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.
By the way, under some conditions evolution does actually predict an upper limit (below 100%) to the accuracy of DNA replication. Known as the drift-barrier hypothesis.
Larry Moran had a blog post about it a little over a year ago: http://sandwalk.blogspot.dk/2016/12/learning-about-modern-evolutionary.html.
Yes, for asexual lineages that works. Allan made a similar point
“Obviously” doesn’t go a long way here at TSZ. Better to make that explicit. Besides, I am not the one who made this distinction. You will find that anagenesis + cladogenesis is a common definition, for example here:
These are the two requirements for a nested hierarchy of species. Given the quality of objections in this thread, I doubt that this is “obvious” for everyone.
I would also like to add that, given the nature of asexual “species”, the only reason we can distinguish separate lineages is because the intermediates have been lost. This is a branching process as well, and I don’t think this automatically follows from semiconservative replication of DNA.
keiths,
Nope, you’re not getting it. I give up.
Rumraket,
I do think there’s another factor not often mentioned – as a polymerase approached perfection, there would be fewer and fewer mutations available to get it any further.
Corneel,
Semiconservative replication means that (ignoring recombination) all DNA molecules will coalesce upon an ancestral sequence – be commonly descended from it – regardless whether there is retention or discard. It may be much harder to establish relationships with retention, but that coalescence – and hence ‘branching’ – is still a prediction of the process.
Anyhoo … still looking for some kind of defence of the ‘Common’ part of this thread. So far, all the Creationists have done (when not word-gaming) is provide arguments for Design, with no indication why we need to add the word ‘Common’, except as a bolt-on in imitation of the evolutionist phrase.
Allan,
I always took it to be the creationists’ way of explaining the similarities among different “kinds”. Instead of designing each new “kind” from scratch, the Designer reused certain design motifs.
Allan,
What, specifically, is the “it” that I’m not getting?
Corneel,
You seem to be focused on nested hierarchies of species, but it’s worth stressing again that those are not the only nested hierarchies produced by semiconservative replication of DNA.
No speciation events are represented in a nested hierarchy of E. coli strains, but it’s still a nested hierarchy, and it’s produced by imperfect DNA replication.
For individual cells, yes. You still have coalescence and will get a nested hierarchy. I conceded as much.
But how do you get distinct population-level lineages if all descendants are retained?
Not going to argue with that. That is correct, except for the part where I am “focused on species”. But I strongly doubt that everybody here immediately grasps that branching automatically follows from certain biochemical processes OR that we switch between nested hierarchies of species, of individuals and of molecular sequences OR that we switch back and forth between evolution as change within a lineage ( e.g. as in Tom’s beautiful simulations) and evolution as lineage change plus speciation. So it doesn’t hurt to be clear what we are talking about.
But perhaps I am being condescending again 🙂
keiths,
You appear to want to restrict the term ‘common descent’ to vertical inheritance. And hence, in that context, HGT is noise at the point of injection, signal after. But in fact ‘common descent’ should, IMO, apply to any sequences that can trace back to a single ancestral sequence, regardless of the path taken. One can point to the common descent of viral sequence, of transposon, of gene duplicate or protein motif – even if these are not always transmitted through the vertical route, they harbour phylogenetic information (provided one accepts the more relaxed sense of ‘phylogeny’ I am advocating in the first place).
That is also the way I understood it. But I haven’t seen any arguments of that type either.
Corneel,
Perhaps this comes from the ‘inside-out’ view I tried, with only limited success, to pursue in the ‘evolution of sex’ thread. If one starts with asexuality (and ignores HGT), one gets common descent and coalescence as a mutually agreed consequence of the semiconservative replication of DNA (one can use ‘the cell’ or ‘the genome’ as one’s unit; cellular encapsulation ensures equivalence).
That’s the situation in the first 1-2 billion years of Life, so not just a special case unless one is a sexual diploid who thinks that the norm 🙂
With the advent of sex (IMO, haploid fusion and separation), one has a different dynamic. First of all, you get independent segregation of chromosomes if n exceeds 1, regardless of crossover. At that point, coalescence ceases to apply at the cell level, but is now at the chromosome level. Now, to get Common Descent of entire genomes, one needs separate fixation of each chromosome (else one has Incomplete Lineage Sorting), which necessarily implies elimination of intermediates.
Then, when one has the addition of crossover, the same argument applies at a lower level still – the level of individual haplotypes. Coalescence at this level is subdivided; each genome is a mosaic of subgenome coalescences/fixations.
So yes, I concede that from the standpoint of a sexual species, there is an extra process, due to the effects of recombination and of the populations it forms – the separate threads of locus history are gathered into a coherent whole by locus-level fixations. But I am arguing from a more fundamental level, on which the sexual mode is something of a late-coming eccentricity.
Does evolution predict speciation, whatever that means?
And Corneel is right to point out that people are talking about different things. When people talk about common descent they are usually referring to it as Darwin did, as transmutation of species.
It’s bait and switch to go from arguing about a nested hierarchy of species to arguing about a nested hierarchy of DNA sequences.
That too is predicted by evolution. 🙂
The poly constraints on proteins are the overlapping binding sites that serve as roadsigns and parking lots that serve the post translational modifications like:
Phospo Proteome
Methyl Proteome
Acetylome
Protein Glycome (protein glycol conjugates).
Here is an illustration of such conjugates which again underscores one can’t assume a protein can just mutate willy nilly from one species to another since the above post translational modifications are species and cell-type specific.
Common design points to ONE creator, not many Intelligent Designers that can’t cooperate. Someone could argue if there are multiple designers, they conspired to plagiarize.
Hold on there, chief. First you have to provide evidence for common design before you can tell us what it points to. How is the nested hierarchy of life evidence for common design? You have avoided all discussion of that question.
John Harshman,
I am not sure how Sal answers this question with clarity until there is a coherent definition of the “nested hierarchy of life”.
Why does the “one designer” exhibit no knowledge of mammalian earbones when it designs birds, and no knowledge of bird optics and lungs when it designs mammals?
Of course there are homologies between mammals and birds, apparently from early tetrapods, as one would expect of evolutionary processes. But it makes no sense from a design standpoint that later changes exhibit no derivative knowledge at all, while earlier derivation is obvious. Why can’t the extremely intelligent designer think between later bird and mammal adaptations?
Strangely, the designer seems as blind to what’s going on around vertical descent as evolutionary processes would be.
Glen Davidson
Your lack of coherence is no problem for those who understand these matters.
Glen Davidson
GlenDavidson,
Glen, you are avoiding argument here. All I can take from your comment is that you don’t have a coherent definition. Your side is making the grand claim that the “nested hierarchy of life” is evidence supporting common descent.
This is mainly an assertion I have heard over and over. Can anyone on this site back up this claim with a real argument? I simply suggest providing a workable definition of the ” nested hierarchy of life” so everyone is on the same page.
Maybe Sal can provide it. If he can’t, then how can he answer John’s question.
But it is a claim that can, in principal, be falsified. For example, if the way fossils were distributed in the various geological layers, the classic example being “rabbits in the Cambrian period” did not comply with the model of bifurcating descent from earlier forms, this would argue against the model.
Alan Fox,
If I were to say trilobites (eyes) in the Cambrian falsify the model how would you make a counter argument?
Can you make a clear definition of the “nested hierarchy of life” ?
No I’m not, I’m commenting on your decided lack of knowledge, and how you try to force everything to fit the ignorance that you use as a weapon against knowledge. The fact is that you’ve been provided copious examples, while you blither on about Macs fitting a nested hierarchy, which is complete bunk. It’s an old ploy by ignorant creationists, to babble on and on about the need for definitions that are well-understood by those not in denial.
Anyway, it’s just a matter of sets. There has to be an intersection of shared characters across a nested hierarchy, with added characters lacking intersection with possible other organisms within other branches. It’s not difficult.
Well, you’re not very good at understanding, obviously. There isn’t a simple definition, but the examples given should explain things to you, if you’re open and intelligent. So far so bad.
It’s simply a matter of derivation. Why don’t you explain why mammals and birds have homologous characters, yet character that arose past a certain fairly early tetrapod stage are not homologous.
Yes, we have, and you’ve just blundered on not understanding anything but your own unenlightened “similarities and dissimilarities” mistake. Your inability to pick up what has been clearly illustrated and explained is not our problem.
See if you can learn something for once.
The real question is why you think you have any kind of handle on evolution vs. design when you lack very basic reasoning skills necessary for understanding this matter. You should be completely without opinion on this matter if you’re committed to an honest answer, since you can’t begin to understand what’s actually at stake, lacking even the simple understanding of what nested hierarchies indicate about life and, say, languages and manuscripts.
Glen Davidson
Just saying trilobites in the Cambrian falsify the model of common descent is not an argument. I don’t know much in detail about trilobites, other than there is a profusion of fantastically preserved specimens. We could look at the evidence of the age and location of these fossils and see if they form a branching tree of descent. Would you be interested in doing that?
ETA grammar
@Bill,
Just looked for info on Trilobites and found this site! I’m having a look now and I may be some time.
It’s been defined for you more than once, each time clearly. I’ve also offered examples, which you have paid no attention to. Even Sal’s favorite flower provided an example when analyzed closely. Your ignorance is not an effective shield. And let me once again remind you of a very simple example:
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.
I’m not going to link to it again; you do the work.
Trilobite branching tree: (link to clearer image)
The claim is actually a misleading claim as to what is the nested hierarchy.
If one means nested as in proteins like Cytochrome-C etc., then superficially it looks like common descent with random modification and some additional constraints like non-erasure of phylogenetic signals.
If one means by nested hierarchy, orphan systems and features defining groups, then common descent is supported if one accepts miracles for the orphan systems and features. Just asserting ‘these orphan features define a nested hierarchy, therefore it evolved” is just a bald assertion that flies in the face of mechanistic difficulties.
Some of the major POOFS:
1. eukaryotes and prokaryotes
2. multicellular animals
3. vertebrates
4. mammals
5. primates
or
3. vascular plants
4. angio sperms (Darwin’s abominable mystery)
These are taxonomic nested hierarchies known since Linnaeus time.
Let me compare a human taxonomic nested hierarchy (which is empirically real) with a supposed human phylogenetic nested hierarchy (which is imaginary and which I argue is likely false).
Here is one human taxonomy polluted by evolutionary thinking where humans nest in a hierarchy that is a FISH. According to some evolutionists, you aren’t just descended from a fish, you ARE a fish. See PZ Myer’s interview with Ray Comfort. Myers echoes the confused thinking as in this wiki article:
https://en.wikipedia.org/wiki/Human_taxonomy
Note for example that evolutionist nest you within this clade with a representative pictured below:
https://en.wikipedia.org/wiki/Teleostomi
Linnaeus was wiser than Darwinists. Just remove the clade nonsense and you get a nicer classification and nesting:
The second rendering is much more sensible, and is a more real taxonomic nested hierarchy without the polluted phylogenetic nested hierarchy.
This is similar to Transformed Cladism:
https://en.wikipedia.org/wiki/Transformed_cladistics
Here is a criticism by Darwinists:
“Pattern cladistics has remained on the fringe because of, first, its implausible assumption that there can be pure observation untainted by theory; and second, its rejection of the evolution assumption. Few systematists now think that a classification not based on evolutionary branching and history has any real signification or justification. The developing consensus is that Darwin was right – a natural classification must be genealogical.”[1]
“The developing consensus is that Darwin was right – a natural classification must be genealogical.” To which I say, balderdash. The so-called “natural” classification is an artifact of imagination. Transformed cladism is the most natural and empirical classification, not common descent.
Common design says:
A conceptual eukaryote gives rise to physical eukaryotes.
A conceptual animal gives rise to physical animal.
A conceptual vertebrate gives rise to physical vertebrate.
A conceptual mammal gives rise to a physical mammal.
etc.
Evolutionary theory says:
A prokaryote-like creature gives rise to a physical eukaryote
A physical fish eventually gave rise to a physical amphibian
A physical amphibian gave rise to a mammal
One can see the distorted viewpoint of evolutionary theory, versus the much more tidy conception provided by common design:
The nesting of humans within a fish clade (teleostomi) does not even make much empirical sense.
Look a human cytochrome-c for example, it’s closer to other mammals than to fish.
Fish cyctochrome-c is like a fish cytochrome-c. Humans don’t nest under fish cytochrome-c, Dab Gummit!
BLAST this sequence, does it look like nests inside of fish. Heck no.
http://www.uniprot.org/blast/uniprot/B201710178A530B6CA0138AFAA6D2B97CE8C2A924F0C8EDQ
If humans are in the fish clade, you ought to see human cytochrome surrounded by fish. It ain’t. Phylogeneticists therefore have to give excuses why it’s not and why REAL fish are so close in sequence to other fish(as in take one fish, and it’s surrounded by other fishes in sequence space), not to humans, goats, and giraffes.
Like I said, MRCA’s don’t look right if one really is more scrutinizing.
Phylogeneticists swear by nested hierarchies, and then build such hierarchies that don’t even accord with the data.
Take a fish cytochrome-C, and you’ll see it is swimming in a sea of other fish, mammals. That’s because mammals aren’t fish, and NOT mammals didn’t descend from fish. At best the descended, er, from another mammal!
Stcordova:
Thanks. John has made the claim that Jesus directed mutations can be part of the theory of common descent. So he has made the observation of the data independent of mechanism. What are your thoughts on this issue?
This is an interesting comment I need to think about. Can you expand on this?
Oh I see, it isn’t falsified, it’s just what one should expect from evolution.
Can you even begin to understand the “nested” part of “nested hierarchies”? Mammals “nest” into the fish clade, they’re all closer to each other than they are to fish, hence cytochrome c is more different between fish and humans than it is between other mammals and humans.
The only thing lacking is your understanding of these issues.
Glen Davidson
Even John Harshman agrees one can define nested hierarchies based on orphan features, that is features that only appear in members of a group.
For example Plants have features that distinguish them from Animals and vice versa. Vertebrates have features that distinguish them from invertebrates. These are orphan features of the group.
Just consider the differences between animals with an Exo-skeleton vs. and Endo skeleton.
https://en.wikipedia.org/wiki/Exoskeleton
https://en.wikipedia.org/wiki/Endoskeleton
These are orphan features from creatures without skeletons. But also creatures with exo skeletons have orphan features that creatures with endo skeletons don’t have, and vice versa. One can see that a TAXONOMIC (not phylogenetic) nested hierarchy can be built with simple accounting of orphan features. The nested hiearachy was seen even by the creationist Linnaeus:
https://en.wikipedia.org/wiki/Linnaean_taxonomy
Skeletal formation involves new gene sets, regulation and development. That involves modifications to the post translation information residing on proteins like:
1. phosphoproteome
2. methyl proteome
3. acetylome
4. glycol proteome
as described above. And lots of other things already mentioned and even more not mentioned.
Creatures with endo-skeletons vs. creatures with exo-skeletons have different developmental programs. It’s more than just pumping out proteins with slight variations on them that make possible those wide differences.
Taxonomic nested hierarchies are real, phylogenetic nested hierarchies are imaginary and often force-fit data as I demonstrated with the cytochrome-C that evolutionists seem to swear by.
Human cytochrome-C is very similar to mammalian cytocochrome C, and fish cytochrome-C is similar to other fish cytochrome C. It implies mammals didn’t descend from fish, at best both fish and mammals descended from a common ancestor that isn’t specified. The fish cytochrome-C is so similar to other fish, the MRCA of extant fish was about as recent as the MRCA of mammals! That doesn’t exactly support the evolutionary story.
Think I’m making stuff up about the conflict between the REAL nested hierarchies of taxonomy vs. the imagined nested hierarchies of phylogeny?
http://www.amjbot.org/content/90/9/1263.full
Which falsified John Harshman’s claim that phylogenetics gives a mechanism for creating taxonomic hierarchies, it doesn’t not. At best it does so with lots of ad hoc epicycles.
Mammals are mammals, they aren’t fish, therefore they don’t belong in the fish (teleosotomi) clade as Darwinists insist.
colewd,
Jesus Fucking Christ, Bill. Do you think, by any chance, that there might be an argument for common descent in a document whose subtitle is The Scientific Case for Common Descent? A document that we’ve referred you to again and again, for that very reason?
Or has the Jebus Effect blinded you even to this most obvious of inferences?
Sal,
Just to keep you on your back foot:
The elephant is still in the room. Would you care to explain to us why, out of the more than 10^38 possible trees for the taxa in Theobald’s Figure 1, we infer the same exact tree from the morphological and molecular data?
Coincidence? The Designer just happens to be an anal-retentive evolution mimic? He hates the eggheads and wants to fool them into accepting common descent?
Be brave and answer the question.
Sal and Bill,
It’s kind of pointless for us to revisit the scientific evidence again and again when your reasons for rejecting common descent are emotional and religious.
This is a psychological issue for you, not a scientific one.
The first step is to stop pontificating on subjects about which you know nothing. It only serves to showcase your ignorance of the subject. Your ability to google, cut, and paste based on key words doesn’t help either.
I hesitate to respond to the Gish gallop in your recent string of posts, purely because of the volume, but there’s hardly anything true in any of them. Perhaps your assumption that it’s intuitively obvious that mammals aren’t fish, so obvious that you don’t even need to make an argument, is the worst. Yes, you actually do have to make an argument, which you have not.
Teleostomi is probably not a group. I would suggest Osteichthyes as an alternative we’re more certain of. Now, what you’re calling “fish” isn’t even fish, just Teleostei, and mammals aren’t teleosts. Mammals are sarcopterygians. Have you tried comparing cytochrome c of various sarcopterygians? One should also not compare raw similarity, since rates of evolution differ among taxa. The question is whether cytochrome c forms a nested hierarchy, one in which there is a branch separating sarcopterygians, including mammals, from what you are calling “fish”. And yes, there is.
Just saying rabbits in the Cambrian falsify the model of common descent is not an argument.
I knew you would say that the minute I read Alan’s post there. what a joke
Allan,
No wonder I didn’t get your point! You were using “common descent” in an idiosyncratic way that included HGT, while I was using it in the standard way.
I think the horizontal/vertical distinction is extremely important and that your usage, by trying to shoehorn HGT into the ‘descent’ category, would only create confusion. I also can’t see any benefit of erasing the distinction and classifying HGT as a form of “common descent”.
Yeah how preposterous. Humans are also eukaryotes. Here’s a representative pictured below:
No indeed! Just saying is not an argument. But Bill was offering (I think) to look at what evidence there is in the fossil record to indicate whether the vast numbers of trilobites that have been found so far fit a nested hierarchy.
He mentioned trilobite eyes, saying:
And my reply was to say I am uninformed (though a little less so after looking at the site I linked to above) on the issue but I’d be interested to explore the evidence and whether it shows a clear evolutionary sequence (or sequences) with him.
One issue is that, though chitin fossilizes beautifully, and trilobite tracks in silt have also fossilized, some tracks predate actual fossil organism specimens (suggesting earliest trilobites did not have armoured exoskeletons), so so far no way to be sure what the most recent common ancestor to the clade was (and I see whether Agnostida should be considered trilobites is still under discussion).
Mung,
Is not (H/T Mung).
stcordova,
Yeah, same objections as before, as you continue to bellow sententiously: “AND ANOTHER THING …”. You equate possible constraint on part of a sequence with constraint on all sequence ever. Again. And again. And again.
colewd,
Yeah, and then Sal will answer with clarity. Chortle.
keiths,
There is nothing particularly idiosyncratic about ‘common descent of DNA sequences’. There is simply a broader set of paths in which they travel, which includes vertical descent – whole-genome copying. Clearly Darwin did not have this in mind, but broader, underlying principles have been discovered that explain the higher-order patterns.
I don’t need to do anything to create confusion – it is already there in the typical gibberings of Creationists, on clear display in this thread, obfuscated by volume or semantic nitpicking.
I’m not really trying to shoehorn HGT in anywhere, I am trying to promote understanding of the fundamental role of DNA replication in the whole shebang. People are so phenotype-focussed, and that loses traction when we are talking about evolution, because phenotypes aren’t inherited.
We can see this focus in the repeated refusal to even look at the molecular evidence. Again and again, we get a brief blink, then a hurried ‘let’s-talk-about-something-else’. Trilobite eyes is but the latest.
I’m definitely not saying that HGT is a form of common descent. I am saying that HGT is one of the paths that commonly descended DNA sequences can take through history. Vertical descent is clearly the major one. But the methods of molecular phylogeny are not restricted to looking at species trees. And, in fact, species trees are simply the predominant signal from gathered-together gene trees. Gene trees are gathered together in vertical descent due to a combination of linkage and fixation.
When people do molecular phylogeny, they are generally looking at gene trees, gathered together by common vertical descent. But that is not the only game in town. If someone wishes to deny the validity of phylogenetic methods, they must do so against its use in areas outside of taxonomy.