Regulating Evolution (Full Version)

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essentialsaltes -> Regulating Evolution (4/17/2008 5:14:13 PM)

Scientific American's May issue has a feature article on gene regulation. "Regulating Evolution" by Sean B Carroll, Benjamin Prud'homme and Nicolas Gompel.

I know Jhud has rhapsodized about gene regulation in the past, and this article provides an excellent explanation of the matter. To quote the article:

"Mutations in DNA 'switches' that control body-shaping genes, rather than in the genes themselves, have been a significant source of evolving differences among animals." "Mutations in regulatory sequences are not the exclusive mode of evolution -- they are just the more likely path when a gene has multiple roles and only one of them is modified." "If humans want to understand what distinguishes animals, including ourselves, from one another, we have to look beyond genes."



Jhud -> RE: Regulating Evolution (4/17/2008 5:26:33 PM)

quote:

Scientific American's May issue has a feature article on gene regulation. "Regulating Evolution" by Sean B Carroll, Benjamin Prud'homme and Nicolas Gompel.

I know Jhud has rhapsodized about gene regulation in the past, and this article provides an excellent explanation of the matter. To quote the article:

"Mutations in DNA 'switches' that control body-shaping genes, rather than in the genes themselves, have been a significant source of evolving differences among animals." "Mutations in regulatory sequences are not the exclusive mode of evolution -- they are just the more likely path when a gene has multiple roles and only one of them is modified." "If humans want to understand what distinguishes animals, including ourselves, from one another, we have to look beyond genes."


Actually, I am reading Carroll's Endless Forms Most Beautiful right now; one thing I have to give him, at least he isn't stuck in Neo-Darwinian la la land.



unclemonkey -> RE: Regulating Evolution (4/17/2008 6:00:25 PM)

ORIGINAL:Jhud
quote:

one thing I have to give him, at least he isn't stuck in Neo-Darwinian la la land.

That could be dangerous for his career.



Bettawrekonize -> RE: Regulating Evolution (4/18/2008 1:46:58 AM)

Which begs the question, how did those gene regulation mechanisms emerge?

This is exactly why teaching only UCD while censoring criticisms and opposing views is harmful to science. Darwin would assume that RM + NS was ultimately responsible for life and all the beneficial mutations that got us to the point that we are now. If RM + NS is able to create enough beneficial mutations to get life to a point where it can create gene regulatory mechanisms, then it's possible for RM+NS to create and maintain beneficial mutations such that it doesn't need gene regulation to accumulate benefits. Hence, a much simpler explanation from that perspective is that RM + NS is perfectly capable of creating and maintaining successive benefits in order to create and preserve life without gene regulation. So there is no reason to assume gene regulatory mechanisms exist (especially since gene regulatory mechanisms would imply that many mutations only apply to certain parts of the genome in certain ways and it would tend to switch genes in one way at one time and back to their original orientation during other times depending on the specific environment. This would place more limits on the rate that mutations create larger net changes since most of the mutations are genes being switched from one orientation to another and then back, which doesn't create any net changes. Hence, many mutations would be switching back and fourth, back and fourth, and many observed mutations would in fact be genes switching from one orientation to another. This would tend to make larger changes within the genome occur much more slowly since most of the changes that we do see are simply genes being switched back and fourth. If larger scale mutations take longer, then evolution must require much more time than previously assumed based on observable mutation rates since most of those observable mutations are simply genes switching back and fourth as needed and not making any net movements).

On the other hand, if life is designed, this would suggest that RM + NS is inadequate to create and maintain life and all the beneficial code and chemical patterns that it consists of. Hence, it makes sense for a designer to put regulatory mechanisms to help create beneficial mutations when needed and preserve the genome when possible.

Had we not assumed UCD to be true, we would have probably have found out the truth of the matter sooner. For example, ID proponents (ie: Dembski) and creationists have long been arguing that Junk DNA is useful (at a time when Junk DNA was defined as and considered useless). We are starting to discover that much of the DNA that was once considered useless is now more useful than once thought. We could have figured this out sooner had the secular community not assumed evolution to be true.

Then again, UCD doesn't really predict anything. It simply accommodates the evidence within its hypothesis after the evidence is known (it makes postdictions), then it claims, "this is what UCD predicts."



essentialsaltes -> RE: Regulating Evolution (4/18/2008 10:17:11 AM)

quote:

ORIGINAL: Bettawrekonize
Had we not assumed UCD to be true, we would have probably have found out the truth of the matter sooner.


Then why didn't the ID crowd make this discovery? As it happens, Zuckerkandl 1981 shows that, despite being blinded by UCD, evilutionists hypothesized that noncoding DNA could serve as "binding sites ... for certain types of regulatory proteins" more than 25 years ago.

Just because a researcher coined the term garbage DNA or junk DNA doesn't mean that the entire scientific community suddenly closed its conspiratorial ranks to deny functionality for all noncoding DNA. It's been an active area of study, not something forbidden by the great evolution conspiracy.



Jhud -> RE: Regulating Evolution (4/18/2008 10:56:21 AM)

quote:

Then why didn't the ID crowd make this discovery? As it happens, Zuckerkandl 1981 shows that, despite being blinded by UCD, evilutionists hypothesized that noncoding DNA could serve as "binding sites ... for certain types of regulatory proteins" more than 25 years ago.

Just because a researcher coined the term garbage DNA or junk DNA doesn't mean that the entire scientific community suddenly closed its conspiratorial ranks to deny functionality for all noncoding DNA. It's been an active area of study, not something forbidden by the great evolution conspiracy.


I am not sure when it was discovered or who researched is all that relevant; in fact, it's fairly obvious lots of folks are involved with it now.

The point is that it deepens complexity, it removes genetic modification one more step away from selective processes, it heightens the need for interoperability throughout the genome, and it indicates a certain degree of anticipatory development of biological structures.



DanJames -> RE: Regulating Evolution (4/18/2008 11:01:10 AM)

quote:

ORIGINAL: Jhud

quote:

Then why didn't the ID crowd make this discovery? As it happens, Zuckerkandl 1981 shows that, despite being blinded by UCD, evilutionists hypothesized that noncoding DNA could serve as "binding sites ... for certain types of regulatory proteins" more than 25 years ago.

Just because a researcher coined the term garbage DNA or junk DNA doesn't mean that the entire scientific community suddenly closed its conspiratorial ranks to deny functionality for all noncoding DNA. It's been an active area of study, not something forbidden by the great evolution conspiracy.


I am not sure when it was discovered or who researched is all that relevant; in fact, it's fairly obvious lots of folks are involved with it now.

The point is that it deepens complexity, it removes genetic modification one more step away from selective processes, it heightens the need for interoperability throughout the genome, and it indicates a certain degree of anticipatory development of biological structures.


What means this "anticipatory development of biological structures"?



Jhud -> RE: Regulating Evolution (4/18/2008 11:07:31 AM)

quote:

What means this "anticipatory development of biological structures"?


Well, for example, a lot of what any vertebrate needs (a fin, a wing, a leg, etc) seems already to have a fundamental genetic foundation already in place before the existence of fins, wings, legs, etc. All that is needed is to regulate the extant genetics in such a way as to produce those structures. That appears to be highly anticipatory - that is, the basic genetic information preceded the survival need for that information.



DanJames -> RE: Regulating Evolution (4/18/2008 11:11:11 AM)

quote:

ORIGINAL: Jhud

quote:

What means this "anticipatory development of biological structures"?


Well, for example, a lot of what any vertebrate needs (a fin, a wing, a leg, etc) seems already to have a fundamental genetic foundation already in place before the existence of fins, wings, legs, etc. All that is needed is to regulate the extant genetics in such a way as to produce those structures. That appears to be highly anticipatory - that is, the basic genetic information preceded the survival need for that information.

Woah, hold it. Are you saying that a fish could grow legs if its genes were regulated, and not necessarily mutated.

You mean predated as in, by generations or by development. If by generations, then you mean that certain sea creatures that would not need legs could grow legs if their genes were regulated in that way.



Jhud -> RE: Regulating Evolution (4/18/2008 11:17:59 AM)

quote:

Woah, hold it. Are you saying that a fish could grow legs if its genes were regulated, and not necessarily mutated.


That appears to be the case.



Bettawrekonize -> RE: Regulating Evolution (4/18/2008 11:42:01 AM)

quote:

ORIGINAL: essentialsaltes
Then why didn't the ID crowd make this discovery? As it happens, Zuckerkandl 1981 shows that, despite being blinded by UCD, evilutionists hypothesized that noncoding DNA could serve as "binding sites ... for certain types of regulatory proteins" more than 25 years ago.


The ID crowed has long predicted junk DNA would be more useful than what the consensus thought, but it isn't the ID crowd that gets research grants from tax dollars to do research, otherwise they probably would have probably made the discovery sooner than evolutionists had. Sure, maybe one evolutionist thought some of it could be useful, but this was not the consensus among the secular community.

This also further demonstrates the unfalsifiable nature of UCD. Few UCD proponents believed junk DNA had much function while most believed it didn't. If it turns out to have function, the evolutionists would then point to the one evolutionist that believed it was more functional than the consensus thought and say, "see, this is what evolution predicts." If they were found to be useless, then evolutionists would point to the consensus and say, "see, this is what evolution predicts."

quote:


Just because a researcher coined the term garbage DNA or junk DNA doesn't mean that the entire scientific community suddenly closed its conspiratorial ranks to deny functionality for all noncoding DNA.


But it did increase their tendency to pre - assume it's non - functional. It wasn't evolutionary presuppositions that predicted they would be functional (ID was what predicted this), it was the course of normal research that discovered them to be useful. However, had the secular community as a whole not presupposed they were mostly useless based on evolutionary presuppositions, chances are they would have found the functions much sooner.

quote:


It's been an active area of study, not something forbidden by the great evolution conspiracy.


Now it's more of an active study after more of it was discovered to have function (which is what Dembski predicted and the ID crowed as a whole predicted would be the case). It was mostly assumed to be useless in the past by the majority of the secular community, most just assumed it had little to no use.



Bettawrekonize -> RE: Regulating Evolution (4/18/2008 11:45:06 AM)

quote:

ORIGINAL: Jhud

quote:

Woah, hold it. Are you saying that a fish could grow legs if its genes were regulated, and not necessarily mutated.


That appears to be the case.


Sounds like front - loading to me, something ID has long indicated would be a good indicator of design (and hence would encourage us to search for it earlier). It's amazing how scientific discoveries continue to confirm ID, ID has made these predictions long before they were found to be true. Evolution would just assume that this would not be the case and hence it would take much longer to discover them to be true from that paradigm.

Obviously, as we continue to research how life works, we will find out that ID predictions turned out to be true even if we assume UCD. However, we could have found it out much sooner had we not simply assumed UCD to be true. Of course, UCD later accommodates the evidence within its hypothesis, further demonstrating its unfalsifiable nature (and the fact that it can make postdictions).



essentialsaltes -> RE: Regulating Evolution (4/18/2008 12:03:31 PM)

quote:

ORIGINAL: Bettawrekonize

quote:

ORIGINAL: essentialsaltes
Then why didn't the ID crowd make this discovery? As it happens, Zuckerkandl 1981 shows that, despite being blinded by UCD, evilutionists hypothesized that noncoding DNA could serve as "binding sites ... for certain types of regulatory proteins" more than 25 years ago.


The ID crowed has long predicted junk DNA would be more useful than what the consensus thought


Sorry, since the cdesign proponentists didn't evolve until the late 1980s, this is a postdiction. It was evolutionists who originally came up with the notion of gene regulation, the ID crowd simply stole it.



DanJames -> RE: Regulating Evolution (4/18/2008 12:05:22 PM)

quote:

ORIGINAL: Bettawrekonize

quote:

ORIGINAL: Jhud

quote:

Woah, hold it. Are you saying that a fish could grow legs if its genes were regulated, and not necessarily mutated.


That appears to be the case.


Sounds like front - loading to me, something ID has long indicated would be a good indicator of design (and hence would encourage us to search for it earlier). It's amazing how scientific discoveries continue to confirm ID, ID has made these predictions long before they were found to be true. Evolution would just assume that this would not be the case and hence it would take much longer to discover them to be true from that paradigm.

Obviously, as we continue to research how life works, we will find out that ID predictions turned out to be true even if we assume UCD. However, we could have found it out much sooner had we not simply assumed UCD to be true. Of course, UCD later accommodates the evidence within its hypothesis, further demonstrating its unfalsifiable nature (and the fact that it can make postdictions).


And the mountain of evidence gets smaller, and smaller, and smaller. Thanks for the article Jack.



DanJames -> RE: Regulating Evolution (4/18/2008 12:07:53 PM)

quote:

ORIGINAL: essentialsaltes

quote:

ORIGINAL: Bettawrekonize

quote:

ORIGINAL: essentialsaltes
Then why didn't the ID crowd make this discovery? As it happens, Zuckerkandl 1981 shows that, despite being blinded by UCD, evilutionists hypothesized that noncoding DNA could serve as "binding sites ... for certain types of regulatory proteins" more than 25 years ago.


The ID crowed has long predicted junk DNA would be more useful than what the consensus thought


Sorry, since the cdesign proponentists didn't evolve until the late 1980s, this is a postdiction. It was evolutionists who originally came up with the notion of gene regulation, the ID crowd simply stole it.

More ID conspiracies. Those n'er-do-wells.



drj11 -> RE: Regulating Evolution (4/18/2008 12:20:20 PM)

quote:

ORIGINAL: DanJames

quote:

ORIGINAL: essentialsaltes

quote:

ORIGINAL: Bettawrekonize

quote:

ORIGINAL: essentialsaltes
Then why didn't the ID crowd make this discovery? As it happens, Zuckerkandl 1981 shows that, despite being blinded by UCD, evilutionists hypothesized that noncoding DNA could serve as "binding sites ... for certain types of regulatory proteins" more than 25 years ago.


The ID crowed has long predicted junk DNA would be more useful than what the consensus thought


Sorry, since the cdesign proponentists didn't evolve until the late 1980s, this is a postdiction. It was evolutionists who originally came up with the notion of gene regulation, the ID crowd simply stole it.

More ID conspiracies. Those n'er-do-wells.


Again, their ideas are just as heretical to creationism as evolution is. Seems a bit hypocritical to me, for creationists to buddy up with them.



Jhud -> RE: Regulating Evolution (4/18/2008 12:21:17 PM)

quote:

Sorry, since the cdesign proponentists didn't evolve until the late 1980s, this is a postdiction. It was evolutionists who originally came up with the notion of gene regulation, the ID crowd simply stole it.


First of, while it is clear that evo-devo began to develop in the '80s (coinciding with greater understanding of the genome) it was not a prediction of evolutionists, and in fact is a criticism in many wasy of Neo-Darwinism which had proposed significantly different mechanisms up until that point.

And evolutionists came up with the notion of junk DNA in the '70s, and clung to the notion until the 2000s; in fact, some still do, despite the many findings to the contrary. It was thought to be a proof for Neo-Darwinism. IDists have been critics of the junk DNA concept for a number of years, long before the trend against it was evident.

And IDists have been almost wholly responsible for the notion of front-loading that Beta referred to above - and this notion seems to gain more and more traction all the time.



Bettawrekonize -> RE: Regulating Evolution (4/18/2008 12:22:39 PM)

quote:

ORIGINAL: essentialsaltes
Sorry, since the cdesign proponentists didn't evolve until the late 1980s, this is a postdiction. It was evolutionists who originally came up with the notion of gene regulation, the ID crowd simply stole it.


You gave an example of one evolutionist vs a much larger consensus from ID proponents (and the fact that the consensus of evolutionists was that Junk DNA was mostly useless). Plus, most creationists (who also believe in design) have been arguing that Junk DNA would have function for a while too (I remember reading it all over their websites years ago before more of it was known to have function) and creationists have been around for a very long time.



Jhud -> RE: Regulating Evolution (4/18/2008 12:23:30 PM)

quote:

Again, their ideas are just as heretical to creationism as evolution is. Seems a bit hypocritical to me, for creationists to buddy up with them.


I always find it odd when evolutionists speak in terms of heresy; I think it belies the religious nature of their evolutionary beliefs.



Bettawrekonize -> RE: Regulating Evolution (4/18/2008 12:24:09 PM)

quote:

ORIGINAL: drj11
Again, their ideas are just as heretical to creationism as evolution is. Seems a bit hypocritical to me, for creationists to buddy up with them.


ID and Creationism are not mutually exclusive.



drj11 -> RE: Regulating Evolution (4/18/2008 12:26:02 PM)

quote:

ORIGINAL: Bettawrekonize

quote:

ORIGINAL: drj11
Again, their ideas are just as heretical to creationism as evolution is. Seems a bit hypocritical to me, for creationists to buddy up with them.


ID and Creationism are not mutually exclusive.


If you believe Behe's version it is.



Bettawrekonize -> RE: Regulating Evolution (4/18/2008 12:29:32 PM)

quote:

ORIGINAL: drj11
If you believe Behe's version it is.


Behe may believe in an old earth form his scientific perspective, but that's not to say ID says anything about the age of the earth. ID says nothing about the age of the earth and Behe believes in an old earth independently of ID.

Think of it this way. Someone could believe in a steady state universe (or the Big Bang) and not biological evolution or vice versa, the two are not mutually exclusive but one doesn't have to believe in one to believe in the other.



DanJames -> RE: Regulating Evolution (4/18/2008 12:43:46 PM)

quote:

ORIGINAL: drj11

quote:

ORIGINAL: DanJames

quote:

ORIGINAL: essentialsaltes

quote:

ORIGINAL: Bettawrekonize

quote:

ORIGINAL: essentialsaltes
Then why didn't the ID crowd make this discovery? As it happens, Zuckerkandl 1981 shows that, despite being blinded by UCD, evilutionists hypothesized that noncoding DNA could serve as "binding sites ... for certain types of regulatory proteins" more than 25 years ago.


The ID crowed has long predicted junk DNA would be more useful than what the consensus thought


Sorry, since the cdesign proponentists didn't evolve until the late 1980s, this is a postdiction. It was evolutionists who originally came up with the notion of gene regulation, the ID crowd simply stole it.

More ID conspiracies. Those n'er-do-wells.


Again, their ideas are just as heretical to creationism as evolution is. Seems a bit hypocritical to me, for creationists to buddy up with them.


Hypocritical seems like a poor choice of words. I agree with some things in the evolutionary camp yet I don't see that as hypocritical. An evolutionist would say that grass is green because of the pigmentation in chloroplasts and I agree. Is that hypocritical for me to agree since he also believes that grass is a product of evolution over millions of years?



benelchi -> RE: Regulating Evolution (4/18/2008 12:58:36 PM)

quote:

ORIGINAL: essentialsaltes

quote:

ORIGINAL: Bettawrekonize
Had we not assumed UCD to be true, we would have probably have found out the truth of the matter sooner.


Then why didn't the ID crowd make this discovery? As it happens, Zuckerkandl 1981 shows that, despite being blinded by UCD, evilutionists hypothesized that noncoding DNA could serve as "binding sites ... for certain types of regulatory proteins" more than 25 years ago.

Just because a researcher coined the term garbage DNA or junk DNA doesn't mean that the entire scientific community suddenly closed its conspiratorial ranks to deny functionality for all noncoding DNA. It's been an active area of study, not something forbidden by the great evolution conspiracy.


However, evolutionary biologists have long argued the presence of "garbage" DNA was proof of evolution because they said that there was no other explanation about why the same "garbage" would be present in "later generations". Such DNA (according to them) would be an indication that design was not part of the process. Now that they have discovered strong indications that this DNA has a function, will they now accept that design is a possibility?



DanJames -> RE: Regulating Evolution (4/18/2008 1:00:47 PM)

quote:

ORIGINAL: benelchi

quote:

ORIGINAL: essentialsaltes

quote:

ORIGINAL: Bettawrekonize
Had we not assumed UCD to be true, we would have probably have found out the truth of the matter sooner.


Then why didn't the ID crowd make this discovery? As it happens, Zuckerkandl 1981 shows that, despite being blinded by UCD, evilutionists hypothesized that noncoding DNA could serve as "binding sites ... for certain types of regulatory proteins" more than 25 years ago.

Just because a researcher coined the term garbage DNA or junk DNA doesn't mean that the entire scientific community suddenly closed its conspiratorial ranks to deny functionality for all noncoding DNA. It's been an active area of study, not something forbidden by the great evolution conspiracy.


However, evolutionary biologists have long argued the presence of "garbage" DNA was proof of evolution because they said that there was no other explanation about why the same "garbage" would be present in "later generations". Such DNA (according to them) would be an indication that design was not part of the process. Now that they have discovered strong indications that this DNA has a function, will they now accept that design is a possibility?

Accept design as a possibility in light of evidence that supports it? That's unscientific!



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