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Author Topic:   Life - an Unequivicol Definition
RAZD
Member
Posts: 19980
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.0


Message 121 of 374 (773198)
11-26-2015 12:53 PM
Reply to: Message 120 by Percy
11-26-2015 7:44 AM


Re: death and extinction -- a part of evolution
Sure, but that's orthogonal to my point, that death isn't necessary for selection. The way you expressed it was a statement that death *is* necessary for selection.

Well curiously, as regards mules in particular, I was not talking selection, I was talking death and drift as an evolutionary mechanism that stochastically removes genes. In the case of mules whole phenotypes are culled, whether their genes are beneficial or not.

The same occurs for any sterile phenotype of any species. The same for any individual that dies before reproducing.

Both those terms are new to me, so I had to look them up. I'm definitely not talking about cladogenic speciation. Anagenic speciation would be closer but because it posits "rapid evolution in the ancestral form without speciation taking place" I don't think it's what I was talking about. I had in mind evolution of a population (slow, fast, doesn't matter) that over time becomes significantly different than the original. Species are a continuum. There was no point in time where the ancestral species became a new species, but at some point it became so different that it must be labeled a new species. ...

Yeah, I was looking at that too, it appears that this article has been edited and changed since last I looked. Looking at the history it was changed 15 April 2015 to make it "rapid" (one of the problems with wiki ... ) and before that it read:

quote:
''Anagenesis'', also known as "phyletic change", is speciation wherein the ancestor species wholly morphs into the new species, such that there are no remaining other populations of the ancestor species and the species can be considered extinct. The ancestor species is therefore superseded by the new species it morphs into. Anagenesis is in contrast to the branching speciation known as cladogenesis.

When enough mutations have occurred and become stable in a population so that it is significantly differentiated from an ancestral population, a new species name may be assigned. A series of such species is collectively known as an evolutionary ''lineage''. The University of California, Berkeley resource on understanding evolution defines a lineage as "A continuous line of descent; a series of organisms, populations, cells, or genes connected by ancestor/descendent relationships." The various species along an evolutionary lineage are chronospecies. ... (edited for readability)


Another definition is:

quote:
an•a•gen•e•sis
[ˌanəˈjenəsis] NOUN
biology: species formation without branching of the evolutionary line of descent. Compare with cladogenesis.

Now I don't think the speed of the evolution really affects the result, so I'll stick with the simpler definition, which is what you were talking about, yes?

... There was no extinction. There was no death of the last individual of a species.

AbE: Granted that once a species no longer exists we do call it extinct, but in the case I'm talking about there is no extinction event, no death of the last individual.

Yet this still requires the death of the "old-timers" (from old age if nothing else) as they are gradually replaced by the newer forms. Again, more of a genetic drift pattern than a selection pattern.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 120 by Percy, posted 11-26-2015 7:44 AM Percy has responded

Replies to this message:
 Message 122 by NoNukes, posted 11-26-2015 2:19 PM RAZD has responded
 Message 127 by Percy, posted 11-27-2015 8:16 AM RAZD has responded

  
NoNukes
Inactive Member


Message 122 of 374 (773204)
11-26-2015 2:19 PM
Reply to: Message 121 by RAZD
11-26-2015 12:53 PM


Re: death and extinction -- a part of evolution
Well curiously, as regards mules in particular, I was not talking selection, I was talking death and drift as an evolutionary mechanism that stochastically removes genes. In the case of mules whole phenotypes are culled, whether their genes are beneficial or not.

Mules are a dead end. But it appears that you are willing to accept a small subset of the evolutionary process as indicating life. Nothing particularly wrong with that. On the other hand, you rely this time on death, and then drift, the latter of which I dispute occuring in mules except by death.

Which leaves for me that you are willing to say that mules are alive because they experience death. Surely that is somewhat of a tautology.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King

If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams


This message is a reply to:
 Message 121 by RAZD, posted 11-26-2015 12:53 PM RAZD has responded

Replies to this message:
 Message 123 by RAZD, posted 11-26-2015 3:31 PM NoNukes has responded

  
RAZD
Member
Posts: 19980
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.0


Message 123 of 374 (773208)
11-26-2015 3:31 PM
Reply to: Message 122 by NoNukes
11-26-2015 2:19 PM


Re: death and extinction -- a part of evolution
Mules are a dead end. ...

As are ALL organisms that don't reproduce. So? Is not failure to reproduce one of the processes of evolution?

It seems you keep thinking of mules as a separate population\species -- they aren't. The come from horses and donkeys. Both parent species also have sterile offspring that you would call horse or donkey, and which would also be dead ends as regards passing their genes to the next generation. So too would be any young offspring killed before reproducing. Is not failure to reproduce one of the processes of evolution?

... But it appears that you are willing to accept a small subset of the evolutionary process as indicating life. ...

Do you seriously think that my definition means that every single organism undergoes every single evolutionary process?

Curiously I see the development of hybrid sterility between subpopulations as part of the process of speciation, and a rather important one at that, as that is the point at which gene flow between the populations ceases.

The horses and donkeys don't share that element of evolution -- would you then say that my definition says that they are not alive? Really?

... . On the other hand, you rely this time on death, and then drift, the latter of which I dispute occuring in mules except by death.

Well duh! Is that not how all drift occurs? -- by the death of the individuals bearing genes that are then not reproduced. That is how genes are lost. That is one of the ways gene frequencies shift.

Genetic drift is an evolutionary process. Mules can also have mutations*, but the point is not how many evolutionary processes need be involved, but that they are "capable of evolution."

Which leaves for me that you are willing to say that mules are alive because they experience death. Surely that is somewhat of a tautology.

It would be if that were what I was saying.

Enjoy

*I also would entertain the thought, for instance, that -- as people keep force mating horses and donkey long beyond any natural inclination for them to mate (google it) -- there is a remote possibility that they could develop a mule that is not sterile: every time a mule is created there is that possibility ... or with Hinneys. Can you say that this would [i]not/i be possible?


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 122 by NoNukes, posted 11-26-2015 2:19 PM NoNukes has responded

Replies to this message:
 Message 124 by NoNukes, posted 11-26-2015 6:22 PM RAZD has responded
 Message 125 by Blue Jay, posted 11-26-2015 7:33 PM RAZD has responded

  
NoNukes
Inactive Member


Message 124 of 374 (773221)
11-26-2015 6:22 PM
Reply to: Message 123 by RAZD
11-26-2015 3:31 PM


Re: death and extinction -- a part of evolution
As are ALL organisms that don't reproduce. So? Is not failure to reproduce one of the processes of evolution?

At this point, I'm just trying to understand your argument. Originally it seemed to be summed up in one sentence, but I don't think our discussion since has confirmed that. It seems now that you are arguing that undergoing one or more evolutionary processes is sufficient.

Yes, mules do participate in some processes that are evolution. They are born and they die leaving their peers behind. But mules don't reproduce. Even in those cases where some female mules are fertile, they are not fertile with male mules which are invariably sterile. So there really are essentially no second generations of mules and there is no feedback from mule survival that would allow nature to produce more mules based on which mules survive. Humans have to intervene. So mules, in my opinion, fail to participate in natural selection (which I take to describe the process of surviving to reproduce and thereby pass on personal traits) and which I also take to mean that mules do not truly evolve.

It seems you keep thinking of mules as a separate population\species -- they aren't.

I respectfully disagree. Mules are a separate population and they are neither the same species as horses nor donkeys.

Edited by NoNukes, : No reason given.

Edited by NoNukes, : No reason given.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King

If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams


This message is a reply to:
 Message 123 by RAZD, posted 11-26-2015 3:31 PM RAZD has responded

Replies to this message:
 Message 130 by RAZD, posted 11-27-2015 8:57 AM NoNukes has responded

  
Blue Jay
Member (Idle past 893 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 125 of 374 (773225)
11-26-2015 7:33 PM
Reply to: Message 123 by RAZD
11-26-2015 3:31 PM


Re: death and extinction -- a part of evolution
Hi, RAZD.

RAZD writes:

Is not failure to reproduce one of the processes of evolution?

This opens a rather large can of worms, and I'm not sure where to begin with it.

As AOkid and NoNukes have pointed out, evolution is a population phenomenon: individuals are all incapable of evolution. So, maybe you could get away with this if you said, "anything whose population is capable of evolution."

Of course, we then have to ask what the mule's population is (does it include horses and donkeys? Or are mules a separate population?); and what happens if that entire population is incapable of reproduction. Surely an entire population that is incapable of reproduction cannot evolve, since there can be no differential reproductive success (change in fitness) within that population.

Also, I'm having a little trouble justifying this in light of what you wrote in Message 56:

RAZD writes:

Crystals can reproduce without change, but are not generally considered life, so I don't see how anything that reproduces without change should be.

This muddies the waters. A mule's inability to reproduce counts as a "process of evolution," thus letting it meet the requirements for "life," but a crystal's ability to reproduce without change disqualifies it?

I think you need to provide some better justification for the dividing line you've chosen.

Intuitively, any valid definition of life should probably include mules and exclude crystals, but you'll need to elaborate on your definition a bit before this is clear.


-Blue Jay, Ph.D.*

*Yeah, it's real

Darwin loves you.


This message is a reply to:
 Message 123 by RAZD, posted 11-26-2015 3:31 PM RAZD has responded

Replies to this message:
 Message 126 by Pressie, posted 11-27-2015 7:54 AM Blue Jay has acknowledged this reply
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Pressie
Member
Posts: 2074
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 2.7


(2)
Message 126 of 374 (773241)
11-27-2015 7:54 AM
Reply to: Message 125 by Blue Jay
11-26-2015 7:33 PM


Re: death and extinction -- a part of evolution
Blue Jay writes:

Intuitively, any valid definition of life should probably include mules and exclude crystals, but you'll need to elaborate on your definition a bit before this is clear.

http://www.wired.com/2013/01/living-crystal/

wired writes:

THREE BILLION YEARS after inanimate chemistry first became animate life, a newly synthesized laboratory compound is behaving in uncannily lifelike ways.

The particles aren’t truly alive — but they’re not far off, either. Exposed to light and fed by chemicals, they form crystals that move, break apart and form again.

“There is a blurry frontier between active and alive,” said biophysicist Jérémie Palacci of New York University. “That is exactly the kind of question that such works raise.”

There's no real distinction between being alive or not. Even from crystals. It all is blurry.
This message is a reply to:
 Message 125 by Blue Jay, posted 11-26-2015 7:33 PM Blue Jay has acknowledged this reply

Replies to this message:
 Message 128 by Tangle, posted 11-27-2015 8:27 AM Pressie has responded

    
Percy
Member
Posts: 18595
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.0


Message 127 of 374 (773242)
11-27-2015 8:16 AM
Reply to: Message 121 by RAZD
11-26-2015 12:53 PM


Re: death and extinction -- a part of evolution
RAZD writes:

Well curiously, as regards mules in particular, I was not talking selection, I was talking death and drift as an evolutionary mechanism that stochastically removes genes. In the case of mules whole phenotypes are culled, whether their genes are beneficial or not.

This may be what you meant to say or wished you said, but it isn't what you actually wrote: "Extinction of species is necessary to evolution just as individual death is necessary to evolution. Without death and extinction selection does not occur." This seemed a little bit too restrictive to me, because selection can indeed occur without death or extinction, and that's all I was saying.

--Percy


This message is a reply to:
 Message 121 by RAZD, posted 11-26-2015 12:53 PM RAZD has responded

Replies to this message:
 Message 134 by RAZD, posted 11-30-2015 11:16 AM Percy has acknowledged this reply

    
Tangle
Member
Posts: 6950
From: UK
Joined: 10-07-2011
Member Rating: 5.1


(3)
Message 128 of 374 (773244)
11-27-2015 8:27 AM
Reply to: Message 126 by Pressie
11-27-2015 7:54 AM


Re: death and extinction -- a part of evolution
Pressie writes:

There's no real distinction between being alive or not.

Oh I think there is. We (science), can agree on 99.9999% of stuff in the world and say for each that it is either alive or dead. And for the rest you can legitimately say:

It all is blurry.

And that's an end to it.

Alternatively you can squabble for weeks on an internet forum attempting to resolve the unresolvable.

But hey, that's life ;-).


Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien.

Life, don't talk to me about life - Marvin the Paranoid Android

"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.


This message is a reply to:
 Message 126 by Pressie, posted 11-27-2015 7:54 AM Pressie has responded

Replies to this message:
 Message 129 by Pressie, posted 11-27-2015 8:38 AM Tangle has not yet responded

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


Message 129 of 374 (773248)
11-27-2015 8:38 AM
Reply to: Message 128 by Tangle
11-27-2015 8:27 AM


Re: death and extinction -- a part of evolution
Exactly Tangle, but we also can read the last paragraph in that article.

As for what’s happening now in Palacci and Chaikin’s lab, a particle currently under development isn’t mobile, but it has a metabolism and is self-replicating. “We’re working on it,” Chaikin said.
It's not a life form as we know it yet but it's getting to it. To define life really is blurry. We're working out the 0.00000001 percent we don't know!

Edited by Pressie, : No reason given.

Edited by Pressie, : No reason given.


This message is a reply to:
 Message 128 by Tangle, posted 11-27-2015 8:27 AM Tangle has not yet responded

    
RAZD
Member
Posts: 19980
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.0


Message 130 of 374 (773249)
11-27-2015 8:57 AM
Reply to: Message 124 by NoNukes
11-26-2015 6:22 PM


equine masochistic necrophilia
At this point, I'm just trying to understand your argument. Originally it seemed to be summed up in one sentence, but I don't think our discussion since has confirmed that. It seems now that you are arguing that undergoing one or more evolutionary processes is sufficient.

Demonstrating "capable of evolution" does not mean demonstrating every single process of evolution.

I respectfully disagree. Mules are a separate population and they are neither the same species as horses nor donkeys.

https://en.wikipedia.org/wiki/Mule

quote:
A mule is the offspring of a male donkey (jack) and a female horse (mare).[1] Horses and donkeys are different species, with different numbers of chromosomes. ...

Species: Equus asinus x Equus caballus


That means hybrid and not a separate species. Mules only exist within a population of horses and donkeys that are made to interbreed, usually by raising the male donkey and the female horse together so that they are their only opportunities to breed. Mules are not a separate species nor a separate breeding population. The breeding population is male donkey and female horse, ie the genus Equus.

Yes, mules do participate in some processes that are evolution. They are born and they die leaving their peers behind. But mules don't reproduce. Even in those cases where some female mules are fertile, they are not fertile with male mules which are invariably sterile. So there really are essentially no second generations of mules and there is no feedback from mule survival that would allow nature to produce more mules based on which mules survive. Humans have to intervene. So mules, in my opinion, fail to participate in natural selection (which I take to describe the process of surviving to reproduce and thereby pass on personal traits) and which I also take to mean that mules do not truly evolve.

Your opinion. You are saying that one specific process is absolutely necessary to show "capable of evolution" and you are beating a dead horse over it.

Is the genetic makeup the same for each mule?

Do the alleles of all the mules change with the introduction of new mules from the breeding population (donkey x horse) and the death of old mules?

... Humans have to intervene. ...

Actually humans "intervene" because it is to their advantage to have mules, let's go back to wiki

quote:
Mules are "more patient, sure-footed, hardy and long-lived than horses, and they are considered less obstinate, faster, and more intelligent than donkeys."[3]:5

A female mule that has estrus cycles and thus, in theory, could carry a fetus, is called a "molly" or "Molly mule," though the term is sometimes used to refer to female mules in general. Pregnancy is rare, but can occasionally occur naturally as well as through embryo transfer.

The mule is a renowned example of hybrid vigor.[9] Charles Darwin wrote: "The mule always appears to me a most surprising animal. That a hybrid should possess more reason, memory, obstinacy, social affection, powers of muscular endurance, and length of life, than either of its parents, seems to indicate that art has here outdone nature."[10] ... Mules exhibit a higher cognitive intelligence than their parent species. This is also believed to be the result of hybrid vigor, similar to how mules acquire greater height and endurance than either parent.[12]


Thus they have different traits than their parents -- evolution has occurred.

The reason they keep being made is because those traits are beneficial to humans. In this sense they have adapted humans to provide their reproduction for them.

There are lots of forced hybrids (humans "intervene") and they have different levels of sterility; mules appear to be the extreme in that regard, but even they are not totally prescribed from reproducing withing their breeding population.

There are also lots of individuals from many many many species that are sterile. What that means is that they have a selection of traits that prevents that phenotype from reproducing, and thus alters the frequency of alleles\traits in the breeding population.

In any breeding population that is evolving some individuals reproduce more than others and some fail to reproduce before dying, and the frequency of alleles\traits changes as a result.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 124 by NoNukes, posted 11-26-2015 6:22 PM NoNukes has responded

Replies to this message:
 Message 131 by NoNukes, posted 11-27-2015 3:36 PM RAZD has responded

  
NoNukes
Inactive Member


Message 131 of 374 (773271)
11-27-2015 3:36 PM
Reply to: Message 130 by RAZD
11-27-2015 8:57 AM


Re: equine masochistic necrophilia
Demonstrating "capable of evolution" does not mean demonstrating every single process of evolution.

In my opinion, 'capable of evolving' ought to mean "undergoing a change in allele frequency in a population from generation to generation". But that is apparently not what you meant. We don't even agree that mules are a population, which is something I find strange. Perhaps we've reached a point where we must simply agree to disagree.

Beyond that, I think agreeing that something less than demonstrating the process of evolution is sufficient might mean that a simpler definition of life is possible.

That means hybrid and not a separate species. Mules only exist within a population of horses and donkeys that are made to interbreed,

You've skipped over something obvious. Horses and donkeys are not the same species. Therefore a mule cannot possibly be the same species as horses and donkeys. It is a hybrid. We can easily discuss a separate population of mules without requiring a separate species.

Besides that, what is a species anyway?

Separate population is not the same thing as separate species. It simply means a group of animals distinct enough to talk about. Like a population with a different number of chromosomes than either horses or donkeys.

Edited by NoNukes, : No reason given.

Edited by NoNukes, : No reason given.

Edited by NoNukes, : No reason given.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King

If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams


This message is a reply to:
 Message 130 by RAZD, posted 11-27-2015 8:57 AM RAZD has responded

Replies to this message:
 Message 136 by RAZD, posted 11-30-2015 11:35 AM NoNukes has responded

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


(4)
Message 132 of 374 (773275)
11-27-2015 4:16 PM
Reply to: Message 115 by RAZD
11-25-2015 12:44 PM


Re: try again
A couple comments on this whole line of discussion... (not just directed at you, but regarding this whole issue)

Yet it doesn't explain the existence or evolution of viruses, nor does it allow for RNA life forms, and this is a failure.

1. This whole "definition of life" discussion is much like discussions about what species are; we intuitively know what constitutes a species, but to create a standard definition that applies in every single case proves to be elusive - biology is just messy. In the end, just as with species distinctions, scientists duke it out arguing in the literature as to whether a particular organism is "alive" or not until eventually there is a consensus reached. Ten to twenty years ago, it was pretty much the consensus that viruses were not alive. Now, it depends on who you ask. I heard a virologist on NPR this morning who referred to viruses as "organisms" that are alive. So the thinking about whether viruses are alive or not is shifting towards the "yes" side; not because definitions are changing or because scientists are being equivocal, but because we are changing how we view these grey areas.

Your definition is like saying only right hands are hands, and left hands don't qualify as hands because they aren't right hands.

2. AOkid's attempt to nail down a definition of "life" strikes me as an attempt to erase the blurry boundary between living things and non-living things in order to claim there is no transitional steps between living and non-living. Just as creationists define Archeopteryx as a bird and then claim it is not a transitional fossil between non-avian, feathered theropods and modern birds. In the same way, by his definition, viruses are not in this blurry area between living and non-living; they are simply defined as non-living.

Your definition shows A boundary event in the evolution of life, just as the evolution of eukaryotes shows a boundary event in the evolution of life, but we don't consider prokaryotes to be non-life because they don't fit the definition of eukaryotic life. This is an arbitrary choice, rather than one based on facts.

3. Right, life cannot be defined it is only described. That is why being overly specific and saying for example, "uses ATP" is inappropriate. Saying "All know life utilizes ATP as the main energy carrying molecule" would be appropriate, because it is descriptive not prescriptive.

4. I think your attempt to define life as "anything capable of evolution" is also problematic, IMO. I am not sure I can explain exactly why I don't like that definition, but it seems to require too many caveats and additional explanations, otherwise it simply means "anything that can change over time."

I think we should stick to the time-tested, simple description of life we all learn in school.

Life has (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

I would argue that viruses ARE capable of all the above within a suitable environment (regulate metabolism is questionable but all the rest seem solid).

I think the above "definition" is simple enough and is thoroughly descriptive of life as we know it. It is not too specific about any of the processes so some as of yet unknown life could still fit this definition.

But who knows, we may someday need to update the definition somewhat to accommodate new discoveries.

HBD


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 115 by RAZD, posted 11-25-2015 12:44 PM RAZD has responded

Replies to this message:
 Message 138 by RAZD, posted 11-30-2015 11:58 AM herebedragons has not yet responded

  
RAZD
Member
Posts: 19980
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.0


Message 133 of 374 (773351)
11-30-2015 11:09 AM
Reply to: Message 125 by Blue Jay
11-26-2015 7:33 PM


review of 'evolution as definition of life'
This opens a rather large can of worms, and I'm not sure where to begin with it.

Every definition opens a can of worms, some more than others. Defining life based on what is observed aspects of life (the 'standard' definition and AOK's definition) all are post hoc definitions. They all leave out one thing or another that then isn't considered life, but which is certainly more than just chemical. Such as evolving viruses.

I'm going to take this opportunity to summarize where I am on this issue, and include some history of how I got here, so this will be loooong.

As AOkid and NoNukes have pointed out, evolution is a population phenomenon: individuals are all incapable of evolution. So, maybe you could get away with this if you said, "anything whose population is capable of evolution."

And I have no problem with that, but I looked back to where I originally developed my definition on the Definition of Life (circa July 2006) and in particular my post A Simple Definition of Life ...:

quote:
Message 24: Which is what makes it so much fun to delve into an actual definition, because this seems to be such an easy question to answer at first.

And yes, I do have an answer, a fairly simple one.

The simple answer is that there is no clear definition of life that always distinguishes life from non-life.

There are examples that we can all agree belong to the category "life" and there are examples that we can all agree belong to the category "non-life" ... and then there are examples where we cannot agree that they belong in "life" or in "non-life" categories, and there are no currently known criteria that can make this distinction.

Personally, I think the best working definition I've seen, is that life is some physical arrangement of atoms and molecules that is potentially capable of evolution (the change in hereditary traits in populations from generation to generation in response to ecological opportunities) and the formation of nested hierarchies of descent.


Now I note that adding "potentially" to my current definition would solve some of the problems raised thus far (it can be argued that mules are potentially capable of evolution, as new mules with new genetic variations are constantly being added to the mix).

Note that this previous definition is rather more restrictive than I have argued here, with the nested hierarchies addendum. Not all species form nested hierarchies whey they are on the track to extinction, yet the individuals are still considered alive, so I am willing to drop that element; successful life-forms will likely speciate and form nested hierarchies but it isn't critical that they do so.

Instead what I have argued here is that all multicellular life is essentially a colony population of cells -- or more specifically an ecosystem of colonies that interact and compete for resources -- that all have generations and evolve during the lifetime of the multicellular life-form, and thus it is alive by my definition. This also works for sterile drones in ant and bee colonies and any sterile offspring within a species.

This also gets into the distinction between multicellular life and single cell life, with colonies of single cells as an obvious, observed, intermediate stage of development\evolution.

There is another aspect that I have also been considering, and that is the transplanting of living tissue upon the death of a donor; part of the organism dies (see What Is the Medical Definition of Death?), but useful parts are still living: they are parts of the colony that are still able to function, and thus they can be transplanted into another support structure (colony/ecosystem), in much the same way endangered species can be transplanted into new ecosystems where they might survive.

Curiously I also listed the 'standard' definition of life on that post, for reference:

quote:
On this thread we see:

quote:
Message 7
One site I ran across in my research into abiogenesis is
http://baharna.com/philos/life.htm
It discusses the different parts of the definitions with pros and cons. Rather interesting, if not too practical in the long run -- the definitions are too frought with problems when they:
(a) includes things that are not (normally) considered alive
(2) excludes things that are normally considered alive

and

quote:
Message 25
See wikipedia
http://en.wikipedia.org/wiki/Life
particularly the "conventional definition
http://en.wikipedia.org/wiki/Life#A_conventional_definition

While there is no universal agreement on the definition of life, scientists generally accept that the biological manifestation of life exhibits the following phenomena:

1. Organization - Living things are composed of one or more cells, which are the basic units of life.
2. Metabolism - Metabolism produces energy by converting nonliving material into cellular components (synthesis) and decomposing organic matter (catalysis). Living things require energy to maintain internal organization (homeostasis) and to produce the other phenomena associated with life.
3. Growth - Growth results from a higher rate of synthesis than catalysis. A growing organism increases in size in all of its parts, rather than simply accumulating matter. The particular species begins to multiply and expand as the evolution continues to flourish.
4. Adaptation - Adaptation is the accommodation of a living organism to its environment. It is fundamental to the process of evolution and is determined by the organism's heredity as well as the composition of metabolized substances, and external factors present.
5. Response to stimuli - A response can take many forms, from the contraction of a unicellular organism when touched to complex reactions involving all the senses of higher animals. A response is often expressed by motion: the leaves of a plant turning toward the sun or an animal chasing its prey.
6. Reproduction - The division of one cell to form two new cells is reproduction. Usually the term is applied to the production of a new individual (either asexually, from a single parent organism, or sexually, from at least two differing parent organisms), although strictly speaking it also describes the production of new cells in the process of growth.

(bold in the original)

(note the second wiki link above works, but it takes you to the same place as the first wiki link and should be replaced by http://en.wikipedia.org/wiki/Life#Biology)

Now AOK's definition is essentially #1 (Organization) plus #2 (Metabolism) in a reductionist extreme, and doesn't include all the other 'standard' observed aspects of currently existing\known terrestrial life. His insistence on including DNA (which the 'standard' definition doesn't) means that he has to consider that there are then three areas of consideration instead of 2, and that the middle one (viruses) behaves just like living things by reproducing and evolving, something that rocks and water don't do. What do you call that -- quasi-life? proto-life? -- and I would think that such a category would be a large problem for your typical creationist type.

In addition, his insistence on a cell raises other problems.

quote:
To my mind, basing a definition on the existence of a cell is begging the question -- the first criteria is basically saying that life is something that has the basic units of life. This is a fairly standard definition of life, and it was reviewed by Joseph Morales (see above), and he ended by concluding that there are degrees of life, different levels that apply.

And that a cell wall was not necessary for life to function. Another post on that thread goes into this in more detail:

quote:
... re membrane your cell:
... we need only find the objective properties of a cell and decide if those are necessary for life. Or so it would seem, but there is something telling me it isn't quite that easy.

No, it isn't quite that easy. That is after all the whole reason why abiogenesis is in the current state of knowledge that it is eh?

Consider Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. (click)

The protein synthesis machinery is too complex to have evolved before membranes. Therefore a symbiosis of membranes, replicators, and catalysts probably mediated the origin of the code and the transition from a nucleic acid world of independent molecular replicators to a nucleic acid/protein/lipid world of reproducing organisms. Membranes initially functioned as supramolecular structures to which different replicators attached and were selected as a higher-level reproductive unit: the proto-organism.

I propose a new theory for the origin of the first cell: fusion of two cup-shaped obcells, or hemicells, to make a protocell with double envelope, internal genome and ribosomes, protocytosol, and periplasm. Only then did water-soluble enzymes, amino acid biosynthesis, and intermediary metabolism evolve in a concentrated autocatalytic internal cytosolic soup, causing 12 new amino acid assignments, termination, and rapid freezing of the 22-acid code.

Before then we had replication and a bunch of stuff going on that is similar to what we think of a cellular life ... is it {life}? Or a stage of "activated chemicals" that responded to certain environmental conditions to catalyse their replication?

We also have no idea how many different kind of replication systems were involved, it could have just taken the right combination in the right place of two or three systems.


So the replicators and catalysts would have existed before the cell evolved, and the cell then enabled DNA to evolve along with the mechanisms to form proteins. And the issue is still - where do you draw the line: after the house is complete and occupied or when the foundation is laid and the building materials are on hand or some magic point in between?

Are viruses "alive" or not? Again this was discussed on the previous thread:

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

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.

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. ... 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?


So it looks like DNA evolved before cell walls in this instance.

There are also several other viruses that self replicate (without using existing cells), and these can be dredged up and posted if necessary; suffice it to say that the biological world is seeing more and more scientists accepting viruses as life/living.

Enough for now (if not too much)

Enjoy.


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
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This message is a reply to:
 Message 125 by Blue Jay, posted 11-26-2015 7:33 PM Blue Jay has not yet responded

  
RAZD
Member
Posts: 19980
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.0


Message 134 of 374 (773353)
11-30-2015 11:16 AM
Reply to: Message 127 by Percy
11-27-2015 8:16 AM


Re: death and extinction -- a part of evolution
This may be what you meant to say or wished you said, but it isn't what you actually wrote: ...

Fine. Still rather a minor point to how life is defined. Consider it clarified.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 127 by Percy, posted 11-27-2015 8:16 AM Percy has acknowledged this reply

  
AlphaOmegakid
Member (Idle past 1071 days)
Posts: 564
From: The city of God
Joined: 06-25-2008


Message 135 of 374 (773357)
11-30-2015 11:25 AM
Reply to: Message 105 by New Cat's Eye
11-24-2015 3:01 PM


Black White or Grey?
Cat Sci writes:

Look at this image:

I can point to the middle of it and say that it is not black.

But nobody can say where white stops and black starts.

Well not to make a big deal about this, but it is done all the time. There is black paint, and there is white paint. Grey is a mixture of the two.

Cat Sci writes:

You're insisting that only the far right edge be called black, and everything else besides that be called white.

Denying the existence of all that grey space is a disservice to everyone.

Why do you insist on it?

Well No! Either you drastically misunderstand or this is a severe strawman. Let's examine your example.

Let's say since black symbolically represents death, that black is dead stuff. Since white is the combo of all colors, let's say that that is life! Anything white is cellular life which is uncontroversial, unequivocal, and meets most if not all of the seven characteristics of life. Now to the naked eye, one cannot differentiate white from grey for about 10% of the gradient on the left side. It all looks white! The same is true for about 10% of the gradient on the right side. That leaves about 80% which is some shade of grey.

My definition is on the grey side of white. It is not 100% white, but very close, and within the 10% gradient line as an analogy. It is a minimalist definition of life. So I disagree with your statement that I am denying the "grey gradient" of life. However, I am saying that "white" (10% margin) and Black (10% margin) is not so fuzzy, and it is definable.

Now let's look at some examples with the current 7 characteristics of Life that are in most Biology textbooks:

1. Homeostasis
2. Metabolism
3. Growth
4. Adaptation
5. Response to stimuli
6. Reproduction
7. Organization / Cellular

Self replicating molecules - 2 and 6 and 4?
Fire - 2 and 3 and 4? and 5? and 6?
Crystals - 3 and 6
virions - 7

The only reason "life is fuzzy" is because of the equivocal terms used to define it. With my definition, only one of these terms is used in a very specific way. My definition allows all of these characteristics, but requires a certain minimal level of self sustainment which is identifiable in living things. No equivocation needed.

My definition does not remove the grey, but it limits what can be identified as white.


This message is a reply to:
 Message 105 by New Cat's Eye, posted 11-24-2015 3:01 PM New Cat's Eye has responded

Replies to this message:
 Message 139 by New Cat's Eye, posted 11-30-2015 4:07 PM AlphaOmegakid has not yet responded
 Message 140 by Percy, posted 11-30-2015 4:30 PM AlphaOmegakid has responded

  
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