Freethought & Rationalism Archive

pz · 10-23-2002, 05:31 PM

Quote:

Originally posted by Doubting Didymus:
It looks to me like both PZ and PeeZ are using the same argument.

"Show me an example of a feauture that genes can produce on their own"

"Show me an example of an evolutionary progression that can occur without genes"

Both of these are very obvious straw men.

Yes, which is why I used it -- it's called the reductio ad absurdam.

The problem is that all too often the environment and epigenetic influences are dismissed as "just the environment" or as incidental by-products of gene action -- that eventually, if you trace it back far enough in development, everything in the organism can be derived from the genome. My point is that that is false.

And yes, the usual response is to say, "oh, so what? I always knew environment influenced the organism. It's still only the genes that are important in evolution."

Quote:

Pz, I want you to clarify your position on heredity, please. See my post on page three, about wolbachia, if you will.

What is there to clarify? There's a bunch of stuff there about Wolbachia, I didn't see anything specifically directed at me. If it helps, yes, it is heredity, and yes, it is evolution, and no, I do not trivialize it by pretending it is reducible to just genes.

pz · 10-23-2002, 05:44 PM

Quote:

Originally posted by Peez:
I would like to ask a question about "evolution", with an eye to clarifying the positions held here:

What would be an explanation for the evolution of birds from "reptiles" that does not require changes in allele frequency?

I do not know whether or not this is a reasonable question to ask, but if it is reasonable then I think that the answer(s) might be enlightening.

I'm confident that changes in allele frequency were involved in the evolution of birds.

Of course, since we're all scientists here, we should then ask how we would evaluate that assertion. I'm afraid that there is no information about the frequency of various alleles in ancestral proto-birds to be found, and barring the discovery of a time machine, such information will never be found. In all but a general theoretical sense, the tools of population genetics are entirely useless in answering the question of how birds evolved, and a definition of evolution that is entirely restricted to terms in population genetics is inapplicable to the question.

So what are you going to do? Can we answer the question of how birds evolved without any knowledge of populations, allele frequencies, or even alleles, or can't we?

Doubting Didymus · 10-23-2002, 06:23 PM

How much do you think can be reduced to the action of genes? As an example, is a cell membrane reducible to the action of genes? if not, what else?

pz · 10-23-2002, 07:22 PM

Quote:

Originally posted by Doubting Didymus:
How much do you think can be reduced to the action of genes? As an example, is a cell membrane reducible to the action of genes?

No.

Quote:

if not, what else?

Nothing. Genes may be necessary, but they are not sufficient.

Why? What do you think is reducible to 'mere' genes?

Doubting Didymus · 10-23-2002, 07:37 PM

I was under the impression that genes are responsible for encoding proteins, which would have made them directly responsible for the creation of cell membranes. (and much else)

If non-genetic factors are as important as you say, why is biotechnology so fixated on genetics, and is largely ignoring cytoplasmic engineering? What kind of heritable phenotypic changes can you induce by manipulating non-genes? (note: this question is genuine and not facecious, as it may sound)

Oolon Colluphid · 10-25-2002, 04:10 AM

Quote:

Originally posted by Doubting Didymus:
I was under the impression that genes are responsible for encoding proteins, which would have made them directly responsible for the creation of cell membranes. (and much else)

<Sticks head above parapet> That's the impression three of my textbooks (Futuyma, Lewin (Genes III -- admittedly an old edition, so maybe I'm missing something) and T A Brown (Genomes) gave me too...

I really don't see the problem. Genes build bodies, but need a previous body to get started. But the previous body was built by copies of similar genes... and needed the previous body to that. And so on. But, um... the 'information' for making another body is coded in the genes, isn't it, and the body amounts to the genes' microenvironment...?

<ducks back below parapet>

Oolon

[ October 25, 2002: Message edited by: Oolon Colluphid ]

RufusAtticus · 10-25-2002, 08:15 AM

Oolon,

But remember in every step of that process gene expression and thus the proteome was influenced by the environment. That is why you just can't simply say that by extracting back far enough there is a point at which the genes can account for everything.

pz · 10-25-2002, 08:59 AM

Quote:

Originally posted by RufusAtticus:

But remember in every step of that process gene expression and thus the proteome was influenced by the environment. That is why you just can't simply say that by extracting back far enough there is a point at which the genes can account for everything.

And if we do trace this chicken/egg sort of question about DNA/cytoplasm way, way back, what we find is that DNA is a relatively late arrival. That is, there was an ancestral organism that used cytoplasmic inheritance exclusively, and didn't have a central nucleotide archive of any kind. The regression argument backfires, because it leads back to the early primacy of the cytoplasm.

I would also mention another error in his post, one that is revealing of the default mindset: "Genes build bodies". This is false. Genes don't build bodies, the cooperative interaction of genes, extra-genetic information, and environment builds bodies.

Peez · 10-25-2002, 09:13 AM

[quote]Doubting Didymus:
It looks to me like both PZ and PeeZ are using the same argument.

"Show me an example of a feature that genes can produce on their own"

"Show me an example of an evolutionary progression that can occur without genes"

Both of these are very obvious straw men.[quote]First, I think that you are making a straw man out of my position. I did not ask for "an example of an evolutionary progression that can occur without genes" until the post immediately before that one, and even then I did not ask it as a challenge to anyone else's position. I was hoping that it might clarify the positions held. What I have asked for repeatedly is a few examples of non-nucleotide inheritance that "make substantial contributions to the form and function of organisms". I asked this because it is my understanding that it is pz's position that there are such examples (the quoted part of the question is directly from his text). I have based my assessment of his position on his posts, including:

Quote:

You can't select for genes. You can only select for a phenotype. It's also trivially false that only genes get passed on to the next generation. The issue is significantly more complex than you are making it out to be.

Lewontin is one of the few authors out there who can lucidly argue against gene-centric dogma, and give the proper weight to a more pluralistic view of biology.

Much more than genes are passed on to the next generation.

Which is why evolution isn't a change in phenotype frequency in a population over time, it is a change in allele frequency.
That is one definition of evolution, yes. It's a pretty good definition. It is not a complete definition, however...I prefer "evolution is a process that results in heritable changes in a population spread over many generations". It's more open about what a heritable change is, and doesn't restrict it to just allelic changes.

You are incorrect to claim that only the genetic component makes it to the next generation. I happen to have inherited a rather complex set of proteins, cofactors, membranes, and carbohydrates from my mom, in addition to a bit of DNA. She also made a substantial investment in my assembly for about 9 months, and then spent many years refining me afterwards.

My point is that there has been continuity of the cytoplasm and membrane as well as DNA, and that those structures also represent a substantial amount of extremely specific information.

The theory of evolution, as biologists understand it, is concerned with "change in allele frequency" evolution.
I would suggest qualifying that as "as SOME biologists understand it". There's more to evolution than that, and many biologists approach it without ever even considering allele frequencies. Some are more interested in mechanisms of morphological change, or the history of change, or the geographic distribution of taxa...

Frequency of alleles in populations just don't matter when you're interested in macroevolutionary differences between species or phyla.

While you are here, pz, could you clarify your position in this thread a little for me? Are you proposing that some non-genetic factors are heritable,
Yes. Of course they are.
or that some non-heritable factors should be considered part of biological evolution?
Yes, that too. There are factors other than the sequence of nucleotides in DNA that make substantial contributions to the form and function of organisms.

Could you please provide a few examples of non-nucleotide inheritance that "make substantial contributions to the form and function of organisms"?
I presume that you've read D'Arcy Thompson's On Growth and Form? There's a whole book full of 'em, and Thompson doesn't mention genetics or genes except to disparage them (not that I agree with that bit of his attitude, of course).

Thompson had part of the story right: a substantial part of the patterns we see are independent of genes, and are 1) a consequence of the physico-chemical structure of the organism and its environment. Another part is due to 2) the epigenetic history of the tissue, which also cannot be described in terms of genes. And yet another part is 3) specifically shaped by gene action. Thompson ascribed almost all of it to (1), with a vague nod towards (2). Much of the recent history of biology ties it all to (3), denies that (1) is even interesting, and dismisses (2) as an inconsequential side effect of gene activity...as we are seeing on this thread.

Meanwhile, could you please provide a few examples of non-nucleotide inheritance that "make substantial contributions to the form and function of organisms"?
All instances of maternal localization of gene products. In Drosophila, for instance, that depends entirely on the proper conformation of the ovary and supporting cells that surround the oocyte. All instances of axis formation. Symmetry-breaking events usually require extra-genetic imposition of information, whether it is maternal localization, sperm entry, gravity, implantation, etc. All instances of induction. This should be obvious: if you have two cells with precisely identical genetic content that are going to have different cell fates, you have to have a non-genetic interaction of some sort to initiate those differences.

Thus do not feel that I am going after a "straw man" at all.

Perhaps pz can comment on whether the first question that you pose ("Show me an example of a feature that genes can produce on their own") represents his position accurately, but I tend to think that it does at least in part. For example, pz posted:

Quote:

Now it's your turn. Give me a few examples of genetic inheritance that are entirely gene-autonomous...that is, no epigenetic contribution is required in order to see the phenotype, and the gene/allele is both necessary and sufficient for expression of the property.

This certainly does miss the mark, as I have never stated or implied that genes act in isolation. My position is that evolution, as understood by every biologist that I have ever discussed it with, is a change in allele frequency over time.

Peez

pz · 10-25-2002, 09:13 AM

Quote:

Originally posted by Doubting Didymus:
I was under the impression that genes are responsible for encoding proteins, which would have made them directly responsible for the creation of cell membranes. (and much else)

How can they be directly responsible? Genes do their work entirely indirectly.

Membranes are an interesting example to choose, though. Perfectly lovely lipid bilayers will spontaneously self-assemble into micelles -- that's an aspect of the physico-chemical nature of the universe that promotes organization. Their assembly is dependent on the chemical nature of their surroundings, so environment is clearly significant. And every cell inherits a complete cell membrane from its parent, with a full array of receptors and cell surface proteins and lipid constituents that influence subsequent cell fate decisions.

Quote:

If non-genetic factors are as important as you say, why is biotechnology so fixated on genetics, and is largely ignoring cytoplasmic engineering? What kind of heritable phenotypic changes can you induce by manipulating non-genes? (note: this question is genuine and not facecious, as it may sound)

Who says cytoplasmic engineering has been ignored? We do it all the time, it's just that we're much more interested in working with somatic cells. Stem cell researchers are acutely interested in non-genetic factors, for instance. However, state of the art is incredibly primitive. It consists of searching for a subset of receptive cells, giving them treatments that are the equivalent of smacking them with a hammer to reset them to a totipotent state, and then following up with basically random exposure to growth factors to trigger development in a particular direction.

Think about it. Why can't we just pluck out a random skin cell and use it to clone a whole individual, or a new liver? It's because skin cells lack the specific extra-genetic programming needed to form a whole 'nother organism or organ. That's a much harder problem than puzzling out the sequence of DNA.

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10-23-2002, 06:23 PM	#83
Doubting Didymus Veteran Member Join Date: Jul 2002 Location: East Coast. Australia. Posts: 5,455	How much do you think can be reduced to the action of genes? As an example, is a cell membrane reducible to the action of genes? if not, what else?

10-23-2002, 07:37 PM	#85
Doubting Didymus Veteran Member Join Date: Jul 2002 Location: East Coast. Australia. Posts: 5,455	I was under the impression that genes are responsible for encoding proteins, which would have made them directly responsible for the creation of cell membranes. (and much else) If non-genetic factors are as important as you say, why is biotechnology so fixated on genetics, and is largely ignoring cytoplasmic engineering? What kind of heritable phenotypic changes can you induce by manipulating non-genes? (note: this question is genuine and not facecious, as it may sound)

10-25-2002, 08:15 AM	#87
RufusAtticus Veteran Member Join Date: Nov 2001 Location: NCSU Posts: 5,853	Oolon, But remember in every step of that process gene expression and thus the proteome was influenced by the environment. That is why you just can't simply say that by extracting back far enough there is a point at which the genes can account for everything.

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