Darwin re-visited

[Biochemist]

More epigenetics, or something else going on?

This process must speed up genetic changes but should't there be more genetically damaged (or exceptional) people?

This is a really interesting development, MA. Your point is valid, but since the retrotransposon activity is embryonic, it also suggests that genetic changes that would result in death of a fertilized ovum now will only result in death of an early embryo cell. Essentially, it raises the probability of embryonic survival, and increases the probability off a functional cell mosaic (whether good or bad).

 

Really interesting. Also, I never saw the numbers (noted in the summary) that L1 retrotransposons are 17% of the human genome. This is roughly six times the portion that transcribes proteins.

 

Bio

[Biochemist]

when we talk about survival of the fittest we do not mean the strongest.

Nice point, Riper. Darwin should probably have said something like "survival of the most opportune variant in the niche", but it doesn't quite roll off of the tongue as well.

[Pyrotex]

Nice post, and nice perspective, Pyro....

2) The degree of "front loading"- The surprising degree of biochemical complexity (completely unknown to Darwin) continues to rise. If you couple the massive chaotic complexity in later phyla with the advent of lysosomes in the first eukaryotes (thus essentially "locking in" the intracytoplasmic machinery at the first eukaryote), it suggests that the "end game" was somewhat decided, or at least limited at the first eukaryote. It remains surprising that the early biochemical cytoplasmic machinery could support such a broad array of body plans, and that such a broad array of body plans could arise without significant change in the cytoplasmic machinery...

Hi Bioch,

and thanks. :Glasses:

 

Again, I am not surprised at the "front loading". Remember, it took from 3 BYrA to .6 BYrA to achieve eukaryotic complexity, with all the cellular machinery that multi-celled plants and animals required BEFORE they could start evolving.

 

Call it 2.5+ BYr to evolve *just* the basic floor plan of the single cell, with its mitochondrial energy-plant, the lysosomes, the cytoplasm, the DNA, the messenger RNA, the standardized use of 4 amino acids to construct all proteins/enzymes which become the "tools", "agents", "end effectors", "sensors", "gateways", "garbage collectors" and "structural elements" of the fantastically complex cell machinery.

 

Yes, there was a LOT of front loading going on. But that front loading took 4 or 5 times longer (~2.5+ BYr versus ~.6 BYr) then the development of ALL the body plans that ALL plants and animals have developed since.

 

Sounds about right to me. :) More later.

[Biochemist]

Again, I am not surprised at the "front loading". Remember, it took from 3 BYrA to .6 BYrA to achieve eukaryotic complexity, with all the cellular machinery that multi-celled plants and animals required BEFORE they could start evolving.

 

Call it 2.5+ BYr to evolve *just* the basic floor plan of the single cell.....[the] "structural elements" of the fantastically complex cell machinery.

 

Yes, there was a LOT of front loading going on. But that front loading took 4 or 5 times longer (~2.5+ BYr versus ~.6 BYr) then the development of ALL the body plans that ALL plants and animals have developed since.

All true, and a good point. I still am surprised (and it seems somewhat counterintuitive) that after "carving into stone" so much of the standardized cell infrastructure, that we could generate such a remarkable diversity in body plans without significant alteration to the standardized machinery.

 

My opinion on this (completely unsubstantiated, of course) is that the tendency toward life (in fact toward the tree of life that we see) is intrinsic in the fundamental molecular structure of the basic molecules. That is, development of life is similar to the order created when solids crystallize. The difference is (of course) that crystallization happens rapidly, so we can test reproducibility.

 

I would hypothesize that if similar conditions arose again, we would get a very similar tree of life again, and arrive at a very similar "end point" again.

 

Bio

[Pyrotex]

All true, and a good point. I still am surprised (and it seems somewhat counterintuitive) that after "carving into stone" so much of the standardized cell infrastructure, that we could generate such a remarkable diversity in body plans without significant alteration to the standardized machinery...

Hmmm, he said while scratching his chin

 

But why would a different body plan (3 body segments vs. 2; 8 legs vs. 6; etc.) need different machinery at the cellular level? The cellular machinery (CM) exists only for the benefit, survival and reproduction of the cell. Well, 99%, anyway. Nothing in the CM "knows" about the "body plan", whether there are 2 heads or 1, or any at all, 2 eyes or 3, antenna or none, etc. The only "external" factors the CM knows about are a select few chemical reactions. Excess potassium or sodium outside the cell will trigger protein gates buried in the cell walls. There exist a few "communication" processes whereby one cell can initiate a process in another. Apoptosis comes to mind. Among some bacteria, if their "wastes" become concentrated enough, all the cells imbedded in that waste change mode or form. Like, growing spores, shutting down metabolism, extruding a protective glue, growing structural fibers between cells, etc.

 

On the other hand, I could argue that multicelled organisms, like duckweed and giraffes, DO have macro large scale functions that demand a "different" kind of cell. Well duh!!!

They evolved a host of NEW CELL TYPES to support those new functions. The nerve cell has a significantly different CM than a blood cell, or a muscle cell or a bone-growing cell.

 

So, you were onto something, but just not what you anticipated.

CM did not have to change to support new body plans.

NEW types of cells with a modified CM evolved to support new body structures.

 

Now, given that any animal needs a nervous system and a digestive system, which are infinitely flexible in terms of size and configuration, animals can evolve an arbitrary number of body plans without any further changes to CM. Kind of a "one size fits all" solution.

 

The paucity of body plans, IMO, is due strictly to the non-viability of most body plans under evolutionary stresses. Eight-legged gazzelles never evolved because eight-legged lizards never evolved because eight-leg-segmented vermicular pseudopedes never evolved because their immediate predecessors took the path of developing a "spine" and becoming chordates at the point where their body plan was 4-symmetric, and mutations toward 8 legs after that point really ****ed up the embryonic nervous system, and left the progeny too clumsy to fend off fangy predators.

 

Once the complexity of the body plan increased past a certain point, older elemental parameters of the body plan (like, number of legs) get frozen in. More recent "emergent" parameters of the body plan (like, scales vs. hair) can still mutate for a few score MYrs, until those too are frozen in.

[Symbology]

It's just amazing what a difference a few courses in zoology, biology, and/or genetics do to the vocabulary, sentence structure, and viewpoints of the posts around here. :)

 

I wonder if we could make that a prerequisite for some threads around here?

 

Or even better the reverse! I mean just think of how much more fun some of the threads could be if we could exclude all the people who actually know something about the subject that is being talked about!

;)

[Michaelangelica]

I'm amused by the various "headlines" quoted in the posts on this page. "Is Darwinism Past its Sell-By Date?" -- "Tree of Life Goes in the Recycling Bin"...

 

They all sound like one-liners on a Creationism website..

yes i know,;) isn't that fun?:)

The reason we get visits from so many 'nice', Yank fundamentalists.

and

the reason I put the new rider in post # one of the thread recently

see riper's post above.

 

Despite all this, I still can't nail the basket, Darwin

[Michaelangelica]

Very interesting conversation Pyrotex and biochemist. Could you break it down a bit for "bears of little brain"

Otherwise I will have to resort to being silly, silly like:-

 

[Pyrotex]

Very interesting conversation Pyrotex and biochemist. Could you break it down a bit for "bears of little brain"...

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

 

Mangel,

I would never in 984,625 years ever think of you as a bear of little brain. Poo!

 

But, assuming that there might be a few lurking around, I will give it my best shot.

 

Evolution: Body Plans and DNA

 

DNA does not code for body parts. There are no genes for a trunk. You cannot, even in principal, splice some genes from an elephant into a giraffe, and get a giraffe with a trunk. What DNA does is code for chemistry -- and 99% of that is code for producing proteins. Proteins have no relation to body parts or body plans. Proteins encode for something else that we might call "Effect" -- this includes the shape of the protein, its ability (if any) to fold or shift into an alternate shape, the charge-density map of its shape, its sensitivity to external electric fields, and its electro-mechanical behavior in the presence of certain "trigger" molecules or levels of acidity (pH).

 

Proteins (by and large) are the Universe's smallest machines. [hypothetical scenario] Along comes an amino acid a nucleotide and a specific protein will respond to its (and only its) electric field and will change shape and "grab" the amino acid nucleotide. This alters the protein's charge-density, which is detected by another protein which attractes protein #1 over to a nest of tightly coordinated proteins that are building a segment of RNA. Protein #1 is leveraged into position by electric fields. A free electron is pumped into Protein #1 and it releases its amino acid nucleotide and reverts to its default shape. Protein #1 drifts away to start the process over again, and the amino acid nucleotide is strung onto the end of the RNA strand.

 

So, at a higher level of abstraction, we can say that proteins have functionality. They "do" things; they make things happen.

 

Now look at a primitive strand of DNA in an organism from the Cambrian Era. The DNA creates proteins in a certain sequence. The proteins take on certain shapes and do certain functions. One patch of DNA generates the shape of a body segment. Another patch of DNA generate a string of proteins that triggers the first patch at a certain "time" in the sequence. Patch #2 typically generates a string of 4 trigger proteins; they trigger the creation of 4 body segments: head, thorax1, thorax2, tail.

 

Thorax1 and thorax2 are nearly identical, containing buds for a pair of legs.

 

Head is quite similar; it also contains buds, but they will develop into antenna/eye complexes. Tail also contains buds, but they develop into orifices.

 

You have the standard 4-leg body plan: lizards and mammals.

 

A mutation occurs, and patch #2 now generates a string of 5 trigger proteins. Bingo, you now have the 6-leg body plan, containing thorax1, thorax2 and thorax3. Thorax2 is the "new" segment, and is identical to thorax 1.

 

Later on, other mutations occur in DNA patch #2, yielding the 8-leg, 10-leg, 24-leg, and 96-leg body plans: spiders, squids, worms, centipedes.

 

Now slip ahead a few tens of Millions of years. The DNA of each body plan has evolved tremendously. The individual "body segments" have to some extent merged, and to some extent, each gone their own way, developing their own refined attributes. Thorax1 and thorax2, among the lizards, have specialized, with thorax1 focused on heart and lung development. Thorax2 focused on digestion and reproduction. The division between these two segments has blurred and disappeared, unless you notice the diaphragm inside.

 

NOW--consider what would happen if we had another mutation in DNA patch #2 at THIS point of evolution. When it happened in the Cambrian Explosion, it resulted in primitive critters with 6, 8, 10, or more legs. Which survived, and each evolved in their own independent direction.

 

NOW--it produces a lizard with six legs, two hearts, two pair of lungs, two diaphragms, a really screwed up spine and nervous system and the agility of a mushroom. It's dead, Jim!

 

Why? Several reasons. The lizard is now 1,000 times larger than its Cambrian ancestor. Mechanical repetition of body segments doesn't scale up. Each segment has evolved its own functions which cannot be improved with mere organ duplication. Each segment has evolved its own internal mechanical, nervous and fluidic structures which can only be botched if you throw in extra components.

 

And so, whereas the proto-critter back in the Cambrian could alter its basic body plan with a single mutation, its descendents tens of MYrs later CANNOT execute the same kind of change and survive. Too much DNA superstructure and organ evolution, and specialization has taken place, and you collapse that "house of genetic cards" if you start slipping in a new pair of arms at the "bottom of the house".

 

A body plan can therefore be "frozen in" by all the changes that take place afterwards. At one time, our arms could have had as many joints as you can imagine. Look at the joints in antennae which are modified limbs. But once 3 joints (shoulder, elbow and wrist) had been around for a while, evolution of muscles, nerves, tendons, veins took place on top of that, to take whatever mechanical and fluidic advantages there were in each arm segment. Each joint evolved to take advantage of its special place and function in the arm. So now, 3 joints is also "frozen in".

 

Given that there are people with 6 fingers and cats with 7 toes, I conclude that the "body plan" of the hand (or paw) is not yet "frozen in". But if specialization and functional extention of the the fingers/toes takes place over a long enough time, then that too will become "frozen in" and a mutant with 6 fingers may not even be able to survive!

 

That, in a nutshell, is how and why body plans can only be created at very early stages in the evolution of any creature. At a stage when no superstructure has been built upon, and is tightly dependent upon, a certain number of: legs, segments, vertabrae, eyes, whatever. But after that superstructure has evolved, the body plan underneath is "frozen in" and cannot change.

 

Metaphor: think of an evolving organism as a personal computer. When it was simple (back in the 80's) you could slap in a new, faster CPU and take off. By the late 90's, peripheral extensions, such as video boards, sound boards, array processors, external drives, etc., had progressed so far that making a new, faster CPU chip that was universally backward compatible was nearly impossible.

 

Thanks for the question!!! :hihi:

[modest]

That, in a nutshell, is how and why body plans can only be created at very early stages in the evolution of any creature. At a stage when no superstructure has been built upon, and is tightly dependent upon, a certain number of: legs, segments, vertabrae, eyes, whatever. But after that superstructure has evolved, the body plan underneath is "frozen in" and cannot change.

 

Thank you, Pyrotex. Your post makes brilliant sense and it's really well explained

 

I'm wondering if it is possible in your estimation for another body plan explosion to happen today. Of course, it wouldn't happen as you say with one of the more complex phyla. But, with one of the early branches of the animal tree like a sponges or flatworms—sponges don't have nervous, digestive or circulatory systems and their cells are very unspecialized—might they find themselves in a position one day to branch out into a new assortment of body plans?

 

My first thought is that this is more unlikely today than it was in the pre-Cambrian because competition is greater now. There aren't as many vacant niches in the ecosystem which would drive such a change. Why, for example, would a sponge develop legs to scurry around the ocean floor if crabs and lobsters are already expertly filling that niche?

 

But, it might be just as likely (and I frankly am not informed enough to know) that sponges and other simple animal phyla are not genetically in a position right now for a body plan explosion. Perhaps one day a species will come to a point where evolving new body plans is easy and favorable.

 

I'm curious what you think.

 

~modest

[Ben]

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]

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]

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]

--- 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]

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. :eek2:

 

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!! :Alien:

[Ben]

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

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]

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