# Making a Tree from Designed Objects?

**URL:** <https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592>\
**Category:** Side Conversation\
**Tags:** Science, Design\
**Created:** [December 11, 2018, 3:03pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592 "2018-12-11T15:03:57Z")\
**Posts on this page:** 20\
**Page:** 3

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [December 13, 2018, 8:03pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/42 "2018-12-13T20:03:38Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/89):
>
> That would seem to depend entirely on what tree we’re considering. Mammals or only great apes?

I don’t understand your point. A gene contradicts the tree if the gene tree is different from the species tree. It doesn’t have to be very different, just different. A gene that supports the tree ((gorilla, chimp), human) contradicts the species tree (gorilla, (chimp, human)). Even if it supports every other node in the accepted tree of life.

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**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [December 13, 2018, 8:06pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/43 "2018-12-13T20:06:11Z")

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I understand that. But in the context of scd’s bad analogy, my point is that there aren’t any genes scd can name that would put gorillas in with, say, amphibians.

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [December 13, 2018, 8:22pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/44 "2018-12-13T20:22:32Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/87):
>
> Really? Name 20 of them then.

About 30% of the human genome is more closely related to gorillas than to chimps. Of course, this is an expected outcome of evolution due to incomplete lineage sorting. In fact, we can predict that ILS will have less of an effect as we move down the tree, and this is what we see. If memory serves, about 5% of the human genome is more closely related to orangutans than to chimps, down from 30% for the gorilla genome.

What we don’t see is extreme departures from the expected tree. For example, we don’t see exact copies of jellyfish genes in the human genome, and absence of these genes in other primates. However, this is exactly what we see in GFP mice that have been designed by humans.

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**Author:** ![T.j\_Runyon](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t.j_runyon/32/9662_2.png) [@T.j\_Runyon](https://discourse.peacefulscience.org/u/T.j_Runyon)\
**Post date:** [December 13, 2018, 8:28pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/45 "2018-12-13T20:28:22Z")

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Even if design is compatible with a tree and phylogenetic signal it doesnt mean that phylogenetic signal isn’t evidence for common ancestry. Common ancestry predicts such signal. Design does not! God could create everything completely different if he wanted to. A phylogenetic signal is more probable on common ancestry than design and therefore is evidence favoring CA over Design. Compatible with != not evidence against. It’s as simple as that.

Edit: before the nitpickers get onto me for terminology, by design I mean no common ancestry

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [December 13, 2018, 8:47pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/46 "2018-12-13T20:47:53Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/92):
>
> About 30% of the human genome is more closely related to gorillas than to chimps.

Is that true? I thought the 30% in question was split between ((gorilla, chimp), human) and ((gorilla, human),chimp).

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [December 13, 2018, 9:00pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/47 "2018-12-13T21:00:25Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/94):
>
> Is that true? I thought the 30% in question was split between ((gorilla, chimp), human) and ((gorilla, human),chimp).

I think you are right.

> [@](#):
>
> In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression.  
> [Insights into hominid evolution from the gorilla genome sequence | Nature](https://www.nature.com/articles/nature10842)

The numbers for the orangutan genome are lower than I remembered:

> [@](#):
>
> Our analyses find that for ∼0.8% of our genome, humans are more closely related to orangutans than to chimpanzees.  
> [Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection - PMC](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044849/)

The second paper is interesting in that it makes predictions of how much of the genome should be affected by ILS.

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**Author:** ![scd](https://avatars.discourse-cdn.com/v4/letter/s/6f9a4e/32.png) [@scd](https://discourse.peacefulscience.org/u/scd)\
**Post date:** [December 15, 2018, 9:05pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/48 "2018-12-15T21:05:18Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/85):
>
> Now, the expectations of your hypothesis, separate creation, would be that gorillas are equally unrelated to cats, frogs, lobsters, and humans, and we would have no reason to expect any genes to show relationship to any of them.

not realy. if they were made by the same designer we actually should expect some similarity. as we see in human designed objects like vehicles. so this not true.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/85):
>
> You may be able to find one or two cases of further exceptions, but one data point doesn’t outweigh all the rest of the data.

if so how we can falsify evolution? for instance: many says that if we will find a mammal with feathers evolution will be false. do you agree with them or disagree?

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**Author:** ![scd](https://avatars.discourse-cdn.com/v4/letter/s/6f9a4e/32.png) [@scd](https://discourse.peacefulscience.org/u/scd)\
**Post date:** [December 15, 2018, 9:11pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/49 "2018-12-15T21:11:09Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/86):
>
> Convergent evolution involves analogous adaptations, not homologous adaptations. There is a huge difference.

there are actually cases of convergent evolution at the molecular level. so this isnt always true.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/86):
>
> A single designer can mix and match parts from other designs which would violate a tree-like pattern.

but again: we find it in nature too.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/86):
>
> I can point to a car and a truck that have the same engine while two cars of the same make and model have different engines

of curse. but we both agree that this is an exception and not the rule. right?

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**Author:** ![scd](https://avatars.discourse-cdn.com/v4/letter/s/6f9a4e/32.png) [@scd](https://discourse.peacefulscience.org/u/scd)\
**Post date:** [December 15, 2018, 9:12pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/50 "2018-12-15T21:12:49Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/91):
>
> I understand that. But in the context of scd’s bad analogy, my point is that there aren’t any genes scd can name that would put gorillas in with, say, amphibians.

so if we will find such a case evolution will be wrong?

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [December 15, 2018, 9:20pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/51 "2018-12-15T21:20:14Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/96):
>
> if they were made by the same designer we actually should expect some similarity.

But we shouldn’t expect any lesser similarity with lobsters than with humans for that reason, should we? After all, gorillas and lobsters were all made by the same designer. Also, “relationship” is not a synonym of “similarity”; phylogenetics isn’t just a count of similarity.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/96):
>
> if so how we can falsify evolution?

“Falsify” is a naive, Popperian term that doesn’t describe how science actually works. You need to think in a statistical framework, whether frequentist or Bayesian. As I said, one data point doesn’t overrule all the rest.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/96):
>
> many says that if we will find a mammal with feathers evolution will be false. do you agree with them or disagree?

Well, of course we’re not going to find any such thing. But I disagree with them. That’s one data point again, and it doesn’t overrule the mass of other data.

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**Author:** ![scd](https://avatars.discourse-cdn.com/v4/letter/s/6f9a4e/32.png) [@scd](https://discourse.peacefulscience.org/u/scd)\
**Post date:** [December 15, 2018, 9:36pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/52 "2018-12-15T21:36:50Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/99):
>
> But we shouldn’t expect any lesser similarity with lobsters than with humans for that reason, should we?

actually we should. why? because gorila and human morphology have more in common then with say a lobster. so we should find (in most cases) that their genome will be more similar too.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/99):
>
> Also, “relationship” is not a synonym of “similarity”; phylogenetics isn’t just a count of similarity.

but you actually conclude that these species related because of their similarity. right?

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/99):
>
> As I said, one data point doesn’t overrule all the rest.

so if we will see a fish evolving into a dog in front of our eyes you will say that too and evolution will be just fine even in such a case?

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**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [December 15, 2018, 10:04pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/53 "2018-12-15T22:04:19Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/96):
>
> not realy. if they were made by the same designer we actually should expect some similarity.

But not twin nested hierarchies. That’s the relationship, not fuzzy “some similarity.”

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/97):
>
> > T\_aq: I can point to a car and a truck that have the same engine while two cars of the same make and model have different engines
> 
> of curse. but we both agree that this is an exception and not the rule. right?

No, it’s a rule, while with living things, it would be the exception.

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [December 15, 2018, 10:57pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/54 "2018-12-15T22:57:51Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/100):
>
> because gorila and human morphology have more in common then with say a lobster. so we should find (in most cases) that their genome will be more similar too.

That doesn’t follow. Only those parts of the genome that influence the particular morphological similarities should be similar by that reasoning. Yet all of the genome is more similar, including the bits that function identically in gorilla and lobster, and even the bits that have no functions at all.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/100):
>
> but you actually conclude that these species related because of their similarity. right?

That’s a common misconception. No, it’s not similarity. It’s nested hierarchy, i.e. the fit of the data to a particular tree. The two most similar species are not necessarily the two closest relatives.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/100):
>
> so if we will see a fish evolving into a dog in front of our eyes you will say that too and evolution will be just fine even in such a case?

Sounds like a hallucination to me. What are you on?

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**Author:** ![scd](https://avatars.discourse-cdn.com/v4/letter/s/6f9a4e/32.png) [@scd](https://discourse.peacefulscience.org/u/scd)\
**Post date:** [December 16, 2018, 2:07pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/56 "2018-12-16T14:07:38Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/102):
>
> Only those parts of the genome that influence the particular morphological similarities should be similar by that reasoning. Yet all of the genome is more similar, including the bits that function identically in gorilla and lobster,

why not? since their morphology is similar i see no problem to conclude that their genes can be similar too. for instance: do you agree that its logical to conclude that the genes for human hands will be more similar to the gorila one instead of a mouse one?

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/102):
>
> That’s a common misconception. No, it’s not similarity. It’s nested hierarchy

as i said above: do you have a specific example?

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/102):
>
> Sounds like a hallucination to me.

you said that a scientific theory like evolution cant be falsify by a single counter evidence. right? so by this criteria even if we will see a fish becoming a dog evolution will be just fine.

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**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [December 16, 2018, 5:07pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/57 "2018-12-16T17:07:12Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/103):
>
> so the majority of these cars are more similar to a truck then to other cars from the same company?

We’re talking about both parts and vehicles.

Why aren’t you including the parts? Because you know that your analogy is false?

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**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [December 16, 2018, 5:24pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/59 "2018-12-16T17:24:54Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/106):
>
> do you realy think that they are more similar to the same parts in a truck rather then to another car?

Your photo omits the engine and smaller parts that could be, and often are, identical.

In the case of Audi, it shares a parent company with Scania AB trucks, so I’m very confident that there are many identical parts. That’s not analogous to biology at all.

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [December 16, 2018, 9:49pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/60 "2018-12-16T21:49:30Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/104):
>
> why not?

For the reasons I pointed out and you ignored.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/104):
>
> as i said above: do you have a specific example?

Of what? If you’re talking about similarity not equalling relationship, there’s a simple example in Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K., Chojnowski J.L., Hackett S.J., Han K.-L., Kimball R.T., Marks B.D., Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences 2008; 105:13462-13467.  
It you examine you will note that ostriches are more similar to rheas, emus, etc. than tinamous, and yet tinamous are more closely related to rheas, emus, etc. than ostriches.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/104):
>
> you said that a scientific theory like evolution cant be falsify by a single counter evidence. right? so by this criteria even if we will see a fish becoming a dog evolution will be just fine.

Sure, because that would be magic, and clearly unlike now dogs usually happen. One bizarre magic situation doesn’t change all our prior knowledge of puppies, parents, and such. And hey, wouldn’t that transformation be even worse for creationism?

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**Author:** ![scd](https://avatars.discourse-cdn.com/v4/letter/s/6f9a4e/32.png) [@scd](https://discourse.peacefulscience.org/u/scd)\
**Post date:** [December 17, 2018, 12:36pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/61 "2018-12-17T12:36:35Z")

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again: i refer to the majority and not to the minority. and the majority of parts among cars are more similar to each other then to a truck. otherwise they were called truck in a car shape.

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**Author:** ![scd](https://avatars.discourse-cdn.com/v4/letter/s/6f9a4e/32.png) [@scd](https://discourse.peacefulscience.org/u/scd)\
**Post date:** [December 17, 2018, 12:41pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/62 "2018-12-17T12:41:47Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/108):
>
> Of what? If you’re talking about similarity not equalling relationship

i actually refer to the nested hierarchy that you said we only find it in living thing but not in designed objects.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/108):
>
> Sure, because that would be magic, and clearly unlike now dogs usually happen. One bizarre magic situation doesn’t change all our prior knowledge of puppies, parents, and such. And hey, wouldn’t that transformation be even worse for creationism?

so if you will see a fish becoming a cat in a single generation it will not be a problem for evolution? is o nothing will be a problem for evolution.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/108):
>
> And hey, wouldn’t that transformation be even worse for creationism?

true. so we can falsify creationism but not evolution?

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<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [December 17, 2018, 2:25pm UTC](https://discourse.peacefulscience.org/t/making-a-tree-from-designed-objects/3592/63 "2018-12-17T14:25:59Z")

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> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/110):
>
> i actually refer to the nested hierarchy that you said we only find it in living thing but not in designed objects.
> 
> ![](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/40/1121_1.png) John\_Harshman:

No problem. My reference works for that too.

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/110):
>
> so if you will see a fish becoming a cat in a single generation it will not be a problem for evolution? is o nothing will be a problem for evolution.

Why would that be a problem?

> [@Tunicates Have Human Like Immune System?](https://discourse.peacefulscience.org/t/tunicates-have-human-like-immune-system/3408/110):
>
> so we can falsify creationism but not evolution?

You’re hung up on falsification, which is not a valid view of science. Creationism doesn’t fit the data; evolution does. One bizarre magic trick doesn’t effect either of them.

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