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Author Topic:   Nothing in biology makes sense except in the light of evolution.
Rrhain
Member
Posts: 6351
From: San Diego, CA, USA
Joined: 05-03-2003


(1)
Message 1141 of 1311 (816123)
07-29-2017 5:10 PM
Reply to: Message 1037 by CRR
07-24-2017 3:49 AM


CRR responds to me:
quote:
quote:
Now, right here and now we can create self-replicating, auto-catalysing, homochiral molecules that evolve.
I'd like a reference for that please.
Why am I not surprised that you didn't do your homework before you started making claims?
A chiroselective peptide replicator
Alan Saghatelian, Yohei Yokobayashi, Kathy Soltani & M. Reza Ghadiri
Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
Correspondence to: Correspondence and requests for materials should be addressed to M.R.G. (e-mail: Email: ghadiri@scripps.edu).
The origin of homochirality in living systems is often attributed to the generation of enantiomeric differences in a pool of chiral prebiotic molecules1, 2, but none of the possible physiochemical processes considered1, 2, 3, 4, 5, 6, 7 can produce the significant imbalance required if homochiral biopolymers are to result from simple coupling of suitable precursor molecules. This implies a central role either for additional processes that can selectively amplify an initially minute enantiomeric difference in the starting material1, 8, 9, 10, 11, 12, or for a nonenzymatic process by which biopolymers undergo chiroselective molecular replication13, 14, 15, 16. Given that molecular self-replication and the capacity for selection are necessary conditions for the emergence of life, chiroselective replication of biopolymers seems a particularly attractive process for explaining homochirality in nature13, 14, 15, 16. Here we report that a 32-residue peptide replicator, designed according to our earlier principles17, 18, 19, 20, is capable of efficiently amplifying homochiral products from a racemic mixture of peptide fragments through a chiroselective autocatalytic cycle. The chiroselective amplification process discriminates between structures possessing even single stereochemical mutations within otherwise homochiral sequences. Moreover, the system exhibits a dynamic stereochemical ‘editing’ function; in contrast to the previously observed error correction20, it makes use of heterochiral sequences that arise through uncatalysed background reactions to catalyse the production of the homochiral product. These results support the idea that self-replicating polypeptides could have played a key role in the origin of homochirality on Earth.
The origin of biological homochirality
Donna G. Blackmond
Philosophical Transactions: Biological Sciences
Vol. 366, No. 1580, The chemical origins of life and its early evolution (27 October 2011), pp. 2878-2884
Published by: Royal Society
Stable URL: JSTOR: Access Check
Page Count: 7
The single handedness of biological molecules has fascinated scientists and laymen alike since Pasteur's first painstaking separation of the enantiomorphic crystals of a tartrate salt over 150 years ago. More recently, a number of theoretical and experimental investigations have helped to delineate models for how one enantiomer might have come to dominate over the other from what presumably was a racemic prebiotic world. Mechanisms for enantioenrichment that include either chemical or physical processes, or a combination of both, are discussed in the context of experimental studies in autocatalysis and in the phase behaviour of chiral molecules.
A cross-chiral RNA polymerase ribozyme
Thirty years ago it was shown that the non-enzymatic, template-directed polymerization of activated mononucleotides proceeds readily in a homochiral system, but is severely inhibited by the presence of the opposing enantiomer1. This finding poses a severe challenge for the spontaneous emergence of RNA-based life, and has led to the suggestion that either RNA was preceded by some other geneticpolymer that is not subject to chiral inhibition2 or chiral symmetry was broken through chemical processes before the origin of RNA-based life3,4. Once an RNA enzyme arose that could catalyse the polymerization of RNA, it would have been possible to distinguish among the two enantiomers, enabling RNA replication and RNA-based evolution to occur. It is commonly thought that the earliest RNA polymerase and its substrates would have been of the same handedness, but this is not necessarily the case. Replicating D- and L-RNA molecules may have emerged together, based on the ability of structured RNAs of one handedness to catalyse the templated polymerization of activated mononucleotides of the opposite handedness. Here we develop such a cross-chiral RNA polymerase, using in vitro evolution starting from a population of random-sequence RNAs. The D-RNA enzyme, consisting of 83 nucleotides, catalyses the joining of L-mono- or oligonucleotide substrates on a complementary L-RNA template, and similar behaviour occurs for the L-enzyme with D-substrates and a D-template. Chiral inhibition is avoided because the 106-fold rate acceleration of the enzyme only pertains to cross-chiral substrates.The enzyme’s activity is sufficient to generate full-length copies of its enantiomer through the templated joining of 11 component oligonucleotides.
The eightfold path to non-enzymatic RNA replication
Jack W SzostakEmail author
Journal of Systems Chemistry20123:2
The eightfold path to non-enzymatic RNA replication | Journal of Systems Chemistry | Full Text Szostak; licensee Chemistry Central Ltd. 2012
Received: 23 November 2011Accepted: 3 February 2012Published: 3 February 2012
The first RNA World models were based on the concept of an RNA replicase - a ribozyme that was a good enough RNA polymerase that it could catalyze its own replication. Although several RNA polymerase ribozymes have been evolved in vitro, the creation of a true replicase remains a great experimental challenge. At first glance the alternative, in which RNA replication is driven purely by chemical and physical processes, seems even more challenging, given that so many unsolved problems appear to stand in the way of repeated cycles of non-enzymatic RNA replication. Nevertheless the idea of non-enzymatic RNA replication is attractive, because it implies that the first heritable functional RNA need not have improved replication, but could have been a metabolic ribozyme or structural RNA that conferred any function that enhanced protocell reproduction or survival. In this review, I discuss recent findings that suggest that chemically driven RNA replication may not be completely impossible.
It goes on and on. Is there a reason why you didn't bother to look this up?
After all, that's how life happens in the first place: It takes dead material and turns it into life. The food you eat isn't alive. It's not like you go out and hunt animals to consume their still-beating hearts. The vegetation you eat dies when you cultivate it. About the only thing that's still alive when you eat it are the bacteria and fungi that are on the food you eat, but it isn't like you get your sustenance from them.
For crying out loud, salt is a rock and yet you continue to incorporate it into your cells in order to keep you alive.
So we can clearly see through simple observation that life is continually created from non-life.
Not quite.
No, really, quite. It's called "digestion." Your body literally breaks everything down to constituent parts and so that they can be passed to the cells which then reincorporate them into whatever is needed. It's why there are things called "essential" nutrients such as certain fatty acids and amino acids: Your body is incapable of synthesizing them on its own. You must get them from your diet. But, your body doesn't need the entire protein the amino acids are making up, so it disintegrates the protein into constituent amino acids that are then transported to your cells which then absorb them and reorganize them into new proteins.
So unless you're saying that amino acids are alive, then my statement stands: Your body takes non-living material and through a chemical reaction converts it into living material. It is nothing but chemistry in action. There is no magic involved.
quote:
In your example something that IS alive is consuming non living matter and incorporating it into its body.
I never said it wasn't. I simply pointed out that the claim that "life from life" is trivially shown to be not true. Instead, life only comes from non-life. Life does not take something living and make new life out of it. Instead, it takes something dead and makes new life out of it. And if what it needs to make that new life is already living, it kills it first.
So since we know that life currently depends upon a chemical reaction based upon non-living reagents and since we know that chemistry doesn't care how the reaction gets started, is it really such a stretch to consider that it might have started all on its own? This is why the concept of "catalysis" is important in the study of biogenesis. Even in chemistry fields that have nothing to do with biogenesis, certain reactions do happen but happen so slowly that they aren't sufficient for what we want or need. Fortunately, we have discovered that there are things that can help make the reaction more efficient. Sometimes, it's as simple as heating it up. And if the reaction itself is exothermic, then the heat of the reaction will help to increase the temperature of the system which will encourage more reaction to take place. And thus, we have a reaction that catalyses itself.
Other types of reactions require a "middle step," as it were. That is, A + B -> C, but that reaction happens slowly or inefficiently. But, there may be a third chemical we can add such that A + X -> Z and then Z + B -> C + X. If this chain of reactions is faster or more efficient, then we say that "X" is a "catalyst" for the reaction. It isn't consumed in the reaction but rather speeds the process of A + B -> C.
A self-catalysing reaction is great because you don't need to look for that extra molecule. If the product is a catalyser for the reagents, then all you need to do is get the reaction started in the first place and it will take off on its own. Thus, even a slow, inefficient reaction will eventually become efficient.
And we seem to be able to make self-replicating, homochiral, auto-cataylsing molecules that evolve. If that isn't life, what is it?
quote:
At best life is creating life.
By first killing and eating something that's dead. Life cannot create life from life. Life can only create life from death. Thus, life does not come from life. Instead, life comes from non-life.
quote:
This is entirely different to abiogenesis; dead matter creating life from dead matter.
But current life is not as you describe it. It is much closer to what we see in abiogenesis: Chemical manipulation of non-living matter into living matter.
Why does it matter where this reaction takes place? The Orion nebula is filled with hydrogen and oxygen which is reacting to form water. More water is made in the Orion nebula in an hour than all the water on earth. Is this water any different than if I were to take hydrogen and oxygen, mix them at STP, and spark the mixture? Is this water any different from the water that my body creates? The oxygen you breathe in is primarily used to make water, after all. Is this "bio water" different from other water?
Are you seriously claiming that the chemistry that takes place inside of a bilipid membrane is fundamentally different from the chemistry that takes place outside it?

Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

Minds are like parachutes. Just because you've lost yours doesn't mean you can use mine.

This message is a reply to:
 Message 1037 by CRR, posted 07-24-2017 3:49 AM CRR has replied

Replies to this message:
 Message 1143 by Adminnemooseus, posted 07-29-2017 9:35 PM Rrhain has not replied
 Message 1145 by CRR, posted 07-30-2017 9:04 PM Rrhain has replied
 Message 1152 by Dredge, posted 07-31-2017 1:41 AM Rrhain has not replied

  
Rrhain
Member
Posts: 6351
From: San Diego, CA, USA
Joined: 05-03-2003


Message 1142 of 1311 (816125)
07-29-2017 5:36 PM
Reply to: Message 1130 by dwise1
07-29-2017 2:14 AM


dwise1 responds to me:
quote:
Well, it's been nearly 40 years since I've done those calculations, so I'm rather rusty. Does anybody see this as a promising tack to take so that they may take it up?
How interesting that you should say that since my undergraduate degree was specifically in Applied Mathematics concentrating in Numerical Analysis. If we could have some idea of what they were using for data, it would help. But off the top of my head, to have an expected value of 10,000 with a potential error term that would allow for 4.5 billion would be such a sloppy data set as to be worthless.

Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

Minds are like parachutes. Just because you've lost yours doesn't mean you can use mine.

This message is a reply to:
 Message 1130 by dwise1, posted 07-29-2017 2:14 AM dwise1 has replied

Replies to this message:
 Message 1163 by dwise1, posted 08-01-2017 5:22 PM Rrhain has not replied

  
Adminnemooseus
Administrator
Posts: 3974
Joined: 09-26-2002


(1)
Message 1143 of 1311 (816129)
07-29-2017 9:35 PM
Reply to: Message 1141 by Rrhain
07-29-2017 5:10 PM


Regardless of whatever CCR's lack of preperation may be...
CRR responds to me:
quote:
quote:
Now, right here and now we can create self-replicating, auto-catalysing, homochiral molecules that evolve.
I'd like a reference for that please.
Why am I not surprised that you didn't do your homework before you started making claims?
...it's still the responsibility of the person making the assertion to supply link(s)/reference(s) (and ?) to support the assertion. Otherwise it's one of those "bare assertions" that is against forum rule 4.
Any replies to the admin message should go here.
Adminnemooseus

Or something like that.

This message is a reply to:
 Message 1141 by Rrhain, posted 07-29-2017 5:10 PM Rrhain has not replied

  
Tanypteryx
Member
Posts: 4344
From: Oregon, USA
Joined: 08-27-2006
Member Rating: 5.9


(2)
Message 1144 of 1311 (816160)
07-30-2017 3:04 PM
Reply to: Message 1105 by Dredge
07-28-2017 1:52 AM


Re: seven "assumptions"
Thanks for the spelling correction.
Dredge writes:
While Gould admits that the fossil record is characterised by "sudden appearance" and "stasis', is seems that it never occurred to him that this is the exact opposite of what Darwinian theory predicts.
Gould wrote extensively about the fossil record AND Darwin's theory during his career. Punctuated Equilibrium was an observation that explains a pattern seen in the fossil record and was a very clever addition to the Theory of Evolution. Paleontologists and biologists recognized that Darwin's theory was incomplete and research and study by hundreds of thousands of scientists during the 150 years since Origin of Species was published has added a tremendous amount of data to our understanding of the mechanisms and processes of biological evolution.
You trying to characterize Punctuated Equilibrium as being the opposite Darwin's theory predicts shows that either you don't know what either of them said or thought on the subject or you are dishonestly quote mining both of them. You may be able to convince some other dimwitted creationists with this bullshit, but that's all.

What if Eleanor Roosevelt had wings? -- Monty Python
One important characteristic of a theory is that is has survived repeated attempts to falsify it. Contrary to your understanding, all available evidence confirms it. --Subbie
If evolution is shown to be false, it will be at the hands of things that are true, not made up. --percy
The reason that we have the scientific method is because common sense isn't reliable. -- Taq

This message is a reply to:
 Message 1105 by Dredge, posted 07-28-2017 1:52 AM Dredge has replied

Replies to this message:
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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 1145 of 1311 (816163)
07-30-2017 9:04 PM
Reply to: Message 1141 by Rrhain
07-29-2017 5:10 PM


Re: self-replicating, auto-catalysing, homochiral molecules
A chiroselective peptide replicator (paywall)
The origin of biological homochirality (requires MyJSTOR account.)
A cross-chiral RNA polymerase ribozyme (paywall)
The eightfold path to non-enzymatic RNA replication (open access)
And Jack W Szostak sums it up pretty well. "Although several RNA polymerase ribozymes have been evolved in vitro, the creation of a true replicase remains a great experimental challenge." and "In this review, I discuss recent findings that suggest that chemically driven RNA replication may not be completely impossible."

This message is a reply to:
 Message 1141 by Rrhain, posted 07-29-2017 5:10 PM Rrhain has replied

Replies to this message:
 Message 1164 by Rrhain, posted 08-01-2017 7:59 PM CRR has not replied

  
Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


Message 1146 of 1311 (816164)
07-30-2017 11:08 PM


New Theory Suggests Life Wasn't a Fluke
Controversial New Theory Suggests Life Wasn't a Fluke of BiologyIt Was Physics
Controversial New Theory Suggests Life Wasn't a Fluke of BiologyIt Was Physics | WIRED
The biophysicist Jeremy England made waves in 2013 with a new theory that cast the origin of life as an inevitable outcome of thermodynamics. His equations suggested that under certain conditions, groups of atoms will naturally restructure themselves so as to burn more and more energy, facilitating the incessant dispersal of energy and the rise of entropy or disorder in the universe. England said this restructuring effect, which he calls dissipation-driven adaptation, fosters the growth of complex structures, including living things. The existence of life is no mystery or lucky break, he told Quanta in 2014, but rather follows from general physical principles and should be as unsurprising as rocks rolling downhill.
More

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
Belief gets in the way of learning--Robert A. Heinlein
In the name of diversity, college student demands to be kept in ignorance of the culture that made diversity a value--StultisTheFool
It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers
If I am entitled to something, someone else is obliged to pay--Jerry Pournelle
If a religion's teachings are true, then it should have nothing to fear from science...--dwise1
"Multiculturalism" demands that the US be tolerant of everything except its own past, culture, traditions, and identity.
Liberals claim to want to give a hearing to other views, but then are shocked and offended to discover that there are other points of view--William F. Buckley Jr.

Replies to this message:
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Dredge
Member
Posts: 2850
From: Australia
Joined: 09-06-2016


Message 1147 of 1311 (816166)
07-31-2017 1:19 AM
Reply to: Message 1123 by dwise1
07-28-2017 2:36 PM


Re: seven "assumptions"
dwise1 writes:
Sage advice to anyone reading a creationist quote: always check to find out what they are hiding in those ellipses (the "..."). Of course, there are some valid uses for ellipses, but creationist use is commonly to leave out necessary context so that they can change the meaning In order to misrepresent the source."
For the sake of brevity, I didn't quote Raup word-for-word, but used only what was necessary to get the point across, without distorting its meaning. You have supplied the full wording of the quote in question, thinking that by doing so you have proven that my abbreviated version is misleading and dishonest. Sorry, no cigar. Anyone (of sound mind, that is) who compares both texts will see that what I left out is irrelevant and what I left in is faithful to the original meaning.
You then supplied Raup's excuses for why there is a lack of transitionals between larger groups of organisms - which I didn't bother mentioning because
a) they're so lame and unconvincing - two of them are just laughable ... the fossil record is incomplete and PE,
and
b) they're irrelevant to the point I was trying to make - that Gould claimed he could point to an abundance of transitionals between the larger groups, but Raup can't.
As for the rest of your bloated post ... er, why did you bother?
So to sum up, your attempt to malign me failed miserably. You got all excited and frothy-at-the-mouth for nothing. Try again some other time.
dwise1 writes:
Why does your religion have to depend almost completely on lies?
I have no idea what you're talking about.

This message is a reply to:
 Message 1123 by dwise1, posted 07-28-2017 2:36 PM dwise1 has replied

Replies to this message:
 Message 1151 by CRR, posted 07-31-2017 1:37 AM Dredge has not replied
 Message 1160 by dwise1, posted 07-31-2017 10:43 AM Dredge has replied

  
CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 1148 of 1311 (816167)
07-31-2017 1:24 AM
Reply to: Message 1146 by Coyote
07-30-2017 11:08 PM


Re: New Theory Suggests Life Wasn't a Fluke
It will be interesting to see if the results of those computer simulations can be replicated in the laboratory. Although the article liberally uses "evolution" this is in the dictionary sense of change over time and is not biological evolution.

This message is a reply to:
 Message 1146 by Coyote, posted 07-30-2017 11:08 PM Coyote has not replied

  
Dredge
Member
Posts: 2850
From: Australia
Joined: 09-06-2016


Message 1149 of 1311 (816168)
07-31-2017 1:30 AM
Reply to: Message 1133 by PaulK
07-29-2017 3:22 AM


Re: Gould's observations do support Creationism
PaulK writes:
Please explain what is laughable about using an idea already widely accepted in evolutionary biology to explain a feature of the fossil record."
Evolutionary biology - real biology's wacko little brother - is notorious for it pseudo-scientific ideas. Relying on evolutionary biology to explain the fossil record is like relying on Jehovah's Witnesses to explain the Bible.
While there are many transitionals - as Gould said - which are evidence for evolution at the higher taxonomic levels.
Yeah, right - if you figure in huge doses of wishful thinking and a very vivid imagination. Take Archaeopteryx, for example:
"Paleontologists have tried to turn Archaeopteryx into an earth-bound, feathered dinosaur. But it's not. It is a bird, a perching bird. And no amount of 'paleobabble' is going to change that." - Dr. Alan Feduccia
Edited by Dredge, : No reason given.

This message is a reply to:
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Dredge
Member
Posts: 2850
From: Australia
Joined: 09-06-2016


Message 1150 of 1311 (816169)
07-31-2017 1:35 AM
Reply to: Message 1122 by New Cat's Eye
07-28-2017 12:07 PM


NewCatsEye writes:
It doesn't say anything about Satan speaking to Judas, but this is way too off topic.
So why do you imagine "Satan entered Judas?" Was it to merely play around in his intestines, or maybe to tickle his ribs from the inside? Probably not. I suggest Satan entered Judas to mess with his mind; to "speak" to Judas in order to make him do his will ... which was to betray Jesus.

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 1151 of 1311 (816170)
07-31-2017 1:37 AM
Reply to: Message 1147 by Dredge
07-31-2017 1:19 AM


Re: seven "assumptions"
Dredge is right Message 1147. The quote did not omit "several pages" as dwise1 claimed and did not substantially distort the meaning.
When Gould said "Transitional forms are generally lacking at the species level, but they are abundant between larger groups." I think he was desperately backpedaling after he let the cat out of the bag.
Edited by CRR, : link added

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Dredge
Member
Posts: 2850
From: Australia
Joined: 09-06-2016


(1)
Message 1152 of 1311 (816171)
07-31-2017 1:41 AM
Reply to: Message 1141 by Rrhain
07-29-2017 5:10 PM


Rrhain writes:
life only comes from non-life.
If you show me an organism arising from sterile mud or sea-water I'll have reason to be believe one half of your claim. The other half of your claim involves proving that life can't come from a Creator God. Good luck with both projects.
In the meantime, I'll just suggest that you don't know what you're talking about.
Humans present their ideas and God laughs.

This message is a reply to:
 Message 1141 by Rrhain, posted 07-29-2017 5:10 PM Rrhain has not replied

  
Dredge
Member
Posts: 2850
From: Australia
Joined: 09-06-2016


(1)
Message 1153 of 1311 (816172)
07-31-2017 1:45 AM
Reply to: Message 1111 by Tangle
07-28-2017 4:01 AM


Tangle writes:
Evolution is a branch of biology.
This statement is at least an improvement on "Evolution is the unifying concept of biology" or "Nothing in biology makes sense except in the light of evolution."
Even better would be to understand this: Evolution needs biology, but biology doesn't need evolution.

This message is a reply to:
 Message 1111 by Tangle, posted 07-28-2017 4:01 AM Tangle has replied

Replies to this message:
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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 1154 of 1311 (816173)
07-31-2017 1:47 AM
Reply to: Message 1133 by PaulK
07-29-2017 3:22 AM


Re: Gould's observations do support Creationism
PaulK writes:
quote:
But what Gould observed DOES call the ToE into question just as Darwin said, and PE is really a laughable way to resolve it, whether Gould believed in it or not.
Please explain what is laughable about using an idea already widely accepted in evolutionary biology to explain a feature of the fossil record.
My impression is that the theory of Punk Eek had a brief moment in the light but is mostly not considered seriously today as a general explanation for the absence of transitional forms in the fossil record. e.g. Punctuated equilibrium - Wikipedia
Edited by CRR, : No reason given.
Edited by CRR, : tidy up

This message is a reply to:
 Message 1133 by PaulK, posted 07-29-2017 3:22 AM PaulK has replied

Replies to this message:
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Dredge
Member
Posts: 2850
From: Australia
Joined: 09-06-2016


Message 1155 of 1311 (816174)
07-31-2017 1:49 AM
Reply to: Message 1138 by Rrhain
07-29-2017 4:27 PM


My dear, poor, dazed and confused fellow,
Please be advised that your comparison between a life-form arising from dead matter and a living organism converting (dead) food into living matter is incompatible with reason, and therefore, science.
Your body takes non-living material and through a chemical reaction converts it into a living material. There's no magic involved.
You could have fooled me. Photosynthesis is "just chemistry" too. A cake is the result of "just chemistry" as well, but can a cake make itself? (Speaking of which, do you find yourself strangely attracted to fruit-cakes?)
What do you mean by "life"?
Just off the top of my head, how about "A thing that grows and performs functions such as obtaining, ingesting and digsting food, expelling waste, reproduction and avoidance of predators?
Edited by Dredge, : No reason given.

This message is a reply to:
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