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Author Topic:   Information and Genetics
wj
Inactive Member


Message 46 of 262 (14550)
07-31-2002 7:09 AM
Reply to: Message 35 by Lewissian
07-22-2002 12:35 PM


quote:
Originally posted by ChaseNelson:

By the way, we don't even have to mention that ultraviolet radiation destroys ammonia and many organic compounds that would have been present in the ocean... oh I just did

Perhaps you were right not to mention it. Here's some relevant comments by Gary S. Hurd at
Account Suspended
"Unfortunately for Sarfati, reality intrudes again. In Noll et al. (1997) for instance it is learned that an atmosphere with less than 10% of the Earth's current oxygen level could have as much as 25% of the Earth's current ozone. Further, without any free oxygen, or ozone, there are several additional means available that could have protected early macromolecules, and life itself. For example, Cleaves and Miller (1998) observe that the prebiotic organic compounds in the oceans would easily absorb the UV radiation flux during the Archean (when the Sun produced less heat [IR radiation] and more UV than today). Earlier, Sagan and Chyba (1997) had shown that methane photolysis could have provided an effective ultraviolet radiation shield for the Earth and prevented, or minimized global glaciation. However, a third model exists, the occasional impact melting of frozen oceans on the early Earth (early to middle Archean approximately 3.9 Ga to 3.5, 1Ga=1 billion years before present) which provides oceanic organic chemical concentration, and an impact heat sink in addition to UV protection of prebiotic chemicals by ice (Bada et al. 1994). Indeed there is strong evidence that these processes could have begun during the Hadean as early as 4.4 Ga (Sleep and Neuhoff 2001, Wilde et al. 2001). "
So UV dissociation of complex organic molecules may not be the problem which creationists suggest.

This message is a reply to:
 Message 35 by Lewissian, posted 07-22-2002 12:35 PM Lewissian has not replied

  
Quetzal
Member (Idle past 5897 days)
Posts: 3228
Joined: 01-09-2002


Message 47 of 262 (14630)
08-01-2002 6:53 AM
Reply to: Message 26 by Lewissian
07-18-2002 1:02 PM


Well, well, well. Welcome back, ChaseNelson. It took me some time to dig up that old thread, since you never replied to my last post.
As to your assertion that I failed to answer any of your questions, I think it would behoove you to re-read the thread in question.
Please respond to:
1. my last paragraph on specified complexity and its problems
2. my citation of Dawkins and why your argument concerning what he said is erroneous
3. my examples of the immune system and cochlear system from the previous post which you have failed to address
4. the three references I provided concerning the evolution of biological information
5. my challenge to you to either accept MY definition of information or provide an operational one of your own
As to your claim that I failed to respond to the final paragraph you cut-and-pasted from some creationist website, I stand by my contention that the paragraph has NOTHING to do with the topic - information and biology - and is rather a transparent attempt to divert the discussion into an abiogenesis/origin of chirality and the availability of oxygen in the early atmosphere. You don't even cite the references on your own - one of them ends in the middle of a sentence, showing not only didn't you READ the references, but merely cut and pasted the whole argument from someone else.
If you want to discuss - we'll discuss. However, this time around there's going to be absolutely no tolerance on my part for straight cut and paste. If you can't synopsize in your own words the arguments, then all you're doing is re-hashing something someone else wrote - and which you may or may not understand.
If you don't want a discussion under those constraints, fine. At least I won't have to wonder for three months what's going on.

This message is a reply to:
 Message 26 by Lewissian, posted 07-18-2002 1:02 PM Lewissian has replied

Replies to this message:
 Message 59 by Lewissian, posted 08-27-2002 7:20 PM Quetzal has replied

  
derwood
Member (Idle past 1901 days)
Posts: 1457
Joined: 12-27-2001


Message 48 of 262 (14647)
08-01-2002 1:27 PM
Reply to: Message 33 by Lewissian
07-21-2002 9:49 PM


quote:
Originally posted by ChaseNelson:
Sorry for the delay--I was gone for the weekend, and I'll be leaving again Tuesday morning for a short camping trip with my dad and cousins.
Me too. I tend to 'cycle' between different boards. That and, after all, it is summer![quote] SLPx:
quote:
I do [claim that science is naturalism]? Well, how are we to examine the supernatural? How does one go about setting up controlled conditions to perform experiments on the same?
In post #28 of this thread you stated that "Of course, naturalism in science - methodological naturalism, that is - also forms the basis of physics, geology, medicine, etc." I read the 'in' as 'is', so I made that mistake, but your point seems basically the same--that naturliasm is foundational to science. We can examine the supernatural by inferring something was designed, and by realizing that natural processes have no ability to explain it.
But that is a non sequitur. Inferring that something was designed (how is that done?) is not examining it. How does one conduct experments to test whether this inferred design really is design? And would not the creationist claim design if/when experiments were performed to show that it can occur naturally? Thios caveat is, in fact, already in place and has been employed by creationists since the early 1970's. Randy Wysong, creationist veterinarian, wrote a book in I think 1972 (The Creation Controversey, or something like that) in which he wrote that life had been created in the lab (news to me) but that rather than it being evidence for natural processes, it was evidence for design. After all, scientists had to add "KNOW HOW" (emphasis his) to the mix to get it to work. This same escape clause has been used on discussion boards recently, in fact. It was claimed by a creationist that indicing speciation in a lab would be a "good place to start" so that we can see how much "intervention" is required. That is, no matter what, the creationist will cry Design!
quote:
Wrong. What is a 'correct' protein? Your reformulated analogy is already moot, as it suffers from the same fatal flaws that all such endeavors do.
Proteins are made of specific amino acids that fold into specific structures. As we know it, life can only be made of the specific proteins--of which I believe there are 19--which it is. That's why I said 19 could work, too. But other than these proteins, none others could support life. Therefore, the 'correct proteins'.
"As we know it." Do we know what the original life was? Do replicating molecules qualify? If so, where are their proteins? Do viruses have these 19 proteins? Do you KNOW that "none others" can support life?
Here is an analogy:
I am going to hang a picture on a wall. I ask my kid to bring me a screwdriver. He brings me a cross-tip. I ask him to bring me some screws. He brings me a box full of assorted screws of every type. I fish around in the box and pull out a hex head. No good. A flat-blade type. No good. A socket head. No good. Ah! A cross-tip screw, the only one I can use.
Does this mean that the only screw types that will hold pictures on walls are cross-tips?
quote:
Meyer the anti-evolutionist philosopher and DI fellow - what were those 'necessary' conditions? Necessary for what? For an after-the-fact specified event? The problem with these scenarios is that were the conditions different, were we based on, I don't know, silicon or something, the exact same arguments could be made!
But we weren't based on silicon.
You missed the point...
quote:
We know what life is made of and what makes it work (at least to a good extent). What needs explaining is how these things came about naturalistically (or else fron an intelligent source). There's a difference in detecting design and simply giving up on all naturalistic explanations and falling back on design. Proteins, DNA, irreducibly complex systems, etc., all contain detectable design.
But THAT is the question, is it not? You are saying that these things DO contian detectible design. Who detected it? How was it done? Where can I read this myself? I do hope, however, that you are not referring to Dembski's "filter"?
quote:
It's not that they aren't explained naturalistically at the time being, it is that they almost can't be--unless a natural process can be shown that can assemble such a system or meet requirements such as left-handedness, which bring us back to my question, and of which neither of us know the answer (you say, "I have no idea. I am not an abiogenesist(?), or a biochemist, or someone who does any sort of research or even pleasure reading on the topic. However, I find the notion of Divine Fiat to be unsatisfying.").
Why does it surprise you that I cannot answer your question? Do you think everyone should be conversant in biochemistry? I understand that any creationist with a degree in anything is an 'expert' in all areas of science by default. Sadly, I do not measure up. I, for one, would feel uncomfortable presenting myself as being 'expert' or even conversant in an area that I am not. But, see my screw analogy above for handedness...
quote:
That is the whole point - you are assuming that some extant protein X was the goal.
I am not saying that a certain protein was the goal--in fact, irreducible complexity relies on evolution as a random, undirected process in which mutations are random, and don't have a certain endpoint in mind (that's why Behe asks how natural processes can explain them). I'm just saying that what we know about what life needs today, and what we know about the only proteins that work for life, evolution doesn't add up.
Allow me to emphasize:
"I'm just saying that what we know about what life needs today..."
Do we know that what we need today was what the first life needed? Subsequent life? I read recently an analogy to a modern automobile. A modern automobile requires certain things to run. If we just start taking parts out, pretty soon - maybe even immediately - the car stops running. Does this mean that the a Model T NEEDED the same parts?
quote:
Meyer's essay (found in the book Mere Creation) shows how design can explain theses designed (or designoid, as Dawkins would refer to them) structures.
I've read some of Meyer's online essays and I find them fairly innocuous. At least he didn't analogize 'Darwinists' to Communists, like Wells does in his 'Icons...' video...

This message is a reply to:
 Message 33 by Lewissian, posted 07-21-2002 9:49 PM Lewissian has not replied

  
derwood
Member (Idle past 1901 days)
Posts: 1457
Joined: 12-27-2001


Message 49 of 262 (14655)
08-01-2002 2:32 PM


Perhaps of interest to Chase and others (re:chirality, other stuff):
This is from a post by Tim Thompson on a board that is now defunct:
Racemic amino acids from the ultraviolet photolysis of interstellar
ice analogues
Nature 416: 401-403, March 28, 2000
Max P. Bernstein, et al.
Abstract: The delivery of extraterrestrial organic molecules to Earth
by meteorites may have been important for the origin and early
evolution of life. Indigenous amino acids have been found in
meteorites - over 70 in the Murchison meteorite alone. Although it has been generally accepted that the meteoritic amino acids formed in
liquid water on a parent body, the water in the Murchison meteorite is depleted in deuterium relative to the indigenous organic acids.
Moreover, the meteoritical evidence for an excess of laevo-rotatory
amino acids is hard to understand in the context of liquid-water
reactions on meteorite parent bodies. Here we report a laboratory
demonstration that glycine, alanine and serine naturally form from
ultraviolet photolysis of the analogues of icy interstellar grains.
Such amino acids would naturally have a deuterium excess similar to
that seen in interstellar molecular clouds, and the formation process
could also result in enantiomeric excesses if the incident radiation
is circularly polarized. These results suggest that at least some
meteoritic amino acids are the result of interstellar photochemistry,
rather than formation in liquid water on an early Solar System body.
Amino acids from ultraviolet irradiation of interstellar ice analogues
Nature 416: 403-406, March 28, 2000
G.M. Muoz Caro, et al.
Abstract: Amino acids are the essential molecular components of living organisms on Earth, but the proposed mechanisms for their spontaneous generation have been unable to account for their presence in Earth's early history. The delivery of extraterrestrial organic compounds has been proposed as an alternative to generation on Earth, and some amino acids have been found in several meteorites. Here we report the detection of amino acids in the room-temperature residue of an interstellar ice analogue that was ultraviolet-irradiated in a high vacuum at 12 K. We identified 16 amino acids; the chiral ones showed enantiomeric separation. Some of the identified amino acids are also found in meteorites. Our results demonstrate that the spontaneous generation of amino acids in the interstellar medium is possible, supporting the suggestion that prebiotic molecules could have been delivered to the early Earth by cometary dust, meteorites or interplanetary dust particles.
Just to make the story complete, earlier studies on the stability of
amino acid molecules in space are encouraging. Once formed, they are
subject to fairly rapid destruction by the same UV that made it
possible, unless they are protected in ice mantles on interstellar
grains, or in a dense cloud protected from UV (The photostability of
Amino Acids in Space, P. Ehrenfreund et al., Astrophysical Journal
Letters 550: L95-L99, March 20, 2001). There is also evidence, as
suggested in both papers, that if the UV impacting the ice is
circularly polarized, the result could be a non-racemic product. There is some experimental evidence to support this view (Mechanism of pH-dependent photolysis of aliphatic amino acids and enantiomeric
enrichment of racemic leucine by circularly polarized light, H.
Nishino et al., Organic Letters 3(6): 921-924, March 22, 2001), and it is also evident that the necessary environment can be found in space (Astronomical sources of circularly polarized light and the origin of homochirality, J. Bailey, Origins of Life and Evolution of the Biosphere 31(1-2): 167-183, Feb-Apr, 2001).

  
Peter
Member (Idle past 1504 days)
Posts: 2161
From: Cambridgeshire, UK.
Joined: 02-05-2002


Message 50 of 262 (15282)
08-12-2002 9:18 AM


... but is there actually any information content
of DNA, or is it just the way we view it?

Replies to this message:
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derwood
Member (Idle past 1901 days)
Posts: 1457
Joined: 12-27-2001


Message 51 of 262 (15301)
08-12-2002 2:49 PM
Reply to: Message 50 by Peter
08-12-2002 9:18 AM


quote:
Originally posted by Peter:
... but is there actually any information content
of DNA, or is it just the way we view it?

Good question. I think that most would say that yes, DNA contains information. However, I don't think anyone competent in any related field would claim that the information in DNA is anything like the 'meaning' definition that creationists append to it.

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Tranquility Base
Inactive Member


Message 52 of 262 (15329)
08-12-2002 11:43 PM
Reply to: Message 50 by Peter
08-12-2002 9:18 AM


Peter & SLPx et al
I think we all agree that genomic sequences are 'special' - they're not random - who cares how they came to be - they are special now - they code for folded and function proteins.
You guys believe that you can get a minimal genome randomly and then that this genome will, over time, end up with new genes that will form organs, limbs and cellualr systems etc. This is where the debate should be focused. Surely we all agree that what we now have in genomes is special and finely tuned.
As we have discussed before, in itself the genomic sequence and the protein sequences look pretty random. But train a neural netweork on it and it will find a systematic lack of randomness. a neural netweork would discover consecutive codons coding for alpha-helical secondary structure and simlar streches for beta-strands. There is definte informaiton content even if analysed by something that doesn't know what to look for. This is exactly the same with a computer. Examining a hard disk in binary it would look loke junk. In ascii one would find patterns.
[This message has been edited by Tranquility Base, 08-12-2002]

This message is a reply to:
 Message 50 by Peter, posted 08-12-2002 9:18 AM Peter has replied

Replies to this message:
 Message 53 by Peter, posted 08-13-2002 3:12 AM Tranquility Base has replied

  
Peter
Member (Idle past 1504 days)
Posts: 2161
From: Cambridgeshire, UK.
Joined: 02-05-2002


Message 53 of 262 (15340)
08-13-2002 3:12 AM
Reply to: Message 52 by Tranquility Base
08-12-2002 11:43 PM


But with a hard-disk we start with the assumption that
the data on it was put there by someone ... and the binary
digits stored are data not information.
The main reason that I started this thread was to discuss the line of reasoning put forward by some YEC's that the information
content of DNA is an indication of design.
DNA contains sequences that are used in the cell to create
proteins etc. and that process in itself is pretty complex,
but does DNA actually, objectively contain information (can you
even have objective information?) ?
The issue of information and genetics is important in the
consideration of design ... but is extremely complex, compounded
by the abstract nature of information.
Another contention, within the context of the information = design
line of reasoning, is that information has to come from an
intelligent source.
Is this true?
If I write a computer program to randomly generate a three letter
sequence, and eventually that comes up with 'cat', and english
reading individual will read that sequence and glean information
from it ... it is related to all things feline in the
consciousness of the observer.
There is no intelligence behind the emergence of the sequence
above, the intelligence is in the observer, who assigns meaning
to it, and thus forms information.

This message is a reply to:
 Message 52 by Tranquility Base, posted 08-12-2002 11:43 PM Tranquility Base has replied

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monkenstick
Inactive Member


Message 54 of 262 (15350)
08-13-2002 5:38 AM


i'll sum up how I see the whole genetics/information/ID argument
Step 1) formulate a series of rules about what information is, does and can do, based on man-made forms of information
Step 2) Identify DNA as a form of information
Step 3) Apply the rules we made for information to show that DNA can't do what the evolutionists say it ca

  
Peter
Member (Idle past 1504 days)
Posts: 2161
From: Cambridgeshire, UK.
Joined: 02-05-2002


Message 55 of 262 (15354)
08-13-2002 7:02 AM


If I have a group of chemicals and I put them together
in a flask, give 'em a whisk, add some heat energy maybe,
and they react to form something else ... does that mean
that the starting molecules contained the information
required to perform the reaction?

  
Tranquility Base
Inactive Member


Message 56 of 262 (15394)
08-13-2002 9:50 PM
Reply to: Message 53 by Peter
08-13-2002 3:12 AM


Peter
I partially agree/disagree.
A study of genomes would discover systemtic non-randomness even without knowing what to look for. This is evidence of specialness which indludes design but I agree it is not proof of design.

This message is a reply to:
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 Message 57 by Quetzal, posted 08-14-2002 2:56 AM Tranquility Base has replied

  
Quetzal
Member (Idle past 5897 days)
Posts: 3228
Joined: 01-09-2002


Message 57 of 262 (15410)
08-14-2002 2:56 AM
Reply to: Message 56 by Tranquility Base
08-13-2002 9:50 PM


quote:
Originally posted by Tranquility Base:
Peter
I partially agree/disagree.
A study of genomes would discover systemtic non-randomness even without knowing what to look for. This is evidence of specialness which indludes design but I agree it is not proof of design.

Hi TB:
I actually partially agree with this (removing the word "design"). There is no question that genomes are pretty well adapted to their current function. Although a case could be made (and has been) that many of the non-coding sections in the genomes of various organisms are pretty good evidence that "random" substitutions and duplications do exist (I'm thinking of the Alu sequence repetition in humans repeated over a million times; the so-called "satellite DNA" in Drosophila which consists of a seven bp sequence repeated 11 million, 3.6 million, and 3.6 million times - comprising over 40% of the genome). Even if these sequences have a structural function now, it may be a question of evolution making use out of something originally "useless".
The other issue with your statement, of course, is to justify the use of the terms "finely tuned" at all. Obviously a leopard or human wouldn't be a leopard or human if their respective genomes didn't "code" specifically for the products necessary to build a leopard or human, by definition. In that sense, of course they're "finely tuned" (to state the obvious). If they sequenced any other way they wouldn't build leopards and humans (duh). (A rose by any other sequence wouldn't be a rose). On the other hand, if by "finely tuned" you mean "perfect" or even "approaching perfection", then you are way off base, and the nonsense sequences present in every genome investigated to date falsify the "perfect" genotype argument.
Which in a round-about way, brings me to my point. The only way we are justified in asserting that the genomes of modern, living organisms are "finely tuned" is by understanding that their current form/sequence represents the end product of billions of years of evolution. Modern organisms with genomes which promote their survival are the beneficiaries of millions of generations of survivors. The organisms whose genomes weren't "finely tuned" for their particular environment and lifestyle aren't around any more. Moreover, simply because the genotypes appear finely tuned NOW, doesn't necessarily mean that a given genotype won't be selected out in the future if conditions change.

This message is a reply to:
 Message 56 by Tranquility Base, posted 08-13-2002 9:50 PM Tranquility Base has replied

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Tranquility Base
Inactive Member


Message 58 of 262 (15414)
08-14-2002 4:34 AM
Reply to: Message 57 by Quetzal
08-14-2002 2:56 AM


Hi Quetzal
I basically agree. The fine-tuning is at various levels of course and I agree that it is happening today via natural selection. I simply don't beleive the ribosome was finally tuned from nothing!

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Lewissian
Member (Idle past 4751 days)
Posts: 18
From: USA
Joined: 04-21-2002


Message 59 of 262 (16126)
08-27-2002 7:20 PM
Reply to: Message 47 by Quetzal
08-01-2002 6:53 AM


Deleted.
Edited by Lewissian, : Outdated.

This message is a reply to:
 Message 47 by Quetzal, posted 08-01-2002 6:53 AM Quetzal has replied

Replies to this message:
 Message 60 by Quetzal, posted 08-28-2002 6:10 AM Lewissian has not replied

  
Quetzal
Member (Idle past 5897 days)
Posts: 3228
Joined: 01-09-2002


Message 60 of 262 (16161)
08-28-2002 6:10 AM
Reply to: Message 59 by Lewissian
08-27-2002 7:20 PM


[QUOTE]Originally posted by ChaseNelson:
Hello,
I am by no means back as this is the first day of a hectic school year. Yes, SLPx, I know exactly what you mean--I find time for one board, and then things get busy again so I end up skipping around.[/b][/quote]
Good luck with school. Hopefully you'll have the opportunity to actually respond to my final post on the original thread.
quote:
However, in this post, I'd like to clear up a few misconceptions that Quetzal has put forth. Most importantly, I never copied and pasted anything. If you can show me what 'creationist website' I pasted from, I'd be... well, confused (seeing I did not do such a thing)! As to the statement that I don't even READ the references I cite, I challenge you to think again. Ask me to type any given sentence on any given page of ANY of the articles/books I cited and I will give them to you. I have everything I cite right here in my room, and I have read them all. By the way, which one ends in the middle of the sentence? I'd just love to complete it for you. Along those lines, how does a mistake I make imply that I did not read the references? I find this very confusing, as well.
Really? How interesting. You are to be congratulated on laboriously retyping all those quotes. Perhaps to avoid such misunderstandings in the future you might want to consider synopsizing in your own words and simply reference the articles.
quote:
Ad hominem doesn't work, Quetzal--at least not with me. For a while I was actually worried I had done something wrong. I see now that my worry was in vain.
That wasn't ad hom. An ad hominem attack would be to call into question your honesty and maturity directly - for example by calling you a liar for cutting and pasting a direct Phillip Johnson misquote of Dawkins here. I'm sure since you are quoting directly from the original source you are fully aware that the ellipses cover 16 full pages (part in the preface, part on page 2, and part on page 18!) - which represents one of the largest ellipse gaps I've ever seen - and weren't drawn from page 2-3 of the book as you cite in your reference. Johnson's misquoting can be found here. Anyone notice the similarities?
However, since I don't engage in this type of tactic, I won't bring it up.
Hopefully someday you will decide to respond substantively. In the meantime, enjoy school.
[This message has been edited by Quetzal, 08-28-2002]

This message is a reply to:
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Replies to this message:
 Message 61 by John, posted 08-28-2002 11:14 AM Quetzal has replied

  
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