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Author Topic:   Life - an Unequivicol Definition
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 114 of 374 (773141)
11-25-2015 10:45 AM
Reply to: Message 90 by NoNukes
11-23-2015 9:47 AM


Mules again ...
It appears that my response was not clear. I agree that speciation between horses and donkeys is complete. ...
Curiously I would say 99% complete -- they can still mate and produce offspring, and almost all are sterile. Some can occasionally mate back with one of their parent stocks.
... But what the infertility of mules does not show is that the mule offspring is on an evolutionary path. ...
When you look at mules in terms of evolution you have to consider what the breeding population is that produces the mule, ie - the horse and donkeys (and zebra and quagga) parent population. This population produces several types of offspring: horses, donkeys, zebras, horse/donkey hybrids (mules, hinneys), horse/zebra hybrids and donkey/zebra hybrids; the quagga is now extinct (fairly recently as there are pictures of them) and thus does not produce any offspring.
Is the recent extinction of the quagga an evolutionary path? I don't see how you can say otherwise -- extinction of species is necessary to evolution just as individual death is necessary to evolution. Without death and extinction selection does not occur.
... The question is whether mules are evolving and thus alive and not whether donkeys and horses are alive. I don't believe it is necessary that mules be able to evolve. They are the reproductive offspring of living creatures. That's enough. And it would be enough even if every single mule offspring were sterile.
The death of sterile animals, or actually of all animals that do not reproduce, is part of the evolutionary process that selects more fit individuals for reproduction. To say that only those that pass on their genes are evolving, while ignoring those that are removing less viable genes, is rather myopic in my opinion. It's like saying people only have right hands.
And the actual question is whether mules are capable of evolution ...
quote:
Message 10: Mine is simpler: anything capable of evolution. (cue definition of evolution ^(1)... ).
(1) The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities for growth, development, survival and reproductive success in changing or different habitats.

This isn't saying that every organism has to undergo every known process of evolution, as that would be absurd.
Removal of less viable traits - the death of any individual organism that doesn't reproduce - changes the frequency of distribution of traits withing the breeding population, whether by selection or drift, and thus they take part in evolution.
The removal of hybrid phenotypes that bridge between diverging daughter populations are necessary to the process of speciation, and are a definite part of evolution. Death is one of the processes for removal of less fit traits.
Message 93: ... There is no such thing as a reproductive pool of mules. ...
The reproductive pool is their parent population, which includes horses and donkeys (and zebras and quaggas and other hybrids).
Mules are sterile. As best as I can tell, males are 100 percent sterile and females are essentially so. ...
And some donkeys and some horses are sterile, some purebred racehorses in particular are sterile. Sterility is a fact of biology and evolution, and is not restricted to hybrids or any one species -- it is an evolutionary process. Any new traits that occur in any sterile individual are not passed on to following generations, and the loss of such a new trait, whether beneficial or not, is genetic drift.
... For that reason, a population of mules does not undergo genetic drift, because there is no random sampling of the characteristics of the mule population to produce a new generation of mules.
Amusing. What you are saying is that there is no fitness\mating selection in the removal of their genes from the breeding (parent) population. They are remove in the same way a tree falling on a colt would remove its genes from the breeding population. That is what drift does.
Enjoy

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This message is a reply to:
 Message 90 by NoNukes, posted 11-23-2015 9:47 AM NoNukes has seen this message but not replied

Replies to this message:
 Message 116 by Percy, posted 11-25-2015 3:46 PM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 115 of 374 (773150)
11-25-2015 12:44 PM
Reply to: Message 91 by AlphaOmegakid
11-23-2015 2:11 PM


try again
Yes, it is. My definition is consistent with cell theory as well as evolution theory.
Yet it doesn't explain the existence or evolution of viruses, nor does it allow for RNA life forms, and this is a failure.
You like to cite (appeal to) authority and pick and choose who you quote, ignoring those that say viruses are alive and are one of 4 branches of life.
Nope, not even close. In your dream world yes, but not according to my definition. You can't just pick and choose which parts of it you like.
Incorrect on two counts: (1) your definition isn't the acid test for life, so your use of it to validate it is tautological, and (2) invalidating any one part of it invalidates the whole as being the definition of life.
Your definition is like saying only right hands are hands, and left hands don't qualify as hands because they aren't right hands.
My definition does show the boundary quite well. It requires a self contined entity in which ATP is used for metabolism and proteins are being synthesized from a DNA to RNA synthesis. ...
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.
... Life does not require evolution. We have plenty of asexual populations which don't vary from generation to generation. That doesn't make them not alive according to your definition.
You make the claim, you provide the evidence. Show me one species that does not show any evolutionary processes from generation to generation.
Or are you picking and choosing what you consider relevant.
Message 92: Amazing. Just Amazing. Not only can you equivocate on what a population is within your own definition, you can distort the meaning of mine. Just amazing!
Curiously, what I was showing you was two different ways your definition fails. That is not distortion, it is pointing out the inadequacy of your definition.
Here is the definition of self-contained which you evidently are unaware...
quote:
1. containing in oneself or itself all that is necessary; independent.
Self-contained Definition & Meaning | Dictionary.com
A living organism, by my definition , has everything within itself to use and synthesize ATP, It has DNA, and RNA, and it has proteins.
NO, A MOLECULE DOES NOT CONTAIN WITHIN ITSELF THESE ABILITIES. This is just one big strawman joke.
And thank you for demonstrating another failing of your definition: cells consume, as part of their living processes, consumption of raw materials is one of the well known elements of life, the raw materials to use in the synthesis of proteins, enzymes, etc ... and thus cells are not self-contained according to your definition.
And if you allow consumption of raw materials from outside the cell, you just allowed the use of raw materials by molecules to reproduce. Either way, fail.
My definition describes, in part, the Central Dogma of Biology. The principles of which are taught in "every" high school Biology book around the world. ...
Big whap. Typical creationist appeal to assumed authority. Definitions, like theories, change all the time, especially when a better one comes along that does a better job of explaining all the evidence.
Your definition does not explain the existence and behavior of viruses, mine does; mine explains more evidence than yours does. That alone makes it a better definition. The fact that the same definition was developed by NASA is more validation of its usefulness. Has anyone else developed a very similar definition to yours in all those Biology text books you appeal to?
... If you read this wiki article you will find the word "information" is used 29 times. It seems the evidence that this is well understood in Biology is overwhelming.
My objection to using "information" is not that it has never been used, but that it needs to be well defined so that everyone understands the meaning. If the use in wiki means one thing and the way you use it means another, then that is the logical fallacy of equivocation.
This is a common source of misunderstanding in IDological circles.
Contrary to yours, the definition of genetic information is quite well defined within a biological context. Here is a definition:
quote:
The genetic potential of an organism carried in the base sequence of its DNA (or, in some viruses, RNA) according to the genetic code.
http://www.oxforddictionaries.com/...ish/genetic-information
And as long as you consistently use that definition for "genetic information" you should not have a problem.
Amusingly, you also need to consider that the "genetic information" is there because of evolution, in both DNA and RNA (whether virus RNA or not).
Message 94: The sign of a good definition is how it relates to it's opposite. You have defined life in relationship to its ability to evolve. So my question is then, using your definition, describe death to us. When does an organism die, ...
When it ceases to function and begins to break down.
Yours?
... and when do populations die? or become extinct?
When every individual of the population dies.
Yours? oh, that's right, your definition doesn't say anything about species ...
So with your molecules that you desire to define as "alive", please describe what makes these molecules die? ...
When they cease to function and begin to break down. And the fact that they can go through this process means they had to be alive to function and hold together, doesn't it?
... With viruses which you desire to define as "alive", please describe the death of a virus. ...
When they cease to function and begin to break down. And the fact that they can go through this process means they had to be alive to function and hold together, doesn't it?
... And finally, describe the death of cellular life in relationship to your definition.
When it ceases to function and begins to break down.
You have said that "death is a part of evolution". Just what exactly does that mean? Do dead things evolve too?
That it is one of the processes of evolution.
Message 97: ... Clearly what you are doing is equivocating on what the "population" is. ...
Saying it does not make it so. Your claims of equivocation are like a broken record to all who disagree with you, and yet you have not shown one actual instance of equivocation.
In the 6 levels of evolution post I clearly described what the population was composed of at each level. Nor am I alone in viewing life at those different levels, check E.O.Wilson for one looking at the evolution patterns of survival and selection of whole species as but one example. Species reproduce by speciation, giving rise to new species in much the same way that asexual bacteria reproduce and evolve.
So what you are doing is equivocating between a population being properly a population of mules or a population being some group of cells within the mule. ...
Nope. Failure to understand is not refutation. Looking at life at different levels is not equivocation, but looking at how each of those different levels fit the same pattern. It is looking and the difference between microevolution and macroevolution ... and sub-micro and super-macro ... at the whole spectrum of evolutionary processes.
I mentioned E.O.Wilson above. He is not alone either. Many scientists talk about the Biosphere:
quote:
The biosphere is the global sum of all ecosystems. It can also be termed as the zone of life on Earth, a closed system (apart from solar and cosmic radiator and heat from the interior of the Earth), and largely self-regulating.[1] By the most general biophysiological definition, the biosphere is the global ecological system integrating all living beings and their relationships, including their interaction with the elements of the lithosphere, geosphere, hydrosphere, and atmosphere. The biosphere is postulated to have evolved, beginning with a process of biopoesis (life created naturally from non-living matter such as simple organic compounds) or biogenesis (life created from living matter), at least some 3.5 billion years ago. ...
Pierre Teillard de Chardin talked about an "Omega Point" of evolution and of the "noosphere" (a sphere of thought/consciousness).
And I can equally go in the other direction, with geneticists, microbiologists and scientists involved in the study of abiogenesis, ... and where they draw the line between life and non-life.
My thought experiment ...
Failed for reasons already discussed. Not accepting that fact does not change that refutation of your argument, its just plain unadulterated denial.
... And clearly many organisms have populations for generation after generation that show no change in alleles either.
Again, please list one. With the evidence to support it.
So evolution has many defeaters which makes it a very poor definition, but I can see why you want it. The faith in naturalism is strong. And the unsuccessful field of OOL needs such equivocation to survive. It's naturalism of the GAPS. Yet no matter what the evidence shows, the imaginations of men want to show something other than what is. It's called magic.
Your opinion, ignoring the facts.
Enjoy
Edited by RAZD, : clrty

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This message is a reply to:
 Message 91 by AlphaOmegakid, posted 11-23-2015 2:11 PM AlphaOmegakid has not replied

Replies to this message:
 Message 132 by herebedragons, posted 11-27-2015 4:16 PM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 117 of 374 (773170)
11-25-2015 4:48 PM
Reply to: Message 116 by Percy
11-25-2015 3:46 PM


death and extinction -- a part of evolution
Concerning death and individuals of a population, what you said feels a little too confined if you're using the definition of selection where it means selecting who gets to reproduce and who doesn't. Death is only one form of selection.
Agreed, but rather than selection death is also necessary for the succession of life, genetic drift and to remove less viable forms from the population to make room for new individuals; without death habitats would become overcrowded. Likewise the extinction of species is necessary to make room for the new species - an ecological view of evolution.
Concerning extinction and species, what you said also feels a little too confined, since a species can cease to exist by evolving to a different species. The fossil record might cease to contain any record of a species, and paleontologists might conclude that it went extinct, but extinction means "the death of the last individual of the species" (Wikipedia), and the population might simply have evolved over time into something else.
In which case you would be talking about anagenic or cladogenic speciation, both leaving the old species behind due to their being less fit species than the new ones. The old species goes extinct and makes room for the new ones. Again this is a necessary part of large view (macro) evolution and ecology (carrying capacity of habitats).
You can think of species as asexual bacteria, reproducing via budding.
Enjoy

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This message is a reply to:
 Message 116 by Percy, posted 11-25-2015 3:46 PM Percy has replied

Replies to this message:
 Message 120 by Percy, posted 11-26-2015 7:44 AM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


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

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

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

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


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?

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

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

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


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.
Mule - Wikipedia
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

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

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

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


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
Psychozoan: The Definition of Life
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
Life - Wikipedia
particularly the "conventional definition
Life - Wikipedia
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 Life - Wikipedia)
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)
Discover Financial Services
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:
Just a moment...
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}80C) 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)
Discover Financial Services
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:
Just a moment...
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}80C) 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 News | BioEd Online
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.

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RAZD
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Posts: 20714
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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

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RAZD
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Posts: 20714
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Message 136 of 374 (773359)
11-30-2015 11:35 AM
Reply to: Message 131 by NoNukes
11-27-2015 3:36 PM


Re: equine masochistic necrophilia
In my opinion, 'capable of evolving' ought to mean "undergoing a change in allele frequency in a population from generation to generation". ...
Again, are you claiming that every new generation of mules have exactly the same distribution of alleles as the previously existing population?
... We don't even agree that mules are a population, which is something I find strange. ...
They are not a breeding population, just as any grouping of all males, or of all females, or of a 'superpopulation' gathering during non-mating times, are not breeding populations.
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.
Feel free to develop one.
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.
But not a separate breeding population ...
Curiously I am not making a claim that they are anything but a hybrid, that individually each mule is the product of (human) breeding a (female) horse with a (male) donkey, and that as such their breeding population includes (female) horses and (male) donkeys.
Do you think mules are a breeding population? If no, then that should clear up your problem.
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.
And there are many non-breeding population groups -- often involving several different species -- but when talking about evolution you need to be talking about the breeding populations.
Enjoy

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
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Message 138 of 374 (773363)
11-30-2015 11:58 AM
Reply to: Message 132 by herebedragons
11-27-2015 4:16 PM


Re: try again - definition as theory ...
... 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. ...
Indeed, especially as we see more and more viruses that are capable of replication without high-jacking cells, and{about the abilities of RNA}, and as we look closer and closer into the possible development of life. Viruses are being more and more accepted as an intermediate stage from first life to modern cellular life.
... 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.
Which then creates a problem with some parts of 'non-living' structures behaving like 'living' structures and unlike what is normally viewed as 'non-living' structures (like rocks). That just moves the blurry area but doesn't get rid of it.
Note that by AOK's definition only cells are alive because only they process\manufacture ATP -- multicellular life-forms consume raw materials and metabolize them by breaking them down and sending the raw materials into the cells which then process them. That puts multicellular life into a gray area when it is usually de facto accepted as life.
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, ...
Perhaps it appears to much like a tautology at first glance.
... but it seems to require too many caveats and additional explanations, otherwise it simply means "anything that can change over time."
As noted before it is modified to "anything capable of (biological) evolution" as I had felt "biological" was understood when discussing life.
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.
There are some life forms that do not exhibit all those elements (see looong post above for link to The Definition of Life By Joseph Morales). I would also delete "self-contained" as that is not entirely correct, and I would consider "metabolism" and "regulate metabolism" to be a subset of replication of molecules from raw materials (some viruses can make proteins for instance, which I would consider regulated metabolism).
But who knows, we may someday need to update the definition somewhat to accommodate new discoveries.
We can also treat definition as theories; they explain evidence, they can be falsified, and they can be altered to accommodate new evidence ... and you can have competing or alternate theories ... and we can investigate to see which one best explains all the evidence.
Enjoy
Edited by RAZD, : .
Edited by RAZD, : ..
Edited by RAZD, : ...
Edited by RAZD, : ....
Edited by RAZD, : link to The Definition of Life By Joseph Morales
Edited by RAZD, : {corrected}

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RAZD
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Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(2)
Message 142 of 374 (773404)
12-01-2015 8:51 AM
Reply to: Message 141 by AlphaOmegakid
11-30-2015 6:26 PM


two gray areas and "dead" tardigrades, seeds and spores
A definition is to create the description that differentiates living organisms from other chemical arrangements. I chose the simplest arrangement that includes the production of metabolic molecules and the production of the enzymes required for their synthesis. A mitochondria's DNA level is much smaller than the entire cell's.
There are two main problems with your definition.
(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); rather it ignores it and pretends that it is non-life, and in the process creates a third category of things: life, non-life that behaves like life (evolves, reproduces, etc, and not what is generally understood as "non-life"), and non-life that doesn't behave like life (rocks, and other non-life as it is generally understood). Not being able to distinguish between these last two cases is a fatal flaw.
(2) Because it is based on microbiological functions inside the cell, it only defines cells as being alive:
Message 1: Life, or a living organism is a self contained entity which uses ATP (adenosine triphosphate) for metabolism and synthesizes ATP with enzymes which are synthesized from a genetic process requiring the transfer of information from DNA to RNA.
... the ATP is only synthesized inside the cell, DNA and RNA are also operating inside the cell (or are viruses); as a result your "mule" is not alive but it's cells are -- a condition you implied was fatal for my definition (Message 97): "So what you are doing is equivocating between a population being properly a population of mules or a population being some group of cells within the mule."
Not being directly applicable to multicellular life is a fatal flaw.
So you've created two gray areas with your definition that aren't life and that aren't really non-life ... as "non-life" is generally understood: one between cellular life and first life, and one built up of multiple cells working together.
And finally, any good definition of life must also identify it's opposite (or death). Life is not the continuum. Death is. ...
Make that 3 problems ...
Consider tardigrades ... Tardigrades:
quote:
Tardigrades (also known as water bears or moss piglets)[2][3][4] are water-dwelling, eight-legged, segmented micro-animals.[2] ...
Tardigrades are notable for being perhaps the most durable of known organisms; they are able to survive extreme conditions that would be rapidly fatal to nearly all other known life forms. They can withstand temperature ranges from −458 F (−272.222 C) to 300 F (149 C), pressures about six times greater than those found in the deepest ocean trenches, ionizing radiation at doses hundreds of times higher than the lethal dose for a human, and the vacuum of outer space. They can go without food or water for more than 10 years, drying out to the point where they are 3% or less water, only to rehydrate, forage, and reproduce.
Seeds and bacteria can also have a phase where there is no metabolism (ie - no production of ATP, no function of DNA\RNA) until conditions become favorable for it's life. Are they dead in between periods of being alive? Your definition would say so. Are they resurrected?
Seeds were recently recovered from an archaeological dig inside a pottery container ~800 years old ...
quote:
Extinct Squash’ Grown From 800-Year-Old Heirloom Seeds
A species of squash believed to be extinct has been grown from 800-year-old seeds found at an archeological dig.
A group of students in Winnipeg, Canada, proved that heirloom seeds can be viable even if they have been buried for centuries. They had a feast in September to celebrate the discovery.
And the oldest known viable seed recovered and grown to date is
quote:
Oldest viable seed
The oldest carbon-14-dated seed that has grown into a viable plant was Silene stenophylla (narrow-leafed campion), an Arctic flower native to Siberia. Radiocarbon dating has confirmed an age of 31,800 300 years for the seeds. In 2007, more than 600,000 frozen mature and immature seeds were found buried in 70 squirrel hibernation burrows 38 metres (125 ft) below the permafrost near the banks of the Kolyma River. Believed to have been buried by Arctic ground squirrels, the mature seeds had been damaged to prevent germination in the burrow, however, three of the immature seeds contained viable embryos. Scientists extracted the embryos and successfully germinated plants in vitro which grew, flowered and created viable seeds of their own. ...
And then there is the bacteria:
quote:
Endospores
Endospores show no detectable metabolism and can survive extreme physical and chemical stresses, such as high levels of UV light, gamma radiation, detergents, disinfectants, heat, freezing, pressure, and desiccation.[79] In this dormant state, these organisms may remain viable for millions of years,[80][81] and endospores even allow bacteria to survive exposure to the vacuum and radiation in space.[82] According to scientist Dr. Steinn Sigurdsson, "There are viable bacterial spores that have been found that are 40 million years old on Earth and we know they're very hardened to radiation."...
And yeasts, moss, and many other life-forms also use spores to propagate ...
By your definition these spores are dead, so is life created from non-life when they revive\grow?
Not being able to distinguish between life and death in such instances is a fatal flaw.
Curiously, these organism are capable of evolving ...
Enjoy
Edited by RAZD, : (3)
Edited by RAZD, : ]
Edited by RAZD, : correction

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 Message 141 by AlphaOmegakid, posted 11-30-2015 6:26 PM AlphaOmegakid has replied

Replies to this message:
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RAZD
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Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


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 similarone 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 knownand 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 RNAssay a D-RNAproved 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 News | BioEd Online
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

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This message is a reply to:
 Message 144 by AlphaOmegakid, posted 12-01-2015 11:02 AM AlphaOmegakid has replied

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

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 179 of 374 (773500)
12-02-2015 8:43 PM
Reply to: Message 162 by AlphaOmegakid
12-02-2015 10:21 AM


Re: self-replicating virus - again ...
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.
Ah, so comprehension of parenthetical statements modifying the main statement of what is posted is also one of your problems in understanding what is said. Do I need to parse it for you?

Do you not see the difference between:
(me): 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), and
(you): you claim viruses can self replicate, metabolize and make proteins outside a host cell.
Perhaps I used a poor choice of wording and structure.
Scientists are increasingly accepting viruses as living, forming a fourth domain of life. This is because of what they are learning.
There are seven types of viruses:
Class 1: Double Stranded DNA Viruses
Class 2: Single-stranded DNA viruses
Class 3: Double-stranded RNA viruses
Class 4: Single-stranded RNA viruses - Positive-sense
Class 5: Single-stranded RNA viruses - Negative-sense
Class 6: Positive-sense single-stranded RNA viruses that replicate through a DNA intermediate
Class 7: Double-stranded DNA viruses that replicate through a single-stranded RNA intermediate
From an RNA world perspective, if (RNA) viruses are "fossils" of the RNA world, and RNA life, then we need to look at RNA self-replication, and we find (learn) that there are (now) several known self-replicating RNA molecules.
Molecule metabolism occurs when available raw materials are converted\combined\catalyzed into larger, more complex structures, which can then be joined in the making of a replicate. We have found (learned) that there are many additional RNA molecules known that are capable of this type of action.
From an early life perspective (before cells evolved) we need to look at how DNA evolved, and (DNA) viruses can be "fossils" of the early evolution of DNA from RNA, able to manufacture proteins to form a protective sheath against UV and other hazards to early life. We see (learn about) this occurring with the (class 1) Mimivirus when it is in a suitable ecology (which in this case is an amoebic cell, but it uses raw materials and not the cell mechanisms or structures). We can also consider cells to be mini remnants, "fossils", of a pre-cellular world. And I note that the scientists that researched the genome of this (DNA) virus seemed quite excited to call it a life form.
Does that mean that DNA viruses can be considered life, but not RNA viruses? Or is it just another matter of degree, of the gray area between living things and never living things?

Curiously, I also see that you have failed to reply to my points that show your definition fails ... (Message 142) ... just as your "reply" (Message 144) failed to address a single one of the problems .... attacking my post without addressing (eg ignoring) those problems doesn't make them go away: do I need to repost them in yellow?
Perhaps you think that discrediting my posts\definition makes your definition stronger. It doesn't.
Enjoy
Edited by RAZD, : added details, clarity
Edited by RAZD, : correction

we are limited in our ability to understand
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This message is a reply to:
 Message 162 by AlphaOmegakid, posted 12-02-2015 10:21 AM AlphaOmegakid has replied

Replies to this message:
 Message 185 by AlphaOmegakid, posted 12-03-2015 10:38 AM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 224 of 374 (773636)
12-05-2015 1:39 AM
Reply to: Message 219 by NoNukes
12-04-2015 12:14 PM


Re: equine masochistic necrophilia
I am claiming that there are no new generations of mules. ...
And yet mules have been around for thousands of years, so either they pop up out of nothing, they are immortal or there are new mules being bred. New mules being bred would be a new generation would it not?
... I am saying that a population of mules does not produce a new generation of mules.
You are saying that it is a population that does not breed, and I am saying that it is not a breeding population. The difference is that you need a breeding population to have evolution and not some other arbitrary population.
A population of all males is not considered a breeding population and cannot produce a new generations with hereditary traits.
A population of all females is not considered a breeding population and cannot produce a new generations with hereditary traits.
A population of individual animals from different species, one per species is not considered a breeding population and cannot produce a new generations with hereditary traits.
A population of mules is not considered a breeding population and cannot produce a new generations with hereditary traits.
ALL of these organisms in each one of these populations are products of reproduction carried out in their respective breeding populations.
I thought at this point we at least understood each others arguments. Let's just end this.
Do you agree that a population of mules is not a breeding population?
Enjoy.
Edited by RAZD, : clrty

we are limited in our ability to understand
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This message is a reply to:
 Message 219 by NoNukes, posted 12-04-2015 12:14 PM NoNukes has seen this message but not replied

Replies to this message:
 Message 226 by dwise1, posted 12-05-2015 4:09 AM RAZD has seen this message but not replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 225 of 374 (773637)
12-05-2015 1:49 AM
Reply to: Message 223 by Tanypteryx
12-04-2015 7:08 PM


Re: Black White or Grey?
A single cell of a dog could not live by itself outside the dog.
A cell wouldn't be able to live by itself (meaning without outside help), but cells can be kept alive and dividing in a lab, invitro.
The HeLa for example, which is generally considered to be living.
Organ transplants and skin grafts fall into the same category. You could say they are transferred from one life support system to another.
Enjoy
Edited by RAZD, : .

we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
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