The Simplest Protein of Life

Just to put a finer point on it, we already know that the random formation of any modern protein out of a prebiotic soup is incredibly unlikely. That's why we don't think they formed that way.If they're interested in some evolutionary conjectures about how the first proteins might have formed then they should just let us know. Suffice to say for now that the first proteins likely bore very little resemblance to any modern protein.--Percy

Maybe you do not understand the Sharpshooter Fallacy. It means you're calculating the probability of the wrong thing. If you fire a gun at a blank target where the goal is to simply hit the target, but you then draw a bulls eye around the bullet hole and calculate the odds of hitting that precise point on the target then you are guilty of the Sharpshooter Fallacy. The proper probability to calculate is the odds for putting a bullet hole anywhere on the target.In the cards analogy the proper probability to calculate is the odds of getting any hand that is better than anyone else's in the game. You're committing the Sharpshooter Fallacy if you instead calculate the odds of getting the specific cards in your hand.When it comes to a protein that successfully carries out a specific biological role, the proper probability to calculate is the odds of producing any protein that successfully fills that role. If you instead calculate the odds of producing the specific sequence of amino acids in that protein then you're committing the Sharpshooter Fallacy.So if Yockey et al's calculation is correct that there are 2.3 x 10⁹³ possible functional cytochrome C protein sequences, the odds of obtaining one of them improve substantially, especially in a process of repeated cycles of selection of mutated candidates.--Percy

You're still misunderstanding the Sharpshooter Fallacy. You can calculate the odds of having the best hand at the table, and that's not a fallacy. And you can calculate the odds of having been dealt the specific cards in your hand, and that's not a fallacy. But if you calculate the odds of having been dealt the specific cards in your hand when what you needed was the odds of having the best hand at the table, then you've just committed the Sharpshooter Fallacy. It means that you calculated the odds of what specifically happened to cause the outcome (winning) instead of calculating the odds of any of the set of things that could have caused the outcome. I don't know why you're having trouble finding it since it's the Yockey citation you provided in your Message 34: So if there are "2.3 x 10⁹³ possible functional cytochrome c protein sequences" then the odds you need to calculate are not for one specific protein sequence (the Sharpshooter Fallacy) but the odds for obtaining any in the set of 2.3 x 10⁹³ sequences.--PercyEdited by Percy, : Fix message link.Edited by Percy, : Fix link to Yockey quote.

Hi Zaius,I take it that your off-topic response means that you don't accept that what you're doing constitutes a fallacy. If it's that you don't understand why it's a fallacy then could you ask some questions so that we can gain some idea of where the problem lies so that we can try to clear this up? Of if you really believe this is an Occam's razor issue then could you explain where the unnecessary complexity lies?But it's important we don't forget your other error of calculating probabilities for sudden de novo creation of proteins. Biologists believe such occurrences are as unlikely as you do. Evolution is a gradual and incremental process.--Percy

Whoops, thanks! I evidently accidentally hit "3" instead of "4", Zaius's was the next message 34. I fixed my link to Zaius's message. I know Taq provided the original citation, but when Zaius quoted it he included it, and since I copied Zaius's quote I unwittingly included a bad link, which I just fixed, and here it is again: Hopefully the correct links will help Zaius explain how his misuse of probability constitutes an example of Occam's razor.--Percy

Hi Alfred,We understand you don't accept evolution, but understanding evolution doesn't require accepting it. In fact, it makes much more sense to reject a position you understand than one you don't.What we're trying to explain in this thread is that evolution doesn't believe that the first proteins just popped spontaneously and randomly into existence. We all agree that that would be incredibly unlikely.As a sort of side issue we're also trying to explain that calculating the odds of a specific protein forming suddenly and randomly is the wrong problem. It's a side issue because evolution doesn't believe that's how the first proteins formed. In this case we're just trying to correct the misunderstanding about probability. Had proteins actually formed suddenly and randomly then you'd want to calculate the odds of obtaining any protein that could be successful, not just the specific protein that was actually created.--Percy

I can use your equation to explain the mistake in thinking that you're making. Let's say you're playing roulette and you bet on red. The ball lands on 34 red, you win. What were the odds of you winning.If you calculate the odds of landing on 34 red, which is 1/38, then you are guilty of the Sharpshooter fallacy. The odds you should be calculating are 18/38, because the ball had 18 chances out of 38 of landing on a red slot.Applied to the spontaneous random formation of a protein (which isn't how evolution believes the first proteins came about, we're just explaining this error in using probability as a side issue), this means that instead of calculating the odds of a specific sequence of amino acids coming together, you must instead calculate the odds of any sequence of amino acids coming together that can perform that function. Here again is the link to webpage where the quote was found: And here's the quote again, which is about 20% down the document: So you're saying that you're not sure you can accept this claim because you can't examine the three citations, one of which is to a book by Yockey titled Information Theory and Molecular Biology. I don't have the book either, but here are links to the abstracts of the papers, and these are the papers that Yockey must have drawn upon for his book, since he's an author on neither paper:

• Amino acid replacements in yeast iso-1-cytochrome c. Comparison with the phylogenetic series and the tertiary structure of related cytochromes c.
  Hampsey DM, Das G, Sherman F.
• Yeast iso-1-cytochrome c: genetic analysis of structural requirements.
  Hampsey DM, Das G, Sherman F.

The abstracts describe research investigating how much variation iso-1-cytochrome can tolerate while still performing its function. The probability of forming one these variations is what must be calculated, not the probability of forming the specific version of the protein that actually happened. If you calculate the probability of forming that specific version of the protein then you're committing the Sharpshooter Fallacy. Independent of whether the 2.3 x 10⁹³ figure attributed to Yockey is correct, what it represents is the number of possibilities, not the number of things that have actually happened. This is basic probability, not sure why you're having a problem with this. I hope you're not falling under Alfred's sway, who seems to reject both math and science.--PercyEdited by Percy, : Grammar.

While there are some conjectures and hypotheses, we don't really know.But one thing we're fairly sure of is that the molecules of life, including proteins, did not form by way of all the necessary atoms and molecules just happening to come together all at once in the right order by chance.--Percy

I'll ignore the rather poetic but scientifically questionable characterization of lifeforms as death avoiding machines and just make a couple comments about the rest. You're reasoning for why the first protein didn't come about by random chance makes perfect sense and is the same as everyone else's: it's too incredibly unlikely.But you're rejection of formation through gradual change by a process of successive cycles of modification and selection has no corresponding rationale, plus one of the biggest dangers in Mother Nature is other life, which was absent before life began. A beaker of proteins dumped into a pond today would be quickly consumed and disappear, but not in the ancient past before there was any life.--Percy

Hi Alfred,You're again drifting off topic. We're not trying to answer the question, "Can we convince Alfred Maddenstein that life developed through a gradual process of successive cycles of modification and selection?" We're trying to answer the question, "How does evolution believe the first proteins came about?" You don't have to believe that the gradual process is the way it really happened, but please do believe that that's what evolution says.About the rest, I'm not sure why you believe water degrades organic molecules. Life requires water, and if water were antagonistic to life then there would be no life on this wet planet whose surface is 3/4 aqueous.If you think the opinions of Kelvin and Helmholtz are relevant (to the actual topic) then you'll have to describe those opinions. And yet just breathing incorporates oxygen into living matter.--Percy

Hi Alfred,If you think something Shapiro has to say is relevant to the thread's actual topic then go ahead and tell us about it.The rest of your post pretty clearly has nothing to do with the topic.--Percy

I again suggest that we only reply to Al when he happens to touch rationally upon the topic.--Percy

Revising my previous suggestion, I now suggest that we only reply to Al or ICANT (or anyone, for that matter) when they happen to touch rationally upon the topic. Something about the simplest protein, I think.--Percy

NoNukes already explained why this isn't the correct question, but let me answer anyway. There's very little 4 billion year-old evidence to be found, but we're very certain that however it happened it followed the same physical laws of the universe that we're familiar with today. It certainly didn't happen anything like the opening post suggests, with all the amino acids coming together in the correct order by chance because that would be incredibly unlikely. The opening post asks about the ribonuclease protein, which is relevant to one of the abiogenesis hypotheses where the first life used RNA instead of DNA. As has been pointed out in this thread many times, the ribonuclease protein of the earliest life may have borne little resemblance to modern versions.--Percy

Hi ICANT,It is believed that the complex molecules of life and the information they contain developed over time through a process of repeated cycles of modification and selection, because this is the kind of process we observe in life today.--Percy