Natural Genetic Engineering

[eversbane]

Originally Posted by Socrates

Re-read the passage (or other material from James Shapiro) and mentally replace the word "evolution" with the word"development".

Do you mean to direct us to misquote and mischaracterize Shapiro?

Why would we do that? Shapiro wrote what he thought was relevant. Why would we change his words?

[eversbane]

Originally Posted by Socrates

For example:

As outlined above, my own experience with E. coli and
its transposons taught me that living cells are prodigious
genetic engineers. For the past 17 years, I have called
mobile elements and the other biochemical complexes
that restructure cellular DNA molecules ‘‘natural genetic
engineering systems’’ and argued further that these
systems fulfill major evolutionary developmental functions

But the evolutionary biology community is resistant
to accepting the fundamental importance of
natural genetic engineering because biologically controlled
genome restructuring does not fit with their
assumptions about the random, accidental nature of
hereditary variation. The use of the word ‘‘engineering’’
has generated further controversy because, some claim,
it suggests the existence of an engineer and might
thereby give comfort to the intelligent design
community.

The second response to arguments against the natural
genetic engineering concept is to reflect seriously on
how living organisms are able to search effectively
through the infinite space of possible genome configurations.
The progenitors of extant organisms have had
to make these searches during the course of repeated
evolutionary developmental challenges. So it should be no surprise that today’s survivors possess evolved developed biochemical systems to facilitate the evolutionary developmental rewriting of genomic information.
These systems have the capacity to reduce the size of
the genomic search space dramatically and to maximize
the chances for success by using a combinatorial process
based on existing functional components. New combinations
of established coding sequences, transcriptional
regulatory signals, and chromatin determinants are far
more likely to prove effective than are a series of random
changes altering individual genetic elements.
We know from genome sequences that evolution development has followed the reliable engineering process of putting
known pieces together in new arrangements. What we
do not yet know is how far cells’ abilities to regulate and
target natural genetic engineering activities may contribute,
as McClintock has suggested, to the generation
of complex and useful evolutionary developmental novelties. Until recently, investigation of this subject has not been
feasible. Today, however, we can activate transposons
and retrotransposons to search for functional multilocus
mutations. If we do indeed find out that regulatory
and targeting mechanisms facilitate the kind of advantageous
genome engineering documented in our databases,
then there is no danger of falling into any
epistemological trap with the natural genetic engineering
concept. We will have identified the responsible
‘‘engineers’’ to be prokaryotic and eukaryotic cells that
have evolved developed capacities to sense danger and rewrite their genomic memory storage systems as best they can
(McClintock 1984). The research agenda will then
be to analyze molecularly and computationally how
those cellular control functions operate. My guess is that
we will be amazed at what we find.

Evolution and Development have different definitions.

[FIGUER]

Originally Posted by VoxRat

The above is confused.

Not at all, that's absurd. Seems you are confusing the process (evolution) with particular mechanisms (current theory). Intelligence would be a particular mechanism for evolution, not a substitute for evolution.

I believe you've missed the point. Did you follow the mitochondrial genome discussion, starting about here?

I believe it does. But you may have to read the previous discussion to follow why.

I don't see how that follows either.

[VoxRat]

Originally Posted by FIGUER

I don't see how that follows either.

whatever.
if you'll pardon the expression.

[Socrates]

Originally Posted by Monad

That's a useful link even if Socrates doesn't seem to really understand it so I've added it to the useful links list sticky:

http://www.talkrational.org/showthread.php?t=7581

Shapiro seems to relate well to authors like Stephen Rose ("Lifelines") who I'm a fan of. He is of course an evolutionist - just not a strong Darwinian (or should I say neo-Darwinian since Darwin himself may well have agreed with much he has to say - remember Darwin = variation + NS/SS - not mutation per se)

It's funny how often we see someone post a sentence like:
"That's a useful link even if Socrates doesn't seem to really understand it".
It is such a foolish thing to say. And so transparent.

[Socrates]

Originally Posted by FIGUER

Well, indeed it suggest an engineer: the cells/living entities themselves. Considering the engineering capacities of humans that shouldn't be a controversial claim.

Agreed.
And consider that human genetic engineers will be even more capable in the future.

[RAFH]

Originally Posted by Socrates

It's funny how often we see someone post a sentence like:
"That's a useful link even if Socrates doesn't seem to really understand it".
It is such a foolish thing to say. And so transparent.

Ah, the sad little mischaracter pops his head up and says nothing. Again.
Now that is funny.

[Socrates]

Originally Posted by FIGUER

Not at all, that's absurd. Seems you are confusing the process (evolution) with particular mechanisms (current theory). Intelligence would be a particular mechanism for evolution, not a substitute for evolution.

I don't see how that follows either.

Figuer, when you say:
"Intelligence would be a particular mechanism for evolution, not a substitute for evolution."

May I suggest that this sentence will have more meaning if you replace the word "evolution" with the word "development".
It would then read:
Intelligence would be a particular mechanism for development, not a substitute for development.

[ericmurphy]

Originally Posted by Socrates

It's funny how often we see someone post a sentence like:
"That's a useful link even if Socrates doesn't seem to really understand it".
It is such a foolish thing to say. And so transparent.

What's "foolish" about it? Anyone who could read that Shapiro passage and thinks it would be improved by replacing the word "evolution" with "development" everyone it appears is clearly incapable of understanding what the passage is on about. It has nothing whatsoever to do with development.

[ericmurphy]

Originally Posted by Socrates

Figuer, when you say:
"Intelligence would be a particular mechanism for evolution, not a substitute for evolution."

May I suggest that this sentence will have more meaning if you replace the word "evolution" with the word "development".
It would then read:
Intelligence would be a particular mechanism for development, not a substitute for development.

What is your fascination with development, "socrates"? Evolution and development are totally different things. You can't just substitute one for the other.

Do you just have some sort of emotional problem with the word "evolution"?

[FIGUER]

Originally Posted by Socrates

May I suggest that this sentence will have more meaning if you replace the word "evolution" with the word "development".

You may indeed suggest it, but I don't see any merit to the suggestion.

[Socrates]

Originally Posted by FIGUER

You may indeed suggest it, but I don't see any merit to the suggestion.

Consider this:

http://www.ncbi.nlm.nih.gov/pmc/arti...0501844102.pdf

"Speciation is the origin of reproductive isolation and divergence
between populations, according to the ‘‘biological species concept’’
of Mayr. Studies of reproductive isolation have dominated
research on speciation, leaving the origin of species differences
relatively poorly understood. Here, I argue that the origin of
species differences, and of novel phenotypes in general, involves
the reorganization of ancestral phenotypes (developmental recombination)
followed by the genetic accommodation of change.
Because selection acts on phenotypes, not directly on genotypes or
genes, novel traits can originate by environmental induction as
well as mutation, then undergo selection and genetic accommodation
fueled by standing genetic variation or by subsequent
mutation and genetic recombination. Insofar as phenotypic novelties
arise from adaptive developmental plasticity, they are not
‘‘random’’ variants, because their initial form reflects adaptive
responses with an evolutionary history, even though they are
initiated by mutations or novel environmental factors that are
random with respect to (future) adaptation. Change in trait frequency
involves genetic accommodation of the threshold or liability
for expression of a novel trait, a process that follows rather
than directs phenotypic change. Contrary to common belief, environmentally
initiated novelties may have greater evolutionary
potential than mutationally induced ones. Thus, genes are probably
more often followers than leaders in evolutionary change.
Species differences can originate before reproductive isolation and
contribute to the process of speciation itself. Therefore, the genetics
of speciation can profit from studies of changes in gene
expression as well as changes in gene frequency and genetic
isolation."

This is just a simple recognition of the fact that we are dealing with a developmental process and not an evolutionary process (in the commonly accepted conception of "evolution").

[FIGUER]

Originally Posted by Socrates

This is just a simple recognition of the fact that we are dealing with a developmental process and not an evolutionary process (in the commonly accepted conception of "evolution").

I don't see any problem with the commonly accepted conception of evolution, which is unrelated to finding some problems or incompleteness in standard evolutionary models.

[Socrates]

Here is a bit more on the idea of development.

http://www.ncbi.nlm.nih.gov/pmc/arti...0501844102.pdf

"Most important for studies of species diversification, the
phenotypic definition of selection permits a more complete
analysis of the origins of new traits. If selectable variation is seen
to be phenotypic variation, then the scope for the origins of
novelty has to be broadened to include environmentally induced
phenotypic variation. Phenotype development, which responds
to both genomic and environmental inputs, is the source of
selectable variation. This analysis brings development, largely
omitted from evolutionary biology during the synthesis era (8),
to the forefront of evolutionary biology as the source of the
variation that fuels natural selection and adaptive evolution."

It is only when we re-orient our minds to correctly see that it is a developmental process that we begin to see this correctly, for what it actually is.
Give it a try. (Even as just an exercise).

[FIGUER]

Originally Posted by Socrates

It is only when we re-orient our minds to correctly see that it is a developmental process that we begin to see this correctly, for what it actually is.

Development is implicit in evolution by definition.

Main Entry: evolution
Part of Speech: noun
Definition: development, progress
Synonyms:
change, enlargement, evolvement, expansion, flowering, growth, increase, maturation, natural process, progression, transformation, unfolding, working out

Concept Thesaurus
Concept: [Motion in the reverse circle] Evolution.
Category: 4. Motion with reference to direction
Synonyms:

-nouns
evolution, unfolding, development; evolvement; unfoldment; eversion (inversion).
-verbs
evolve; unfold, unroll, unwind, uncoil, untwist, unfurl, untwine, unravel; disentangle; develop.
-adjectives
evolving; evolved.

http://thesaurus.reference.com/browse/evolution

Give it a try. (Even as just an exercise).

That's stupid (the idea that you need to suggest it as if it was something remarkable).

[ericmurphy]

Originally Posted by Socrates

Consider this:

http://www.ncbi.nlm.nih.gov/pmc/arti...0501844102.pdf

"Speciation is the origin of reproductive isolation and divergence
between populations, according to the ‘‘biological species concept’’
of Mayr. Studies of reproductive isolation have dominated
research on speciation, leaving the origin of species differences
relatively poorly understood. Here, I argue that the origin of
species differences, and of novel phenotypes in general, involves
the reorganization of ancestral phenotypes (developmental recombination)
followed by the genetic accommodation of change.
Because selection acts on phenotypes, not directly on genotypes or
genes, novel traits can originate by environmental induction as
well as mutation, then undergo selection and genetic accommodation
fueled by standing genetic variation or by subsequent
mutation and genetic recombination. Insofar as phenotypic novelties
arise from adaptive developmental plasticity, they are not
‘‘random’’ variants, because their initial form reflects adaptive
responses with an evolutionary history, even though they are
initiated by mutations or novel environmental factors that are
random with respect to (future) adaptation. Change in trait frequency
involves genetic accommodation of the threshold or liability
for expression of a novel trait, a process that follows rather
than directs phenotypic change. Contrary to common belief, environmentally
initiated novelties may have greater evolutionary
potential than mutationally induced ones. Thus, genes are probably
more often followers than leaders in evolutionary change.
Species differences can originate before reproductive isolation and
contribute to the process of speciation itself. Therefore, the genetics
of speciation can profit from studies of changes in gene
expression as well as changes in gene frequency and genetic
isolation."

This is just a simple recognition of the fact that we are dealing with a developmental process and not an evolutionary process (in the commonly accepted conception of "evolution").

Highlighting occurrences of the word "development" or "developmental" in this passage does not mean the author is talking about development, "socrates." Evolution and development are completely different things. Developmental processes do evolve over time; the development of arthropods is very different from the development of chordates.

We are NOT talking about a "developmental" process here. We are talking about an evolutionary process. That the word "development" shows up in the above passage does not change that fact.

If you knew what "development" means in the current context, you'd realize this. But once again, you are tripped up by your own ignorance.

[Socrates]

Originally Posted by Socrates

Here is a bit more on the idea of development.

http://www.ncbi.nlm.nih.gov/pmc/arti...0501844102.pdf

"Most important for studies of species diversification, the
phenotypic definition of selection permits a more complete
analysis of the origins of new traits. If selectable variation is seen
to be phenotypic variation, then the scope for the origins of
novelty has to be broadened to include environmentally induced
phenotypic variation. Phenotype development, which responds
to both genomic and environmental inputs, is the source of
selectable variation. This analysis brings development, largely
omitted from evolutionary biology during the synthesis era (8),
to the forefront of evolutionary biology as the source of the
variation that fuels natural selection and adaptive evolution."

It is only when we re-orient our minds to correctly see that it is a developmental process that we begin to see this correctly, for what it actually is.
Give it a try. (Even as just an exercise).

The other powerful thing in this line of thinking is where she uses the phrase:
"..largely omitted from evolutionary biology during the synthesis era "
Here is a specific reference to the "synthesis era". The "synthesis era" corresponds to the "synthesis paradigm.
The passing of that paradigm marks the end of that era.
You can see it happening right here in this thread and in this forum.

[ericmurphy]

Originally Posted by Socrates

Here is a bit more on the idea of development.

http://www.ncbi.nlm.nih.gov/pmc/arti...0501844102.pdf

"Most important for studies of species diversification, the
phenotypic definition of selection permits a more complete
analysis of the origins of new traits. If selectable variation is seen
to be phenotypic variation, then the scope for the origins of
novelty has to be broadened to include environmentally induced
phenotypic variation. Phenotype development, which responds
to both genomic and environmental inputs, is the source of
selectable variation. This analysis brings development, largely
omitted from evolutionary biology during the synthesis era (8),
to the forefront of evolutionary biology as the source of the
variation that fuels natural selection and adaptive evolution."

It is only when we re-orient our minds to correctly see that it is a developmental process that we begin to see this correctly, for what it actually is.
Give it a try. (Even as just an exercise).

This is just stupid. You've never heard of "evolutionary development theory"?

"Development" refers to the process by which a single cell develops into a complete organism. You can't just replace the word "evolution" with the word "development" and come up with some new theory. Evolution is a process acting on populations. Development is a process acting on individual organisms. You and Guzman have the same mental block over the difference. And I think all it is is some sort of knee-jerk distaste for the word "evolution."

[Socrates]

Originally Posted by FIGUER

Development is implicit in evolution by definition.

http://thesaurus.reference.com/browse/evolution

That's stupid (the idea that you need to suggest it as if it was something remarkable).

A lot of people have this confusion. And it is purely a semantic confusion.
The word "evolution" has a general common-usage meaning and in that sense it includes development.
As in "Let me tell you how my thinking has evolved". "Or let's see how the design of the airplane evolved".
Here in the common usage sense there is no sense of randomness nor mindlessness. Quite the opposite. In fact, it is what we all would call DEVELOPMENT.

However when the word "evolution" is used in evolution theory it has a specific meaning as everyone here knows and randomness and mindlessness are at the heart of it.
So in the evolution theory meaning of the word "evolution" DOES NOT INCLUDE DEVELOPMENT. (It is pretty much the opposite of it).
As I say this is just a semantic confusion.

That is why the ideas of West-Eberhard and Shapiro and others is DEVELOPMENTAL and not "evolutionary".

[ericmurphy]

Originally Posted by Socrates

The other powerful thing in this line of thinking is where she uses the phrase:
"..largely omitted from evolutionary biology during the synthesis era "
Here is a specific reference to the "synthesis era". The "synthesis era" corresponds to the "synthesis paradigm.
The passing of that paradigm marks the end of that era.
You can see it happening right here in this thread and in this forum.

You have no idea what the author is talking about. You have no idea what she's even talking about when she says "the synthesis era." Evo-devo dates from the 1990s. The "synthesis era" is an historical period in evolutionary theory that dates from roughly the mid-thirties until almost the end of the twentieth century.

None of this means that evolutionary theory is wrong (or, even more stupidly, that common descent is false). It means that evolutionary theory is evolving, as do all scientific theories.

You're so deep in the weeds we can't even see the top of your head, "socrates."

[ericmurphy]

Originally Posted by Socrates

A lot of people have this confusion. And it is purely a semantic confusion.
The word "evolution" has a general common usage meaning and in that sense it includes development.
As in "Let me tell you how my thinking has evolved". "Or let's see how the design of the airplane evolved".
Here in the common usage sense there is no sense of randomness nor mindlessness. Quite the opposite. In fact, it is what we all would call DEVELOPMENT.

However when the word "evolution" is used in evolution theory it has a specific meaning as everyone here knows and randomness and mindlessness are at the heart of it.
So in the evolution theory meaning of the word "evolution" DOES NOT INCLUDE DEVELOPMENT. (It is pretty much the opposite of it).
As I say this is just a semantic confusion.

That is why the ideas of West-Eberhard and Shapiro and others is DEVELOPMENTAL and not "evolutionary".

You have no idea what you're talking about. Evolution and development have well-defined meanings in evolutionary theory. You don't know what either of those meanings are, and you're conflating them in profoundly stupid ways.

[Socrates]

Originally Posted by Socrates

A lot of people have this confusion. And it is purely a semantic confusion.
The word "evolution" has a general common-usage meaning and in that sense it includes development.
As in "Let me tell you how my thinking has evolved". "Or let's see how the design of the airplane evolved".
Here in the common usage sense there is no sense of randomness nor mindlessness. Quite the opposite. In fact, it is what we all would call DEVELOPMENT.

However when the word "evolution" is used in evolution theory it has a specific meaning as everyone here knows and randomness and mindlessness are at the heart of it.
So in the evolution theory meaning of the word "evolution" DOES NOT INCLUDE DEVELOPMENT. (It is pretty much the opposite of it).
As I say this is just a semantic confusion.

That is why the ideas of West-Eberhard and Shapiro and others is DEVELOPMENTAL and not "evolutionary".

In fact here is a more comprehensive definition
http://www.thefreedictionary.com/evolution
ev·o·lu·tion (v-lshn, v-)
n.
1. A gradual process in which something changes into a different and usually more complex or better form. See Synonyms at development.
2.
a. The process of developing.
b. Gradual development.
3. Biology
a. Change in the genetic composition of a population during successive generations, as a result of natural selection acting on the genetic variation among individuals, and resulting in the development of new species.
b. The historical development of a related group of organisms; phylogeny.
4. A movement that is part of a set of ordered movements.
5. Mathematics The extraction of a root of a quantity.

The distinction I am highlighting is the difference between:
definition 1 which is the common-usage definition I was referring to
and
definition 3 which is the evolution theory definition.

Also see
http://dictionary.reference.com/browse/evolution
where again this distinction is made.

The links I have given are the first ones that come up on Google and on Yahoo.

[FIGUER]

Originally Posted by Socrates

However when the word "evolution" is used in evolution theory it has a specific meaning as everyone here knows and randomness and mindlessness are at the heart of it.

Utterly wrong: Evolution as used in evolutionary theory denotes the basic concept of transgenerational change in biological entities, period. Randomness and mindlessness are particular to the mechanics by which the basic concept is considered to operate by most biologist. If purposefulness and mindfulness became part of standard evolutionary theory, the basic concept of evolution would remain the same, since it is not dependent on mechanics for its definition.

That is why the ideas of West-Eberhard and Shapiro and others is DEVELOPMENTAL and not "evolutionary".

Do tell them, please.

[ericmurphy]

We're all aware that the term "evolution" has a different meaning in evolutionary theory than it does in the general sense. Just as the term "square" has a different meaning in plane geometry than it does in, say, civic planning.

Do you have a point? Or are you just doing your usual meandering?

[Socrates]

Originally Posted by FIGUER

Utterly wrong: Evolution as used in evolutionary theory denotes the basic concept of transgenerational change in biological entities, period. Randomness and mindlessness are particular to the mechanics by which the basic concept is considered to operate by most biologist. If purposefulness and mindfulness became part of standard evolutionary theory, the basic concept of evolution would remain the same, since it is not dependent on mechanics for its definition.

Do tell them, please.

If the definition of evolution is simply:
"transgenerational change in biological entities"
then ID would fit within that definition.