The Difficulty with Detecting Design

before we will continue, can you give an example of nested hierarchy that exist in nature? i will show you that such hierarchy exist in vehicles too.

true. so we can also look at a truck wheel. in general a truck wheel is more similar to other truck wheel than to a car wheel. and a car wheel is more similar in general to other car wheel than to a bicycle wheel. we can check other traits and get the same result in many other traits. eventually we will get the nested hierarchy.

https://tree.opentreeoflife.org/opentree/argus/opentree10.4@ott93302

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Now let’s do engines.

There are engines shared by trucks and cars, but two different cars of the same make and model will have different engines. The phylogeny based on engines will be very different than the phylogeny based on wheels. The same happens when we look at transmissions. It will happen again when we look at radios, or mufflers. You will get very different phylogenies for different features in vehicles. You do not see this with life.

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Don’t you with ‘convergent evolution’?

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I could, but since you’ve already been given links to such examples in this very thread, I’m not going to waste time searching for further examples of something you’ve already had.

Then quit stalling and making excuses, and just get on with it. Because so far your responses exactly match those I’d expect from some-one who can’t back up their claim but doesn’t want to admit it.

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No. Convergence usually applies only to gross morphology; examination of the detailed structures that produce that morphology show differences that match the common phylogeny, such as shark flippers containing cartilage while dolphin flippers contain bones similar to those of other mammals. Even in convergence at the genetic level the proteins may be the same but the underlying nucleotide sequences won’t be.

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actually we do and that is the problem. here are 2 papers about this problem:

https://onlinelibrary.wiley.com/doi/full/10.1111/zsc.12213

so we can solve these contradictions by convergent evolution or convergent loss. and there is no real difference between a vehicles tree and a biological one.

How would you possibly know? You haven’t produced a vehicles tree yet, just lots of excuses and diversions.

(Also, the trees in that article are not “very different”; they differ in the order of some branching points. They don’t make the tree completely different, as would be the case if you tried to generate a tree for vehicles based on (i) spark and glow plugs, (ii) doors and windows.)

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They’re an obvious attempt to divert from the fact that you claimed “there is no real difference between a vehicles tree and a biological one” even though you’ve shown no sign of ever having attempted to produce the former.

Either produce nested hierarchies for vehicles that are similar to those available for life, as you have repeatedly claimed is possible, or admit that you can’t. I’m not interested in a perpetual distraction machine.

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As @Roy stated, this is only seen on a superficial level with morphology. At the genetic level there will be slight noise from convergence, and this noise is expected due to the same mutation happening in different lineages on rare occasions, incomplete lineage sorting, and strict requirements for function at specific positions in genes. However, the phylogenetic signal should swamp the noise caused by these known mechanisms, and it does.

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They don’t differ by as much as the different vehicle phylogenies. For example, none of those trees have chimps in the fish clade. There are only small differences between the trees for life while there are massive differences in the tree of vehicles.

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Once again you have no goddamn clue what you’re talking about. Yes, the phylogenies don’t always come out completely identical, just like you dont’ always measure the exact same temperature in a room with two different but highly sensitive thermometers.

That is basically the situation with phylogenetic trees. Even where they are not identical, they are still so incredibly similar that it is a fact in need of an explanation. The gene sequences being constrained by a real shared genealogical history is the best explanation for that fact.

Some clades are difficult to resolve when the bifurcations they represent took place very long ago, but very close to each other in time. It’s like trying to find out which is the oldest of two fossils from two different organisms born less than one week apart, 10 million years ago. Some times the data simply isn’t good enough yield that level of resolution.

None of these facts actually cast any doubt on the reality the overwhelmingly tree-like history of life.

With respect to your latter point it hasn’t met it’s burden of proof. You simply declare that we’d get the same result with vehicles as we do with life, by which you must be implying there is as much tree-like structure in vehicle character data, and that we should expect the same low degrees of phylogenetic pitfalls such as HGT, convergence, polytomies, and so on. That’s just not obvious at all, and in fact highly doubtful if you have even the slightest insight.

Theobald explained all this and more all the way back in 1999 in his 29+ Evidences for Macroevolution: The Scientific Case for Common Descent article. That was 20 years ago.

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They don’t contradict what he said at all. You are focusing on the frequency of disagreement (how often do we find trees that disagree?) but failing to consider the magnitude of disagreement(how much do they disagree?).

Go back to the thermometer analogy. Suppose I give you ten thousand thermometers which are sensitive to the 15th decimal place and I ask you to go measure the temperature in a room. How many of those will produce the exact same temperature? Probably very few. The slightest pertubations can give 12-13 decimal disagreements. Does that mean the thermometers don’t really agree? No.
Is the fact that there are trillionth of one-degree differences in their measurements mean the thermometers can’t be trusted? No.
Should we abandon the idea that the room has a relatively uniform temperature that we can measure? No.

It’s the same situation with incongruent branches in phylogenetic trees. They reduce our certainty in our knowledge of what exactly the genealogical history of life is like, they don’t amount to reducing our certainty that there IS a genealogical history of life. You understand the difference?

Another analogy: We might be uncertain about which of two twins were born first (that might even be impossible to determine), but we’re pretty sure they’re twins. You are effectively saying that because we can’t determine to a high degree of certainty which of them were born first, that we must abandon the idea that they’re even twins, or related. It’s fatuous in the extreme.

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here is something similar by looking at cytochrome b phylogeny ( Michael S. Y. Lee, “Molecular phylogenies become functional,” Trends in Ecology and Evolution , Vol. 14:177-178):

i dont think so. if we can find the same engine between a truck and a car they will still belong to the same group basically. but we will not find that engine in say a bicycle or a jet fighter. so we still get a similar tree basically where cars and trucks are still closer to each other than to airplanes or bicycle.

First, cytochrome b is a mitochondrial gene which has limited application in deeper nodes due to increased mutation rates in the mitochondrial genome. Second, I don’t see any mammals in the fish clade separate from other mammals.

The point is that you get very different groups when comparing different features in vehicles. You have a car and truck in the same group and a different car in a distant group for one tree. In another tree, those two cars are in the same group and the truck is in a distant group. The trees are all over the place.

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First, whales aren’t usually grouped with fish. Nor are cats, except when bowls are involved.

Secondly, the paper says:
“The most reasonable conclusion is that this is no coincidence: rather, these functionally related parts of the mitochondrial genome have undergone concerted, adaptive evolution and lost their historical signal.”
Or, put another way, phylogenies built on features that evolve rapidly aren’t reliable because the historical commonality is swamped buy the changes.

Thirdly, this is just another distraction from your claim that hierarchies for vehicles are similar to those for life, a claim that can never be supported by looking only at hierarchies for life.

Bollocks. Piaggio used the same basic engine for both scooters and garbage trucks.

Either produce nested hierarchies for vehicles that are similar to those available for life, as you have repeatedly claimed is possible, or admit that you can’t.

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Seems to me there’s one, mabe two non-canonical branches in that tree. How many possible topologies are there for a rooted phylogeny of 9 species? Over 2 million. One to two incongruencies between two trees out of 2 million is equivalent to a magnitude of error of 0.5-1 part per million.

You are basically complaining that the thermometers disagree by at most one millionth of a degree centigrade, and that we should now throw away the thermometers as being incapable of estimating the temperature in the room.

And in any case, the placement of species in that tree could very well be an artifact of poor taxon sampling. One feline and one whale in a tree with 7 primates is rather weak. It would be interesting to see how a bigger and more diverse set of cytochrome b sequences affects the picture.

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This is especially true for mitochondrial genes due to the higher per generation mutation rate in the mitochondrial genome. Cytochrome b is actually a good gene for building phylogenies between closely related species.

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and this is exactly what happen when we check the cytochrome b phylogeny- the whale is group with primates. a very different group. now, we can say that its happen only in the minitory of cases. but its also true for vehicles. most cars traits in general are more similar to other cars than to a truck. so in most cases they will group with the car group. again- like animals phylogeny.