" of this is simple. DNA is not a "blueprint" in any sense of the word. It is not a symbolic representation of the structure (layout, plan, map, components, sizes, relative positions, breakdown) of the critter (plant, animal or fungi). A blueprint of an office building or an aircraft carrier IS a symbolic representation of the structure of the final product.

Now, a blueprint or map is, in fact, a visual representation. You can look at a blueprint and tell that it "encodes" for an aircraft carrier. So, let's remove that attribute. Let's create a digital document (say, a JPEG) of the blueprint. Now we have a string of 1's and 0's. We'll group the bits into packets of 8 (bytes) and assign each byte an (ASCII) alpha-numeric symbol. We now have a string of alphabetic characters (...j39KK&q#3,[gK...) that looks NOTHING like an aircraft carrier. But it STILL encodes for an aircraft carrier. Technically, it encodes for the blueprint of an aircraft carrier.

Okay so far?

On the one hand, we have a string of characters that encode for an aircraft carrier.
On the other hand, we have a string of codons that encode for an elephant.

It would be plausible at first glance to assume that the "encoding" is similar for these two objects, and that we can assume analogies from one to the other. But not so.

Let's take any arbitrary and contiguous sequence (a sub-string) out of each string.

For the aircraft carrier sub-string, we run it through a decoder (a JPEG imaging application) and it will show a piece of the blueprint. Perhaps a side view of the bridge, showing placement of windows and electrical conduits.

For the elephant sub-string (assuming it is a full "gene"), we run it through a decoder (elephant cell machinery) and out comes... a protein.

We have no idea what the function of this protein is, or where it goes, or what it does, or how it relates to the animal's size or shape -- because the sub-string of codons does not give us this information. It just gives us a protein. There is nothing in the elephant codon string that "maps" this protein to any specific feature of the elephant, like a blueprint would.

That's why any given gene, a single gene, can truthfully be described by my blue statement above. A gene encodes for a protein. Pure and simple.

Wherefore come body parts, then? IMHO, body parts are "emergent structures". They are an ad hoc manifestation of an incredibly complicated process that turns genes into proteins in a specific order in a specific environment (the critter's womb or seed).

So genes do not encode for "body parts" -- because DNA is not a "blueprint".

Thanks for keeping me honest!!

[Ben]

Having been unpardonably rude to Pyro, let me try and make amends with a windy and slightly philosophical reply to this........

Originally Posted by Pyrotex

I would appreciate knowing how a PhD MolGen interprets and uses the word "gene".

So. Classically, the term "genetics" refers to the study of heredity, with the gene as the unit. Now, it is a fact that all the "laws" of genetics were well worked out before anyone even thought to ask about the chemistry of the mediators of genetic phenomena. I would even venture to suggest that the early greats (Fisher, Haldane, L. Penrose (Roger's father)), who were after all applied mathematicians, would have scoffed at the idea, saying that this knowledge was completely superfluous.

I think this (if true) would be an extreme view, but nonetheless one with which I have more that a little sympathy. Specifically, there is a tendency, especially in pop-science books, to maintain that genetics is the study of genes, meaning it is the study of the stuff that genes are made of.

This creates the following difficulty. What, then is meant by a "gene"? How do you define it? Is it just, as you suggest, just a sequence of nucleotides that has the potential to code for a protein? It cannot be, since in any individual organism, there are many such sequences for which, even if such a protein were produced (it need not be) it has no discernible effect on what's called the "phenotype"

Moreover, what if we know that 2 (or more) sequences produce different proteins and result in different phenotypes, how different must they are to be called different genes? Since we no longer allow the classical definition, say, we cannot assert that they are simply alleles at the same locus i.e. different forms of the same gene. Only the study of how they are inherited can do this.

Which brings us back to the classical definition.

To be precise, a codon (three contiguous nucleotides in DNA or RNA) encodes for an amino acid.

Yes, this correct.

A contiguous sequence of codons encode for a sequence of amino acids that constitute a protein.

This is not - in almost all eukaryotes, coding sequences are interrupted by (sometimes huge) stretches of non-coding DNA called "introns"

Is there any other "name" that specifically refers to this sequence of codons? If it's okay with you, I will call this sequence of codons a (singular) "gene".

From all the above, you may anticipate my response to this - it is perfectly good description of the structure of something we already have decided is a gene, by other means. Or if you prefer, it is a necessary but not sufficient condition for something to be called a gene.

[maddog]

Originally Posted by Pyrotex

Back to body parts. The statement that "genes do not encode for body parts" is indeed true and correct. The "proof" of this is simple. DNA is not a "blueprint" in any sense of the word. It is not a symbolic representation of the structure (layout, plan, map, components, sizes, relative positions, breakdown) of the critter (plant, animal or fungi). A blueprint of an office building or an aircraft carrier IS a symbolic representation of the structure of the final product.

I don't believe you make that as a general assertion (at least not for all animals). I don't
claim to be a geneticist at all. I have read some books as you and viewed some science
shows. There was an experiment that documented on Discovery on the common housefly.
The scientist(s) interviewed on the show had manipulated the genetic code of a housefly
(in particular a single gene) and was getting results like wings on the head of the fly
and eyes down the back of the fly. It would imply that by this scientist moving that moving
parts around they were able to manipulate morphology of that fly (and his descendants).
I can not say this would be for all animals. It did appear to be so for the Insectivore
phyla. I will also grant that were I to generalize, I would think Morphology control has
to be mediated by multiple genes simultaneously, especially for higher order animals.

maddog

[Galapagos]

Originally Posted by maddog

There was an experiment that documented on Discovery on the common housefly.
The scientist(s) interviewed on the show had manipulated the genetic code of a housefly
(in particular a single gene) and was getting results like wings on the head of the fly
and eyes down the back of the fly. It would imply that by this scientist moving that moving
parts around they were able to manipulate morphology of that fly (and his descendants).
maddog

I believe you are referring to homeotic genes.
I think you also mean to refer to fruit flies(drosophila), rather than house flies, and the genes you refer to specifically are Hox genes:

Hox genes are a group of related genes that specify the anterior-posterior axis and segment identity of metazoan organisms during early embryonic development. These genes are critical for the proper number and placement of embryonic segment structures (such as legs, antennae, and eyes).

These two pages may contain some of the mutations/genes you heard/read about in particular:
Regional specification - Wikipedia, the free encyclopedia
Drosophila embryogenesis - Wikipedia, the free encyclopedia
Homeobox - Wikipedia, the free encyclopedia

I just skimmed this review from Heredity, but for those more looking for more technical talk than appears on wikipedia, it would certainly suffice:
Heredity - Building divergent body plans with similar genetic pathways


On a related note, scienceblogger PZ Myers recently did a review of a journal article about miRNAs and the role they may have played in the evolution of metazoan body plans:

What caused the Cambrian explosion? MicroRNA! : Pharyngula
Blogging on Peer-Reviewed Research

No, not really — my title is a bit of a sensationalistic exploitation of the thesis of a paper by Peterson, Dietrich, and McPeek, but I can buy into their idea that microRNAs (miRNAs) may have contributed to the pattern of metazoan phylogenies we see now. It's actually a thought-provoking concept, especially to someone who favors the evo-devo view of animal evolution. And actually, the question it answers is why we haven't had thousands of Cambrian explosions.

[Pyrotex]

Originally Posted by Ben

Having been unpardonably rude to Pyro, let me try and make amends with a windy and slightly philosophical reply to this...

Thanks, Ben.
As I said before, your criticism was justified, and I should have known better. My background in MolGen is similar to Galapagos', overlying a degree in physics, and a LOT of Scientific Magazine articles.

This "brouhaha" between us has had some very positive results, given the wealth of resources that the last few posts have made available. It will take me a day or two to digest them.

It may be that I might have to adjust my infamous blue law:

"Genes do not primarily encode for body parts or structural description; they primarily encode for chemistry (largely the production of proteins). However, some genes (when modified) apparently manifest themselves in observable morphological changes to the phenotype."

Further negotiations may be necessary after deliberating on the proffered resources.

[Michaelangelica]

Originally Posted by Pyrotex

Mangel,
Thanks for the question!!!

Thanks for the new name; which is also a description of what i do !?

OK I think I am there-- the third reading i might get it-- but lets go for first reading mow
I have an image in my head of a chicken with teeth.
I have a sentence in my brain which says ' "orientation" is important'

Now lets try to see what the mangle-brain is about. The proteins that 'do things" or make things that make things happen must talk to each other right?
Otherwise how do you get chickens with teeth when you put the wrong activated / 'turned on' DNA next to an other. (The research is somewhere here??)

Now the proteins have to know where they are right? Otherwise we would have feet were the head it?
So that means some overall "gestalt' or organising principle?? Who or what is that?

So 'orientation' and "talking to neighbors" is important? How does it happen?

How does epigenetics 'stir the pot' ? I am told it is most active at this early phase of development.

My brain hurts.