You are right that the function of the peptide sequence is unknown and probably garbage. You are wrong about the analogy and the point of Taq’s post. It was clearly and simply this: the unlikelihood of a particular protein, or a particular DNA sequence, or (to borrow from Richard Dawkins) a particular arrangement of atoms that looks like Mont Blanc, is completely irrelevant to whether the protein or anything else was designed, or evolved, or whatever. Every particular thing in the universe is fantastically unlikely. This means nothing.
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Not sure to understand your point here, but I’m sure you don’t understand mine.
My point is that @T_aquaticus is wrong when he uses his webtool example to show that the ID argument is flawed.
Look. He used a random sequence generator, came across a rare sequence and then claim that « according to ID arguments, there is no way that a random sequence generator could have produced that rare of a sequence ». But this is a profound misunderstanding of ID argument. IDers understand perfectly well that playing @T_aquaticus game, you will come across a rare sequence. In fact, the probability to get a rare sequence is 1. Now, what IDers are saying is that if playing @T_aquaticus game you come across let’s say the first 100 aa of the human myoglobin gene, then you would be warranted to doubt that the random generator is a random generator. IOW, you would be warranted to draw a design inference. Why? Because that new sequence would match a specification and you would be able to calculate the probability of getting it. And since this probability is so small (1x20^100), you can eliminate the chance hypothesis.
As an aside, I would say that intuitive arguments are not always to be dismissed.
Indeed, what would you say in front of Mount Rushmore ? Would you refrain from inferring design because it is intuitive?
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I hope this isn’t going to far outside the scope of this particular discussion, but I think part of the challenge we have is different frame of references. From a naturalist / atheist / scientific (I’m not sure the right word to use) perspective, the outcome of evolution we see around us, is one random possibility out of essentially an infinite number of outcomes. From this perspective when someone identifies what we have as being only possible because of design, it is an example of the sharpshooter fallacy.
However a Christian does not see the world around us as the result of pure randomness. He/she see’s the specific outcome of evolution that we see around us, as the bull’s eye that God wanted to hit, the specific outcome he wanted. From this perspective we don’t have a sharp shooter fallacy, we have a perfectly designed shot that was on target.
So I think a part of the failure of the analogies is differences in the frame of reference being used by different people. And once again, I think we arrive at point that the only way to reconcile these two frame of references is to accept the limitations of science. To me this means accepting that from the frame of reference of science, evolution is completely random, while also accepting that as a Christian, looking at it from a Christian’s perspective, nothing is random, everything is designed, we just can’t be sure exactly where / how God has interacted with his creation to arrive at the target he planned.
In practice however, as a Christian non-scientist, it is difficult to have a purely scientific discussion, that assumes randomness, when I know that this isn’t the complete picture, and there is design involved.
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Science does have limitations. However, they do not limit its abilities to answer this particular question. The evolutionary model is correct. The particular Christian model defended by ID is not.
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Now I’m definitely headed off in a bit of a different direction, mods can feel free to split the thread.
First off, I completely disagree with ID (as opposed to id) so I won’t disagree with that part of your statement.
However in the interest of trying to improve discussion between the camps I wanted to comment on your statement “The evolutionary model is correct.”
As a Christian non-scientist (and especially as one raised in YEC only environment), this statement provokes an emotional reaction in me, that I suspect I share with many other Christian non-scientists. My initial reaction is one of complete disagreement, similar (I would guess) to your reaction to my statement “There is a God”, or “Jesus rose from the dead”. I immediately want to argue with you 
But I accept that the evolutionary model is correct within the perspective of science. So why do I have that reaction? It’s because it’s not clear that your statement is within the context of science, or a much wider context where you are stating God did not design the world we see today (id as opposed to ID).
If we want good discussion, I would suggest we need to make sure we are clear about the context of such statements (and this applies to id statements being clear that their inference of design is outside of the context of science).
I’ve replied to you, but this is really more of a general comment, to anyone interested in reaching across the barriers of the various camps for peaceful discussion.
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Thank you very much Stephen. I don’t mind being wrong about the analogy and T’s post or anything else for that matter. As I said, I’m trying to learn something. In this case, what it means (the example of characters generated by the webtool) and why it is significant.
Let’s recap what has transpired:
Gilbert said: The random self-assembly of this thing is so statistically improbable that it could not have occurred on its own. (summary, in my words)
T_Aquaticus said: Look, I just created this 100 aa protein using a random character generator. The odds against creating such are astronomical, there’s no way a random sequence generator could make such a thing, and yet it did. (summary)
I said: Wait, this seems like a bad example to me, because the protein created does not seem to be anything at all. It seems like it is garbage. Please explain why this is a good example, if I’m incorrect.
Stephen said:
So, what I’m understanding you to say is this: The unlikelihood of X is irrelevant to whether X was designed or evolved. X is fantastically unlikely. The fact that it is unlikely means nothing. Is that what you are saying?
If so, I understand and thank you for the explanation. That said, my original question was regarding the efficacy of the example that had been put forth. My gut reaction was that the randomly generated characters represented “nothing” rather than “something” and it seems that you have confirmed this. So, in my mind, to provide an example of a random generated text that is insignificant (because it results in a nothing) is not a good example to use. That’s all.
But there is a reason why I’m being persistent. Not because I want to be right, but because this is what I think that scientists need to understand about the general public. Due to the complexity of the subject matter, we laypersons are always trying to reduce the complex concepts to comprehensible ones. So, when someone puts forth an example like the random character generator, we will tend to see that as an analogy for evolution or an evolutionary process.
If this is ever not the case, it would behoove those in the scientific community to say so. Because, as you already know, we have a penchant for glomming onto analogies like “motors” and “propellers” and the like, to our own detriment. So being careful to clarify that an example is a negative control, not an analogy, for instance, will help to advance the conversation in a way that fosters greater communication.
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I have a couple of thoughts on that.
First, we have no way of knowing if a protein is functional by looking at just the sequence. The tools we do have are somewhat crude and will give us a lot of false negatives. Empirically determining activity would be extremely difficult since there are millions if not billions of potential substrates that a protein can interact with. As shown with antibodies, it is also rather easy for proteins to bind to one another, so I would expect that it wouldn’t be too difficult to find a different protein that my random protein can bind to.
Second, ID supporters claim that most, if not all, of the human genome is functional. Most of that sequence is equally jumbled and lacks the type of function you are probably thinking of. There are also cases of orphan genes that have just a handful of mutations that were added to previously random sequence. Therefore, ID supporters should probably conclude that almost every sequence is specified.
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The chances of coming up with my random protein is equally improbable. That’s the point. If you don’t believe me, then try it.
https://www.bioinformatics.org/sms2/random_protein.html
In the first box, enter 100 for the number of residues, then hit submit. I guarantee that over many, many trials you will not get my random protein. Does this mean my protein is specified?
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Many intuitive arguments run afoul of logical fallacies, and this ID argument is one of them. In this case, it is the Sharpshooter fallacy:
What ID supporters tend to ignore is all of the possible proteins that could have evolved, but didn’t. How many possible proteins are there that could transport oxygen in a circulatory system? Frankly, we don’t know. Just looking around the animal kingdom we find many different proteins that serve this function, such as hemocyanin in molluscs that uses copper instead of iron to transport oxygen. Just among hemoglobins there is a wide number of sequences that are equally functional. So how do you calculate the odds of a protein evolving the ability to transport oxygen? Well, you can’t because we don’t know how many different proteins can fill that role.
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As @swamidass states, no apology needed. I assume that any disagreement or misunderstanding we have is an honest one.
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Yes, that’s my point.
It’s a perfect example to use whenever someone offers an unlikelihood-based argument against evolution, and this happens every minute or so. It is, in fact, so common in ID circles that we have no choice but to address it as an “ID argument.” At the risk of appearing to speak for @T_aquaticus, I note that this is what the post said: “According to ID arguments, there is no way that a random sequence generator could have produced that rare of a sequence…” and he was responding to an argument of exactly that type.
Because this kind of ID argument is so common, we find ourselves in conversations like this one, in which the way scientists actually think is obscured (deliberately, often) by red herrings that are designed to affect non-specialists. This matters because the rest of your post is about how scientists need to be more careful when using analogies, but you seem to ignore the entire context of the conversation, which is an incessant drip-drip-drip of confusing nonsense about evolution, design, probability, and scientific thought.
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In my opinion, the takeway from this (and similar) threads is that naive likelihood calculations that are not based on some sort of reasonable biological model tell us essentially nothing about whether something could evolve or not.
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That’s a straw man and a creationist trope.
Evolution has components that are random, but natural selection is anything but random. The reason why ID is bad Christian theology is that it puts God into an ever-shrinking box, diminishing Him.
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Science says that every hypothesis should be rigorously tested. By doing that, we have dismissed many intuitions.
Again, no one in the ID movement is willing to take the step of testing an ID hypothesis. They have no faith and fall back on intuition.
I agree.
They are telling you that the proposed mechanisms of change are very limited relative to the problem of biological transitions and that in itself is valuable information.
This is not true.
@Michael_Callen, in the presence of comments like this, it is difficult to have intelligent conversation about probability and design. Do you see the challenge?
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“Random” is the wrong word then. As a non scientist my understanding is that random changes at the level of the DNA (or building blocks of DNA), result in evolutionary change through mechanism like selection. Feel free to insert your own word / sentence or statement that better describes the evolutionary model.
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Part of the problem may be that biologists tend to take shortcuts in their explanations because of their knowledge base. We may not take the time to fill in the lines between concepts when talking to the general public. So, to that end, perhaps we could take a step back and explain the basic problem.
The ID argument is plagued by false equivalencies. This is where you say that two things are the same when they actually are different. This is the case with “specified”.
Let’s start with how evolution works. Random mutations are constantly ticking away in the background, and selection/drift affects the rate at which those mutations are passed on to further generations. Mutations that produce a beneficial effect will be selected for. Evolution is NOT looking for a specific sequence. Evolution is looking for a beneficial phenotype. Evolution could care less what the sequence (i.e. genotype) is. This means that if we rewound history and let evolutionary history play out once again from the very first life we would expect to have very different genomes 3.5 billion years later than what we see now.
This is where the ID argument plays its trick. It tries to draw a false equivalency between “function” and “this specific sequence”, and they used “specified” to link them together. Someone has mentioned hemoglobin before, and this is a good example. Evolution doesn’t have to evolve hemoglobin. Evolution could evolve many other proteins that function in oxygen transport, or possibly evolve entirely different anatomical structures that don’t even require a circulatory system.
This is where my initial post came from. I can come up with a random sequence, but the chances of coming up with that random sequence again is extremely unlikely. There would be numerous random sequences that could have function, and once that function is found it would be conserved in later generations. That function would then be refined within that protein’s sequence and added to as other proteins evolved to work with it. So what if a different protein with a different sequence evolved at that early point? The same thing would happen. What evolved is just one protein out of many that could have evolved.
The ID argument fails because it states that evolution must produce hemoglobin. Well, it doesn’t. All it has to produce is beneficial mutations. Evolution doesn’t have to produce specific proteins, just functional proteins.
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I’m not ignoring anything… there are dozens of threads here dedicated to discussing the efficacy of the ID arguments. I set this thread up for the purpose of trying to understand the meaning and significance of the random character example as it pertained to the probability argument. Further, I explained that we (laypersons) tend to glom onto concepts that we can comprehend, and, often times, utilize them beyond their intent. So, isn’t understanding the degree to which an example can be used important?
I see this happen and bristle when it does. This is the very reason why I pursued this conversation.
Thanks, this makes a great deal of sense!!
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