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Author Topic:   Evolving New Information
traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 128 of 458 (519107)
08-11-2009 11:12 AM
Reply to: Message 1 by Percy
05-01-2009 8:57 AM


Condons
(As a proponent of ID I want you to know that I am not attempting to start a fight. At least I have not been provoked here yet. I am asking questions and exposing my ignorance on genetics.)

GGAACG (green eyes)

GGAACA (blue eyes)

GGCACG (yellow eyes)

GGCACA (brown eyes)

All of the above appear to be variation of two amino acids correct?

GGA or GGC - glycine
ACG or ACA - threonine

I wonder what would happen if some of those amino acids had mutations that changed into any of the other 18 new amino acids???

Am I right in thinking that mutations at the beginning of each condon would more likely result in larger mutations? Or would the eyes start to lose some particular functions?

For example: ACG becoming UCG instead of ACG becoming AAG


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 131 of 458 (519117)
08-11-2009 12:43 PM
Reply to: Message 130 by Theodoric
08-11-2009 12:32 PM


Re: Codon!!!!!! not Condom?
I didn't quite use that word. But I suppose some of you have guessed what was on my mind.

codon, codon, codon, codon, codon, codon, codon, codon, codon, codon...

Some of you get me on technicalities but can any of you answer my questions in my post or really refute many of my main arguments in others?


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 138 of 458 (519213)
08-12-2009 11:54 AM
Reply to: Message 132 by Theodoric
08-11-2009 12:53 PM


Re: Off Topic Theodoric
Many times. As a matter of fact, you have pulled out of a few threads when things were not going your way.

I will state this one time here because it is off topic. There have been many times when I just stopped the debate when it turns in to an argument. I really think it starts to become childish when people carry on with arguments on these threads. Other times I pull out when the person who is debating me is/or employing the use of various types of equivocations, strawman agruments, off topic, or just doesn't get my point for whatever reason. Sometimes I hold off hammering my points because part of me doesn't want to disturb some of you. Also, just because I don't answer doesn't necessarily mean that I am stuck. I know about five ID websites where I go for researching some of topics on posts around here.

Go back through the threads. I know I am looking for a response on at least a couple.

OK I will go back to the Expelled forum to see what you said. What do you think of my post #390?


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 139 of 458 (519221)
08-12-2009 12:34 PM
Reply to: Message 134 by pandion
08-11-2009 6:30 PM


Re: Codons
Don't know what you are asking. ACG encodes threonine, UCG encodes serine, and AAG encodes lysine. The changes may or may not change the function of the protein.

You partly answered it here:

A point mutation of one of the bases in either the first or second position, and only sometimes in the third position will produce a different amino acid in the protein sequence.

For example: ACG becoming UCG instead of ACG becoming AAG

The ACG becoming UGC was a change in the first postition and ACG becoming AAG was change in the second position. It seemed to me the differences in eye color were from variations in the first positions. But as you stated, it is more complicated than that.

Thank You

Edited by traderdrew, : No reason given.


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 175 of 458 (520850)
08-24-2009 1:31 PM
Reply to: Message 171 by Arphy
08-24-2009 4:24 AM


Re: What is information?
Sorry this doesn't solve the problem. You still have the problem that the kids are using a language that already exists. Yes, you might get a more spectacular sentence but this doesn't mean that you've created anything new, you are still limited to the vocab the kids posess in the first place. One kid might add some gibberish but this doesn't help the message as none of the kids will be able to understand what it means. It just makes things more confusing and distorts the message. It becomes useless (yes, it may serve for some amusement, but generally I'd say most cells in an organism don't tend to make up gibberish to entertain their neighbouring cells)

I'm glad to read a post from someone who can see. The information inside DNA must be specified with little margin for error. If it isn't specified, then why does transcription even take place? If it isn't specified, then genetic information viruses inject into cells wouldn't be effective.

It is amazing how random mutations supposably get it right with specific information at specific places within the genome. So far I remain unconvinced that the genome rolls dice. If it is random, then there should be a lot of trial and errors in the genome but I don't think it is random. I think it is for the most part due to natural genetic engineering.

This is a challenge to Darwinian evolution and especially the spontaneous forming of specified information in any origin of life model.

The genome also uses dual overlapping coding.

As W.Y. Chung, a bioinformatician at the Center for Comparative Genomics and Bioinformatics at Penn State University, has noted, the existence of "dual coding" and overlapping protein-coding reading frames, just one of many cellular innovations for concentrating genomic information, is "virtually impossible by chance." - Signature in the Cell

use [qs] to quote someone at the start. At the end of the quote add a / at the second position in the [qs].

Edited by traderdrew, : No reason given.

Edited by traderdrew, : No reason given.


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 178 of 458 (520861)
08-24-2009 2:47 PM
Reply to: Message 176 by Perdition
08-24-2009 2:12 PM


Re: What is information?
Down's Syndrome, genetic deformations, Sickle Cell anemia, the sheer number of pregnancies that don't even make it to term

That is a fairly good counterpoint. However, some of those problems are rather rare and of course the sickle cell is something that protects against a specific serious disease. I'm not saying the sickle cell was designed. I'm saying it is probably the result of blind natural Darwinian evolution.

And how do some of these accidental mutations arise in the first place? Could they be the result of toxins or the problem with defenses stemming from insignifigant nutrition?

You are probably not seeing this the way I am seeing this. Look at a amino acid code table. In order to acheive a specific effect that is beneficial to the organism, you must have specific changes at specific places within long strings of codes. How many generations does it take a self replicating cell to acheive this with a few random mutations? Can't random mutations occur anywhere in the genome?

We learned that Darwinian conjecture doesn't always explain things. Rather it seems to mislead us or even delude us. (See message #390 in the Expelled thread in links & information.) Darwinian conjecture is a way of thinking but it doesn't seem to represent reality very well. At least it doesn't seem to do it for me.

I also sometimes get the impression there exists confusion of ID with Creationist thought. The science behind ID doesn't tell us what the intentions of the designer were. If the Japanese won WWII, we probably would have been worshiping the God of the Rising Sun.

Edited by traderdrew, : No reason given.

Edited by traderdrew, : No reason given.


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 180 of 458 (520866)
08-24-2009 4:05 PM
Reply to: Message 179 by PaulK
08-24-2009 3:25 PM


Re: What is information?
Your problem here is that you are thinking in terms of how a designer would do it. A designer might look for a specific change, but evolution doesn't. Thinking in this way leads to the "hindsight" problem I referred to in the probability thread.

I'm not saying that a designer inserted/subsituted/deleted the mutations in many cases. Take the example of the nylonase enzyme example, the frameshift that resulted in the new enzyme didn't result in any stop codons along the way. In other words, the frameshift didn't inhibit the system from creating a new enzyme. This suggests the codon sequences were predesigned or evolved from Darwinian processes for new functions. (Two competing ways of looking at it.)

A better question is what is the probability of hitting on a beneficial mutation.

I agree. If you could prove that it can only be done (not, can it be done?) with Darwinian processes and not (NGE) natural genetic engineering, then it would shut me up.

If you accept that Wounded King's suggestion is correct, then it would mean that a layman using "Darwinian conjecture" got closer to the truth than the ID "experts". That isn't bad going.

I don't remember that being the case. It is a matter of perspective I guess.

That isn't even possible. All the major creationist positions are accepted parts of ID. Including Young Earth Creationism. Creationist thought IS ID.

Once again, that is a matter of perspective and you're entitled to it. I believe in evolution. I just don't believe a totally blind process is behind it.


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 202 of 458 (521001)
08-25-2009 10:02 AM
Reply to: Message 189 by Dr Adequate
08-25-2009 12:32 AM


Re: What is information?
That ol' burden of proof is getting a bit heavy for you, isn't it?

Not at all. I'm just simply drew another line to see if anyone could cross it. There should be a way to prove if certain mutations are random or if James Shapiro's natural genetic engineering can do the trick. If you repeat the same experiment in the lab over and over again and look at the results, it should be able to support it either way. Here is a quote from Shapiro's website:

Examining the fate of Mudlac DNA in sectored colonies
showed that these same functions are subject to developmental control, like controlling elements in maize. All these experiences confirmed McClintock’s view that cells frequently respond to stimuli by restructuring their genomes and provided novel insights into the natural genetic engineering processes involved in evolution.

Another reason why I stop the debate is that it just goes on and on. If I don't stop then someone else will come along. Also, debate such as, "Your view is just religion." doesn't render my debate as false or irrelevant. Everyone has an agenda but the only agendas of irreducibly complex structures and CSI in DNA are the specific functions these things perform. These things are just there and they have no religious agendas.


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 218 of 458 (521204)
08-26-2009 1:12 PM
Reply to: Message 214 by Wounded King
08-26-2009 6:44 AM


Re: What is information?
I'm not trying to start another round of debate. I am attempting to learn through comments and inquiry with this post.

Aoccdrnig to rscheearch at Cmabrigde uinervtisy, it deosn’t mttaer waht oredr the ltteers in a wrod are, the olny iprmoetnt tihng is taht the frist and lsat ltteres are at the rghit pclae. The rset can be a tatol mses and you can sitll raed it wouthit a porbelm. Tihs is bcuseae we do not raed ervey lteter by it slef but the wrod as a wlohe.

Wounded King: Clearly this is technically nonsense but I very much doubt that you can't understand what it says.

We can understand the above because I think we know the English language enough to be able to discern the meanings. It is sort of a pattern recognition ability that we have.

So the question becomes, does the machinery in the cell have pattern recognition abilities in spite of serious misplacements and errors? If it does, it would seem to me it would have limited utility. I think that because I am considering the genetic information injected by viruses.

When for the most part we have no ideas what the allowable margins for error are because we don't know what the functional effects of most possible mutations on a protein/sequence would be.

I don't understand that because mutations within RNA could be transcribed in different ways depending on where they fall. It seems to me the mutations in the first or second positions of each codon can have larger effects than mutations at the third position of a codon. Of course this understanding hinges on pattern recognition and an a possible ID answer for it.

I may never understand the complex machinery in the cell. Stephen Meyer has made references to its incredible machinery. I just heard one of his interviews he did with George Noory on You Tube.

Edited by traderdrew, : No reason given.


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 228 of 458 (521404)
08-27-2009 11:28 AM
Reply to: Message 225 by greyseal
08-27-2009 6:41 AM


Re: What is information?
And just because you don't understand it, doesn't mean somebody else doesn't. Saying "godidit" because you don't understand it, doesn't make it so. One scientist with a will and the means can unlock this "machinery", a thousand ID apologists who don't want to know never will.

I guess you do understand it. If so, I would surely like to hear how an origin of life model factored in the arrangements of nucleotide sequences in DNA or RNA in order for the complex interacting proteins and coherent machinery of the first living and replicating cell.


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 230 of 458 (521427)
08-27-2009 12:23 PM
Reply to: Message 229 by Dr Adequate
08-27-2009 11:35 AM


He did not claim to understand it. What he said was that not understanding it is not a basis for the Great Big Fundie Fallacy: "I don't understand this perfectly. Therefore, no-one else in the world understands it perfectly or ever will. Therefore, I do understand it perfectly --- God did it by magic".

I don't think there is anything wrong with "God did it" and I will tell you why. There will always be skeptics of the "God did it" idea. This is what science is for. Science should challenge itself and if and when it fails to find a unambiguous example of an explanation then, perhaps we could credit intelligent design as a casual explantion. The process shouldn't dumb down participants. The process should be an exporation and an excercise of intelligence and philosophy.

Francis Crick's sequence hypothesis is apparently more than just a hypothesis. Anyone who thinks the sequences in DNA are nothing more than Shannon information fails to explain how the precise functions and coherence within the cell formed without it.

Also, labeling me as a creationist is off the topic and an argument more from philosophy. I guess some people wish to define their opponents in certain ways in hopes to create certain impressions on others. The ID paradigm is distinct from creationism. It is sort of a hybrid between science and creationism but more toward science. It is a particular way of thinking and once you start to use the paradigm, the differences become obvious. See link below which helps discern the differences.

http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&t=752

Edited by traderdrew, : No reason given.

Edited by traderdrew, : No reason given.


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 248 of 458 (521814)
08-29-2009 11:11 AM
Reply to: Message 242 by greyseal
08-28-2009 8:57 AM


...and fail. No. That's called "god of the gaps" and your own theist thinkers and philosophers warned you creationists not to do that because then for every single forward step by the scientific method, you god is similarly reduced.

That is understandable. We shouldn't resort to lame explanations for phenomenon. In the case of information, I am not going there. The information in DNA is precise with little margin for error. The information needs to serve specified functions indicative to particular organisms and overall functions. Shannon information does not explain how the machinery in the cell can work together coherently and how it all was built.

The chances of the nucleotides landing in specific sequences in an origin of life model are extremely unlikely. Adding to this are the forces that are detrimental or potentially damaging to the chemical constituents which were precursors to the model such as UVB radiation, high temperatures, hostile organic molecules and gases. It compounds the already insurmountable chances of the information arising from an accidental process that much more. All of these factors reduce it to a extremely unlikely event of just bare possibility and so -

Bare possibility is a poor basis for forming a judgment about nature. A rational person doesn't give credence to a claim based on bare possibility--a rational person demands positive reasons to believe something. - The Edge of Evolution

We know that CSI can be generated by an intelligence. We do not infer intelligence due to lame explanations. We infer intelligence because materialistic explanations fail and we know of another cause that can produce CSI.

Some on this forum say that we have an agenda to push. However, I can turn the motive mongering game right back on some the participants here. I can say some of you have gone down the road to perdition or have become Devil's advocates (puns intended) who wish to abolish religion or wish to perpetuate the seeds of other ideologies.

Posters should engage the substance and the content of the messages and not the motives behind them.

If scientists don't know, they say...gasp... "we don't know". And then they try to find out. If they said "godidit", they'd stop there.

On the other hand, if they keep trying maybe they will uncover more evidence for the existence of a creator. The trend for ID is up and going. We do not infer explanations based on the bible or the koran. If the evidence isn't there for those historical events, then we don't infer them. On the other hand, some of us believe when there are multiple causes for phenomenon, tends to render the ability to accurately reconstruct history as impossible.

Edited by traderdrew, : No reason given.

Edited by traderdrew, : No reason given.

Edited by traderdrew, : Just adding more "complex specified information" to the post


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 250 of 458 (521827)
08-29-2009 12:38 PM
Reply to: Message 249 by Wounded King
08-29-2009 12:01 PM


This is the sort of claim that really requires substantial evidence. Didn't we just cover the fact that ~30% of a coding DNA sequence could be changed without even changing a single amino acid in the primary sequence of its protein product? That seem like a pretty big margin of error right there.

I just looked for this but I couldn't find it. It kind of sounds like you are referring to a frameshift mutation. I did find this in your message #223

You were doing well up until here. There are a number of forms of mutation which could in fact stop a protein being created. The most obvious is a mutation which removes the start codon for the gene.

I also found this in message #214

When for the most part we have no ideas what the allowable margins for error are because we don't know what the functional effects of most possible mutations on a protein/sequence would be.

I'm sure there is documented research on how to induce mutations. I have read about it in hox gene research and among other research.

We do have ideas of what information from viruses can do. I wonder what would happen if we replace RNA from bacteria with human or insect RNA.

Please show your working.

You know that I don't have working model but in turn I could ask you to provide a working model that shows the bonding affinities in an origin of life model which produces a specified sequence of nucleotides. How would those specific arrangements or the lack of them enable protein binding sites to form?

No, you infer it even in the absence of lame explanations. You just infer it from nothing but you own incredulity basically.

Is that a low blow? If any of you infer that something doesn't exist, are you inferring it from your own incredulity also?

You could say that, but you would look like an idiot to do so. There are vast numbers of people of faith who support modern evolutionary theory and see it as the best explanation of life's history on Earth.

True, true and I would wonder why they would invest in both. Perhaps they realize this:

Interestingly enough though, the scientific method does not detect truth directly. The power of the scientific method comes from its ability to detect error, thereby limiting the places where truth may be found. - Sean Pitman

You could probably count on the fingers of one hand the people who aren't religiously motivated who want Intelligent Design taught in schools or put on an equal footing with evolution despite its lack of substantiating evidence.

I think there is a lack of substantial evidence for us to have evolved from blind natural forces. Should we debate this further?

Yes, every couple of years someone publishes a theoretical maths/informatics paper that subsequently sinks without trace. Its not what I'd call a really constructive research cycle.

You should know that we have done better than that.

It needn't unless one of these causes is ineffable, intangible, indescribable or in some other way inconsistent with our whole understanding of nature.

Well then, I would say that you or someone else should have been able to persuade those scientists would believe in a god that materialistic or natural explanations do the trick.


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 253 of 458 (521911)
08-30-2009 1:00 PM
Reply to: Message 251 by Wounded King
08-29-2009 2:07 PM


There is, but surely it is obvious to you that this doesn't translate into knowing what the functional effects of most mutation in most proteins are, it would take an inconceivable amount of work just to screen all the possible single nucleotide substitutions for 1 gene.

I think you have an indirect point. It is one thing to say what I have posted and another to understand it biochemically. I can sit here and argue it with you and it would be another thing to seek a greater understanding of it. I think it would be better if I took the latter.

It isn't about a working model. You said you knew the probabilities of 'the nucleotides landing in specific sequences in an origin of life model are extremely unlikely'. I wanted to know how you had calculated them.

It is based on common sense and deduction as well as reading about the material. If there were certain bonding affinities where the sugar phosphate backbone preferred certain nucleotides over others then, I would expect a certain amount of redundancy. Proteins have specific complex shapes and their overall structures are not assembled or conform to standard Euclidean mathematics. Specified sequences within DNA determine their specific shapes and functions. There is that problem of coherence also. Common sense says throwing the amino acids together randomly is highly unlikely to generate functional coherence. DNA is also a very complex molecule.

I imagine rather from an absence of evidence. But you aren't inferring an absence you are inferring a presence which surely requires stronger support or at least positive evidence?

I imagine this relies on a certain amount of perspective. You can weigh the evidence that supports a higher intelligence to the what is against it. The problem with that is us thinking, "If I was a god then this is the way I would run things."

Again, this would be a really good place to pull out all of your supporting evidence, particularly the published practical research papers.

Even though I a tendency to venture off the topic, I was trying to pretty much stay on the topic of information in the cell. If I was going to post some of them, I would be giving you bare links without commenting on them. Stephen Meyer has some on his website. The one that was published in the Smithsonian's journal mentioned the term "intelligent design" in it. I read the article online.

1. information in the cell and all of its complexities. 2. Irreducibly complex systems 3. Fine-tuning in the physics of the universe. 4. Fine-tuning in cosmology 5. Unusual patterns and appearances of organisms in the fossil record. And a sixth one might be unusual dispersion patterns of phyla in marine life. On a side note, I have an interest in sea life and I find it amazing how well adapted certain creatures are in that environment and their designs, and their symbiotic relationships. I sometimes try to see it from a Darwinian perspective but that is still hard to believe. One example is the leafy sea dragon off Australia. There is more also. I have been slowly investigating the inverted vs verted retina of the eye. I think I have found a very good counterargument for the Darwinists.

How many articles do proponents of ID need? What arbitrary figure would any of you put on it? There is obviously a certain amount of chaos and change or entropy (whatever you want to call natural processes) that would tend to obscure evidence of an intelligent designer. There is also the subject of resistance or pressure organizations may apply against articles that support ID.

I might get rhrain or (whatever he posts as) criticizing Behe again here. If I saw him in person I would put my hand up to interrupt him and say, "All you have to do is show me or direct me to a model of how one of them evolved with a step by step Darwinian fashion." I will investigate it myself. I believe I understand the concept of dogma. I think we are all guilty of it to a certain extent. RAZD posted a model to me (I call it the pilus model) and it was a nice try.

Unfortunately this makes no sense to me, are you saying evolution should make everyone an atheist if it is true?

I would think Richard Dawkins would argue for that. I think his books belong in philosophy but this being the case, I would think ID books belong there also.

Edited by traderdrew, : No reason given.


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traderdrew
Member (Idle past 3470 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 258 of 458 (521997)
08-31-2009 10:49 AM
Reply to: Message 254 by Wounded King
08-30-2009 3:37 PM


Wouldn't it be a good thing to have a good understanding of something before criticising it and telling us all what is possible or impossible?

Of course it would. However, one reason why I am here is to learn more about the subject matter. The debate helps me gain understanding.

Oh, a guess.

Your 30% substitution rate in the third position of each codon wasn't a guess? I wonder what are the chances of a series of random mutations hitting only the third position in a chain of amino acids.

You know that I really do not understand the language of DNA. This doesn't say that others don't understand it better than me. Your point doesn't say the code isn't specified. I think it is specified enough. Here are some quotes.

Some have also argued that alterations in sequencing would likely result in loss of protein function before fundamentally new function could arise (Eden 1967, Denton 1986).

Maybe we study Eden's and Denton's work we will get to understand it better. Somehow I doubt they are creationists.

Too many processes in the cell depend upon particular proteins having just the right shape and sequence of amino acids to leave the assembly of these molecules to chance. "Signature in the Cell"

Recently, experiments in molecular biology have shed light on these questions. A variety of mutagenesis techniques have shown that proteins (and thus the genes that produce them) are indeed highly specified relative to biological function (Bowie & Sauer 1989, Reidhaar-Olson & Sauer 1990, Taylor et al. 2001).

In particular, Axe (2000) has shown that multiple as opposed to single position amino acid substitutions inevitably result in loss of protein function, even when these changes occur at sites that allow variation when altered in isolation. Cumulatively, these constraints imply that proteins are highly sensitive to functional loss as a result of alterations in sequencing, and that functional proteins represent highly isolated and improbable arrangements of amino acids -arrangements that are far more improbable, in fact, than would be likely to arise by chance alone in the time available (Reidhaar-Olson & Sauer 1990; Behe 1992; Kauffman 1995:44; Dembski 1998:175-223; Axe 2000, 2004).

Oh yes, boo hoo. Mainstream science was mean to ID so it is taking its theory and going home.

I'm not whining. The article Meyer wrote that was published in Proceedings of the Biological Society of Washington (volume 117, no. 2, pp. 213-239). I believe the man who had PhDs who authorized it had his keys taken away and was transferred to a hostile supervisor. Most everyone would fear negative reprocussions for publishing an ID article in a journal like that one.


This message is a reply to:
 Message 254 by Wounded King, posted 08-30-2009 3:37 PM Wounded King has responded

Replies to this message:
 Message 263 by Wounded King, posted 08-31-2009 2:59 PM traderdrew has responded
 Message 270 by Rrhain, posted 09-01-2009 11:09 PM traderdrew has responded

  
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