Why are We Disagreeing with ID?

[Rumraket (Mikkel R.)]

@Tim

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.

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.

[Roy (30-year veteran)]

@scd

@Paul_King

So what if a useful function is at 333333332 ? Since evolution has no target it doesn’t care which function it finds.

the problem is that we know that function A is very different from function B in both sequence and structure.

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

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

[scd]

@Paul_King

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

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?

@Faizal_Ali

What would we expect to see if an organism had the beginnings of what would eventually be a “new organ”?

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

@Tim

That person is you. So where is your substantiation? Where are your probability calculations for each and all these functions?

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.

@Roy

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

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

[Paul_King]

@scd

@Paul_King

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

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?

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.

[RonSewell (RonS)]

@scd

one in how many births we can get a new anatomical trait in a direction of a new organ?

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.

[Faizal_Ali]

@scd

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

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”?

[Dan_Eastwood]

@scd

@Dan_Eastwood

This is true. Further, we know of no other source for gears and motors.

i dont think so. if gears exist in nature, and we know that human didnt made nature- we can conclude that other designer was involve.

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.

[Roy (30-year veteran)]

@scd

@Paul_King

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

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?

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.

@Paul_King

So what if a useful function is at 333333332 ? Since evolution has no target it doesn’t care which function it finds.

the problem is that we know that function A is very different from function B in both sequence and structure.

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

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

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

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

[Tim]

@scd

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.

That is not how it works scd. You plucked “one in about 1000 births” from thin air without evidence, so per the aphorism I quoted to you before, I can simply dismiss that claim without evidence. The need for this evidence is a large part in why I asked you for “your probability calculations”, so that your calculation would, of necessity, include this evidence.

I would also note that you ignored my point about the wide range of probabilities, by continuing to treat all functions as being of equal probability.

The first step is for you to decide which evolutionary convergent function you wish to calculate the probability for.

The second step is to decide what evolutionary starting point you wish to choose. Do you want to give echo-location to a mouse, for example? The starting point will make a very large difference, as for example the aerodynamic properties of feathers gave birds a considerable leg up over mammals in developing flight – with the result that bats need to keep flapping their wings all the time in order not to drop out of the sky.

Then you have to start looking at evolutionary pathways – not just the one that is most likely to have been the one that happened, but also ones that would have yielded a functionally similar result.

Then you have to calculate the probability of each of these pathways, and sum them up. As probability of the steps will depend on whether each of these steps are beneficial, neutral, or adverse will depend on the environment, the environment will also have to be specified – and may change over time.

Do this for a large number of convergences – both ones that have occurred, and might have occurred, and you will start to develop an understanding on what is or is not likely to happen.

Only then would a general claim along the similar lines to this earlier claim of yours start to become credible:

@scd

so how you explain convergent evolution? if we know that function X is rare as one in 10^30 sequences then what is the chance to get that function twice?

Until you do this, your claim will have been made without evidence – so it is likewise dismissed without evidence.

[scd]

@Paul_King

Obviously then your answer is “no”. So in that case “we know” is not really applicable - it’s just an assumption

its not an assumption. we know that a motion system needs few parts.

@RonSewell

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,

great. so if its so rare to get a new anatomical trait, then a rate of one in 1000 births to get a new anatomical trait is very generous. right?

@RonSewell

First, do we need a new organ?

a new anatomical trait which suppose to be a part of an organ. we do need to start from something after all.

@Faizal_Ali

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”?

if it has no function then the organ should not evolve, because the small steps are neutral in that case.

@Roy

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.

in this case the motor has no advantage without that rod. so why it should evolve in the first place? remember that we are talking about a living creature. so that scenario will not work, unless the motor was already in the organism with no function at all.

@Tim

That is not how it works scd. You plucked “one in about 1000 births” from thin air without evidence

no. i base my claim on something we do see (or actually not see) in nature. if we check out for instance about 1000 random fish and see no beginning of a new anatomical trait, then we can conclude that the chance to get a new anatomical trait is less than 1000 births. very simple and base on empirical evidence.

@Dan_Eastwood

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.

if we will see a motor on an empty planet. we cant conclude design base on that motor since we have no material evidence for that designer?

[Dan_Eastwood]

@scd

@Dan_Eastwood

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.

if we will see a motor on an empty planet. we cant conclude design base on that motor since we have no material evidence for that designer?

The difference is the artifact is (presumably) constructed by the unknown designer. In biology we know the construction occurs biologically within the biological system. We know that biology can build motors (if we want to call them that).

Also, finding a material artifact makes us suspect a material designer, not an immaterial one. We ask questions and seek answers about this designer - something that ID insists it cannot do.

[Paul_King]

@scd

its not an assumption. we know that a motion system needs few parts.

Please try to keep track of the discussion. I asked for a real example where a large change of structure was required with no intermediate stages. It doesn’t matter how many parts a “motion system” needs. You need to know what it’s immediate precursor was. The large change is simply assumed.

[scd]

@Dan_Eastwood

The difference is the artifact is (presumably) constructed by the unknown designer.

and this is what we need to know. i doesnt matter who the designer is. just that he exist.

@Dan_Eastwood

. We know that biology can build motors

only if we already have the complex genes\systems to do that.

@Paul_King

Please try to keep track of the discussion. I asked for a real example where a large change of structure was required with no intermediate stages.

so if I understand you correctly, you suggest that a motion system might evolved from a simpler system that wasnt a motion system? an easy way to test that is by removing some parts of the motion system and see if we get a different function. but we know its impossible since by removing some parts out of a motion system give us non working system and not a different system. so this cant be done.

[Tim]

@scd

no. i base my claim on something we do see (or actually not see) in nature. if we check out for instance about 1000 random fish and see no beginning of a new anatomical trait, then we can conclude that the chance to get a new anatomical trait is less than 1000 births. very simple and base on empirical evidence.

Where did you dissect “1000 random fish”? If you didn’t do it yourself, and you cannot point to a peer-reviewed article showing somebody doing this (with proper sampling methodology), then this is not evidence.

For that matter how do you know that the new function involves “a new anatomical trait”, rather than being a metabolic change, or dozens of other changes that would not show up under dissection?

Also your claim demonstrates one of the more pervasive creationist misunderstandings about evolution – evolution involves populations not individuals – so the fact that one of the fish doesn’t differ from the other members of the same population is not indication that the fish haven’t evolved – determining that would require comparing the current population with a population from the distant past.

This all leaves you without even the semblance of evidence.

[Faizal_Ali]

@scd

if it has no function then the organ should not evolve, because the small steps are neutral in that case.

Why do you think it is impossible that a series of neutral steps could occur? This is a very common misconception among evolution deniers, and for the life of me I cannot see what is so difficult to understand here.

[Paul_King]

@scd

so if I understand you correctly, you suggest that a motion system might evolved from a simpler system that wasnt a motion system? an easy way to test that is by removing some parts of the motion system and see if we get a different function. but we know its impossible since by removing some parts out of a motion system give us non working system and not a different system. so this cant be done.

I’m saying that your assertion that “a motion system” directly evolved from something very different is in need of support, And your “test” is ridiculous. If the system was very similar the necessary change was more likely a change in one or a few parts rather than the addition of a new part. Further, unless the modern “motion system” is unchanged since it first developed it will be further from the immediate precursor so we can’t expect to recover the precursor through simple changes.

[Dan_Eastwood]

@scd

@Dan_Eastwood

The difference is the artifact is (presumably) constructed by the unknown designer.

and this is what we need to know. i doesnt matter who the designer is. just that he exist.

Then all you need is to find a 289 V8 Small Block on Titan and your all set.

@scd

@Dan_Eastwood

We know that biology can build motors

only if we already have the complex genes\systems to do that.

Congratulations on moving the goalpost for detecting design to the very existence of biology. Again, no complaint about your beliefs, only the validity of your argument. You are making a theological claim, not a scientific or logical claim.

[Rumraket (Mikkel R.)]

@scd

an easy way to test that is by removing some parts of the motion system and see if we get a different function.

That’s literally how the system works already now. Part of the flagellum functions as a protein translocase, and some bacteria use them as protein translocases. Others use them as receptors/docking sites for extracellular molecules, sensors of local conditions or what have you. They lack the flagellin proteins that make up the filament yet the system still performs other functions.

The Evolution of the Flagellar Assembly Pathway in Endosymbiotic Bacterial...

Sense and sensibility: flagellum-mediated gene regulation

In addition to motility, flagella have roles in other microbial processes, such as adherence to host cells, host cell invasion, protein secretion, autoagglutination (i.e. clumping or self-adherence of bacterial cells) and biofilm formation [2–6]. For some of these processes a direct involvement of flagella is clear. For example, Campylobacter jejuni flagella are responsible for secretion of several non-flagellar proteins [7–9]. Interestingly, some obligate intracellular symbionts of insects (e.g. Buchnera aphidicola ) have lost many of the genes needed for assembly of the flagellum and appear to use the remaining flagellar assembly gene products for export of bacterial proteins to the host [10–12].

[lee_merrill]

@Mercer

@lee_merrill

But there being only a few known new interactions…

There aren’t. You’re making that up.

Well, I haven’t seen more than a few, even by people eager to disprove Behe’s claim.

[lee_merrill]

@Rumraket

@lee_merrill

@Rumraket

I agree that your entirely hypothetical and imaginary piece of complete fiction would be a big problem for evolution to overcome. It would also be a problem to travel across the ocean if boats and planes were impossible. It’s just boats and planes aren’t impossible.

So there are selectable pathways to structures of half-a-dozen parts?

Are you conceding that you merely imagined that there aren’t but have no evidence for that?

No, I was commenting on your “boats and planes” claim.

@Rumraket

@lee_merrill

With dozens of parts?

Do they have to have dozens? Isn’t the idea that even one protein-protein binding spot is beyond Behe’s edge?

No, the edge is at two new binding sites, I mention dozens because dozens of parts are typical of flagella.

@CrisprCAS9

You still haven’t demonstrated a single interaction in this system is ‘new’ rather than a modification of an existing interaction.

That’s a fair point, how about MotA and MotB? But wouldn’t it still be rather miraculous if the two dozen proteins in flagella somehow assembled (with modification) in a bacterium? The flagellum would not seem to be useful until all the components were assembled.