Micro to Macro: Working Backwards

[Loudmouth]

Well, we predict how viruses mutate with enough accuracy to make functioning vaccines.

Just for a bit of context. . .

When epidemiologists decide what the vaccine strains will be for the upcoming flu season, they actually look at what mutations have already occurred. They look for mutations that have resulted flu strains which very few people carry antibodies for. These mutations most often occur in their hemagglutinin and neuraminidase genes which are responsible for the two major surface protiens, which is also where you get the HxNx notation. If few people have active antibodies that recognize a virus, and the virus passes easily from person to person, then you have a strong candidate for vaccine production.

 

[PsychoSarah]

Just for a bit of context. . .

When epidemiologists decide what the vaccine strains will be for the upcoming flu season, they actually look at what mutations have already occurred. They look for mutations that have resulted flu strains which very few people carry antibodies for. These mutations most often occur in their hemagglutinin and neuraminidase genes which are responsible for the two major surface protiens, which is also where you get the HxNx notation. If few people have active antibodies that recognize a virus, and the virus passes easily from person to person, then you have a strong candidate for vaccine production.

Of course, viruses have to be able to attach to proteins on the surface of human cells, so that helps.

 

[OllieFranz]

Ollie, I agree with you up to a point as well. ID looks for specific commonalities in things that are designed, yes. (I recall one paper looking for proverbial genetic trademark stamps in our dna.) It also seeks to rule out chance occurrences, and find evidence of insight in biology among a number of other methods. Since these are about inferring and discussing the design itself, I see no way that your criticism applies. When you said it's abandoning science and logic to not expand the scope of ID to make inferences about the designer, you weren't clear exactly what scientific and/or logical principles have been violated by not doing so. What are these principles?
Did you consider the possibility (and I'm not entirely sure yet) that the idea of manufacture you have has a similar definition to the design ID proponents use even if you disagree with their use of the term?

I have never, until now,seen an IDer give a definition of Design that could be both objective (under the same circumstances independendent observers would all agree whether or not an object meets the criteria in the definition) and helpful in constructing a falsifiable scientific theory --one that can be tested. There is no way to test for IC, since every complex system contains subsystems that combine differently for different purposes.

Both the other poster's "evidence of being manufactured" and your "evidence of insight" may, if more carefully defined, become objective. I don't know if any theorems that use them will be testable, but they very well could be.

The principles to which I referred, and which have been the foundation of scientific inquiry ever since its founding by people like Newton, Descartes, Bacon, and Pascal, most of whom were Christians, include, among other things, a naturalistic approach, reproducible results, and the rule of parsimony (aka Occam's Razor). All ID "theories" that I have seen start with the assumption of a Designer, and attempt to prove His existence. This violates both parsimony and naturalism.

 

[OllieFranz]

OK then, but you're using it in a different way than Ollie was when I first responded to him, and I was trying to respond to Ollie based upon his position of natural selection, which seems to be that it in some sense mimics intelligence.

It in no way mimics "intelligence" or even "intelligent design." There are some constraints on an organism, and certain mutations produce traits that make an organism unviable..Its mutations are not propagated into the population. "Beneficial" and neutral traits are.

As Sarah says, "fitness" and fecndity are different concepts. The fittest organism of its generation might have an accident, or get eaten before having the chance to produce offspring. But evolution is not something that happens to individual organisms, but to entire populations. The fittest 20% of one generation may produce 40 or even 60% of the next generation, so there is a strong correlation between fit traits and fecundity.

If the climate is getting colder, "fitness" might mean a heavier coat. Esch generation a greater percentage of the population has heavy coats. God may be overseeing the process, but He is not actively interfering with the natural workings of an unintelligent Nature. There is no reason for a scientific hypothesis to insist on accounting for God or even an intelligent Nature to explain the Shaping of the population. That is why Shaping is evidence of neither Intelligence nor Design.

 

[OllieFranz]

Well, we predict how viruses mutate with enough accuracy to make functioning vaccines.

Also, don't expect Ollie to have the same view as me, he isn't an atheist so he is more likely to pair an intelligence to evolutionary processes.

Actually, I do agree with you far more than I agree with PG. He was reading my position incorrectly.

 

[PsychoSarah]

Actually, I do agree with you far more than I agree with PG. He was reading my position incorrectly.

My bad, I have issues with trying to read large walls of text, so I usually don't read what you say, sorry X/

 

[OllieFranz]

My bad, I have issues with trying to read large walls of text, so I usually don't read what you say, sorry X/

No problem.

I hope its not my posts you meant by large walls of text. I try to keep my paragraphs small --usually four sentences or less -- and well spaced.

 

[PsychoSarah]

Separating it into paragraphs is minimally helpful for someone with ADHD as bad as mine.
It actually makes it look like more text.

 

[PhantomGaze]

I have never, until now,seen an IDer give a definition of Design that could be both objective (under the same circumstances independendent observers would all agree whether or not an object meets the criteria in the definition) and helpful in constructing a falsifiable scientific theory --one that can be tested. There is no way to test for IC, since every complex system contains subsystems that combine differently for different purposes.

Both the other poster's "evidence of being manufactured" and your "evidence of insight" may, if more carefully defined, become objective. I don't know if any theorems that use them will be testable, but they very well could be.

The principles to which I referred, and which have been the foundation of scientific inquiry ever since its founding by people like Newton, Descartes, Bacon, and Pascal, most of whom were Christians, include, among other things, a naturalistic approach, reproducible results, and the rule of parsimony (aka Occam's Razor). All ID "theories" that I have seen start with the assumption of a Designer, and attempt to prove His existence. This violates both parsimony and naturalism.

It in no way mimics "intelligence" or even "intelligent design." There are some constraints on an organism, and certain mutations produce traits that make an organism unviable..Its mutations are not propagated into the population. "Beneficial" and neutral traits are.

As Sarah says, "fitness" and fecndity are different concepts. The fittest organism of its generation might have an accident, or get eaten before having the chance to produce offspring. But evolution is not something that happens to individual organisms, but to entire populations. The fittest 20% of one generation may produce 40 or even 60% of the next generation, so there is a strong correlation between fit traits and fecundity.

If the climate is getting colder, "fitness" might mean a heavier coat. Esch generation a greater percentage of the population has heavy coats. God may be overseeing the process, but He is not actively interfering with the natural workings of an unintelligent Nature. There is no reason for a scientific hypothesis to insist on accounting for God or even an intelligent Nature to explain the Shaping of the population. That is why Shaping is evidence of neither Intelligence nor Design.

According to IDers, ID theor(y)ies infer the designer(s) from the evidence, then don't talk about the designer, but the design. I am aware that a lot of it's critics claim ID assumes a designer first, but if I uncritically accepted every accusation I heard, I'd think IDers were armed terrorists bent on world domination. Ollie, you said that the fact that id does not identify the designer makes it violate principles of science and logic. But I still see no reason to think that. You know, any idea will look silly if you let its critics define it for you.

Anyway, let me try to clarify a few things.

Which part of the following do you disagree with and why?

1. ID and Evolution can predict different things regarding how tuned/fit/shaped/whatever an organism is to its environment.
2. If ID makes a prediction, and is correct, that would provide evidence that ID is right, (or at the very least useful in science)
3. Therefore in the right context, evidence of 'shaping' as you defined it can be evidence for ID.

What do you take issue with?

 

[PhantomGaze]

You aren't a bad guy. You simply don't understand the science, which puts you in the same boat as 95% of the general public. Like I said, I fully accept that you believe what you say you believe. The problem is that your beliefs don't match upwith or even address the facts that science has come to discover. That is the disconnect.

I'm certainly aware of a number of facts science has discovered, whether it's sufficient to provide me with an accurate picture of the field of biology, I assume time will tell. For the record though, I have a science degree, I'm not just some silly hick who's giving you grief because "mah pass ter told meh to". As for my 'beliefs,' as they relate to ID, aside from the facts I'd cite in support of them, I see various positions as hypotheses to be tested, not some kind of theological proposition, and that goes for every position on the issue.

It's possible that leprechauns secretly plant evidence at crime scenes so that it is indistinguishable from the occurrence of a real crime. It is possible that we have everything wrong with respect to gravity, and that it is really caused by invisible pink fairies in such a way that it is indistinguishable from natural processes.

We could go on and on about possibilities that we can dream up that would be indistinguishable from the processes that currently hold a consensus in science. The problem is that these are just fantasies. What we are much more interested in is evidence, or even a methodology that would allow us to test for these possibilities.

Except that we have directly observed these mechanisms, and what they can do, and we also know that nature seems to show examples of insight and complexity the more we look, the more complex and organized things seem to get. Of course when I said 'non-random with respect to fitness' I should have included things like 'important for regulating future evolution' or altering the way some proteins are formed... I guess 'purposeful' was the term I was looking for.

We certainly can't find any changes that are inconsistent with the observed mechanisms of mutation. In fact, that is the whole point of this thread.

Interesting way to phrase it. I am not taking issue with the 'observed mechanisms of mutation' I'm asking for the reasons that you (or anyone for that matter) think one particular mechanism is responsible for the balance of change as opposed to other observed mechanisms (aside from the fact that we didn't know of others for quite some time).

The biggest piece of evidence is the ubiquitous nested hierarchy found in the genetic data for complex life. If mutations were non-random, then we would expect specific gene sequences to more closely related to environment than lineage. This isn't what we see. We don't see bats sharing more DNA with birds than they do with dogs. We don't see adaptations moving wholesale from one branch of life to another. Instead, we see each lineage coming up with their own solutions to a problem at a genetic level.

I see no reason to think that in the event the balance of change in evolution is non-random (based upon pre-existing information), that all creatures would need to generate entirely new body plans every time the environment shifts a little. That sounds pretty wasteful. Furthermore, I think we should expect a nested hierarchy given common descent, but that still doesn't inform us which of our mechanisms of generating novelty are the most influential.

We can also detect negative selection of mutations in genes by looking at Ka/Ks ratios. Another piece of evidence is that mutations continue to cause species to diverge, even in areas of junk DNA where mutations do not change fitness.

With Ka/Ks ratios, I know we can detect negative selection in theory, but this seems to be given certain assumptions about the mutations themselves that seem to undermine the point of bringing them up. If you want to go a little further on why they’re relevant, that would be helpful.
It’s also interesting you say that mutations cause species to diverge, how exactly do you/have you quantified that?

 

[PhantomGaze]

Well, we predict how viruses mutate with enough accuracy to make functioning vaccines.

Also, don't expect Ollie to have the same view as me, he isn't an atheist so he is more likely to pair an intelligence to evolutionary processes.

My principle argument hinges upon whether ID can have different predictions about the environment and organisms, than evolution, I'm not saying it does necessarily all the time.

 

[PsychoSarah]

Which part of the following do you disagree with and why?

1. ID and Evolution can predict different things regarding how tuned/fit/shaped/whatever an organism is to its environment.
2. If ID makes a prediction, and is correct, that would provide evidence that ID is right, (or at the very least useful in science)
3. Therefore in the right context, evidence of 'shaping' as you defined it can be evidence for ID.

What do you take issue with?

I disagree with all but the first one.

2. If I make a guess to the answer of an equation without doing the proper work, and lucky me I happened to guess right anyway, is that a good measure of my understanding of how to do those equations? Of course not. You can't just have 1 prediction be correct and consider that to be good supporting evidence for a theory, especially if the methodology is flawed and lacks consistency. If the same process by which the first time I got the answer correct won't work well in the future (obviously, there is no way I would get that lucky) it fails.

3. Shaping isn't even an evolution term, it is a psychology term which describes a certain method of teaching a person or another animal to do a trick or perform a function by rewarding them every time they progressively get closer to doing the action you want ( used for more complex tasks). It has nothing to do with evolution as far as the terminology goes.

 

[PhantomGaze]

Both the other poster's "evidence of being manufactured" and your "evidence of insight" may, if more carefully defined, become objective. I don't know if any theorems that use them will be testable, but they very well could be

Good. XD seems like we're making some progress then aren't we?

 

[PsychoSarah]

My principle argument hinges upon whether ID can have different predictions about the environment and organisms, than evolution, I'm not saying it does necessarily all the time.

ID, well, actually if you adhered to it the world wouldn't match up with the predictions.

If something is intelligently designed for its environment, then these rules should be followed:

1. Traits which do not make an organism better suited for their environment or make them less so should not appear in individual organisms or populations.

2. Organisms should not become so specialized that inevitable climate changes should not place them at risk of extinction.

3. Breeding shouldn't result in potential death of the parent organism ever.

Because if design were intelligent, then it stands to reason these kinds of mistakes shouldn't happen, and yet we see none of this followed in the slightest.

 

[PhantomGaze]

I disagree with all but the first one.

2. If I make a guess to the answer of an equation without doing the proper work, and lucky me I happened to guess right anyway, is that a good measure of my understanding of how to do those equations? Of course not. You can't just have 1 prediction be correct and consider that to be good supporting evidence for a theory, especially if the methodology is flawed and lacks consistency. If the same process by which the first time I got the answer correct won't work well in the future (obviously, there is no way I would get that lucky) it fails.

3. Shaping isn't even an evolution term, it is a psychology term which describes a certain method of teaching a person or another animal to do a trick or perform a function by rewarding them every time they progressively get closer to doing the action you want ( used for more complex tasks). It has nothing to do with evolution as far as the terminology goes.

2. Ok obviously if you only have one successful prediction you're not getting anywhere, but a series of accurate predictions in succession means you're onto something. This is a principle issue, you can't refute it by saying "Well you're just always going to be wrong." That's disingenuous, and we can't have fruitful discussions that way. Why would you even think I meant something like that?

3. Once again, I was using the word Ollie used, it's not what I would have preferred, but I like to communicate to be understood. If you don't like it, talk to him about it, or stop responding to stuff I write to him.

 

[PsychoSarah]

2. Ok obviously if you only have one successful prediction you're not getting anywhere, but a series of accurate predictions in succession means you're onto something. This is a principle issue, you can't refute it by saying "Well you're just always going to be wrong." That's disingenuous, and we can't have fruitful discussions that way. Why would you even think I meant something like that?

3. Once again, I was using the word Ollie used, it's not what I would have preferred, but I like to communicate to be understood. If you don't like it, talk to him about it, or stop responding to stuff I write to him.

The thing is, ID rarely makes predictions which are correct. That is the issue. Plus, generally it is hard to make predictions from that theory in the first place, due to the nature of it.

I just want to know what you mean by shaping or what you think Ollie means by it.

 

[PhantomGaze]

ID, well, actually if you adhered to it the world wouldn't match up with the predictions.

If something is intelligently designed for its environment, then these rules should be followed:

I think you're trying to envision a more perfect world or something. You
do understand that there can be intrinsic limits to a mechanism that a designer employs to cause his/her/its designs to unfold in the world.

The designer may be limited to certain possibilities, or a desire for certain functional outcomes might require things that would otherwise need to be corrected, or a number of other reasons. We really don't know, but this I think is why it's necessary to come up with more specific outlines and hypotheses for ID before we start comparing too many predictions.

 

[PsychoSarah]

I think you're trying to envision a more perfect world or something. You
do understand that there can be intrinsic limits to a mechanism that a designer employs to cause his/her/its designs to unfold in the world.

The designer may be limited to certain possibilities, or a desire for certain functional outcomes might require things that would otherwise need to be corrected, or a number of other reasons. We really don't know, but this I think is why it's necessary to come up with more specific outlines and hypotheses for ID before we start comparing too many predictions.

The issue is that if the system is designed intelligently, then we really shouldn't see so many pointless, stupid, and harmful developments in nature.

 

[OllieFranz]

According to IDers, ID theor(y)ies infer the designer(s) from the evidence, then don't talk about the designer, but the design. I am aware that a lot of it's critics claim ID assumes a designer first, but if I uncritically accepted every accusation I heard, I'd think IDers were armed terrorists bent on world domination. Ollie, you said that the fact that id does not identify the designer makes it violate principles of science and logic. But I still see no reason to think that. You know, any idea will look silly if you let its critics define it for you.

Anyway, let me try to clarify a few things.

Which part of the following do you disagree with and why?

1. ID and Evolution can predict different things regarding how tuned/fit/shaped/whatever an organism is to its environment.
2. If ID makes a prediction, and is correct, that would provide evidence that ID is right, (or at the very least useful in science)
3. Therefore in the right context, evidence of 'shaping' as you defined it can be evidence for ID.

What do you take issue with?

Every IDer I have read treats the teleological argument (aka the watchmaker argument) as a valid scientific basic principle. It is not a basic principle, it is a conclusion, and it violates parsimony. Science simply does not need the assumption. Further, no IDer I have read has even attempted to "do science" with the assumption. No observation of data, no testing of data, no predictive hypotheses, no fulfilled predictions.

Therefore your first premise is wrong because ID, as presented by the professional ID apologists, does not predict anything. Your second premise is wrong because the non-existent predictions are not "correct." If both premises are incorrect, then the conclusion is invalid.

As a philosophical thought experiment (not a scientific one, though), it is possible that shaping could be the result of a God guiding the process toward a specific design,. But not only is there no scientific evidence for ID, to suggest that we look for such evidence is to abandon the very principles of science.

 

[Loudmouth]

I'm certainly aware of a number of facts science has discovered,

No you aren't. If you did, you would be able to answer the questions in the opening post.

As for my 'beliefs,' as they relate to ID, aside from the facts I'd cite in support of them, I see various positions as hypotheses to be tested, not some kind of theological proposition, and that goes for every position on the issue.

I keep hearing about testable ID hypotheses, but they never materialize.

Except that we have directly observed these mechanisms,

We observe deities designing species? Last I checked, we don't.

Of course when I said 'non-random with respect to fitness' I should have included things like 'important for regulating future evolution' or altering the way some proteins are formed... I guess 'purposeful' was the term I was looking for.

How do you differentiate between a purposeful mutation that is important for regulating future evolution and changing protein structure and a non-purposeful mutation that does the same?

How do you differntiate between an evolutionary pathway that was taken with purpose and one that was blindly found by evolution? Do we conclude that rainclouds were guided over millions of years with th express purpose of producing the exact shape of the Colorado river and the Grand Canyon?

Interesting way to phrase it. I am not taking issue with the 'observed mechanisms of mutation' I'm asking for the reasons that you (or anyone for that matter) think one particular mechanism is responsible for the balance of change as opposed to other observed mechanisms (aside from the fact that we didn't know of others for quite some time).

We knew that mutations were random with respect to fitness before we had discovered DNA. This was based on the work of Luria, Delbruck, and the Lederbergs.

Evolution 101: The Lederberg Experiment

Luria–Delbrück experiment - Wikipedia, the free encyclopedia

Now that we can sequence genomes, we also observe that massive portions of genomes (~90% for mammals) diverge from other species at a rate consistent with neutral drift. In genes, we see negative selection of deleterious mutations.

I see no reason to think that in the event the balance of change in evolution is non-random (based upon pre-existing information), that all creatures would need to generate entirely new body plans every time the environment shifts a little. That sounds pretty wasteful. Furthermore, I think we should expect a nested hierarchy given common descent, but that still doesn't inform us which of our mechanisms of generating novelty are the most influential.

The nested hierarchy does tell us. It screams evolution. A designer would be able to move a sequence anywhere in the tree of life. Evolution can't do that. That is how to tell the difference between ID and evolution, a nested hierarchy.

When a car designer creates a new car model, they don't worry about lineages, or common ancestral rules of which adaptations can and can't go with each other. They mix and match from a wide array of designs to produce something they want without one iota of care about a nested hierarchy. What do we find? Cars do not fall into a nested hierarchy. Life does.

Are you going to argue that if ID is true then it will look exactly like evolution occurred?

With Ka/Ks ratios, I know we can detect negative selection in theory, but this seems to be given certain assumptions about the mutations themselves that seem to undermine the point of bringing them up.

And those assumptions are . . .?

It’s also interesting you say that mutations cause species to diverge, how exactly do you/have you quantified that?

It logically follows from the evidence.

P1. DNA sequence determines the morphology of a given species.

P2. Mutations are changes in DNA sequence.

P3. Humans and chimps have different morphology.

C. The difference in morphology is due to differences in DNA caused by mutations.