Why are We Disagreeing with ID?

This says that your evidence does not have broad significance. What is missing is a general purpose model which is missing from all these papers. @RonSewell posted several interesting papers on anti freeze proteins in arctic fish. The problem with these papers is evolution is assumed and the most probable pathway is chosen.

What is missing is a feasible process… Where plants can change gene form by mixing exons through recombination I have not seen this in vertebrates. Mixing exons is a reasonable explanation for some de novo genes. A random walk through many improbable mutations is not a likely conclusion…

In the case of anti freeze genes there is extreme selective pressure but on the other hand the paper 1. suggest a long improbable road to arrive at the point of that selective pressure. While this could possibly happen I think ID is the better explanation for the origin of the arctic anti freeze gene given the current available evidence.

1.https://www.pnas.org/doi/10.1073/pnas.1817138116

That doesn’t even make sense as a response. You can’t justifiably make any conclusion on probabilities on the information given.

Small steps are very different from completely random jumps to anywhere in sequence space. The distribution of function matters - a lot. So what if a useful function is at 333333332 ? Since evolution has no target it doesn’t care which function it finds.

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A better analogy. Let’s say that 777777777 has a specific function X, and 333333333 has function Y. And let’s say you can mutate to be something like 777777377. It retains function X despite the mutation (functional robustness, which is observed in proteins), but it now it does a bit of function Y (functional promiscuity, which is also a property seen in proteins). By continuous mutations it becomes more specialized until it becomes 333333333.

That way, proteins are able to traverse the fitness landscape of the sequence space, while in a non-directed manner, it nevertheless allows for the discovery of new fitness peaks. Here below is a real life example. Take your time to comprehend the illustration.

Duplication events and changes in specificity and activity during the evolution of Saccharomyces cerevisiae MALS enzymes.The hydrolytic activity of seven modern MAL and IMA enzymes and of key ancestral enzymes (prefix anc) is given. The width of the colored bands corresponds to the k cat/K m-value of the enzyme for a specific substrate. For details see Voordeckers et al. (2012).

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we can deal with that too. if indeed all biological systems where near each other in sequence space, all of them should be very similar to each other. but we know that this isnt the case. olfactory system for instance is very different from heme synthesis, which is very different from a motion system etc. thus many biological systems are indeed isolated in sequence space, and we cant move from one system to another by small steps.

so you basically agree that motors and gears are the result of design or not?

If proteins can traverse the sequence space over time, that means they don’t have to remain “near each other”. Also, that doesn’t mean that every single proteins evolved from one another. That is not what I am saying ether.

Sure, unless you want to define “motor” so broadly, such that you would call some protein complexes “motors”… which is likely what you were getting at with this… then I would say that SOME motors are designed. We can conclude that THOSE motors are designed, because we have the background knowledge. This isn’t the case for the other “motors” and we can’t conclude they are designed because they “look” designed.

Although, I wouldn’t call any biological system “motors” since such analogies poorly describe biological processes. Organisms are not machines.

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10 posts were split to a new topic: Analogies to Motors

so what do you think is the rate of a new biological function? one in a million mutations? something similar to that? one in how many births we can get a new anatomical trait in a direction of a new organ? do you agree for instance that a rate of one in 1000 births to get a new anatomical trait is generous?

the problem is that we know that function A is very different from function B in both sequence and structure. thus we do need to change 333333333 to 777777777.

they need to be near each other in order to evolve from each other in small steps. but its clearly not the case with complex biological system. you cant change a non-motion system into a motion system by small steps. and you cant get a motion system from a random sequence either. so in any case a motion system is isolated in sequence space. and its true for many other biological systems.

do you agree with me that a watch which is made of organic components is still a watch?

The definition of “motor” is pretty broad. The dictionary definition and the engineering understanding of a motor as any transducer which converts a form of energy to mechanical motion agree well enough. While it is analogous to compare the flagella to specifically induction motors or internal combustion motors, I think that it is within usage to term some biological processes literally as motors. This is no concession to ID.

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Assuming that you mean “structures that have function A are all very different from those that have function B’ I have to ask if this reflects any real situation. And by that I mean a case where the evolution from function A to function B happened despite the large difference - and happened directly, without intermediate stages that served some other function.

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I’m pretty sure we have discussed this before, but I don’t recall you answering the question. If you did, please remind me: What would we expect to see if an organism had the beginnings of what would eventually be a “new organ”?

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I think treating all “new biological function” as homogeneous and having the same probability is absurdly silly and simplistic.

I think the probabilities will vary radically depending on things like:

  1. the complexity of the function;

  2. the degree to which the new function can co-opt existing functions (flight is a lot more easy if you’ve already got feathers, for example); and

  3. the number of different evolutionary pathways leading to the new function.

(This is just a few factors that I could think up off the top of my head – I’m sure that there are dozens of others if we look in sufficient detail.)

But that is not my problem – as I’m not the person making claims about how unlikely these functions are. It is the problem of the person who is making those claims to provide substantiation for them. That person is you. So where is your substantiation? Where are your probability calculations for each and all these functions?

Without such substantiation, we get back to:

That which can be asserted without evidence, can be dismissed without evidence.

… and your entire argument can therefore be dismissed out of hand.

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No, they don’t. They can evolve to be far away after numerous small steps.

Just an assertion with no evidence to back the statement up.

A tautologically stupid question.

This.

Consider the space of all possible nucleotide sequences. Simply picking some long genome sequence at random and then working out (if we imagine we can do this) what sort of organism some randomly picked nucleotide sequence is going to result in.
I think we can agree that randomly and blindly picking a genome sequence that corresponds to a highly anatomically streamlined fish is unfathomably remote. In the space of all possible nucleotide sequences that vast majority must either be nonfunctional, as in not result in a viable form of life at all, or at the very least result in something very, very different from a highly streamlined fish.

Yet it should also be very clear that in so far as we have an organism that can live and swim in water, it is essentially guaranteed that under natural selection this species can and will evolve ever more streamlined body morphology. So the real question isn’t whether it is likely to pick a streamlined fish from among all possible genomes, that’s just not how anything evolves. The real question is what is the probability that a mutation occurs that affect body morphology in a way that reduces aquadynamic drag, in a member of the species? Given that these obviously occur in large quantities every generation (the drag coefficient of fish is a variable and heritable trait in any population), one can move gradually towards extremely rare genotypes.

This is the power of cumulative selection, and why an attractor in a space can vastly affect the probability of obtaining something that is a priori very unlikely.

It is an entirely reasonable and interesting question to ponder what that attractor might be in protein sequence space. It doesn’t actually have to be(and probably isn’t, in many cases) a persistent selection for a specific function. If certain functions are extremely rare in protein sequence space then you obviously can’t select for those functions right out of the gate, but you can select for something else that might lead to such rare functions as an unavoidable byproduct. Some of the rarest functions in protein sequence space might in fact have begun long after the protein’s first origin, as spandrels that resulted as a byproduct of some other selection pressure, such as the long-term consequence of selection against the inherent aggregation propensity of polypeptide sequences.

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You might think that, but we know it’s not true.

Two proteins can have different functions and different sequences but very similar structure.

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well, take the motion system as example. can you as a designer made a motion system that is base on a single part? i mean, can you add a single part to an object (that cant move) and it will start to move from A to B on its ownf?

i guess that any new and different bump that serve a new function might be a good start.

ok. so i will say that the average rate to get a new anatomical trait is one in about 1000 births, and probably more then that. why? because we have seen billions of living creatures (human population alone is about 8 billion). and as far as im aware only in rare case (if any) we see a new function. let alone a begining of a new organ. so i think that a rate of one in 1000 births is very generous and even contradict empirical reality.

i refer to the cases that its true. which is a lots of cases.

Obviously then your answer is “no”. So in that case “we know” is not really applicable - it’s just an assumption in a purely fictional example with no apparent relevance to anything that actually happened.

First, do we need a new organ? To what purpose? Why should we expect a new organ in any event?

Billions of years of evolution, and humans have wound up with 78 organs give or take. That is compatible with the development of organs being exceedingly rare, so we would not necessarily expect to witness that.

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Why not a “new and different bump” that has no new function whatsoever? Can you provide some reason that this could not be a step in the evolution of what will eventually become a “new organ”?

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We don’t know that humans or some human-like creature didn’t make nature. While unlikely, that would be impossible to prove. We accept human design where we have material evidence that human design is feasible. We have material evidence supporting design-by-evolution, but no material evidence for any other. (That’s OK, we should not expect material evidence of immaterial designers).

More, concluding some unspecified"other designer" causes problems. Literally any other possibility can be concluded, including silly things like Flying Spaghetti Monsters. I do not mean to mock, but this puts the idea of God as the designer on equal footing with FSM. None of the more theologically-minded people I have discussed this with find this idea acceptable. Reason include mockery of God, “putting the Bible on a pedestal of science,” and more.

Still more, if you hadn’t noticed - science has left the building. The possibility of a supernatural explanation, based on a lack of material evidence, if simply a no-go for science. If you are not content with the theology you have, I really don’t think try to “science it up” if going to help you. IOW, it’s OK to have faith, but it is not reasonable, or helpful, to pretend that science backs up one’s faith.

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Trivially. One example would be adding a connecting rod between two gears, one linked to an engine and the other to a set of wheels. The object would not move previously because the engine wasn’t connected to the wheels, but now it will.

Had you thought about your question at all before asking it, you might have come up with this example yourself.

No you weren’t. You were referring to an analogy involving strings of numbers, not to any actual cases.