Uncommon or Common Descent?


(S. Joshua Swamidass) #46

A post was merged into an existing topic: Missing the Point on Ewert


(S. Joshua Swamidass) #47

No it does not. Remember…


(Bill Cole) #52

Joe
There is a chance to advance ID here. Just pounding the weaknesses of common descent is not enough. You are right there is no tested mechanism. This is not the issue at hand that Ewert is challenging it is much bigger…can ID explain the pattern in the data better the CD.


(Bill Cole) #53

I agree but again this is not the issue being worked on. Lets ask another question. Can Winston’s model give us a better line of demarkation between design and descent? We don’t know where that line is right now but wouldn’t it be interesting to find out?


(S. Joshua Swamidass) #54

Thanks for being a voice of sanity @colewd. @JoeG is limited to just 10 more posts today, but he’ll be back tomorrow.


(Bill Cole) #55

I think that the software design pattern fitting the tree shows a hierarchal pattern. What more do you think he has to show here?


(S. Joshua Swamidass) #56

You are right that in principle a software design pattern could fit a hierarchical pattern. That is not the question right now.

In this paper, the question is whether or not he is demonstrating that this explains the presence or absence in genes.(which is merely one type of nested clade). He has not demonstrated this yet, but he might if he handles objections well and is lucky.

The larger question is whether this can explain the full cohort of patterns in genetic data that falls in nested clades. He is very far from that.

The largest question is whether he can explain the even larger cohort of patterns in genetic data that neutral theory explains. He is even farther from this.

Only at that point is there a true alternative to common descent in sight.


(Bill Cole) #57

Common ground :slight_smile:

Again, I need an education here.


(Eric Michael Holloway) #58

I think this is correct. Here’s an example.

The data is a string of 16 1s: 1111111111111111

The first model is 1100000000000000, which only fits 1/8 of the data.

The second model is 1111111100000000, which fits 1/2 of the data.

Our final model is 111111111111100, which fits 7/8 of the data.

The -log Bayes factor for #1/#2 is 2, and #2 explains 2^2=4 times more of the data than #1.
The -log Bayes factor for #2/#3 is ~ 0.8, and #3 explains 2^0.8=7/4 times more of the data than #2.

So, this means that if Dr. Ewert’s analysis shows the -log Bayes factor for tree/dependency is 10,000, then that means the dependency graph explains the data 2^10,000 times better than the tree graph. That means P(Data|Tree)/P(Data|Dep.) = 2^-10,000. 1.7% difference in explanation, on the other hand, means that P(Data|Tree)/P(Data|Dep.) = 0.98. Big difference.

Unless I’m misunderstanding all this, it looks like Dr. Swamidass is incorrect saying that Dr. Ewert’s results show the dependency graph only explains 1.7% more than the tree.

We can also think about this in terms of edit distance. In order to turn the best fitting tree into the best fitting dependency graph, then 2^10000 edits the size of the tree must be made to make the transition. More than a factor of 2 already seems implausible, let alone 2^10000. So, I would say this makes common descent a non workable solution, regardless of a few homoplaises here and there.


(S. Joshua Swamidass) #59

Common misunderstanding. I’ll have to explain later.


(Bill Cole) #60

Your example matches what he claims in his paper.


(Intelligent Design Deist) #61

Without a mechanism Common Descent cannot explain any pattern or it can explain every pattern. Not really much use there. Common design explains patterns of similarities. We would follow the pattern laid down by Linnaean taxonomy to see what organisms should have more similarities than others.

Common Design was the original model. All evos did was steal it, change “archetype” to “common ancestor” and called it their own:

Blockquote
“One would expect a priori that such a complete change of the philosophical bias of classification would result in a radical change of classification, but this was by no means the case. There was hardly and change in method before and after Darwin, except that “archetype” was replaced by the common ancestor.”-- Ernst Mayr

and

Blockquote“From their classifications alone, it is practically impossible to tell whether zoologists of the middle decades of the nineteenth century were evolutionists or not. The common ancestor was at first, and in most cases, just as hypothetical as the archetype, and the methods of inference were much the same for both, so that classification continued to develop with no immediate evidence of the revolution in principles….the hierarchy looked the same as before even if it meant something totally different.” - G Simpson


(Curtis Henderson) #62

Does Common Design offer a mechanism that is missing from Common Descent?


(Intelligent Design Deist) #63

Design is a mechanism. And as the name implies, common design, means there will be at least some commonality- look at cars and PCs for examples. I don’t need to know how either was built to uncover all of the similarities based on a common design.

That said, Common Descent by means of intelligent design is something to consider, as at least some IDists have. But what is being changed? Is it the genetics? Or is it something else? That is what I don’t know yet. What could possibly be changed in a chimp-like organism to allow it to evolve into a human? (worded wrong but hopefully people get the point)


(Jon Garvey) #64

Sympathetic as I am to the question, it may be less than fair to some versions of common design. Evolution was proposed as a mechanistic alternative to non-mechanistic special creation, which is not a mechanism but a supernatural act of God. In other words, the whole aim was to bring biological form into the mechanical realm and out of the supernatural for the first time. So in that case the question is like an atheist asking for a mechanism of the resuurection - the question presupposes certain assumptions, ie that “common design” would be a process of efficient material cause and effect.

But even outside purely supernatural special creation, it would seem that similar issues apply. Take Louis Agassiz’s belief that there was a kind of divine evolution of platonic forms, rather than common descent. I’ve not read Agassiz, so am not sure how he fleshed out the idea (one for the reading list, maybe), but it was a scientific theory, shared in some ways by Owen, another anti-evolutionist. I doubt, though, that it was susceptible to a “mechanism of design”, because that was occurring in a non-material realm.

That said, there could be somewhat to be discovered about the content of common design - which I take to be the potential hope in Winston Ewert’s work.


(Bill Cole) #65

I may be splitting hairs here but I think the mechanism is conscious intelligence. Conscious intelligence is the mechanism used to design.

Conscious intelligence can create large quantities of functional information something that neutral mutations cannot.


(Eric Michael Holloway) #66

Technically, intelligent design cannot have a mechanism. Otherwise, it would be another form of chance and necessity.

However, we can talk about the capability of intelligent design. For example, chance and necessity cannot increase algorithmic mutual information, due to the law of independence conservation. See the following article section 1.2 for the law’s definition and proof.

So, intelligent design possesses the capability to increase algorithmic mutual information, which is measurable to some degree, and exemplified by empirical signatures. Examples of such signatures are irreducible complexity, large scale homoplaises, hierarchical design patterns, modularity, codes, communication channels, etc.

We see many of these signatures in engineering disciplines and biology. However, we never see natural processes originate these signatures. Hence why intelligent design seems a persuasive and helpful theory.


#67

In a rarefied sense, I suppose. However, I can machine a gear. I think ‘turned on a lathe from a block of aluminum’ would be a distinct mechanism of its creation or at least the means by which the design is ‘implemented’. This would be distinct from a method where I forged a gear in a mold or punched one out using a press. Similarly, progressive creation could be brought about via gene editing using CRISPR. The processes behind specific, past manipulations may be discernible. Likewise the specific changes introduced may be discernible or leave a mark not just of a change but the means by which the changes were implemented.


(Intelligent Design Deist) #68

Yes, design as a mechanism is the general sense- as in you can build a house by design or wing it. By design means there was a plan, process and/ or procedure. Intentional agency volition would be what carried out the design


(Intelligent Design Deist) #69

Technically a mechanism is just a way or means of accomplishing a desired result. That refers to a process and surely ID is OK with that. True we may never know the exact design mechanism used- that is why ID isn’t a mechanistic theory.