Evolution and Creation an Honest Question

[drkitten]

"Handed-ness", and "racemic: Of or relating to a chemical compound that contains equal quantities of dextrorotatory and levorotatory forms and therefore does not rotate the plane of incident polarized light. ... courtesy of dictionary.com .. more handed-ness" ... I'm sure interesting to some.

Perhaps that's posturing as well, or perhaps these attribues directly address the sanctity of neo-Darwinism; I admit I don't know.

They directly address the issue of multiple biogenesis events.

Specifically, "normal" (laboratory) chemical processes will always produce racemic forms, since there's an even chance of a methyl group attaching to the left side or the right side of any given (symmetric) molecule. Biochemistry appears to be different. Nature has a 'preferred' side; for example, your DNA has a right-handed twist, not the equally plausible but for some reason unfound left-handed version. Similarly, the amino acids that make up your proteins are all levorotary.

We can explain this fairly simply as the result of a single evolutionary coin flip, way back when. The first DNA molecule that happened to form had to be either left- or right-handed, since there's no intermediate choice. But a hypothetical second DNA molecule would only have a 50% chance of being left-handed. If there were a thousand different abiogenesis events that led to the independent creation of DNA, the odds against all the DNA that we see today being left-handed would be the same as the odds of getting heads each time for a thousand coin flips -- essentially negligible.

If, as you suggest, DNA/RNA chemistry was independently reinvented several times, why was it only ever invented on the right side?

We could extend this even further. There's no known reason why left-handed DNA (which we don't have) couldn't work properly with levorotary amino acids (which we do), or why right-hand DNA couldn't work with dextrorotary amino acids. So there's really at least two coin flips involved here.

Similarly, there's really at least twenty coin flips, since there's no known reason why we couldn't use a mixture of dextro- and levorotary acids; biochemistry would probably still be possible with l-cysteine and d-histidine, for example. (In fact, as was pointed out, there are many more than two variations on most amino acids.) But we don't see that combination, either. And the combinations that we do see are the same for all life forms, suggesting a single biogenesis event.

And should separate trees actually exist, how would one differentiate them?

One way was answered above. A tree based on left-handed DNA and dextrorotary amino acids would be notably different, and probably win the Nobel prize for the discoverer. But so far, that doesn't seem to be the case.

ETA: typo fix.

 

[blutoski]

Could you be a bit more specific in the tenet you specifically refer to?

"Each codon represents one of 21 amino acids. The translation is identical in all living things."

The discovery of two, then two more amino acids refutes this, since some codons appear to have different translations in different kingdoms.

 

[blutoski]

And should separate trees actually exist, how would one differentiate them?

The passage you dismissed as irrelevant above was an answer to this question.

Apparently you can lead a horse to water...

 

[sphenisc]

...
your DNA has a right-handed twist,
...
There's no known reason why right-handed DNA (which we don't have)
...

What is this, the hokey-cokey ??

 

[drkitten]

What is this, the hokey-cokey ??

Sorry. Typographic mistake.

Natural DNA is indeed right-handed.

 

[hammegk]

You asked a specific question, and I answered you. This is what you do with answers? Not even a thanks?

My apologies. You have presented in interesting and understandable form several things I was completely unaware of, and I do thank you.

At least pretend you ask questions because you're interested in learning.

Sorry. As I said, I didn't see the significance of chirality until your follow-up. Again, I thank you.

My impression is that you were suggesting that an underlying physics would guide independent abiogenesis events to identical chemistry, such that these biomes may merge without the ability to detect their unique origins.

Yes, although the merge vs did-not-merge would be unanswered, even after accepting your likely/unlikely scenario given below.

You proposed that alterations in rna/dna would impact functionality.

Yes, and it appears that is absolutely correct once we move from chemical compounds to life (or better said, biochemistry).

My counterargument is that abiogenesis events would be subject to ordinary laws of physics which do not thermodynamically favour any particular chirality. Organic reactions outside a living organism produce optically inactive racemic outcomes, so mirror-images are possible. As are enantiomers. But enantiomers are thermodynamic equals outside of a biome. Nucleic acids have several chiral centers, and could exist and function identically in, at my count, any of 512 different combinations each.

Although if I understand you correctly, only 1 of the 512 results in 'life'.

Yet only one configuration exists in the biome. Two explanations are possible: the other 511 varieties either did not originate (unlikely), or were outcompeted by our common ancestor (likely).

A number of things that science has examined were once, incorrectly, deemed unlikely.

Abiogenesis biochemistry is a mature scientific field, not just fru-fru philosophy. Optical activity is key to exactly the field of research you are discussing.

And I again that you for a cogent discussion of same.

"Each codon represents one of 21 amino acids. The translation is identical in all living things."

The discovery of two, then two more amino acids refutes this, since some codons appear to have different translations in different kingdoms.

I wondered if that was what you were referring to -- different aminos from the same source code, is perhaps another way to say it. Again, thanks.

They directly address the issue of multiple biogenesis events.

Specifically, "normal" (laboratory) chemical processes will always produce racemic forms, since there's an even chance of a methyl group attaching to the left side or the right side of any given (symmetric) molecule. Biochemistry appears to be different. Nature has a 'preferred' side; for example, your DNA has a right-handed twist, not the equally plausible but for some reason unfound left-handed version. Similarly, the amino acids that make up your proteins are all levorotary.

Thanks for the clear explanation.

We can explain this fairly simply as the result of a single evolutionary coin flip, way back when. The first DNA molecule that happened to form had to be either left- or right-handed, since there's no intermediate choice. But a hypothetical second DNA molecule would only have a 50% chance of being left-handed. If there were a thousand different abiogenesis events that led to the independent creation of DNA, the odds against all the DNA that we see today being left-handed would be the same as the odds of getting heads each time for a thousand coin flips -- essentially negligible.

Offset somewhat by the fact that poking & prodding in the lab indicates that viability ceases if the wrong chirality is present.

If, as you suggest, DNA/RNA chemistry was independently reinvented several times, why was it only ever invented on the right side?

Unknown, but we back to right-hand is life, left-hand is not.

We could extend this even further. There's no known reason why left-handed DNA (which we don't have) couldn't work properly with levorotary amino acids (which we do), or why right-hand DNA couldn't work with dextrorotary amino acids. So there's really at least two coin flips involved here.

Similarly, there's really at least twenty coin flips, since there's no known reason why we couldn't use a mixture of dextro- and levorotary acids; biochemistry would probably still be possible with l-cysteine and d-histidine, for example. (In fact, as was pointed out, there are many more than two variations on most amino acids.) But we don't see that combination, either. And the combinations that we do see are the same for all life forms, suggesting a single biogenesis event.

Again, suggestive, but not absolute.

One way was answered above. A tree based on left-handed DNA and dextrorotary amino acids would be notably different, and probably win the Nobel prize for the discoverer. But so far, that doesn't seem to be the case.

I finally see the point that was being made above; yet again the fact is that only right-hand compounds 'live'.

My thanks to both of you for an interesting, concise, and sfaik factual, discussion.

 

[drkitten]

Although if I understand you correctly, only 1 of the 512 results in 'life'.

You have the wrong end of the stick here.

Any of the 512 could result in life, biochemically speaking. It would simply be life that is different than (and incompatible with) our current biochemical processes.

We have no reason to believe -- in fact, every reason not to believe -- that an independently evolved biosphere (say, the Vulcan's, with their pointy ears and their green, copper-based blood) would also have right-handed DNA if they even had DNA at all.

In fact, even stating that different chiralities would necessarily be "incompatible with" our current biochemical processes is overstating it. We know, for example, that the human systems will partially respond to molecules of the wrong chirality -- for example, sucrose of the wrong chirality tastes sweet, but doesn't digest properly (and therefore has zero calories, a fact that has not been lost on the diet soft drink industry). So the chemical processes in our taste buds can handle "wrong" molecules, but our digestive enzymes can't. If there were some kind of plant that had independently evolved to use the wrong chirality, we would almost certainly see some kinds of herbivores (for example) that had evolved enzymes to digest those plants.

Offset somewhat by the fact that poking & prodding in the lab indicates that viability ceases if the wrong chirality is present.

No, viability doesn't cease. It's simply incompatible with life as we experience it.

One of the key things that lets us know, for example, that Mac and Windows computers are independently designed are the key differences, for example, in the instruction set. A program for a Windows machine won't execute on a Mac, and vice versa -- but that doesn't mean that "functionality ceases" if you have a Mac program. My Mac programs work just fine, thank you -- but I run them on a Mac.

Unknown, but we back to right-hand is life, left-hand is not.

Again, wrong end of the stick.

It's not "right-hand is life." It's "life is right-hand." There's nothing necessary about life being right-hand. And the observation that all life is right-handed strongly suggests a single abiogenesis event that happend to be right-handed.

If you want to focus on "suggestive," be my guest. But this evidence strongly suggests a single abiogensis event. Probability theory suggest that the chance of multiple abiogenesis events is of the order of 2^100 or more to one against. Nothing except perverse nihilism suggests otherwise. We're back to the "well, science strongly suggests that yeast causes bread to rise, but we don't have absolute proof that it isn'f fairies" issue.

It gets back to evidence in support of alternatives. The believe that all life shares a single common ancestry is a conclusion from the data, not an axiom or an assumption. It's been questioned many times, but no evidence against it has ever surfaced.

 

[blutoski]

Although if I understand you correctly, only 1 of the 512 results in 'life'.

No, the point was that any of the 512 would have worked equally well. Any one of these could have founded a biome such as we have today.

Yet only one is present.

If we were to rewind and restart, and for some reason rna was involved in life again (an assumption I'm willing to make for this exercise), then any of the other 511 setups would be equally viable. In a world where no life exists yet, no orientation has an advantage.

The roiss machines used in abiogenesis lab demos operate pefectly well, regardless of which enantiomer starts replicating like gangbusters.

This is old material for abiogenesis models. The specialists have been tossing this around, along with exobiology scenarios, for three generations now.

 

[hammegk]

Thanks again for interesting comments and data.

You have the wrong end of the stick here.

Any of the 512 could result in life, biochemically speaking. It would simply be life that is different than (and incompatible with) our current biochemical processes.

Apparently life disagrees with that assessment.

We have no reason to believe -- in fact, every reason not to believe -- that an independently evolved biosphere (say, the Vulcan's, with their pointy ears and their green, copper-based blood) would also have right-handed DNA if they even had DNA at all.

I'd say you have no data to make such a judgement, and what data you have says the opposite.

In fact, even stating that different chiralities would necessarily be "incompatible with" our current biochemical processes is overstating it. We know, for example, that the human systems will partially respond to molecules of the wrong chirality -- for example, sucrose of the wrong chirality tastes sweet, but doesn't digest properly (and therefore has zero calories, a fact that has not been lost on the diet soft drink industry). So the chemical processes in our taste buds can handle "wrong" molecules, but our digestive enzymes can't. If there were some kind of plant that had independently evolved to use the wrong chirality, we would almost certainly see some kinds of herbivores (for example) that had evolved enzymes to digest those plants.

Er, yes, the miracles of modern chemistry and nutritional food.

No, viability doesn't cease. It's simply incompatible with life as we experience it.

Do you state this based on in-vitro -- I'd guess -- viable lifeforms (with suitable sustenance) being a reality?

Again, wrong end of the stick.

It's not "right-hand is life." It's "life is right-hand." There's nothing necessary about life being right-hand. And the observation that all life is right-handed strongly suggests a single abiogenesis event that happend to be right-handed.

The fact being, again, that life is right-hand.

If you want to focus on "suggestive," be my guest. But this evidence strongly suggests a single abiogensis event. Probability theory suggest that the chance of multiple abiogenesis events is of the order of 2^100 or more to one against.

Do you have a cite?

Nothing except perverse nihilism suggests otherwise.

LOL. From my view, your view is the epitome of perverse nihilism.

We're back to the "well, science strongly suggests that yeast causes bread to rise, but we don't have absolute proof that it isn't fairies" issue.

Nope, I don't see even 2^100 against. Nor I suspect do you. What life can accomplish and what life is are different questions.

It gets back to evidence in support of alternatives. The believe that all life shares a single common ancestry is a conclusion from the data, not an axiom or an assumption. It's been questioned many times, but no evidence against it has ever surfaced.

Agreed that it's a strongly held conclusion, but as I've indicated before, we are now discussing the magnitude each person assigns to epsilon.

 

[Lamuella]

Apparently life disagrees with that assessment.

Repeat after me: there is a difference between what can happen and what has happened.

The fact that all life as we know it has this particular biome does not mean that no other biome would result in life. If you are stating that it does mean this, you need to present evidence to support your viewpoint.

 

[drkitten]

Apparently life disagrees with that assessment.

No. We've done experiments with replicators with differing chirality, and they happily beaver away.

You're assuming that because a path wasn't taken, that it couldn't have been.

And you have no basis to make that assumption.

I'd say you have no data to make such a judgement, and what data you have says the opposite.

This from a man who six hours ago had never heard of chirality....

Do you state this based on in-vitro -- I'd guess -- viable lifeforms (with suitable sustenance) being a reality?

Self-replicating biochemical systems being a reality, yes.

We haven't yet gotten to the point where I can make a redwood tree from scratch in the lab. We would need a very large beaker, for example....

Do you have a cite?

I have a calculation. Each nucleic (there are five) acid has at least eight chirality points. A typical amino acid (there are 20) has three or so. There's also no reason that RNA should use the same chirality as DNA in its versions of nucleic acids, so there's three more acids, twenty-four more chirality points. Between the 60 chirality points in the amino acids and the 64 in the nucleic acids, there are 124 different binary left/right decisions that are consistent across all known life-forms.

124 coin flips.

An independent re-invention of DNA/RNA/protein chemistry would therefore have one chance in two to the hundred and twenty fourth power of making identical guesses in the reinvention.

 

[hammegk]

Repeat after me: there is a difference between what can happen and what has happened.

The fact that all life as we know it has this particular biome does not mean that no other biome would result in life. If you are stating that it does mean this, you need to present evidence to support your viewpoint.

I choose what is fact over what might be fact. That assumes that other chirality life is not growing in a testube somewhere.

I see drk has provided added data which I've not yet considered. Am I proved in error by the latest post?

 

[Lamuella]

I choose what is fact over what might be fact.

no, you choose what supports your prejudices over what better informed people (like Dr Kitten) tell you is the case.

 

[Hellbound]

Of course, I personally find it interesting that someone in this thread had never heard or chir, while simultaneously claiming to have studied evolution and abiogenesis extensively.

I have not studied them extensively, but I have a good, solid layman's understanding of the major points. Chir is one of those major points.

Was wondering if anyone else noticed this discrepancy, and agreed with my analysis of it.

 

[Yahzi]

To me to believe that every thing needed to bring life into existence on this planet(both the chemical reactions and for that matter the aspects of our solar system) happened by random chance is to big a stretch.

It is a stretch. But all the other alternatives are even more of a stretch.

Consider this: if you push the design on life onto God, then what do you push the design of God onto? In other words, if it strikes you as a stretch that random luck created life, why doesn't it strike you as a bigger stretch that random luck created God?

And if you are going to claim that God was not created... isn't that even more of a stretch?

How much stretch are you going to embrace to avoid this little problem of random chance?

No and I'm well aware of that but its some thing I've taken the time to think through and it makes sense to me.

Then why wouldn't it make sense to us?

If we all start with the same premises, then we must achieve the same result. Unless you're repudiating all logic, reason, and math.

So really, all we need to discuss are the premises. Here are my premises: 1) there is a real world, 2) it is non-arbitrary, 3) we can know it to approximation, and we can tell the difference between approximations.

Now I willing to bet that you share those premises. I bet the problem is that you add one additional premise: 4) God exists. So the real question becomes: how do you justify adding an additional premise?

 

[hammegk]

Of course, I personally find it interesting that someone in this thread had never heard or chir, while simultaneously claiming to have studied evolution and abiogenesis extensively.

Not immediately seeing the application of an idea -- handedness, say -- to a topic has little to say on one's general knowledge of chirality.

I have not studied them extensively, but I have a good, solid layman's understanding of the major points. Chir is one of those major points.

Obviously so, today. It wasn't when my knowledge of evolutionary theory was significantly better than 'layman level', but never delved deeply into genetic chemistry. As I said, I appreciate learning something new; it happens damn seldom here even though we have a fairly large number of posters who could provide valuable info.

Was wondering if anyone else noticed this discrepancy, and agreed with my analysis of it.

Yeah, I'm a stupid man. You got me. Feel better now?

I'm happy to be on board that terran life, so far, is right-handed. What have we found in comet debris, and deep space material returned to earth?

no, you choose what supports your prejudices over what better informed people (like Dr Kitten) tell you is the case.

Opinions are variable, facts are not. As you've noticed I'm disinclined to accept anecdotes no matter how 'well-informed' the source. Inheritance, and modification, are facts.


eta: http://www.talkorigins.org/faqs/comdesc/section1.html
is full of interesting data that I admit I'm not really up on, and appears to comment on some of my questions.

Real world examples that cannot be objectively classified in nested hierarchies are the elementary particles (which are described by quantum chromodynamics), the elements (whose organization is described by quantum mechanics and illustrated by the periodic table), the planets in our Solar System, books in a library, or specially designed objects like buildings, furniture, cars, etc.

In particular touches on an earlier question I posed.

 

[Hellbound]

Hammegk:

No I don't feel better. But considering the number of times you've intruscted us to go "learn about your theory", and the number of times you've repeatedly claimed "I already know what your theory says, and I've looked at the evidence", it shows a certain intellectual dishonesty on your part.

In short, it shows your ignorance, dogmatic attitude, and bias.

It supports the contentions that you have nothing constructive to add, that you are a simple nay-sayer, with very little thought put into the subject at all.

Chirality is one of the major points supporting common ancestry, and I've seen it covered in multiple works that address the question. SO how does someone whose "knowledge is extensive" miss this major point? I know, for a fact, that the discussions of chir in regards to abiogenesis have been around for at least 10 years now.

 

[drkitten]

I know, for a fact, that the discussions of chir in regards to abiogenesis have been around for at least 10 years now.

More like 40; my first exposure to the chirality discussion was an old paper of Isaac Asimov's dating from the 1960s. Now, granted, Asimov was a polymath of the first water, and his first and primary field was biochemistry -- but still, he was a professional writer, not a bench scientist. I assume he didn't make up the idea out of his own fertile imagination....

 

[drkitten]

Not immediately seeing the application of an idea -- handedness, say -- to a topic has little to say on one's general knowledge of chirality.

No, but not immediately seeing the application of an idea that has been extensively discussed in the recent literature speaks of an unfamiliarity with that literature.

Which also suggests an unfamiliarity with the rest of the recent literature doncerning evolutionary theory.

Obviously so, today. It wasn't when my knowledge of evolutionary theory was significantly better than 'layman level', but never delved deeply into genetic chemistry. As I said, I appreciate learning something new; it happens damn seldom here even though we have a fairly large number of posters who could provide valuable info.

My sympathies are limited.

If your knowledge of evolutionary theory is that out-of-date, then you shouldn't be making cathedral pronouncements about "butterfly collecting" and "just-so stories." Evolutionary biology, especially with the tie-in to molecular genetics and bioinformatics, is arguably the largest and fastest moving field in modern biology. The amount of information gained in the past six years dwarfs the total biological knowlege gained between Linneus and the recent millenium.

And it more or less all supports the theory of evolution. There have been a few surprises, yes. We now know (based on the story of the molecules) that whales are a form of artiodactyls, and in fact, are close relatives of hippos (and not so close relatives of pigs). There are some interestingly suggestive findings about our relationship to different kinds of bacteria (in particular, we appear to be descended from archaebacteria, while our mitochondria are descended from proteobacteria).

But what we haven't found -- and we've looked for -- is any evidence that materially refutes the overall story of "descent with modification" from a single common ancestor.

The information has been presented to you multiple times across the threads. You simply refuse to accept the experimental evidence when it's described to you, and reflexively deny the conclusions that have become routine within the community. Instead, you tell just-so stories that have long been refuted among the active scientists, or retreat to unfalsifiable 'fairies at the bottom of the garden" stories, without bothering to assess how utterly improbable they are.

You dogmatically assert that you are entirely familar with the theory of evolution, but it's obvious that if your knowledge ever rose above "layman's level" (which I doubt), it certainly hasn't done so since most of the current practitioners of evolutionary biology were alive.

 

[hammegk]

eta:

You dogmatically assert that you are entirely familar with the theory of evolution, but it's obvious that if your knowledge ever rose above "layman's level" (which I doubt), it certainly hasn't done so since most of the current practitioners of evolutionary biology were alive.

Guilty as charged vis-a-vis this topic, although I am making an effort to become better informed.

Thanks to all.

Hammegk:

No I don't feel better. But considering the number of times you've intruscted us to go "learn about your theory", and the number of times you've repeatedly claimed "I already know what your theory says, and I've looked at the evidence", it shows a certain intellectual dishonesty on your part.

It highlighed a glaring lapse in my education. I should have done more homework when challenged to examine the 'common ancestor' hypothesis.

In short, it shows your ignorance,

Agreed.

dogmatic attitude, and bias.

I also admit to dogmatism and bias; as an objective idealist my analysis must differ from the conclusions a physicalist must reach.

It supports the contentions that you have nothing constructive to add, that you are a simple nay-sayer, with very little thought put into the subject at all.

For most audiences I'd agree; simple? ummm, perhaps not; as to the amount of thought I put into things, you are wrong. GIGO effects me no more or less than anyone else.

Chirality is one of the major points supporting common ancestry, and I've seen it covered in multiple works that address the question. SO how does someone whose "knowledge is extensive" miss this major point? I know, for a fact, that the discussions of chir in regards to abiogenesis have been around for at least 10 years now.

Feel free to equate lack of current (and that could mean decades )education with stupidity.

Repeat after me: there is a difference between what can happen and what has happened.

The fact that all life as we know it has this particular biome does not mean that no other biome would result in life. If you are stating that it does mean this, you need to present evidence to support your viewpoint.

No. We've done experiments with replicators with differing chirality, and they happily beaver away.

Do you assert these self-replicators qualify as life?

You're assuming that because a path wasn't taken, that it couldn't have been.

And you have no basis to make that assumption.

Nor, apparently, do you to assume the opposite.

I have a calculation. Each nucleic (there are five) acid has at least eight chirality points. A typical amino acid (there are 20) has three or so. There's also no reason that RNA should use the same chirality as DNA in its versions of nucleic acids, so there's three more acids, twenty-four more chirality points. Between the 60 chirality points in the amino acids and the 64 in the nucleic acids, there are 124 different binary left/right decisions that are consistent across all known life-forms.

124 coin flips.

Awesome odds indeed, iff any of the alternates can be demonstrated to be 'life'. However, I suggest the burden of proof for that assertion rests with you.

Until that proof is incontrovertible, your ID opponents will just note what you admit are the incredible odds of random occurence.


KevinM: I am unqualified to address the accuracy of the author -- who appears to be a Christian as you are -- as he attempts to address many questions opponents of neo-Darwinism consider.

http://www.evanwiggs.com/articles/reasons.html#primer