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.
Glen Davidson
That’s an example of why I prefer: Everything causes everything.
Or, in more detail, everything is a contributory cause to everything.
Just like design then!
What is the entailment (or what are the entailments if there are more than one) of the addition of function that require design? What does design actually explain regarding the addition of function?
Well, that’s what some of you keep asserting, but oddly no one who supports the design notion has been able to show any entailments that lead to that design conclusion.
But not in terms of cause and effect, because those are just verbal games.
Sure, assuming that “everything” is analogical to crankshaft and combustion. But is it?
There is no need for a causal link to justify common design.
Ommmmmmmmmmmm…
Do you or do you not see how substantially this changes what the term “common descent” entails? You evidently don’t. As some ephemeral asbtract label, I can accept “common descent” any time to slap it on anything, for example in the sense “those things there have certain undeniable commonalities – and we can draw a graph”.
How ridiculous. Now I am definitely done.
If you want to know the basics of the mainstream understanding of speciation, I recommend checking out http://evolution.berkeley.edu/evolibrary/article/evo_40
If you are familiar with that, but disagree, I’m not sure what you think speciation needs to fit into.
Your problem with the mainstream understanding seems to be that you can’t imagine how, for example, a fish population could evolve into a mammal population, and you don’t see anything like that going on now. Is that accurate?
Ah, Erik flounces once more. I doubt that will last long. Yes, “common descent” certainly means something different for manuscripts than for species. But it should nevertheless be quite clear that there is only one sensible meaning for species, so I don’t know why we’re having this little talk. It’s certainly logically possible that the nested hierarchy was produced by god acting as a poorly performing xerox machine, occasionally poofing a new species into existence by using a previous species as a model, with incorporated errors, but that seems like nothing more than an attempt to counterfeit common descent (in the usual meaning of the term). And you are apparently not proposing that model anyway, or any model at all.
Good thing I didn’t mention anything about causal links then…
Gravitation fields and electromagnetic fields extend everywhere. So why not?
Our ordinary use of “cause”, in my opinion, has to do with what we can cause either directly or indirectly. But that does not extrapolate back to “first cause” arguments. And it does not support arguments that claim we cannot cause anything.
Just enough knowledge to misunderstand biology and think it ridiculous.
More than adequate for Erik.
Glen Davidson
Cause is more of a stand-in for an observed sequence. We repeatedly observe a before b and conclude a causes b. This works in everyday life, but is inadequate in describing feedback systems and systems involving loops of causal sequences.
I’m thinking of a recent article in which researchers announced breathlessly that they had found a cluster of genes that accounted for differences in intelligence.
Reading the article it seems that the number of genes involves was a couple dozen, and combined, they accounted for about five percent of observed differences.
Except of mutation that cause catastrophic metabolic disease, I suspect most mutations have subtle effects, easily swamped by environmental effects, or drowned in population statistics. Animal breeders that try to short circuit evolution by rapid selection frequently wind up with lots of unwanted side effects.
The mills of drift grind slow, but they grind exceeding fine.
When you look at what happens when you try to design organisms, only the observed process makes sense. There simply too many dimensions of fitness in play.
John, to Erik (post-flounce):
God mimicking unguided evolution; the Rain Fairy mimicking unguided meteorology. Equally idiotic, yet somehow, the former is acceptable to folks like Erik, while the latter is not.
I disagree. We don’t know what’s acceptable to Erik, since he has never said. Like most creationists, he’s all anti with nothing to be pro.
Robin,
The requirement of a very large set of DNA sequences that can interrupt the cell cycle and trigger programmed cell death or apoptosis. A mission critical process in multicellular organisms.
What’s up with evolutionists and their being all anti providing evidence for their speculations?
keiths:
John:
The evidence points to common descent and away from common design. Erik’s only rational options are to
1) accept common descent;
2) give a plausible and non-ad-hoc explanation of why his Designer mimics common descent so exactly (to a precision of better than 38 decimal places in the case of Theobald’s Figure 1), when trillions of other options are open to him; or
3) come up with another explanation that fits the evidence better than common descent.
Good luck to him.
keiths,
He did a lousy job mimicking common descent. Just look at Sal’s flower. Genes appearing in a Zebra fish and not re appearing until a primate does not look like a very good imitation of common descent. The varied use of genes scattered through lineages does look like design activity. Descent with modification, not so much.
38 decimal places, Bill.
Creationism is flat-earth, Rain-Fairy stupid.
You don’t even explain how you get Sal’s “flower” so wrong. No one knows how you can think that such a normal evolutionary article could be taken as showing genes “re appearing” in primates. It neither shows that nor is it possible to see why you think that, except for the fact that you’re out to find anything wrong with evolutionary theory, no matter how incorrect.
Why don’t you for once explain your “reappearing” genes? Clearly you’re very wrong about that, but it remains to be seen how you’re so amazingly mistaken about a relatively simple and straightforward diagram.
Glen Davidson
Glen, to colewd:
Yes, please do. That’s a laughable misinterpretation of the diagram, as we’ve explained to you again and again.
keiths,
73 Genes are found in the Zebra fish are lost in the chicken lost in the mouse and re appear in the human. Wow, where did those genes go? Evolutionist denial is on full display.
Bill,
Where did you get the “reappear” bit? Why not draw out a diagram and tack it on to your next comment?
keiths,
Here is the image address.http://theskepticalzone.com/wp/wp-content/uploads/2017/08/image_103611.jpg
Humans ate zebrafish. Chickens and mice did not. An obvious case of symbiosis.
Do you think that we evolved from chickens and mice, according to theory?
That’s the only way that your statement could make any sense with respect to genes “reappearing” in humans? It’s as wrong as anything I’ve ever seen, of course, but I have to suspect that you actually think that we evolved from mice and chickens.
So far you’ve made no sense at all, unless you believe something so wrong as the notion that the theory suggests that we evolved from mice and chickens.
Glen Davidson
Yes, we know the diagram. We can’t figure out your “thinking.” And we can even figure out Byers and J-Mac a lot of times.
Glen Davidson
colewd,
I’m talking about the tree, Bill. Show us exactly where you think the genes were lost and where they reappear, in your interpretation.
keiths,
Use the flower Keiths. It shows the problem clearly. The genes are shared by humans and zebra fish and are not in chicken and mice. Most trees show zebra fish ancestral to chicken and mice which exist in separate lineages birds and mammals. So the deletion event with the same genes happened in two parallel lineages. A miracle 🙂
colewd:
Bill,
Did you actually think I wouldn’t notice when you quietly dropped your claim about the genes reappearing in humans?
I did notice.
So are you retracting that claim?
Most trees don’t show the common ancestors. We’re supposed to just pretend as if they are there.
Un-poof!
OMG that’s stupid!
There isn’t a “deletion event” responsible for anything, there are just genes being lost and gained. And most “lost” genes aren’t “deletion events” at all, the genes just become non-functional, pseudogenes. You could probably find in mice and chickens any number of pseudogenes of the 79 genes we share with zebrafish and not with mice or chickens.
Chickens share 129 genes with zebrafish and not with mice or humans, while mice share 57 genes with zebrafish and not with mice or humans. There’s nothing magical about two lineages losing the same genes, it’s just a matter of probabilities (well, it’s more than that, but one wouldn’t do badly to think of it as just probability for the sake of simplicity). They’re not special genes to be lost by two species, they’re just ones that happened to mutate in both mice and chickens to become pseudogenes (in most cases, anyway) and didn’t happen to mutate in humans to lose their functions. Meanwhile, humans, mice, and chickens share 10.660 genes with each other as well as with zebrafish. It would be surprising if mice and chickens didn’t lose a few tens of genes that humans did not.
I can’t see how you think there’s any problem at all.
Glen Davidson
One more thing in Bill’s odd little post that nobody has yet commented on. No, Bill. No tree shows zebra fish ancestral to chicken or mice. What one might hope you meant to say (but failed) is that chickens and mice are more closely related to each other than to zebrafish, so that there is a lineage ancestral to chickens and mice that isn’t ancestral to zebrafish. Or perhaps you actually meant what you said, which would be unfortunate.
John, to colewd:
That’s why I’d like him to draw the tree and show us exactly where he thinks the “deletions” and “reappearances” occurred.
Meanwhile Mung is floundering on the sidelines, as usual.
John’s wrong. Again. I commented on it in the post immediately prior to his. Doh!
Miraculous insertion to the tree of life explain everything as needed and they were also predicted by evolution…. but first by Hashman in his delusion of an imaginary tree of life lol…
Thank you all… That’s it for me…
You’ve been great…
Good night everybody! lol
Seriously, just ignore him.
Nevermind, I think I figured this one out for myself.
@John Harshman, or Joe Felsenstein, or whoever else knows:
Suppose we include an organism like Tiktaalik in a phylogenetic analysis of a large number of taxons of extant fish and terrestrial tetrapods.
My guess is the algorithm would put an ancient and extinct lineage on a node closer to the root of the tree, with a short(er) branch. Is that correct?
Erik,
Educate me! Google’s bust! I won’t listen, but educate me anyway!
Mung,
Just like flat earth, too, if ‘being a conclusion’ is the bar for explanatory power. One would hope one could do better.
John Harshman,
I disagree with your disagreement. He has elsewhere argued the commonality of Flood stories in global cultures to be evidence of an actual historical Flood. So, he accepts common descent sometimes, without a particularly exacting standard of corroboration.
colewd,
But how many different ways does a cell actually need to die? Clutching its chest, staggering dramatically? With an audible pop? Surrounded by tear-stained loved ones?
The thing to be explained is the variation in cytochrome c among different organisms. Just saying ‘apoptosis’ does not come close to that, any more than saying ‘electron transport’ would.
You are effectively doing that which you criticise evolutionists for – a ‘just so story’ regarding a possible adaptive difference, seized eagerly and uncritically through confirmation bias. Far more work would need to be done to establish that the nested differences within taxa all relate to a ‘design requirement’ in the cytochrome c’s themselves. Explain it in animals, there’s a whole biosphere left to go at.
Bill, they don’t “re-appear” in humans. The lineage leading to humans and to zebrafish, from their common ancestor, has retained those 73 genes for all that time. They were gradually lost in the lineages leading to mouse and chicken. In all likelihood, as you get closer to the common ancestor of all birds, you will find a greater and greater proportion of those 73 genes still present. And the same for the mouse, as you get closer and closer to the common ancestor of all rodents, again that number will get smaller, as you go further back in time.
It’s not like one day there were mice, and from one generation to the next, from “non-mice to mice”, 73 genes were lost, and the same thing happened in chicken. That’s a misreading of that graph.
There has been lots of independent gene-gains since the common ancestor of all vertebrates, in the lineages leading to all four species in the diagram. Which you probably find equally preposterous to the gene-loss.
But many of those genes are not really “novel” protein coding genes in the sense you think. A large proportion of those gene-gains are simply duplications of already existing genes.
The authors of the study from which that graph originates also note that the Zebrafish lineage, after the split from amniotes (the three other species in that graph are amniotes), has probably undergone whole genome duplication at least once, which would also significantly inflate the total number of protein coding genes.
They write: “Zebrafish are members of the teleostei infraclass, a monophyletic group that is thought to have arisen approximately 340 million years ago from a common ancestor(11). Compared to other vertebrate species, this ancestor underwent an additional round of whole-genome duplication (WGD) called the teleost-specific genome duplication (TSD)(12). Gene duplicates that result from this process are called ohnologues (after Susumu Ohno who suggested this mechanism of gene duplication)(13). Zebrafish possess 26,206 protein-coding genes(6), more than any previously sequenced vertebrate, and they have a higher number of species-specific genes in their genome than do human, mouse or chicken. Some of this increased gene number is likely to be a consequence of the TSD.”
Source of the graph is this The zebrafish reference genome sequence and its relationship to the human genome.
Mung,
As you know, John has you on ignore, so … doh! I’d have been far more impressed if you’d actually corrected Bill, particularly on the ‘reappearing’ thing.