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Author Topic:   Simultaneous Evolution?
Dr Adequate
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Posts: 12742
Joined: 07-20-2006
Member Rating: 2.3


(1)
Message 16 of 42 (575763)
08-21-2010 1:30 AM
Reply to: Message 15 by sac51495
08-21-2010 12:55 AM


Re: RNA World?
Dean Kenyon went on to reject his own hypothesis, and become a prominent YEC and an ID proponent.

He seems to have built an entire career on being wrong.

This anecdote demonstrates the difference between postulation and empirically-based claims. One may postulate that there is a remote possibility of something occurring, or they may make claims backed by evidence.

This is exactly why I recommended that you study examples of "simultaneous evolution" that would show up in the fossil record.

Rather, if evidence is brought, the evidence is confined exclusively to the possibility that evolution could provide a plausible, naturalistic explanation for the world around us.

No. This is why you had to try to think up a question for which, by its nature, any answer no matter how correct would be unsupported by evidence.

Okay, maybe my sequencing of events was not perfect, but please notice something about all of this: besides from some difficulties with the actual steps, one must realize that the steps are mere possibilities (if that), and really only serve as an escape device for evolutionists.

Alternatively, your unevidenced speculation that DNA and RNA would both be required is nothing but an "escape device" for creationists; especially as we can observe (in RNA viruses) that RNA is quite capable of performing the function of DNA.

But after all what is creationism but one big escape device: "We can't think of a mechanism ... so God did it by magic!"

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 15 by sac51495, posted 08-21-2010 12:55 AM sac51495 has responded

Replies to this message:
 Message 18 by sac51495, posted 08-21-2010 3:24 AM Dr Adequate has responded

  
crashfrog
Inactive Member


(1)
Message 17 of 42 (575776)
08-21-2010 2:44 AM
Reply to: Message 15 by sac51495
08-21-2010 12:55 AM


Specificity of proteins
it must be noted that amino acids must be sequenced precisely the right way in order to form a protein

"Precisely"? No, not even remotely true. As much as 80% of the primary sequence of a protein contributes only structurally; 20% or less of most proteins is the crucial "active site" that actually interacts chemically with the enzyme's substrates.

While there are 20 amino acids mainly involved in protein biosynthesis, they're easily grouped into about 5 or 6 groupings based on their acidic or basic side chains, hydrophilicity, nucleophilicity/electrophilicity, steric hindrance, and so on. Within those groups they're usually quite interchangable; an enzyme like a serine protease may be as much as 300 residues, but only depends on three of those being specific amino acids at specific positions (the so-called catalytic triad actually involved in the chemical reaction that the enzyme catalyzes.)

The fact is that proteins are incredibly non-specific for most of their structure, and specific to any degree only at the protein's active site. In fact, analyzing the same homologous protein across several species to find the most conserved (least varying) areas in the protein is one way we elucidate protein structure and identify active sites.


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sac51495
Member (Idle past 1148 days)
Posts: 176
From: Atlanta, GA, United States
Joined: 04-02-2010


Message 18 of 42 (575790)
08-21-2010 3:24 AM
Reply to: Message 16 by Dr Adequate
08-21-2010 1:30 AM


Re: RNA World?
Dr. Adequate,

we can observe (in RNA viruses) that RNA is quite capable of performing the function of DNA.

I assume that you are not referring to the reproductive function of DNA; right? Because a virus is, by definition, "a small infectious agent that can replicate only inside the living cells of organisms." Viruses are not considered to be life-forms. Why? Because they cannot reproduce, unless they attach themselves to a living organism, or, "host". This is absolutely, 100% necessary in order for a virus to replicate itself. So we find that RNA in viruses depends on the genetic material of living cells, further proving the fact that we have no in vivo examples of an "RNA world".


This message is a reply to:
 Message 16 by Dr Adequate, posted 08-21-2010 1:30 AM Dr Adequate has responded

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Dr Adequate
Member
Posts: 12742
Joined: 07-20-2006
Member Rating: 2.3


Message 19 of 42 (575796)
08-21-2010 3:54 AM
Reply to: Message 18 by sac51495
08-21-2010 3:24 AM


Re: RNA World?
I assume that you are not referring to the reproductive function of DNA; right?

No, I meant storage.

But we should note that RNA is capable of base-pairing just like DNA.


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 Message 18 by sac51495, posted 08-21-2010 3:24 AM sac51495 has not yet responded

  
haleyonline 
Suspended Member (Idle past 1397 days)
Posts: 1
From: USA
Joined: 08-21-2010


Message 20 of 42 (575841)
08-21-2010 10:21 AM
Reply to: Message 15 by sac51495
08-21-2010 12:55 AM


Re: RNA World?
a bit beyond me

Edited by Admin, : Let his new sig be expressed!


I'm a damn sorry spammer!
This message is a reply to:
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Blue Jay
Member (Idle past 31 days)
Posts: 2615
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 21 of 42 (575852)
08-21-2010 11:44 AM
Reply to: Message 15 by sac51495
08-21-2010 12:55 AM


Re: RNA World?
Hi, Sac.

sac51495 writes:

Typically, mRNA gets information for amino acid sequencing (this is slightly generalized) from the DNA, and then tRNA and rRNA may act as catalyzers [sic] for the process of protein synthesis.

Since marking your own mistakes with “sic” is rather inexplicable, and since I can’t find the word “catalyzer” anywhere else on this thread, I'm curious as to whether this is actually your own writing.

-----

sac51495 writes:

...but please notice something about all of this: besides from some difficulties with the actual steps, one must realize that the steps are mere possibilities (if that), and really only serve as an escape device for evolutionists.

When other valid possibilities are brought onto the table, your assertion that RNA and DNA must have evolved simultaneously loses its automatically-assumed-as-true status, and becomes nothing more than one of the mere possibilities itself.

When autocatalytic ribozymes are known to exist, it’s difficult to take seriously your argument that RNA can’t function without DNA.

-----

sac51495 writes:

Dr. Adequate mentioned that "a lot of the most basic nuts and bolts of the process of making proteins consist of RNA enzymes such as tRNA and rRNA". This is indeed true, but it does not support the notion that RNA, in and of itself, can carry out all of the necessary functions for life, including reproduction.

You’re missing the basic point. What “necessary functions of life” did RNA have to carry out on its own other than self-replication?

A “ribo-organism” would have been nothing more than an autocatalytic ribozyme, a molecule that replicates in a pool of water. Such an “organism” did not have to do anything but self-replicate. It could become intermingled with DNA and proteins later.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


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crashfrog
Inactive Member


(1)
Message 22 of 42 (575874)
08-21-2010 2:42 PM
Reply to: Message 18 by sac51495
08-21-2010 3:24 AM


Re: RNA World?
Viruses are not considered to be life-forms. Why? Because they cannot reproduce, unless they attach themselves to a living organism, or, "host". This is absolutely, 100% necessary in order for a virus to replicate itself.

That doesn't mean they're not alive; that just means they're parasites.

Vaccines, as you may know, are made from dead viruses. How can you have a dead virus if it was never alive?


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 Message 18 by sac51495, posted 08-21-2010 3:24 AM sac51495 has responded

Replies to this message:
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shalamabobbi
Member (Idle past 113 days)
Posts: 396
Joined: 01-10-2009


(1)
Message 23 of 42 (576605)
08-24-2010 6:09 PM
Reply to: Message 1 by sac51495
08-14-2010 2:38 AM


another example
The topic name - simultaneous evolution - indicates that this is to be a discussion of those characteristics that we see in the world around us which are mutually supportive of one another, and necessary to one another. The question is this: how would these things evolve in the world of an evolutionist?

msg 16 Dr A: I recommended that you study examples of "simultaneous evolution" that would show up in the fossil record.

The specificity of proteins is another example. But note how it is resolved..

quote:
What the authors did was mine existing databases of DNA sequence data, pulling out the sequences of the steroid receptors from 29 different vertebrate species.
Then they charted the changes in the DNA sequence in the context of the tree of life as sketched out in the fossil record. The tree they assembled includes all the steroid receptors.
They used this tree to guide ... an analysis of the 3-D structure of the various postulated intermediates in the evolutionary pathway.
The authors accomplished this by making proteins from the "resurrected" genes, then crystallizing them and using X-ray diffraction techniques to determine their precise structures.

Examination of their receptor family tree revealed something interesting. Most vertebrates have highly specific receptors: the corticosteroid receptor isn't strongly stimulated by aldosterone, and vice versa. But some living vertebrates (skates, in particular) show a different pattern: the corticosteroid receptor isn't all that specific for cortisol. Because the ancestral receptor also lacked specificity (as shown in the 2006 paper), the authors concluded that the receptor acquired its discriminating taste at some point between the branching-off of skates (and their kin) and the separation of fish from tetrapods. Their Figure 1 is a little crowded, but it illustrates this nicely:


To follow the evolutionary narrative in this graph, start at the blue circle, which represents the ancestral receptor that was "resurrected" in the 2006 paper and that happily binds to both corticosteroids and aldosterone. (The graphs on the right side of the figure demonstrate the specificity, or lack thereof, of the receptors at different times in history.) There's a branch leading up and to the left, to the various GRs (corticosteroid receptors), and one leading up and to the right, to the MRs (aldosterone receptors). At the green circle, another branching event occurred, 440 million years ago, at which point certain groups of fishes (skates among them) branched off, up and to the right. The receptor at that point is an ancestral corticosteroid receptor, and it still isn't specific for corticosteroids. But the receptor at the yellow circle, in the common ancestor of tetrapods and bony fishes, is specific. The authors conclude that specificity arose between those two points, between 420 and 440 million years ago.

source:
http://sfmatheson.blogspot.com/...ew-protein-in-about-8.html

I don't necessarily plan to get really into this discussion

of course not.. you might get pinned down..
This message is a reply to:
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sac51495
Member (Idle past 1148 days)
Posts: 176
From: Atlanta, GA, United States
Joined: 04-02-2010


Message 24 of 42 (576639)
08-24-2010 9:40 PM
Reply to: Message 21 by Blue Jay
08-21-2010 11:44 AM


Re: RNA World?
Bluejay,

Since marking your own mistakes with “sic” is rather inexplicable, and since I can’t find the word “catalyzer” anywhere else on this thread, I'm curious as to whether this is actually your own writing.

Heh. I did worry about that myself, but hoped it wouldn't lead to any difficulties: yes, that is my own writing. Apparently, the word "catalyzer(s)", is not found in the dictionary. But, I figured that given the situation I was using it in, the meaning was rather obvious. I hope that this will lead to no further confusion.

it’s difficult to take seriously your argument that RNA can’t function without DNA.

I may be nit-picking, but (here I go ), I wouldn't say that RNA can't "function" without DNA; rather, I would say:

  • RNA (particularly mRNA) has no "survival" benefits, unless DNA is present to be interpreted.

  • There are many problems with getting RNA to evolve at all, even if DNA were present.

  • Both RNA and DNA contain information, which is an incredibly difficult problem to deal with when it comes to evolution.

    Once again, let me iterate that all the postulation of an RNA world has come as a result of highly controlled experimentation, or, in vitro. Why is this a difficulty? Because we know relatively little about the functions and properties of RNA, so highly controlled experiments mean little.

    And further, this hypothetical "RNA world" seems little more to me than pseudo-science, since, after all, science is the the study of the material world around us, or the environment that we see around us. Postulations about historical events (possibilities) through controlled experimentation has nothing to do with the environment around us. Hence the adjective "pseudoscience".

    Edited by sac51495, : No reason given.


    "Oh, the depth of the riches both of the wisdom and knowledge of God! How unsearchable are His judgments and His ways past finding out! For who has known the mind of the LORD? Or who has become His counselor? Or who has first given to Him and it shall be repaid to him? For of Him and through Him and to Him are all things, to whom be glory forever. Amen." (Romans 11:33-36) ~ Sola Deo Gloria
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  • sac51495
    Member (Idle past 1148 days)
    Posts: 176
    From: Atlanta, GA, United States
    Joined: 04-02-2010


    Message 25 of 42 (576640)
    08-24-2010 9:45 PM
    Reply to: Message 22 by crashfrog
    08-21-2010 2:42 PM


    Re: RNA World?
    crashfrog,

    That doesn't mean they're not alive; that just means they're parasites.

    One could perhaps say that, although biological textbooks that I have read refer to viruses as non-life. Personally, I disagree with the notion that viruses are life forms.

    But whether they are alive or not really has no bearing on this discussion. Even if they are alive, they do not have the ability to self-replicate without a host cell, all of which contain DNA (in vivo).

    Edited by sac51495, : No reason given.


    "Oh, the depth of the riches both of the wisdom and knowledge of God! How unsearchable are His judgments and His ways past finding out! For who has known the mind of the LORD? Or who has become His counselor? Or who has first given to Him and it shall be repaid to him? For of Him and through Him and to Him are all things, to whom be glory forever. Amen." (Romans 11:33-36) ~ Sola Deo Gloria
    This message is a reply to:
     Message 22 by crashfrog, posted 08-21-2010 2:42 PM crashfrog has responded

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    sac51495
    Member (Idle past 1148 days)
    Posts: 176
    From: Atlanta, GA, United States
    Joined: 04-02-2010


    Message 26 of 42 (576643)
    08-24-2010 9:52 PM


    Hmmmm
    This is indeed an interesting thread, but it hasn't exactly generated the type of discussion I had in mind; particularly, I've been a bit of a loner (as on other threads). So I may not have time to respond to all posts, as I was not intending to spend a lot of time on this thread anyways...

    Shalamabobbi said that I don't want to spend a lot of time on this thread for fear that I may be pinned down...

    If you wish to look at it that way, then you may.


    "Oh, the depth of the riches both of the wisdom and knowledge of God! How unsearchable are His judgments and His ways past finding out! For who has known the mind of the LORD? Or who has become His counselor? Or who has first given to Him and it shall be repaid to him? For of Him and through Him and to Him are all things, to whom be glory forever. Amen." (Romans 11:33-36) ~ Sola Deo Gloria
      
    crashfrog
    Inactive Member


    (2)
    Message 27 of 42 (576651)
    08-24-2010 10:38 PM
    Reply to: Message 24 by sac51495
    08-24-2010 9:40 PM


    Re: RNA World?
    . Apparently, the word "catalyzer(s)", is not found in the dictionary.

    "Catalyst" is the word you're looking for, I think - something that makes a chemical reaction occur faster or under more favorable conditions, but is not itself consumed in the reaction.

    RNA (particularly mRNA) has no "survival" benefits, unless DNA is present to be interpreted.

    RNA has largely the same survival benefit that DNA has; it's an easily-replicatable molecule that can store the primary sequence of a protein. Also, unlike DNA, RNA is more reactive and capable of acting as a catalyst for some chemical reactions (aka "ribozymes"), and it adopts a greater diversity of physical conformations (due to its single-strandedness) that allow it to engage in some regulatory activity without any proteins at all.

    DNA has the advantage that, lacking the 2' hydroxyl, it's considerably more stable and less reactive, making it more suited for its role in the cell as the genetic "archive".

    There are many problems with getting RNA to evolve at all, even if DNA were present.

    Because RNA is both replicatable and catalytic, it's actually the easiest of the biomolecules to evolve on its own. In fact it's so easy to get RNA to evolve on its own that doing exactly that in vitro to produce custom ligands is a well-known lab procedure called "SELEX": Systematic Evolution of Ligands by Exponential Enrichment.

    DNA can't replicate without proteins; proteins can't replicate themselves at all, they can only be synthesized from nucleic acids. RNA bridges both worlds and is therefore the logical precursor to both.

    Both RNA and DNA contain information, which is an incredibly difficult problem to deal with when it comes to evolution.

    Evolution of information in a system subject to random mutation and natural selection is trivial. Under such a system it's simply inevitable that you will produce information that reflects adaptation to the selective environment. That's how SELEX works, by replicating and mutating RNA strands and then selecting them according to their affinity for a certain ligand.

    Because we know relatively little about the functions and properties of RNA, so highly controlled experiments mean little.

    Those are precisely the circumstances under which highly controlled experiments mean a lot, actually. That's why they're so highly controlled - to increase the value and quality of the information they produce. It's an uncontrolled experiment that gives you little to any useful knowledge.

    But, come on. You may not know all that much about RNA but biochemists know quite a bit, actually.

    And further, this hypothetical "RNA world" seems little more to me than pseudo-science, since, after all, science is the the study of the material world around us, or the environment that we see around us.

    Life didn't evolve in the environment we see around us. It evolved in the environment that existed 3.5 billion years ago, before living things had caused immeasurable change to the planet Earth. Other than that, I think you're taking "the material world around us" a little too literally. Science explains observations. Logically, that must mean that science is able to elucidate and study the past, since by the time you've made any observation, the observation you've made is of an event that occurred in the past.


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    crashfrog
    Inactive Member


    (1)
    Message 28 of 42 (576652)
    08-24-2010 10:50 PM
    Reply to: Message 25 by sac51495
    08-24-2010 9:45 PM


    Re: RNA World?
    Personally, I disagree with the notion that viruses are life forms.

    I'm not prepared to say that anything without a metabolism is "alive", but that's probably a function of the biochemistry I'm studying. To me viruses occupy an intermediate realm between living organisms and inorganic chemistry, a realm they share with prions.

    I'm prepared to accept that opinions on this differ, I merely hope you'll consider a perspective different than your own.

    Even if they are alive, they do not have the ability to self-replicate without a host cell, all of which contain DNA (in vivo).

    Many species of intracellular parasite, for instance Rickettsias, cannot replicate or survive outside of a host cell, but Rickettsias are certainly not viruses (they don't rely on the host cell for all protein expression, for instance.) While there are no living examples of RNA-based cellular life (they were outcompeted by the superior qualities of DNA-based genetics), the very existence of RNA-based viruses implies that they must have existed at some point. If DNA has always been the molecule of genetic storage, expression, and heredity, all viruses would be DNA-based as well.

    Evolution predicts that the fitter species will outcompete the less-fit ones, who may go extinct. It shouldn't surprise us that the robust combination of DNA-based genetics and protein-based enzyme chemistry outcompeted the organisms that relied on unstable RNA for both genetic storage and chemical catalysis. Especially given the marked advantage that DNA-based species would have had against an panopoly of viruses that, at the time, were based solely on RNA. It's certainly not a reason to reject the RNA world.


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    barbara
    Member (Idle past 1231 days)
    Posts: 167
    Joined: 07-19-2010


    Message 29 of 42 (581874)
    09-17-2010 9:25 PM
    Reply to: Message 28 by crashfrog
    08-24-2010 10:50 PM


    Re: RNA World?
    What is the difference between a DNA virus and RNA virus that is seen today?
    This message is a reply to:
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    crashfrog
    Inactive Member


    Message 30 of 42 (581882)
    09-17-2010 10:41 PM
    Reply to: Message 29 by barbara
    09-17-2010 9:25 PM


    Re: RNA World?
    What is the difference between a DNA virus and RNA virus that is seen today?

    RNA viruses, as the name implies, have no DNA but instead store their genes in the form of RNA.


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