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Author Topic:   Definition of Life
RAZD
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Message 46 of 77 (337469)
08-02-2006 5:44 PM
Reply to: Message 45 by Wounded King
08-02-2006 8:52 AM


Re: Optical isomer issues
I'm not sure that these would be neccessary for your concentration to occur, I'd have thought some material with a chirally selective adsorption would be more likely.

Or just that one important ingredient was more predominant in L-form to start.

If all the aminos were clumping into multi-aminos, D-form with D-form and L-form with L-form, this would tend to (a) reduce the 'toxicity' of one to the other and (b) prep the soup for the next step. Then if one had a {superlink} that the other didn't, and that started replication ...


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RAZD
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Member Rating: 3.8


Message 47 of 77 (337527)
08-02-2006 7:15 PM
Reply to: Message 1 by Jon
07-20-2006 8:32 AM


Here's some more 'mud' in the 'mix'
From (accessable Discover Mag article)
http://www.discover.com/issues/mar-06/cover/

Few things on Earth are spookier than viruses. The very name virus, from the Latin word for "poisonous slime," speaks to our lowly regard for them. Their anatomy is equally dubious: loose, tiny envelopes of molecules - protein-coated DNA or RNA - that inhabit some netherworld between life and nonlife. Viruses do not have cell membranes, as bacteria do; they are not even cells.

Less an organism than a jumbled collection of biochemical shards, the virus eventually yielded Wendell M. Stanley, the leader of the research team that exposed it, a Nobel Prize in chemistry rather than biology. The discovery also set off an intense scientific and philosophical debate that still rages: What exactly is a virus? Can it properly be described as alive?

The usual Discovery Magazine hype eh?. Notice the seeming equation of {life} with have a cell or cell membrane -- the "netherworld" may be one of definition rather than something mysterious.

The sheer prevalence of viruses, however, is forcing a reconsideration about how these entities fit into the biological world. Researchers have characterized some 4,000 viruses, from several dozen distinct families. Yet that is a tiny fraction of the number of viruses on Earth. In the last two years, J. Craig Venter, the geneticist who decoded the human genome, has circled the globe in his sailboat and sampled ocean water every couple of hundred miles. Each time he dipped a container overboard, he discovered millions of new viruses - so many that he increased the number of known genes 10-fold.

That's a lot of viral matter out there. Now consider this:

http://www.pnas.org/cgi/content/full/101/20/7716

The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life

Of the three domains of life (Eukarya, Bacteria, and Archaea), the least understood is Archaea and its associated viruses. Many Archaea are extremophiles, with species that are capable of growth at some of the highest temperatures and extremes of pH of all known organisms. Phylogenetic rRNA-encoding DNA analysis places many of the hyperthermophilic Archaea (species with an optimum growth {gtrsim}80°C) at the base of the universal tree of life, suggesting that thermophiles were among the first forms of life on earth. Very few viruses have been identified from Archaea as compared to Bacteria and Eukarya. We report here the structure of a hyperthermophilic virus isolated from an archaeal host found in hot springs in Yellowstone National Park. The sequence of the circular double-stranded DNA viral genome shows that it shares little similarity to other known genes in viruses or other organisms. By comparing the tertiary and quaternary structures of the coat protein of this virus with those of a bacterial and an animal virus, we find conformational relationships among all three, suggesting that some viruses may have a common ancestor that precedes the division into three domains of life >3 billion years ago.

Essentially that viruses that adapted to each of the different domains of life had a common ancestor virus that predates the separation of life into those 3 (for now) domains.

But here's the interesting part (discover again).

Now, with the recent discovery of a truly monstrous virus, scientists are again casting about for how best to characterize these spectral life-forms. The new virus, officially known as Mimivirus (because it mimics a bacterium), is a creature "so bizarre," as The London Telegraph described it, "and unlike anything else seen by scientists . . . that . . . it could qualify for a new domain in the tree of life." Indeed, Mimivirus is so much more genetically complex than all previously known viruses, not to mention a number of bacteria, that it seems to call for a dramatic redrawing of the tree of life.

"This thing shows that some viruses are organisms that have an ancestor that was much more complex than they are now," says Didier Raoult, one of the leaders of the research team at the Mediterranean University in Marseille, France, that identified the virus.

Or from
http://www.bioedonline.org/news/news.cfm?art=1288

Giant virus qualifies as 'living organism' - Huge genome allows mimivirus to make its own proteins.

Roll up, roll up, to meet Mimi, the biggest virus in the world. This monster has just had its genome sequenced, and scientists say that, unlike its fellow viruses, it may truly be called 'alive'.

Although it shows all the trademark features of a virus, the mimivirus is much more complex, says Jean-Michel Claverie, a biologist from the Institute of Structural Biology and Microbiology in Marseilles, France, who worked on the sequencing effort.

Mimi carries about 50 genes that do things never seen before in a virus. It can make about 150 of its own proteins, along with chemical chaperones to help the proteins to fold in the right way. It can even repair its own DNA if it gets damaged, unlike normal viruses.

The new study shows that its genome contains 1.2 million bases, which is more than many bacteria contain and makes it several times bigger than the largest DNA viruses. The bases make up 1,260 genes, which makes it as complex as some bacteria, the scientists say.

What's more, viral DNA often contains lots of 'junk' sequences, genetic material that does not seem to serve any useful function. Mimi, on the other hand, is lean and mean: more than 90% of its DNA does something specific.

Although biologists sometimes divide life into three categories, the team says that Mimi is sufficiently different that it deserves a fourth branch of life all to itself.

Bacteria are the simplest branch, because they lack a nucleus to gather their genetic material together. Archaea are very similar, but are thought to have evolved separately because of their unusual cell membranes. Every other living thing is a eukaryote, that is, an organism that groups its genetic material into a nucleus inside its cells. But Mimi carries seven genes that are common to all cellular life, putting it on a par with the other life-forms, says Raoult.

Arguing that viruses should be a (new) 4th domain ... less than 50 years after the last domain was added?

Enjoy.

Edited by RAZD, : — changed to " - "


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
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RAZD
Member
Posts: 18653
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.8


Message 48 of 77 (337537)
08-02-2006 7:31 PM
Reply to: Message 40 by inkorrekt
07-31-2006 10:44 PM


Re: ... re membrane your cell
I like the last part of your post that "we do not know".

That is essentially the difference between a scientific\rational approach (when confronted with a lack of data\information): admit that the data\information is insufficient, and because it is insufficient, we don't know.

The alternative is to make some assertion that is supported more by {the lack of knowledge\datainformation} and {belief in what should be}, as in concluding that it MUST be an intelligent designer.

The soup of D-and L-forms of amino acids will be biologically useless as the D-forms act as biological poisons.

We are not talking biology yet, but active chemicals that predate biology.

Also D-forms are still prevalent in the world and do not seem to have a toxic effect on the continuation of life, thus the existence of D-forms is not a barrier to life as we know it now, and presumably would be no greater barrier (other than being in the way) back then.

As noted on another thread, I think it may be possible for early life to be more of a hodge-podge than we see now - what we see now has been honed and fiddled and refined for 3.5 billion years after all - and may have included D-forms at least in some portions: we don't know.

Enjoy


Join the effort to unravel {AIDSHIV} with Team EvC! (click)

we are limited in our ability to understand
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RebelAAmericanOZen[Deist
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to share.


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inkorrekt
Member (Idle past 3521 days)
Posts: 382
From: Westminster,CO, USA
Joined: 02-04-2006


Message 49 of 77 (337552)
08-02-2006 9:36 PM
Reply to: Message 43 by Wounded King
08-02-2006 3:05 AM


Re: Optical isomer issues
The substrate of an enzyme can be any one of a huge number of molecules indeed there are enzymes that convert L-amino acids into D-amino acids.

Yes, you are right on. these enzymes are known as racemase enzymes. They are not present in every cell.If they are present, then all reactions will proceed. There will not be any enzyme inhibition. But, in nature, this is not the case. Threre are specific control mechanisms modulating cellular activity. What happens if there is no control? This is when we develop some diseases known as Metabolic disorders. For example, if Phenyl alanine is not metabolized, then it accumulates. The clinical condition is known as Phenylketonuria.

Random chemical reactions cannot and should not occur. If they did, then there will be chaos and severe metabolic disorders.


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inkorrekt
Member (Idle past 3521 days)
Posts: 382
From: Westminster,CO, USA
Joined: 02-04-2006


Message 50 of 77 (337553)
08-02-2006 9:39 PM
Reply to: Message 43 by Wounded King
08-02-2006 3:05 AM


Re: Optical isomer issues
Do you have any evidence to support your contention that D-amino acids are general inhibitors of enzyme activity?

In the brain, Phenylalanine is converted into hydroxy phenylalanine by the enzyme phenyl alanine hydroxylase. L-Phenylalanine is the substrate. But, D-Phenylalanine is an inhibitor of this enzyme.


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Wounded King
Member (Idle past 1534 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 51 of 77 (337587)
08-03-2006 2:54 AM
Reply to: Message 50 by inkorrekt
08-02-2006 9:39 PM


Re: Optical isomer issues
But, in nature, this is not the case.

What do you mean 'in nature', are you claiming that racemases are synthetic? these enzymes occur in nature, but I have no problem agreeing that they would not have been present when life first arose, if that is what you were getting at.

Threre are specific control mechanisms modulating cellular activity. What happens if there is no control? This is when we develop some diseases known as Metabolic disorders. For example, if Phenyl alanine is not metabolized, then it accumulates. The clinical condition is known as Phenylketonuria.

I don't see what this has to do with chirality.

Random chemical reactions cannot and should not occur. If they did, then there will be chaos and severe metabolic disorders.

Well actually they occur a lot, and there are a number of systems in the cell to cope with them when they do. The entire point of many enzymes is to catalyse reactions which might otherwise occur randomly but only rarely.

In the brain, Phenylalanine is converted into hydroxy phenylalanine by the enzyme phenyl alanine hydroxylase. L-Phenylalanine is the substrate. But, D-Phenylalanine is an inhibitor of this enzyme.

Which is interesting but one D-amino acid acting as an inhibitor of a specific enzyme is by no means clear evidence that D-amino acids are general inhibitors of enzyme activity.

TTFN,

WK


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inkorrekt
Member (Idle past 3521 days)
Posts: 382
From: Westminster,CO, USA
Joined: 02-04-2006


Message 52 of 77 (337950)
08-04-2006 4:43 PM
Reply to: Message 51 by Wounded King
08-03-2006 2:54 AM


Re: Optical isomer issues
Which is interesting but one D-amino acid acting as an inhibitor of a specific enzyme is by no means clear evidence that D-amino acids are general inhibitors of enzyme activity
.

You are wrong. Go and check any basic text book in biochemistry.


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Wounded King
Member (Idle past 1534 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 53 of 77 (338058)
08-05-2006 2:46 AM
Reply to: Message 52 by inkorrekt
08-04-2006 4:43 PM


Re: Optical isomer issues
I can't find anything saying that in Stryer.

Why not try and back your claims up for once and provide an actual reference, even from a textbook, which supports your claim.

TTFN,

WK


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inkorrekt
Member (Idle past 3521 days)
Posts: 382
From: Westminster,CO, USA
Joined: 02-04-2006


Message 54 of 77 (339883)
08-13-2006 8:56 PM
Reply to: Message 53 by Wounded King
08-05-2006 2:46 AM


Re: Optical isomer issues
My time is valuabe. If you are so serious in learing, go to any library. I am not your teacher.
This message is a reply to:
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Iname
Junior Member (Idle past 1324 days)
Posts: 28
Joined: 06-08-2006


Message 55 of 77 (339890)
08-13-2006 10:09 PM
Reply to: Message 54 by inkorrekt
08-13-2006 8:56 PM


Re: Optical isomer issues
[/lurk]

quote:
My time is valuabe. If you are so serious in learing, go to any library. I am not your teacher.

Nice combo, three dodges in one, bravo! Though your choices are a bit overused, you pull it off quite well. Also I would suggest you reread the forum guidelines since I'm about 99% sure there's something in there about substantiating your claims with links.

[lurk]

Edited by Iname, : code error


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Wounded King
Member (Idle past 1534 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 56 of 77 (339922)
08-14-2006 3:15 AM
Reply to: Message 54 by inkorrekt
08-13-2006 8:56 PM


Re: Optical isomer issues
Stryer is pretty much one of the standard university level Biochemistry textbooks, it says nothing in line with your claims. You claimed that I would find something supporting your claims in...

any basic text book in biochemistry.

Since this claim seems to be false why not try to show that your prior claim was not also false. The full text of Stryer is available in a searchable format online so you don't even need to go to the library to show me where I'm wrong. Just find the evidence in this standard biochem texbook, which I have apparently missed, supporting your claim.

I am not your teacher.

You're right, you aren't. I am the one teaching you, because I am the one who has a clue what they are talking about. You just seem to grab hold of some plausible sounding argument and keep repeating it regardless of whether there is actually any truth in it or any evidence suggesting it is a valid argument. As Iname has suggested this is going against the forum guidelines and is also very much debating in bad faith.

TTFN,

WK


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42
Inactive Member


Message 57 of 77 (357916)
10-21-2006 8:31 AM


How about: "life as distinct from existence is a myth?" or:
Life: "That which has not yet been destroyed by chaos: the (increasingly diverse) results of continuous accidental experiments in stability?"

The advent of reproduction is a significant step in this increasing stability, but I feel that non-reproductive stability is usually excluded from definitions of life because "alive" is deemed to require complex activity. Perhaps these are prejudices that we use to separate ourselves from other stable forms of energy.

Am I alive? Are my cells alive? Are their organelles alive and are the molecules they are made of alive? I feel the question is ultimately about self-perception. I must be alive - surely? I hope I am, but that doesn't really help the debate.


Replies to this message:
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RAZD
Member
Posts: 18653
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.8


Message 58 of 77 (357924)
10-21-2006 9:51 AM
Reply to: Message 57 by 42
10-21-2006 8:31 AM


a thin line?
Welcome to the fray, Douglas Adams fan.

... but I feel that non-reproductive stability is usually excluded from definitions of life because "alive" is deemed to require complex activity.

Perhaps the line of stability is the line between organising life and disorganising matter.

Below that line loss of organization occurs with time, above that line increasing organization occurs with time.

Something is acting to increase organization, ergo life.

Am I alive? Are my cells alive? Are their organelles alive and are the molecules they are made of alive? I feel the question is ultimately about self-perception.

The molecules aren't alive, as they continue to exist after cell death. But when does cell "death" occur? The question comes down to the organization of the molecules, and whether increased organization occurs with time or decreased organization.

Enjoy.

btw: type [qs]quote boxes are easy[/qs] and it becomes:

quote boxes are easy


Join the effort to unravel {AIDS/HIV} {Protenes} and {Cancer} with Team EvC! (click)

we are limited in our ability to understand
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... to learn ... to think ... to live ... to laugh ...
to share.


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Phat
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Posts: 9425
From: Denver,Colorado USA
Joined: 12-30-2003
Member Rating: 2.0


Message 59 of 77 (358030)
10-21-2006 7:28 PM
Reply to: Message 4 by Jon
07-20-2006 3:56 PM


Jon writes:

I would have to guess that there is somehow an objective scientific way to determine whether or not something is alive; seeing as how there are so many different and unfamiliar ways things can come into living.

In Japan, they did just that! They placed ten inanimate objects minus one animate hidden object in a room.

Pizza was placed in the middle of the room, and the lights were dimmed. Only in the animated room was the pizza missing at the conclusion of the test.


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AdminPD
Inactive Administrator


Message 60 of 77 (358081)
10-22-2006 9:03 AM
Reply to: Message 57 by 42
10-21-2006 8:31 AM


Welcome to EvC
Glad you decided to add to our diversity. We have a wide variety of forums for your debating pleasure, but I warn you it can become habit forming.

In the purple signature box below, you'll find some links that will help make your journey here pleasant.

Pay particular attention to our Forum Guidelines and all will go well.

Again welcome and fruitful debating. Purple


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