The Importance of Potentially Disconfirming Evidence

quote:

---

Really? Any specifics? Would it matter if the aforementioned organisms were related via Common Creator or due to a design or does it matter only if they shared a common ancestor?

---

This is a paper on current Multiple Sclerosis research:Chavanas S, Mechin MC, Takahara H, Kawada A, Nachat R, Serre G, Simon M. Comparative analysis of the mouse and human peptidylarginine deiminase gene clusters reveals highly conserved non-coding segments and a new human gene, PADI6. Gene. 2004 Apr 14;330:19-27.This research group is using equivalent genes in mice to try and find the root cause of MS. The reason we pick mice, and not reptiles or birds, is because we share a more recent common ancestory with mice. Also, I could point you in the direction of human-chimp-mouse pseudogene and gene comparisons that could lead to major breakthroughs in a host of genetic diseases. To say that common ancestory is not needed in medical research is like saying a wing isn't needed for flying.Also, evolutionary mechanisms are used to guide research in epidemiology and infectious diseases:Bredenbeek PJ, Snijder EJ, Noten FH, den Boon JA, Schaaper WM, Horzinek MC, Spaan WJ. The polymerase gene of corona- and toroviruses: evidence for an evolutionary relationship. Adv Exp Med Biol. 1990;276:307-16.Karlsson AC, Younger SR, Martin JN, Grossman Z, Sinclair E, Hunt PW, Hagos E, Nixon DF, Deeks SG. Immunologic and virologic evolution during periods of intermittent and persistent low-level viremia. AIDS. 2004 Apr 20;18(7):981-989.As you can see, evolution is a vital part of biological and medical research. You might want to look into what people are actually researching. A good place to start is http://www.pubmed.com (where I got the above citations BTW). Of course, we are moving quickly away from the topic. I am hoping these few examples out of many are enough to pique your curiosity about what scientists are actually studying and how they use common ancestory and evolutionary mechanisms to better our health and further our knowledge of the natural world.

quote:

---

Lets say a million testified against terror without qualification.

​

My wrath was and still is against the ones who justify Palestinian suicide bombings.

​

Why are these university elites given a free ride from the stain of Nazis and skinheads ?

---

Why are you giving Israeli's a free ride for indiscriminate bombings that kill civilians? Black kettle meet black pot.If you are lumping the "university elites" into one group, I could just as easily lump "christians" together with the Aryan Nation Church and proclaim that "christians" are racist, fascist pigs and that they to carry the stain of Nazism.

quote:

---

[Common ancestory between humans and mice] is an assertion. Just because we and mice have some similarity in our DNA doesn't equate to common ancestry. Common Creator is just as viable.

---

Common Creator is not viable, since a common creator doesn't include the same mistakes in different designs. It would be like a carmaker putting the same number of loose bolts under the floorboards of two different car models. ERV's and pseudogenes fit into the common ancestory theory. This theory could be falsified if the pattern of ERV and pseudogene mutations did not fit phylogenies constructed from the fossil record. The patterns do fit, and therefore the theory is viable. How do we potentially falsify the Common Creator theory? I have offered a potential falsification for common ancestory, it is only fair that you do the same for the theory you feel is also viable.

quote:

---

One thing you need to remember- there IS a huge difference between a change in allele frequency over time, mutations occurring and being passed on AND all of life's diversity owing its collective common ancestry to some unknown LUCA.

---

No difference, just a matter of degree. We can trace common ancestory by mutations, and differentiation in allele distributions. No amount of whining will change this fact.

quote:

---

If these alleged pseudogenes represent evidence for common ancestry than that notion should fall very soon. We are now finding that DNA sequences we thought did nothing actually do something. The ToE was started out of our ignorance and it appears has stayed strong for the same reason.

---

Some pseudogenes do have a function, but the origination of the gene is still very obvious. For instance, if the pseudogene for vitamin C synthase was found to have a function, its previous life as a broken gene is still very obvious. A pseudogene with function is much like a vestigial organ. As an analogy, if you used your computer keyboard to pound in a nail, would that make the keyboard a hammer? Of course not, and using the same logic, functional pseudogenes are still very important in tracing common ancestory. Common ancestory gains more evidence the closer we look at DNA sequences between extant and extinct organisms, it is far from falling.

quote:

---

First, how do you know they are mistakes seeing we haven't deciphered any genome? Second how do you know those alleged mistakes were included and aren't the result of mutations culled by selection?

---

First, how do you know that these pseudogenes and ERV's have function? The fact that most of these genes are not transcribed into mRNA should tell you something. The fact that these genes are not transcribed, but very similar sequences in other organisms do have function, it is easy to see where the pseudogenes and ERV's came from. Could a pseudogene come about by chance to resemble a functional gene in another organism? Given a 2,000 base pair sequence, this is very doubtful. Could ERV's be non-viral related. Given that the partial genome and long terminal repeats take up about 20,000 base pairs, no. Are pseudogenes and ERV's (both somatic and germ line ERV's) beneficial, harmful, or neutral? All three, hence they are described as random mutations (changes in genome sequence without regard to benefice or lack thereof). The only theory that is able to describe the presence of pseudogene and ERV patterns in different organisms is common descent and evolution. Since pseudogenes and ERV's can be a benefice, neutral, or harmful, maybe you could answer this multiple choice question:The Common Designer uses pseudogenes and ERV's to ____________:a) Cause disease.
b) Cause design.
c) Add useless junk DNA.Also, one ERV sequence has been found to be involved in mammalian placental development. This sequence and protein product are found in all mammals tested so far. ERV's are responsible for some functions, but the vast majority are not transcribed. ERV's can be culled by natural selection, and the mutations seen in these genes follows already established (by fossil record) lines of ancestory. ERV's could have falsified evolution, but they haven't. Instead, they support common ancestory and evolution.

quote:

---

Do we really know that the alleged ERVs are in all actuality ERVs?

---

Yes, since they share homology to known retroviruses, including env, pol, and gag genes, not to mention long terminal repeats found in almost all retroviruses known.

quote:

---

Just because somatic cells are infected it doesn't follow that the sex cells would be.

---

Why? Cells are cells, and DNA integration is not affected by a diploid or haploid DNA structure.

quote:

---

We can look at HIV. Does it infect the sex cells? No.

---

YES. You might actuall want to do some research. http://www.pubmed.com is a great place to start.

quote:

---

Yet when looked at we see the same % of difference in some molecules in bacteria and all other organisms. Cytochrome C comes to mind. Not exactly what the ToE would predict.

---

It is not the percentage difference, but the pattern of differences. Until you can understand the process of constructing genetic phylogenies, this discussion will be fruitless. As an analogy, think of a civilization that splits up. They share the same myths, but these myths will change overtime, with different changes being made in each separate culture. This process proceeds over many civilizations and creation of new civilizations. The ancestory of these myths (if there is a written record) can help us trace the ancestory of each civilization. Language can also help us trace the roots of each civilization (again, with a written record of the languages). The same can be said for DNA sequences. Immediately after a speciation event, the DNA sequences between the two new species is very similar. Over time, the two separate gene pools will accrue different mutations, but will still have sequences in common. It is the pattern of mutations, not mutations themselves, that allow us to trace common ancestory. The differences in cytC is exactly what the ToE predicts. Given that not every organism has been sequenced for cytC sequence, there is still the possibility that the ToE could be falsified. Finding the same cytC sequence in a fish and mammal would do just that. Maybe you should talk to your creation science friends and do a survey and prove the ToE wrong.

quote:

---

And if these alleged pseudogenes do NOT have a function then why were they kept and passed on?

---

Because they have no affect on the organism, other than creating more DNA bases. Pseudogenes are often used as molecular clocks to give us the mean mutation rate in certain taxa. This is because any mutations that occur in the pseudogenes are neutral. Why would a commmon creator include junk DNA that resembles functional DNA to such a high degree? Is it a joke of some kind? Or is God just deceptive, in that he set up pseudogenes and ERV to reflect how he planted the fossils in the ground?

quote:

---

John Paul:
And that shows us that ID can get around IC. Afterall it takes ID to make the computer, the program and the parameters.

---

This is a cop out. The mechanism, mutation and selection, happens whether it is in a computer or in an organisms DNA. If we create a computer model that shows how difference in air pressure and temperature cause hurricanes, does this mean that natural hurricanes are intelligently designed? Of course not. The computer simulation is merely a model constructed to reflect reality. The process of mutation and selection is capable of producing design. Period.

JP,I put your material out of order, hope it's not too confusing.

quote:

---

Do you know why Dobzhansky stated that "..prebiological natural selection is a contradiction in terms"?

---

I agree with Dobzhansky. Without life there is no natural selection. Without a language, the language can't change and split off into local dialects. Without a car, car design can't change over time. Without matter, the evolution of star formation can't proceed. The same contradiction can be seen in this phrase: "Star formation pre-Big Bang?" People have been telling you over and over, evolution only starts once there is an imperfect replicator. The theory that covers the formation of that first replicator is Abiogenesis, not evolution. Abiogenesis works by different mechanisms than does evolution, hence prebiological natural selection is a contradiction in terms.

quote:

---

Show me one place where that mechanism produced design from scratch.

---

Just as an organism starts with unmutated DNA, this circuit started out as a mass of transistors and other hardware. Through mutation and selection, it assembled itself into a radio receiver.News articles and features | New ScientistThe amazing thing is that they were trying to pressure the evolution of the circuit to produce an oscilloscope. What happened is that the evolved circuit tuned into the radio frequencies of a neighboring computer to output the needed oscillations. Even more stunning, the circuit wasn't even provided an antenna. Instead, the circuit used what it had available, a long piece of wire that was part of the circuit board. Again, design is produced via mutations (in this case, random connections between transistors and other paraphenalia) and selection (each connection that bettered the circuit was kept). Although it isn't mentioned in the article, how much do you want to bet that IC was created in this process?

quote:

---

The process doesn't require intelligence. The information to produce IC systems is programmed in at the beginning. That is what IDists such as Behe suggests.

---

So Behe should be able to predict future changes in morphology and function. Where are those predictions? Where is the evidence for front-loaded adaption and change? Dare I say "figment of Behe's imagination".Secondly, you have put forth the following falsification for ID: If life can be shown to rise from non-life, then ID is falsified. I really don't see how this falsifies ID. Firstly, we are limited to life as it appears on Earth. There might be intelligent life elsewhere that is constructed in a way that could quite plausibly arise from non-living matter. All they have to do is construct an imperfect replicator that isn't front-loaded in the manner that you and Behe contend. Therefore, life arises on Earth artificially, but evolves naturally without the input of an intelligent designer. This is all wild fancy, but it does leave a loophole that your falsification doesn't cover.

quote:

---

LM:
So Behe should be able to predict future changes in morphology and function.
John Paul:
I love conclusion jumpers. 99% they are wrong. Behe can't predict changes because evolutionists won't allow ID in the door. Until ID is allowed no one will decipher any genome. That is what would be required to predict changes. Right now all evolutionists can predict is change- why do we need a theory for that?

---

So, in other words, front-loaded instructions in DNA are an unsupported, empty assertion. Thanks for clearing that up.Also, evolutionists have found the MECHANISM behind the change. This is very useful, especially in searching for hereditary diseases by comparing genomes between species. It is also useful in studying ecological dynamics. What discoveries has ID lead to?

quote:

---

John Paul:
The issue here is that it had ALL of the components necessary at its disposal. That is the basic premise Behe is getting to. IF organisms had all the information and material handy then IC could come about.

---

And within the theory of evolution, all the material you need is a self-replicating organism. "Front-loading" is not necessary.

quote:

---

The circuit "survived" because of what? If they were trying to get an o'scope, what we allow it to survive until it got to that stage?

---

I misread the article a tad. They were actually trying to evolve an oscillator, not an oscilloscope. IOW, they were trying to evolve a circuit that would produce an electrical sine wave. The circuit layouts that were able to produce a signal that was closer to a sine wave were kept (beneficial mutations), and those that were poorer at producing a sine wave were thrown out (detrimental mutations). This would be the same thing seen in a predatory species, those that are better able to catch prey are kept in the population. It was not the design that the selection was choosing, but rather the outcome of the mutations. The funny thing about this experiment is that they circuit did just what the scientists wanted (output an oscillating signal) but the way in which the circuit did it (by reinventing the radio) was quite a shock.If design can be created by the process of change and selection in non-biological systems, why shouldn't it apply to biological systems as well. This is a counter-example to your assertion that all design is due to intelligence, since this radio/oscilator was designed by an algorithm based on evolutionary mechanisms and not direct manipulation of an intelligence.

quote:

---

LM:
If design can be created by the process of change and selection in non-biological systems, why shouldn't it apply to biological systems as well.

​

John Paul:
As I have already posted- the computer was designed by humans. The program was written by humans. The parameters were input by humans. And all the parts needed were granted to the program by humans. IOW there wasn't anything natural about the simulation.

---

Again, lets look at other computer simulations. As an analogy, lets look at tornadoes. The mechanisms behind tornado formation are understood, maybe not well but understood nonetheless. Now, someone wants to simulate tornado formation using a computer. They come up with a plausible model that takes into effect wind speeds, humidity, and air pressure. They set the simulation into motion and on the screen they see a tornado form. Now, are we to argue that tornadoes are intelligently designed? According to your argument, yes we should. It took human intelligence to simulate the tornado, and therefore tornadoes are a product of intelligent design.Of course, what you and Behe often miss is that genetic algorithms in computer science model reality, and the mechanisms found in reality. In the example of the evolved oscillating circuit, the system started out with zero information. By the end, it had both information and design. We could say the same thing about genetic systems. If we start with the simplest DNA sequence, a self-replicating molecule of DNA, and put this sequence under selective pressure we will also end up with an increase in information and design. It is the mechanisms of evolution, not the intelligence of man, that cause the ultimate changes in information and design. Man supplies the environment, in this case software, hardware, and selective pressure. The algorithm of evolution takes it from there. No front-loading is necessary. In fact, the circuit wasn't even supplied an antenna, but it created one on its own. The circuit wasn't even given instructions to make an antenna, but it did so anyway.Sorry, but the excuse of intelligence being input into the investigation of genetic algorithms is a cop-out. It fails to explain the ultimate power of the algorithm, whether within the confines of man-made technology or within the larger natural world. The only way to investigate ANY mechanism in the natural world is to apply our intelligence. If in doing so we strip the phenomena under investigation of it's natural state, then everything known to man would by definition have to be intelligently designed. This is a piss poor way to define what is natural and what isn't.

quote:

---

JM:
Others are able to see through the smoke screen and realize that ID/IC is just a backdoor for creationists.

​

John Paul:
Does lying and bullsh!t come easy for you Meert? It sure does flow freely in your posts.

---

JP, surely you know the intentions of the ID movement. It is not the pure pursuit of knowledge, but rather the overthrow of materialism. It doesn't matter if it is ID or YE creationism, just as long as religion gets its shot at inserting God into scientific investigation. From the Wedge Document: You may notice that they start with the presupposition that God MUST have a role. They only look for things that seem to support this presupposition, and ignore everything else. The fact that ID theory is untestable makes it even better, since it can't be falsified like YE creationism. ID isn't a movement that started with the evidence, but rather a movement that is looking for an excuse to exist. IC just seems to be the latest invocation of "God-did-it".Please tell me that you are not as naive as you sound. ID theory is the foothold that creationists have been looking for for about 30 years. Their ultimate plan is to introduce other creationist theories once ID is established in high school curicula. Denying this is indeed turning a blind eye.

quote:

---

LM: Again, lets look at other computer simulations. As an analogy, lets look at tornadoes.

​

John Paul:
Tornadoes don't fit the criteria for being designed. They may be specified but they are not complex and they do form regularly. IOW they would stop at the first block of the design explanatory filter.

---

Firstly, the explanatory filter has yet to find a function in describing design, even design in nature. Even its proponents have yet to show how it can be applied to biological or natural phenomena. Therefore, it is pretty useless at explaning anything.Secondly, my analogy was attempting to show that no matter how much intelligence is put into modelling nature, that doesn't mean that the phenomena being modelled has to be intelligently designed. Therefore, no matter the amount of intelligence that goes into genetic algorithms it still doesn't mean that biological genetic systems have to be intelligently designed, as you seem to be insinuating.

quote:

---

LM:
Of course, what you and Behe often miss is that genetic algorithms in computer science model reality, and the mechanisms found in reality.

​

John Paul:
Excuse me, the issue is they don't model reality. I can point you to the refutations to show you that they don't.

---

Could you point me in the right direction?

quote:

---

LM:
In the example of the evolved oscillating circuit, the system started out with zero information. By the end, it had both information and design.

​

John Paul:
That is NOT true. That program started out with plenty of information. It had plenty at its disposal too.

---

And biomolecules start with the information found within chemical reactions. DNA has specificity because of the specificity of chemical reactions. Carbon, oxygen, nitrogen, and phosphate don't randomly come together willy nilly, instead they follow the rules of chemical reaction. This is the information that Abiogenesis started with, and this is the information found within DNA as well. Compare atoms to transistors, and the evolution of the circuit will become clear (hopefully). So even abiogenesis had plenty of information available to it.

quote:

---

DNA, first wouldn't form outside of a cell and second wouldn't do much of anything outside of the cell.

---

So perhaps DNA wasn't part of the first replicator. There is catalytic RNA, as well as reactions between polypeptides and catalytic RNA. They react just find outside of the cell.

quote:

---

The circuit didn't create an antenna, the antenna was a by-product of the design. The algorithm had a goal- nature does not. That is all that is required to show that the simulation does not simulate nature.

---

Lets go over how the circuit evolved. The components were connected randomly. Each random set of connections was passed through a selection filter. The selection filter was for an oscillating signal. If the signal was closer to a true sine wave, then that set of connections was kept. The goal was for a circuit that created an oscillating signal ON ITS OWN. What happened instead was that the computer used a long stretch of wire as an antenna to recieve oscillating signals from near by computers. In other words, it became a parasite. This wasn't part of any of the scientists goal in evolving the circuit. The goal was an oscillating circuit.Lets compare this to bacteria. The selective pressure is for bacteria to move towards food sources. Each mutation either increases this ability or decreases this ability. Over time, the selective pressure creates the BacFlag. Just as the antenna above, the BacFlag is a consequence of the SELECTIVE PRESSURE, or the selective filter. The selective pressure is what I would call pseudo-goal oriented. As soon as there is movement towards that goal, it will change more and more towards that goal. Just as an analogy, you wouldn't call a falling rock "goal-oriented" just because it is affected by a physical force to fall towards the ground. Such is the force of selective pressure (in a figurative sense).What may help your case is to show changes in morphology or cell function in current times that could only be explained by a teleological goal oriented mutation. This mutation would have to be a consequence of your proposed "fron-loaded" instructions imbedded within DNA.

quote:

---

John Paul:
The EF process works fine with detecting design.

​

And . . .

​

LM:
Even its proponents have yet to show how it can be applied to biological or natural phenomena.

​

John Paul:
Why would biology be exempt from a design inference? Right now all you have is credulity that certain biological systems can evolve via purely natural processes.

---

This isn't meant to be rhetorical, but could you point me to a place where the EF has been able to detect design in biological structures/systems? And could you also show how the EF excludes evolutionary mechanisms as the design agent?

quote:

---

There isn't any laws of chemistry that would allow DNA to form in the first place. The bonds just won't happen in nature.

---

Then how do cells replicate? Also, RNA does form spontaneously given the right environment. RNA can have catalytic properties that could lead to RNA replication in early earth environments. DNA could be the product of RNA catalyzed reaction.

quote:

---

Comparing to bacteria- odd that after billions of generations of bacteria, bacteria remain bacteria.

---

Bacteria are the most successful organisms on Earth, why should they change. The only thing that drove multi-cellularity was the opening of new niches. The bacterial niche has and will always be available, and therefore there will always be a selective pressure for the presence of unicellular life. Just to give you an idea of how successful bacteria are, from the top of your head to the tip of your toes, bacteria outnumber your human cells about 1,000 to one. It is only your misrepresentation or misunderatanding of evolution and science that keep you from understanding the importance of unicellularity in an ecosystem and the niches open to bacteria.

JP,Let's take a step back and look at the whole picture. First of all, lets define "nature" so that we can agree on at least something. When is use the word "nature" I am referring to the things that can be touched, measured, or observed using the 5 senses. Things that can not be sensed witht the 5 senses, or through instrumentation that relates back tot he 5 senses, is by definition "supernatural" or beyond nature. Therefore, within nature new DNA is formed through the mechanisms of DNA replication in cells. It occurs through natural mechanisms, since we have been able to determine the enzymatic and chemical reactions that are required for DNA replication and elongation. I will agree that the first replicator is quite a different story, but nonetheless there are viable mechanisms for creating a self-replicator that does not involve manipulation by an intelligence. Whether or not these are plausible pathways should probably be discussed in a different thread on Abiogenesis.Secondly, anything that happens in a cell is the direct or indirect result of protein function (ignoring catalytic RNA for the moment). Protein function specificity is derived from the amino acid sequence, which is derived from DNA/RNA. Ignoring amino acid sequence for the moment, lets focus on DNA. It has been shown that mutations in DNA are random and you have yet to show how mutations are teleological in nature. The established fact is that mutations are random with respect to benefice, detriment, or neutrality.So, we have a system that results in mutations that directly affect protein function. This protein function then affects cellular morphology, cellular function, and cell to cell communication as well as extracellular reactions. Given a selective pressure, those mutations that offer a benefice to the carrier are spread through the population via differential reproduction. Do you agree with this so far? If not, this might be a good place to stop. But being the stubborn SOB I am, I will keep going.We now have a system that keeps beneficial mutations, and hence beneficial protein function, while detrimental mutations are pruned from the population. Given enough time, there is no limit to the number or specificity of different protein functions. Also, protein function can change within a system resulting in IC. Although I don't have direct evidence of this, but changing protein function over time has the innate ability to create just that. There is no reason why a protein should keep its present function over time. There is no reason why other proteins could be subtracted away from a system, and therefore masking prior relationships.In other words, changing protein function can result in IC systems. The cause of a change in protein function is due to a change (mutation) in the DNA sequence. All evolutionists have to do to evidence IC as a result of evolution is to show random, non-teleological, mutations. This has been done. To show that IC is a result of an intelligent designer, you must show how these mutations are non-random and teleological. Otherwise, your claim in the absence of these goal-oriented mutations is your incredulity about the ability of proteins to change function due to DNA mutation.

quote:

---

Actually it is our ignorance that determined the mutations are random. Someone not versed in computer code would think it jumps around randomly but when an educated person looks he sees that it is the loops, go to instructions and other pieces of code that are actually making those jumps.

---

Where are the go to's instructions in the DNA code?Take Rrhain's now infamous example of phage resistance in E. coli. If there are preprogrammed, front-loaded resistance "go to" instructions, then all of the clonal organisms should be resistant due to the same mutation. However, we find that only a random few contain the necessary mutations. If the DNA sequence was a pseudo-program, then they should all of the analogous "go to" command that creates the same mutation due to the same stimulus. It's simply not there.Just to get back to the topic, what would falsify the theory of front-loaded (ie go to commands) instructions in DNA?

quote:

---

Proteins come from DNA. Life requires proteins. Which came first the protein or the DNA?

---

You forgot catalytic RNA which has the properties of both protein and DNA.

quote:

---

No one can predict what is selected for at any point in time- Dan Dennett.

---

Believe it or not, I agree. However, selective pressures do cause differential spread of alleles. Sometimes the relationship between phenotype and selective pressure is easy to figure out (eg peppered moths) and others times it is less obvious. However, allele frequencies do shift (fact) in different environments.

quote:

---

Proteins change shape and they no longer function in the system, the system fails and the organism dies.

---

Not always true. Just among humans there are different types of hemoglobin, many different alleles in MHC class proteins, etc. There are so many examples of different protein configurations just among species as to totally negate your argument. One of the enzymes of interest that I work with can lose 30% of its amino acid sequence without losing any function whatsoever. Proteins are extremely flexible.

quote:

---

Proteins rely on a "hand/ glove" fit.

---

Yes they do, and which proteins fit together can change with a change in protein shape. This is an important aspect for creating protein cascades, such as found in blood clotting. If you want I can search for specific references on the protein function/binding changes as a result of mutation. I didn't feel like putting the work in unless you disagreed.

quote:

---

You can't change a protein without affecting something- in a negative way.

---

Absolutely false. Beneficial mutations are known.

quote:

---

LM:
All evolutionists have to do to evidence IC as a result of evolution is to show random, non-teleological, mutations. This has been done.

​

John Paul:
When and where? Not in biology that's for sure.

---

Well, in microbiology it has been done. From this website: In other words, mutations have been known to be random since 1943.Now, show me how they aren't random with respect to benefice, detriment, or neutrality.