Evolution and Intelligent Design

[Ivellious]

You keep asserting this argument over and over again and frankly I am just sick and tired of it.

And frankly, I'm sick and tired of saying it, but I'll explain it again.

How is what ID proposes any different than claiming evolutionary progressions without the ability to test them?

There's a massive difference, but go on, I'll get to it. It's not about "ability to test" in this case.

If you want to claim it's unscientific because it's untestable then at a minimum be intellectually honest enough to admit that TE's claims are unscientific because they are just as untestable.

Not at all. I'm not asserting that it is untestable (though it is). The problem is when you say that evolution and ID make the exact same assertions. Here's why that is incorrect:

Evolution proposes that all species had a common ancestor. ID proposes life is only related by their designer. Huge difference. Now what else do they say, in terms of scientific statements?

Evolution proposes mechanisms and reasons why species evolve. ID says questions about mechanisms are not important, and therefore don't need to be explored.

Evolution predicts/explains the presence of transitional "cross-breed" fossils. ID has no explanation for them, aside from the vague "the designer must have just done it" answer.

Evolution predicted before genetics that we could find strong homologies between related species. We did, and the results of genetic "mapping", if you will, are a staggering demonstration if how we can trace lineages. ID

The mechanisms for evolution can be demonstrated, even if we can't speed up time to witness broad scale macroevolution in progress. ID, once again, says that questions of when/how/why/where/what are irrelevant.

Evolution explains that evolution has not "stopped" at any point in time, though ID has no explanation for why this supposed "designer" has just decided to stop ever since we showed up.

Evolution started within the scope of mainstream science over a hundred years ago and has only gotten stronger as evidence proceeds. ID aims to rewrite science (as admitted by Behe and the Discovery Institute) into a realm where astrology is a mainstream science. The main point here is that ID started with its conclusion (things did not evolve, they were designed) and then scrambled to find evidence supporting that claim. Which is bizarre and unscientific at best. Darwin, on the other hand, proposed evolution by natural selection using the data and evidence he found, just like every other scientist.

In short, it's not about "ability to test", but rather just what is being proposed and not proposed.

Who is rewriting what? It seems, based on what I've read, you guys have to be given (repeatedly) a definition on operational versus forensic science.

Again, for ID to become scientific, the definitions of scientific exploration need to be changed. Namely, they need to be able to justify asking no scientific questions beyond "It happened" and they need to justify mangling the scientific method into a "conclusion first, evidence later" approach.

The constant argument given that ID is the exact same thing as archaeology and forensic crime science is simply wrong. It seems right to say that they are both seeking out "intelligently designed" materials, but in terms of science, that's where the similarities end. An archaeologist doesn't just stop at "it was designed" as ID does, they seek out the other questions too. Who or what people made this? How did they make it? Why did they make it or what was its purpose? When did they make it? While at its core, yes, both groups are seeking out an intelligent agent, archaeologists scientifically explore their discoveries, instead of finding a jar, labeling it as designed, and then tossing it out because that's all they needed. Same goes for forensic scientists.

Can you imagine a world where ID's rules of science applied to forensics? Screw actually identifying a culprit or examining how they did it for a trial, all we need to know is that it happened! Again, in principle the first step is the same between ID and forensics, but after that, the difference is that forensic scientists continue to perform scientific inquiry, and ID "scientists" just sit back and call it a day.

As K has said, we can observe thousands of instances of intelligence accounting for 3-D spatial positioning.

You know what? I don't have an answer for this. Honestly, I can admit that. I'm not saying evolution is iron'clad. But just because K has one example of this doesn't mean ID is automatically correct. Especially when nearly no biological research has been done on the topic and frankly no ID research has been done on it either.

You've got a double standard and you stubbornly refuse to acknowledge.

Where is the double standard? That I expect ID to answer the same questions as evolution if it expects to overcome evolution? Or the same questions as any field of science for that matter?

You will stand before God one day, and all of this will be evidence of how you shook your fist in the face of reason, and people who actually care about your eternal destiny. If you have nothing new to add, I'd say, move along, because from my perspective you are only embarrassing yourself as K has laid out his case, and you guys keep attacking red herrings.

Well, considering ID isn't a religious stance....wait, maybe you are admitting that it, in fact, is? Look, this has been thrown around so often, but it baffles me how ID can talk out one side of its mouth and claim no religious/Christian origins or leanings, and then turn around and blatantly demonstrate that it is nothing but re-packaged creationism.

[jlay]

Evolution proposes that all species had a common ancestor. ID proposes life is only related by their designer. Huge difference. Now what else do they say, in terms of scientific statements?

Yep, they have different presuppositions. So, please explain why ID must embrace Darwiniam presuppostions to be legit?

Evolution proposes mechanisms and reasons why species evolve. ID says questions about mechanisms are not important, and therefore don't need to be explored. ??What?? I surely hope you realize how ridiculous this sounds.

Again, this presupposes Darwinism and commits the fallacy of equivocation. It is a QUESTION BEGGING hypothesis. You only expose how insance this has become. One must embrace a question begging hyposthesis to be considered legit in the scientific community. I am sooooooooooo glad you made this last post, because it only confirms how strong the religious committment really is to Darwinism. Sadly, you can't see this yourself.

Evolution predicts/explains the presence of transitional "cross-breed" fossils. ID has no explanation for them, aside from the vague "the designer must have just done it" answer.

Evolution presupposes transitional fossils. Why would ID attempt to explain such a thing? Can you not see the insanity of this?
for example. I reject the concept of transitional fossils. Fossils exist. People dig them up. In fact many expeditions have been funded with the intent of FINDING transitional fossils. Is that scientific, or ideological? Uh, the later. A fossil NEVER says when it was buried or what it is. That must be interpreted, such as 'this animal exist today,' or, 'it is extinct.' The term 'transitional' is an interpretation. Sometimes these interpretations are made by people funded to FIND TRANSITIONAL FOSSILS, or who expect to find them in the record. Sure, you believe in Darwinism. You expect transitions. Your worldview DEPENDS on it. So, you see archeoptryx as transitional. But you can't tell me what it was and what it transitioned into. It is extinct. A dead animal.
I see archeoptryx as an extinct creature. As far as we know, that's a fact. So, please explain why I am obligated to explain it as a transitional fossil, when that would be question begging? Assuming what one expects to find.

[KBCid]

How is what ID proposes any different than claiming evolutionary progressions without the ability to test them?

There's a massive difference, but go on, I'll get to it. It's not about "ability to test" in this case.

Lol. it is not about the "ability to test". IT is not in this case because it deals with the ToE but as soon as it becomes a question of ID then it is all about the "ability to test" and mostly its about the ability to test the designer.

If you want to claim it's unscientific because it's untestable then at a minimum be intellectually honest enough to admit that TE's claims are unscientific because they are just as untestable.

Not at all. I'm not asserting that it is untestable (though it is). The problem is when you say that evolution and ID make the exact same assertions.

But you are asserting its untestable with every breath and yet you have been shown that ID is used scientifically in a number of sciences; Forensic sciences, Archeology, Cryptanalysis, Arson investigation, Search for Extraterrestrial Intelligence. Each of these accepted sciences use ID detection as a foundational aspect to make determinations. The fact that you deny that they are relevant is simialar to a flat earth POV which would even deny a personal view of the curved earth rotating.

Here's why that is incorrect: Evolution proposes that all species had a common ancestor.

Which is both untested and untestable. Science uses the scientific method. Religion is based on belief.

ID proposes life is only related by their designer. Huge difference. Now what else do they say, in terms of scientific statements?

ID proposes that all life exhibits the same common design principles used in all life. Same reason chevrolet has a wide array of vehicles but similar mechanics as their basis. This is an observable evidence of the type of detectable information intelligent design forms as it operates. This is what is known as engineering principles. Engineering after all is a foundational scientific aspect of intelligent design.

Evolution proposes mechanisms and reasons why species evolve.

mechanism 1 - mutation. Show by scientific method exactly how mutations occured in order to form all life
mechanism 2 - natural selection. Show by scientific method exactly how NS affects the origination of the variety of life.
So far no testable explanation for how species evolve has been defined.

ID says questions about mechanisms are not important, and therefore don't need to be explored.

ID says that the mechanism that causes variety are mechanistically designed into the operation of the organisms DNA. 3 dimensional spatiotemporal control of the formation of matter is the mechanism that not only implements the formations defined by that variation mechanism but also allows for the mechanistic control of the variation system.

Evolution predicts/explains the presence of transitional "cross-breed" fossils.

lol
The problem with the cross-breeding test for transitional forms is that transitional forms are found in the fossil record: they are dead. You can not cross-breed animals that are dead. This is why appearance is often used for identifying transitional forms. Appearance is related to genetics, so the idea is that two animals that share many similar characteristics will have much of the same genes, and therefore they may very well be able to cross-breed. However, is it true that two animals that bear many similarities are closely related genetically?
Evolutionists have a term for when two different animals that are not supposed to be related happen to look very much like each other. Such an unrelated similarity is said to be the result of convergent evolution. A classic example of convergent evolution is the similarities between the Tasmanian wolf and a true wolf. Both of these animals have the classic dog-type body. Both are about the same size. However, one is a marsupial, and the other is a placental.
Now based solely on outward appearances, it might be thought that the Tasmanian wolf represents a transitional form between marsupials and dogs. Of course, we are told that it is not. The similarities that exist between Tasmanian wolves and true wolves exist simply because they were subjected to similar selective pressures, and they adapted to those pressures by evolving similar traits. A legitimate question to ask is: why are the similarities between these two animals not representative of a genetic relationship while the similarities between Archaeopteryx and dinosaurs show that they are related? http://stevendking.blogspot.com/2010/02 ... ified.html

This understanding leads to the obvious question "how was the cross-breeding determination tested by scientific method"

ID has no explanation for them, aside from the vague "the designer must have just done it" answer.

An IDer like me who made a number of designs that look very similar but use different internal structuring would say "this is a typical intelligent designer type of information. This is the original designers answer to the saying "if it walks like a duck and quacks like a duck".(it may not actually be a duck)
Would a car look much different if it used this for propulsion; Shockwave-Generating Wave Discs Could Replace Internal Combustion Engines
http://www.popsci.com/cars/article/2011 ... on-engines
One of the many aspects of intelligent designers is their ability to be artistic. Fortunately for us we are also intelligent and can recognize these possible types of evidence left behind from the action of inteligent agency.

Evolution predicted before genetics that we could find strong homologies between related species.

What other choice did it have but that prediction? small changes culminating into a new species. I think they would have been hard pressed to predict that each variation was absolutely different. You don't even need to be an engineer to follow the obvious implications of "small changes".
What has evolution predicted that doesn't owe its existence to the original assertion of small changes.
Has evolution by chance predicted the necessary existence of a spatiotemporal control system in order to form matter into specific shapes?
ID predicts its necessity and you know there should be a fairly common understanding about this. If you aren't a crystal or a snowflake then how does your 3 dimensional form replicate?
Here is a prediction from ID for you; "The replication of 3 dimensional formations of matter... 'REQUIRES' an irreducibly complex spatiotemporal control system". no replication, no evolution.

If you choose to believe that everything can be explained by natural forces then you will one day have to say that such an irreducibly complex system (which is now being revealed) happened by random chance alone. no replication, no evolution.

[KBCid]

we can observe thousands of instances of intelligence accounting for 3-D spatial positioning.

Our creator from the very beginning expounded on forming spatially positioned systems of matter. This is his trademark action as an intelligent designer.For early observers of his handywork it was wonderous to simply detect the range of the varities of forms that resulted from his action.
In this time we can now go beyond just the appreciation of his artistic forms and consider rationally how such forms were designed to persist. Life persists because God caused living systems of matter to be able to replicate their 3 dimensional form.
This is the true dividing line from the evolutionary rationale. God formed an irreducibly complex automated spatiotemporal control system into the physical design of life so that it may persist.

My part here and now is to help reveal this system for his believing creations to consider. The non-believer is left with being forced to assert that such an irreducibly complex system occured by chance.
I feel lucky to be taking part in continuing what Isaac Newton started. He simply wanted to understand and convey how the Creator caused things to persist.

The law of gravity became Isaac Newton's best-known and most important discovery. Isaac warned against using it to view the universe as only some machine like a great clock. He said, "Gravity explains the motions of the planets, but it cannot explain who set the planets in motion. God governs all things and knows all that is or can be done."
http://www.doesgodexist.org/NovDec01/Is ... avity.html

[Neige]

Hello,

I'm new to this forum and I find some of the topics discussed in this thread quite astounding. KBCid, I want to know if I understand correctly what you're saying. I'm not very familiar with all the scientific terminology (+ English is not my native language), but let's get this straight - you're main points are:

1. According to abiogenesis, the first living organism did NOT come into being by reproduction (but had a chemical origin).
2. Without reproduction, there can be no evolution.
3. That means this 3D positioning system existed within the first organism (or collection of organisms) before evolution could possibly occur.
4. Since, unlike DNA, cells have no inherent natural form of organisation, 3D positioning system within cells has no naturalistic explanation.
5. Since there is no other logical explanation and since our empirical experience (Craig Venter cell experiment) affirms such a possibility, an intelligent agent could have caused the system to be created.

Is that about right?

[Pierson5]

This is exactly the issue I have with your "evidence." You are taking a small, specific aspect of biology not completely understood and claiming it as evidence for design.

...The evidence is plainly showing that there is a system of spatiotemporal positional control functioning within all life.

I'm not arguing that the system isn't there. I'm arguing that you are jumping to a conclusion when we are still left with a mystery. Just as Behe had his flagellum. No one was arguing that the flagellum wasn't there, or that it didn't express machine-like characteristics. Even if we didn't know how the flagellum evolved, this would not be evidence for design. You are taking this structure that is not completely understood (an unsolved problem) and claiming it as evidence for design. If you have an unanswered question, you have an unanswered question. Not evidence. Once you and your colleagues have actually discovered evidence for design in this system, then you can claim it is designed. People building systems that are similar is not evidence for biological design.

The citation you gave says NOTHING about ID in the regards of this discussion. Your whole argument is just a rehashed version of Paley's watchmaker argument. Just as Behe used the flagellum (motor), you are using the same argument with 3 dimensional spatial organization. Paley's argument is flawed, Behe's argument was flawed and yours is flawed for the same reasons.

Then you should have no serious problems defining how it is flawed just like all the others. Right?

Sure. For the sake of argument, let's say we have the same amount of knowledge of 3 dimensional spatial organization as we do the flagellum (so removing some information we know about the flagellum). I'll provide analogies through the rest of this post.

The question I asked was specifically about the so called research you and your colleagues are currently doing. As you said above, you have presented your ideas to your colleagues and they are implementing it. Why not give us a run down of the type of experiments they are doing to test your hypothesis?

They are testing the system mostly by knockout experimentation. Determining how the positional control is being implemented and observing how cellular components are being controlled in space and time. This is an exciting field and there is some very neat new technologies that are allowing them to observe the functioning of the cell in vivo with 3 dimensional detail...
If you want names of people and specific experiments then you can look through the references I gave, there is one cited from a colleague.

Cutting edge research is exciting, I agree. The issue I have is with your conclusion. From the citations you have provided thus far, no one has come to the conclusion you are promoting (biological design). As I said above, I'm not arguing these systems don't exist. You are taking this cutting edge research and jumping to the conclusion about the origin of these systems when the answer is still inconclusive (again, going off your previous citations).

When I was asking if you presented your ideas to your colleagues, I meant the biology department. And just so we're clear, you don't have any type of experiments to test your hypothesis?

My collegues are the biology department? and just so we are clear I have a number of experimental evidences to validate the hypothesis that it requires an irreducibly complex system of spatiotemporal control of matter in order to allow for 3 dimensional replication. You simply have to look within the field of mechanical engineering to see the testing and applications of the systems.
As for the hypothesis that such a system requires an intelligent designer the observable evidence speaks for itself there since only intelligent design has ever been observed to form such systems. So how would one test to prove that the system in life was designed? for that matter how would one test to prove that it evolved? We have a common problem. Neither of us can test the past... it is beyond the scientific method. Our only choice is to infer from current observable evidence.
You argue for natural occurance which you have never seen to form such a system and I argue for ID based on the observable evidence left behind as intelligent designers form such systems.

You mentioned before you were working on a bioengineering degree. So I assume you have some sort of affiliation with the biology department, even if you aren't doing research in their particular field. Since your conclusion would have major ramifications in the field of biology, I guess I assumed you would have at least discussed this, researcher to researcher, with others in that field.

The experimental evidence I'm looking for is biological evidence. Not mechanical engineering. If we use the same argument Behe had used with regards to the flagellum, it's not hard to see the similarities. The system requires a designer because the flagellum is irreducibly complex. We only have seen intelligent agents give rise to the type of design we see in the flagellum. As our understanding of the flagellum grew, however, this was shown to be false. You can test for these sort of things. For example, if the flagellum evolved, we should be able to see some sort of gradual transition. This may be a bit lengthy, I'll try to sum it up the best I can. From the trial:

A. So this is, in a way, a summary of Dr. Behe's argument. And one of the things that I think is important to make clear to the Court is that, it is absolutely true that there are many, many structures in the living cell, many biochemical pathways for which we don't have a detailed biochemical -- excuse me, a detailed evolutionary explanation. That is a point that all scientists will concede. Do Doctor --

Q. I'm sorry. Is that true just about evolutionary theory or is that true about any science?

A. That's true about anything. In cell biology, for example, I think most people and the court are aware that when a cell divides, the chromosomes that carry the genetic information of a cell are moved apart and separated into the two daughter cells. We have enormous arguments in the field of cell biology as to what the exact mechanism is by which that force is generated. We can all see it happen. Any high school student can watch the separation of chromosomes under a microscope in a high school laboratory. But we still don't know exactly what the motor or the mechanism is that moves these apart. There are many, many other unsolved problems in biology.

Q. I'm sorry. Please continue.

A. Sure. So it's important to note that Dr. Behe's argument does not say simply, well, there are complex structures within the cell for whom we do not understand the detailed evolutionary origin of, that's absolutely true.

Now what I wrote here is that, Dr. Behe has made very clear in what I think is fairly called his biochemical argument from design, that that argument depends upon a much bolder claim than simply saying, scientists have not completely explained how this structure evolved. And that bolder claim is shown in the next animated section of this slide. And that is that, the evolution of complex biochemical structures cannot even or ever be explained in principle. And, of course, what he means by that is, there is some aspect of this complexity, which means we can say not just, we haven't figured it out yet, but we will never figure it out, and that's where the evidence for design lies.

The reason that evolution cannot explain, he says, the origin of such structures is because they have a property, which he calls irreducible complexity.

So in the lower part of the the slide, I have a quotation from page 39 of his book, Darwin's Black Block. And I will read that to the Court. Quote, By irreducibly complex, I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.

And now, from my point of view, the key part of the argument, and I'll continue to read. An irreducibly complex system cannot be produced directly by slight, successive modifications of a pre-cursor system -- and that's how evolution would have to produce it -- because any pre-cursor to an irreducibly complex system that is missing a part is by definition non-functional.

So his argument is that, if you have a multi-part system, and all the parts are necessary to function, you can't produce that system five parts at a time, six, seven, and gradually build up the complex system, because there is no function possible until the last part is snapped into place. And that's why evolution cannot produce that system.

But the reason I like the way that Dr. Behe has put his argument, and I like sort of describing it this way, is because it actually is amenable to a scientific test. Something that most arguments for intelligent design are not.

Q. I'm sorry. This is -- is Dr. Behe's argument for irreducible complexity, is that an argument directly for design?

A. That's a good point. The answer is, no, it's not. It really is an argument that says why such systems are not produceable by evolution. So it's a negative argument against evolution. It is in itself not evidence. Even if the argument were correct, it's not evidence of a designer, it's not argument for design, it simply is an argument that the evolutionary mechanism wouldn't work in this case.

Q. So that's why this argument is testable?

A. That is correct. As I mentioned earlier, one of the problems with intelligent design is that it doesn't make any testable predictions. This actually isn't a testable prediction of design either. This is simply an argument as to why evolution wouldn't work. And that can be subjected to a test.

Q. Please continue.

A. Thank you. Next slide, please. So what I have done in this slide is to place the graphic summaries of the argument from irreducible complexity that I just made in the upper left-hand corner of the slide, and in the upper right-hand corner, I have basically put the evolutionary explanation using the same graphic convention. And the nature of the test that I or any other scientist would propose is pretty simple.

If you animate the slide, you'll see that Dr. Behe's prediction is that the parts of any irreducibly complex system should have no useful function. Therefore, we ought to be able to take the bacterial flagellum, for example, break its parts down, and discover that none of the parts are good for anything except when we're all assembled in a flagellum. If evolutionary theory holds, however, and we can animate again, and we'll show that in the right-hand side, evolution makes an extremely straight forward prediction. And that is, when we look at these irreducibly complex structures, we ought to be able to find parts of those systems that actually do have useful functions within them.

So we can do a very straight forward either/or test to distinguish between these two alternatives. So what I'd like to show in the next slide is how such a test can be conducted. This is a -- in the upper right-hand corner of the slide is a graphic representation from a review article showing some of the proteins involved in the construction of the bacterial flagellum.

I cited a paper earlier in this thread regarding the evolution of the flagellum. Also, after removing 30 parts, leaving 10, we have a type 3 secretory system, which falsified Behe's argument. This is why, before we had an in depth understanding of the flagellum and it's parts, the argument: "People build motors for cars and boats, therefore the flagellum is designed," is a flawed argument.

They continue to have similar examples such as blood clotting and the immune system, which I don't think I need to go into. The point is, these ARE testable claims. I understand that you are on the cutting edge of the current research being done in this field. But, you are coming to a conclusion (biological design) before your research is complete. When you or your colleagues actually publish your research which concludes biological design, THEN you will have evidence for what you are promoting.

Q. I'm listening to the arguments that you have described Dr. Behe is making, that these components are irreducibly complex, and that science cannot explain them. And in some cases, he's been shown wrong. But is that essentially the argument, that scientists currently can't explain some aspects of evolution?

A. In essence, that is the argument. It is what a philosopher might call the argument from ignorance, which is to say that, because we don't understand something, we assume we never will, and therefore we can invoke a cause outside of nature, a supernatural creator or supernatural designer.

Q. And is this not a completely negative argument? I mean, it sounds like this is an attack on evolution?

A. This is in every respect a completely negative argument. And if one combs the pages Of Pandas and People or, for that matter, if one looks at Dr. Behe's book or if one looks at the writings of other people who consider themselves to be intelligent design advocates, all that one finds is example after example, argument after argument, as to why evolution couldn't produce this, didn't make that, and doesn't provide an explanation for the following. I have yet to see any explanation, advanced by any adherent of design that basically says, we have found positive evidence for design. The evidence is always negative, and it basically says, if evolution is incorrect the answer must be design. Never considers an alternate idea.

Another point. If you do end up showing this structure is, in fact, irreducibly complex, this is not evidence for design. It is merely a problem for evolution.

Q. And what about in Dr. Behe's work?

A. As far as I can tell, there is no affirmative evidence for a designer in Dr. Behe's book either. Both books rely entirely on negative inferences by saying that, if evolution has problems, if evolution is wrong, if evolution cannot provide complete explanations, then we can go ahead and say it's a designer.

Q. So how do they make that argument? I mean, even if there's no evidence? What's the rationale? What's the reasoning for getting to that designer?

A. Well, with all due respect, I believe I've already answered that question, which is, I don't find there is any reasoning in that area at all. It's the
sort of logical fallacy in which you might say, well, I have theory A, and I have theory B. And I can prove theory B by showing theory A is wrong. And in science, you say, excuse me, just a minute.

Besides theory B, there's an infinite number of other possible theories. So you don't, quote, prove one by showing that another one is wrong. If you show another one is wrong, you've shown that it's wrong. All other alternative theories are now equal contenders. So the logic of picking out intelligent design, which is inherently untestable, and saying that any evidence against evolution is evidence for intelligent design employs a logical fallacy that I think most scientists reject.

Replication is that simple little thing most everyone understands as the reproduction of material form. You do understand that in order to replicate material form it requires both spatial and temporal control of matter right?

I'm not disagreeing with you that it is a requirement, and it does happen. I don't see how you go from: 1. Here is a requirement
2. We don't understand it 3. People build stuff similar 4. Therefore design

Point 2 isn't true... the fact is 'You' don't understand it. I understand it quite well since the type of system you don't understand is what I make for a living and since these systems have only ever been observed as a result of ID I have every right to hypothesize that ID would be required for them to come into existence. What have you observed that forms such a system? really show me what kind of system like this you have personally observed nature forming?

We don't understand it 'completely.' There are still unsolved mysteries about this system, I think you'll agree. That is what we are arguing about and is what I was referring to. Before we understood a lot of the intricate details of the flagellum, we still had a pretty good understanding of the flagellum itself. Before our further understanding of the flagellum, you could make the same argument in your last sentence. "Show me nature forming this system." And eventually they did. This goes back to my previous point as well. This is merely a problem for evolution. NOT evidence for design.

As far as forming such a system, doesn't this happen every time an organism reproduces and grows? If you are asking for a cause at a molecular level, as far as I've read, it's still unknown, like many things in the field of biology.

I also agree with what others have said before. The citations you provide are not relevant. They do not come to the same conclusions you do. None of these papers address what our current discussion entails. One citation is discussion engineering of viable tissue and says nothing about ID in the sense you are promoting.

Ok let's review what I have been saying "The evidence is plainly showing that there is a system of spatiotemporal positional control functioning within all life" and I further state that "a system of spatiotemporal positional control is required for 3 dimensional replication" here is a sampling of
the evidence provide to back these statements;

http://genesdev.cshlp.org/content/24/11/1086.full

http://nar.oxfordjournals.org/content/e ... lowres.pdf

So in your opinion none of these references says anything like what i'm saying right?

No, because that is not what we are discussing. As I've said many times, I am not arguing these things don't happen/exist. I am arguing that you are jumping to a conclusion. Your first statement left out: "Therefore, biological intelligent design." THAT is what you are saying and is NOT mentioned in ANY of your reputable citations.

By definition a stone archway is "irreducibly complex."

Really? So you think a stone archway is the equivalent of a 3 dimensional spatiotemporal control system? Have you ever seen a stone archway replicate itself?

Behe's famous mouse trap example doesn't replicate itself. I was pointing out by definition the archway is irreducibly complex. If you take a stone away, it falls apart.

Behe's mouse trap arguement is not mine nor is the stone archway. These are your strawman arguments. How about you define where my arguments are wrong.

lol. Come on. You were the one citing the reference with the mouse trap analogy, as you said later to "define irreducible complexity." You could have just taken an excerpt from Behe's book and given a short definition instead of citing multiple articles that you claim have nothing to do with what you are arguing now.

Couldn't I use this same argument against your "evidence" for ID? Have you ever seen something built by humans that has 3 dimensional spatiotemporal control systems and was also able to replicate itself with slight modifications?

http://www.telegraph.co.uk/science/7745 ... g-god.html

Observable evidence - good

I don't see any mention of 3 dimensional spatiotemporal control. If I may point to the post directed to neo and ask you to expand on this? My point about the arch-way may have fell through, but this still says nothing about biological design. It's interesting evidence about human innovation for sure.

This may be relevant: http://www.ncbi.nlm.nih.gov/pubmed/21683595
CONCLUSIONS:
The genetic separability of spatial and temporal control modules in Caulobacter reflects their evolutionary history. DnaA is the central component of an ancient and phylogenetically widespread circuit that governs replication periodicity in Caulobacter and most other bacteria. By contrast, CtrA, which is found only in the asymmetrically dividing α-proteobacteria, was integrated later in evolution to enforce replicative asymmetry on daughter cells.

In what way is someones opinion of what may have happened relevant? Do you or they have any evidence from scientific method?

Here is the full publication: http://www.ncbi.nlm.nih.gov/pmc/article ... ool=pubmed

They define the background/observation, perform tests and published their conclusion. It doesn't appear to just be "their opinion" if it's supported by experimental testing. I have yet to see any of your research conclude biological design... In what way is your opinion relevant?

Now, if you are claiming that 97% of scientists who accept evolution are mistaken in their evaluation of this sort of evidence, we now have a testable claim!! Feel free to re-evaluate the methods used by evolutionary/molecular/geneticists and other scientists and prove them wrong.

ok... how many genetic markers do they use to ascertain relatedness?

Here is one from the Tree of Life project, using the 16S rDNA method:
http://tolweb.org/accessory/Trees_Based ... ?acc_id=54

Here's a few more publications using the exact same method:
http://www.ejarr.com/Volumes/Vol4/EJBS_4_01.pdf
http://www.ncbi.nlm.nih.gov/pubmed/9783450
http://www.ncbi.nlm.nih.gov/pubmed/10508537
http://www.ncbi.nlm.nih.gov/pubmed/9326623
http://www.sciencedirect.com/science/ar ... 3911800830
http://www.ncbi.nlm.nih.gov/pubmed/8401474

Shall I continue?

thus homology = relatedness. OR, homology =/= relatedness

Homology which describes the condition of being homologous or the similarity of position or structure is not defined by 16 separate genetic markers to provide a reasonable assumption of relatedness. Homology therefore is not the equivalent of a paternity test. It does not have the same logical or rational power that a paternity test gives based on 16 genetic markers.

The genetic markers are based on the differences in the DNA sequences. DNA is the bases of heredity and, I can't tell if you agree, the number of shared markers is a good measure of relatedness (accepted by courts of law and the scientific community).
There are a variety of ways to test for distinctive variations in DNA.

Yup there certainly are "ways to test for distinctive variations in DNA", Variations are one thing and relatedness is another. Now tell me how many genetic markers are used to define relatedness?

A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like (as I mentioned before) minisatellites.

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

There are many different methods. I just touched on the 16S rDNA method above, as you seem to like that one.

Comparing two people's genetic variations determines heredity. Biologists use the same process for classifying populations of organisms. This is known as phylogenetics, and wouldn't you know it, matches up perfectly with common characteristics, biogeography and the fossil record (among others, see pg 1). So, if two organisms have the same genetic variations/markers in the same location (#3 on your definition of homologous), I fail to see the false analogy there... Maybe I'm missing something?

Comparing two peoples genetic markers... 16 of them determines heredity.
Yup your missing something;

The problem posed by phylogenetics is that genetic data are only available for living taxa, and the fossil records (osteometric data) contains less data and more-ambiguous morphological characters.[6] A phylogenetic tree represents a hypothesis of the order in which evolutionary events are assumed to have occurred. http://en.wikipedia.org/wiki/Phylogenetics

I was addressing your claim that I made a false analogy. It appears there isn't one and you now move onto an issue with phylogenetics.

http://www.sciencemag.org/content/320/5875/499.short
Molecular Phylogenetics of Mastodon and Tyrannosaurus rex

Analyzed protein sequences extracted from Mastodon and Tyrannosaurus rex fossil fragments. As expected, when these sequences were compared with those of modern organisms, Mastodons were found to be most closely related to modern elephants, while T-rex was genetically similar to modern birds. This confirmed scientists' hypotheses that the taxa were evolutionarily related.

What do you know, a scientific hypothesis confirmed with experimentation. Scientific method you say?

In genetics, there are homologs and paralogs in gene structure. Either homology implies relatedness and paternity testing works, OR all that is wrong, in which case the experiment I provided earlier should be easy for you to conduct.

Homology is not a paternity test since it isn't based on 16 distinct genetic markers

The two are one and the same. As I cited above, it is based on the EXACT SAME METHOD.

[sandy_mcd]

The evidence is plainly showing that there is a system of spatiotemporal positional control functioning within all life.

No one is denying that. [And your citations show scientists have been aware of this for some time.]

You would like us to believe that evolution was functioning prior to life, prior to the existence of alleles? Prior to replication?

Evolution in the sense of competitive chemical reactions, a mixture of thermodynamic and kinetic products.

There is no ID research into the background of design. ID addresses none of these issues. Scientists would be researching these questions.

Intelligent Design as a Theory of Information

Your references are only to the detection of design, not any studies of the designer. The Antikythera mechanism is only interesting because of when it was designed. Without this background investigation, it would not be important. I posed several questions a scientist studying designers would be interested in. There seems to be absolutely no research in this area whatsoever. How was this design implemented?

As K has said, we can observe thousands of instances of intelligence accounting for 3-D spatial positioning.

Again, no one is denying that. But they are all just observations, there is no underlying explanatory theory. Organisms change naturally, but very slowly. Men can change organisms very quickly; note the number of different dog breeds. Nature without man works on a much slower time scale with fewer instruments. Without man's help, numerous species would not exist. That does not mean all or most of them could not have occurred naturally without man's assistance. The same is true for design.

God formed an irreducibly complex automated spatiotemporal control system into the physical design of life so that it may persist.

Assertion. How does this control system work? Does it change with time? What kind of evolution occurred? Do all life forms have the same system? How does it work? Enquiring minds want to know.

The law of gravity became Isaac Newton's best-known and most important discovery. Isaac warned against using it to view the universe as only some machine like a great clock. He said, "Gravity explains the motions of the planets, but it cannot explain who set the planets in motion. God governs all things and knows all that is or can be done."

Noting that the sun comes up at different times every day is just observation. Gravity explains why. The observation that men can design spatio-temporal control systems is just an observation. It does not explain all such systems.

[sandy_mcd]

I'm not arguing that the system isn't there. I'm arguing that you are jumping to a conclusion when we are still left with a mystery. Just as Behe had his flagellum. No one was arguing that the flagellum wasn't there, or that it didn't express machine-like characteristics. Even if we didn't know how the flagellum evolved, this would not be evidence for design. You are taking this structure that is not completely understood (an unsolved problem) and claiming it as evidence for design. If you have an unanswered question, you have an unanswered question. Not evidence. Once you and your colleagues have actually discovered evidence for design in this system, then you can claim it is designed. People building systems that are similar is not evidence for biological design.

And that in a nutshell, is the disagreement. Some feel that not seeing any such real time natural phenomena is all the proof needed.

[sandy_mcd]

And yes, "chemical evolution" is an accepted phrase, in which "evolution" does not have exactly the same definition as in "biological evolution".http://pubs.rsc.org/en/content/articleh ... c2cs35073d

Chemical evolution from simple inorganic compounds to chiral peptides 

Thomas A. E. Jakschitz and Bernd M. Rode

First published on the web 25th June 2012

Numerous experiments performed in the past 50 years have strongly changed ideas of how life could have emerged on the primitive Earth. This review deals with the synthesis of biomolecule precursors under the conditions prevailing on the primordial Earth, and describes possible scenarios for their combination and elongation to form peptides and proteins. Furthermore it proposes different answers to one of the big secrets of nature: why DNA-coded biohomochiral life emerged using amino acids in their L-form?

Primordial Earth scenario

The primordial Earth was formed about 4.6 billion years ago by accretion of material surrounding the sun. About 700 million years later, at the end of the heavy meteoritic bombardment the primarily very hot and molten Earth cooled down to temperatures around the boiling point of water. The presence of liquid water seems to be the most important condition for chemical evolution to have started and, therefore, the most basic precondition for life to develop on Earth. Enormous thunderstorms formed hot primordial oceans, lakes and lagoons with numerous salts and a variety of small organic compounds dissolved in them. The base for their formation were reactions of atmospheric gases with different energy inputs like UV irradiation or thermal energy in the form of volcanic heat and lightning. The atmospheric gases were mainly supplied by volcanic outgassing, thus containing carbon dioxide, nitrogen as well as traces of sulfur dioxide. Furthermore, small amounts of oxygen were formed by decomposition of water and carbon dioxide by UV irradiation and lightning.
Previous papers have already shown that in such a scenario RNA/DNA is not a suitable starting point due to the very limited stability in a primordial ocean and for information-theoretical reasons. On the other hand peptides have shown to be able to carry and transport information, to replicate from their constituents and to be stable under the harsh conditions of the primordial ocean.

[sandy_mcd]

The problem is when you say that evolution and ID make the exact same assertions. Here's why that is incorrect:

Evolution proposes that all species had a common ancestor. ID proposes life is only related by their designer. Huge difference.

The common ancestor concept can be falsified. There could be many totally chemically unrelated forms of life. The design concept cannot not be. What scenario can not be explained by design?

[Byblos]

I'm not arguing that the system isn't there. I'm arguing that you are jumping to a conclusion when we are still left with a mystery. Just as Behe had his flagellum. No one was arguing that the flagellum wasn't there, or that it didn't express machine-like characteristics. Even if we didn't know how the flagellum evolved, this would not be evidence for design. You are taking this structure that is not completely understood (an unsolved problem) and claiming it as evidence for design. If you have an unanswered question, you have an unanswered question. Not evidence. Once you and your colleagues have actually discovered evidence for design in this system, then you can claim it is designed. People building systems that are similar is not evidence for biological design.

And that in a nutshell, is the disagreement. Some feel that not seeing any such real time natural phenomena is all the proof needed.

Please show me a real time natural phenomenon (preferably backed up by scientific experiments) of a species transitioning into another (that could not also be explained by common design). THAT, in a nutshell, is where the real disagreement is.

[Pierson5]

I'm not arguing that the system isn't there. I'm arguing that you are jumping to a conclusion when we are still left with a mystery. Just as Behe had his flagellum. No one was arguing that the flagellum wasn't there, or that it didn't express machine-like characteristics. Even if we didn't know how the flagellum evolved, this would not be evidence for design. You are taking this structure that is not completely understood (an unsolved problem) and claiming it as evidence for design. If you have an unanswered question, you have an unanswered question. Not evidence. Once you and your colleagues have actually discovered evidence for design in this system, then you can claim it is designed. People building systems that are similar is not evidence for biological design.

And that in a nutshell, is the disagreement. Some feel that not seeing any such real time natural phenomena is all the proof needed.

Please show me a real time natural phenomenon (preferably backed up by scientific experiments) of a species transitioning into another (that could not also be explained by common design). THAT, in a nutshell, is where the real disagreement is.

You can refer back to my post regarding reptiles and birds if you want that. I also assume you accept paternity testing as a reliable method of determining relatedness. Go ahead and tell me what issue you have with using the exact same method on other living organisms.

Here is an brief/simple example of how the scientific method is used with regards to the ToE:
Observation: Fossil record apparently shows a transition from reptile like creatures to bird like creatures
Hypothesis: Evolution?
Prediction: If the ToE is true, DNA fingerprinting (like that used in paternity testing) will show modern reptiles and birds to be related
Experimentation/Test
Analysis/conclusion: Genetic evidence confirms prediction

Obviously it's a lot more complicated than this, but you get the idea. Scientific method at work. You can also tell me a prediction made by ID that has been confirmed. The ToE has tons.

Maybe you could be a little more specific about what you are asking. You want to see examples of speciation? You need to elaborate on "species transitioning into another." What do you expect to see exactly?

[KBCid]

The evidence is plainly showing that there is a system of spatiotemporal positional control functioning within all life.

I'm not arguing that the system isn't there. I'm arguing that you are jumping to a conclusion when we are still left with a mystery.

'we' aren't left with a mystery. I know precisely what it takes to systematically replicate 3 dimensional formations of matter. This system is irreducibly complex. 'IT' requires a control to form the system and chance alone does not logically explain it. Thus you are left with 2 choices either it arose by a chance occurance or it was designed since only ID has shown the ability to initiate such a complex form.

Just as Behe had his flagellum. No one was arguing that the flagellum wasn't there, or that it didn't express machine-like characteristics. Even if we didn't know how the flagellum evolved, this would not be evidence for design. You are taking this structure that is not completely understood (an unsolved problem) and claiming it as evidence for design. If you have an unanswered question, you have an unanswered question. Not evidence. Once you and your colleagues have actually discovered evidence for design in this system, then you can claim it is designed.

Behe wasn't arguing simply for the existence of the flagellum. What he was arguing for was that it was irreducibly complex and essentially beyond the possibiity of random chance to generate in small steps. his error was choosing a mechanical formation that is believed to have come into existence after evolution was already underway.
Evidence for historic occurance can only be derived from what is observable in the present. Only one cause has formed the types of systems that even come close to the systems in life.
Have you ever seen natural forces form such a system? Then by what evidence do you presume to infer that such a system is naturally forming?

People building systems that are similar is not evidence for biological design.

Wrong. People building systems that are similar learn what is minimally required for a system to provide a function. In this case it is the formation of matter into precise 3 dimensional arrangements and since the ONLY cause observed to have formed such systems is ID.

The citation you gave says NOTHING about ID in the regards of this discussion. Your whole argument is just a rehashed version of Paley's watchmaker argument. Just as Behe used the flagellum (motor), you are using the same argument with 3 dimensional spatial organization. Paley's argument is flawed, Behe's argument was flawed and yours is flawed for the same reasons.

Then you should have no serious problems defining how it is flawed just like all the others. Right?

Sure. For the sake of argument, let's say we have the same amount of knowledge of 3 dimensional spatial organization as we do the flagellum (so removing some information we know about the flagellum). I'll provide analogies through the rest of this post.

In your case you don't have the same knowledge of 3 dimensional spatial organization as I do and really what do you know about the formation of the flagellum? Since it is clear that it requires a system of spatiotemporal control to form the flagellum then the two systems are not the same. The flagellum is the result of programmed spatiotemporal controlled construction. Thus it is simpler than the system that allows it to form and simpler than the system I am pointing out to you.

Cutting edge research is exciting, I agree. The issue I have is with your conclusion. From the citations you have provided thus far, no one has come to the conclusion you are promoting (biological design). As I said above, I'm not arguing these systems don't exist. You are taking this cutting edge research and jumping to the conclusion about the origin of these systems when the answer is still inconclusive (again, going off your previous citations).

One does not have to provide citations to opinions that match their own. My references are there for the observable evidence being shown in their experiments. Most of them realize that a system exists but don't say anything about how inclusive it may be which is probably because they are not looking for the forest that the trees are a part of.
I am using logic and reason based on already understood scientific understanding of replication and showing that the same system is functioning within life. All you have to do is follow the logic to its rational conclusion.
Tell me what does it take minimally to systematically replicate a 3D formation of matter? remember... no replication, no evolution. If you don't know then you have no business arguing this thread with me as your counter POV would be an argument from ignorance.

You mentioned before you were working on a bioengineering degree. So I assume you have some sort of affiliation with the biology department, even if you aren't doing research in their particular field. Since your conclusion would have major ramifications in the field of biology, I guess I assumed you would have at least discussed this, researcher to researcher, with others in that field.

I have and as I said they are implementing the concept. Looking scientifically for evidences to back it. Let me tell you their POV in their own words "It is best to start by uncovering as much of the system as possible before stating the implications it will evoke." This system isn't just another flagellum concept. This system would be required before evolution could function. This has paradigm changing extent and since a system which is capable of replicating 3 dimensional formations of matter is exceedingly complex and irreducible then it will pretty much leave chance as a rediculous assumption for its origination.

The experimental evidence I'm looking for is biological evidence. Not mechanical engineering.

You can no longer separate biology from mechanical engineering since the formations of life works mechanically as well as chemically and electrically. Life is not as simple as you would like rationalise it.
The evidence I am bringing to the table with the cited references are showing how the system is an inherent part living systems and they know a system exists. Their major failure is that they have not ever had to form a replication system. This is where I have an advantage. I see the connections from the individual references and recognise that they are all part of one system. Soon they will have to make the same rationalization as they start to connect the dots.
So if you don't accept my references as evidence for an irreducibly complex system of control for spatial positioning then I invite you to define how chance makes it happen at every replication event.

If we use the same argument Behe had used with regards to the flagellum, it's not hard to see the similarities.

As I pointed out my argument is not the same as Behe's concerning the item constructed. My argument is the same as Behe's as concerns the irreducible complexity of a system. It's not hard to see the differences if you pay attention to what I'm writing.

The system requires a designer because the flagellum is irreducibly complex. We only have seen intelligent agents give rise to the type of design we see in the flagellum. As our understanding of the flagellum grew, however, this was shown to be false. You can test for these sort of things. For example, if the flagellum evolved, we should be able to see some sort of gradual transition.

Indeed if something was formed by evolutionary mechanism then you should be able to test for it and yet no such test has confirmed such a thing and Behe's rationale still stands. However, since my argument is not the same as Behe's then you have to deal with the specifics that I am pointing out if you hope to refute it.
Again my position is that
1) in order to have evolutionary function as you conceive it to be you must first have alleles and replication.
2) 3 dimensional formations of matter cannot be replicated without a defined system of spatiotemporal control
3) No replication, no evolution.
Unlike Behe's critics you cannot invoke the conceptual magic wand of evolution to bypass the forming of the minimal irreducible complexity of the system I am revealing. You are simply left with 2 choices... It occured by chance or it was designed. I would really like to see you try to formulate how it could have happened by chance.

This may be a bit lengthy, I'll try to sum it up the best I can. From the trial:

Your attempt to make Behe's argument the same as mine is a strawman argument. You are making a strawman by avoiding the plain understanding of differences that I have repeatedly pointed out.

And now, from my point of view, the key part of the argument, and I'll continue to read. An irreducibly complex system cannot be produced directly by slight, successive modifications of a pre-cursor system -- and that's how evolution would have to produce it -- because any pre-cursor to an irreducibly complex system that is missing a part is by definition non-functional.
So his argument is that, if you have a multi-part system, and all the parts are necessary to function, you can't produce that system five parts at a time, six, seven, and gradually build up the complex system, because there is no function possible until the last part is snapped into place. And that's why evolution cannot produce that system.

Mostly correct except that in this case you don't get to invoke the (pre-cursor system) conceptual magic wand of evolution since there is no evolution systematically functioning until there is replication. You sir are logically cut off at the pass with your strawman since 3 dimensional replication cannot proceed without the spatiotemporal control system, and evolution cannot begin until replication does.

They continue to have similar examples such as blood clotting and the immune system, which I don't think I need to go into. The point is, these ARE testable claims. I understand that you are on the cutting edge of the current research being done in this field. But, you are coming to a conclusion (biological design) before your research is complete. When you or your colleagues actually publish your research which concludes biological design, THEN you will have evidence for what you are promoting.
Another point. If you do end up showing this structure is, in fact, irreducibly complex, this is not evidence for design. It is merely a problem for evolution.

You are invited to provide rationale for how my irreducibly complex system came about by chance since 3 dimensional replication cannot proceed without the system, and evolution cannot begin until replication does.

Point 2 isn't true... the fact is 'You' don't understand it. I understand it quite well since the type of system you don't understand is what I make for a living and since these systems have only ever been observed as a result of ID I have every right to hypothesize that ID would be required for them to come into existence. What have you observed that forms such a system? really show me what kind of system like this you have personally observed nature forming?

We don't understand it 'completely.'

What don't 'we' understand completely?

There are still unsolved mysteries about this system, I think you'll agree.

The only thing not understood completely by anyone is the extent of the paths that the system works through.

That is what we are arguing about and is what I was referring to. Before we understood a lot of the intricate details of the flagellum, we still had a pretty good understanding of the flagellum itself. Before our further understanding of the flagellum, you could make the same argument in your last sentence. "Show me nature forming this system." And eventually they did. This goes back to my previous point as well. This is merely a problem for evolution. NOT evidence for design.

lol 'a problem for evolution'. yes it is... since 3 dimensional replication cannot proceed without the system, and evolution cannot begin until replication does.
How does one try and invoke a theoretical cause (evolution) that doesn't logically exist prior to the system necessary for the cause to function?

Ok let's review what I have been saying "The evidence is plainly showing that there is a system of spatiotemporal positional control functioning within all life" and I further state that "a system of spatiotemporal positional control is required for 3 dimensional replication" here is a sampling of the evidence provide to back these statements; http://genesdev.cshlp.org/content/24/11/1086.full
http://nar.oxfordjournals.org/content/e ... lowres.pdf
So in your opinion none of these references says anything like what i'm saying right?

No, because that is not what we are discussing. As I've said many times, I am not arguing these things don't happen/exist. I am arguing that you are jumping to a conclusion. Your first statement left out: "Therefore, biological intelligent design." THAT is what you are saying and is NOT mentioned in ANY of your reputable citations.

I am discussing an irreducibly complex system of spatiotemporal control which could not evolve since it's existence is required before evolution can proceed. The logical inference is that it must be designed since it is far beyond a chance ability to form such a complex interacting system. You of course are free to assert that chance could form such a system and then I will begin laying out all the necessary components of the system that would have to arise and interact "by chance".

Behe's mouse trap arguement is not mine nor is the stone archway. These are your strawman arguments. How about you define where my arguments are wrong.

lol. Come on. You were the one citing the reference with the mouse trap analogy, as you said later to "define irreducible complexity." You could have just taken an excerpt from Behe's book and given a short definition instead of citing multiple articles that you claim have nothing to do with what you are arguing now.

The references show how irreducible complexity is being applied. You are choosing to try and use the objects that it was applied to as a means to refute.

Couldn't I use this same argument against your "evidence" for ID? Have you ever seen something built by humans that has 3 dimensional spatiotemporal control systems and was also able to replicate itself with slight modifications?

http://www.telegraph.co.uk/science/7745 ... g-god.html Observable evidence - good

I don't see any mention of 3 dimensional spatiotemporal control.

The post mentions quite clearly "They manufactured a new chromosome from artificial DNA in a test tube, then transferred it into an empty cell and watched it multiply – the very definition of being alive."
How do you suppose it multiplies?
by chance maybe?

If I may point to the post directed to neo and ask you to expand on this? My point about the arch-way may have fell through, but this still says nothing about biological design. It's interesting evidence about human innovation for sure.

Expand on my entire post to Neo?

This may be relevant: CONCLUSIONS:
The genetic separability of spatial and temporal control modules in Caulobacter reflects their evolutionary history. DnaA is the central component of an ancient and phylogenetically widespread circuit that governs replication periodicity in Caulobacter and most other bacteria. By contrast, CtrA, which is found only in the asymmetrically dividing a-proteobacteria, was integrated later in evolution to enforce replicative asymmetry on daughter cells.

In what way is someones opinion of what may have happened relevant? Do you or they have any evidence from scientific method?

Here is the full publication: http://www.ncbi.nlm.nih.gov/pmc/article ... ool=pubmed
They define the background/observation, perform tests and published their conclusion. It doesn't appear to just be "their opinion" if it's supported by experimental testing. I have yet to see any of your research conclude biological design... In what way is your opinion relevant?

They gave an opinion on how a part of the system they see may have occured without having any understanding of how replication itself could begin. My proffesional opinion is relevant since it is based on evidence from existing designed replication systems. You have two options to explain it chance or design. I choose the most logical choice, Design, which is refutable by showing logically how chance could have done it.

Now, if you are claiming that 97% of scientists who accept evolution are mistaken in their evaluation of this sort of evidence, we now have a testable claim!! Feel free to re-evaluate the methods used by evolutionary/molecular/geneticists and other scientists and prove them wrong.

ok... how many genetic markers do they use to ascertain relatedness?

Here is one from the Tree of Life project, using the 16S rDNA method:
http://tolweb.org/accessory/Trees_Based ... ?acc_id=54 ... Shall I continue?

You should by all means continue since you have not shown how the 16S rDNA/ 16S rRNA method is the equivalent to a paternity test.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
How Close Is Close: 16S rRNA Sequence Identity May Not Be Sufficient To Guarantee Species Identity
Abstract
16S rRNA sequence comparisons were conducted with the following three psychrophilic strains: Bacillus globisporus W25T (T = type strain) and Bacillus psychrophilus W16AT, and W5. These strains exhibited more than 99.5% sequence identity and within experimental uncertainty could be regarded as identical. Their close taxonomic relationship was further documented by phenotypic similarities. In contrast, previously published DNA-DNA hybridization results have convincingly established that these strains do not belong to the same species if current standards are used. These results emphasize the important point that effective identity of 16S rRNA sequences is not necessarily a sufficient criterion to guarantee species identity. Thus, although 16S rRNA sequences can be used routinely to distinguish and establish relationships between genera and well-resolved species, very recently diverged species may not be recognizable.
http://ijsb.sgmjournals.org/content/42/1/166.full.pdf

Ribosomal RNA or protein sequences for phylogenetic inference?
Comparative analyses of rRNA sequences, initiated in the 1970s, suggest that the living world is divided into three domains:
Eucarya, Archaea (formerly archaebacteria), and Bacteria (formerly eubacteria).
...recent data using phylogenetic methods based on protein-coding genes have shown that classical methods of molecular phylogeny using rRNA genes may fail to delineate phylogenetic relationships between domains or between major lineages of these domains.
During the last five years, investigators have analysed an increasing number of protein sequences from Archaea, Bacteria and Eukarya, furnishing many more representative examples from each of the domains. At first, these new trees were expected to support the idea of amitochondriate Archaezoa to have preceded all mitochondriate eukaryotes. However, much of the new information does not support this idea. As data accumulate, a drastically different pictures emerges.
http://www.icp.ucl.ac.be/~opperd/private/tree_o_l.html

RNA Editing
The DNA sequence doesn't always translate into amino-acid sequence. The pre-mRNA may require alteration of its coding sequence before it can be translated into a funtional protein. This is called post-transcriptional editing. In post-transcriptional editing several different mechanisms are known. These are:
RNA editing in the Kinetoplastida.
This involved the insertion or deletion of one or more Us in the pre-mRNA, using guide RNAs as templates. This way non-coded initiation codons or amino acids are added or coded amino acids are removed during the editing process. This could lead to major differences between DNA and mature mRNA sequence. In some extreme cases (in Trypanosoma brucei sometimes more than 50% of a genes is edited. Such genes are called pan-edited genes). DNA and mature mRNA do not hibridise anymore to each other. Nevertheless this leads to roughly the same protein sequence after final editing. (Some details about editing in Trypanosomatidae can be found here or on the RNA editing site of Larry Simpson).
Post-transcriptional base modification in some gene products.
Examples of these are: Modification of rRNAs, Modification of tRNAs Modification of the apo-lipoprotein B mRNA creating an additional termination codon
Conclusion: Peptide sequences are not always identical to what is predicted by the corresponding genes!
http://www.icp.ucl.ac.be/~opperd/private/arguments.html

Comparison of biochemical and molecular methods for the identification of bacterial isolates associated with failed loggerhead sea turtle eggs
Abstract
Aims: Comparison of biochemical vs molecular methods for identification of microbial populations associated with failed loggerhead turtle eggs.
Methods and Results:
Two biochemical (API and Microgen) and one molecular methods (16s rRNA analysis) were compared in the areas of cost, identification, corroboration of data with other methods, ease of use, resources and software. The molecular method was costly and identified only 66% of the isolates tested compared with 74% for API. A 74% discrepancy in identifications occurred between API and 16s rRNA analysis. The two biochemical methods were comparable in cost, but Microgen was easier to use and yielded the lowest discrepancy among identifications (29%) when compared with both API 20 enteric (API 20E) and API 20 nonenteric (API 20NE) combined. A comparison of API 20E and API 20NE indicated an 83% discrepancy between the two methods. Conclusions: The Microgen identification system appears to be better suited than API or 16s rRNA analysis for identification of environmental isolates associated with failed loggerhead eggs.
http://cat.inist.fr/?aModele=afficheN&cpsidt=20291825

Guidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria
Abstract
This study is believed to be the first to provide guidelines for facilitating interpretation of results based on full and 527 bp 16S rRNA gene sequencing and MicroSeq databases used for identifying medically important aerobic Gram-positive bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 24 and 40% of medically important Gram-positive cocci (GPC), and 21 and 34% of medically important Gram-positive rods (GPR) confidently to the species level...
Since its first use three decades ago, 16S rRNA gene sequencing has become one of the indispensable pillars in the polyphasic approach to bacterial classification and novel bacteria discovery (Woo et al., 2008a). In the last decade, the technology has further developed beyond the research realm and matured into a clinical application for bacterial identification. Despite its increasing use in reference laboratories, one of the major limitations to its wider use is the difficulty associated with interpretation of 16S rRNA gene sequence results. The use of 16S rRNA gene sequencing for bacterial identification depends on a significant inter-species difference and a small intra-species difference in 16S rRNA gene sequences. Therefore, one of the major limitations is that when two different bacterial species share almost the same 16S rRNA gene sequence; this technique alone would not be useful for distinguishing them confidently.
For species identification, 16S rRNA gene sequence results of aerobic Gram-positive bacteria should be interpreted cautiously with basic phenotypic tests results, and additional biochemical tests or sequencing of additional gene loci are often required for definitive identification.
http://jmm.sgmjournals.org/content/58/8/1030.full

Shall I continue?

Yup there certainly are "ways to test for distinctive variations in DNA", Variations are one thing and relatedness is another. Now tell me how many genetic markers are used to define relatedness?

A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like (as I mentioned before) minisatellites.

How exactly does a genetic marker define an individual or specie? How do you know that 2 separate species which have a very similar marker in a similar place were not designed that way?

Comparing two peoples genetic markers... 16 of them determines heredity.
Yup your missing something; The problem posed by phylogenetics is that genetic data are only available for living taxa, and the fossil records (osteometric data) contains less data and more-ambiguous morphological characters.[6] A phylogenetic tree represents a hypothesis of the order in which evolutionary events are assumed to have occurred. http://en.wikipedia.org/wiki/Phylogenetics

I was addressing your claim that I made a false analogy. It appears there isn't one and you now move onto an issue with phylogenetics.

You have made a false analogy. I was just showing how limited the test actually is besides what I just posted above. You have yet to show how the 16S rRNA method is equivalent to a paternity test.

Analyzed protein sequences extracted from Mastodon and Tyrannosaurus rex fossil fragments. As expected, when these sequences were compared with those of modern organisms, Mastodons were found to be most closely related to modern elephants, while T-rex was genetically similar to modern birds. This confirmed scientists' hypotheses that the taxa were evolutionarily related.
What do you know, a scientific hypothesis confirmed with experimentation. Scientific method you say?

So how did the scientific method absolutely define relatedness? I think I'll refer you to a creationist site here as I tire of performing the research to keep knocking down your conceptual truths;
Dinosaur Protein Sequences and the Dino-to-Bird Model
by Jeffrey Tomkins, Ph.D.
Those sequences of high enough quality to be usable were then analyzed using dino-to-bird evolution as a filter.10 Interestingly, an external laboratory re-analyzed the data using a computational technique called Neighbor-Net analysis that was better suited to the type of data collected.8 Their results showed that the T. rex protein grouped more closely with amphibians and did not show a close relationship with either chicken or ostrich--two birds that evolutionists like Jack Horner claim actually have dinosaur genomes with just a few minor differences to make them birds.
http://www.icr.org/article/4949/

[sandy_mcd]

Please show me a real time natural phenomenon (preferably backed up by scientific experiments) of a species transitioning into another (that could not also be explained by common design). THAT, in a nutshell, is where the real disagreement is.

It can't be done. And the same reasoning can be applied, as pointed out often before, to plate tectonics, non-volcanic mountain formation, existence of atoms, stellar processes, sub-atomic particles, etc including much or most of what mainstream scientists have no trouble believing they have explanations for. Why single out species?
And again, as pointed out before, consider ring species, where space and not time is the variable:
Why is this not a credible counter-argument? [And/or, describe some scenario for which "that's the way the designer did it" isn't a potential explanation. I know this is considered flogging a dead horse, but to my knowledge there has never been any response. "That's the way the designer did it" adds nothing; any scientific explanation (if there is one) which reduces the description is preferable. ]

http://www.pbs.org/wgbh/evolution/libra ... 52_05.html

Ring Species: Salamanders:



Some critics of the theory of evolution argue that it doesn't convincingly explain the origin of new species. They say that members of one species couldn't become so different from other individuals through natural variation that they would become two separate non-interbreeding species.

One of the most powerful counters to that argument is the rare but fascinating phenomenon known as "ring species." This occurs when a single species becomes geographically distributed in a circular pattern over a large area. Immediately adjacent or neighboring populations of the species vary slightly but can interbreed. But at the extremes of the distribution -- the opposite ends of the pattern that link to form a circle -- natural variation has produced so much difference between the populations that they function as though they were two separate, non-interbreeding species.

In concept, this can be likened to a spiral-shaped parking garage. A driver notices only a gentle rise as he ascends the spiral, but after making one complete circle, he finds himself an entire floor above where he started.

A well-studied example of a ring species is the salamander Ensatina escholtzii of the Pacific Coast region of the United States. In Southern California, naturalists have found what look like two distinct species scrabbling across the ground. One is marked with strong, dark blotches in a cryptic pattern that camouflages it well. The other is more uniform and brighter, with bright yellow eyes, apparently in mimicry of the deadly poisonous western newt. These two populations coexist in some areas but do not interbreed -- and evidently cannot do so.

Moving up the state, the two populations are divided geographically, with the dark, cryptic form occupying the inland mountains and the conspicuous mimic living along the coast. Still farther to the north, in northern California and Oregon, the two populations merge, and only one form is found. In this area, it is clear that what looked like two separate species in the south are in fact a single species with several interbreeding subspecies, joined together in one continuous ring.

The evolutionary story that scientists have deciphered begins in the north, where the single form is found. This is probably the ancestral population. As it expanded south, the population became split by the San Joaquin Valley in central California, forming two different groups. In the Sierra Nevada the salamanders evolved their cryptic coloration. Along the coast they gradually became brighter and brighter.

The division was not absolute: some members of the sub-populations still find each other and interbreed to produce hybrids. The hybrids look healthy and vigorous, but they are neither well-camouflaged nor good mimics, so they are vulnerable to predators. They also seem to have difficulty finding mates, so the hybrids do not reproduce successfully. These two factors keep the two forms from merging, even though they can interbreed.

By the time the salamanders reached the southernmost part of California, the separation had caused the two groups to evolve enough differences that they had become reproductively isolated. In some areas the two populations coexist, closing the "ring," but do not interbreed. They are as distinct as though they were two separate species. Yet the entire complex of populations belongs to a single taxonomic species, Ensatina escholtzii.

Ring species, says biologist David Wake, who has studied Ensatina for more than 20 years, are a beautiful example of species formation in action. "All of the intermediate steps, normally missing, have been preserved, and that is what makes it so fascinating."

RickD, what are the odds of a substantive response this time around?

[KBCid]

lol another attempt to back the ToE with the ring species argument... you would think that this concept would have some traction buut, just as we see commonly happening with many of the evolutionary concepts, they hang around for awhile like the assertion that the herring gull is a ring species and then bam;

The herring gull complex is not a ring species
http://www.ncbi.nlm.nih.gov/pmc/article ... 255043.pdf

It all unravels as time and information progress.
Richard Lenski thought he had shown evolution in progress with E. coli until it was found out that a loss of information caused normal channels to break down and allowed an already existing processor of the food source to be open to the source. lol ergo, evolution is a loss of information.
So we have another allegation of evolution in action. Has anyone performed an empirical test to see if the alledged 2 ends of the ring cannot produce offspring?.