# Uncommon or Common Descent?

(Ashwin S) #110

Of course chromosomes don’t know anything. Its just that change beyond a limit causes things like death, or the inability to reproduce…
Besides the process of reproduction in animals is designed to transmit existing genes… not create novelty…

George, didn’t I tell you in my earlier conversation at Biologos that I am not an young earth creationist?
Did you forget?

(Guy Coe) #111

At approximately 50-40 kya there was a noticeable “bump” in the levels of human conceptual sophistication, as evidenced by a proliferation of artifacts in cultural anthropology. Also, at approximately 15-13 kya, the rise of irrigation agriculture and animal domestication marked the beginnings of a transition from mainly hunter-gathering to more settled forms of human lifestyle, coinciding with the beginnings of the rise of ancient civilizations. I suspect the latter as the first evidence of the “Adam” effect.

(Eric Michael Holloway) #112

He’s taking the negative log of a 0.01 p-value.

Interesting point you make about the values increasing arbitrarily, but the proportion being stable. It is true any result can be made statistically significant with enough data. That could be what is going on here.

On the other hand, as the number of vertices grows, an exponentially smaller proportion of configurations will form pure trees vs dependency graphs (most other configurations). The formula for labeled trees with N vertices is N^{N-2}=2^{\log N (N-2)} whereas the number of labeled graphs is 2^{N(N-1)/2}. So, the log of number of trees grows at rate O(N \log(N)) and for graphs it is O(N^2). Since \lim_{N\rightarrow \infty} \frac{\log N}{N} = 0, tree configurations become a vanishingly small proportion of the possible graphs as vertices increase.

With directed edges the difference between the two models becomes even more pronounced, since for every possible undirected graph with E edges there are 2^E possible directed graphs. Common descent can only use a subset of the directed trees, since the arrows will only point down the trees. Thus, the theory can only use 1 of 2^E possible graphs. However, with the dependency graph model, as with human innovation in general, the restriction is not as stringent on which way the arrows can point. Hypothetically, cycles could even exist, such as with inventions that are mutually inspired.

In this way, the pure tree hypothesis is very brittle. Common descent is likewise more brittle than a dependency graph. So, Dr. Ewert’s result could be a function of common descent’s brittle nature. Counter intuitively, this suggests that as long as a fair amount of ignorance remains about the true source of biological diversity, maximum entropy over the two theories makes the dependency graph the preferred model. One would have to achieve almost absolute certainty with genealogical data to prefer a tree of some sort.

The question in my mind, then, is what is the edit distance growth rate between a tree and a dependency graph as the vertex count grows? I think this question could be answered with some combinatoric math. It could be as the tree grows in complexity there is more opportunity for edits to make a significant difference, and the number of available edits grows, so tree + some variants becomes more salvageable as the vertex count grows. However, thinking about the combinatorics involved makes this seem less likely.

Thus, my interpretation of Dr. Ewert’s result is absent almost certain knowledge of the true model, the dependency graph model is always epistemically preferable to the tree model, and probably also preferable to any kind of common descent model (since the arrows only go down the tree).

(Jon Garvey) #113

Rightly or wrongly, I’ve taken Ewert’s paper to comment on the incompleteness of common descent explanations via nested hierarchies, rather than its denial. It’s certainly useful to view it that way. @Ashwin_s is right to say how many have taught (eg on BioLogos) that the prevalence of neat nested hieracrchies is strong evidence for common descent, and I’ve pointed out in reply that they were considered strong evidence of the principle of plenitude (Linnaeus) before evolution was ever proposed.

In other words, even perfect nested clades do not necessarily show common descent, and I suspect the “Creationist” application would be that if they are sufficiently disrupted by other mechanisms not easily explained, the application to CD is far less secure.

But whatever additional explanations are found for apparently non-inherited features, if they are suffciently common, they point to other possible causes being severely underestimated, just as the theory of divergent human races separating from common stock is undermined by genetic evidence of extensive interbreeding. Drawing an anthropological tree like the Eugenicists is simply a false understanding of even a single human race.

Joshua’s example of the human race might, I think, possibly be misleading. What human nested hierarchies we find are the result of tribalism and geography and, as he implies, are disrupted by interbreeding (hence genealogical Adam). Humanity is a freely breeding single population, for all its genetic variation.

Now, the same is certainly true of closely related species: they’ve had a glut of reclassifying bird species since genomics, and our own species is known to have hybridized with Neanderthals etc, so that it’s hard to define the species, but easy to spot incomplete lineage sorting, etc. Likewise, many bird of paradise species are hybrids (thus demolishing the long-favoured sexual selection theory of their evolution, since females regularly breed outside the genus, let alone outside the most perfect displayers).

But these ideas seem far less tenable at higher taxonomic levels, where diagnostic features even of orders or classes crop up in the wrong groups: the recent big example was the diagnostic pelvic anatomy of the two major dinosaur groups suddenly being overturned after a century - the explanation being that it must have evolved twice, tens of millions of years apart. The diagnostic homology is no longer a homology at all.

On The Hump, whenever my attention happens to be drwan to a taxon, I like to look at its phylogeny. It virtually always turns out that the origin is disputed. There are two or more entirely different proposals for turtle origins. Three for the pterosaurs. And the reason for dispute is that they share diagnostic features (or in some cases genetic markers) with groups that supposedly separated millions of years before - no incomplete lineage sorting there, surely, no chance of hybridization, and horizontal gene transfer, currently, is though to be minimal in these higher animals.

Convergent evolution is left, but is, after all, only an epicycle to explain away the particular anomalies left when you finally plump for one phylogeny over its rival theories. Even its major proponent, Simon Conway Morris, proposes some kind of emergent laws governing, it which are no less mysterious and undemonstrated than anything Winston Ewert might have in mind.

One of my favourite examples is the bat, or bats. The first theory was that they derive from primates, based on the anatomy and brain structure of diurnal bats. But the oldest bat fossils are just as specialized as the modern nocturnal echo-locating bats, which seem derived from insectivores. Needless to say, the trail disappears at the beginning of both groups, and the phylogeny is “disputed.” That is, where it matters the nested hierarchy doesn’t exist until you create it.

Apparently genetic studies affirm the monophyletic nature of both groups of bats, and the conclusion is that they must have diverged very early for one group to have echolocation, insectivorous habits and nocturnal lifestyle, and the other group to be much bigger “winged primates”, with good vision, eating fruit and flying by day. Yet the first fossil of these larger, and so more likely to be fossilized, bats is 15 million years later than the oldest bat (which looks to be able to echolocate).

Personally, I doubt if anyone would consider these two groups to be related apart from the uncomfortable fact that they both have the same wing-plan.Nobody, it seems, is willing to bet on neutral change or natural selection producing such a specalisation twice, when birds and two branches of pterosaurs had quite different solutions for flying.

But on current theory, there must be a nested hierachy, and it seems one has to choose more or less arbitrarily what major anomalies to ignore. The decision to make bats monophyletic seems to be based on the human decision that a clade can include apparent insectivore descendants and apparent primate descendants, so long as the wing plan and some gene families are similar. Bat wings can’t evolve twice - though echolocation can, but nobody derives bats from dolphins, of course. That would be absurd.

(Eric Michael Holloway) #114

This is exactly what Dr. Ewert says. Those taking his conclusions further to deny common descent (such as myself) are extrapolating beyond the author’s own modest conclusions.

(S. Joshua Swamidass) #115

What if capabilities did not change, just knowledge?

(S. Joshua Swamidass) #116

I would agree he may be showing the incompleteness of trees (but not common descent). More later.

(Ashwin S) #117

So you equate the “tree of life” with a body of knowledge… for example some kind of tech transfer?

I wonder if that is enough. I would assume that things like language/farming etc would develop rapidly once the basic abilities are present. Are you proposing that modern humans wouldn’t be able to come up with things like languages and farming on their own in hundreds of thousands of years unless somebody taught it to them?

(S. Joshua Swamidass) #118

Language And farming if one sort or another existed for a long time before. CiviliZation is new.

(Ashwin S) #119

You will have to commit to some kind of change brought about by introducing Adam into the human genealogy… is there anything specific you could venture forth?
Or is it case of no detectable change… and hence an unverifiable matter of faith?

(Mark M Moore) #120

I have been lurking here on an excellent thread, but your comments take things in a direction I want to chip in on…

I say that’s the case particularly with farming. And so did the ancient Sumerians who claim “the gods” taught them about farming and civilization. I think those “gods” were near descendants of Adam, who was not only taught farming by God, but provided with more domesticated versions of a number of animals and plants. That is a lot of what Gen. 2 is talking about.

I do think agriculture needed a jump start. There may have been a few efforts to get there before, but why tend crops for months when locusts or the neighboring clan would just take it from you just as it was ready for harvest? It takes more than tools or mental ability to sustain agriculture. It takes a certain environment protected from both natural calamity and the evil that men do (even if they don’t see it as such because God had not given man any “thou shalt nots”).

There is a ton of evidence that true farming and the domesticated versions of many plants and animals came about in just the time frame and place I am suggesting for Adam. That is to say NE Anatolia and NE Iran around 13K ago. When I was researching it I thought “somebody ought to do a book on this” but the theology aspects that I was working on already took 350 pages and I thought “this is someone else’s book to write”.

(Ashwin S) #121

Hi @Revealed_Cosmology
Thanks for the information. Can you point me to any sources on this. I would love to read more on this.

(Mark M Moore) #122

With Goats I found a pattern repeated with dogs and pigs. There was more than one point of origin for the domestication of goats but almost all extant domestic goats come from the group close in time and place to my proposed location for Adam. So it was not, in these cases, that domestication wasn’t being tried elsewhere (though this could have been in imitation of what Adam was doing) but the domestic varieties available in Anatolia/NW Iran were superior to those obtained elsewhere and eventually almost totally replaced them.

@Ashwin_s all I did was a google search on “earliest domestication of ________” and put in the blank a common crop or herd animal. The answer is usually the same.

#123

Well… I care. At least that provides some interesting challenges with detection. This isn’t to say that many bacteria can’t be grouped into trees of solid relationships. It’s just that the ultimate grounding of any tree is currently up for grabs, as is the question of whether there is a single root.

Humans and mammals are easy cases, in comparison.

(Bill Cole) #124

[quote]So you have some company there with respect to skepticim of evolution… Though their solution is kinda crazy.
I really don’t see why some versions of special creation cannot be published if stuff like panspermia can [/quote]

I think the real answer is we don’t know. The big problem with the evolutionary hypothesis is trying to figure out the origin of new functional information. Large amounts have appeared suddenly as you point out and there is no explanation for the source of this.

Panspermia pushes the problem back but does not solve it as the only known cause of FI (functional information) is conscious intelligence. So this kills the simple to complex model as even the simplest life has lots of FI.

(George) #125

@Ashwin_s

You seem oblivious to the idea that a long string of little mutations is the more successful version of evolution… and there is no indication that chromosomes know when they are exceeding YOUR acceptable threshold for net change.

(George) #126

@EricMH

Are you a Young Earth denier of shared descent? Or an Old Earth denier of shared descent?

(George) #127

Yes, @Ashwin_s, I did forget… most likely because you never provided a clear discussion for your personal stance.

If you are Old Earth then where do you even begin to explain where a global flood fits in … if you even accept the idea of a global flood.

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(Ashwin S) #128

Haven’t decided on any particular model as of yet.

(George) #129

@Ashwin_s… I would expect this answer any time a person has a problem fitting real world evidence into any kind of creationist paradigm.

The idea that you can just deny god-led processes of speciation … when you have no idea how else to explain the data is pretty much the norm.