Here is one reason I don’t think life as we know it is the result of ordinary processes.
From Wiki:
https://en.wikipedia.org/wiki/Stop_codon
In the genetic code, a stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation.[1] Proteins are based on polypeptides, which are unique sequences of amino acids. Most codons in messenger RNA (from DNA) correspond to the addition of an amino acid to a growing polypeptide chain, which may ultimately become a protein. Stop codons signal the termination of this process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain. While start codons need nearby sequences or initiation factors to start translation, a stop codon alone is sufficient to initiate termination.
Now what happens when there is no stop codon?
A nonstop mutation is a point mutation that occurs within a stop codon. Nonstop mutations cause the continued translation of an mRNA strand into an untranslated region. Most polypeptides resulting from a gene with a nonstop mutation are nonfunctional due to their extreme length.
….
Nonstop mutations have been linked with several congenital diseases including congenital adrenal hyperplasia,[15] variable anterior segment dysgenesis,[16] and mitochondrial neurogastrointestinal encephalomyopathy.
In other words, it would be bad juju if there are no means of reading of DNA and recognizing where one gene ends and the other begins. In fact, without stop codons, it looks like a DNA-RNA-protein-based life on Earth would be dead.
One could postulate a DNA-RNA-protein-based life that had an alternate stopping mechanism that eventually evolved a stop codon. But that just moves the problem elsewhere in as much as a DNA translation system that contains multiple genes needs a gene delimiting mechanism. A stopping mechanism needs proteins to implement it, but without a stopping mechanism to implement proteins, there is no stopping mechanism. We have then a chicken and egg paradox.
One could postulate proteins arose by a method outside of DNA translation and somehow recruited DNAs and RNAs and then defied all probability and somehow figured out how to code the next generation of proteins using DNAs that just happen to be coding the proteins like the ones that miraculously recruited them. At some point, such scenarios are so out of the ordinary they are not distinguishable from miracles.
Some will argue Darwinian evolution in the origin of life. That’s problematic for at least two reasons.
1. even most evolutionists don’t view the origin of life and origin of the protein translation cycle as part of typical evolutionary theory. So in that sense of the word “evolution”, stop codons didn’t evolve.
2. something dead can’t evolve by Darwinian mechanisms, and if this is an origin of life scenario we’re dealing with dead pools of chemicals.
So Darwinian evolution isn’t a solution. Chemistry isn’t a solution. Physical laws aren’t a solution. Probability isn’t a solution. In fact what we know of physical process would work against evolution of stop codons, not for it. Hence stop codons and life that depend on stop codons did not arise out of ordinary physical processes.
Sal, have you ever read anything at all on the origin of life? You really make us tug and strain at the assumption of honestly rule.
Sal,
What’s an “ordinary process”?
I think you forgot to show your working.
Sal,
Given your “explanation” is basically “a miracle occurred” why do you have a problem with miracles in general?
I don’t understand the point of this post.
Yes, it’s true that origin of life is not yet explained. Maybe it will never be explained. But why do we need to invent gods to explain it?
There’s a trivially obvious explanation of life. It happened. It is predicted by Murphy’s law.
The chemistry of our cosmos is such that life is possible. If somebody had tried to construct such a cosmos without life the, according to Murphy’s law, life would break out anyway — Whatever can go wrong will go wrong.
It is equally true that if somebody attempted to build an entirely religion free community, then Murphy’s law predicts that religion would break out anyway.
Petrushka,
Yes, I’ve read some stuff on the origin of life.
But I was posting this hoping the TSZ crowd that is so eager to disagree with me could provide some credible literature that I can give my ID students to review.
I’ve not found much if anything on the mechanical details of how something like a DNA to RNA to protein translation system without a gene delimiting mechanism (like start and stop codons) would come to exist — except for hand-waving assertions that are not much better than “we exist, therefore we evolved.”
Hey, no need to make accusations of dishonesty. If I’m ignorant and I’m teaching science students, I was hoping if my literature search was incomplete this essay might induce some of you all Skeptics to provide some links.
I’ll happily refer my students to this free and open website where ID and creation science are freely critiqued. So give it your best shot. My kids may be visiting, and here is your chance to change their minds. If you can persuade them I’m wrong, hats off to you.
You could at least acknowledge that things won’t go so well for an organism that has a multigene DNA strand but has no means of delimiting the genes (with things like start and stop codons, translation initiation sites, etc.).
C’mon petrushka, can you acknowledge it is ordinary for something that is dead to stay dead, and that it is extraordinary for something to rise from the dead?
To paraphrase an ancient saying, “they will not be convinced even if something rises from the dead”.
It seems more likely that RNA or something close to it recruited amino acids. Indeed, there was one paper that found the nucleotides are non-randomly correlated with amino acids that would have greater affinities to them–apparently with some shifting since actual coding took the place of chemical attractions.
Sal doesn’t go and learn (who needs that when ‘God did it’ is the sole answer considered worthy?), however, he makes up his own version of evolution and tries to rubbish it. The last thing we’ll get from ID is a sincere attempt to explain anything using our knowledge of design, of course, since life doesn’t even begin to fit the purposes and methods of known designers.
Glen Davidson
You think what you just did in that OP is science do you? You are mistaken!
I could define “ordinary” as something within theoretical expectation.
For some, a phenomenon within 3 or for 4 sigma would be in the realm of believability from ordinary processes, but just to be conservative we could go to 10 or 20 sigma.
But apparently for some here at TSZ, even phenomenon at 22-sigma from expectation and a major violation of the law of large numbers would be considered in the realm of “perfectly consistent” with the physics of a well-defined system. See:
and
Don’t you think defining it should have been the first thing you did, not as an afterthought?
You forgot to mention how that was relevant. You have not demonstrated that processes at the OOL are relevant to your claims of improbability.
Your problem is that you are assuming the first life was anything at all like extant life.
Disagree with what? Your un-sourced, speculative claims? Why would anyone bother?
Here, give your “students” this link: http://origins-of-life-fg.arc.nasa.gov/resources/
You’re more than welcome to elaborate, many of my students have or will be exposed to bio chemistry and molecular biology.
That’s just a bald assertion and doesn’t address the emergence of stop codons. Why would stop codons emerge to make multigene loci out of a strand of DNA?
You could argue “well maybe lots of genes mRNA transcripts just floated around and were not connected by stop codons and random mRNAs were just free floating and despite all probability these mRNAs just happened to code for the right genes and do so in the right amounts without any regulation and do so without a functioning ribosome and then some how somewhere random DNAs started popping up along with transcription proteins and stop codons to connect the DNAs that previously had no role in making mRNAs” etc. etc. etc.
Don’t you guys see this whole sequence of events and conditions would have to be way out of the ordinary? Are you going to argue this would be an ordinary sequence of events or not? If you say extra ordinary, then you’ve agree with my basic point.
Thank you anyway for commenting and trying to help educate the next generation of science students why the should believe life can naturally arise from something dead.
I argue however, if you teach them that these sequences of events are well within scientific expectation, you are doing them a disservice in the cause of truth.
Well, that’s up to you to believe what your conscience dictates. But the origin of life or stop codons is not explained and maybe never will be explained, then believing no miracle (or extra ordinary set of events) is involved is formally a belief, not proven fact. We have a word for a body of beliefs that cannot be proven but which we swear by, “religion”.
I have no beef with you personally Neil, I appreciate your intelligence and knowledge, but I just don’t intuitively think Murphy’s law will evolve stop codons nor originate life, I’ve stated the reasons why, and I can say I echo what a lot of my ID colleagues feel about such matters.
No one really cares what you think, Sal. But if your students are interested in biology they could do worse that read this:
Intellectual filth.
Sal, all of science, from Galileo onward, has assumed that regular processes can be found. It is perhaps a mistake to call regular processes “explanations,” but they are useful and lead to further regularities.
Your aversion to regularity might carry some weight if you could cite a single episode in the history of science where “miracle” won the day.
If you cared about “proven fact” in the slightest, you’d not have posted the OP.
Theres absolutely no justification for invoking miracles on this.
Its likely that 3 1/2 billion years ago during the period of quasi-life proteins were much simpler. According to Trifonov they might have been mostly sticky repetitive sequences of amino acids. Protein size might have been determined by the random falling off of a pre-ribosome. So some would be a bit too short, some would be a bit too long but most would get the job done. The only reason nonstop mutations cause a problem now is that proteins are so exquisitely fine-tuned to their function, and because there is cellular machinery that rapidly degrades misfolded proteins ( which would always be the case for a nonstop mutation)
You might say there is no evidence for this ( there is some) You might say this is just storytelling. It doesn’t matter. When you chose to explain something via a miracle then any plausible scenario is enough to reject the necessity for miracles- at least in this case. I would suggest that there are deeper reasons for rejecting the very notion of ‘miracle’
You’re more than welcome to study, rather than expect others to do your work for you.
And who said it was addressing your “problem” that you don’t even begin to understand?
It wasn’t a bald assertion, it’s what the paper states, and I don’t claim to be an expert on such things. Quit stating untrue things about others, and learn something, you ignorant bozo.
And really, I’ve wasted enough electrons on someone as uncivil, unlearned, and unchristian as yourself.
Glen Davidson
The fundamental problem with assuming miracles as an explanation is not that miracles can’t happen. We can’t prove that.
The problem is that such assumptions are useless.
Cite an exception.
Sal,
Great news! The origin of life has been solved! It turns out it was “a miracle”.
Thanks for putting us on the right track. Do you have any other solutions to outstanding mysteries? Is there a limit on the number of times I can use “a miracle” as an explanation for something? I don’t want to wear it out…
Will you be pointing at anything else and saying “it’s a miracle!” any time soon? I’d like to be there when you do, it’s so illuminating!
The problem however is we can’t just take a random set of poly peptides, “proteins”, if you will and expect them to become a self-replicating DNA translation machine. Such a thing happening is would be out of the ordinary, which is exactly my point.
You may not like the miracle explanation. Fine. Will you buy that origin of life is an out of the ordinary set of events and circumstances?
Anyway, thank you for responding. Personally I like Trifanov’s work on non-coding DNA. I’m sure he wouldn’t have a high opinion of the anti-ENCODE crowd, so I count Trifanov as one of the more reasonable evolutionists.
I love how Sal becomes an expert overnight in these things.
No.
What part of the word regular are you incapable of understanding?
The origin of life as a protein translation-cum-replication system with 61 of 64 codon positions occupied by real tRNAs is so implausible as to be not worth considering. Since the rest of the post hinges on that, there is nothing to refute but straw.
stcordova,
How do you know what the probabilities were, such that you can assign particular values? If the original form life took is unknown, you can hardly say how improbable it was.
The old show me your pathetic level of detail gambit.
Won’t work. The ID scenario is preserved in horseshit, like mummies in peat bogs.
Sal
I don’t think anyone suggests something that simple actually happened.
It seems to me that we have bits and pieces of evidence that strongly support life originating by natural mechanism, along with huge gaps in our knowledge. The reasonable approach is to accept the natural explanation and work on closing the gaps, but creationists and IDers ignore what we do know and only focus in on the gaps.
I’d have to agree with you here ( and disagree with petrushka). At least we can say that life has not originated on any of the other bodies in our solar system and probably not on most or all of the exoplanets we know about
Yes, obviously
I’m not sure why you say that about Trifonov. Just because he works on non-coding DNA doesn’t mean he agrees with the no-junk encode people. Even they have retracted some of their more careless statements.
Come to think of it, most biologists work on or with non-coding DNA at least some of the time. The DI has created this false dichotomy: scientists who think all DNA is coding ( no one like this actually exists) vs scientists who accept non-coding DNA but think its all functional ( probably a minority)
By regular process, I mean consilient with known laws and processes of physics and chemistry. I imply nothing about how common an event might be. I am somewhat pessimistic about finding life on other planets, and extremely pessimistic about finding civilizations on other planets.
A regular process is contrasted with god/designer twiddling with the knobs.
I don’t need to establish absolute zero probability to defend the claim on extra ordinary process or set of circumstances. I didn’t argue impossibility, I argued extra ordinary.
I assigned a probability of approximately zero to something dead evolving a stop codon. There might be chemical change, but nothing resembling heritable change. Biotic materials actively degrade in the dead state, so its not like it has a billion years for chemical evolution to work.
Do think an unlikely event or inevitable?
Given some at TSZ can swallow a 22 sigma event as perfectly natural, it reminds me of this:
I’m surprised no one mentioned blood cells. They don’t have DNA!
That of course raises the question how DNA translation and stop codons emerge in a proteins first scenario.
stcordova,
You spattered around sigma values like you had the slightest clue what they might be at the OoL. You don’t, so stop bullshitting.
stcordova,
Jesus Christ. What in hell is this supposed to mean? You know the first organisms probably didn’t have blood, right?
stcordova,
Who has ever suggested that such a thing happened?
stcordova,
See? There you go again. Show your bloody working.
petrushka,
My guess is that asexual, prokaryotic life is probably quite common. The kind of life we are interested in – the likes of us – much, much less so.
Sal,
Christ, not this again. Will you ever learn?
Every specific sequence of 500 coin flip outcomes is equally (and vanishingly) unlikely, assuming a fair coin flipped fairly. Is it therefore impossible to flip a coin 500 times, Sal?
Is every outcome “unnatural”?
Oh yeah? Well then how did they bleed, smarty pants?
Mung,
er … I think I need another drink.
I have. Lots of books on it. Not sure how they are relevant though.
Why doesn’t someone explain to Sal how the process actually works?
It’s not like protein synthesis just keeps going. The Designer was smarter than that.
Mung,
So you’d have to be a bit dim to invent a process that just keeps going?
Would the existence of polypepdtides of infinite length provide evidence of intelligent design?
🙂
We need to develop a list of ID axioms. Sal here has made a good start:
1) All extremely unlikely events are probably miracles (every bridge hand is a miracle).
2) The way life works today is the only possible way it can work (evolution has us as a target, and evolving us is extremely unlikely).
3) There was no long sequence of increase in organic complexity, leading to proto-life over millions of years. The first life appeared POOF just as we see it today, complete with stop codons!
4) The goal of proper science isn’t to explain how things work, it’s to generate some explanation of why everything not yet known must be impossible, so goddidit.
That stcordova has “students” is the most concerning part of this post. If you’ve taken a basic college level biochemistry class, a reasonable scenario isn’t too hard to come up with.
So you’ve never taken a basic college level biochemistry class.
It was to show the fact a cell can operate without DNA.
You guys have done so poorly refuting the basic point, I felt sorry for you and tried to give you and out with the “proteins first” and a “metabolism first”scenario and showing a life-form that functions without DNA. Are you aware enucleated (cells missing DNA) cells can function?
You instead took my little helping suggestion and criticized it. Oh well, guess you guys lose another one.
By the way, Sal, I addressed your latest quotemine while you were away.
I have that book and posted on it before Larry Moran did. See:
No sooner is one misrepresentation pointed out than Sal is on to the next.
Michael Lynch does not “disdain” natural selection, Sal. He just laments an overemphasis on natural selection at the expense of other evolutionary mechanisms:
Kind of spoils your story, doesn’t it?
I already linked to it, you apparently missed it. The math applies quite well to the question of homochirality in proteins (and you’re out of the mainstream actually since you think living things can work without homochirality):
you can extend the math to a functional protein or DNA sequences necessary for a system. If you need help doing this exercise I can try spoon feeding it you.
Btw, in that link you can see the dopey view Keiths holds:
A more than 22 sigma deviation from experimental expectation is “perfectly consistent” in Keiths book. Too funny man.
Note the word “all” in that quote, Sal:
As I said:
And of course, no one will be surprised to hear that you quotemined Lynch. Here’s the quote again, including the part you carefully excised:
What a piece of work you are, Sal. If God is on your side, why does he let you make an idiot of yourself over and over?
Mung,
Ah, that’s what you meant by ‘keeps going’! 🙂
Yep, it’s way beyond nature to have a gap in the codon set. Design it is, then.