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Author Topic:   Simultaneous Evolution?
crashfrog
Member (Idle past 257 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


(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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crashfrog
Member (Idle past 257 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


(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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crashfrog
Member (Idle past 257 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


(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
Member (Idle past 257 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


(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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crashfrog
Member (Idle past 257 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


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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Replies to this message:
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crashfrog
Member (Idle past 257 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 32 of 42 (581890)
09-17-2010 11:23 PM
Reply to: Message 31 by barbara
09-17-2010 11:22 PM


Re: RNA World?
Does a RNA virus have enough genes to form a chromosome?

They have a single chromosome comprised of single-stranded RNA.


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 Message 31 by barbara, posted 09-17-2010 11:22 PM barbara has responded

Replies to this message:
 Message 33 by barbara, posted 09-17-2010 11:59 PM crashfrog has responded

  
crashfrog
Member (Idle past 257 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 35 of 42 (581987)
09-18-2010 2:29 PM
Reply to: Message 33 by barbara
09-17-2010 11:59 PM


Re: RNA World?
Since a RNA virus is a single chromosome then isn't logical to think that since we have 23 chromosomes X2 each parent that our chromosomes are actually RNA viruses linked together with all of their information put into DNA storage?

Why would that be reasonable? Animal-infectious RNA viruses have circular chromosomes; eukaryotic chromosomes are linear.

And if our chromosomes are viral why aren't we viruses? No, there's nothing logical about your notion.

Can science identify each chromosome for what it does?

Yes, that was the Human Genome Project which you may have heard of. You can browse it at the UCSC Genome Browser.


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