I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.
Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.
If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.
One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.
Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.
That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).
Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.
The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”
So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.
So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.
Are you talking about asexual species? That’s the only way I can interpret individuals being reproductively isolated. Or are you trying to say something else?
Yes, drift results in divergence between isolated populations. What does that have to do with genetic diversity within species?
Enough for what? Due to coalescence, the divergence between individuals is likely to be much less than the age of the species. Or it could be more than the age of the species but less than the age of the divergence from the closest other living species. I think you’re also confused about the difference between those two things.
I don’t know what genomes you’ve been browsing, the the average intraspecific difference between humans is around 0.1%. Again, coalescence. That has nothing to do with the age of Homo sapiens, just like mtEve and Y-Adam have nothing to do with the age of Homo sapiens. You have to understand that coalescence necessarily happens within lineages, at a rate unrelated to speciation events.
Now that’s something different: divergence among species rather than diversity within species. It’s not due to coalescence but to something more or less analogous: extinction. For whatever reason, only a small clade of cycads has survived to the present day, while most lineages have gone extinct. But that’s you cherrypicking again. There are plenty of taxa with MRCAs at every conceivable age, including 300 million years.
stcordova,
Incidentally, cycads aren’t ferns, they aren’t a species but a class, and living cycads are an order. Learn some biology.
Which contradicts your earlier statement,
You just explained your own error.
Name one, and I mean an MRCA for the species, not some split between species. There is a difference.
As mentioned phylogeny doesn’t explain orphan systems. One of them is flowering plants.
http://www.bbc.com/earth/story/20141017-how-flowers-conquered-the-world
One can neglect the BBC’s Dariwnist spin that they evolved gradually after all.
There are physiological barriers to evolving angiosperms from plants that weren’t angiosperms. This is yet another example of common descent needing miracles indistinguishable from special creation.
Angiosperms supposedly split off from gymnosperms:
Yet another poof.
One can see the taxonomic nested hierarchies in terms of the gymnosperms versus the angiosperms. The hierarchical division can easily be seen by recognition of the orphan systems, namely the non-encased condition of seeds vs. encased. No need of phylogeny to create the nested hierarchical relationships. One only needs to recognized the common taxaonomical designs among groups. Yet again another example of the fact a nested hierarchical relationship can be seen without any assumption of phylogeny!!!
But this poof in plants was preceded by 6 other poofs, namely the evolution of multicellularity in eukaryotes.
https://en.wikipedia.org/wiki/Multicellular_organism#Evolutionary_history
Darwin’s abominable mysteries are only abominations to those who hate the idea of creator.
Uh, you are aware that DNA consists of two antiparallel strands right? The lagging strand can be replicated by the same enzymes that processed the leading strand.
Apart from that, I don’t see the relevance of this to the OP, since all domains are able to produce Okazaki fragments.
Explain everything! Right now!
stcordova,
Those statements are not contradictory. The variants lost in two isolated populations are not likely to be the same, hence they diverge. And of course mutation is adding novel variants for drift to operate on in the same uncorrelated manner, driving divergence still further.
The evidence for common ancestry implies common ancestry, that alone does not explain all the differing organismal features.
To understand how whatever entity in question evolved it is not enough to know that two species share common ancestry. Nobody is under any illusions about this.
The fact that I and a cow have mammary glands, while a shark does not, does not explain how mammary glands evolved.
The evidence from common descent can in some cases help shed light on that, like monotremes (for example) can with the evolution of mammary glands.
The fact that some species have properties other species do not, is not evidence AGAINST common descent. They’re just not explained merely by the fact that those species descended from a common ancestor.
For example, we can have good evidence that you an I share a distant ancestor. Even though you are asian and I am caucasian, we can have genetic evidence that implies we both branch from the same ancestral node. Maybe a very distant great great great great (etc.) grandmother.
Yet the fact of the matter that we share this ancestry does not explain why you are asian, and why I am caucasian. But just because the evidentially implied fact of our shared descend does not explain why we are different in the ways we are, in itself does not contradict the fact of our shared descent. Do you really not understand this? Suppose you had a half-brother with blonde hair and blue eyes. Then you’d share descent through one of your shared parents. Yet both of you would have features not found in the other. Black hair and brown eyes contra blonde hair and blue yes. Is that mere fact evidence against your common descent from a shared parent? Of course not!
The explanation for the various “orfan” systems you allude to is found in the evolutionary process. That is where you find the in principle explanations. The mechanisms that have the requisite explanatory power to account for much of the physiology of life.
As in genetics, population dynamics and natural selection, over geological timescales. THAT is where orfan systems are explained. When those mechanisms are combined with evidence from comparative anatomy, comparative genetics and so on, (in so far as we have data on that) we get the history of how various things evolved. If we don’t have the data, if there are gaps in the data, then we are merely left with in principle explanations, which while they are at least capable of accounting for the entity, we can’t be sure which account is the correct one, as the mechanisms we know operate on life can be combined in many different ways to account for the data.
So if you want to really contradict common descent, what you need isn’t just things common descent doesn’t explain (like you being asian and me being caucasian), but that it cannot be compatible with. For that, you need statistically significant incongruent phylogenetic trees build from data you would EXPECT to be statistically significantly congruent if common descent was true. Only then can you have evidence against common descent.
You really, really don’t understand this, and no creationist ever has even come close to addressing it.
What are those barriers? Remember, an argument from ignorance is not a barrier. That you, Salvador Cordova, can’t immediately think of how it could have evolved, is not evidence that there is a barrier. So please inform us what the barrier is.
The idea that hating the idea of a creator has any relevance to this discussion is a total fantasy, as there are theistic evolutionists who love the idea of a creator (and in fact believe in and worship the same dying and resurrecting one you do), yet are completely convinced that evolution and common descent is true.
Forgot Kenneth Miller already?
Rumraket, to Sal:
Hence my assessment in the other thread, in a comment to J-Mac:
And of course Sal has already revealed his true motivation, which has nothing to do with the search for truth:
Sal:
My incredulous response:
Ruminating a bit on your comment, I think I figured out what you are trying to say:
DNA polymerases can only elongate DNA strands from an preexisting 3′ OH-group so now you think that the need for priming is somehow an unsurmountable hurdle to evolution of organisms with a double-stranded DNA genome.
Am I warm?
It’s all well and fine to sit back and try to poke holes and claim evolutoin can’t explain X. Where is Sal’s experimentally testable alternative hypothesis for the origin of replication? Oh I forgot, Goddidit, and it can’t be tested.
Once more, what are you trying to say? Why won’t you explain? No, there is no contradiction. Drift lowers diversity within populations and increases divergence between populations. Why is this hard to understand?
And yet you wander back and forth between them without seeming to notice. Of course there’s a difference, and there I was talking about the split between species, which should have been obvious. As I have explained several times without you acknowledging at all, MRCAs for genes within species are subject to coalescence, which makes them often younger than the species, and certainly younger than their divergence from some other species 300 million years ago. Now, there are coalescences that are older, first because there’s a fairly large variance, but more importantly because selection for genetic diversity — frequency-dependent seletion —can maintain diversity for a long time. I’ve already mentioned HLA alleles shared between humans and chimps. There are other systems in which coalescence can be delayed for a long time, for example the difference between male and female mitochondria in mussels, because the leakage of mitochondria between male and female lineages is a rare event.
Anyway, to summarize: your amazing discovery does not point toward young life, only to coalescence within populations.
Separate populations of the same species doesn’t necessarily make them different species. Learn some biology.
No. How did the Okazi fragment system specifically come about. Rolling Circle Replication could have kept replicating double stranded systems without the Okazaki like system. So how did the Okazaki system come about.
stcordova,
They’ll still diverge, and that’s due at least in part to drift. When there’s an ocean between, it makes little practical difference whether they could breed if they met or not. Ocean, physical compatibility, zygotic compatibility, meiotic compatibility. A progression from ‘macro’ to ‘micro’ barriers to gene flow. LSB.
Sorry, you’re asking me to learn some biology? Yes, isolated populations are not necessarily different species, though if they remain isolated long enough they inevitably will be. Drift alone will eventually result in speciation, even in the absence of selection. But what does this have to do with anything you’re talking about? How is this the zinger that confounds the evolutionists?
It seems that Erik and Sal are both, knowingly or otherwise, pursuing the line that reproductive incompatibility cannot evolve. Indeed, that nothing can, since if microevolution happens then so must divergence, absent some constraint or correlation between the separate populations in both mutation and fixation.
What’s the evidence that it can evolve? And I mean evidence, not something like “If it can’t, then how did all the species get here?”
Erik,
OK, you won’t appreciate this angle, but reproductive compatibility is ultimately dependent upon genes. If microevolution can occur in two separated populations – that is, their genes can undergo independent mutation and fixation – how can reproductive incompatibility not evolve? What reason would we have for excluding reproductive processes from microevolution?
Let’s pretend nobody knows. Now what? – Therefore God?
https://en.wikipedia.org/wiki/Argument_from_ignorance
I don’t understand why you are fazed by this particular issue. Okazaki fragments start of as small stretches of RNA synthesized by specialised RNA polymerases (“primases” ). Why couldn’t these have evolved from some ancestral enzyme with RNA polymerase activity? That doesn’t seem much of a problem.
You were talking about creatures unable to replicate the lagging strand. That specific problem stems from DNA polymerase as it cannot initiate DNA synthesis de novo. It does not need specifically Okazaki fragments to get going, just some sort of priming system.
The evidence for common descent is evidence that reproductive isolation can evolve.
I suggest reading a book in which the literature on speciation is ably summarized: the aptly titled Speciation, by Jerry Coyne and H. Allen Orr. Among other things, the book mentions a number of laboratory experiments in which reproductive isolation was induced by selection on ostensibly unrelated traits.
Common descent too is a miracle. It’s all miraculous.
You can see an analogy to reproductive isolation in the base-pairing capacity of iteratively mutating replicated DNA strands. After enough mutations have accumulated, the ancestral strand can no longer base-pair with the distant descendant. As eventually any base from the ancestor that could pair with the distant descendant have been replaced. At some point a threshold is reached where they simply can’t stably associate.
So is your definition of miraculous, if by miraculous you mean unobserved and supernatural. 🙂
Allan Miller,
You are quite right: I don’t appreciate that angle, because it doesn’t answer the question. By evidence I meant something like an observation or experiment, not “if descendants are a little bit different from ancestors, then they can surely be a lot too, eventually totally different.” The hypothesis looks good, but has it been tested?
John Harshman,
Fruit flies?
Hahaha…Good one John!
Jesus, Mary and the apostles. The least you can do is get the theory right.
Erik,
If I showed it happening, would it convince you it happened in any other case? Show me a monk producing illuminated manuscripts, or I say it was done by aliens. Show me the monk, I still say it was done by aliens.
Allan Miller,
Thanks for being very unambiguous this time. Saves time.
I do wonder if people have a sensible idea what they are asking for. If one population grew to 10 feet tall and another shrunk to an inch, would that be a demonstration of the evolution of reproductive incompatibility?
One can measure rates of introgression. One can see that reproductive compatibility diminishes upon an apparent continuum when comparing within- and between-population fertility. But what one cannot show – to Erik’s satisfaction – is ‘reproductive incompatibility evolving’. Heh heh.
The hypothesis that tectonic plates can move great distances looks good, but has it been tested?
No, but observations of phenomena that would exist if they had most certainly have occurred.
Sort of like evolution, there is only one explanation for the derivative nature of life, which is derivation by normal reproduction with modification under selective pressure.
That whole “were you there” line doesn’t work, and would wipe out much crucial information if it were adopted as a meaningful objection. Not to mention screwing up judicial decisions.
Glen Davidson
And so one has the rather frustrating situation whereby, armed with two genomes 99% identical, and asking whether we can legitimately infer common descent, Erik says: “I just need one more piece of information. Somewhere buried in those genomes are the sites that affect reproductive compatibility. I need to know which way they go before I can give my provisional assent”.
lol
What about them?
We don’t need to pretend Rumrakat. We know that we don’t know. Haven’t you been paying attention?
John Harshman,
They aren’t humans and chimps.
Allan Miller,
As far as I am concerned at 99.9% identity common descent is a reasonable inference.
I wonder what they think would be good evidence for evolution. Complete different DNA sequences? Different genetic codes across species? Different kinds of genetic material?
No, somehow I think they’d demand what we see in life now if it didn’t exist. But because evolution “can’t be true,” the fact that what we see is (roughly) what would have to be the case if evolution occurred means nothing, because they can always demand evidence to show that the evidence matters.
Basically, it’s resort to the toddler’s gambit, just keep asking why, or to sound slightly more sophisticated, demand evidence past the point of possibility and necessity.
Glen Davidson
What controversy?
But if two students’ essays differed by 10%, how could anyone properly infer that derivation was responsible for the identical 90%?
Glen Davidson
Personally. I’d like to see an eye evolve. Or a von Neumann self-replicating automaton.
colewd,
I’ll let the world know.
Why did you pick that number?
Mung,
Personally, I’d like to see an eye arise by something other than evolution. Although even that would just be reverse engineering. Something new.