An Alternative to Mutations

[mark kennedy]

It just seems to me epigenetics can produce more variation with lower physiological costs. I did some looking around an found this little gem:

Evolution requires phenotypic variation, selection, and heritability. It is generally assumed that mutation provides the single source of biological diversity that fuels evolution. In this report we describe evolution without mutation...What distinguishes these few cells and allows them to grow rather than die? In this report we show that the mechanism is not based on DNA mutation or plasmid uptake. Instead, within an isogenic population, without significant genotypic variation, there exists selectable phenotypic variation based on stochastic differences in gene expression patterns. That is, heritable epigenetic variation creates phenotypic diversity for natural selection to act upon...For example, over 95% of cells taken from a single colony growing on a 2.5 μg/ml amp plate were unable to grow when immediately transferred to a new plate with the same 2.5 μg/ml amp concentration (Fig. 1). This immediate reversion rate of over 95% to amp sensitivity argues strongly in favor of an epigenetic inheritance based mechanism, and against the involvement of DNA mutation...Altered gene expression patterns in resistant cells might reveal epigenetic based survival mechanisms...he evolution of resistance within the population is driven by a powerful antibiotic selective pressure coupled with phenotypic diversity created by heritable epigenetic variation. The extreme instability of the observed low level antibiotic resistance argues strongly that it does not involve DNA mutation events, or induced gene expression survival mechanisms...he evolution of resistance within the population is driven by a powerful antibiotic selective pressure coupled with phenotypic diversity created by heritable epigenetic variation. The extreme instability of the observed low level antibiotic resistance argues strongly that it does not involve DNA mutation events, or induced gene expression survival mechanisms.(Epigenetic inheritance based evolution of antibiotic resistance in bacteria BMC Evolutionary Biology 18 Feb 2008)

I have never been comfortable with mutations being the only source for evolution, adaptation and variation. The epigenetic diversity is heritable as well as reversible. I like it for a viable adaptive mechanism that is not mutually exclusive with the role of random mutations in heritable adaptive patterns.

Providence is a kind of watchmaker theology where the Creator's role as provider is understood as a completed work and a divine fiat. It is contrasted by but not mutually exclusive with God's miraculous interventions and events in time and space. Even with the processes being exclusively naturalistic their purposes and origins are preordained with a teleological end. Providence does not negate the miraculous any more then epigenetic sources of variation negate the role of mutations as a source of variation.

Recombination, transcription factors and gene expression are all highly efficient genetic mechanisms for producing inheritable adaptive traits. Without the cumulative mutations of Darwinism over mind numbing spans of time there are obvious limits to how much one species can transpose into an altogether different species.

I'm gong to keep a running total of the responses I get and score how many substantive points were actually made. I predict that the substantive scientific arguments will be far out weighed by the ad hominem attacks, rhetorical devices used to derail the topic and other logical fallacies evolutionists employ shamelessly.

Have a nice day
Mark

 

[Loudmouth]

It just seems to me epigenetics can produce more variation with lower physiological costs.

Then why don't we find a cephalopod with DNA 98% identical to that of humans?

 

[Vene]

It just seems to me epigenetics can produce more variation with lower physiological costs. I did some looking around and my, did you ever ask a good question. Found this little gem:

I was under the impression that without constant pressure that epigenetic traits tend to disappear after a couple of generations. How is this a stronger evolutionary force? And does epigenetic variation prevent sexual reproduction?

I have never been comfortable with mutations being the only source for evolution, adaptation and variation. The epigenetic diversity is heritable as well as reversible. I like it for a viable adaptive mechanism that is not mutually exclusive with the role of random mutations in heritable adaptive patterns.

I can see epigenetic traits accounting for some diversity, but I'm unconvinced that it would lead to the degree of diversity that is observed.

Providence is a kind of watchmaker theology where the Creator's role as provider is understood as a completed work and a divine fiat. It is contrasted by but not mutually exclusive with God's miraculous interventions and events in time and space. Even with the processes being exclusively naturalistic their purposes and origins are preordained with a teleological end. Providence does not negate the miraculous any more then epigenetic sources of variation negate the role of mutations as a source of variation.

(emphasis mine)
Irrelevant as far as a scientific discussion is concerned.

Recombination, transcription factors and gene expression are all highly efficient genetic mechanisms for producing inheritable adaptive traits. Without the cumulative mutations of Darwinism over mind numbing spans of time there are obvious limits to how much one species can transpose into an altogether different species.

Right, which is why mutations as a mechanism for variation cannot be discounted. It's too good of an explanation to throw away.

I'm gong to keep a running total of the responses I get and score how many substantive points were actually made. I predict that the substantive scientific arguments will be far out weighed by the ad hominem attacks, rhetorical devices used to derail the topic and other logical fallacies evolutionists employ shamelessly.

So, by telling others not to use ad hominem attacks, you employ one. How righteous of you.

Have a nice day
Mark

You have a good one too.

 

[mark kennedy]

Then why don't we find a cephalopod with DNA 98% identical to that of humans?

It has to be at least 25% identical because there are only 4 nucleotides. A better question would be how the actin gene families diverge from one another and what the regional variations are within known taxa:

The Actin I gene appeared to be less saturated than might be expected based on the highly conserved nature of the amino acid sequences. While first- and second-codon-position substitutions were rare, third-codon-position substitutions tended to accumulate linearly with increasing sequence divergence (fig. 4a ).Actin Gene Family Evolution and the Phylogeny of Coleoid Cephalopods (Mollusca: Cephalopoda)​

 

[DrRotmos]

It has to be at least 25% identical because there are only 4 nucleotides. A better question would be how the actin gene families diverge from one another and what the regional variations are within known taxa:

Actually, the nucleotides in question is irrelevant, because similarity at a genetic level isn't measured by which nucleotides are used, but rather by sequence.

Saying that it has to be 25% identical is like saying that any two given english sentences has to be at least 3.8% identical because there are only 26 letters.

 

[mark kennedy]

I was under the impression that without constant pressure that epigenetic traits tend to disappear after a couple of generations. How is this a stronger evolutionary force? And does epigenetic variation prevent sexual reproduction?

They do tend to disappear but they provide a selective advantage without high physiological costs like mutations. I really have no idea what you mean by the second question, does it prevent sexual reproduction in what exactly? Sexual reproduction helps to maintain and repair DNA stands through recombination.

I can see epigenetic traits accounting for some diversity, but I'm unconvinced that it would lead to the degree of diversity that is observed.

I would have to say that it depends on the diversity that is observed. Mostly I'm wondering about adaptive traits and clearly, not all of them are going to result with changes in the gross structure of the genes. The epigenetic variation can keep the costs of changes down while other complementary mechanisms produce other kinds of changes. My real point of contention is that epigenetic variation sounds a lot more viable then random mutations.

(emphasis mine)
Irrelevant as far as a scientific discussion is concerned.

Then don't worry about it, the question of how this fits into a Creationist perspective might of come up which is why I mentioned it.

Right, which is why mutations as a mechanism for variation cannot be discounted. It's too good of an explanation to throw away.

Who knows how many adaptive mechanisms exist, this could be one of dozens. Something else that keeps me wondering about this. Do you think it's possible that there are genetic mechanisms that can restructure parts of the genes purposely, even mechanically? See, I'm looking around for genetic mechanisms for adaptations and this one was far more appealing to me then random mutations.

So, by telling others not to use ad hominem attacks, you employ one. How righteous of you.

It's just that they are inevitable, sometimes if you keep score of them you can keep them to a minimum.

You have a good one too.

Grace and peace,
Mark

 

[mark kennedy]

Actually, the nucleotides in question is irrelevant, because similarity at a genetic level isn't measured by which nucleotides are used, but rather by sequence.

Saying that it has to be 25% identical is like saying that any two given english sentences has to be at least 3.8% identical because there are only 26 letters.

It's not just the sequence but also where and how regional variation is allowed. In an amino acid sequence in a protein coding gene the nucleotides used can be very important. One misplaced base pair and the reading frame can be shut down, you could have a nonsense mutation. I didn't ask the question about sequence variation, I just responded to it.

 

[Vene]

They do tend to disappear but they provide a selective advantage without high physiological costs like mutations. I really have no idea what you mean by the second question, does it prevent sexual reproduction in what exactly? Sexual reproduction helps to maintain and repair DNA stands through recombination.

By preventing sexual reproduction I'm talking about speciation. I'm asking if epigenetic changes would ever be enough to cause a population to break into multiple species.

I would have to say that it depends on the diversity that is observed. Mostly I'm wondering about adaptive traits and clearly, not all of them are going to result with changes in the gross structure of the genes. The epigenetic variation can keep the costs of changes down while other complementary mechanisms produce other kinds of changes. My real point of contention is that epigenetic variation sounds a lot more viable then random mutations.

I'm not convinced that it is more viable. A source of variation? Sure. But, if epigenetic variation cannot yield speciation isn't not enough.

Who knows how many adaptive mechanisms exist, this could be one of dozens. Something else that keeps me wondering about this. Do you think it's possible that there are genetic mechanisms that can restructure parts of the genes purposely, even mechanically? See, I'm looking around for genetic mechanisms for adaptations and this one was far more appealing to me then random mutations.

There may be other mechanisms, there's a lot to the world. But, just because mutations are 'appealing' isn't a good reason to discount them. Especially when they do happen and there are documented cases of mutation bringing benefits to an organism link

It's just that they are inevitable, sometimes if you keep score of them you can keep them to a minimum.

But then why single out evolutionists? That part was the attack. Do I really have to point out examples of bad logic that creationists use?

 

[mark kennedy]

By preventing sexual reproduction I'm talking about speciation. I'm asking if epigenetic changes would ever be enough to cause a population to break into multiple species.

Not working independent of of other adaptive mechanisms like cis-regulatory elements or gene regulatory change.

I'm not convinced that it is more viable. A source of variation? Sure. But, if epigenetic variation cannot yield speciation isn't not enough.

Maybe not but it can produce inheritable change that escapes the physiological costs of mutations with deleterious pleiotropic effects.

There may be other mechanisms, there's a lot to the world. But, just because mutations are 'appealing' isn't a good reason to discount them. Especially when they do happen and there are documented cases of mutation bringing benefits to an organism link

I don't doubt that and I know of even more significant changes. The thing is that mutations are more often neutral or deleterious and the beneficial effects don't last are only fixed if the benefits outweigh the costs.

Among the mutations that affect a typical gene, different kinds produce different impacts. A very few are at least momentarily adaptive on an evolutionary scale. Many are deleterious. Some are neutral, that is, they produce no effect strong enough to permit selection for or against; a mutation that is deleterious or advantageous in a large population may be neutral in a small population, where random drift outweighs selection coefficients. Rates of Spontaneous Mutation

But then why single out evolutionists? That part was the attack. Do I really have to point out examples of bad logic that creationists use?

Creationists typically don't respond to my posts.

 

[Loudmouth]

It has to be at least 25% identical because there are only 4 nucleotides.

But why not 98%?

A better question would be how the actin gene families diverge from one another and what the regional variations are within known taxa:

How is this related to your first post? Wouldn't you rather compare the transcription factors and regulation of actin genes?

 

[Loudmouth]

For example, over 95% of cells taken from a single colony growing on a 2.5 μg/ml amp plate were unable to grow when immediately transferred to a new plate with the same 2.5 μg/ml amp concentration (Fig. 1). This immediate reversion rate of over 95% to amp sensitivity argues strongly in favor of an epigenetic inheritance based mechanism, and against the involvement of DNA mutation...Altered gene expression patterns in resistant cells might reveal epigenetic based survival mechanisms...he evolution of resistance within the population is driven by a powerful antibiotic selective pressure coupled with phenotypic diversity created by heritable epigenetic variation.

This is not what was observed in the Lederberg-Lederberg plate replica experiment (.pdf file 1.2M). In this experiment only a very few bacteria (all of whom shared a common ancestor) displayed amp resistance. Of those, they all came from the same spot on the parent plate meaning that the amp resistance existed before exposure to amp and that it was not present in the common ancestor. Also, the amp resistance persisted even after several rounds of growth in non-selective media.

Why is it that the amp resistent bacteria originated from the same spots on the parent plate (which had not been exposed to amp) every time?

 

[Naraoia]

I'm quite certain epigenetic variation is not a true alternative to mutation. It may play a very important role in evolution (for example in cell differentiation), but without mutations there would be no substance for epigenetic mechanisms to act on.

While epigenetic modifications can affect the expression of existing genes, how would they produce novel traits that aren't just about a different expression pattern?

As far as I can tell, for something like a novel enzyme you are going to need mutations.

 

[Blayz]

Why does epigenetics have to be a mutually exclusive alternative to mutation-type evolution?

They both occur, and they are both covered by current evolutionary theory. Trying to separate them is about as silly as considering genetics in the absence of evolution.

 

[ReverendDG]

hey mark what do you think epigenetics is? what do you think it relates to?
evolution affects genes, well epigenetics is purely a change of the expression of genes, in fact epigenetics is thought of as being part of evolution theory

seems to me, that only those who build a strawman of evolution think this a problem for the ToE

 

[Gawron]

See guys, this is a debate.

"That is, heritable epigenetic variation creates phenotypic diversity for natural selection to act upon"

In an example I cited before, Italian wall lizards introduced into a new environment underwent a change in snout-vent length, body mass, and head dimensions. Yet when DNA ayalysis was done from tail clips taken from the displaced lizards, it was found these lizards were genetically identical to the source population still living in the pervious environment. What accounts for this phenotypic alteration without a genotypic alteration?

"I'm asking if epigenetic changes would ever be enough to cause a population to break into multiple species."

Maybe, but this would not be the only factor in the equation. Staying with the lizards above, if the two populations were to be re-intergrated, the effect of geographic isolation (allopatric spciation) over time may cause the displaced lizards (B) to refuse to mate with the source population (A) even though they could still produce viable offspring.

 

[BrainHertz]

Poll:

Epigenetics is the result of research pursued by:

a) Biologists who (still) accept evolution
b) Creation scientists (sic)

 

[Gawron]

Posted by Naraoia:

"While epigenetic modifications can affect the expression of existing genes, how would they produce novel traits that aren't just about a different expression pattern?"

It has recently been demonstrated that RNA plays a role in paramutation in mice. I am trying to find a full access link to the paper.

In addition, another aspect of epigenetic regulation has been demonstrated in that the memory of exposure to stress is transferred through several generations in plants.

"Why is it that the amp resistent bacteria originated from the same spots on the parent plate (which had not been exposed to amp) every time?"

I didn't read the paper you linked to but off the top of my head it could be DNA methylation. DNA methylation is called an epigenetic modification because it is not encoded in the DNA sequence itself. It is a form of cellular memory, particularly when applied to CG-rich promoter sequences, has been shown to silence gene expression in a heritable manner.

Quote:

"Although many nonmethylated GATC sites have been identified in E. coli, methylation in only a subset has been shown to control the expression of linked genes."

http://iai.asm.org/cgi/content/full/69/12/7197

 

[ReverendDG]

whats your point gawron?
epigenetics is not a problem for evolution, science has known about it longer than creationists have harped over it.
like what 30-35 years now?
as i said before epigenetics is not a problem for evolution or the ToE, only people who are building a strawman argument are claiming it is

 

[Naraoia]

See guys, this is a debate.

"That is, heritable epigenetic variation creates phenotypic diversity for natural selection to act upon"

In an example I cited before, Italian wall lizards introduced into a new environment underwent a change in snout-vent length, body mass, and head dimensions. Yet when DNA ayalysis was done from tail clips taken from the displaced lizards, it was found these lizards were genetically identical to the source population still living in the pervious environment. What accounts for this phenotypic alteration without a genotypic alteration?

I'm not sure about this, but wasn't the "identicalness" based on markers that had nothing to do with the phenotypic traits in question? Wait, I've downloaded the paper, let me check... (this is the Podarcis sicula on Pod Mrcaru, right?) Yes, the analysis was based on mitochondrial rDNAs. I wouldn't imagine mitochonrdial ribosomes have a lot to do with the changes the lizards underwent. So from this genetic analysis alone it's impossible to decide whether the changes were genetic or epigenetic.

 

[Naraoia]

whats your point gawron?

As far as I understand it's not that epigenetics is some huge problem for the ToE