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.
@colewd
Notice that thing there I highlighted in bold in my previous post:
“antimutator alleles”. As in variations of genes that cause reductions in the mutation rate.
That means there are spontaneous mutations that happen that reduce the spontaneous mutation rates. In other words there are multiple ways to reduce the mutation rates besides mismatch repair.
So the real world demonstrates that reproduction can function without DNA repair, and that reduced mutation rates can even evolve in hypermutable lineages.
They have even found some of the mutations that cause the mechanism responsible for the later reduction back down towards normal mutation rates, after the repair pathway lost function.
From: Wielgoss et al.: Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load.
Proc Natl Acad Sci U S A. 2013 Jan 2; 110(1): 222–227. doi: 10.1073/pnas.1219574110
“Identification of Antimutator Alleles and Mutational Spectra.
The MutT protein is a hydrolase that purges the cellular nucleotide pool of oxidized guanine nucleotides (8-oxo-dGTP), which can mis-pair with adenine and lead to A:T→C:G (adenine or thymine to cytosine or guanine) transversions after DNA replication. Loss-of-function mutations in mutY, which encodes a DNA repair glycosylase that excises mis-paired bases from DNA helices, also lead to elevated mutation rates on their own (29). However, mutY mutations have an antimutator effect in the context of a MutT defect because MutY mis-repairs 8-oxoG:A base pairs in DNA. The 60% reduction in overall mutation rates reported in mutT mutY double mutants compared with mutT single mutants (29) is similar to the rate changes we observed in both the phylogenomic analysis (Fig. 1B) and fluctuation tests (Fig. 1C). Indeed, genome resequencing showed that different mutY mutations had occurred along the two mutT branches
sampled at 40,000 generations (Fig. 1A).”
It is quite amazing how many of your creationist canards have been experimentally refuted in this single experiment.
That has to do with a method of sequencing DNA that allows for multiple reading passes of the same DNA molecule. Not relevant I’m afraid.
Blimey Eric!
There’s a gulf of incomprension between you and people like Allan who think in terms of chemistry and biology. He’s trying to get some basic ideas across to you but you seem to be deaf to his efforts.
So you reject the tutor’s best efforts at getting you to understand? Then it’s no wonder you don’t understand.
Basic ideas can be summarized in a few sentences, preferably without basic errors of logic. You can pick up from here.
But phylogenetics is complex. You may have to put in significant effort, but you appear to want spoonfeeding instead. Why not do some independant learning first before rejecting an entire field?
I’m okay with complexity. I only require that the basics make sense. Demand to forget basic distinctions of A and B do not make sense. Correlation is not causation in any science I know of, so why should biology be an exception?
How basic do we need to get? The structure of DNA is such that replication is an inherent property. We can start from there.
No, I said that populations need to occasionaly acquire unique novel distinguishing characters. That has the “fixed” baked into it, as Mikkel already explained to you. As before, it is your lack of grasp of basic genetics that is causing your confusion; it has nothing to do with me not being open in any way.
No, it’s not. I was referring to baraminology that holds that certain groups of species (say all felids) descended from some “original kind”. I was hoping that you agreed with this position, since it entails lineage splitting and divergenge and then we would be on the same page. Given your reluctance to commit to this or any position, I take it that you simply don’t have a position?
Fine. And how do you know *how* it was replicated across the biosphere? Something like, “It replicates along species with some variation, so let’s extrapolate that the whole biosphere is a result of the same variation on grand scale over Very Long Time.” Right? Anything more to it than this?
Paul C, to Erik:
If Erik were the type to do that, it’s doubtful that he’d be a creationist in the first place.
Right, we are 1211 comments into the thread and we only have Mungs comment that actually recognises that the nested hierarchy is something worthy of an explanation (I am not even talking about, you know, giving an explanation).
Is there anybody here willing to concede that you won’t get a nested hierarchy under every conceivable version of common design?
Is there anybody here willing to concede that, even for versions of common design that will result in a nested hierarchy, the actual pattern that is expected depends on the ecological requirements of a species?
Corneel:
And just to be clear here, Corneel is talking about an objective nested hierarchy, such as in Theobald’s Figure 1, where independent morphological and molecular data yield the same hierarchy.
It seems to me under your schema we cannot know anything. And yet scientists science and other scientists science on top of that original science. If it was a house of cards based on nothing we’d have noticed by now.
Extrapolations are legitimate in some cases. We’ve identified a mechanism (differential reproduction) and it seems capable.
It seems to me Erik has not understood this point. When we observe the nested hierarchy it’s perfectly possible that the designer did it, but that’s not a useful assumption as every data point can be “explained” by that assumption.
If we saw that sometimes we cannot observe the nested hierarchy then Erik’s objection would have some weight – we cannot extrapolate to cover everything as there are datapoints not covered by that extrapoliation. But we don’t observe that and so the extrapoliation seems legitmate as far as it goes.
We use plate tetonics to explain the movement of the continents. We don’t demand that we rule out other forces or designers doing the same until we actually observe some evidence of those forces or designers. Plate tetonics seems sufficent.
Erik, I don’t believe you’ve actually answered my question – has there been any speciation events that you accept as such? Last time I asked you simply asked me a question in return. I think it’s fair that you answer this now, given I did respond to your questions.
Biologists define species and speciation. Erik rejects those definitions, it seems, and demands proof beyond what the biologists themselves demand. Does this make Erik more “honest” then those bioloigsts, not being willing to take things on faith?
No, I don’t think so. I think it just illustrates Erik’s hubris.
I know, he’s just colossally wrong about almost everything, yet thinks that he makes good arguments when he merely regurgitates old tripe from pseudoscientists, the IDists. I wrote:
And he replied:
The truth is, I’m being amazed at how closed creationists are to evidence and how they can be wrong about almost every fact while thinking that they have to be right about their “conclusions.” It’s more about sociology, psychology, and cognition than anything, because of course the creationists aren’t very exceptional among pseudoscientists, aside from the fact that they may have attacked the core values of science and of evidence-based thinking more destructively (at least to themselves) than has any other group of nonsense-believers.
Bill stumbles at every turn, failing constantly at reading comprehension, the understanding of graphs, and of basic principles of evidence-based thinking, yet he supposes that he makes reasonable arguments all the same. How does anyone think that this could even be possible? For me it’s an eye-opener, because I really was never like that when I was a believer (to be sure, that was only up to around age 15), and I never plumbed that level of denial when arguing with the religious as I was doubting their theology, especially creationism.
Denialism that I knew never seemed so deep, thorough, and utterly incapable of recognizing how badly it was floundering. Even UD seems to be composed mostly of people who like echo chambers and fear getting out to anywhere that could really threaten their beliefs, a more familiar denialism in my experience. Only here do we seem to run into people like Erik and Bill who appear unable to get anything right about science and evidence, yet think that they possess a wholly superior ability for getting at the truth.
Glen Davidson
Let me see if I understand this.
A butterfly mated with a daffodil. And the offspring was similar to a dog. So we said it was a dog, and put it into a tree. From such similarities, we conclude that there is common descent.
That is what Erik seems to be suggesting. And if biology were done that way, I would be just as skeptical as Erik.
It seems to me that he is missing something.
Erik,
I knew exactly what I was doing and what I wanted to achieve. The fact that you are either struggling to grasp this, or doing your damnedest to avoid grasping it, is the issue here. You don’t know genetics, you don’t want to know genetics, you don’t want to see what relevance genetics has. So – what exactly are you doing, beyond, as that last comment suggests to me, trying to get a rise out of me?
No, they aren’t. Likewise the genes for a trait are not the same thing as the trait. One can build trees on either. Lo and behold, they are typically congruent. Isn’t that strange? But the important thing about gene sequences is that they are digital. If there is a change, particularly a large-scale change such as an indel, that provides extra information not available to simple ‘trait analysis’.
Lure you? Fucksake Erik. You seem to think everyone knowledgable is Satan in disguise. Get real.
zzZZ no, another in a long line of errors and misconceptions. Gene-duplications are not restricted to whole gene-copies, where a complete gene with all exons and introns (speaking of eukaryotes) from one end to the other, is copied.
Many duplications involve copying smaller fragments (of variable sizes) of already existing genes and inserting them into new genes, or simply extending the original gene.
There can be “exploration” of sequence space by duplications and insertions, essentially without requiring single nucleotide substitutions, by replication errors extending sequences with multiple tandem duplications.
“New” genes don’t have to evolve single nucleotide by single nucleotide. Duplications are a substrate for further blind sampling of sequence space, but that sampling doesn’t have to proceed exclusively by SNPs.
“come with me if you want to sin”
It’s hilarious. Try the actual thing, Erik blinks in incomprehension. Try an analogy, it’s a dismissable ‘category error’.
Congratulations to all the folks who tried to get across the evidence for common ancestry. It always seemed to me that it was the “elephant in the room”, with evolutionary biologists spending far too little time on it, as compared to fossils, development, biogeography, and population genetic evidence. Even Jerry Coyne’s Why Evolution Is True spends too little time on it.
But from the mid-1700s on, biologists (almost all of them creationists) became more and more impressed with the reality of an hierarchical pattern of groups in the classification system. That was the concordance of phylogenies for different aspects of morphology, although describing it that way is much more recent. Doug Theobald has done an excellent job of documenting it, following up and extending the work of David Penny and Peter Lockhart in the 1980s.
Creationists who deny common ancestry find themselves in a dilemma, since in their present incarnation many of them accept “baraminology” which does accept evidence for common ancestry within “baramins” (where it also accepts the effectiveness of natural selection). “ID Theorists” who are really relabeled creationists have the same problems. When confronted with the evidence they either stick their fingers in their ears, or run away to the Origin Of Life. or just run away. The minority of ID advocates who say they accept common ancestry become surprisingly vague when asked about particular examples.
I wish that people understood the centrality of concordance of phylogenies in the history of evolutionary biology. Fossil evidence was important, but by the mid-1800s a majority of biologists had abandoned the fixity of species and the idea of Special Creation. The stage was set for Darwin and Wallace. The folks on the other side of the debates here are 200 years behind the times.
Okay, so the tree argument makes evolution. No need for anyone else to beat around the bush anymore. Thanks for the lecture.
I do think Darwin would have been delighted with the molecular evidence. It is an elegant corroboration of his fundamental hypothesis on descent.
Molecules and DNA strings not being actual objects themselves of course. 🙂
There’s nothing you can say that will make Erik budge the slightest little bit. He’s determined not to learn anything, and you can’t make him. “La la la, I can’t hear you.” I even suspect he’s put me on “ignore”.
But just in case he hasn’t, once again I offer an example of how this tree thing actually works, which I suppose he will ignore even if he sees this:
Harshman J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and false gharials: A nuclear gene phylogeny of Crocodylia. Systematic Biology 2003; 52:386-402.
Perhaps Bill will bite.
Blimey Alan!
There’s a gulf of incomprension between Allan and people like Erik who think in terms of actual objects and causes and categories. He’s trying to get some basic ideas across to Allan but Allan seems to be deaf to his efforts.
LoL. Allan’s the one being tutored and Allan’s the one who doesn’t understand.
It’s a two-way conversation going on. Let’s not just blame Erik.
This is blatantly false. If we are going to teach Erik biology, let’s not teach him nonsense.
For those kinds of arguments to be effective, you have to be right. Simply mirroring a valid response just makes you look silly
I see that as a strength of common design. It’s a more comprehensive explanation. It can explain far more than common descent. It’s explanatory power is greater. Therefore it’s to be preferred.
So the pattern is not caused by common descent.
And as I pointed out previously, there are an untold number of other nested hierarchies other than the actual nested hierarchy that common descent could be used to explain.
So common descent doesn’t really explain the actual pattern. For common descent to explain the actual pattern, it would need to do so to the exclusion of other patterns, and this it does not do.
I’ve always been the class clown.
Given common descent, in what sense are the data sets independent? And what do we do with the “independent” data sets that yield a different hierarchy, just ignore them?
Common design is not an assumption, it is a conclusion. How many times do we have to explain this?
Sometimes we cannot observe the nested hierarchy. Erik’s objection has some weight.
I must be God in disguise then. 😀
No, Alan is correct.
Upon the elucidation of the structure of DNA, it immediately was obvious to James Watson and Francis Crick that genetic information could be copied by using the complementary strands as templates:
I started a thread here at TSZ in which I pointed out this very thing. I wanted to know how to convince someone else that common descent is true. Even after reading through all this thread I’m still at a loss.
Which theory of common design? There are so many!
payback time!
Mung,
Would it be possible for you to link to where common design explains a specific thing comprehensively?
I’m fairly familiar with ID but I can’t recall actually seeing a specific case where common design provides an explanation more detailed then the alternative evolution based explanation.
For you to say it’s a comprehensive explanation presumably means you have such an example to hand? If so I’d be very interested to see it.
What Alan wrote was Salvador level nonsense. And focusing solely on the double-stranded helix leaves out a lot of the actual structure of DNA. And even given the double-stranded helix it doesn’t make replication an “inherent property” of DNA.
#Bafflegab
😀
It’s incoherent even!
Mung,
Sure they are, but a gene for a trait is not the trait. Ceci n’est pas une pipe.
OK then!
Basics first. Though I see Corneel has pointed out to you the basic structure of DNA was enough to put Crick and Watson on the trail of the genetic code. The clue was in how an association of hydrogen bonding, an inherent property of the four nucleotides found in DNA, results in them forming matching complementary pairs in the chain (Chargaff’s rules). So in a double helix, you have a chain of nucleotides and its matching complement. This inherent property can be exploited in vitro using PCR where you can produce many copies of a particular DNA sequence from a tiny sample.
Mung,
Another cracker for Polly.
I think you misunderstood by what I meant by comprehensive. I didn’t mean it provided an exhaustive step-by-step mechanism. I meant it explained far more cases.
I think it’s common knowledge here that common design explains anything and everything. So I don’t see why I need to defend that claim. That’s what I meant by comprehensive.
What I mean, for example, is that you cannot show me a phylogenetic tree where the pattern cannot be explained by common design.
Mung,
I am being tutored that the entirety of molecular phylogeny is wrong, because Erik doesn’t understand genetics, and ‘you can build a tree on anything’. ‘kay.
Was the ever a Creationist whose coat you didn’t hold, while going rah! rah! rah! from the sidelines?
Mung,
You appear to be saying that an ‘independent’ dataset would be one based on some feature that was not possessed by the organisms in question …
Erik is not trying to tutor you on molecular phylogeny.
Salvador. BA77. Swamidass. keiths. I’m sure there have been others.
Such fertile soil here at TSZ. How could I not grow and prosper and bring forth fruit.
Is your knowledge of biochemistry sufficient to make that judgement?
I’ve started but I haven’t finished. Broad brush first, details later. And Yes the double helix is an emergent property of the chemistry of the DNA structure in aqueous solution. I’ve performed this technique and rolling up semi-liquid DNA “superstrands” on a glass rod gives a wonderful impression of the constituent DNA molecules.