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Author Topic:   The "Digital Code" of DNA
Rob 
Suspended Member (Idle past 3201 days)
Posts: 2297
Joined: 06-01-2006


Message 106 of 143 (410112)
07-13-2007 9:25 AM
Reply to: Message 103 by ringo
07-13-2007 3:30 AM


Re: Dean Kenyon
Ringo:
The only "code" involved is a shorthand invented by scientists to describe complex molecules.

Scientists did not invent DNA Ringo.

By one process or another (because God spoke, or because of some 'as yet unknown / unscientific self-organizational process)... that shorthand is what invented scientists.

It is the epitomy of what digital code means. And that is precisely why, it is in the dictionary.

It's no big deal... we didn't invent 'code'. We didn't invent the electric motor either: http://www.detectingdesign.com/flagellum.html

We did invent war and other things though. most of our 'real' discoveries are just that... 'discoveries'.

I am not even going to argue any longer about it. Hoot Mon made the point long ago.

Let's move on ok?


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Rob 
Suspended Member (Idle past 3201 days)
Posts: 2297
Joined: 06-01-2006


Message 107 of 143 (410117)
07-13-2007 9:59 AM
Reply to: Message 102 by Wounded King
07-13-2007 2:55 AM


Re: Dean Kenyon
Come on Rob, just reading this it comes out as either stupid or disingenuous.

Surely it should say ...

"But... the fact is that there are approximately 30 thousand different known proteins based upon the arrangement of sequences of lengths varying from hundreds to thousands of digits composed of four distinct chemical digits."

Well, actually.... it should have said:

"But... the fact is that there are approximately 30 thousand different known proteins based upon the specified arrangement of 20 different amino acid sub units (the number of sub units varying from hundreds to thousands depending on the protein being constructed). The order (and possibly the relative position) of the sub-units is based upon the arrangement four chemical digits code in the DNA."

I guess we are all learning how to dot all the 'T's without being insulting.

Which brings a question to mind. Does anyone know if the shape of amino acids adds to the complexity of the arrangement mixture?

Or put another way... as three dimensional sub-units, are the twenty amino acids always linked to the same port (if we can call it that) on their surface to other acids, or are there multiple positions also possible?

I bring it up... because if the genetic code contains the information for the proper sequence in -let's say not just two dimensions but three, and actually specifies that as well, then we have an even more emense level of complexity to contend with. What would the number of possible positions for each amino acid be? Does each amino acid have the same number of ports?

I simply do not know the answer to those questions (and don't know if anyone does, but would love to know).

The startling (frankly alien) complexity of genetic information and the potential for a 'quaternary' code to specify enormous detail, leads me to infer that this is likely the case. Biology is after all, three dimensional.

Edited by Rob, : No reason given.


This message is a reply to:
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Fosdick 
Suspended Member (Idle past 2852 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 108 of 143 (410127)
07-13-2007 10:45 AM
Reply to: Message 100 by ringo
07-12-2007 8:11 PM


Digital polio
Hoot Mon writes:

You can order genes through the Internet....

Ringo asks:

And what can those genes do? Can they produce proteins?


Yup. To wit: US Scientists Create Polio Virus With Mail Order Chemicals

quote:
Scientists in the US have, for the first time, fabricated a working copy of a dangerous disease virus from scratch in the lab, using chemicals obtained by mail order and the publicly available knowledge of the virus's code.

Using harmless pieces of DNA they received through the post [office], researchers at the State University of New York built a synthetic version of the polio virus so like the real thing that it infected mice and made them ill…

The New York team's work, published yesterday in the online version of the journal Science, alarmed polio specialists, but also prompted concerns that other viruses more suitable for biowarfare, such as smallpox, could be synthesised.

Written down, the genetic code for polio is only 7,741 letters long…



Show me the Fordness

How about a Ford owner's manual? There's digital Fordness in there.

—HM


This message is a reply to:
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Replies to this message:
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ringo
Member
Posts: 12820
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 2.6


Message 109 of 143 (410137)
07-13-2007 11:21 AM
Reply to: Message 108 by Fosdick
07-13-2007 10:45 AM


Re: Digital polio
Scientists in the US have, for the first time, fabricated a working copy of a dangerous disease virus from scratch in the lab, using chemicals obtained by mail order and the publicly available knowledge of the virus's code.

So, using chemicals and publically available knowledge of those chemicals, scientists have been able to alter those chemicals. Once again, how is the "code" anything other than the structure of the molecule?

How about a Ford owner's manual? There's digital Fordness in there.

Now you're confusing advertising with code.


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This message is a reply to:
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Wounded King
Member (Idle past 1447 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 110 of 143 (410139)
07-13-2007 11:23 AM
Reply to: Message 107 by Rob
07-13-2007 9:59 AM


Protein structure
Well, actually.... it should have said:

"But... the fact is that there are approximately 30 thousand different known proteins based upon the specified arrangement of 20 different amino acid sub units (the number of sub units varying from hundreds to thousands depending on the protein being constructed). The order (and possibly the relative position) of the sub-units is based upon the arrangement four chemical digits code in the DNA."

So instead of just something stupid or disingenuous it should have been something irrelevant to start off with and then the same stupid/disingenuous elision? Well, its your sentence. Maybe when you were dotting the 'T's you shouldn't have had your 'I's crossed.*I'm sorry*.

Funnily enough the sort of high level protein structure we are talking about her includes structural levels up to the quaternary.

What is specified by DNA is the primary structure of the amino acids, i.e. which one comes next in the polypeptide sequence. The higher levels are the secondary, which covers the various basic structural fold and loop elements of protein conformation, the tertiary, which is the exact spatial form the protein will take and includes the sort of residue and atomic positional relationships you mentioned. The quaternay structure is the way several seperate polypeptide products can combine to produce larger functional proteins, i.e. the way 4 haeme bearing subunits combine in haemoglobin.

But all of these higher levels and other modifications of the protein are based at root upon its primary structure. In fact it is almost as if the chemical characteristics of the amino acids in that primary structure encode information for the way the peptides should be folded in the cell to make a functional protein, now what does that remind me of.

TTFN,

WK


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Fosdick 
Suspended Member (Idle past 2852 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 111 of 143 (410142)
07-13-2007 11:58 AM
Reply to: Message 109 by ringo
07-13-2007 11:21 AM


Re: Digital polio
Once again, how is the "code" anything other than the structure of the molecule?

Because structure alone does not explain the genetic code—the molecular structure must be arranged to hold its genetic information. You can have a DNA molecule with any arrangement of nucleotides and it's still a DNA molecule. The structure of a DNA molecule is not the primary concern here, because the arrangement of nucleotides into coded information goes a huge step beyond mere structure. You want a DNA molecule to work like a quartz molecule. You want to see all of the information contained in the electromagnetic bonding. You fail to see how a rock is different from sea urchin, because you pull the shade down on anything that is more than just bonding chemistry.

But I suppose you will say, ignorantly, that molecular arrangement is only structure. That's like saying 'a jelly doughnut is only food.' What's the point? ...futility is a bad feeling.

—HM


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ringo
Member
Posts: 12820
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 2.6


Message 112 of 143 (410144)
07-13-2007 12:16 PM
Reply to: Message 111 by Fosdick
07-13-2007 11:58 AM


Re: Digital polio
Hoot Mon writes:

The structure of a DNA molecule is not the primary concern here, because the arrangement of nucleotides into coded information goes a huge step beyond mere structure.

You seem to think the "structure" of the DNA molecule is just the framework. The arrangement of nucleotides is the fine structure. Every DNA molecule has the same framework, but it's the fine structure that holds the information.

You seem to be saying that "a building is a building" and there's some magic code that distinguishes one building from another. In reality, it's the arrangement of the rooms - the fine structure - that distinguishes one building from another.

Yes, the molecular arrangement, the fine-structure arrangement of the nucleotides is only structure.


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Fosdick 
Suspended Member (Idle past 2852 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 113 of 143 (410147)
07-13-2007 12:39 PM


Tautology 101
...and the arrangement of a song is only music.

—HM


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Wounded King
Member (Idle past 1447 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 114 of 143 (410150)
07-13-2007 12:53 PM
Reply to: Message 113 by Fosdick
07-13-2007 12:39 PM


Re: Tautology 101
Actually the arrangement of a song should be ...

OUP Music Encyclopedia writes:

The reworking or adaptation of a composition, usually for a different medium from that of the original.

TTFN,

WK


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Matt P
Member (Idle past 2127 days)
Posts: 106
From: Tampa FL
Joined: 03-18-2005


Message 115 of 143 (410165)
07-13-2007 2:57 PM
Reply to: Message 101 by Rob
07-13-2007 2:18 AM


Re: Dean Kenyon
Hi Rob,
Isn't it interesting that he remains silent.

I'm quite busy and tend not to respond instantaneously, what with work, research, homelife, and all. I also don't have sound on this computer, so I can't listen to the video here, though I did listen to the first half of it at home when you posted it. All I can recall is that the first half completely ignored the role of RNA. I will need to listen to fully engage in this discussion.

I stand by my claim of disingenuous, especially with regards to the way the website you linked to that introduced the video. I've investigated a bit further, and Dean Kenyon was never trained as an evolutionary biologist. His training is in prebiotic/organic chemistry. He also was never a "leading" researcher, he has a grand total of two first author publications (journals and major books), of which one was his book "Biochemical Predestination". The way the website presents may be considered grandstanding, but it's grandstanding to a deceptive degree.

Again, I will try to watch your video again once I get more time at home to do so.


This message is a reply to:
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Rob 
Suspended Member (Idle past 3201 days)
Posts: 2297
Joined: 06-01-2006


Message 116 of 143 (410261)
07-14-2007 2:15 AM
Reply to: Message 115 by Matt P
07-13-2007 2:57 PM


Concession + not so fast...
Matt P:
I've investigated a bit further, and Dean Kenyon was never trained as an evolutionary biologist. His training is in prebiotic/organic chemistry. He also was never a "leading" researcher, he has a grand total of two first author publications (journals and major books), of which one was his book "Biochemical Predestination". The way the website presents may be considered grandstanding, but it's grandstanding to a deceptive degree.

Well after looking around myself, I concede that you are correct. Deceptive or not, I don't see what the point would be in defending it directly.

You seem to be a reasonable man, so bear with me for a moment as I appeal to more than the surface image (personally, I don't worship the image).

The Documentary (in clip 1) also clearly refers to Kenyon as an 'evolutionary biologist'. I think Sean Pitman took them at their word as did I. So if there is any deception, then it is on the part of the producer (though I do believe Steven Meyer made Kenyon out to be so also in one of the other clips).

It's the evil PR firms I tell you... it's a conspiracy Man! :eek:

Seriously now... Kenyon's actual credentials are as follows: Professor Emeritus of Biology at San Francisco State University. He received his Ph.D. in Biophysics from Stanford University. He was a National Science Foundation Postdoctoral Fellow in Chemical Biodynamics at the University of California at Berkeley, a Research Associate at NASA-Ames Research Center, and a Visiting Scholar at Trinity College, Oxford University. (source / The Discovery Institute) (if you'd like a more derogatory slant on his credentials, Wikipedia is your best bet...)

What troubles me more yet... is that the producers of the documentary feel the need to compete for attention in a marketplace dominated by 'experts' by using 'titles' that are actually irrelevant to the arguments themselves. This worship of the title of 'expert' is another matter that is a sociological issue in our intellectually dead, entertainment culture.

Nonetheless, it is the argument itself and the paradox within it that is the real issue; the question that converted Dean Kenyon (which you claimed to be skeptical of, fine). That is what you need to address. I appriciate your inclination to attend to it. I thank you for your corrections, but let us not lose sight of the arguments. It's time I raised and enunciated that issue so that Wounded King can mock my lack of legality.

The question is this: [b]how such a sophisticated molecule as RNA (or worse DNA) could emerge (and for this particular discussion... the fact that it is a digital code).

Dean Kenyon is not alone... I easily found two other scientists who are not to my knowledge affiliated with Intelligent design .

Please pay close attention to the bolded sections.

The attractive features of RNA World prompted Gerald Joyce of the Scripps Research Institute and Leslie Orgel of the Salk Institute to picture it as "the molecular biologist's dream" within a volume devoted to that topic. They also used the term "the prebiotic chemist's nightmare" to describe another part of the picture: How did that first self-replicating RNA arise?
(source / Robert Shapiro http://www.sciam.com/print_version.cfm?articleID=B7AABF35-E7F2-99DF-309B8CEF02B5C4D7 )

Notice that Dean Kenyon's training was in this very area of brebiotic chemistry. So evolutionary biologist or not, he was working in the very field that had to deal with the question. The public doesn't know the difference between a biologist and a prebiotic chemist...

If anything, a prebiotic chemist is more a 'true scientist' (at least theoretically) than a biologist. Biologists get to use 'more' imagination... chemists work more with facts and laws. So this doubt you raise of deception, is in itself very cleverly positioned.

I will give you the benefit of the doubt by saying I don't think you considered all of these angles. In fact, I hadn't either frankly... until pushed by this 'spirit of unbridled skepticism' to translate my intuition into coherent thoughts.

As for Gerald Joyce and Leslie Orgel, consider some of their other comments on the question:

Scientists interested in the origins of life seem to divide neatly into two classes. The first, usually but not always molecular biologists, believe that RNA must have been the first replicating molecule and that chemists are exaggerating the difficulties of nucleotide synthesis...The second group of scientists are much more pessimistic. They believe that the de novo appearance of oligonucleotides on the primitive earth would have been a near miracle. (The authors subscribe to this latter view). Time will tell which is correct.

This discussion... has, in a sense, focused on a straw man; the myth of a self-replicating RNA molecule that arose de novo from a soup of random polynucleotides. Not only is such a notion unrealistic in light of our current understanding of prebiotic chemistry, but it should strain the credulity of even an optimist's view of RNA's catalytic potential...Without evolution (are you listening Percy?) it appears unlikely that a self replicating ribozyme could arise, but without some form of self-replication there is no way to conduct an evolutionary search for the first, primitive self-replicating ribozyme.

(source / Darwin's Black Box / Joyce, G.F., and Orgel, L.E. (1993) "Prospects for Understanding the origin of the RNA World" in The RNA world, ed. R.F. Gesteland and J.F. Atkins, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, p. 19, 13.)

So that is the question / problem Matt...

In retrospect, I think the intention by the producers was to get the concept across to the public... they do in fact do so as I am a truck driver with a 'hi scule' degree. And once again, the matter raised is one that is clearly the realm of prebiotic chemistry... Dean kenyon's expertise!

As Forest Gump said after a long run, "I'm pretty tired... think I'll go home now".


This message is a reply to:
 Message 115 by Matt P, posted 07-13-2007 2:57 PM Matt P has responded

Replies to this message:
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Rob 
Suspended Member (Idle past 3201 days)
Posts: 2297
Joined: 06-01-2006


Message 117 of 143 (410262)
07-14-2007 2:18 AM
Reply to: Message 113 by Fosdick
07-13-2007 12:39 PM


Re: Tautology 101
...and the arrangement of a song is only music.

"... The cool intellect must work not only against cool intellect on the other side, but against the muddy heathen mysticisms which deny intellect altogether." (Lewis / Learning in War-Time 1949, pg51)


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anglagard
Member (Idle past 51 days)
Posts: 2157
From: Big Spring, TX, USA
Joined: 03-18-2006


Message 118 of 143 (410267)
07-14-2007 3:07 AM
Reply to: Message 117 by Rob
07-14-2007 2:18 AM


Re: Tautology 101
Rob, one difference between a HS grad and one of those college smartasses is that the college educated person has been trained to express their ideas in their own words and only use quotes to support their argument.

After all, CS Lewis is available in any library. No need to post it here without interpretation or context.


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Matt P
Member (Idle past 2127 days)
Posts: 106
From: Tampa FL
Joined: 03-18-2005


Message 119 of 143 (410277)
07-14-2007 5:15 AM
Reply to: Message 116 by Rob
07-14-2007 2:15 AM


Re: Concession + not so fast...
Hi Rob,
Fair enough- I'm basing my assessment of Kenyon solely on what he has published. As far as I can tell, he's never done any biological research, which is the qualifying characteristic of someone labeled a biologist. Still, it's definitely not the point at hand.

I'm glad for your redirect into the field of prebiotic chemistry. You quote Shapiro:

The attractive features of RNA World prompted Gerald Joyce of the Scripps Research Institute and Leslie Orgel of the Salk Institute to picture it as "the molecular biologist's dream" within a volume devoted to that topic. They also used the term "the prebiotic chemist's nightmare" to describe another part of the picture: How did that first self-replicating RNA arise?

Shapiro is the author of "A skeptic's guide to the origin of life", which he wrote in part to combat the irrational exuberance exhibited by many of his contemporaries (including some of what's in "Biochemical Predestination"). A lot of what he discusses includes the random assembly of amino acids to form proteins, or the spontaneous assembly of a strand of RNA. His counter-proposal is that life began with short monomers, wherein proto-metabolic processes eventually led to life (he's termed it "Garbage bag world" if you'd like to look it up- I'm not sure if it's published, this is just what I saw him present at a conference).

I think it's extremely important to raise the points that 1) the weak RNA world is nearly universally accepted by prebiotic chemists, and 2) the strong RNA World is only accepted by about half of prebiotic chemists. Sorry for the confusion, but there are two fundamental tenets of the RNA-World.

The weak RNA world holds that an RNA-based system preceded the DNA/Protein world we have today. This is pretty well evidenced in biochemistry, from RNA fragments dominating metabolic cofactors, to ribozymes playing key roles, and in the fact that ribosomal peptide synthesis is an RNA catalyzed reaction. Cech and others won the Nobel prize for the discovery of the ribozyme, and not even Shapiro doubts that RNA preceded the DNA/protein world of today.

Conceptualize the weak RNA world as follows, with "?" being the gap in our knowledge:
?--> RNA --> DNA/Protein

Shapiro's main beef is with the "strong RNA World", which suggests that the origin of life corresponds to the de novo synthesis of an autocatalytic, self-replicating ribozyme. The strong RNA world provides a very definite view of the origin of life, and frankly, Shapiro is justified in his skepticism. The de novo synthesis of this ultimate ribozyme from random nucleotides is highly unlikely, as is the specific formation of those nucleotides in quantities high enough to proceed. However, it's still a common theme encountered in the prebiotic chemist/origin of life community, mainly due to the strong emphasis of DNA and genetics in biology. It's kind of funny- among prebiotic researchers, pure chemists are the most likely to follow the strong RNA world, whereas geochemists, cosmochemists, and even some physicists don't agree (I'm in this latter camp).

Conceptualize the strong RNA world as follows:
non-life --> RNA --> DNA/Protein

However, this does reveal a counter straw-man: the RNA world (weak version) is extremely well supported, and fairly well fits into the idea that catalysts and replicators can be the same thing. When researchers like Shapiro dismiss the RNA world, they're usually dismissing the "strong" version. The weak version is quite well supported, and be cautious that broad dismissals of the RNA world are usually dismissals of only the strong version, not the whole thing. This also kind of dampens the idea that there's a mystical relationship between DNA and protein (I know you didn't say that, but this is something I got from the title of the video, "Unlocking Life's Mysteries"). However, the RNA world (strong version) is much more difficult to conceptualize, though it's still a fairly active area of research. As much as I doubt the strong version of the RNA world, the spontaneous assembly of nucleotides into RNA is remarkably easy- you can do it on the surface of clays, by drying bubbles, on PAHs, even with a bit of heat. It's not dismissable out of hand (don't dismiss what hasn't been tried yet!). What we don't know with this may still come around to be demonstrable- for example, I think the smallest autocatalytic RNA strand is currently clocked at about 30 nucleic acids, which is starting to get past that "miraculous" and move into the realm of only "difficult".

What Shapiro doesn't like is the strong version of the RNA world. He's fine with the weak version (based on my personal conversations). Many who don't like the strong RNA world suggest instead a metabolic-focused life which would form the chemicals that lead to replicative material through specific chemical reactions. It's easy to do chemistry when something is making the starting materials. This already-developed metabolism assisted with the eventual appearance of RNA, giving it the necessary support for the origin.

So, my main point here is that there are two views of the RNA world- one that is immensely well supported (and which solves the chicken/egg problem of DNA/protein), the other of is still in the realm of "unlikely, but maybe."

Hope this helps!


This message is a reply to:
 Message 116 by Rob, posted 07-14-2007 2:15 AM Rob has responded

Replies to this message:
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Rob 
Suspended Member (Idle past 3201 days)
Posts: 2297
Joined: 06-01-2006


Message 120 of 143 (410315)
07-14-2007 10:20 AM
Reply to: Message 119 by Matt P
07-14-2007 5:15 AM


Re: Concession + not so fast...
Thank you for bringing me up to speed on the debate. Small RNA world it is... What will they think of next?

Matt P:

What we don't know with this may still come around to be demonstrable- for example, I think the smallest autocatalytic RNA strand is currently clocked at about 30 nucleic acids, which is starting to get past that "miraculous" and move into the realm of only "difficult".

When we do know... then all of this 'theo' may actually be worth something more than the title of science fiction. All of the technical jargon is not useful at all other than for the purpose of intimidation, of which I am not inclined.

You boys speak often of testability (the hallmark of science) yet you are far from it...

This smallest autocatalytic strand you talk of, with 30 amino acids... is that a computer generated model? If so, were the computer and the software not designed by intelligent agents for the purpose of creating this cenario? If not, was it found within the confines of an already complete organism?

One might tend to think it was found all alone in some swamp the way you referred to it. As though it were anything more than grand speculation. What do you mean clocked? Do you mean postulated by a computer 'virtual creation' with intelligent agents at the helm who's purpose is to show that we don't need intelligent guidance?

The spirit of Dawkins is alive and on the move; morph, twist, spin and laugh.

I'm not laughing. They're trying to steal your most excellent brain. Or... are you trying to steal mine?

Matt P:

Many who don't like the strong RNA world suggest instead a metabolic-focused life which would form the chemicals that lead to replicative material through specific chemical reactions.

Suggest = 'theo'. We already have a multitudes of self replicating cycles that are emperically affirmed. They are called 'organisms'.

Matt P:

It's easy to do chemistry when something is making the starting materials.

Like intelligent agents in a lab coat? You might succeed some day... but don't count your chickens until you first design a fertile egg (and keep it nice and warm in an incubator specifically designed for that egg).

Matt P:

This already-developed metabolism assisted with the eventual appearance of RNA, giving it the necessary support for the origin.

Isaac Asimov would be proud of the way you refer to imaginary things as though they are real.

Matt P:

So, my main point here is that there are two views of the RNA world- one that is immensely well supported (and which solves the chicken/egg problem of DNA/protein), the other of is still in the realm of "unlikely, but maybe."

Hope this helps!

Not really...But thank you for helping me to keep my eye on the pea. I was unaware of the re-invention of the same dilemma.

When you say 'immensely well supported' do you mean that it is a very popular 'theo'ry'? Because you almost give the impression that there is actually evidence that self exists out there... like some uncaused, self evident truth (better known as logic).

Matt, fate takes some strange twists... these arguments they give you are not just exaggerations, but beyond conjecture presented as fact, they are pure deception; clever, pea palming magic. They are miraculous signs and wonders...

And not about one's credentials, but in the arguments themselves.

Gaurd your mind friend. There are wolves who seek to devour you.

Edited by Rob, : No reason given.


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