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.
No, it just isn’t evidence for common descent. Common descent is not a theory that says there won’t ever be “features with no ancestors”. So finding such features can’t be evidence against it. At best it just fails to be evidence for it.
You need to understand this distinction. Some observations can be compatible with a theory, without being evidence for or against the theory.
To make an analogy here. There is nothing in christianity that says that the dwarf-planet Pluto should exist, or not exist. Finding the dwarf-planet Pluto therefore isn’t evidence for christanity, nor is it evidence against it.
3900 comments in, this thread is still nothing but a showcase of creationist incompetence and the Jebus Effect.
I was expecting something more enticing than a gene list after this.
Maybe some, not all, especially ones that I put forward in this discussion.
You mean it pretends to, but doesn’t actually, not where it counts.
Bill,
Doesn’t it bother you that you still have no idea what the rest of us are talking about?
Has the stupidity of “I don’t know what you’re talking about, but it requires Jesus” escaped your notice?
You do realize that isn’t an explanation, right? An explanation is a hypothesis that fits the data considerably better than other hypotheses. “God did it” can’t fit the data because it has no expectation of what we will see or of what we won’t see. What you need is a reason why separate creation would be expected to produce a nested hierarchy but common descent wouldn’t. Try again.
Disagree. Quantum Mechanics suggests there is a supreme intelligence equivalent to the God of ancient religions in power and ability. If a probability barrier is big enough for an event to happen, and the event happens, it’s a miracle. You can call that a miracle of God if you want. It’s at least a historical hypothesis albeit not a predicting hypothesis.
But there’s a bit of hypocrisy on your part, you don’t have explanations either. You’ve shown the absence of them time and again in this discussion. You only pretend you have explanations, when you don’t, especially for complex novel features that define entire taxonomic groups.
No, but that was a convenient, simple example to illustrate why homoplasy is an expectation, which is what you asked for.
That depends on the mutation rate and how much time elapses. Why do you ask?
First, it doesn’t have to be simultaneous. It only has to be after their divergence and before the present. Second, the chance at any single site may be small, but as you point out there are 3.2 billion sites. And it increases over time.
What sort of calculation did you use to determine this? Or are you just pulling numbers from nowhere? But anyway, that’s irrelevant to common descent, which you have confused with the cause of mutation again. Why can’t creationists keep this straight?
Rumraket,
Why?
The probability is so remote of there mutations occurring. Lets say each there are 50 million mutations that separate two species. With a 3 billion total nucleotides the chance of on common mutational site is 3 billion/10000 (estimated population) between two species times the population times the probability of the same mutation is 1/9 or 1/2.7 million of a single mutation occurring in a single generation or about 1/100 occurring in over the time of the split say 6 million years. So the chance of two simultaneous mutations occurring is 1/10000. To fix the adaption you would need the mutation to fix in a single generation in at least two specific species which is about 1/3 billion. Your chance of this adaption is 1/ 3 x 10^14 assuming it takes with only two species obtaining it. With effective populations of 100000 you reduce it to 1/3x 10^13.
I’m not even going to ask how QM proves Jesus. It’s irrelevant. The argument isn’t over whether Jesus intervenes to create changes. We’re talking (and why do I have to keep reminding you?) about the nested hierarchy, not about mutation.
Once again, this discussion isn’t about the causes of novel features. It’s about the cause of the nested hierarchy of life. That’s the pattern formed by the features, not the features themselves. Why can’t you keep this straight?
And of course common descent explains, predicts, expects, whatever word you like, this pattern. That is indeed an explanation. Nested hierarchy is what we expect from common descent, and we don’t expect something else. You have not given any reason why we should expect nested hierarchy to result from separate creation of kinds, whatever those kinds might be. Why, you have even hinted that common descent explains nested hierarchy within kinds. What you call hypocrisy is just me knowing what the subject is, which you have consistently failed to address or even understand.
Bad calculation. Let’s simplify. Let’s assume a genome of 3*10^9 bases. Let’s further assume that there are 3.5*10^7 neutral fixations (that’s the difference between human and chimp). That’s 1.75*10^7 in each lineage. The probability of a given site having a fixed difference from the ancestor in each lineage is thus 1.75*10^7/(3*10^9), or 5.8*10^-3. The probability of the same site getting a fixed difference in both lineages is the square of that or 3.4*10^-5. Assuming the crude model of equal probabilities for each change, the chance of identical bases at that site is 1/3 of that number, or 1.1*10^-5. The expected number of homoplasious mutations is 1.1*10^-5*3*10^9, or 3.4*10^7. Not exactly vanishingly small, though certainly a very small percentage of the whole.
John Harshman,
It is irrelevant to the common descent you are claiming which includes divine intervention as a possible mechanism but it contradicts orthodox common descent which claims the cause of the pattern is mutation plus natural selection.
If through this discussion we agree divine intervention is likely then common design does surface as a real alternative since divine modification of extant animals is one of many possible ways diversity occurred.
If you can show that common design does not fit the observed pattern then your version of common descent would be the best candidate.
Even if that were true it would STILL not make the vacuous phrase “God did it” an explanation. For anything. There is no actual explanation going on. There is nothing about the data set that is being explained why it is the way it is.
A probability barrier? What the heck is that?
It’s not a hypothesis of any sort. It is completely vacuous. It is equivalent to Mung’s well-worn phrase “it just happened, that’s all”.
Bill, why don’t you feel any shame about just saying things on subjects you don’t really understand?
Do you not have friends and colleagues, or family members, among whom it is frowned upon to pretend to know things that you actually don’t? Have you never been taught that you shouldn’t just say stuff?
And if you don’t really feel any shame about just blathering ignorantly and incompetently all the time, don’t you then at least understand at an intellectual level why you still shouldn’t do it?
John Harshman,
Irrelevant calculation. Homoplasy is about features that are common to the species that are not common to the ancestor. These features require changes to DNA that can point to the specific adaption. You are modeling history not predicting the probability of a specific convergent adaption occurring given the observed conditions.
You are surfacing the chimp and human hypothesis fallacy. The theory needs to explain the origin of new features and how the genetic changes occurred that point to those features not just counting mutations agains time and mutation rate.
Since your theory allows for divine intervention, divine common descent is a candidate for this event.
That’s not how I see it.
So every time that the random number generator in your computer produces a random number, that is a miracle occurring?
Miracles are easier than I had ever realized.
My version of common descent is just common descent. We can and do study common descent without thinking about the origin of mutations one way or the other. It isn’t a question of orthodoxy.
Now I’m pretty sure that common design could fit any pattern whatsoever or no pattern at all, so your attempted test is useless. Until common design can come up with some expectations, nothing can be done to falsify it. However, since common descent explains the data very well, I would think that any theory of common design would have to involve intentional mimicry of common descent. But who would do that, and why?
As is so often the case, I have no real idea what you’re trying (and failing) so say.
The issue is, and has been, imho is this: Short of you seeing a miracle with your own eyes, is there any way the features within the universe can be constructed that would persuade you a miracle happened during the course of history?
If you say, “there is no way any feature of the universe could be constructed that would persuade me a miracle happened unless I saw something like it with my own eyes,” then if a miracle really did happen, you would never ever be able to make the correct inference about the past.
If on the other hand you said you could believe in a miracle in the past without seeing it with your own eyes, what would be your criteria? My criteria is mechanistic improbability (like tornados passing through a junkyard building a 747 jetliner).
We may not be able to explain why a miracle took place, the question is whether a miracle took place. If you don’t think miracles are detectable nor possible, then even if they happened, because it doesn’t satisfy your requirements for “an explanation” you wouldn’t make the correct inference. For the record, I actually don’t know what you believe about the detectability of miracles in the past, at least in principle.
I’m putting on the table why I think certain events like the emergence of complex features of life are not the ordinary statistical, physical, chemical expectation of the antecedent systems. A lungfish-like Sarcopterygiian fish is the supposed antecedent of a Parrot and an Elephant. That transformation, even over geological time, seems mechanistically improbable to me. I’ve articulated some of the reasons I believe it is mechanistically infeasible.
Paul Nelson said, Universal Common Ancestry is a really a theory of transformation. I look at some of those gene trees, and I said, superficially that’s reasonable support for common descent, but it may fall apart upon further scrutiny (like problems the various -omes pose).
The problem of Universal Common Ancestry isn’t the gene trees so much as the problem of complex novel features that define taxonomic groups.
I accept that Universal Common Ancestry can be falsified by the presence of improbable complex novel features that are far beyond ordinary statistical expectation, so that means to me “God did it because evolution can’t.” Therefore to me, the patterns of similarity, such as those shown by the gene trees that even I was able construct, are the result of Common Design not Common Descent.
John Harshman,
Lets postpone this specific conversation.
The real question: What would ever suggest to anyone in the first place that design would produce a nested hierarchy?
In other words, why would older and more basic “designs” be similar in bats and birds, yet newer and more recent “designs” exhibit no homologies beyond the older similarities? Why are the bones of bats and birds homologous, but hair and feathers not, nor are wings adapted similarly?
What designer refuses to use newer ideas in newer models, while refusing to throw out older ideas in the same models (even if it will modify them)?
Of course “common design” doesn’t fit the observed pattern, because the pattern isn’t smart, and it’s not even stupid, it’s something entirely else–it’s the sort of pattern that common descent would produce and that no smart or stupid designer would produce (unless it was trying to make things look evolved–in which case, bravo!).
Glen Davidson
So now you’re agreeing that common descent needs to explain the differences. Because if it doesn’t explain the differences it can’t possibly be evidence for macroevolution.
I am pretty sure that there are more than four possible states as soon as you stop thinking about one specific position in a DNA sequence.
So let’s agree that the limit on possible states is not a single given position in a DNA sequence, because that’s just silly, and ask what the actual number of possible states is and what the limit is on that. Because that would be what is relevant.
LoL.
There ought to be an award for anyone who can make sense of Salvador’s ramblings. Seriously. I’m not sure Gish Gallop even describes it.
What if we all just started quoting stuff that we read that may or may not be tangentially related just to show how much we know about the subject. Make Salvador wade through piles of crap searching for anything of relevance for a change.
Oh wait. You guys already do that. 😉
There can only ever be evidence for common descent. How convenient.
I took you off “ignore” because you had a post that might have been interesting. I’ll probably put you back on pretty soon, since you haven’t said anything since then that was other than trolling. By “macroevolution” I was referring to common descent. Sorry if that wasn’t clear.
John Harshman,
If you could really validate common descent then common design would be falsified. The only issue is that your version, divine common descent, which includes all possible mechanisms is not falsifiable.
My version isn’t divine common descent. How many times must I tell you? The point is that the evidence of common descent is independent of the mechanism by which new features arise. I don’t know what you would consider as “validating” common descent. Common descent predicts a certain pattern. That pattern is observed. Nothing else predicts that pattern. What more is needed?
John Harshman,
Common descent does not predict the pattern we see. Common descent does not predict homoplasy. Common descent does not predict the pattern of new features yet we see new features. Common descent fails to predict all the aspects of the pattern we see. Common descent is a claim about transitions of new species by reproduction. What we see when we witness reproduction is species striking similarity to the ancestors. Over the diversity of life we don’t see this.
Again, common descent is about transitions and your claim is a certain pattern is evidence that the pattern is caused by reproduction. Maybe the pattern is partial evidence that may support the claim but you are ignoring the contradictory evidence such as new features and homoplasy.
The appearance of a nested hierarchy is not conclusive evidence that the pattern is created by reproduction alone.
You cannot conclude common descent based only on supporting evidence without addressing the contradictory evidence.
And Jesus said, “The unteachable ye shall always have with you.”
Well, it was really the “poor,” not the “unteachable,” but you know…
Glen Davidson
No it’s not, unless you cherry pick.
Features without ancestors or features without mechanistically feasible transitions from ancestors are a violation of that predicted pattern.
Sigh. The origin of a feature is not relevant to the nested hierarchy. There is no cherry-picking, but if a gene is absent, its sequence must be treated as missing data. A tree constructed from binary presenc/absence data would still give you the standard nested hierarchy, as even your “flower” shows. You still haven’t figure out the subject of this thread.
Plus, a creationist found it first.
So there, it was first observed by non-evolutionists and it doesn’t really exist.
The power of creationist thought demonstrated!
Glen Davidson
John Harshman,
The nested hierarchy is only a partial explanation of the overall pattern and a new feature is a relevant part of the overall pattern. You have to explain the overall pattern, not just a single feature of it.
The thread is not named nested hierarchy vs common design. It is named common descent vs common design. All evidence for both hypothesis must be examined.
The nested hierarchy isn’t an explanation of the overall pattern; the nested hierarchy is the overall pattern that needs explanation. Common descent is the explanation. The origin of features is something else.
Common design is a synonym of separate creation of kinds. Please explain how separate creation of kinds predicts a nested hierarchy. What evidence is there for separate creation of kinds?
Look at the supposed prediction of gene tree hierarchies. So what you suggest then is genes will evolve in fashion that create descendants that can be arranged in a nested hierarchy based on patterns of similarity and diversity. So far so good. I have no problem with that, I showed I can build such trees right here at TSZ.
So how is that process going to create an orphan gene? How then do you account for the absence of any trace of the ancestor of such orphans or taxonomically restricted genes. The ad hoc explanation is gene evolves so fast no trace of the ancestor of the orphan is left, or that the trace of the ancestors got wiped out.
So you’re theory is that it common descent makes homologs that can be hierarchically arranged EXCEPT when it doesn’t. Not much of a prediction.
It doesn’t predict a nested hierarchy, but it doesn’t predict a non-hierarchy either.
If the pattern you are talking about is the taxnonomic nested hierarchy then that isn’t the same as the phylogenetic nested hierarchy. Your phylogenetic nested hierarchy says birds are Sarcopterygiian fish, the taxonomic nested hierarchy says birds aren’t fish.
Birds and fish-like Sarcopterygiians share different characters. Learn some biology.
Once again, common descent is not invoked to explain orphan genes, though in fact orphan genes do arise through descent, either from cooption of junk sequences or duplication of genes. In the former case we expect the non-gene sequences in related species to degrade fairly quickly. Still irrelevant, though. The pattern of orphan genes is still a nested hierarchy and, as you admit, separate creation does not predict a nested hierarchy but common descent does.
But in that case, isn’t it useless as a scientific hypothesis? I see this as a very damaging admission.
This distinction between taxonomic and phylogenetic nested hierarchies is your own invention, and it’s a distinction that doesn’t exist, or rather it’s really a difference between what we thought a hundred or more years ago and what we know now.
There’s your overweening arrogance again. You want me to learn some biology? Now the fact is that birds and fish-like sarcopterygians share a number of characters that the sarcopterygians don’t share with actinopterygians. And that’s what nested hierarchies are based on. You and old-time systematists had the problem that they didn’t distinguish between derived and primitive characters. We know better now.
You’re spouting gibberish again. Common descent doesn’t predict homoplasy, but it can account for homoplasy. Common descent doesn’t completely predict the pattern of new features, but it does predict that new features will form a nested hierarchy. It doesn’t predict all aspects of what we see, just the nested hierarchy. Common descent isn’t a claim about transitions but about relationships, though it’s true that in order for different species to be related there must have been transitions. Still, the nature of those transitions isn’t relevant. I am unable to interpret the last two sentences.
Again, common descent is not about transitions, though it implies that transitions happened. “Caused by reproduction” is a weird thing to say. New features fit the nested hierarchy, and homoplasy can be accommodated.
No idea what you mean by “by reproduction alone”. What alternatives do you have that might create the pattern?
Makes sense. But you misunderstand what contradictory evidence would look like or how it would be addressed.
John Harshman,
The pattern is an arrangement of data that describes the species relationship to each other. A nested hierarchy is a description of the pattern and evidence of common descent. New features are evidence that contradict common descent. All evidence that helps evaluate the hypothesis of common ancestry should be included.
Your attempt to make the nested hierarchy the only relevant point to determine if the evidence points to common ancestry is misleading.
John Harshman,
Common descent is a claim about transitions. If you are saying in your argument the nature of transitions isn’t relevant then your claim is about something different then common ancestry.
Some of your understanding is outdated, and you presume when we disagree the problem is with me. Some of the stuff I put on the table just floats over you head. You seem to define so much of biology in terms of phylogeny, not structure and molecules. I put examples here of structures that are better classified in terms of chemical structure, not phylogeny, such as protein domains. It just seems to float over your head as if I didn’t mention it.
You referred once to the various “-omes” as bad science.
The problem is John I’ve quoted issues from other evolutionary biologists who are more up-to-date than you, one example is promiscuous domains. You seem quite eager to close your eyes to the way biology works. I was fascinated by Histone readers, writers, and eraasers. When I put the concept on the table, you disputed that they existed. I thought to myself, “what a fricking amateur.”
I pointed out enhancers on exons. It just floated over your head. I pointed out the Phosphoproteme, the Acetylproteome, the Methylproteome, glyco congjugation,etc. These put constraints on the evolution of proteins from one species to another. I provided examples where it would obviously put functional constraints on the protein sequence in terms of taxonomic groups. It just floated over your head and you complained that I was doing a Gish Gallop. It’s a rather convenient way for you to avoid dealing with the problem that the hierarchical pattern in genes can’t be just a random walk but is the result of functional diversity rather than random changes of no functional consequence.
It just floats over your head. I’d have expected a little more interest in science and how things operate in biology. But you focus so much on looking at biology through the lens of (a likely mythical) phylogeny than structure.
Birds have structures that are not shared by fish. That’s a old-school taxonomic viewpoint, not a phylogenetic one. I discussed that at the molecular level, when structural biologists are trying to elucidate structure, structure takes priority, not some supposed phylogeny.
Birds have structures that make birds a structurally similar group, mammals have structures that make mammals a structurally similar group. The nested hierarchies formed by these patterns of structural similarities and differences (which are relatively stable) shouldn’t be conflated with the nested hierarchies of phylogenetic speculations (which are conflicted, unstable and uncertain).
I respect people with open minds and eager to learn about other fields (like those -omes you consider bad science). It’s not so much arrogance about me in general, I just find it hard to take what you say seriously because you show so little interest in other fields of biology than phylogeny, like structural/molecular biology.
For the reader’s benefit:
https://en.wikipedia.org/wiki/Structural_biology
Note in that wiki entry, there was no mention of John’s specialty of phylogeny. It however mentioned fields I’m acquainted with : informatics, physics, chemistry.
I put lots of structural biology terms in this discussion. You just ignore it as if some supposed phylogeny takes precedence over structure. You’ve got it backward John, structure takes precedence over phylogeny, therefore the real issue of nested hierarchies is the nested hierarchy created by old-school style structural comparisons. It’s in these old-school style structural comparisons that the problem of novel complex features becomes a barrier for common descent. You just don’t get it. That’s the problem.
I have to hope that Sal has me on ignore, otherwise he’s even further removed from reality than I had supposed.
I wrote:
The next day he writes:
Woot!
Seriously, though, there are a bunch of biochemists commenting here, and I really doubt that anything you have posted at TSZ has been news to any of them (Zinc fingers! OMG!). Nor has it been coherent, or even constituted the beginning of an argument.
In pretty much every interaction Sal has had here, he has been wrong. Currently he is indulging in his favorite escape technique, posting swathes of tangential or irrelevant quotes so that he can claim he has “put stuff on the table”. Oh, and getting all huffy and condescending.
It’s sad.
I’m not going to pay any attention to someone who, when talking about relativity, claims
</Sal Mode>
Perhaps Sal was referring to the small ‘n’ newton who posts here rather than Isaac Newton. newton is correct.
But it’s working well on Bill Cole, who understands neither what we, or what Sal is saying. But there’s them technical terms and buzzwords innit.
This is it. This is why creationism persists. A viscious circle of dishonesty and incompetence. Round and round it goes.
stcordova,
Trouble here is that, when I pointed out the silliness of supposing every single residue in a protein being constrained by its participation in the widdleyome, it just floated over your head. Ditto the idea that introns must form by point mutation, etc. You talk, you don’t listen.
Oh-err, Mung, that’s a rather effective way of getting Sal to take me off ignore.
Thank you, sir. Here’s your popcorn.
Allan Miller,
I like it the most when he touts “arguments” that are mutually exclusive, like the widdleyome vs the high levels of intra-species variation. However, I only mark my bingo card if he contradicts himself in the SAME COMMENT.
So you’re saying that the nested hierarchy is evidence for common descent. But the nested hierarchy is that which is to be explained. The explanandum. Common descent is supposed to be the explanation. The explanans.
To appeal to the nested hierarchy as evidence for common descent is to confuse the explanans with the explanandum. It makes the argument circular.
So it really does make much more sense for you to have said that the nested hierarchy is evidence for macroevolution. But then we are back to having to explain the differences without which there would be no nesting. There is no nesting without the appearance of those differences.
So while I disagree with Salvador on so much, on this at least he seems to have a valid point. IF common descent doesn’t explain the origin of the differences upon which the nesting is based then it does not explain the nested hierarchy.
See. I can do things other than trolling. I’m not OMagain. 🙂