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Author Topic:   Irreducible Complexity, Information Loss and Barry Hall's experiments
traderdrew
Member (Idle past 1628 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 90 of 136 (515353)
07-17-2009 12:15 PM
Reply to: Message 57 by DevilsAdvocate
07-14-2009 9:06 PM


Re: Irreducibly Complexity and a True Acid Test
Here is someone else who is attempting to play a game of deception by equivocating the information in my post.

If you look at the post that this post is responding to, you will see that I was mostly kidding. Aren't we all wasting time with attempting to equivocate each others points?

If you want to, you can take the historical account of junk DNA from the Devil's Advocate, an interesting avatar by the way, or you can take it from the Natural Standard below:

http://www.naturalstandard.com/index-abstract.asp?create-abstract=/monographs/genomics/genomic-junkdna.asp

Researchers originally called these sections of DNA "junk DNA" because they thought they served no functional purpose.

Better Yet

http://www.sciencedaily.com/releases/2009/05/090528203730.htm

Scientists used to believe that most of the DNA outside of genes, the so-called non-coding DNA, is useless trash that has sneaked into our genome and refuses to leave. One commonly known example of such 'junk DNA' are the so-called tandem repeats, short stretches of DNA that are repeated head-to-tail. "At first sight, it may seem unlikely that this stutter-DNA has any biological function," says Marcelo Vinces, one of the lead authors on the paper. "On the other hand, it seems hard to believe that nature would foster such a wasteful system."

Why would they think it is "junk"? Because the theory that says life emerged by unintelligent causes says that it there should be evidence that supports it. Hence, junk DNA is evidence for neo-Darwinism.

Edited by traderdrew, : No reason given.

Edited by traderdrew, : No reason given.


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traderdrew
Member (Idle past 1628 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 92 of 136 (515357)
07-17-2009 12:28 PM
Reply to: Message 79 by RAZD
07-15-2009 6:59 PM


Re: Sticking to the topic/s, and avoiding deceptions.
At least it would have not been done without simultaneous multiple coherent mutations and that would arguably be entering into the realm of metaphysical miracles.

I didn't write that correctly. I should have stated something like this:

At least it would have not been done without simultaneous multiple coherent mutations. If this occurred then the possibility of many IC systems, which would have required this, would arguably be entering into the realm of metaphysical miracles.

I am working on a final response in this thread.


This message is a reply to:
 Message 79 by RAZD, posted 07-15-2009 6:59 PM RAZD has responded

Replies to this message:
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traderdrew
Member (Idle past 1628 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 93 of 136 (515360)
07-17-2009 12:34 PM
Reply to: Message 91 by Rahvin
07-17-2009 12:23 PM


Re: Sticking to the topic/s, and avoiding deceptions.
That question wasn't a question that I was asking her. The question was a question in an attempt to clarify one of my points.

HIV isn't even cellular. It uses RNA instead of DNA, and it mutates at a rate that puts human cells to shame. If your definition of "sophistication" is "susceptibility to copying errors," HIV is one of teh most "sophisticated" things on the planet.

HIV mutates at a rate of about 10,000 times faster of multicellular lifeforms. It seems to me that the lack of the sophisticated error correction mechanisms (which is there in the cell) plays a part in the rapid mutations in the HIV virus. By the way, what has all of these rapid mutations done to the HIV virus anyway? Has it evolved into a new type of virus?


This message is a reply to:
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Replies to this message:
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traderdrew
Member (Idle past 1628 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 98 of 136 (515479)
07-18-2009 10:10 AM
Reply to: Message 94 by themasterdebator
07-17-2009 12:41 PM


Re: Sticking to the topic/s, and avoiding deceptions.
This is from my memory:

I also believe that some humans are naturally immune to the HIV virus. Has the virus found a way around this particular defense?

The virus also bonds to a particular type of protein. Has the virus found another type of protein to bond with?

Once again, the virus mutates at the evolutionary speed limit (10,000 times faster than we do) far faster than we can keep up with it.


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traderdrew
Member (Idle past 1628 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 99 of 136 (515482)
07-18-2009 10:29 AM
Reply to: Message 97 by RAZD
07-17-2009 9:08 PM


Re: what's special about IC?
Actually, it is relevant, because it appears that you do not fully understand evolutionary biology and have only a surface impression of it, yet you freely make assertions about scientists being wrong or "irrational" - something that can only be properly stated from a strong foundation in the science.

No it is not. What I post is relevant and not my education. Defeat my debate on substance, not who I am. I think Perdition knew he or she was cornered and Perdition tried to equivocate a way out of it. Think of it, how many people remember much of what they learned in biology class years ago?

Science itself is not irrational but I think that depends on how you define it. If science is defined by ONLY citing natural causations that you must analyze with methodological processes, then that definitely automatically disqualifies certain possibilities.

By the way despite one of your previous posts, irreducible complexity is a test for an unguided process of evolution not intelligent design. Nobody in their right mind says, "OK creator, you can't make an irreducibly complex system."

Mayr says that neutral mutations are not part of evolution because they are not subject to being selected - either for nor against. That means that their survival and spread within a population is due to purely stochastic processes, such as piggy-backing on a beneficial gene.

Thanks for being honest and citing something. Now can it build a flagellum?

If you or Perdition or anyone else can show me a peer reviewed science journal that realistically demonstates this with a step by step process, then I will leave this forum.

Common sense told me that a lot of scientists don't like what Michael Behe has to say. Obviously, some people around here don't like what I have written. Behe is a target.


This message is a reply to:
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Replies to this message:
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traderdrew
Member (Idle past 1628 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 100 of 136 (515485)
07-18-2009 10:37 AM
Reply to: Message 95 by Rahvin
07-17-2009 1:03 PM


Re: Sticking to the topic/s, and avoiding deceptions.
But you chose to ignore everything I said on that subject

Probably because I didn't disagree with it.

Your concept of the "goal" of evolution seems to be rather misguided. Forming a "new type" of virus is not necessarily the "goal." There is, in fact, no goal at all.

I'm wondering how you thought that I think that evolution has goals. In fact, this is my biggest issue I have with evolutionists. Why would I be here if the current prevailing paradigm says that there is no need for an intelligent designer?

I think the "dirty little secret" is that all the other theories that attempt to explain evolution leave at least a small gap for the possibility of a creator being involved.


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traderdrew
Member (Idle past 1628 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 102 of 136 (515666)
07-20-2009 12:35 PM
Reply to: Message 101 by RAZD
07-18-2009 2:40 PM


Re: issues and how to resolve them
Sorry, but the issue I have, is that you have criticized scientists from an apparently weak knowledge basis -- if your schooling and accumulated knowledge in the field IS weak then you have no basis for criticism.

Do you claim to be a scientist? I have the impression that you are a student. It wouldn't be the first time that I have pissed off a scientist.

It is when you criticize others that you need to show your credentials. Of course you could instead follow your own advice, and attack the evidence and the argument, rather than attack the scientists, especially with silly blanket statements that are inane to begin with.

I have not attacked scientists on this forum to my knowledge. I believe that many Darwinists are irrational but that doesn't mean that scientists are. Everyone is irrational including ME. Some are just more rational than most of the others.

So if you agree to follow your own advice, and refrain from criticizing others, I will allow you to refrain from exposing your (weak) knowledge of evolution.

Feel free to point out the flaws in my knowledge on this forum. This way I can correct my thinking. Do you see that I am not trying to be totally dogmatic here? I think Darwinists (not all scientists) can get dogmatic.

I believe that Darwinism has transcended into metaphysical implications inside the minds of certain amount of Darwinists. I think Daniel Dennett was partly correct that Darwinism is a "universal acid". I think that "Darwinian Dogma" is the universal acid.

Ah, so you agree that it is not an argument for ID. Excellent. Now all you need to do is admit that IC systems arise all the time by natural processes, and we can agree that there is essentially no point to IC.

IC is not a test for ID. IC is an argument for ID. This isn't rocket science.

The TTSS Pilus Model

I never heard of that argument before. I have learned many things from Stephen Meyer and one of those things is that models like those typically conceal a host of problems and/or questions. I just researched it and I see that William Dembski refuted it.

Also, I saw a BIG problem with it.

Science has become sophisticated enough to provide a body of evidence that shows the flagellum was precursor for the TTSS. This means that the TTSS devolved from the flagellum. Sean Pitman provides the information. I also saw a reference of some documented evidence of it somewhere in "Signature in the Cell".

During cross-examination Behe even stated that the definition of 'theory' as he applied it to intelligent design was so loose that astrology would qualify as a theory by definition as well.[43]

Behe is a biochemist. I never had the impression that is a philosopher of science. What is to stop science from investigating astrology? Maybe the gravitational and electromagnetic forces of the moon and the sun could affect something inside of ourselves???

Also while under oath, Behe admitted that his simulation modelling of evolution with Snoke had in fact shown that complex biochemical systems requiring multiple interacting parts for the system to function and requiring multiple, consecutive and unpreserved mutations to be fixed in a population could evolve within 20,000 years, even if the parameters of the simulation were rigged to make that outcome as unlikely as possible.

OK,... You just MIGHT have gotton me on that one. I am still not sure what that statement means. I believe that a flagellum can evolve. I believe Smoke coauthored a paper with Behe. I will have to research on this sometime. Do you see now that I am not totally dogmatic with this?

In addition to failing to produce papers in peer-reviewed journals, ID also features no scientific research or testing.

Ever heard of the lab called Biologic???

Edited by traderdrew, : No reason given.

Edited by traderdrew, : Minor corrections


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Replies to this message:
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traderdrew
Member (Idle past 1628 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 104 of 136 (515671)
07-20-2009 1:15 PM
Reply to: Message 103 by Theodoric
07-20-2009 1:09 PM


Biologic
Biologic is a laboratory at the Discovery Institute. News media reporters once demanded to see the laboratory as though (pointed out by Stephen Meyer) doing experiments was the only kind of activity that scientists pursue.
This message is a reply to:
 Message 103 by Theodoric, posted 07-20-2009 1:09 PM Theodoric has responded

Replies to this message:
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traderdrew
Member (Idle past 1628 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 105 of 136 (515672)
07-20-2009 1:20 PM


Evolving an Irreducibly Complex System
I don’t understand the perspective that an irreducibly complex system can’t evolve through minor mutations. This perspective probably comes from the idea that if God made an IC system, it is therefore sufficient in function and has no need for any other mutations or finishing touches. Logically, biological IC systems are subject to the same forces that proteins are. What is stated is an IC system can’t evolve through a step by step process of natural selection acting on random mutations.

The intelligent design perspective is different than that of a Creationist. A proponent of ID has the room to contemplate the possibilities. In fact, a system that can make necessary mutations in adaptation or response to environmental factors is further testament to a creator. It would add to what is already irreducibly complex.

A Hypothetical Story

Certain species of bacteria use flagellum for locomotion as they propel themselves through liquids such as water or liquids primarily of water. Consider it if the flagellum would be forced into a new habitat of liquid of higher tension such as oil. Let’s say that the flagellum wouldn’t be able to function very well in this particular oil. But scientists are able to tinker with the struggling flagellum. They induce the right mutations which make the flagellum evolve a stronger rod and a larger heavy duty filament (propeller). But still the colonies of bacteria don’t quite have the torque to propel themselves through the oil. What do the bacteria do?

They call upon their natural genetic engineering and resurrect something their ancestors used over 2 billion years ago. A stronger motor evolved in response to the other factors. Scientists quickly realized why they didn’t have a stronger motor to begin with since it would have to utilize more energy. (The same is the case with automobiles. More powerful motors use more fuel.) So the previous motor, which as sufficient for movement through water, didn’t use as much power.

Wait,.. there was something that wasn’t mentioned in the experiment. At first, the bacteria had problems finding food in the oil. The scientists had to thoroughly mix a solution of organic food called “LPGT” in the oil in order for the bacterial colonies to survive.

It is true that this was just a story but it gives the reader somewhat of idea of how a flagellum could evolve.

Back in the real world, there are different variations of the flagellum. Some have extra parts such as extra rings for example. But the mutated flagellum is still a flagellum.

Inside the book “The Edge of Evolution” describes another IC system discovered fairly recently. It is called a “gene regulatory network” or “kernel”. Kernels specify the embryonic development of body plans. To me, their schematic drawings look like a complex electrical schematic of a circuit board. Unlike the five or six part system of the E.coli above, any interference of this network will destroy the overall function.


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traderdrew
Member (Idle past 1628 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 108 of 136 (515678)
07-20-2009 1:30 PM


Back to the True Acid Test
This thread started with a post by RAZD. I think that I offered at least one solid counter argument to it above and that was the system was irreducibly complex to being with but RAZD and I continue to agree to disagree. I don't expect anything to change.

An operon consists of several genes which are transcribed together. It turns out that E. coli has many operons and the lac operon is just one of them. (See link below)

http://www.cib.nig.ac.jp/dda/taitoh/ecoli.operon.html

So what did E. coli do in response to the deletion? It took a part from the ebg operon that was homogenous to the lacZ gene.

This experiment was beginning to painting a picture that E. coli could evolve an irreducibly complex system through natural selection acting on random mutations. There is a problem I have with the random mutation thinking as applied or derived from this experiment. If this experiment can be conducted over and over again with the same results occurring every time, then where were the random mutations? The 1st time says it helps support the current paradigm. The 2nd casts a shadow of a doubt so it was a coincidence. The 3rd time says, “What is going on here?” By the 5th time I would say that the mutations were not random.

However, it wasn’t until years later when Hall made some conclusions that didn’t support that hypothesis. It resurrected genes from over 2 billion years ago to fill in for the one that was removed. I

A comparison of Ebg beta-galactosidase with those 13 beta-galactosidases shows that Ebg is part of an ancient clade that diverged from the paralogous lacZ beta-galactosidase over 2 billion years ago. (Hall, 1998)

The new system did not evolve the ability to bring lactose into the cell. The lac-permease (in the lac operon) already does this. However, the E. coli were on life support due to the artificial drug called IPTG. The results can’t be reproduced without IPTG.

IPTG cannot be broken down by the enzyme that degrades lactose. Consequently IPTG continues to induce the lac operon over the long term, whereas natural inducers would only induce the genes of the lac operon for a short period of time before they are broken down.

This doesn’t really answer the question that the IPTG was really necessary but I can assume that it was if it is used against irreducible complexity. Why not attempt to form a more convincing argument for Darwinism by taking the IPTG out of the experiment?

Instead of this experiment supporting the mechanisms for neo-Darwinism, I really think this supports is natural selection acting on NGE (natural genetic engineering), with the help of IPTG of course. The cell obviously had the ability to find replacement parts and engineer them into a useful system. (NGE is the result of years of research done by James Shapiro.)

This is what I recently realized when I studied this experiment.

What E. coli did was use “adaptive mutations” in order to respond to the immediate environment.

It is one thing to reengineer and existing system by removing a single part of a five or six part system 1. Find familiar genetic substitutes 2. Force IPTG into it in order to keep it alive. 3. Give E. coli a challenge so it had a particular aim or foresight – (Not Darwinian).

It is something else for a bacteria (without an irreducibly complex system such as a flagellum) to have the foresight and know how (master control genes in collaboration with body part genes) in order to build an irreducibly complex system from scratch from so-called junk DNA.

Why wouldn't an intelligent designer program life with the genetic versatility to make necessary changes???

Not only that, Barry Hall stated that this system in E. coli had limited evolutionary potential years later. Let’s look at what Barry Hall stated years later after this experiment.

In a trivial sense, each genome’s potential is infinite, because given enough additions, deletions, rearrangements, and base substitutions, any sequence can evolve into any other sequence. In reality, however, evolution is subject to a variety of constraints that limit this potential, and understanding evolutionary processes amounts to understanding those constraints. (Hall, 1998)

Evolutionary biologists are usually forced to infer historical evolutionary processes by examining the present day outcomes of those processes. That is an unsatisfactory means of understanding a dynamic process, partly because neither the historical selective constraints nor the detailed molecular functions of ancestral states are well understood. (Hall,1998)

Just from those two statements, I can say that you either have “faith” that this experiment proves macroevolution through a neo-Darwinian process or you have “faith” that it can’t.

Because multiple mutations require that the organism traverse one or more intermediate steps, evolutionary potential is limited by the fitness associated with those intermediate steps. For some possible protein changes, it may well be the case that ‘‘you can’t get there from here’’ because the intervening single-step mutations are too deleterious. (Hall,1998)

“Too deleterious” was in reference to the E. coli experiment. Obviously Hall doesn’t seem to be very optimistic that the E. coli can evolve any further.

The experiment demonstrates that the E. coli system had certain flexibility but that flexibility only allowed the E. coli to evolve before it was faced with barriers.

Do you want to believe the words of the one who ran the experiment or, do you want to believe the words of the Darwinists around here?

Conclusions

This experiment does not disprove microevolution. However, this experiment does not falsify intelligent design.

It also seems to support another one of Michael Behe’s statements that says evolution isn’t an arms race; it is more like trench warfare.

Edited by traderdrew, : Title

Edited by traderdrew, : Minor HTML corrections

Edited by traderdrew, : Just more "intelligently designed complex specified information"


Replies to this message:
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traderdrew
Member (Idle past 1628 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 109 of 136 (515680)
07-20-2009 1:41 PM
Reply to: Message 107 by Theodoric
07-20-2009 1:27 PM


Re: Biologic
That is what you are here for. There is so much information out there that it is hard for me to keep up with it. I'm spending enough time with this forum. I read part of your link. Care to start a thread about Robert Pennock's work?
This message is a reply to:
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traderdrew
Member (Idle past 1628 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 111 of 136 (515694)
07-20-2009 3:30 PM
Reply to: Message 110 by NosyNed
07-20-2009 2:09 PM


Re: The topic is IC
If I roll a pair of dice and they come up 11, roll again and they come up 3, again and they come up 6 are they random?

If I roll 11, 3 and 11 are they random?

No but I don't think it would disprove that the dice were rigged.

You are forgetting that there are billions of "rolls" involved in the case of the bacteria. Many do not produce a "win". The fact that one "number" comes up a 2nd or 3rd or 5th time doesn't show they are not random.

This is true. But are you insinuating that the mutations were random? If so, why?

Why not show that mice can not evolve by taking oxygen out of the experiment? This is as silly as your first argument.

I don't think so.

If you think that intelligent design is falsified if the idea that IC can't evolve is wrong then ID is, indeed, falsified. I don't know how you make that connection though. It is also a topic for another thread.

You are entitled to your point of view and so we agree to disagree on some things. I wonder if you can elaborate on your belief. I already made that connection and explained it in the form of one large post today that I'm sure you read.

Edited by traderdrew, : No reason given.

Edited by traderdrew, : No reason given.


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