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Author Topic:   Nothing in biology makes sense except in the light of evolution.
Rrhain
Member (Idle past 703 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


(2)
Message 1021 of 1311 (815716)
07-23-2017 3:41 PM
Reply to: Message 1018 by Faith
07-23-2017 9:42 AM


Faith writes:

quote:
The evidence for old age is hardly "massive," it's all radiometric dating.

Incorrect.

For example, you are ignoring the cosmological data (the stars and galaxies really are that far away and the light from them really does take billions of years to reach us in order for us to see it; analysis of star clusters given their mass will indicate how old they are) and even simple kinematic data (we can plot the motions of objects such as asteroids and determine where they were in the past and thus determine their origin...such as from a collision that broke it into two...and when that event happened)

And if you want to look at just the earth, you are ignoring the biological data and geological data. We have tree rings and ice cores and varves that show ages much greater than YEC claim. And since those three methods are all independent of each other, the fact that they align with each other to indicate an earth at least 100,000 years old is evidence that it is at least that old (the ice cores show nearly a billion years.)

The fact that you think "radiometric decay" is insufficient is telling. You don't actually care what the evidence says.

quote:
There IS evidence for the Flood

No, there isn't. The Great Pyramids were built hundreds of years before the flood, but there is no water damage to them. Civilizations outside of the Middle East such as the Central and South American natives as well as China had thriving civilizations at the time of the flood, and there is no interruption in their documentation of their history. Not even Egypt seemed to notice.

And that ignores the topological impossibility of a global flood. If it were mathematically possible to flood the earth, it would be flooded right now.

quote:
and I continue to think it really funny that such obvious evidence as sedimentary strata and bazillions of fossils is just flatly refused while the absurd and impossible interpretation of time periods assigned to various blocks of strata is treated as reasonable.

And yet, you continue to refuse to recognize the obvious evidence from sedimentary strata and bazillions of fossils as evidence of an old earth while the absurd and impossible interpretation of time periods assigned to various blocks of strata as if they were young you claim to be reasonable. This sort of "science" you put forward really is laughable.

quote:
Oh, also that wishfulness that calls the non-life of replicating molecules "building blocks of life."

This would be where you define what you mean by "life" and "non-life," then. We can create self-replicating, auto-cataylsing, homochiral molecules that evolve, Faith. If that isn't "life," then what is?

quote:
unlike the sciences of the past for which most of the information is irretrievably lost.

Then we had better open up the prisons, Faith, for that same "sciences of the past for which most of the information is irretrievably lost" is what is used to convict people. For most crimes, there is no witness. We only have the "sciences of the past" to determine what happened and by whom.

And we had certainly stop trying to claim we can determine paternity, for that is the same "sciences of the past."


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 1018 by Faith, posted 07-23-2017 9:42 AM Faith has responded

Replies to this message:
 Message 1025 by Faith, posted 07-23-2017 4:00 PM Rrhain has responded

  
Rrhain
Member (Idle past 703 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


(1)
Message 1023 of 1311 (815720)
07-23-2017 3:51 PM
Reply to: Message 1007 by Dredge
07-23-2017 4:59 AM


Dredge writes:

quote:
Firstly, the fact that you consider it possible that science could one day produce life from dead matter says a lot about your grip on reality.

Yep. That it's pretty tight. 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. Life is merely a chemical process that takes certain reagents and produces certain products in a long-term reaction. And as we all know from chemistry, it doesn't matter how the reaction gets started and there is no magic to it. You simply need the appropriate reagents with sufficient activation energy to start the reaction.

Now, right here and now we can create self-replicating, auto-catalysing, homochiral molecules that evolve. If that isn't "life," what is it? What is your definition of "life"?


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 1007 by Dredge, posted 07-23-2017 4:59 AM Dredge has responded

Replies to this message:
 Message 1036 by Dredge, posted 07-24-2017 3:31 AM Rrhain has responded
 Message 1037 by CRR, posted 07-24-2017 3:49 AM Rrhain has responded

  
Rrhain
Member (Idle past 703 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 1127 of 1311 (816074)
07-28-2017 8:46 PM
Reply to: Message 1025 by Faith
07-23-2017 4:00 PM


Faith responds to me:

quote:
Tree rings, varves and ice cores do not support an ancient earth, they add a few thousand years at most to the YEC timing.

YECs claim the earth is at least a billion years old? Because that's what the ice cores say.

Do you have evidence otherwise? Now is the time to bring it forward.


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 1025 by Faith, posted 07-23-2017 4:00 PM Faith has not yet responded

Replies to this message:
 Message 1130 by dwise1, posted 07-29-2017 2:14 AM Rrhain has responded
 Message 1136 by RAZD, posted 07-29-2017 7:14 AM Rrhain has not yet responded

  
Rrhain
Member (Idle past 703 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 1138 of 1311 (816120)
07-29-2017 4:27 PM
Reply to: Message 1036 by Dredge
07-24-2017 3:31 AM


Dredge responds to me:

quote:
quote:
So we can clearly see through simple observation that life is continually created from non-life. Life is merely a chemical process that takes certain reagents and produces certain products in a long-term reaction. And as we all know from chemistry, it doesn't matter how the reaction gets started and there is no magic to it. You simply need the appropriate reagents with sufficient activation energy to start the reaction.

Such thoughts are standard fare for your garden-variety, raving Darwinist space-cadet. Humans, with all their intelligence and scientific knowledge and technology, can't produce life from inanimate matter, yet you think mere chance can achieve the feat. It takes a special talent to believe such dreamy nonsense.


You mean food is alive? Salt, a rock, is alive? Sugar is alive? Even assuming that the things you eat are alive when they enter your mouth, are you saying you don't understand what happens to them when you eat them? The very first thing that happens is you grind it up with your teeth in order to make it easier to swallow. Anything that was alive is now being crushed and is on its way to being dead real soon. Enzymes in your saliva start breaking things down.

And when it gets to your stomach, the food is bathed in acids to further break down whatever it is you ate into its constituent parts. If it was still alive when you swallowed, it isn't going to stay alive for long. And then when it gets into the small intestine, more enzymes and chemicals are added to literally break the food down into individual molecules. Proteins are ripped apart into their constituent amino acids. Long chain carbohydrates are broken down into simple sugars. Water is extracted. Minerals are leached out. What enters your blood is nothing but a set of parts. Your cells then take those parts and integrate them in order to continue the biochemistry of life. There is no magic in this.

Are you saying that those parts are still alive? We're back to the question that I directly asked you and that you failed to answer...one would say deliberately refused to answer:

What do you mean by "life"?


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 1036 by Dredge, posted 07-24-2017 3:31 AM Dredge has responded

Replies to this message:
 Message 1155 by Dredge, posted 07-31-2017 1:49 AM Rrhain has not yet responded

  
Rrhain
Member (Idle past 703 days)
Posts: 6349
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: http://www.jstor.org/stable/23035657
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
https://doi.org/10.1186/1759-2208-3-2© 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 responded

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

  
Rrhain
Member (Idle past 703 days)
Posts: 6349
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 responded

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

  
Rrhain
Member (Idle past 703 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


(1)
Message 1164 of 1311 (816257)
08-01-2017 7:59 PM
Reply to: Message 1145 by CRR
07-30-2017 9:04 PM


Re: self-replicating, auto-catalysing, homochiral molecules
CRR responds to me:

quote:
A chiroselective peptide replicator (paywall)

So you're unwilling to do the work to find out by going to your local library and reading the copy there. It won't cost you a thing other than getting out of your chair. Why am I not surprised that you are unwilling to do your homework?

quote:
The origin of biological homochirality (requires MyJSTOR account.)

So you're unwilling to do the work to find out by signing up? It won't cost you a thing other than typing. Why am I not surprised that you are unwilling to do your homework?

quote:
A cross-chiral RNA polymerase ribozyme (paywall)

So you're unwilling to do the work to find out by going to your local library and reading the copy there. It won't cost you a thing other than getting out of your chair. Why am I not surprised that you are unwilling to do your homework?

quote:
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."

It seems you didn't understand that last sentence. What part of "may not be completely impossible" are you having trouble with? You do understand that that means that it is possible, yes? You do understand how double negatives work in English, yes? If something is "not impossible," that means it's possible.

Yes, the work into abiogenesis is still ongoing, but this comes back to the question that you are steadfastly refusing to answer despite me having asked it multiple times:

What do you mean by "life"?

That is not a trivial question. Even biologists have a hard time defining it. Again, if a self-replicating, auto-catalysing, homochiral molecule that evolves isn't life (and I'm not saying it is), then what is it?

When are you going to do your homework?


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 1145 by CRR, posted 07-30-2017 9:04 PM CRR has not yet responded

  
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