RE: Regulating Evolution (Full Version)

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Jhud -> RE: Regulating Evolution (4/21/2008 2:25:30 PM)

quote:

None of the discoveries that you have mentioned or that are in the SciAm article were made by people who didn't bother to look. Go ask them why they bother. They may respond that it's part of science to test our understanding of nature. Or they may respond that they had a hunch. Or they may respond that a piece of data jumped out at them, violating their expectations and inspiring a closer look. Despite the pejorative term 'junk DNA', scientists haven't stopped looking into the matter.


One wonders how much time they have wasted because it was thought to be junk.

Nonetheless, I think it suggests two possible interesting paradigms:

The genome is the product of intention and we should expect the majority of it to be significantly functional.

And

The genome is the product of incidental modification and we should expect functionless portions to represent the major portion of the structure.

One more way by which we can test the conclusions of ID and evolution.



BVZ -> RE: Regulating Evolution (4/22/2008 2:46:38 AM)

Lets assume for the sake of the argument that there is absolutely NO junk DNA.

Now what?



DanJames -> RE: Regulating Evolution (4/22/2008 1:00:29 PM)

quote:

ORIGINAL: BVZ

Lets assume for the sake of the argument that there is absolutely NO junk DNA.

Now what?

Now the evolutionists have to stop using it as evidence for evolution, that's what. And the higher we climb this mountain of evidence, the more we realize we aren't getting very high off the ground.



BVZ -> RE: Regulating Evolution (4/24/2008 2:00:22 AM)

quote:

ORIGINAL: DanJames

quote:

ORIGINAL: BVZ

Lets assume for the sake of the argument that there is absolutely NO junk DNA.

Now what?

Now the evolutionists have to stop using it as evidence for evolution, that's what. And the higher we climb this mountain of evidence, the more we realize we aren't getting very high off the ground.


How did they use junk DNA as evidence for evolution?



Bettawrekonize -> RE: Regulating Evolution (4/24/2008 2:10:53 AM)

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ORIGINAL: BVZ
How did they use junk DNA as evidence for evolution?


quote:


Although the high content of "junk DNA" was initially surprising when it was discovered, our current understanding of the mechanisms of genome expansion (duplication and insertion) and the apparent lack of significant selective pressure to minimize genome size combine to make the accumulation of useless sequences in our DNA seem inevitable.


http://www.talkorigins.org/faqs/molgen/



Bettawrekonize -> RE: Regulating Evolution (4/24/2008 2:23:43 AM)

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So which is it? Can anyone tell me some fact we might uncover, or process we might observe that the theory of Evolution could not be stretched around?

And just what DOES Evolution predict? (seems we don't know until we find out what's there, and then conlude that's EXACTLY what the theory predicts!)
...
While it is true that these types of predictions are based on prior observations of the evidence, so are the predictions of any scientific theory. In the scientific endeavor, observations are collected, a theory is built to explain them, and the theory is tested by comparing its predictions with further observations.


http://www.talkorigins.org/origins/feedback/sep96.html

Wow, did talkorigins just indirectly acknowledge the unfalsifiable nature of UCD? They are saying, we first observe the evidence and then we determine that evolution predicts that evidence. IOW, it doesn't matter what the evidence is, that's what evolution predicts and hence, UCD is unfalsifiable.

It would be great if students were exposed to what I just quoted from their site.

Student
"So, no matter what the evidence, that's what evolution predicts?"

Teacher
"Yes, that's how science works. We claim evolution predicts A. If not A, we claim it predicts B."

ROFLOL. Students should be exposed to this logic.

Another example from that site
quote:


Case in point: Evolution predicts a lot of "junk" in our DNA code (as a random process would leave, as opposed to an intelligent designer). OR (now that we're finding that "junk DNA" may actually have elaborate purpose, and is not junk) Evolution now predicts a code free of junk, because Natural selection is so efficient.


Forget the fact that ID, as a consensus, has long argued that most of this DNA would turn out to be useful (long before evolution). If this DNA is useful, it's evidence for evolution. If it's useless, that's also evidence for evolution. Long live evolution for predicting everything, anything, and nothing at the same time.



essentialsaltes -> RE: Regulating Evolution (4/24/2008 11:44:54 AM)

quote:

ORIGINAL: Bettawrekonize
Wow, did talkorigins just indirectly acknowledge the unfalsifiable nature of UCD?


No. You are quoting letters and comments written to talk origins, not by the people who contribute to talk origins. You should read the response parts more carefully, since it answers the objections you (and the letter writer) raised:

"Evolution and common descent are certainly falsifiable. One way to disprove them would be to show that the Earth is only a few thousand years old. Not surprisingly, many creationists are trying to do just that. One could also falsify evolution by showing that the various forms of life have not changed significantly over time. Finding strong evidence that humans coexisted with dinosaurs or trilobites, organisms that are currently known to have gone extinct millions of years ago, would be one way to do this.

In addition to being falsifiable, evolution makes a large number of verifiable predictions. It predicts that closely related organisms will share a large amount of the same genetic material. It predicts an ordering of the fossil record, in which animals like mammals never appear before the first reptiles. It predicts that isolated regions of the planet will be populated by living organisms that are unique throughout the world. It predicts anatomical similarities between genetically similar organisms. It predicts the existence of atavisms and vestigial structures that were useful to ancestral forms but are much less useful to present forms. And so on."



Bettawrekonize -> RE: Regulating Evolution (4/24/2008 11:52:22 AM)

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ORIGINAL: essentialsaltes
No. You are quoting letters and comments written to talk origins, not by the people who contribute to talk origins. You should read the response parts more carefully, since it answers the objections you (and the letter writer) raised:

"Evolution and common descent are certainly falsifiable.
...
In addition to being falsifiable, evolution makes a large number of verifiable predictions...



I know what I was quoting. The first two sentences I quoted were to talkorigins. The last paragraph was an editors response that came after what you quoted. Notice how it's below the part that says, "Response from the editor:" and that's what I was responding to.

quote:


One could also falsify evolution by showing that the various forms of life have not changed significantly over time.


The thread Stasis as a criticism of evolution addresses this (in part). Punctuated equilibrium itself seeks to address the stasis. Interestingly, the editor doesn't seem to realize this. He seems to have not corrected the person that said,

quote:


Case in point: Evolution predicts many transitional forms in the fossil record. OR Evolution predicts the systematic gaps in transitional forms (punctuated style). I see that, Stephen Gould notwithstanding, whether the gaps are there or not is not a settled issue. But it doesn't seem to matter, either way Evolution suvives (a theory more adaptable than any known life form - thus proving it correct I presume...)


Darwin himself acknowledged the gaps and attempted to address them. Gould did not need to address something Darwin already allegedly addressed. Gould wasn't trying to address the gaps, he was trying to address the stasis. The fact that the editor said, "One could also falsify evolution by showing that the various forms of life have not changed significantly over time." suggests that he did not know this.

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Eldredge and Gould proposed that the degree of gradualism championed by Charles Darwin was virtually nonexistent in the fossil record, and that stasis dominates the history of most fossil species.


http://en.wikipedia.org/wiki/Punctuated_equilibrium

So either way, if we have stasis, it's punctuated equilibrium. Non - stasis, it's gradualism. The editor seems to be wrong about this one too.

quote:


Finding strong evidence that humans coexisted with dinosaurs or trilobites, organisms that are currently known to have gone extinct millions of years ago, would be one way to do this.


http://www.talkorigins.org/origins/feedback/sep96.html

Again, the editor says, "While it is true that these types of predictions are based on prior observations..." which really means, it's a postdiction. It's not what evolution predicts, it's what we observe and then evolution accommodates it in the hypothesis. We can come up with a hypothesis, "humans never existed before dinosaurs" and this maybe falsifiable (lets assume it is). This is similar to saying, "gravity pulls things towards objects," again, a falsifiable prediction that we may now consider to be a law of physics. If we falsify this, it won't falsify evolution. Likewise, if we falsify the notion that humans never existed before dinosaurs (assuming that's true), there is no reason to say it would falsify UCD. It would only falsify the notion that humans never existed before dinosaurs. See, that's the difference between operational science and origins science. With operational science, we make observations and call them laws. If future observations contradict them, we change the laws (ie: add qualifiers). With evolution, we make observations (ie: the alleged observation that human fossils are never observed below dinosaur fossils) and say this is what evolution predicts. No, even if the statement is true, the only thing it tells us is that human fossils are never found below dinosaur fossils. If true, we can predict that future human fossils won't be found below dinosaur fossils, not based on evolution, but based on the alleged fact that current human fossils are never found below dinosaur fossils. Same with gravity, we can predict that if I throw a baseball in the air, it will come back down. This prediction is not based on evolution or the big bang or cosmological evolution, it's based on the fact that, in the past, when I threw baseballs in the air, they came back down. So I can predict that, in the future, when I throw baseballs in the air, they will come back down.

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It predicts anatomical similarities between genetically similar organisms.


This isn't so much a prediction of evolution as it is a prediction that genetic material is what controls our morphology and phenotypes. If genes are what code for our characteristics, then we expect that more similar organisms should have more similar genes. Evolutionists base the alleged relationships of organisms on their similarities, but that's not to say similarities in genes and phenotypes are evidence for evolution.

The other alleged predictions suffer similar problems.



Real_Solitude -> RE: Regulating Evolution (4/26/2008 6:17:48 AM)

quote:

ORIGINAL: Bettawrekonize
"Darwin himself."

Not addressing anything you said, but this line has always confused me a bit. It seems like a silly thing to say. Darwin has been dead and gone for a long time. The theory that he proposed has moved on. It has expanded and become more refined than what he originally proposed. To say that the first person to publicize a field didn't expect X, or couldn't see how X could happen is irrelevant to modern knowledge.
It would be like me saying "Even the Wright Brothers believed trans-continental flight to be impossible." (Doubt they did, but it's a simile, not a direct example.) Or "Even Bill Gates doubted that anyone would ever need more than 640k memory."
Just because they're pioneers in their fields, and they made great contributions to those fields, doesn't mean that they're the be-all-end-all authority. Darwin didn't know everything. He was brilliant for proposing the idea, but anything he said on the subject that was wrong can be chalked up to the newness of the field.

Creationists, IDer's, please stop using "Darwin himself." It's a bad argument.



Bettawrekonize -> RE: Regulating Evolution (4/26/2008 8:10:42 PM)

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ORIGINAL: Real_Solitude
The theory that he proposed has moved on.


UCD is unfalsifiable.

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It has expanded and become more refined than what he originally proposed. To say that the first person to publicize a field didn't expect X, or couldn't see how X could happen is irrelevant to modern knowledge.


If the first person is wrong, we say that his hypothesis was falsified. UCD, OTOH, is unfalsifiable.

quote:


It would be like me saying "Even the Wright Brothers believed trans-continental flight to be impossible." (Doubt they did, but it's a simile, not a direct example.) Or "Even Bill Gates doubted that anyone would ever need more than 640k memory."


Bill Gates was wrong. His prediction has been falsified. Darwin was wrong yet it didn't seem to falsify UCD, which demonstrates the unfalsifiable nature of UCD.

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Just because they're pioneers in their fields, and they made great contributions to those fields, doesn't mean that they're the be-all-end-all authority.


But their hypotheses should be falsifiable. UCD doesn't seem to be.

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Darwin didn't know everything.


He should have known that UCD is wrong.

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He was brilliant for proposing the idea, but anything he said on the subject that was wrong can be chalked up to the newness of the field.


It could be chalked up to the fact that either UCD has been falsified or it is unfalsifiable. There is no reason to suggest it makes predictions.

quote:


Creationists, IDer's, please stop using "Darwin himself."


Sorry, this is probably not going to happen.

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It's a bad argument.


Nope, it demonstrates the unfalsifiable nature of UCD. Darwin was wrong, it didn't falsify UCD (and it should have), which suggests that UCD is unfalsifiable. It's not like evolutionists wouldn't complain if ID or Creationism was wrong about anything and later refined itself.



gluadys -> RE: Regulating Evolution (4/26/2008 8:35:41 PM)

quote:

ORIGINAL: Jhud

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.


I've read it. But I didn't find it to be out of step with neo-Darwinism. What do you see as the significant differences?


quote:

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.


I am puzzled here. Jhud, do you understand a change in regulatory DNA to be something other than a mutation?



Bettawrekonize -> RE: Regulating Evolution (4/26/2008 9:31:52 PM)

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ORIGINAL: gluadys
I am puzzled here. Jhud, do you understand a change in regulatory DNA to be something other than a mutation?


Darwin claimed that random mutation (or variation) was responsible for all of the diversity of life.

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Regulation of gene expression (or gene regulation) refers to the cellular control of the amount and timing of changes to the appearance of the functional product of a gene.


http://en.wikipedia.org/wiki/Gene_regulation

Cellular control. ie: not random. Which begs the question, how did these regulatory mechanisms emerge?

This also seems to suggest that the net movement of change would be very slow. For instance, if you have 100 bytes and you keep switching the same bit back and forth, back and forth millions of times as the environment changes from one condition to another (over millions of years), then there is little to no net change over time (you may have a lot of speed but little to no velocity). All the other bits stay the same and you have one bit that simply changes back and forth as needed. This maybe exaggerated, but the point still stands. It begs the question, how did all the other bits get to where they are?

Not only that, but more mutations are harmful than are beneficial. If a substantial portion of beneficial mutations are controlled by the cell (as more recent research seems to be suggesting), then that suggests that a larger proportion of random mutations are harmful. This would suggest that the ratio of beneficial random mutations to harmful random mutations is much lower than was once anticipated (ie: there are far more harmful random mutations to beneficial random mutations than was once thought). This makes it even more difficult for evolution to explain the existence of the regulatory mechanisms (and the genes that are not controlled by regulatory mechanisms).



gluadys -> RE: Regulating Evolution (4/26/2008 11:25:41 PM)

quote:

ORIGINAL: Bettawrekonize

quote:

ORIGINAL: gluadys
I am puzzled here. Jhud, do you understand a change in regulatory DNA to be something other than a mutation?


Darwin claimed that random mutation (or variation) was responsible for all of the diversity of life.


This doesn't answer my question as to Jhad's understanding of what a mutation is. Is a change in regulatory DNA not a mutation?

It is also incorrect. Darwin did not claim to know the origin of variation--only that it existed. His claim was that some variations would be preferentially preserved. He had no knowledge of genes, DNA or mutations or the manner by which traits are inherited.

quote:

quote:


Regulation of gene expression (or gene regulation) refers to the cellular control of the amount and timing of changes to the appearance of the functional product of a gene.


http://en.wikipedia.org/wiki/Gene_regulation

Cellular control. ie: not random. Which begs the question, how did these regulatory mechanisms emerge?


Yes, I know what regulation is. But the various regulators bind to sites on the DNA molecule and the binding will vary if the DNA varies. Naturally, this will also affect the regulation process. So I am still not seeing it as outside of the evolutionary framework. And I know Sean Carroll did not. After all, he deliberately chose his title from the closing of Origin of Species.

quote:

This also seems to suggest that the net movement of change would be very slow. For instance, if you have 100 bytes and you keep switching the same bit back and forth, back and forth millions of times as the environment changes from one condition to another (over millions of years), then there is little to no net change over time (you may have a lot of speed but little to no velocity). All the other bits stay the same and you have one bit that simply changes back and forth as needed. This maybe exaggerated, but the point still stands. It begs the question, how did all the other bits get to where they are?


Yes, it is very exaggerated, because, of course, the other bits do not remain constant, nor does an environment simply shift back and forth, back and forth. Living things themselves generate novel ecological niches. Time's one-way arrow applies to biological history as it does to all history. That is why current biologists are so keen to preserve what diversity we have. You can't get it back again once it is gone.

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Not only that, but more mutations are harmful than are beneficial.



That will be true in any species that is well adapted to its current environment. If a species is at or near its fitness peak, there are many more ways to move away from the peak than farther toward it.

It will not necessarily be true in a changing environment. "harmful" and "beneficial" are always relative terms in biology. Mutations are not really harmful or beneficial in and of themselves, but only in relation to the environment (internal as well as external to the organism) in which they function.

Also, strictly speaking, it is not the mutation that is harmful or beneficial, but the character trait which is associated with the gene expression that raises or lowers the fitness level of the organism. And what is beneficial today may be harmful in a changed situation or vice versa.


quote:

If a substantial portion of beneficial mutations are controlled by the cell (as more recent research seems to be suggesting), then that suggests that a larger proportion of random mutations are harmful.


Again this would seem to relate to how well the species is adapted to its current environment. Remember, the cellular control acts on gene expression, not the gene itself. The gene is still there when it is not being expressed. And, as far as I know, the cellular action to control gene expression is itself programmed genetically. So it makes sense that if a certain pattern of gene expression enhances fitness, cellular control of that expression be selected to ensure it.

In a changed situation where this pattern of gene expression is deleterious selection would favor a different regulatory pattern.



Bettawrekonize -> RE: Regulating Evolution (4/27/2008 12:05:09 AM)

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ORIGINAL: gluadys
This doesn't answer my question as to Jhad's understanding of what a mutation is. Is a change in regulatory DNA not a mutation?


but it's not necessarily random.

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It is also incorrect. Darwin did not claim to know the origin of variation--only that it existed. His claim was that some variations would be preferentially preserved. He had no knowledge of genes, DNA or mutations or the manner by which traits are inherited.


I know, which is why I put variation. Mutation just means change.

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Yes, I know what regulation is. But the various regulators bind to sites on the DNA molecule and the binding will vary if the DNA varies. Naturally, this will also affect the regulation process. So I am still not seeing it as outside of the evolutionary framework. And I know Sean Carroll did not. After all, he deliberately chose his title from the closing of Origin of Species.


Does not explain how these regulatory mechanisms emerged.

quote:



Yes, it is very exaggerated, because, of course, the other bits do not remain constant, nor does an environment simply shift back and forth, back and forth. Living things themselves generate novel ecological niches. Time's one-way arrow applies to biological history as it does to all history. That is why current biologists are so keen to preserve what diversity we have. You can't get it back again once it is gone.


Another problem for evolution.

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That will be true in any species that is well adapted to its current environment. If a species is at or near its fitness peak, there are many more ways to move away from the peak than farther toward it.


If you put a virus in a petri dish for many many generations, it eventually loses its ability to survive as well as its ancestors in humans. When you put it back in humans, the virus is further away from its fitness peak than its ancestors, yet it does not get closer to its fitness peak and survive as well as its ancestors would. One can claim that the immune system gets to it beforehand, but claiming that it would otherwise get towards its fitness peak like its ancestors have is unfalsifiable. Many dogs who have been modified by artificial selection may get put back in the wild and they would be away from their fitness peak (despite the fact that their ancestors were able to survive just fine). They won't eventually evolve back to the fitness peak of their ancestors unless they acquire genes from ancestors that are able to survive in the wild. One can make up excuses for this, but the notion that their ancestors have reached the level of adaptation that they have through RM + NS is unfalsifiable. Even mutations in organisms that are less than optimal (for their environments) tend to be more harmful than beneficial. Bacteria survive much better than humans and other organisms yet most mutations in humans and other organisms are harmful. Bacteria are closer to the fitness peak. One can claim, "well, bacteria serve a different niche" but coming up with all these excuses, in effect, makes your claim that being close to some fitness peak is what makes mutations harmful unfalsifiable. We have organisms that are more fit than humans (that are closer to a fitness peak), why would evolution produce something much further away from a fitness peak? After all, we see many organisms going extinct, breaking down over time, yet bacteria seem to be surviving just fine, suggesting that they are closer to a fitness peak, yet evolution claims to have produce humans? Bacteria seem to be much closer to a fitness peak (since they survive much better), why haven't mutations caused us to become closer to that peak?

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Also, strictly speaking, it is not the mutation that is harmful or beneficial, but the character trait which is associated with the gene expression that raises or lowers the fitness level of the organism. And what is beneficial today may be harmful in a changed situation or vice versa.


Some mutations cause these characteristic changes. More mutations are harmful than beneficial.

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Again this would seem to relate to how well the species is adapted to its current environment. Remember, the cellular control acts on gene expression, not the gene itself. The gene is still there when it is not being expressed. And, as far as I know, the cellular action to control gene expression is itself programmed genetically. So it makes sense that if a certain pattern of gene expression enhances fitness, cellular control of that expression be selected to ensure it.

In a changed situation where this pattern of gene expression is deleterious selection would favor a different regulatory pattern.


The act of regulating is not selection. The act of selecting what's there is selection. You may claim that natural selection would favor an organism that is capable of responding to its environment by method of gene regulation, but you still haven't demonstrated that evolution would produce these regulatory mechanisms (and don't claim that it would because they exist because then I can claim that God would produce them because they exist). Show me evolution producing these regulatory mechanisms or the DNA that codes for them.



Jhud -> RE: Regulating Evolution (4/27/2008 5:55:54 PM)

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I am puzzled here. Jhud, do you understand a change in regulatory DNA to be something other than a mutation?


They aren't one and the same.



gluadys -> RE: Regulating Evolution (4/27/2008 6:16:41 PM)

quote:

ORIGINAL: Jhud

quote:

I am puzzled here. Jhud, do you understand a change in regulatory DNA to be something other than a mutation?


They aren't one and the same.


How so? What is the difference?



gluadys -> RE: Regulating Evolution (4/27/2008 6:46:12 PM)

quote:

ORIGINAL: Bettawrekonize

quote:

ORIGINAL: gluadys
This doesn't answer my question as to Jhad's understanding of what a mutation is. Is a change in regulatory DNA not a mutation?


but it's not necessarily random.


Would that mean it is not a mutation (change)?

quote:

but, coming up with all these excuses, in effect, makes your claim that being close to some fitness peak is what makes mutations harmful unfalsifiable.


That is not my claim. Mutations can be harmful in any circumstances, but the probability that a mutation is harmful is likely higher for species that are well-adapted to their niche. The fact that they are well-adapted does not "make mutations harmful". It just means there are not many ways for a mutation to add a benefit and lots of ways for it not to.



quote:

We have organisms that are more fit than humans (that are closer to a fitness peak), why would evolution produce something much further away from a fitness peak?


Fit for what? Remember fitness is relative to the fitness landscape. Every species, every population, has a difference landscape. It is difficult to compare fitness across species unless they are very closely related. Fitness is ordinarily measured against conspecifics, not against other populations.

Natural selection never produces something further away from a fitness peak. However, other types of selection may introduce less fitness in one respect or another. Sexual selection may tend to favour traits that are not conducive to survival if only ecological adaptation is being considered. However, since finding a mate is as essential to evolution in many species as surviving to maturity, we see species making trade-offs, balancing the need to attract a female against the need to avoid the attention of a predator for example.

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After all, we see many organisms going extinct, breaking down over time, yet bacteria seem to be surviving just fine, suggesting that they are closer to a fitness peak, yet evolution claims to have produce humans? Bacteria seem to be much closer to a fitness peak (since they survive much better), why haven't mutations caused us to become closer to that peak?


Again, fit for what? You can't talk about fitness in abstractions. Bacteria survive all over the place because they have diversified to establish themselves in many different niches. A bacterium that thrives in one environment will fail to thrive in another. So it is not that all bacteria are clustered around a single fitness peak. Rather different bacteria are situated around different fitness peaks.

Humans have a different fitness landscape.


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Some mutations cause these characteristic changes. More mutations are harmful than beneficial.


How does a population respond to harmful mutations as opposed to beneficial mutations? (NOTE the term "population". I am not asking how individuals respond.)

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The act of regulating is not selection. The act of selecting what's there is selection.


And what may be there are alternate mechanisms of regulation. That provides something to select.

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You may claim that natural selection would favor an organism that is capable of responding to its environment by method of gene regulation, but you still haven't demonstrated that evolution would produce these regulatory mechanisms (and don't claim that it would because they exist because then I can claim that God would produce them because they exist). Show me evolution producing these regulatory mechanisms or the DNA that codes for them.



I understand that at least some of these regulators are proteins that bind to particular spots on a gene or upstream of a gene. Protein production is regulated by RNA which transcribes and translates the relevant coding in DNA. Hence a mutation in the DNA which codes for the protein would modify the protein produced, and that in turn would modify how (or whether) it binds to the regulatory section of the genome.

I am not a biochemist so I don't have access to studies on the DNA that codes for particular proteins or other cellular mechanisms. However, I see no reason to suppose that the proteins involved are not coded for by DNA, nor any reason why they are not subject to evolutionary change.



Jhud -> RE: Regulating Evolution (4/27/2008 6:48:40 PM)

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How so? What is the difference?


I provide a pretty comprehensive discussion of the issue here.



Jhud -> RE: Regulating Evolution (4/27/2008 6:57:55 PM)

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I understand that at least some of these regulators are proteins that bind to particular spots on a gene or upstream of a gene. Protein production is regulated by RNA which transcribes and translates the relevant coding in DNA. Hence a mutation in the DNA which codes for the protein would modify the protein produced, and that in turn would modify how (or whether) it binds to the regulatory section of the genome.

I am not a biochemist so I don't have access to studies on the DNA that codes for particular proteins or other cellular mechanisms. However, I see no reason to suppose that the proteins involved are not coded for by DNA, nor any reason why they are not subject to evolutionary change.


Well, most biological structures are the product of multiple proteins working in concert. When we talk about substantive change in organisms (changes in body plans, the generation of new organs, or structures like skeletal systems, or nervous systesm, etc) then we are talking about multiple specific proetiens working together in concert on a cellular level and in terms of a gross morphological level.

These structural changes simply aren't explainable through the gradual and incremental modification of extant proteins via genetic change.



gluadys -> RE: Regulating Evolution (4/27/2008 6:58:13 PM)

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ORIGINAL: Jhud

quote:

How so? What is the difference?


I provide a pretty comprehensive discussion of the issue here.



Thanks. I'll comment over there.



Bettawrekonize -> RE: Regulating Evolution (4/30/2008 12:51:00 PM)

quote:

ORIGINAL: gluadys
That is not my claim. Mutations can be harmful in any circumstances, but the probability that a mutation is harmful is likely higher for species that are well-adapted to their niche. The fact that they are well-adapted does not "make mutations harmful". It just means there are not many ways for a mutation to add a benefit and lots of ways for it not to.


In general, mutations tend to be more harmful than beneficial and there is really no reason to suggest fitness peak has anything to do with it.

quote:


Fit for what? Remember fitness is relative to the fitness landscape. Every species, every population, has a difference landscape. It is difficult to compare fitness across species unless they are very closely related. Fitness is ordinarily measured against conspecifics, not against other populations.


Which further helps make your fitness peak argument unfalsifiable. The fact is, with any organism, mutations tend to be more harmful than beneficial and are more likely to be harmful than beneficial.

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However, other types of selection may introduce less fitness in one respect or another.


Other types of selection are subject to natural selection.

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Sexual selection may tend to favour traits that are not conducive to survival if only ecological adaptation is being considered.


Which is also subject to natural selection. Why would natural selection favor an organism that desires an inferior spouse? This makes no sense and further demonstrates the unfalsifiable nature of evolution.

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However, since finding a mate is as essential to evolution in many species as surviving to maturity, we see species making trade-offs, balancing the need to attract a female against the need to avoid the attention of a predator for example.


But the organism that is better able to avoid the predator is more fit and would be favored by natural selection (and other types of selection because they are also subject to natural selection).

quote:


Again, fit for what? You can't talk about fitness in abstractions. Bacteria survive all over the place because they have diversified to establish themselves in many different niches. A bacterium that thrives in one environment will fail to thrive in another. So it is not that all bacteria are clustered around a single fitness peak. Rather different bacteria are situated around different fitness peaks.

Humans have a different fitness landscape.


Again, excuses such as these further demonstrate the unfalsifiable nature of your arguments. We know that mutations are more likely to be harmful than beneficial, yet you make up difficult to test reasons. We know that viruses that have lost the genetic information needed to survive well in humans won't gain the ability to live in humans as well as their ancestors, and the same is true with dogs that have lost the genetic information required to live in the wild (unless they get it from their ancestors). Again, they are not at their fitness peak, their ancestors are closer to their fitness peak, and further mutations do not bring them back to their fitness peak. There is no evidence suggesting that the reason why mutations tend to be more harmful than beneficial is because they are close to their fitness peak and the simple fact that there are organisms that live more successfully in the same environment as other organisms and mutations are still more harmful than beneficial to the less successful organisms suggests that this is not the case. I see no reason to believe otherwise.

Aside from the fact that post 89 destroys your fitness peak argument, I forgot to mention it is often evolutionists that argue that life is inefficient and far from perfect, hardly a trait of an organism close to its fitness peak. This is another reason why imperfect organisms are evidence against evolution (aside from the fact I have mentioned other reasons why on other threads), because mutations tend to be more harmful than beneficial yet organisms are far from perfect so it is more difficult to argue that mutations are harmful because organisms are close to their fitness peak.



essentialsaltes -> RE: Regulating Evolution (4/30/2008 1:24:10 PM)

quote:

ORIGINAL: Bettawrekonize
it is often evolutionists that argue that life is inefficient and far from perfect, hardly a trait of an organism close to its fitness peak.


In the fitness landscape, species can only migrate toward 'local' peaks, not necessarily the optimal peak. A cheetah with wheels and an internal combustion engine might be more fit than its normal cousins, but that part of the landscape is inaccessible. Similarly, once vertebrate eyes got locked (through historical accident of development) into a system with the nerves and blood vessels blocking the retina, it probably would take too much of a mutational leap to make the system better 'designed'. Evolution doesn't make intelligent leaps toward the absolute optimum, just unintelligent shifts along the slope of the fitness landscape toward the better than last year's model.



Bettawrekonize -> RE: Regulating Evolution (4/30/2008 1:38:06 PM)

quote:

ORIGINAL: essentialsaltes
In the fitness landscape, species can only migrate toward 'local' peaks, not necessarily the optimal peak. A cheetah with wheels and an internal combustion engine might be more fit than its normal cousins, but that part of the landscape is inaccessible. Similarly, once vertebrate eyes got locked (through historical accident of development) into a system with the nerves and blood vessels blocking the retina, it probably would take too much of a mutational leap to make the system better 'designed'. Evolution doesn't make intelligent leaps toward the absolute optimum, just unintelligent shifts along the slope of the fitness landscape toward the better than last year's model.


Of course, this further demonstrates the unfalsifiable nature of UCD. Again, the fact is that mutations tend to be more harmful than beneficial which suggests that things are breaking down. Your arguments that it is because all organisms are close to their local fitness peak and there is no pathway to get closer to an optimal peak is unfalsifiable. It doesn't explain how organisms got to the state that they're in and lack of observable pathway doesn't seem to be a problem for evolution in this regard, so it shouldn't be a problem in other instances. Also, why haven't other organisms found different pathways earlier on that have lead to an organism that is very close to optimal and why hasn't natural selection favored those organisms such that they eventually take over the niches of the less optimal organisms? The fact is, when viruses and dogs lose their genes to live in the wild, they do not gain it back (unless they acquire it externally) as well as their ancestors even if one does try to slowly re - select a dog that can live in the wild just as well. If UCD is true, there is a pathway by which it is possible for dogs to reach the local peaks of their ancestors, yet once a dog has lost their ability to do so they do not gain it back. The problem is that you assume a pathway to get to the fitness peaks of their ancestors, but we can never observe one. There is no evidence supporting your (unfalsifiable) hypothesis and lots of evidence contradicting it.



essentialsaltes -> RE: Regulating Evolution (4/30/2008 1:57:43 PM)

quote:

ORIGINAL: Bettawrekonize

Also, why haven't other organisms found different pathways earlier on that have lead to an organism that is very close to optimal


They have. Squid eyes, for instance, do not suffer from the defects of vertebrate eyes that I mentioned.



gluadys -> RE: Regulating Evolution (4/30/2008 5:04:54 PM)

quote:

ORIGINAL: Bettawrekonize

In general, mutations tend to be more harmful than beneficial and there is really no reason to suggest fitness peak has anything to do with it.


So you don't think it might be because most species are relatively near a fitness peak?

quote:

Other types of selection are subject to natural selection.


They certainly co-exist with natural selection, but they are not always subject to natural selection. In some situations, neutral selection is thought to be more dominant than natural selection.

quote:

But the organism that is better able to avoid the predator is more fit and would be favored by natural selection (and other types of selection because they are also subject to natural selection).


By natural selection, yes. But not by other types of selection. So it depends on which mode is in the driver's seat. That is what the guppy experiment was about. Females tend to prefer brightly coloured males. But brightly coloured males are an easy target for predators. So one would expect guppies not to be brightly coloured if natural selection prevails over sexual selection. And we do find that many guppies are not brightly coloured.

However we also find in nature--sometimes in the same stream as the dull-coloured guppies, male guppies that sport bright colours. How can this be? The researchers theorized that in places where the guppies were brightly coloured there were few if any predators. Then they began a census of predator species and found they were right.

They also added experimentation. They took dull-coloured guppies and placed them in an area of the stream (in some cases in a tank in a laboratory) where they were shielded from predation. After a few generations, the males were sporting bright colours. They also tried this experiment in reverse, adding predators to a tank or moving bright coloured guppies to regions where there were high numbers of predators. And after a few generations, these one lost their bright colours.

So whenever the pressure of natural selection was lessened because of lack of predators, sexual selection took over and generated brighter colours.


quote:

Aside from the fact that post 89 destroys your fitness peak argument


I think you must mean a different post. That one says nothing relevant to this conversation.


quote:

I forgot to mention it is often evolutionists that argue that life is inefficient and far from perfect, hardly a trait of an organism close to its fitness peak.


Actually no. If an organism were actually at the optimum fitness, for every characteristic, it would follow that every mutation which could possibly happen would remove it from the optimum. So that actually agrees with the fitness thesis. Most organisms are not at optimum for every characteristic. They may be at or very near the optimum for one characteristic, but fairly well down for another. If there is no strong pressure to maintain optimum fitness, the whole species may be a fair distance down the slope. If the fitness landscape changes (because of some environmental difference) a species that was near a fitness peak may find itself somewhat removed from a fitness peak.

The main point to remember is that there is not just one fitness peak, even for one species. Overall fitness for an organism then does not usually mean optimum fitness, but some sort of balance in the fitness of various traits.

Combined with historical constraint, such as essentialsaltes has discussed, this means organisms are generally not perfect.


quote:

it is more difficult to argue that mutations are harmful because organisms are close to their fitness peak.


And again you have misread the argument.



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