evolution question

[BH]

when we see a change in an animal or plant from generation to generation, a new body part or trait, how do we know if new genetic information has added to its gene sequence or whether the genetic information was always there to begin with and just manifested itself for some reason in one offspring?

 

[Loren Pechtel]

If it simply manifested in one offspring then there are still changes--something changed to switch it on.

 

[bilby]

when we see a change in an animal or plant from generation to generation, a new body part or trait, how do we know if new genetic information has added to its gene sequence or whether the genetic information was always there to begin with and just manifested itself for some reason in one offspring?

Mostly we don't.

Although in recent years it's become possible to sequence nucleic acids fairly quickly and cheaply, so if the funding and time are there to do it, a comparison between the genomes can be made, and the changes investigated.

My understanding is (and I am probably waaaay out of date, as I haven't been trying to keep up, and Molecular Biology has been moving very fast) that a lot of phenotypic change is epigenetic - that is, mediated not by the genetic material itself changing, but by changes in what genetic material is read.

Methylation was getting a lot of press a while back - a gene can be turned on or off by the removal or addition of methyl groups, without a change in the underlying sequence of base pairs.

Ultimately the answer to any question in biology, and certainly any question in molecular biology, is "it's more complicated than you think it's going to be, even after you take into account the fact that it's more complicated than you think it's going to be".

The popular narrative of a simple string of base pairs, in three base groups each coding for a specific amino acid, which is then assembled into a protein, with the changing of one base pair thereby having the potential to change the properties of the final protein, and thereby ultimately the phenotype of the individual in which that change occurs, is not untrue, but it's such a dramatic oversimplification of the hyper-complex reality that on a clear day, you can see 'untrue' from there, if you squint a little.

 

[Cheerful Charlie]

I suggest checking out Sandwalk occasionally. A science blog by Laurence Moran, professor emeritus of University Of Toronto. There is a lot of good science going on and a lot of bad science also. Moran is a hard nosed biochemist who digs into this. Epigenetics, junk DNA etc get examined critically. Plus well aimed kicks at sloppy science, sloppy science journals who should know better, and occasionally, creationists. Warning, Sandwalk can get quite technical.

 

[BH]

I'm really interested in this subject. can anyone here give me about ten book titles to start off reading?

 

[Cheerful Charlie]

What you are asking about is evo devo. Evolutionary development. Probably might be a good idea to start with an introductory college text book on that subject. Be warned. It is a vast field that some people have studied their entire lives and still do not know all the details.

https://www.quantamagazine.org/in-test-tubes-rna-molecules-evolve-into-a-tiny-ecosystem-20220505/

...
When researchers gave a genetic molecule the ability to replicate, it evolved over time into a complex network of “hosts” and “parasites” that both competed and cooperated to survive.
...

 

[Swammerdami]

The popular narrative of a simple string of base pairs, in three base groups each coding for a specific amino acid, which is then assembled into a protein, with the changing of one base pair thereby having the potential to change the properties of the final protein, and thereby ultimately the phenotype of the individual in which that change occurs, is not untrue, but it's such a dramatic oversimplification of the hyper-complex reality that on a clear day, you can see 'untrue' from there, if you squint a little.

For example,  RNA editing makes various changes to the RNA codons after the RNA has been transcribed from the DNA. This is one way eukaryotes' nuclear membrane is useful: the editing process is much slower than protein construction so keeping the RNA contained for the editing prevents premature translation.

In vertebrates, editing is rare.... In other organisms, such as squids, extensive editing (pan-editing) can occur; in some cases the majority of nucleotides in an mRNA sequence may result from editing.
. . . An example of C-to-U editing is with the apolipoprotein B gene in humans. Apo B100 is expressed in the liver and apo B48 is expressed in the intestines.

 

[Peez]

There is a great deal to sift through here. When we see a change in an organism (plant, animal, or any other), we do not typically see “a new body part”. Whether or not we see a new “trait” is going to depend on how that term is defined.

Quantifying “information” can be quite technical, and complex. That said, we can say that new information is generated by genetic mutation, and then increased in sexually-reproducing organisms by shuffling and mixing genes. This results in genetic variation in the population.

Some of this genetic variation contributes to variation in traits. Selection on these traits can then reduce variation in traits, and in genes.

That’s it. It is not a question of a mutation generating a trait in one offspring, rather it is selection (and drift) acting on variation in a population.

 

[Gun Nut]

when we see a change in an animal or plant from generation to generation, a new body part or trait, how do we know if new genetic information has added to its gene sequence or whether the genetic information was always there to begin with and just manifested itself for some reason in one offspring?

because we know how bodies know how to build body parts... through the blueprint that is the genetic code. so if a body is doing something new it is because the body is reading new instructions.
Edited to add in light of bilby's post..
.. reading new instructions because they're newly added instructions, or due to a change in the mechanism that reads the instructions that were already there... as in epigenes.

 

[bilby]

when we see a change in an animal or plant from generation to generation, a new body part or trait, how do we know if new genetic information has added to its gene sequence or whether the genetic information was always there to begin with and just manifested itself for some reason in one offspring?

because we know how bodies know how to build body parts... through the blueprint that is the genetic code. so if a body is doing something new it is because the body is reading new instructions.
Edited to add in light of bilby's post..
.. reading new instructions because they're newly added instructions, or due to a change in the mechanism that reads the instructions that were already there... as in epigenes.

Yeah, it's far more complicated than that. Genes aren't an instruction set or a blueprint for making a phenotype, and the influences on phenotype are myriad. Sure, genetics and epigenetics are a big-ish part of that, but there's a stack of other influences, which is why identical twins aren't identical.

Many developmental steps exhibit chaotic responses to apparently trivial environmental conditions, so that a tiny variation in conditions (from being on this side of the uterus, and not that side) result in very large differences in final appearance, form, or function.

Bilby's first law of biology applies: Every accurate statement about biology can be rendered even more accurate by adding "...but in reality, things are more complicated than that".

 

[Bomb#20]

Bilby's first law of biology applies: Every accurate statement about biology can be rendered even more accurate by adding "...but in reality, things are more complicated than that".

Your so-called "law" grossly underestimates biology's complexity.

 

[Swammerdami]

Genes aren't an instruction set or a blueprint for making a phenotype, and the influences on phenotype are myriad. Sure, genetics and epigenetics are a big-ish part of that, but there's a stack of other influences, which is why identical twins aren't identical.

I think you are underestimating the influence of DNA. Many of the "non-DNA" influences are themselves a result of genes. For example the RNA editings I mentioned upthread are controlled by special RNA's and proteins which are themselves transcribed or translated from the genome.

Identical twins ARE rather ... identical! Watch the Three Identical Strangers documentary. (It's an interesting story for reasons other than showing identical triplets to be very similar to each other. Do NOT abandon the film half-way through; that's when the big "plot twist" occurs!)

 

[bilby]

Genes aren't an instruction set or a blueprint for making a phenotype, and the influences on phenotype are myriad. Sure, genetics and epigenetics are a big-ish part of that, but there's a stack of other influences, which is why identical twins aren't identical.

I think you are underestimating the influence of DNA. Many of the "non-DNA" influences are themselves a result of genes. For example the RNA editings I mentioned upthread are controlled by special RNA's and proteins which are themselves transcribed or translated from the genome.

Identical twins ARE rather ... identical! Watch the Three Identical Strangers documentary. (It's an interesting story for reasons other than showing identical triplets to be very similar to each other. Do NOT abandon the film half-way through; that's when the big "plot twist" occurs!)

I think you are underestimating the influence of the environment.

Identical twins aren't identical. People who know them well can almost always tell them apart.

 

[Peez]

Genes aren't an instruction set or a blueprint for making a phenotype, and the influences on phenotype are myriad. Sure, genetics and epigenetics are a big-ish part of that, but there's a stack of other influences, which is why identical twins aren't identical.

I think you are underestimating the influence of DNA. Many of the "non-DNA" influences are themselves a result of genes. For example the RNA editings I mentioned upthread are controlled by special RNA's and proteins which are themselves transcribed or translated from the genome.

Identical twins ARE rather ... identical! Watch the Three Identical Strangers documentary. (It's an interesting story for reasons other than showing identical triplets to be very similar to each other. Do NOT abandon the film half-way through; that's when the big "plot twist" occurs!)

I have no doubt that bilby understands the role of DNA in directing the production of RNA. It would add that, as far as we can determine, epigenetic effects are limited and are themselves influenced by DNA. That said, bilby is correct that so-called identical twins are not actually identical. They are not even genetically identical (in fact different parts of your body are not genetically identical to each other), but they are even more different in their traits. I refer you to bilby's first law on biology.

 

[Swammerdami]

Wow. Obviously when I wrote "identical" this was whimsical shorthand for "ALMOST identical." Are you guys unusually pedantic? Or intent on pretending Swammerdami is an idiot?

I'll give you credit and assume you knew that "almost identical" was the intended meaning, but felt even this was an exaggeration. In that case you are simply wrong at least in some cases.

In the documentary I mentioned, the boys had very similar interests, very similar appearance, answered questions in unison, thought they were looking in a mirror, and so on. This despite that they (and their adoptive parents) were unaware they were triplets until they met by chance at age 19. And the adoptive parents were deliberately chosen to have very different income levels: this was part of a 'nature vs nurture' experiment.

I personally knew two identical twins whom very few people could tell apart. There is an amazing anecdote that proves they were almost indistinguishable; I won't recite it here because it is a very personal story with possible legal implications.

 

[bilby]

Wow. Obviously when I wrote "identical" this was whimsical shorthand for "ALMOST identical." Are you guys unusually pedantic? Or intent on pretending Swammerdami is an idiot?

I'll give you credit and assume you knew that "almost identical" was the intended meaning, but felt even this was an exaggeration. In that case you are simply wrong at least in some cases.

In the documentary I mentioned, the boys had very similar interests, very similar appearance, answered questions in unison, thought they were looking in a mirror, and so on. This despite that they (and their adoptive parents) were unaware they were triplets until they met by chance at age 19. And the adoptive parents were deliberately chosen to have very different income levels: this was part of a 'nature vs nurture' experiment.

I personally knew two identical twins whom very few people could tell apart. There is an amazing anecdote that proves they were almost indistinguishable; I won't recite it here because it is a very personal story with possible legal implications.

And such close similarity is the exception, not the rule.

So clearly genetics ain't everything.

 

[Jokodo]

Genes aren't an instruction set or a blueprint for making a phenotype, and the influences on phenotype are myriad. Sure, genetics and epigenetics are a big-ish part of that, but there's a stack of other influences, which is why identical twins aren't identical.

I think you are underestimating the influence of DNA. Many of the "non-DNA" influences are themselves a result of genes. For example the RNA editings I mentioned upthread are controlled by special RNA's and proteins which are themselves transcribed or translated from the genome.

Identical twins ARE rather ... identical! Watch the Three Identical Strangers documentary. (It's an interesting story for reasons other than showing identical triplets to be very similar to each other. Do NOT abandon the film half-way through; that's when the big "plot twist" occurs!)

I think you are underestimating the influence of the environment.

Identical twins aren't identical. People who know them well can almost always tell them apart.

Identical twins are identical mostly in their looks. There's this set of twins I know long enough that a hypothetical offspring of a hypothetical union between me and one of them would be allowed to vote and drink alcohol, and I've been close friends with half of it for the better part of that time. I still sometimes struggle to tell them apart in photos. As soon as you meet them in real life, all doubt is gone. They have different goals in life, different hobbies, different mannerisms, different ways to talk, walk, move. And they've lived together for most of their lives.

 

[Peez]

Wow. Obviously when I wrote "identical" this was whimsical shorthand for "ALMOST identical." Are you guys unusually pedantic? Or intent on pretending Swammerdami is an idiot?

I'll give you credit and assume you knew that "almost identical" was the intended meaning, but felt even this was an exaggeration. In that case you are simply wrong at least in some cases.

In the documentary I mentioned, the boys had very similar interests, very similar appearance, answered questions in unison, thought they were looking in a mirror, and so on. This despite that they (and their adoptive parents) were unaware they were triplets until they met by chance at age 19. And the adoptive parents were deliberately chosen to have very different income levels: this was part of a 'nature vs nurture' experiment.

I personally knew two identical twins whom very few people could tell apart. There is an amazing anecdote that proves they were almost indistinguishable; I won't recite it here because it is a very personal story with possible legal implications.

Please stop. The difference between "identical" and "almost identical" is not pedantic at all (particularly in this context: "identical twins aren't identical"... "Identical twins ARE rather ... identical!"). Why did you not think that bilby meant "almost identical"? Would you agree that all humans are genetically "almost identical" to each other (99.9% is almost 100%)? Do you understand how important the difference is between "almost identical" and "identical" in evolution?

 

[Swammerdami]

Please stop. The difference between "identical" and "almost identical" is not pedantic at all (particularly in this context: "identical twins aren't identical"... "Identical twins ARE rather ... identical!"). Why did you not think that bilby meant "almost identical"?

No, YOU stop. My writing "Identical twins are ... identical!" was obviously whimsy, intended to be slightly humorous. "Identical twins are ... similar!" would not have the same effect.

Obviously I use much different diction when I'm writing for submission to technical journals. But I don't plan on self-censoring here to cope with boring sophomoric pedantry.

As for why bilby did NOT mean "identical twins aren't almost identical" the question rather answers itself, no? Get a grip.

Would you agree that all humans are genetically "almost identical" to each other (99.9% is almost 100%)? Do you understand how important the difference is between "almost identical" and "identical" in evolution?[/I]

What??? What possible relevance does this have to a discussion of identical twins? If I indulged in sophomoric disingenuity I'd caricature this "argument" as "Neanderthal/Sapiens 99.7%. Identical twins 99.9+%. Same-same."

Weren't you the one who didn't understand the huge gulf between prokaryotes and eukaryotes? How does Professor Nick Lane's thinking compare with yours? Or are you just going to quibble that he begins a chapter by discussing cuckoo clocks?

 

[skepticalbip]

I know diddly-squat about biology but I think that I have gleaned from this thread that identical twins aren't.