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Author Topic:   Life - an Unequivicol Definition
Genomicus
Member (Idle past 139 days)
Posts: 852
Joined: 02-15-2012


Message 151 of 374 (773441)
12-01-2015 6:44 PM
Reply to: Message 150 by AlphaOmegakid
12-01-2015 6:22 PM


Re: Black White or Grey?
You've got to be kidding, Right?

Don't you realize that every atom, molecule, and chemical combination has an architecture or shape associated with it?

So you don't think heat and light affect chemical reactions? Would you like to research this a little before I embarrass you?

The only embarrassing thing here is that you're ignoring the question marks at the end of Percy's sentences -- so his/her sentences are interrogative, not declarative, as you would have the reader believe.


This message is a reply to:
 Message 150 by AlphaOmegakid, posted 12-01-2015 6:22 PM AlphaOmegakid has not yet responded

  
Tanypteryx
Member
Posts: 2250
From: Oregon, USA
Joined: 08-27-2006
Member Rating: 5.4


Message 152 of 374 (773443)
12-01-2015 8:03 PM
Reply to: Message 150 by AlphaOmegakid
12-01-2015 6:22 PM


Re: Black White or Grey?
If they are not alive, then they are dead.

Then you must decide your definition of life and the differentiation between life and death. And both must make sense.

I think you are misusing death here and several others have referred to non-living matter as "dead." Death is something that happens to living organisms when they stop functioning.

Non-living material may not be the same thing as dead material. If it was never alive then it is just "non-living material." If it was once an organism that has died then it is dead. Dead material is the remains of a living organism that has gone through the process of death.


What if Eleanor Roosevelt had wings? -- Monty Python

One important characteristic of a theory is that is has survived repeated attempts to falsify it. Contrary to your understanding, all available evidence confirms it. --Subbie

If evolution is shown to be false, it will be at the hands of things that are true, not made up. --percy


This message is a reply to:
 Message 150 by AlphaOmegakid, posted 12-01-2015 6:22 PM AlphaOmegakid has responded

Replies to this message:
 Message 157 by AlphaOmegakid, posted 12-02-2015 7:59 AM Tanypteryx has responded

    
New Cat's Eye
Inactive Member


(1)
Message 153 of 374 (773445)
12-01-2015 11:01 PM
Reply to: Message 150 by AlphaOmegakid
12-01-2015 6:22 PM


Re: Black White or Grey?
I clearly identified entities in the grey area. You are just unhappy, because I don't call them alive.

You're misunderstanding us.

It's not that you're discounting grey areas of non-life.

It's that you're not counting grey areas of life.

Yes, much of life is chemical, and all of life is physical, but life is more than just chemical processes.

Not really.

I mentioned this before, that biology is like a derivative of chemistry.

Behind that, chemistry is like a derivative of physics.

There is no chemistry that is not just ridiculously complex phyisics.

And there is no biology that is not just ridiculously complex chemistry.

You cannot draw a line between that which is chemistry and that which is biology.

It's like how you can't draw a line between that which is chemistry and that which is physics.

Those lines are fuzzy.

That's the reality that we have to deal with.

Your attempts at nailing down an non-equivocal definition of life for the field of biology has been doomed from the get-go.

It's totally unnecessary, unproductive, nonessential, and actually would be worse for the field of biology.

My OP asked a sarcastic question of what to do with the professional virologists that work for the biology departments, given your definition of what life is.

It was kinda tongue-in-cheek, but what I've repeatedly asked is: Why? What is the point?


This message is a reply to:
 Message 150 by AlphaOmegakid, posted 12-01-2015 6:22 PM AlphaOmegakid has not yet responded

  
Dr Jack
Member (Idle past 302 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


(2)
Message 154 of 374 (773446)
12-02-2015 3:48 AM
Reply to: Message 146 by AlphaOmegakid
12-01-2015 12:33 PM


Re: Mercy Me!
Seems to me that's exactly what a good scientific definition would be

No, quite the opposite. Good science synthesizes observations into coherent theory that can then be used to understand things that have not been observed before and make predictions beyond observation. Your definition does not do this.

Why not suppose a planet where water is HeO2? Diamonds are made from lead? we would still call the diamonds and water, right? Do you see any difference in "supposing an imaginary" observation, and real observations? I guess not.

HeO2 is not a possible compound. Diamond is a compound of Carbon and cannot be made from lead. This is basic chemistry. There is every reason, on the other hand, to suppose that the selection of DNA and ATP are arbitrary rather than necessary. On another planet they are unlikely to be repeated.

Your definition is so far removed from what we think of as life that it will produce absurd conclusions; the imaginary world of Delton-four is a simple illustration of where it is likely to break down. It's called a "thought experiment" and is a key part of science.


This message is a reply to:
 Message 146 by AlphaOmegakid, posted 12-01-2015 12:33 PM AlphaOmegakid has not yet responded

Replies to this message:
 Message 156 by Pressie, posted 12-02-2015 7:12 AM Dr Jack has acknowledged this reply

  
Percy
Member
Posts: 18611
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 155 of 374 (773447)
12-02-2015 7:11 AM
Reply to: Message 150 by AlphaOmegakid
12-01-2015 6:22 PM


Re: Black White or Grey?
AlphaOmegakid writes:

You said "You're attempting to create a definition where everything is either living or dead with no shades of gray in between."

That just isn't so. I clearly identified entities in the grey area. You are just unhappy, because I don't call them alive.

No, I'm saying there's a region between alive (white in the image analogy) and not alive (black) that is neither living nor non-living (a shade of gray).

You and RAZD want the grey area to be living.

Speaking just for myself, no, I don't want the gray area to be living. Giving the gray area a clear and unambiguous designation such as "living" would be the opposite of a gray area.

Then you must decide your definition of life and the differentiation between life and death.

No. I merely recognize that there's a gray area between living and non-living.

Percy writes:

That's it? Just blindly declare it a faith-based premise and be done with it?

No. I said a lot more than that which you ignored. Read it again.

Well, yes, you did say more in your very next sentence, and I quoted that next. You have responded:

Percy writes:

Chemicals don't have "organization, architecture or shape"?


You've got to be kidding, Right?

Don't you realize that every atom, molecule, and chemical combination has an architecture or shape associated with it?

My sentence wasn't a statement. Didn't you see the question mark? My question was rhetorical.

Now that you've made it obvious that you understand that chemicals have "organization, architecture and shape," I'll have to reinterpret your original statement from Message 141:

quote:
It ignores the many things in life that are not chemical. ie organization, architecture or shape, electromagnetic radiation, and gravity. ( none of which are chemical)

Are you saying that the view of life as a continuum ignores "organization, architecture or shape, electromagnetic radiation, and gravity"? Why do you think that?

Percy writes:

Chemicals aren't subject to "electromagnetic radiation, and gravity"?


So you don't think heat and light affect chemical reactions? Would you like to research this a little before I embarrass you? And gravity also?

I was asking another rhetorical question. When you quoted me you removed my question mark and replaced it with a period, and you left out the close-quote. I fixed it in my above quote region.

I may as well comment on one more thing from your Message 141:

quote:
And finally, any good definition of life must also identify it's opposite (or death).

This is just another bald declaration. We do have opposite ends of a continuum. A dog is obviously living. A block of lead is obviously non-living. Some things inhabit the region between living and non-living, like perhaps prions and viruses.

--Percy


This message is a reply to:
 Message 150 by AlphaOmegakid, posted 12-01-2015 6:22 PM AlphaOmegakid has responded

Replies to this message:
 Message 161 by AlphaOmegakid, posted 12-02-2015 9:57 AM Percy has responded

    
Pressie
Member
Posts: 2074
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 2.7


(2)
Message 156 of 374 (773448)
12-02-2015 7:12 AM
Reply to: Message 154 by Dr Jack
12-02-2015 3:48 AM


Re: Mercy Me!
Mr Jack writes:

HeO2 is not a possible compound.

The fact that AOk suggested HeO2 is a reason to know that there's no way of even attempting to have a rational conversation with AOk. Basic chemistry.

But, maybe Aok thinks that electrons flying around and not flying around in S1 and P1 and all those orbitals around Oxygen is just a theory...

Edited by Pressie, : No reason given.

Edited by Pressie, : No reason given.

Edited by Pressie, : No reason given.

Edited by Pressie, : No reason given.


This message is a reply to:
 Message 154 by Dr Jack, posted 12-02-2015 3:48 AM Dr Jack has acknowledged this reply

    
AlphaOmegakid
Member (Idle past 1073 days)
Posts: 564
From: The city of God
Joined: 06-25-2008


Message 157 of 374 (773450)
12-02-2015 7:59 AM
Reply to: Message 152 by Tanypteryx
12-01-2015 8:03 PM


Re: Black White or Grey?
Tany writes:

I think you are misusing death here and several others have referred to non-living matter as "dead." Death is something that happens to living organisms when they stop functioning.

Thanks Tany, I agree completely in a biological sense. So when does a virus die? No one is questioning that it is "alive" in the host cell (actually it is the infected cell that is alive). But outside the host, is it alive or dead? As a virion, is it alive, non-living, or dead?

And how about self replicating molecules? When are they dead? etc etc.? Or are they ever alive?

This is the reason that we need a good unequivocal definition of life.

Tany writes:

Non-living material may not be the same thing as dead material. If it was never alive then it is just "non-living material." If it was once an organism that has died then it is dead. Dead material is the remains of a living organism that has gone through the process of death.

Bingo! By George, me thinks he's got it!

Maybe, I was too quick in the semantics by using the term "dead", but you can see that the term non-living is almost a synonym of "dead". I've been trying to semantically identify the so called grey area. "Non-living" is a perfectly good designation as far as my definition is concerned.

The best term is abiotic! https://en.wikipedia.org/wiki/Abiotic_component

So now we (you and I) have clarified the grey area. We have categories:

(1) White=Living==>by some unequivocal definition of life
(2) Grey=Abiotic=non-living
(3) Black= Dead

Within this model dead organisms are also abiotic material, but abiotic material that has never been alive is just abiotic material. I think this model works very well within Biology and especially well with my definition of life.

The problem I was having was everyone else in this forum was referring to the grey area as "life" (the "grey area of life"). This makes no sense, because every abiotic thing would be on the pathway to life which is obviously false. The reality is that most abiotic things have no chance at life, many are dead, and some have some of the characteristics of living things.

Thanks for your post! It was revealing.

Now look at your last sentence, and consider a virus. If it is considered alive within the host cell. Then when the cell is destroyed and the virus is released again, then all life functions would be gone. It would be dead. Both abiotic and dead. This makes a lot of sense using this model. So a virus would not be in the grey area at all. It would be black.


This message is a reply to:
 Message 152 by Tanypteryx, posted 12-01-2015 8:03 PM Tanypteryx has responded

Replies to this message:
 Message 158 by Pressie, posted 12-02-2015 8:08 AM AlphaOmegakid has not yet responded
 Message 159 by Percy, posted 12-02-2015 8:30 AM AlphaOmegakid has responded
 Message 164 by herebedragons, posted 12-02-2015 12:57 PM AlphaOmegakid has responded
 Message 170 by Tanypteryx, posted 12-02-2015 4:02 PM AlphaOmegakid has responded
 Message 229 by RAZD, posted 12-05-2015 5:34 PM AlphaOmegakid has responded

  
Pressie
Member
Posts: 2074
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 2.7


(3)
Message 158 of 374 (773451)
12-02-2015 8:08 AM
Reply to: Message 157 by AlphaOmegakid
12-02-2015 7:59 AM


Re: Black White or Grey?
AOk writes:

Thanks Tany, I agree completely in a biological sense. So when does a virus die? No one is questioning that it is "alive" in the host cell (actually it is the infected cell that is alive). But outside the host, is it alive or dead? As a virion, is it alive, non-living, or dead?

Thank you for admitting that there's no clear definition for what is alive and what is not alive.

Edited by Pressie, : No reason given.


This message is a reply to:
 Message 157 by AlphaOmegakid, posted 12-02-2015 7:59 AM AlphaOmegakid has not yet responded

    
Percy
Member
Posts: 18611
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


(1)
Message 159 of 374 (773452)
12-02-2015 8:30 AM
Reply to: Message 157 by AlphaOmegakid
12-02-2015 7:59 AM


Re: Black White or Grey?
AlphaOmegakid writes:

The best term is abiotic! https://en.wikipedia.org/wiki/Abiotic_component

So now we (you and I) have clarified the grey area. We have categories:

(1) White=Living==>by some unequivocal definition of life
(2) Grey=Abiotic=non-living
(3) Black= Dead

Within this model dead organisms are also abiotic material, but abiotic material that has never been alive is just abiotic material. I think this model works very well within Biology and especially well with my definition of life.

The Wikipedia definition lists some examples of abiotic components, making clear just what an abiotic component is:

quote:
In biology, abiotic factors can include water, light, radiation, temperature, humidity, atmosphere, and soil.

You're saying that, for example, water that was once but is no longer part of a living creature is "dead", but that water that has never been part of a living creature is "abiotic". I don't think that definition is going to work for anybody.

The problem I was having was everyone else in this forum was referring to the grey area as "life" (the "grey area of life"). This makes no sense, because every abiotic thing would be on the pathway to life which is obviously false.

Why do you think a gray area between living and non-living implies that "every abiotic thing would be on the pathway to life." Water is an "abiotic thing," but most water in the universe is not likely on its way to becoming part of a living creature.

Now look at your last sentence, and consider a virus. If it is considered alive within the host cell. Then when the cell is destroyed and the virus is released again, then all life functions would be gone. It would be dead. Both abiotic and dead.

And then the virus enters another cell and is alive again? Really?

Look at the list of examples of abiotic components from Wikipedia again. Why do you think a virus outside a host cell belongs on that list?

--Percy


This message is a reply to:
 Message 157 by AlphaOmegakid, posted 12-02-2015 7:59 AM AlphaOmegakid has responded

Replies to this message:
 Message 163 by AlphaOmegakid, posted 12-02-2015 11:46 AM Percy has responded

    
RAZD
Member
Posts: 19981
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.9


Message 160 of 374 (773453)
12-02-2015 9:09 AM
Reply to: Message 144 by AlphaOmegakid
12-01-2015 11:02 AM


self-replicating virus - again ...
RAZD writes:

(1) It doesn't address the issue of viral life, which is increasingly being accepted as life forms as more is found out (self replication without host, metabolism and making of proteins used to encase it, etc)

You have claimed this several times now. Admittedly, I am totally unaware of this. Evidence Please! Hopefully papers I can access on the web. Not journalistic articles I hope.+

Rather than go back to old posts to find this material I did a search on this topic to also see what the current status is. My original information involved the first paper\article, and I am pleased to see that further progress has been made on this.

Start with these two articles (bold added for emphasis):

Astrobiology: Test-Tube RNA, 2001

quote:
A new RNA enzyme, or ribozyme, synthesized by David Bartel, Wendy Johnson and colleagues at MIT’s Whitehead Institute for Biomedical Research, opens a door to create a path for the earliest evolution to have happened without either DNA or proteins in the primordial soup. Since first described in the journal Science, the Whitehead ribozyme, or RNA catalyst, has filled in the picture of early chemical evolution and how life might have arisen.

... When aligning the master and copy molecules upon themselves, they tested their fidelity to the original design. The key feature showed 95% accuracy.

... “The reaction must be accurate in incorporating nucleotides based on the template strand, general enough that any template can be copied, and efficient enough to add on a large number of nucleotides,” says Johnston. In fact, one complete RNA helix turn, a chain length of 14 code letters (or nucleotides) was able to replicate itself.

One key piece for a RNA World scenario is now available: a laboratory version of a master and copy molecule, 95% fidelity to the master, and independence from RNA chain length or sequence order. ...


I haven't found the Science article yet, perhaps you would like to try.

Follow up research leads to (bold added for emphasis):

The Daily Galaxy: "Evolution in a Test Tube" -Scientists Create Immortal Genetic Molecule, 2010

quote:
For the first time, scientists have synthesized RNA enzymes – ribonucleic acid enzymes also known as ribozymes - that can replicate themselves without the help of any proteins or other cellular components.These simple nucleic acids can act as catalysts and continue the process indefinitely.

... The goal was to take one of the RNA enzymes already developed in the lab that could perform the basic chemistry of replication, and improve it to the point that it could drive efficient, perpetual self-replication.

Lincoln synthesized in the laboratory a large population of variants of the RNA enzyme that would be challenged to do the job, and carried out a test-tube evolution procedure to obtain those variants that were most adept at joining together pieces of RNA.

Ultimately, this process enabled the team to isolate an evolved version of the original enzyme that is a very efficient replicator, something that many research groups, including Joyce's, had struggled for years to obtain. The improved enzyme fulfilled the primary goal of being able to undergo perpetual replication. "It kind of blew me away," says Lincoln.

The replicating system actually involves two enzymes, each composed of two subunits and each functioning as a catalyst that assembles the other. The replication process is cyclic, in that the first enzyme binds the two subunits that comprise the second enzyme and joins them to make a new copy of the second enzyme; while the second enzyme similarly binds and joins the two subunits that comprise the first enzyme. In this way the two enzymes assemble each other — what is termed cross-replication. To make the process proceed indefinitely requires only a small starting amount of the two enzymes and a steady supply of the subunits.

"This is the only case outside biology where molecular information has been immortalized," says Joyce.

The researchers then generated a variety of enzyme pairs with similar capabilities. They mixed 12 different cross-replicating pairs, together with all of their constituent subunits, and allowed them to compete in a molecular test of survival of the fittest. Most of the time the replicating enzymes would breed true, but on occasion an enzyme would make a mistake by binding one of the subunits from one of the other replicating enzymes. When such "mutations" occurred, the resulting recombinant enzymes also were capable of sustained replication, with the most fit replicators growing in number to dominate the mixture. "To me that's actually the biggest result," says Joyce.

Joyce says that only when a system is developed in the lab that has the capability of evolving novel functions on its own can it be properly called life. ...


So as long as there was substrate (food to metabolize) the RNA enzyme\catalysts replicated, competed, evolved. In other words QED -- independent self-replicating RNA molecules.

For an overview of the RNA world current status see Wikipedia: RNA world (accessed Dec 2015) (bold in original):

quote:
RNA as an enzyme

RNA enzymes, or ribozymes, are found in today's DNA-based life and could be examples of living fossils. Ribozymes play vital roles, such as those in the ribosome, which is vital for protein synthesis. Many other ribozyme functions exist; for example, the hammerhead ribozyme performs self-cleavage[21] and an RNA polymerase ribozyme can synthesize a short RNA strand from a primed RNA template.[22]

Among the enzymatic properties important for the beginning of life are:

Self-replication. The ability to self-replicate, or synthesize other RNA molecules; relatively short RNA molecules that can synthesize others have been artificially produced in the lab. The shortest was 165-bases long, though it has been estimated that only part of the molecule was crucial for this function. One version, 189-bases long, had an error rate of just 1.1% per nucleotide when synthesizing an 11 nucleotide long RNA strand from primed template strands.[23] This 189 base pair ribozyme could polymerize a template of at most 14 nucleotides in length, which is too short for self replication, but a potential lead for further investigation. The longest primer extension performed by a ribozyme polymerase was 20 bases.[24]

RNA in information storage

RNA is a very similar molecule to DNA, and only has two chemical differences. The overall structure of RNA and DNA are immensely similar—one strand of DNA and one of RNA can bind to form a double helical structure. This makes the storage of information in RNA possible in a very similar way to the storage of information in DNA. However RNA is less stable.

Prebiotic RNA synthesis

Nucleotides are the fundamental molecules that combine in series to form RNA. They consist of a nitrogenous base attached to a sugar-phosphate backbone. RNA is made of long stretches of specific nucleotides arranged so that their sequence of bases carries information. The RNA world hypothesis holds that in the primordial soup (or sandwich), there existed free-floating nucleotides. These nucleotides regularly formed bonds with one another, which often broke because the change in energy was so low. However, certain sequences of base pairs have catalytic properties that lower the energy of their chain being created, enabling them to stay together for longer periods of time. As each chain grew longer, it attracted more matching nucleotides faster, causing chains to now form faster than they were breaking down.

These chains have been proposed by some as the first, primitive forms of life.[59] In an RNA world, different sets of RNA strands would have had different replication outputs, which would have increased or decreased their frequency in the population, i.e. natural selection. As the fittest sets of RNA molecules expanded their numbers, novel catalytic properties added by mutation, which benefitted their persistence and expansion, could accumulate in the population. Such an autocatalytic set of ribozymes, capable of self replication in about an hour, has been identified. It was produced by molecular competition (in vitro evolution) of candidate enzyme mixtures.[60]

Implications of the RNA world

The RNA world hypothesis places RNA at center-stage when life originated. This has been accompanied by many studies[citation needed] in the last ten years that demonstrate important aspects of RNA function not previously known—and supports the idea of a critical role for RNA in the mechanisms of life. The RNA world hypothesis is supported by the observations that ribosomes are ribozymes: the catalytic site is composed of RNA, and proteins hold no major structural role and are of peripheral functional importance. This was confirmed with the deciphering of the 3-dimensional structure of the ribosome in 2001. Specifically, peptide bond formation, the reaction that binds amino acids together into proteins, is now known to be catalyzed by an adenine residue in the rRNA.


[22] Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP (May 2001). "RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension" (PDF). Science 292 (5520): 1319–25. Bibcode:2001Sci...292.1319J. doi:10.1126/science.1060786. PMID 11358999.

[23] Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP (May 2001). "RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension". Science 292 (5520): 1319–25. Bibcode:2001Sci...292.1319J. doi:10.1126/science.1060786. PMID 11358999.

[24] Hani S. Zaher and Peter J. Unrau, Selection of an improved RNA polymerase ribozyme with superior extension and fidelity. RNA (2007), 13:1017-1026

[60] Lincoln TA, Joyce GF (Feb 2009). "Self-sustained replication of an RNA enzyme". Science (American Association for the Advancement of Science) 323 (5918): 1229–32. Bibcode:2009Sci...323.1229L. doi:10.1126/science.1167856. PMC 2652413. PMID 19131595. Lay summary – Medical News Today (January 12, 2009).


[22] and [23] would be the Science articles related to the first article above; it doesn't appear that the wiki article has been updated with the information from the second article above. I'll have to look into that.

See also Science: Mirror image RNA enzymes may hold clues to origin of life:

quote:

Much as in M. C. Escher's famous lithograph, novel RNA enzymes can assemble mirror image versions of themselves.

Like a pair of hands that appear as mirror images of one another, biomolecules, such as DNA and RNA, come in left-handed and right-handed forms. Normally, enzymes that recognize one mirror image form won’t touch the other. But researchers have isolated RNA enzymes, known as ribozymes, that synthesize RNAs of the opposite handedness. As esoteric as this may sound, similar mirror image–making RNAs may have played a role in the early evolution of life.

Researchers consider RNA a likely central figure in the origin of life. That’s because, like DNA, the molecule can store genetic information, and like proteins it can act as a chemical catalyst that speeds up normally slow reactions. Many researchers believe that life likely got its start in an “RNA world” where RNAs evolved to replicate other RNA molecules. In this scenario, the more specialized DNA and proteins arose later.

Now, Joyce and his postdoc Jonathan Sczepanski have found a possible solution. Online this week in Nature, they show that by using a technique called test-tube evolution they were able to generate ribozymes capable of assembling RNA strands of the opposite handedness in the presence of a mixture of D- and L-RNA nucleotides. What’s more, when they started with a D-RNA ribozyme, they found that it preferred to work on an L-RNA template to synthesize an L-RNA complementary strand. Likewise, they prepared L-RNA ribozymes that synthesized D-RNA complementary strands from D-RNA templates. And both the D- and L-RNA ribozymes were able to make mirror image copies of themselves.

... the new work does suggest that if these cross-copying ribozymes arose early on, they could have copied both mirror versions of RNA to propel the evolution of more complex RNAs. If one of those later, more complex RNAs—say a D-RNA—proved more capable, it could have encouraged the copying of its own kind, and promoted the single-handedness in nucleotides that we see today.


A possible path to chirality.

In between self-replicating RNA and modern cell life would be self-replicating DNA molecules, with DNA viruses as 'living fossils' of their pre-cell existence.

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

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

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.

1. Raoult D., et al. Science, published online, doi:10.1126/science.1101485 (2004).
2. La Scola B., et al. Science, 299. 2033 (2003).

This isn't self-replication and it is inside a cell, but it is the RNA virus acting alone to make its proteins, another step on the road to RNA world.

And now I will add a copy of this post to Self-Replicating Molecules - Life's Building Blocks (Part II)

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
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This message is a reply to:
 Message 144 by AlphaOmegakid, posted 12-01-2015 11:02 AM AlphaOmegakid has responded

Replies to this message:
 Message 162 by AlphaOmegakid, posted 12-02-2015 10:21 AM RAZD has responded

  
AlphaOmegakid
Member (Idle past 1073 days)
Posts: 564
From: The city of God
Joined: 06-25-2008


Message 161 of 374 (773456)
12-02-2015 9:57 AM
Reply to: Message 155 by Percy
12-02-2015 7:11 AM


Re: Black White or Grey?
Percy writes:

No, I'm saying there's a region between alive (white in the image analogy) and not alive (black) that is neither living nor non-living (a shade of gray).

No. I merely recognize that there's a gray area between living and non-living.

OK, then show me the semantics that clarify "alive" and "non-living" or the model of a grey area makes no legitimate scientific sense. There is no grey area unless white and black, which are unequivocal, are defined!

So please make sense of this or drop the analogy.

My sentence wasn't a statement. Didn't you see the question mark? My question was rhetorical.
Yes, I recognized that. However you were being quite selective in your quoting of my argument. I responded in kind. This post is much more civil!

This is just another bald declaration. We do have opposite ends of a continuum. A dog is obviously living. A block of lead is obviously non-living. Some things inhabit the region between living and non-living, like perhaps prions and viruses.
See post 152
This message is a reply to:
 Message 155 by Percy, posted 12-02-2015 7:11 AM Percy has responded

Replies to this message:
 Message 165 by Percy, posted 12-02-2015 1:40 PM AlphaOmegakid has responded

  
AlphaOmegakid
Member (Idle past 1073 days)
Posts: 564
From: The city of God
Joined: 06-25-2008


Message 162 of 374 (773457)
12-02-2015 10:21 AM
Reply to: Message 160 by RAZD
12-02-2015 9:09 AM


Re: self-replicating virus - again ...
I didn't enjoy anything about this post. It is meaningless elephant hurling to the claims you made. You quoted my request....

RAZD writes:

(1) It doesn't address the issue of viral life, which is increasingly being accepted as life forms as more is found out (self replication without host, metabolism and making of proteins used to encase it, etc)

You have claimed this several times now. Admittedly, I am totally unaware of this. Evidence Please! Hopefully papers I can access on the web. Not journalistic articles I hope.+

You have claimed several times now that viruses can self replicate, metabolize and make proteins outside a host cell. I claim your bluffing or sadly misinformed on this. I have asked for supporting evidence to support this claim. You provided a bunch of non-relevant material.

I will give you the benefit of a doubt. Please provide supporting evidence for your specific claim in yellow above, or withdraw it.


This message is a reply to:
 Message 160 by RAZD, posted 12-02-2015 9:09 AM RAZD has responded

Replies to this message:
 Message 179 by RAZD, posted 12-02-2015 8:43 PM AlphaOmegakid has responded

  
AlphaOmegakid
Member (Idle past 1073 days)
Posts: 564
From: The city of God
Joined: 06-25-2008


Message 163 of 374 (773458)
12-02-2015 11:46 AM
Reply to: Message 159 by Percy
12-02-2015 8:30 AM


Re: Black White or Grey?
Percy writes:

You're saying that, for example, water that was once but is no longer part of a living creature is "dead", but that water that has never been part of a living creature is "abiotic". I don't think that definition is going to work for anybody.

No, I said nothing similar to that. But using the example of water, it is clear that water is essential to living things. Every abiogenetic hypothesis requires water!. So water by itself is in the non-living category (abiotic). It is not dead, because it has never been alive. But it is necessary and affects all life.

Why do you think a gray area between living and non-living implies that "every abiotic thing would be on the pathway to life." Water is an "abiotic thing," but most water in the universe is not likely on its way to becoming part of a living creature.

I don't think that, nor do I imply that. I have provided an unequivocal definition of life. And recently, I have embraced the grey scale analogy to identify living, non-living, and dead. It works. All non-living things are in the grey area, living things are white, and dead things are black.

The faithful evolutionary continuum from non-living to living through some form of chemical evolution is just speculative hypotheses at this moment. So I reject that there is a "pathway to life'. Water is abiotic, and of course necessary for life.

And then the virus enters another cell and is alive again? Really?

Yes, really. That's exactly what we observe! All life comes from pre-existing life. This concept is perfectly consistent with cell theory and the law of biogenesis. We have a perfectly normal cell, and we have a viral infected cell. The virus is only alive in the sense that it is part of the original cell, and that now that it is within the cell it is disturbing and disorganizing the cell usually until it explodes the cell and releases the virions. Then those non-living virions hang around until they find another host.

I think you would agree that poisons are abiotic and non-living. Yet they affect cells by disturbing their organization to such and extent that they destroy the cell. I think many doctors would agree that a virus can be interpreted as a very specific type of organic poison. In fact, they use the term "viral food poisoning" all the time.

Look at the list of examples of abiotic components from Wikipedia again. Why do you think a virus outside a host cell belongs on that list?

That list is miniscule, but their definition is clear...

quote:
In biology and ecology, abiotic components or abiotic factors are non-living chemical and physical parts of the environment that affect living organisms and the functioning of ecosystems. Abiotic factors and phenomena associated with them underpin all biology. https://en.wikipedia.org/wiki/Abiotic_component

I think a virus is a perfect example by observational evidence that it is a "non-living chemical and physical part of the environment that affects living organisms and the functioning of ecosystems."

And at the same time there is no evidence that a virus is "on the pathway to life".


This message is a reply to:
 Message 159 by Percy, posted 12-02-2015 8:30 AM Percy has responded

Replies to this message:
 Message 184 by Percy, posted 12-03-2015 9:55 AM AlphaOmegakid has responded

  
herebedragons
Member
Posts: 1513
From: Michigan
Joined: 11-22-2009
Member Rating: 10.0


(3)
Message 164 of 374 (773460)
12-02-2015 12:57 PM
Reply to: Message 157 by AlphaOmegakid
12-02-2015 7:59 AM


Re: Black White or Grey?
So now we (you and I) have clarified the grey area. We have categories:

(1) White=Living==>by some unequivocal definition of life
(2) Grey=Abiotic=non-living
(3) Black= Dead

Your position just keeps getting stranger. Why would you put abiotic materials (which means "not biotic" or "not derived from living organisms") as the "grey" area between living and dead? That make NO sense at all.

I'm pretty sure Tanypteryx will spit out his coffee when he sees that you think he was agreeing with you.

The grey scale should be interpreted as:

White = living - meets ALL the criteria for living creatures. I listed my version of this list in Message 132

quote:
(1) self-contained and organized structures (2) the ability to convert chemicals into metabolic and structural components (3) the ability to regulate it's metabolism (4) the ability to grow (5a) the ability to reproduce (5b) heritable traits (6) the ability to adapt to its environment (7) the ability to respond to stimuli

Black = Non-living - meets NONE of the criteria listed above

Grey = Meets SOME of the criteria listed above, but not all of them.

Viruses exhibit at least 5 of the above criteria and arguably all of them when it is within a suitable host cell. So then viruses are in this grey area between living organisms and non-living, abiotic materials - NOT between living and dead. Abiotic materials are not dead, they never were alive in the first place. If viruses are not alive, then they cannot be killed.

ABE: Crystals may have only 1 (or maybe 2) of these characteristics. Self-replicating RNA may have 3 of these characteristics, etc.

Dead organisms become organic matter, which when broken down may become part of abiotic substrates, such as soil, but they are still considered different from actual abiotic materials. We can recognize matter that originated in living organisms because of the way they can use carbon atoms. I know of no abiotic processes that can use carbon like living organisms do. Which makes me wonder why did you not include "carbon-based" in your definition of "living"?

I think this model works very well within Biology and especially well with my definition of life.

I wasn't aware there was really a problem in Biology regarding this issue. Sure some things are hard to classify, even when it comes to a seemingly simple question as to whether the subject is a living organism or not. But such is Biology. As much as we would like everything to fit in nice neat categories, things just are reluctant to allow us such amenities.

So this all makes me wonder what your motive is for wanting such a cut and dried definition of "life." What would such a definition accomplish that cannot be accomplished using the standard criteria?

HBD

Edited by herebedragons, : added ABE portion


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 157 by AlphaOmegakid, posted 12-02-2015 7:59 AM AlphaOmegakid has responded

Replies to this message:
 Message 167 by AlphaOmegakid, posted 12-02-2015 2:39 PM herebedragons has responded

  
Percy
Member
Posts: 18611
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 165 of 374 (773461)
12-02-2015 1:40 PM
Reply to: Message 161 by AlphaOmegakid
12-02-2015 9:57 AM


Re: Black White or Grey?
AlphaOmegakid writes:

OK, then show me the semantics that clarify "alive" and "non-living" or the model of a grey area makes no legitimate scientific sense.

By "show me the semantics" are you asking for definitions of "living" and "non-living" of a specificity that we keep telling you doesn't exist? Dogs are living, a lead block is non-living. That's pretty unambiguous. The area between is ambiguous.

See post 152

See Message 155.

--Percy


This message is a reply to:
 Message 161 by AlphaOmegakid, posted 12-02-2015 9:57 AM AlphaOmegakid has responded

Replies to this message:
 Message 168 by AlphaOmegakid, posted 12-02-2015 3:05 PM Percy has responded

    
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