So what is Entropy?
To follow in the tradition of Maimonides. Entropy is NOT a tendency to disorder! I need to thank Joe Felsenstein for directing me to Frank L. Lambert’s insights on a previous thread probably best left alone. Here is a great site to elucidate Lambert’s insights:
http://entropysite.oxy.edu/
What about Evolution? Can complex systems arise naturally and spontaneously into higher tiers of complexity and order and opportunity—according to the Second Law of Thermodynamics— and all without divine intervention commonly described as Intelligent Design or Irreducible Complexity?
Sean Carroll has much to offer on this question:
Participants should refrain from arc-reflex boiler-plate diatribes echoing previously held opinion and first examine what Carroll has to say. Failure to do so will merit cyber-smack downs.
DNA and RNA sequences both fold up on themselves into a blob due to molecular interactions. So what template strand are you talking about?
Sounds like a poor design
So you never heard about DNA as a double helix? Of about double-stranded RNA viruses?
No. They’re demonstrable facts.
That depends on temperature. All DNA and RNA strands have what is called a melting temperature where the strands separate and unfold.
This fact is rouninely exploited in the Polymerase Chain Reaction method.
Rumraket,
Here is a critique of the hypothesis. The 1% number came from a paper I had read previously and am still searching for it.
Rumraket,
This paper highlights the issue with non enzymatic coping of RNA which is inaccurate and slow. They are trying to come up with a modified pre biotic replicator.
It appears my 1% may be very conservative relative to non enzymatic RNA coping accuracy.
Sure, but neither of these is a template strand, and you were talking about a template strand.
Do you think double-stranded DNA and double-stranded RNA were there from the beginning? A double-stranded virus, for example, has a lot of prerequisites.
My. Why didn’t evolution think of that. If we just up the temperature in this cell this stuff will come apart automagically.
Each strand in a double helix, aka, double-stranded molecule, is a template strand. Your comment about “blobs” indicated some of ignorance on your part, but not clearly what kind of ignorance. This one indicates that your ignorance, or misunderstanding, might be much worse than I suspected.
Nope. I’ve heard there’s a proposal that at some stage there was an RNA-world, but not “from the beginning.” So, maybe there was such an RNA-world stage. Maybe it included double-stranded RNAs. It’s not as if it was impossible for replicating RNA molecules to stay together, at least for a while.
But why do you ask? You think that “neither of these is a template strand.”
Why are you so desperate to portray yourself as a fool? High temperature doesn’t make stuff come apart “automagically,” but naturally.
Well, Tom has convinced me that evolution can’t happen due to entropy. Thanks Tom!
To serve as a template it can’t be in a double helix. It has to be a single strand. I should have to tell you this?
I explicitly said that each strand is a template strand, I didn’t say that a double helix is a template strand. Seems like your illiteracy and your forgetfulness can be quite a problem.
Moved a post to guano.
Right, then get back to us when you find it. None of the papers you reference here speak about the replication fidelity of RNA replicators.
Yes but Bill, that is non-enzymatic replication. You said a replicator (that is an RNA enzyme) would have a 1% replication fidelity. I don’t believe that number is correct. In fact I’m pretty sure I’ve seen estimates that even low-fidelity RNA polymerases are much more accurate than that. On the order of one mutation in about ten thousand bases. Which is the mutation rate of some RNA viruses.
The abstract in the first one reads like a demand to provide a complete explanation from what the RNA-world was exactly like, how to go from an RNA-world to today’s life forms, all of that before considering the possibility of an RNA-world. Pretty much what a creationist would do: blind themselves by demanding the complete history, and all the possible details, and thus reject whatever route might be proposed.
I’m more of the “lets study those possibilities until either we get to the point where we have to reject that pice of the puzzle, or we get better insight about how it could have happened,” which is exemplified by your second abstract, which reads like “maybe primitive nucleic-acid-replicators didn’t have exactly the same nucleotides as those of today,” which doesn’t contradict anything we’ve explained to you. We have lots of potential pieces of the puzzle. maybe all wrong, maybe some wrong, some right. But they still exemplify ways in which life could have started.
No, here’s what you wrote:
They are not template strands when they are in a double helix aka double stranded molecule. The double helix has to be taken apart to create two separate individual strands before they can be used as a template.
They don’t just automagically serve as templates as you seem to think.
So you have to have some mechanism already in place to separate the strands and then how do you keep each one from a) folding up on itself and b) reattaching to the partner strand that already matches up perfectly.
There is far more to replication than simply having a “template strand.” You have to over-simplify things in order to hide the complexity because otherwise sensible people would laugh at your explanations.
It just happened, that’s all, is not a route to anything but ignorance. If you had details you’d gladly provide them, but you don’t have details. What you have is speculation and wishful thinking. Blind belief based on ignorance and imagination.
It’s how I know you’re a true skeptic.
Entropy,
The article in the first paper showed that the RNA world hypothesis is highly improbable given what we know now. The second article confirmed that the RNA molecule needed modification in order to replicate with the fidelity and speed required to be part of a primitive living cell. This crosses over to intelligent intervention. The reality is the simple to complex model has never been validated in either OOL or evolutionary experiments. Just because something can replicate does not mean that it can repeatably generate new functional features.
Sorry, pretending to be that much of an illiterate won’t work.
Really? Woa! I guess that separation must require magic, since it surely never happens! Shit! You’ve got me!
No. Of course not. They separate naturally.
You mean like what happens in that phenomena dubbed DNA breathing? Like that?
Because that folding up could not possibly unfold naturally either, right?
How could it reattach to the partner if it is folding in itself and the self-folding is indestructible (according to your fantasies)?
Somebody should tell those replicating RNAs that some scientists have in their laboratories. Hey RNAs! Stop! It’s not that simple! So don’t keep replicating!
I don’t know about them, but I would not be laughing at my explanations.
Not really. The first abstract shows a pretty much creationist-style rejection of the idea of an RNA world. the claims are suspiciously creationist-like. I’d read it, but I don’t really care if there was an RNA world or not.
It provided an alternative. The article proposes RNA-like molecules that might work better than RNA. That’s it.
No, it doesn’t. This is the poor philosophy I was talking about. The work just proposes that if RNA is too slow, then maybe something other molecule was there. A molecule is not an intelligence. Sorry.
Curious, because I have seen plenty of validation in evolutionary studies, and because I doubt, very much, that life could have started as we see it today. There’s plenty of experiments that show that cells-as-we-know-them don’t suddenly appear, which means it must have been simpler at the beginning. But fell free to show me experiments showing that the sudden appearance of life-as-we-know-it is possible.
This is also curious, because we see the variety of life everywhere around us. That means, pretty much, that generating new functional features is not that much of a problem for replicating entities. If that wasn’t enough, there’s directed evolution experiments showing new functional features out of replicating entities.
You understand that cycling temperatures (like from a day-night cycle, or convective flows in a pool or hydrothermal mineral enclosure of some sort), is suggested to be how strand-separation took place before helicase enzymes first evolved. Under that model it’s not that evolution had to “invent” the process of strand-separation by temperature, rather that is what made recursive copying and therefore evolution possible in the first place.
Speculative to be sure, but I’m just pointing this out because you seem to have reversed the suggested chronology of events, when you say evolution was already happening and then had to somehow invent strand separation with cycling temperatures.
And that, my dear, is what is called psychological projection.
Rumraket,
Mung equated separation of DNA strands at high temperatures to magic. That pretty much shows that the poor guy doesn’t understand that temperature separates strands naturally. He might imagine that the PCR reaction proceeds by elevating the temperature, some tiny intelligent designer feels the heat, and runs towards the molecules to separate them.
So, your explanation will not help Mung. You still assumed that Mung understands that high temperatures naturally separate strands, despite he clearly declared that such a thing would be magic.
I doubt that Mung has the background, or the literacy, to understand.
TSZ should have a drinking game. Every time Entropy writes the word illiterate, you take a decent shot of scotch and let out a big belly roaring laugh.
In no time whatsoever, you will have an entire gaggle of hebefrenic drunk fools, cackling and shouting, look, look, HE DID IT AGAIN, gurgle gurgle, drool, AHHAHA !
Rumraket,
Yeah, cycling temperatures, or cycling salt concentrations (tidal pool at low humidity) will do it…
Strand separation is the easy bit. What’s tricky is actually getting strand pairing, when you haven’t just got a complementary template pair knocking around.
Entropy,
The selection and modification of the molecule is what required intelligence.
The only data we have of simpler functioning life is a gene reduced living cell
in Venters Lab which is pretty close to simple bacteria.
Evolutionary evidence of new function is very rare and the evolution of a new enzyme or new cell type from scratch has never been demonstrated. All new function so far is a result of a few adaptive mutations. Based on the structure of the genome and the transcription translation mechanism, this is exactly what we should would expect.
For the experiments? Sure. For life’s origin? How could it? There was no life-as-we-know-it back then (remember that contradiction of terms?), and the only intelligent beings we can actually talk about are life-as-we-know-it. That rules out an intelligence. But, for the safest part, numerous experiments about potential natural chemistries for an early earth produce different kinds of organic molecules, among those different kinds of nucleotide-like ones.
Yep. For life-as-we-know-it, yes. But that wasn’t my request. You seem to think that life started as we know it today. So, I asked for evidence that life-as-we-know-it springs out of the nonliving stuff in a single swoop. If there’s no such thing, then the first life forms must have been simpler. It’s a very logical inference.
Yet scientists have isolated functioning catalysts from random sequences of RNA, and there’s at least one case where a large part of a new enzyme derived from a non-coding sequence. I suspect that examples will come more frequently as we sequence more and more organisms.
One of your most coherent posts in months.
Rumraket,
Way ahead of him. Every ‘lucky accidents’, ‘what survives survives’, or a lengthy post about something complex with a picture at the end, it’s down the hatch. I had to come to India just to dry out.
I tried a sip of beer every time a creationist here wrote something stupid, but ended up in the emergency room with acute alcohol poisoning in a couple of hours.
Glen Davidson
Entropy,
I don’t know how life started but the evidence is the simplest form is a bacteria that we can observe. Your are insisting on the simple to complex hypothesis with no evidence of a simple living organism. You have a hypothesis you need to validate. An argument from incredulity is going to fall short of confirming your hypothesis.
Can you provide a citation of this experiment?
I have no argument from incredulity. On the one hand, by mere logical inference, since life-as-we-know-it doesn’t appear all of a sudden, the only option seems to be that there was a route from much simpler to what we see today. After all, so far there’s no data about how a complex one as-we-know-it would arise all of a sudden.
If that wasn’t enough, I have already told you, there’s lots of proposals about routes from simpler to complex, from something that maybe we cannot describe as life proper, to life-like, to etc. Lots of proposals about simpler membranes, simpler replication-prone chemistries, about chemical reaction systems / metabolisms, etc.
For an RNA catalysts evolved in the lab, The last author of the second paper you quoted has some interesting articles. If you check the web page of that author, you might find some good examples. There’s also a kind-of-old review from a different author.
For the enzyme, I think it was a nylonase example, or maybe another I cannot currently remember. You can try and find it yourself. If I find it later I’ll let you know.
Entropy,
There is no data how it arose. You are trying to drive a material answer here as the only answer without data. The experiments so far are too rudimentary to claim the high ground of the simple to complex. Until you have a simple living organism in the lab generating work and reliably self replicating your hypothesis is untested.
The partial experiments are interesting but fall short of validating the concept. Assuming the simple to complex without validation makes your argument circular.
I would expect that small catalytic activity is possible with short RNA’s. The problem is complex catalytic activity necessary for life that are currently performed by amino acid based enzymes.
The nylonese experiment, the favorite of the theistic evolutionists is a claim that an existing bacterial enzyme was modified by a frame shift mutation to allow the bacteria to break down nylon. This is not an enzyme from scratch but a mutation of an existing enzyme.
It turns out that the nylonese enzyme had existed well before the observation and the frame shift story is probably wrong. Sal has written a paper on this and there is general agreement here at TSZ that Sal’s analysis is correct.
No, I didn’t.
I bet you think that in extremophiles don’t have their DNA in a double helix.
There’s lots of data for “material” answers all over the place for all kinds of questions. So far I haven’t seen an answer to anything involving something other than “material.” So my question would be: why consider something that cannot even be described? I’d find that much more questionable than expecting an answer that involves the very same things every other answer has involved. How would we go about it? More importantly, why? What would be the justification for “we should try this question assuming something other than material answers, even thought there’s no way to test for any of it”?
Where are the rudimentary experiments showing a potential route other than simpler to complex?
That depends on what’s claimed. If the claim was that we have a complete route from non-licing to today’s life forms, then I would agree, but if the claim is that potential routes might involve this, and that, and that, and that. and there’s demonstrations for chemistries that show such events to be at least possible, then I’d think we’re going well. But, regardless, without experiments showing the potential for other kinds of routes, where organisms can spring out of the non-living, at the complexity levels we see today, we have no option but assume the most logical routes, from simpler to complex. The closest to a semi-complex thing is the metabolism first thing, and even that one involves systems much simpler than today’s cells.
I disagree. I think you have irrational standards because you don’t like the idea that the origin of life might look essentially solved. That would thus refute what you perceive as the “default” “option.” An “option” that complies with much lower philosophical and scientific standards, but that you like very much over anything else.
But I’m not doing that. I told you already: I have philosophical, scientific, and experimental validation.
This is what’s called “moving the goalposts.”
Even if your standards towards philosophically and scientifically reasonable answers are too high, you should understand why I remain optimistic that we’re learning something about potential routes towards understanding the origin of life, and why I don’t feel like you’re offering me a reasonable counterpoint. All you do is refuse to accept any evidence in exchange for something that has much lower quality.
Since I don’t have time to look up for the example I was semi-remembering, then I accept your judgement on this one.
Anyway, as I keep saying, we’re here. As far as we can see we’re natural. As far as we can understand, we have not always existed. Life has not always existed. Therefore, there must be ways in which natural processes started “producing” life forms. Otherwise we could not be here discussing it.
What prevents a strand from folding up on itself in the absence of a complementary strand? And what prevents the strands, once separated, from just pairing back up given that you’ve got a handy complementary strand right there?
But maybe Entropy understand now that just having a template strand isn’t nearly enough.
I bet that’s been proven by experiment.
I bet you meant to say that life as we know it has not always existed.
Haha.
Yes you did when you wrote this:
As you can read, you clearly said that separation at high temperatures is magic.
Nice try. But you’re contradicting yourself. You’re implying that if thermophiles’ DNA remains double stranded, then separation of any DNA strands at high temperature must require magic.
When the extermophiles were discovered, one of the first questions scientists thought about was how their DNA remained stable, because these scientists knew that high temperatures denature the DNA of mesophilic organisms. What they discovered was that higher stabilities are attained by tendencies towards higher GC content, by DNA super-coiling, and by association to some proteins.
Now, I doubt that you understood that explanation. I suspect that you imagine that the two strands of DNA are solidly fused together. That you really have no idea, and thus my explanation above was completely wasted on you. That the words I used, “stability,” “super-coiling,” “GC content,” “higher,” are like hieroglyphics to you.
He has philosophical, scientific, and experimental validation.
Q.E.D
phoodoo,
Thanks phoodoo. I hadn’t caught on that repetition.
FFS. I was mocking the idea that separation by temperature was the way things work in the cell.
Again? Nothing prevents them from folding into themselves. You must imagine that once folded in themselves the fold is indestructible. You really have no idea what you’re talking about, do you?
Again? You must think that these get solidly fused. Once paired, it must be impossible for the strands to separate, right? According to your fantasies, that is.
So you were mocking your own sarcastic nonsense by adding that separation at high temperature would be magic? Well, that’s even worse. At least your imagining that DNA strands are inseparable can be justified as simple ignorance.
But I don’t know what I am talking about. Why do they fold on themselves?
Must I?
No, by some magic they can fold and unfold at will. And by some magic they just happen to choose to do so at the exact moment at which a complementary strand just happens to be floating by that by some magical means is not folded. POOF! A COPY!
This is simply not the way that template copying takes place. Don’t you get that yet? Your idea of how DNA replication takes place is laughable.
Must I?
Right. But only on the second pairing.