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.
In other words, because reproduction? That’s not what I asked. And that’s not what genetic inheritance a la common descent means.
So the answer you have is misdirection. You can try again with some better answer.
What is shown by the diagram is often explained away by Incomplete Lineage Sort and Loss of Genes and Emergence of Orphan Gene or Taxnomically Restricted Genes. There is a lot of ad hoc patchwork epicyclic apologetic tautology and flimsy excuse making for a failing theory, not a forceful scientific hypothesis like say Netwonian Mechnics within classical domains. In otherwords UCA sucks.
But consider all the orphan genes in the diagram. Now in the diagram it looks like 2963 orphan genes are in the human. That’s not exactly correct because it probably represents a lot of primate-specific genes. But it is known there are a lot of orphan genes for each species or group. They just sort of POOF onto the scene. There isn’t direct evidence of smooth continuous increases and changes between supposed ancestors, it looks PUNCTUATED. The absence of direct evidence of the smooth continuity is explained away by saying we don’t have direct evidence nor can we because we don’t have genetic fossil records of all the transitional steps, blah blah blah. Well, in that case, UCA is a statement of faith in absences fact.
But each grouping of organisms shows the common ancestor of the group has a POOF of genes that then get either lost or create an incomplete lineage sort as seen in diagrams like the one shown. So at every step of a new common ancestor of a some group, there is a POOF. Evolution to work requires POOF, POOF, POOF… at every emergence of each group.
As I said, UCA requires statistical miracles to make it acutally work, except naturalists strenuously avoid admitting it and dogmatically assert it’s quite natural for something like a fish (sarcopterygii) to eventually give rise to a bird.
https://en.wikipedia.org/wiki/Orphan_gene
It’s not just orphan genes, but orphan systems where homologous genes are used for different purposes. The synthesis initiation factors for example are homologous in Eukaryotes and Prokaryotes, but they are used in different ways. IF-1 in prokaryotes is “homologous” to eIF-1 in eukaryotes, but they are used differently.
Compare this
https://liarsfordarwin.files.wordpress.com/2017/05/prokayote_protein_synthesis_initiation.png
with this:
OK, perhaps a longer response might be in order (though I do find the effort of explaining things to the determinedly intransigent to be increasingly lacking in interest):
We have a routine observation that changes to DNA are inherited by descendants. It could hardly be otherwise: if a genome ‘loses’ a gene, there is nothing to inherit. You don’t infer this from phylogenetic analysis, but from the known mechanism of inheritance.
Whether a given difference in DNA is or is not a useful phylogenetic signal depsnds upon what else you have in the analysis. Obviously, it’s not just the descendants of a given individual that lack a gene; it’s all the ones whose ancestors never had it in the first place. So, you must add in other potential phylogenetic signals, in order to establish the likely phylogeny, and against which the discordance stands out.
Repeatedly, Creationists make the mistake of thinking that phylogeny is only about commonality, or only about difference. It’s about the pattern – the tree-like pattern, entirely an expectation of genetic copying, but not at all an expectation of ‘design’ – your favourite analogy of cups vases and mugs nothwithstanding.
De novo origination? If this is a thing, then common descent isn’t. The question that I keep asking – how do biologists know this (other than just assuming that the ability to draw a tree and to give it names like phylogeny/nested hierarchies/common descent has causal powers)?
Erik,
In the piece to which you were responding, I was talking about a very simple model of single-generational inheritance. If that is repeated across many generations, with bifurcation, then it is very much what ‘genetic inheritance a la common descent’ means.
Ah, the arrogance of ignorance.
How do you know it’s repeated with bifurcation?
This is the second time I am asking the same question, because you failed to answer the first time.
Now Erik has leapt on the carousel, like the rest failing completely to indicate why common design explains the data better than common descent, and adding to the confusion by not recognising that common descent is about genetic inheritance.
That doesn’t explain the appearance of orphan genes.
Erik,
I said If it is repeated with bifurcation. That is what the common descent of two species means, in biology.
You’d be as well just trying to understand what you are criticising, rather than repeating demands that others clear up your ignorance by slow, painful degrees.
Mung,
Doesn’t explain the size of your gas bill either. But hey ho.
Yes, but genetic inheritance is not (only) about common descent. You pretend that it is. Hint: Felsenstein’s phylogenetic script is said to be able to detect common ancestry, but it cannot detect the direct parents.
Very sad from you, Harshman and Felsenstein to pretend that reproduction is the same thing as common descent and adaptation is the same thing as speciation, when they clearly are not.
Common design trumps common descent as an explanation of the nested hierarchy because it is a better explanation. Happy now?
Erik,
If a stretch of DNA is template copied, and two individuals inherit that DNA, after however many generations, that is common descent. Fill me in; what’s missing?
You might do better than drop hints; you might actually lay out an argument why that is even necessary. You don’t need to know the parents in order to infer common descent. My brother and I can be inferred to be closely related (ie: commonly descended), by DNA, without any reference to any ancestor at any remove.
stcordova,
So you take a sledgehammer to the dimension of time and conclude that the result is flat?
If there are n differences between 2 extant taxa, what forces us to suppose that they all happened at once? What happens when you subdivide the taxa? 2000 becomes 1000, becomes 500, becomes 50 … could it be that gross suppositions were based on a flawed premise in the first place?
Well, it’s a start 🙂
Allan Miller,
This was not your question. Again your question:
The big difference is between singled celled organisms and multicellular organisms, The addition of the binding capability for apoptosis explains this difference.
It indeed isn’t necessary. That’s the whole point. It means that reproduction is not the same thing as common descent, so stop pretending that it is. If you want to “infer” common descent, then “the basics of template-directed DNA replication” is the wrong answer. How is this unclear?
Alan Fox,
After your read this paper, I am interested in your opinion of how this experiment supports the emergence of de novo proteins in multicellular organisms.
I note that whenever evolutionary biologists say “common descent”, the other folks immediately change it to “Universal Common Descent”. The screeching noise as the goalposts move is deafening. But the evidence for common descent on a much smaller scale of, say, the Golden-Crowned Sparrow, the White-Crowned Sparrow, and the White-Throated Sparrow is of the same sort as for more distantly related species.
In fact many contemporary creationists accept common ancestry within what they call “baramins”. After the two (or seven) representatives get off the Ark, they undergo a mind-boggling burst of high-speed evolution that also involves lots of differences arising between their descendants. Presumably with natural selection acting, though they tend not to say.
Using ordinary phylogenetic methods, and examining congruence of evolutionary trees made from different parts of the genome or using different phenotypes, it is just as possible to confirm within-baramin trees as for more widely separated forms. The unanswered question is why those methods are suddenly meaningless when used on more distantly related forms.
So they are not the same thing? Is UCA a thing or is it not? And if it is, is it proven by hand-waving to any sort of “common descent” or does it require separate demonstration?
That’s the best.
It’s a total fail, just like all of the other total fails.
But he who fails last, fails best.
Erik,
I still don’t know what it is I’m ‘pretending’. I don’t regard reproduction as the same thing as common descent; I regard being commonly descended as being at the ends of series of reproduction events (reducible to template copyings of DNA) tracing back to a common ancestor.
By not being clear.
If the basics of template-directed DNA replication indicate that a change, once it has happened, will be inherited by all descendants, then common descent can be inferred for all organisms in which that change is found (subject to some caveats, but the fundamental logic remains sound).
Neil Rickert,
Why is it a total fail?
It’s not supposed to. Bill was showing signs of radical confusion regarding what gene-loss, particularly considering he thought they some times “re-appear”.
Exactly what I was wondering about. I asked Sal about it further down the thread, but he seems to have missed it or didn’t bother to answer.
Many YECs accept some level of branching evolution after the deluge, so they also need to accept some level of common descent, at least up to the founders of the baramins.
Compare what you said earlier,
…”with bifurcation”, i.e. speciation. That’s the difference. And this is what you keep including and omitting randomly as if it were a non-issue. In reality, it’s the whole issue. It needs a definition so that it’s different from mere reproduction across generations and then it requires separate demonstration according to the definition to establish that it’s a thing in reality, not wishful thinking.
Joe Felsenstein,
How close are these birds genetically?
colewd,
That’s not ‘the big difference’ at all. Do you see a discontinuity in the accumulation of differences when protists are added to the Dayhoff diagram? And anyway, my point was actually about the little differences.
Every point on the Dayhoff diagram indicates a different cytochrome c sequence. You would have it that apoptosis explains the difference between rabbit and wombat cytochrome c, that which supposedly cannot be explained by electron transport requirement alone. But apoptosis is no more fundamentally a species-specific thing than electron transport. These are low-level housekeeping functions. There is a possibility that the shape of a rabbit and wombat are ’caused’ by differential apoptosis, and this is entirely due to cytochrome c, but I seriously doubt that.
You got that one wrong. IF-3 in prokaryotes is homologous to eIF1 in eukarotes. They’re used in the same way.
The sheer incompetence being demonstrated by the creationists in this thread is staggering.
Erik,
Actually, it doesn’t. If two sequences are commonly descended, then they are commonly descended. One does not have to ‘demonstrate speciation’ for that – iterated reproduction in 2 lineages – to remain the very essence of the definition of common descent.
This is what you need to find a ‘common design’ alternative to. Design does not become a viable alternative simply because speciation has not been evidenced to your particular standards.
One should note that the evidence for common descent is actually itself evidence for speciation. That is not circular. If two species share a gene, common descent is a viable explanation for that commonality, which can be supported by looking at another sequence – and then another. Common descent predicts that pattern Common design does not.
Allan Miller,
This is your opinion. Can you support the claim? The paper I cited shows a binding difference between humans and mice. The genetic distance in AA similarity in most cases among mammals is not that great. In some cases reptiles are closer to humans then primates.
Isn’t that obvious?
It doesn’t say anything. It merely declares common design to be the best explanation.
… and was intended, I surmise, to be taken tongue-in-cheek.
colewd,
To the same standard you support yours, I reckon I can, yes …
A test of the ‘apoptosis’ hypothesis for variation in animals would be if animals had a different pattern of differences to the rest of Life. I bet they don’t.
That’s because they are closely related, and only about 5,000 species to pick from.
And?
What diagram? The diagram you show has nothing to do with incomplete lineage sorting.
https://en.wikipedia.org/wiki/Psychological_projection
Heh, you think orphan genes somehow contradict the nesting hiearchy pattern, when in fact it confirms it. The greater the distance between species, or between groups, the more orfan genes.
The funny thing is you sorta refer to the solution to your non-issue without realizing it. As you correctlty state, there are less orfan genes separating one primate from another, than there are separating fish and primates. And the more closely related the species are, the less orfan genes will separate them.
Even better, the closer the distances, the higher the likelihood that we can even see a phylogenetic signal of the process by which those ORFan genes arose. For example, putative ORFan protein coding genes in the human lineage, have detectable DNA orthologoues in the chimpanzee and gorilla lineages. So we can literally see how protein coding regions emerged by the accumulation of mutations in non-coding DNA.
You think ORFan genes somehow contradict common descent, when in reality they are just another layer of confirmation.
The problem is you think exclusively in terms of absense-presence, and you believe there is some sort of great obstacle to evolution producing new genes. These two things in combination is your problem. It isn’t a problem with the theory of evolution or common descent.
No, they simply don’t. The evidence we have shows that ORFan genes usually emerge from random accumulations of mutations in non-coding DNA, often junk-DNA or other types of intergenic DNA.
In some cases we can literally see, by comparing lots of closely related species, how transcription factors emerge and mature from what is at first spurious transcription, and how it eventually results in translatable regions.
So when you write: “There isn’t direct evidence of smooth continuous increases and changes between supposed ancestors, it looks PUNCTUATED.”
The facts are literally the diametrically opposite.
The signal for emergence of ORFan genes, or taxonomically restricted genes, however will gradually erase with inferred age of divergence. Exactly like you would expect if common descent was true, as mutations continue accumulating over long time scales, particularly in the absense of purifying selection.
No, it’s exactly as expected. The more time separates two species, the more erasure of a signal of descent you’d expect for a region not under strong purifying selection.
It isn’t ad-hoc, it literally follows from our understanding of the mechanism of inheritance when extrapolated over sufficiently long timescales.
What the fuck does that gibberish even mean? Incomplete lineage sorting is a predicted out come of the process of speciation. It is almost unavoidable.
When two subpopulations of a bigger ancestral population become isolated, it is EXTREMELY unlikely for both subpopulations to have ended up with an identical distribution of the total set of alleles in the ancestral population.
Besides, incomplete lineage sorting is about explaining how it is that a small subset of alleles (those would be variants of the same gene, hence alleles, not ORFan genes) in a more distantly related cousin species are more similar to the species in question, than the same alleles in the same species.
Sal for fucks sake man. You need to get these terms right. This is fucking pathetic.
No actually its shows the long-term, gradual accumulation of new protein coding genes over deep time. And the closer we get to the present, the better the signal for how these genes emerge get (see attached picture), so that we can see simply from comparative genetics how ORFan and taxonomically restricted genes emerge.
It doesn’t contradict common descent, it confirms common descent.
At this stage I will only note the irony of someone who believes that ALL genes that exist in the entire biosphere, were literally POOFED into existence, in an instant, 6000 years ago, complains about percieved “poofing” in a theory that actually accounts for their slow, gradual emergence and accumulation over deep geological time.
Yes, I thought so.
Neil Rickert,
So we can hold evolutionists to the same standard when they make the claim that common descent is the best explanation of the nested hierarchy?
This is true. But does it follow that they must therefore accept the methods of phylogenetic inference as Joe seems to think?
If someone accepts DNA testing, does that mean she must accept the methods of phylogenetic inference, as many people here seem to think?
Being used in the same way doesn’t mean it’s homologous. If evolutionary theory were coherent you wouldn’t make this mistake. 🙂
Allan Miller,
And your argument that cytochrome c evidence supports common descent is going in circles.
Yes, you’ll just have to show how it’s not the best explanation, when it’s the only process known that would inevitably produce it.
Any chance that you’ll ever think these things through, rather than merely cheering any stupid creationist comment, including one that was apparently meant to be an obvious joke that you managed to miss?
Glen Davidson
colewd,
A mechanism from which a nested hierarchy would fall as a matter of course kind of is the best explanation for the nested hierarchy, isn’t it?
If something is true, then it is true. If common design is the best explanation, then it is the best explanation.
Neither of us has pretended (or even claimed) any such thing. You are suffering from serious misunderstandings, though their extent is not completely clear.
I agree that “poofing” over long periods of time in many small bursts is much better than “POOFING” everything all at once in one big burst.
#Poofolutionism
colewd,
It is not a prediction of common descent that the total number of differences will always increase with time. So if you find an instance where the number is less than expected, you haven’t turned cytochrome c into a circular argument. (‘Circular argument’ – yet another term subject to abuse by Creationists).
It’s like saying that all twigs should always get further away from their fellows on an actual tree, otherwise there is no actual tree.
Allan Miller,
Mung said is isn’t you say it is. Whats the difference? Both are equivalent un supported assertions. I just guess thats the point Mung was making.
Would you take no for an answer?