Unsatisfactory Scientific Explanations?

[whois]

Human genome paper:
http://www.nature.com/nature/journal/v409/n6822/full/409860a0.html

Chimp genome paper:
http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html

Both used Sanger sequencing and pyrosequencing. Once the genomes were sequenced, they compared the sequence in silico (using computers). They didn't use hybridization.

thanks, i'll look into it.

 

[whois]

How can we get to presenting evidence when you refuse to even define your terms?

You either need to start using standard meanings of words or you need to start defining terms.

you are avoiding the issue.
i gave you the examples and the source i got them from.
anyone that honestly wanted to debate the issue would have no problem with what i presented.

 

[[serious]]

you are avoiding the issue.
i gave you the examples and the source i got them from.
anyone that honestly wanted to debate the issue would have no problem with what i presented.

You were using nonstandard meanings. You said starfish evolved from centipedes (false using normal meanings of words) then only recently said you mean they both have a common ancestor. That's an entirely different statement. I can't just guess at when you are going to stop using normal definitions, and when you stop using normal definitions, it's on you to actually provide a new definition.

To recap:
You said macroevolution doesn't occur
I pointed out that macroevolution has been observed using the normal meaning of the term.
You then said you didn't mean that definition of macroevolution, but a different one. Instead of defining it, you gave examples, including the starfish/centipede nonsense.

All of that could have been avoided if you would just define macroevolution.

 

[Loudmouth]

you are avoiding the issue.
i gave you the examples and the source i got them from.
anyone that honestly wanted to debate the issue would have no problem with what i presented.

This is the definition that scientists use.

"Macroevolution is evolution on a scale of separated gene pools.[1] Macroevolutionary studies focus on change that occurs at or above the level of species, in contrast with microevolution,[2] which refers to smaller evolutionary changes (typically described as changes in allele frequencies) within a species or population.[3]"
https://en.wikipedia.org/wiki/Macroevolution

 

[FrumiousBandersnatch]

first of all, why doubt that he said it?

Just naturally skeptical, I guess. It sounds like publicity or media blurb, not the same tone or import as the article.

IOW, the concept of common descent HAS NOT BEEN PROVEN, it's an assumption.

Strictly speaking, nothing is ever proven in science; we just have levels of confidence. Multiple independent lines of evidence, a simple, elegant explanatory mechanism, and no plausible evidence for alternatives, make common descent more than an assumption - it's beyond all reasonable doubt.

according to the modern synthesis, it's by accumulating gradual changes.
smith directly discounts that.

It's not a binary choice. Mutation rates are relatively constant (though they do vary), but selection pressures vary directly with environmental changes. This implies that environmental disruption will be a powerful driver of evolution. When you're dealing in clock ticks of millions of years, what is and isn't gradual is relative.

in fact, his hypothesis seems to support PE, but goes a step further by stating it was accomplished by a few major changes instead of accumulation.

What was accomplished? how many mutations in how much time make a major change? A single mutation in a regulator gene can produce major changes, like an extra pair of legs, or eyes, etc., but major phenotypic changes of that kind would generally require an available and compatible niche to have a selective advantage, so would be more likely to succeed in times of environmental change, when new niches more are likely to be available. So you might expect major developments to correlate with environmental upheavals - which is what we see.

this implies that macro evolution is a different animal than micro evolution.
they are 2 distinct processes

Not really, it's the same underlying mechanism, with different contributions from the different drivers of selection, over varying timescales. As I understand it, the debates and arguments are about the mechanisms that generate selection pressures.

it's my guess that HGT (or some form of it) is responsible for these transitions, some of them anyway.
but here again, HGT can hardly be called gradual, nor can it be strictly accumulating.

You need more than a guess. To be taken seriously, you need a plausible model that predicts and explains the observed gene frequencies and distribution, and does it better than current models. HGT is an important factor in prokaryotes, but not so much in eukaryotes; if you want to show otherwise, you'll need find some solid evidence for it, or at least, a well-reasoned and testable argument for it.

that's the point, there are no missing fossils, because the changes were major changes, not accumulating ones.

Or the changes accumulated in a shorter time. Only the last three transitions in the list had a significant chance of fossilization, and I'd argue the last as a major transition.

what if common ancestry isn't true?

Then we'd have a vast amount of evidence from multiple independent sources that are entirely consistent with common ancestry, and no other explanation for it - we'd probably be querying the meaning of 'true'.

 

[FrumiousBandersnatch]

I would define a mind as the Immaterial principle (spiritual) of the body that has 4 faculties (powers) namely: the intellect, will, memory and imagination.

So does it have these properties independent of the biological brain?

If so, we might expect that while brain damage or manipulation might limit their expression in various ways, we wouldn't expect it to significantly change the quality or content of those faculties when expressed. Is that reasonable?

[I'm assuming some kind of mind-as-transmitter & brain-as-receiver model crudely analogous to a TV receiving and displaying a transmitted programme].

 

[FrumiousBandersnatch]

... It can't all be dismissed as rubbish.

I've already explained - including a link to a detailed explanation from leading expert in the field - why the standard model of physics, and quantum field theory in particular, - the very science you hope to recruit to support your wishful fantasy - actually shows it to be impossible.

By all means speculate about amazing ideas, but it's unwise to to try to bolster them with science that disallows them - that's like claiming you can use the laws of thermodynamics to make a free energy device.

 

[whois]

Human genome paper:
http://www.nature.com/nature/journal/v409/n6822/full/409860a0.html

Chimp genome paper:
http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html

Both used Sanger sequencing and pyrosequencing. Once the genomes were sequenced, they compared the sequence in silico (using computers). They didn't use hybridization.

okay, i'm concluding that this is not empirical evidence of the major transitions of evolution.
in examining smiths paper, you will note that he proposes these transitions happened by how information is stored and transmitted.
the graphics smith presents indicates some kind of "mechanical" process, how DNA is wound around histones for example.
in my opinion, this does not equate to a statistical analysis.
smiths conclusions indicate that all of these transitions involved basically the same process by saying "enough similarities".

 

[whois]

furmious,
first of all, i want to commend you on your civility.
you are one of the most civil people i've debated in a very long time.
you seem to understand perfectly my meaning, while others go into the "define it" mode.
for that, i graciously thank you.
second is that name of yours, it conjures up all sorts of wildness.

Just naturally skeptical, I guess. It sounds like publicity or media blurb, not the same tone or import as the article.

believe me, i understand the naturally sceptical bit.
also, i believe i've seen this very same article posted on respected sites.

Strictly speaking, nothing is ever proven in science; we just have levels of confidence. Multiple independent lines of evidence, a simple, elegant explanatory mechanism, and no plausible evidence for alternatives, make common descent more than an assumption - it's beyond all reasonable doubt.

i understand this too.
science is not a method of proof, but of discovery.
also, it's a method of elimination, eliminating contenders until you arrive at the only thing left.

It's not a binary choice. Mutation rates are relatively constant (though they do vary), but selection pressures vary directly with environmental changes. This implies that environmental disruption will be a powerful driver of evolution. When you're dealing in clock ticks of millions of years, what is and isn't gradual is relative.

maybe.
the ability of the genome to adapt negates a large part of this.

What was accomplished? how many mutations in how much time make a major change? A single mutation in a regulator gene can produce major changes, like an extra pair of legs, or eyes, etc., but major phenotypic changes of that kind would generally require an available and compatible niche to have a selective advantage, so would be more likely to succeed in times of environmental change, when new niches more are likely to be available. So you might expect major developments to correlate with environmental upheavals - which is what we see.

this is one of the most befuddling aspects of evolution i've run across.
we talk about genomes (basically DNA), and the corresponding changes to it (mutations).
then we go into phenotypes, where the previous argument doesn't correlate.
in my opinion, this is an attempt to confuse the issue.

Not really, it's the same underlying mechanism, with different contributions from the different drivers of selection, over varying timescales. As I understand it, the debates and arguments are about the mechanisms that generate selection pressures.

not according to smith.
these transitions were few and major.
furthermore, it seems they are "mechanical" in nature instead of mutation driven.
granted, some of these transitions probably happened by HGT, but again HGT can hardly be called gradual.
i seriously question the "gradual accumulating changes", in regards to macro evolution, for 2 major reasons.
first it has been mentioned by at least one scientist.
second, and more importantly. is gene mutation by HGT and base insertions.
these 2 processes would negate any "accumulating"

You need more than a guess. To be taken seriously, you need a plausible model that predicts and explains the observed gene frequencies and distribution, and does it better than current models. HGT is an important factor in prokaryotes, but not so much in eukaryotes; if you want to show otherwise, you'll need find some solid evidence for it, or at least, a well-reasoned and testable argument for it.

i don't buy this line of reasoning, and the apparent presence of ERVs in humans is the reason.
if HGT is not that frequent in humans, then these ERVs had to come from deep time, and they would be present in every lineage from the moment of acquisition.
to my knowledge, this has not been proven.
yes, it appears this has been shown between ape and man, but that's it
for example, it hasn't been shown to exist between lungfish and apes (reference the TOL upload for source, post 405.)
so no, common ancestry has not been empirically proven.
i use common ancestry in the macro evolution context.

 

[Loudmouth]

not according to smith.
these transitions were few and major.

Why can't major transitions be produced by the gradual accumulation of small changes?

furthermore, it seems they are "mechanical" in nature instead of mutation driven.

How so?

granted, some of these transitions probably happened by HGT, but again HGT can hardly be called gradual.

As your own references have demonstrated, there has only be one gene acquired by humans through HGT since diverging from the chimp lineage. Therefore, the transition of language was not influenced by HGT in any meaningful way.

i seriously question the "gradual accumulating changes", in regards to macro evolution, for 2 major reasons.
first it has been mentioned by at least one scientist.
second, and more importantly. is gene mutation by HGT and base insertions.
these 2 processes would negate any "accumulating"

HGT has been mentioned by more than one scientist, so does that mean you don't accept it?

Secondly, why do you have a problem with indels? I still don't understand that one. While most indels will cause frame shift mutations within the transcribed regions of genes, they don't pose the same deleterious risk in upstream and downstream regulatory DNA which is just as important for the evolution of phenotype. And as we have shown you multiple times now, HGT is very rare in complex eukaryotes.

i don't buy this line of reasoning, and the apparent presence of ERVs in humans is the reason.
if HGT is not that frequent in humans, then these ERVs had to come from deep time, and they would be present in every lineage from the moment of acquisition.

Many of them are in every lineage. We can find ERV's shared by distantly related primates because those retroviruses inserted long ago in a distant common ancestor. Through time, ERV's can recombine and accumulate mutations which makes the most ancient insertions hard to distinguish. However, more recent insertions are much easier to find.

In fact, here is part of a figure from a paper that compared ERV's between distantly related primates. They showed the expected divergence between the 5' and 3' LTR's of an ERV shared by humans, other apes, baboons, and macaques.

http://www.pnas.org/content/96/18/10254.full

for example, it hasn't been shown to exist between lungfish and apes (reference the TOL upload for source, post 405.)
so no, common ancestry has not been empirically proven.

It has been proven for humans and primates.

 

[whois]

Why can't major transitions be produced by the gradual accumulation of small changes?

they probably could, and that is what the modern synthesis says.
but according to smith, these transitions happened not by "gene mutation/ accumulation", but by "mechanical" process, for example how tightly DNA is wound around histones.
a review of smiths paper will give you the general process that he proposes, see post 389 for link.

As your own references have demonstrated, there has only be one gene acquired by humans through HGT since diverging from the chimp lineage. Therefore, the transition of language was not influenced by HGT in any meaningful way.

as smith states, this was no doubt caused by some kind of "mechanical mutation" of DNA.
these transitions do not seem to be gene mutations.
plus, smith states in the conclusion that there are similarities in these transitions, which indicates a separate process from micro evolution.

HGT has been mentioned by more than one scientist, so does that mean you don't accept it?

i was referring to accumulating gradual changes in regards to macro evolution.
the one scientist i'm referring to is ayala, and he had this to say:
"We would not have predicted stasis from population genetics, but I am now convinced from what the paleontologists say that small changes do not accumulate"
this quote has been hotly contested, but i believe it was legit.

as to HGT, science says it happens.
i fail to understand how they can empirically demonstrate this, especially in regards to deep time.

Secondly, why do you have a problem with indels? I still don't understand that one. While most indels will cause frame shift mutations within the transcribed regions of genes, they don't pose the same deleterious risk in upstream and downstream regulatory DNA which is just as important for the evolution of phenotype. And as we have shown you multiple times now, HGT is very rare in complex eukaryotes.

i believe i have provide valid sources that say the opposite.
all of the sources i've seen considers HGT in vertebrates as a major factor in their evolution.
one such source had this to say:
"An example of HGT in animals is the transfer (through consumption) of fungal genes into insects called aphids, which allows the aphids the ability to make carotenoids on their own."

so, not only can this happen through viral infection, it can happen by food consumption.
in this regard, HGT is probably more common than one thought.
one specific example involves a certain blood group in humans, which didn't exist until it was HGT acquired.
this sort of thing demonstrates that change doesn't necessarily require millions of years.

Many of them are in every lineage. We can find ERV's shared by distantly related primates because those retroviruses inserted long ago in a distant common ancestor. Through time, ERV's can recombine and accumulate mutations which makes the most ancient insertions hard to distinguish. However, more recent insertions are much easier to find.

this is the type of destruction that i refer to in the analysis of gene history.
it's this destruction that would make the ability to trace genes through deep time impossible, but yet science says it can do exactly that.
this same type of reasoning applies to ancient HGT events as well.
how can science possibly know an ancient HGT event as opposed to mutation?
but yet science says they can.

In fact, here is part of a figure from a paper that compared ERV's between distantly related primates. They showed the expected divergence between the 5' and 3' LTR's of an ERV shared by humans, other apes, baboons, and macaques.

View attachment 166847
http://www.pnas.org/content/96/18/10254.full



It has been proven for humans and primates.

all you have done here is prove they are all primates.
this does nothing in regards to empirical proof of macro evolution.

 

[Loudmouth]

they probably could, and that is what the modern synthesis says.
but according to smith, these transitions happened not by "gene mutation/ accumulation", but by "mechanical" process, for example how tightly DNA is wound around histones.

From my reading, he is saying that histones had to evolve first, not that the DNA sequence stayed the same and histones somehow bound differently. Why couldn't histones evolve through a process of gradual accumulation of small DNA mutations?

as smith states, this was no doubt caused by some kind of "mechanical mutation" of DNA.
these transitions do not seem to be gene mutations.

From my reading, the mechanical systems came about through the mutation of DNA.

plus, smith states in the conclusion that there are similarities in these transitions, which indicates a separate process from micro evolution.

I think we all agree that macroevolution includes mechanisms not found in microevolution, such as speciation. However, I don't see how this rules out the gradual accumulation of mutations as part of that process.

i was referring to accumulating gradual changes in regards to macro evolution.
the one scientist i'm referring to is ayala, and he had this to say:
"We would not have predicted stasis from population genetics, but I am now convinced from what the paleontologists say that small changes do not accumulate"
this quote has been hotly contested, but i believe it was legit.

Was he referring to genetic or phenotypic changes? What is the context of the quote?

as to HGT, science says it happens.

Scientists say that people get hit by lightning. That doesn't mean that every death is caused by lightning.

If I say that most buffalo are brown, that is not refuted by saying that people have found white buffaloes.

Do you understand how finding a few rare HGT events does not refute the statement that HGT events are rare?

i fail to understand how they can empirically demonstrate this, especially in regards to deep time.

They use phylogenetics. Genes that don't follow the expected species tree are suspected of being transferred through HGT.

i believe i have provide valid sources that say the opposite.
all of the sources i've seen considers HGT in vertebrates as a major factor in their evolution.
one such source had this to say:
"An example of HGT in animals is the transfer (through consumption) of fungal genes into insects called aphids, which allows the aphids the ability to make carotenoids on their own."

so, not only can this happen through viral infection, it can happen by food consumption.
in this regard, HGT is probably more common than one thought.

If HGT is responsible for 0.1% of the changes in the human genome compared to VGT, that would be more common than we thought, but it is still a small amount. You could claim that people getting killed by lightning strikes may happen more than we think, but you still can't claim that most people die from lightning strikes. Do you understand what I am saying?

Afterall, we have the chimp and human genome sequences. We know that VGT from a shared ancestor is responsible for the vast majority of each genome. This isn't a mystery.

one specific example involves a certain blood group in humans, which didn't exist until it was HGT acquired.

One gene out of how many in the human genome?

this sort of thing demonstrates that change doesn't necessarily require millions of years.

It doesn't demonstrate that all changes must happen through HGT.

this is the type of destruction that i refer to in the analysis of gene history.
it's this destruction that would make the ability to trace genes through deep time impossible, but yet science says it can do exactly that.

The destruction is slow enough that we can detect ERV's that were present in the common ancestor of primates, including humans. ERV's can survive for 10's of millions of years.

Your argument is like saying that fingerprint evidence will disappear after a few years, so fingerprints can't ever be used in a court of law.

this same type of reasoning applies to ancient HGT events as well.

For conserved genes, this isn't true. Negative selection can preserve sequence and allow us to determine if it was transferred by HGT.

how can science possibly know an ancient HGT event as opposed to mutation?

As mentioned earlier, HGT is detected when the gene tree differs greatly from the expected species tree. Finding a gene in humans that is identical in sequence to a dog gene while being quite different in sequence in chimps would point to an HGT event.

all you have done here is prove they are all primates.

I have proven that they share a common ancestor.

this does nothing in regards to empirical proof of macro evolution.

It is empirical proof that all primates, including humans, descended from a common ancestor. How is that not macroevolution?

 

[FrumiousBandersnatch]

furmious,
first of all, i want to commend you on your civility.
you are one of the most civil people i've debated in a very long time.
you seem to understand perfectly my meaning, while others go into the "define it" mode.
for that, i graciously thank you.

Thanks - maybe I'm learning to follow your trains of thought...

second is that name of yours, it conjures up all sorts of wildness.

Rightly so; for I am rehabilitating the shunned Jabberwock - the eyes of flame, jaws that bite, the claws that catch!

the ability of the genome to adapt negates a large part of this.

It's not the genome that adapts but the population; populations adapt through changes in the genome. That's exactly what I've been talking about, it negates nothing.

this is one of the most befuddling aspects of evolution i've run across.
we talk about genomes (basically DNA), and the corresponding changes to it (mutations).
then we go into phenotypes, where the previous argument doesn't correlate.
in my opinion, this is an attempt to confuse the issue.

The basics are simple enough - the phenotype is the expression of the genome. Mutations of the genome can change it's expression - i.e. they can change the phenotype.

not according to smith.

Yes, according to Smith - it's precisely what he's talking about; he's discussing the relevance of information in evolutionary biology and in explaining the particular mechanisms of evolution by natural selection that these transitions have in common. Here's some relevant quotes from the article:

"The transitions must be explained in terms of immediate selective advantage to individual replicators. We are committed to the gene-centred approach outlined by Williams and made still more explicit by Dawkins."

[when there are a large number of small groups and effective competition between groups], ".. there will be genetic differences between groups, but individuals in a single group will be similar. If so, the groups will be units of evolution and will evolve by natural selection.
The principle of the small number of founders is important at the time of transition."

A small number of founders means a high degree of genetic similarity, making for a distinct population.

These transitions were few and major.

Quite, that's what makes them notable...

furthermore, it seems they are "mechanical" in nature instead of mutation driven.

I don't know where you got that from. Mutations are the underlying means of variation; what is being discussed is the 'mechanisms' underlying the various selection pressures and their effects on the populations.

granted, some of these transitions probably happened by HGT, but again HGT can hardly be called gradual.

As mentioned previously, HGT may have a significant role in prokaryotes, but less so in eukaryotes - think it through: if significant HGT occurred between lineages, we'd see less distinct lineages and more genes in common between them. But what we see in eukaryotes is consistent with limited viral and bacteriophage insertion.

i seriously question the "gradual accumulating changes", in regards to macro evolution, for 2 major reasons.
first it has been mentioned by at least one scientist.
second, and more importantly. is gene mutation by HGT and base insertions.
these 2 processes would negate any "accumulating"

HGT doesn't cause gene mutations - it's horizontal gene transfer. And if HGT was significant in these transitions, it would still be necessary to accumulate enough changes to differentiate the populations - a problem for this idea of HGT driven transition, if it had happened, is that it would mean swapping genes between populations supposedly transitioning apart - it would work against differentiation.

i don't buy this line of reasoning, and the apparent presence of ERVs in humans is the reason.
if HGT is not that frequent in humans, then these ERVs had to come from deep time, and they would be present in every lineage from the moment of acquisition.

Sure, ERVs are present, and many have been around since the earliest times; they give us an independent measure of genetic relatedness, they are another strand of evidence in support of a tree of lineages of common descent.

 

[FrumiousBandersnatch]

...this sort of thing demonstrates that change doesn't necessarily require millions of years.

We already know this - in the right circumstances, speciation can occur in a few thousand years or less; isolated bird populations can evolve mating differences, a step towards speciation, in less than 50 years. Is it any wonder that after hundred of millions of years there is such diversity of life?

 

[stevevw]

I used to spend a lot of time as a child wishing I could affect things with the power of my mind, like a comic-book hero... but wishful thinking is one thing and the real world is something else. We know enough about quantum mechanics and the brain to know they don't work magic together; if the brain uses quantum effects outside of normal biochemistry, it will be for small-scale functional optimizations. Biology apart, quantum physics itself tells us you won't see mind remotely affecting matter; the only field or force with the range and strength to have significant effect over human-scale distances (besides gravity) is electromagnetism, and we know what it can and can't do, and what is needed to generate a significant influence with it. Electric eels can pack a remote electrical wallop, but human biology isn't up to it.

I am not sure we know enough about quantum mechanics and our brains to understand how they may connect together to influence things. We know a lot about them individually but I think the area of quantum effect is still fairly unknown. Afterall even science itself still talks about quantum tunneling , time travel, parallel, hologram worlds and other possibilities. The point is we just dont know what our minds can effect because maybe we are not aware of what is effected by he quantum world yet. You say that you use to try and wish things into effect when you were a kid. I am not sure it is that obvious that you expected to get a magical response there and then. It maybe that some of the things that happened in your life that maybe fell into place which you thought were good luck or the right timing ect were influenced by something that you did through your mind that influenced things.

The point is we just dont know yet. We may not even have the right sort of equipment or test to find that out yet. It just seems that if at the quantum level things can operate in a different way that there are many possibilities before a end result that the brain may also be able to tune into this and have an influence. If the brain begins its effects at a quantum level as well then who knows if the two cannot link up and have some effect on things.
Discovery of quantum vibrations in 'microtubules' corroborates theory of consciousness
http://phys.org/news/2014-01-discovery-quantum-vibrations-microtubules-corroborates.html

 

[whois]

The basics are simple enough - the phenotype is the expression of the genome. Mutations of the genome can change it's expression - i.e. they can change the phenotype.

it's slowly being realized by a large number of biologists that genomes do not follow the simple principle of a "gene library".
IOW, phenotypes aren't constructed on the basis of a DNA blueprint.

Yes, according to Smith - it's precisely what he's talking about; he's discussing the relevance of information in evolutionary biology and in explaining the particular mechanisms of evolution by natural selection that these transitions have in common. Here's some relevant quotes from the article:

"The transitions must be explained in terms of immediate selective advantage to individual replicators. We are committed to the gene-centred approach outlined by Williams and made still more explicit by Dawkins."

this is a typical example of my preceding response.
since phenotypes do not follow a DNA blueprint, this allows individual adaptation to the environment.
for example, the ability to acclimate to low oxygen levels.

[when there are a large number of small groups and effective competition between groups], ".. there will be genetic differences between groups, but individuals in a single group will be similar. If so, the groups will be units of evolution and will evolve by natural selection.
The principle of the small number of founders is important at the time of transition."

i'm not sure what you mean by "unit of evolution", a certain scientist introduces a similar term "fundamental unit of evolution", but does so in a discussion about the tree of life.
unfortunately i have been forbidden by the mods of discussing this particular authors papers.
also, it seems i am the only one that this honor has been bestowed on.

I don't know where you got that from. Mutations are the underlying means of variation; what is being discussed is the 'mechanisms' underlying the various selection pressures and their effects on the populations.

okay, there must be a distinction between "mechanisms" and "mutations"
if mutations are the cause, then why discuss mechanisms?
don't forget, in the conclusion smith says there are enough similarities in these transitions to hope for a theory behind them.
it's my opinion that this theory is going to entail a "mechanical" basis, how proteins are folded, or how DNA is transcribed.
i guess you could say this is a result of mutations, but i think you need to apply goulds concept of spandrels to this.
the groundwork is laid, then the final mutation happens that results in the major transformation.
this concept is probably applicable to all of evolution, not just to major transitions.
IOW, macro evolution is the result of the clockwork nature of genetics, not because of any kind of adaptation.

As mentioned previously, HGT may have a significant role in prokaryotes, but less so in eukaryotes - think it through: if significant HGT occurred between lineages, we'd see less distinct lineages and more genes in common between them. But what we see in eukaryotes is consistent with limited viral and bacteriophage insertion.

a single HGT event can be significant, and it's certainly far from gradual.

HGT doesn't cause gene mutations - it's horizontal gene transfer. And if HGT was significant in these transitions, it would still be necessary to accumulate enough changes to differentiate the populations - a problem for this idea of HGT driven transition, if it had happened, is that it would mean swapping genes between populations supposedly transitioning apart - it would work against differentiation.

HGT can certainly be seen as a mutation of a particular germline.
a single HGT event affecting regulatory or HOX genes can have major impact.
speaking of which, regulatory and HOX genes seems to be relatively immune to these types of events.
this sort of immunity had to evolve.
when you start delving into this stuff and start giving it scrutiny, you suddenly realize that science is very far from any kind of coherent theory for it.
this alone almost demands a different process for macro evolution.

Sure, ERVs are present, and many have been around since the earliest times; they give us an independent measure of genetic relatedness, they are another strand of evidence in support of a tree of lineages of common descent.

this is another area that makes no sense.
science says they can trace gene history through deep time, but how can the do this with such things as base pair insertions, transposons, and other mutations that wouls soon destroy any kind of gene history.

 

[FrumiousBandersnatch]

I am not sure we know enough about quantum mechanics and our brains to understand how they may connect together to influence things. We know a lot about them individually but I think the area of quantum effect is still fairly unknown. Afterall even science itself still talks about quantum tunneling , time travel, parallel, hologram worlds and other possibilities. The point is we just dont know what our minds can effect because maybe we are not aware of what is effected by he quantum world yet.

You may not know enough, but physicists do; quantum field theory tells us that the only field with a range and strength relevant to human-scale interactions is the electromagnetic field. The brain does produce EMF, but it's a barely detectable (e.g. by EEG) bioelectric sum of all neural activity. Quantum tunneling, quantum entanglement, time travel, parallel worlds, holographic universe, and so-on, are all irrelevant to this. If you want to know what researchers are speculating about concerning the brain and quantum effects, check out the latest New Scientist issue - it's a 'highly speculative' (and to me unconvincing) hypothesis about the contribution of molecular level quantum effects to neural function in thought and memory.

The point is we just dont know yet. We may not even have the right sort of equipment or test to find that out yet. It just seems that if at the quantum level things can operate in a different way that there are many possibilities before a end result that the brain may also be able to tune into this and have an influence. If the brain begins its effects at a quantum level as well then who knows if the two cannot link up and have some effect on things.
Discovery of quantum vibrations in 'microtubules' corroborates theory of consciousness
http://phys.org/news/2014-01-discovery-quantum-vibrations-microtubules-corroborates.html

We do know; everything is quantum mechanical at the lowest level and the theory describing how it behaves is the best tested theory we've ever had. We know very precisely how it behaves; what we don't know is why it behaves like that.

We know some molecular-scale quantum effects are used to optimize some biological functions (e.g. photosynthesis, bird navigation). But the Penrose & Hameroff Orch-OR theory of quantum consciousness mediated by cellular microtubules is more than highly speculative, it's quite implausible; there's no evidence for it, it stretches QM way outside its known bounds, it makes no testable predictions, and it is redundant. If you look for the original paper that phys.org item is based on, you'll find it wasn't a peer-reviewed paper published in an acknowledged journal, but a report of a claimed discovery by a colleague of theirs in a review by Penrose & Hameroff themselves. It was media puffery, an attention grab - but there was nothing to see - which is why, after a brief flurry of interest, it was put back in the 'speculative pseudoscience' bin.

 

[FrumiousBandersnatch]

it's slowly being realized by a large number of biologists that genomes do not follow the simple principle of a "gene library".
IOW, phenotypes aren't constructed on the basis of a DNA blueprint.

The concepts of DNA as a blueprint or a recipe have always been inaccurate analogies. No news there.

this is a typical example of my preceding response.
since phenotypes do not follow a DNA blueprint, this allows individual adaptation to the environment.
for example, the ability to acclimate to low oxygen levels.

It was a quote from the paper you linked to. But anyhow, lets clarify adaptation. Individuals in a population will attempt to adapt to their environment - for example, acclimatising to low oxygen, as you point out, or building muscle and thickening bones to accommodate heavy physical labour. The degree of such adaptation is limited by the physiological capabilities of the individual. When a whole population is exposed to a novel and stressful environment to which they have to adapt, the genetic variation in the population means that some are able to adapt more fully than others; these individuals will generally be more successful, and produce more viable offspring with the genetics that enable them to adapt better than the original population average. In time, the population genetics will be shifted in favour of these adaptations. So the individuals in the genetically adapted population will have a genetic advantage over the original population - they'll be able to adapt to their environment more quickly and to a greater extent. In this sense, population evolution follows in the footsteps of individual adaptation.

i'm not sure what you mean by "unit of evolution"...

It's a quote from Smith's paper - the one you linked to; if you'd read the paper carefully, you'd know this - if you'd read my post carefully, you'd know this. Smith is referring to a 'unit of selection' - in this case a small group of closely genetically related individuals, on which natural selection can act.

if mutations are the cause, then why discuss mechanisms?

Mutations provide the variation; the discussion is about how natural selection acts on those variations to produce the observed transitions. That's what the whole paper is about...(!)

...science says they can trace gene history through deep time, but how can the do this with such things as base pair insertions, transposons, and other mutations that wouls soon destroy any kind of gene history.

Well, no. If you had really delved into this stuff and given it the scrutiny you claim, you'd know that critical areas of the genome are highly conserved, unchanged since the earliest times. The level of gene conservation is roughly proportional to their fundamental importance. This conservation hierarchy gives us one kind of genetic history. There are also large amounts of the genome that are not strongly conserved. These have mutations, insertions, ERVs, etc. scattered through them. As these accumulate over evolutionary time, they provide another kind of genetic history.

Your posts show that you really need to get a coherent understanding of the fundamentals of genetics and the theories you're arguing for (or against) before you can make reasonable arguments and suggestions about them. Just hopping around finding papers on particular topics won't give you that basic understanding. I'm no expert (my formal grounding was at degree level 35 years ago), but I've spent a fair bit of time trying to explain this stuff, and it's become clear that it's not going to help unless you can think through the implications for yourself, and you can only do that if you understand the foundations of these ideas.

 

[whois]

I'm no expert (my formal grounding was at degree level 35 years ago), but I've spent a fair bit of time trying to explain this stuff, and it's become clear that it's not going to help unless you can think through the implications for yourself, and you can only do that if you understand the foundations of these ideas.

yes, it does seem you know a lot about the modern synthesis, and its foundations.
unfortunately genomics and other disciplines have overturned many important assumptions of the modern synthesis in the last decades of the 20th century.
give the following a read:
www.ncbi.nlm.nih.gov/pmc/articles/PMC2222615/

edited to add:
since some genes are conserved, then science apparently know what these genes are.
what are these genes specifically, HOX genes perhaps?

 

[[serious]]

yes, it does seem you know a lot about the modern synthesis, and its foundations.
unfortunately genomics and other disciplines have overturned many important assumptions of the modern synthesis in the last decades of the 20th century.
give the following a read:
www.ncbi.nlm.nih.gov/pmc/articles/PMC2222615/

edited to add:
since some genes are conserved, then science apparently know what these genes are.
what are these genes specifically, HOX genes perhaps?

Epigenetic might be new in popular culture, but non genetic effects, even heritage ones, have been known about for a while. A decade ago when I was an undergrad we covered them. I even had a professor who got a paper rejected because a reviewer felt he hadn't adequately controlled for maternal effects. This is after he weighed the seeds to specifically control for that.

One thing I've learned is that the more impressive a title or press release sounds, the more certain it is to be minor, procedural gains in a well studied field. Sometimes, as appears to be the case here, it's strictly commentary on decades of work by others.

It is not that the paper is wrong or bad, it just over sells it's point. Let's begin by defining modern synthesis. Wikipedia has a good run down of the key points:

• All evolutionary phenomena can be explained in a way consistent with known genetic mechanisms and the observational evidence of naturalists.

• Evolution is gradual: small genetic changes regulated by natural selection accumulate over long periods. Discontinuities amongstspecies (or other taxa) are explained as originating gradually through geographical separation and extinction. This theory contrasts with the saltation theory of William Bateson (1894).[7]

• Natural selection is by far the main mechanism of change; even slight advantages are important when continued. The object of selection is the phenotype in its surrounding environment.

• The role of genetic drift is equivocal. Though strongly supported initially by Dobzhansky, it was downgraded later as results from ecological genetics were obtained.

• Thinking in terms of populations, rather than individuals, is primary: the genetic diversity existing in natural populations is a key factor in evolution. The strength of natural selection in the wild is greater than previously expected; the effect of ecological factors such as niche occupation and the significance of barriers to gene flow are all important.

In palaeontology, the ability to explain historical observations by extrapolation from microevolution to macroevolution is proposed. Historical contingency means explanations at different levels may exist.Gradualism does not mean constant rate of change.

Now, the paper objects to the following:

The genome is always a well-organized library of genes.

• Genes usually have single functions that have been specifically honed by powerful natural selection.

• Species are finely adjusted to their ecological circumstances due to efficient adaptive adjustment of biochemical functions.
The durable units of evolution are species, and within them the organisms, organs, cells, and molecules, which are characteristic of the species.

• Given the adaptive nature of each organism and cell, their machinery can be modeled using principles of efficient design.

you will note that the objections he raises don't line up with the central tenants of the modern synthesis. The points he address are legitimately simplification that exist in biology, but they are simplification we are aware of and use for certain uses. This is akin to using newtonian physics to model something. Is it a simplification? Yes. But that doesn't mean it isn't appropriate to use when relativistic effects aren't significant.

Same here. There are times when epigenetic factors are critical to understanding an observation, and there are times when they are not. Finding that balance is important.