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.
One can also see many sequence alignments are almost non-existent! The homology of NYLB is “structural” where certain critical residues are located. Ordinary BLAST will not detect the homologies, but rather PSI-BLAST, MUSCLE and Position-Specific PSSM profiles.
Confirmation of functional similarity has been partially confirmed by enzymatic activity to the same substrate, namely nylon-6. But anyway, here is a snap shot of how different the homolgous sequences are, but where 2 critical amino-acid positions (of Serine “S” and Lysine “K”) are conserved.
You can zoom in on the image here:
http://theskepticalzone.com/wp/wp-content/uploads/2017/08/serine_position_v31.png
Corneel,
Different design. Prokaryotes have simpler genomes and are functionally simpler organisms then eukaryotes. The design on eukaryotes makes multicellular organisms possible and alternative splicing makes new animal designs simpler.
Are you a young ark creationist or an old ark creationist?
It’s obvious that prokaryotes evolved from eukaryotes.
I wish you would stop posting that figure, since you have ignored all the responses to your claims about it, responses that completely dismantle your claims. You have yet to suggest how common design would explain any of it. If common ancestors didn’t exist, how do you explain the nested hierarchy? Now I see that you have started to deny that there actually is a nested hierarchy, so I wish you would make up your mind on that point. I have quite a few wishes about your behavior, none of which are likely to come true.
John Harshman,
3 out of 8 trees have multiple events which clearly violates the nested hierarchy. 8 out of 8 have single events which may violate the nested hierarchy.
What we have here is a partial nested hierarchy that points to the design strategy of re using components.
Mung,
Fits the Occum’s Razor analysis 🙂
Are you at all familiar with the Einstein definition of insanity?
I don’t count dubious ad hoc rationalizations as dismantling my claims. I pointed out the problem of the common ancestor having an absurd number of genes not to mention orphans. Objections you ignored.
So I’d wish you’d learn something and concede you didn’t refute the issues except with flimsy arguments.
Btw, have you learned yet the situations when coalescence theory isn’t applicable? Can you state it for the readers?
Notice that I didn’t post a complete analysis of all 15 areas. It’s actually 4 out of 15 trees that have multiple events. Single events do not violate the nested hierarchy, by definition. And note that if you count genes rather than areas, the ones that violate the nested hierarchy become a ridiculously tiny proportion of the total. Of course we would predict a certain amount of homoplasy given the known mechanisms of evolution, so that small number of violations isn’t a problem for the model.
And notice that you still didn’t answer the question. Why should this “strategy of re-using components” fit a nested hierarchy so well? Why should the number of genes that require two changes to explain be so many fewer than the number that require only one change?
I didn’t ignore them. I explained why they were wrong. The common ancestor doesn’t require an absurd number of genes, because genes are gained as well as lost. “Orphans” is a meaningless term, or at least a term that you are mis-applying with regard to the figure. Most of the genes in it have clear homologs, either paralogs or pseudogenes or both, in other species. All “absence” means here is that the sequence doesn’t code for a protein, not that it doesn’t exist.
If the arguments are flimsy, why did you ignore them?
Sure. Coalescence theory isn’t applicable if there’s selection. It is, however, applicable to large populations. You should probably discuss this with Joe, if he’s willing to talk to you.
John Harshman,
It’s a partial nested hierarchy which points to a design strategy and violates what we would expect from inheritance. If the mechanism was inheritance I would not expect this pattern.
As one would expect from a design strategy, to reuse components as much as possible.
Any change challenges your hypothesis. Inheritance should copy genes and move them to the next generation along with variation from recombination.
You are aware that deletion mutations happen, and so do gene duplications? Yes you are, you have been told as much in this very thread and many others. So gene loss or gain can’t be a challenge to common descent.
Rumraket,
Do you have experimental evidence beyond single celled organisms?
Yes. In humans even. Here’s a nice overview: http://www.molevol.org/the-range-of-rates-for-different-genetic-types-of-mutations/
This paper (cited in the linked blogpost) also gives a nice overview:
Campbell CD, Eichler EE.:Properties and rates of germline mutations in humans.Trends Genet. 2013 Oct;29(10):575-84. doi: 10.1016/j.tig.2013.04.005 Epub 2013 May 16.
“CNV mutation rate
In addition to SNVs, there has been considerable effort in estimating the rates of formation of CNVs. Although CNVs are operationally defined as deletions and duplications of 50 bp or more [17] , most studies have assessed de novo events only in the multi-kilobase pair range. As with SNVs, initial studies in this area focused on only a few loci. These analyses found that the locus mutation rate was higher for CNVs (2.5 × 10 −6 –1 × 10 −4 mutations per locus per generation) compared with SNVs and that the rate varied by more than an order of magnitude between loci [18 19] ; data from mice suggest that the difference in rates between loci are even larger [20] . A genome-wide analysis of large CNVs (>100 kbp) revealed a mutation rate of 1.2 × 10 −2 CNVs per generation based on approximately 400 parent–offspring trios [21] . A significantly higher mutation rate of 3.6 × 10 −2 mutations per generation was observed for individuals with intellectual disability, probably because some of these de novo CNVs were influencing the development of the disorders observed in these individuals [22] . Using high-density microarrays and population genetic approaches, the rate of CNV formation was estimated to be 3 × 10 −2 for variants >500 bp [23] . However, this rate is likely a lower boundary because selection will remove deleterious mutations from the population and most large CNVs are estimated to be deleterious [21 23] .
Notably, when considering the total number of mutated base pairs between SNVs and CNVs, CNVs account for the vast majority. New large CNVs (>100 kbp) are relatively rare compared with SNVs: one new large CNV per 42 births (95% Poisson CI: 23–97) [21] compared with an average 61 new SNVs per birth (95% CI of the mean: 58–64) 5 6 7 8 ( Figure 1 ). The average number of base pairs affected by large CNVs is 8–25 kbp per gamete (16–50 kbp per birth) [21] , which is larger than the average of 30.5 bp per gamete observed for SNVs (61 bp per birth; Figure 1 ). It is important to note that the estimates for CNVs are based on microarray data that could not be used reliably to detect smaller CNVs (<100 kbp); therefore, the mutational properties and rates of formation of these smaller variants remain unknown."
So now you are going to explain to me why unicellular eukaryotes need that type of design?
I don’t know what you mean or what your argument is. Could you try to state both your claim and your argument for it more clearly?
But why should the pattern of that re-use be a nested hierarchy? Why should those re-used components differ among species in a way that fits the same nested hierarchy? And why isn’t “as much as possible” not “in every case”?
That isn’t my hypothesis. That’s your strawman hypothesis. I expect there to be changes because mutation happens, despite your attempts to deny that it does. Anyway, as I have perhaps mentioned, the source of variation isn’t relevant. Why should that variation fit a nested hierarchy? You still haven’t answered the question, after three attempts to dodge it.
John Harshman,
Sal’s flower shows a partial nested hierarchy of genes. This is the pattern that I would expect from design.
Again:
Because a design based on the transcription translation mechanism 4 nucleotides 20 amino acids would easily explain the data in Sal’s flower. The reuse of key components (genes) across generations. This pattern points to design and not inheritance.
Again:
Again: It does not as you pointed out with your trees on October 13. It fits a partial nested hierarchy that supports the pattern of a design strategy.
1. It’s better for them.
2. It’s better for their evolution.
How? Please do it then, explain it using those facts.
Why?
Rumraket,
The use or reuse of a DNA sequence is a design decision
With design the skipping of generations is not a problem. With inheritance (excluding the addition of new genes) I would expect genes to move forward from the earlier ancestor (fish, birds and mammals) and be present in the animals that share a common ancestor like mammals.
Yes.
Why doesn’t “design” skip generations?
Why must you repeat this garbage endlessly? If you could support it, I suspect you would.
Glen Davidson
Why would you expect that pattern from design?
Why should that variation fit a nested hierarchy? You still haven’t answered the question, after three attempts to dodge it.
Why would a design explain Sal’s flower? How does a design explain Sal’s flower? Whatever does “reuse of key components across generations” even mean?
No, what I pointed out is that it fits a nested hierarchy very well with only a very few exceptions. Here, let me quantify that for you: out of 27,607 genes in the figure, 10,660 are present in all species and would fit any tree. Of the remaining 16,047, 16,726 require only one change, i.e. fit the tree perfectly, and 221 require 2 changes. So what you’re saying is that you are going to believe the 221 and disbelieve the 16,726. And yet, there is an obvious reason for the great discrepancy in numbers: one event is much more likely than two independent events. But that only makes sense if there’s a tree.
No, you still haven’t answered the question.
colewd:
Jesus H. Christ.
I think we’d have better luck teaching this to Byers than to Bill.
John Harshman,
2059 genes are common in Zebra Fish Humans and Mice but not chickens. 2059 genes that inheritance could not preserve in one case and preserved in another. The design argument does not have this issue to deal with.
colewd,
And it was trying so hard! I wonder what went wrong.
The design “argument” has no issues to deal with, since design predicts nothing. That isn’t a virtue.
Chickens have lost 2059 genes present in the common ancestor of the four species. How is that a problem? Please try very hard to be clear. Harder than before.
I guess it’s best to plan ahead:
That is an excellent choice of RNA polymerase, sir. With that key component you can convert your model to multicellular at any time. If you take on the splicing apparatus as well, you are all set when the new line of animal designs comes out.
Yes, it is comes with DNA OS installed.
John Harshman,
Design predicts the repeatable processes we see in the cell.
-transcription
-translation
-splicing
-cell division
-cell regulation
.
10% of the genes lost in one lineage and preserved in another. How do you explain this based on inheritance?
The problem is that you don’t recognize there is a problem.
And yet Archaea use RNA polymerases that are similar to those used by eukaryotes:
You will undoubtedly present me with a good design reason for it. But maybe it would be nice if you concoct one after checking the actual biology.
How does design predict that?
I don’t. Again, changes are not due to inheritance. The pattern of distribution of characters is explained by inheritance. Genes, once around, are inherited unless lost. Once a gene is lost, its absence is inherited (and is so unlikely to be reversed that we don’t have to think about that). Loss is explained by mutation in the absence of selection.
I conclude that you are incapable of saying what you mean, knowing what you mean, arguing for your position, or understanding the arguments for my position. That makes it hard to get any real discussion going.
If you really want discussion, use the Ignore feature.
DNA_Jock:
keiths:
DNA_Jock:
Because it’s the central point I am trying to make. We all agree that the evidence is fatal to ‘common design’. My point is that it’s also fatal to guided evolution. Guided meteorology (aka the Rain Fairy) is ridiculous, even though it’s logically possible for it to produce meteorological evidence of the kind we see. Guided evolution is ridiculous for the same reason, even though it’s logically possible for it to produce biological evidence of the kind we see.
Now for some debate advice. You tried to condescend above by writing
Yet it was you who failed to comprehend what you were reading, bizarrely concluding that I regarded the four of you as closet IDers who were arguing for guided evolution.
It should be obvious that your attempts at condescension will fail if you are the one who is mistaken, and not your opponent.
Put somewhat differently, you are more likely to succeed if you condescend downward. You are trying to condescend upward, and it’s splatting in your face.
DNA_Jock,
That’s incorrect, and it’s the same mistake that John made here:
Rather than reinvent the wheel, I’ll quote my response to John:
keiths,
There are no additional entailments for guided evolution.
Here’s another:
And:
Let me provide some perspective here, because I sense some bias: The vast majority of eukaryotes are single celled organisms. Whatever features eukaryotes possess as a group, they are unlikely to be requirements for multicellularity or developmental processes.
Regarding unguided or guided evolution. Seems clear that adaptation and other non-random processes are guided by the environment. The difference between a theist and an atheist who agree that evolution is a reasonable theory that fits observation is that the theist believes that the universe was created by God to achieve his ends and the atheist doesn’t have a reason for why things are why they are. No explanation vs unfalsifiable explanation.
Alan,
We are using ‘guided evolution’ to refer to evolution that is guided by an intelligent agent.
Guidance usually implies a trajectory that is made steady by adjustments. Probably the most simple guidance system that has parallels in biology and the man-made world are temperature control and thermostats. If the environment gets cold a heating system comes into play and if the environment gets hot a cooling system comes into play.
A monarch butterfly navigates over long distances correcting for wind or whatever along the way. That is guidance.
In terms of developmental biology, there are a variety of self-healing and alternative developmental pathways to correct for changing environments and damage to the system. Development is guided, internally and mechanistically.
For evolution then to be guided, there are at least two or three schools of thought. One is that it works like development, it is somehow mechanistically programmed, front loaded. The other that is close in idea is that it is a physical law. That idea was promoted by Leo Berg (Dobshanzky’s mentor). That idea doesn’t work so well because we now know physical law, like tornadoes going through a junk yard, is against such self-organization. The third notion of guidance is external as in “God guided” or “space alien guided” where the course corrections toward a goal a imposed from an intelligent external source.
Approximating who believes what and who believes neither:
1. Internally guided: Michael Behe, Mike Gene, Leo Berg, maybe Gunter Bechly
2. Physical law guided: Leo Berg, Michael Denton
3. God or Space Alien Guided: Theistic evoltutionists, Directed Pan Spermists
4. Neither: typical creationists and ultra Darwinists (evolution didn’t happen, or evolution is unguided)
Naturally guided, imho, is a bit of an oxymoron. It’s like saying a tornado guides the destruction of a house. Dawkins says natural selection guides the evolution of complexity. I would say that what Dawkins and Darwin call “natural selection” isn’t what actually happens naturally, therefore it is a misnomer and a mis-label.
To select means to interevene against natural tendency or where there is no inherent tendency. Tornados going through a town don’t select how to dismantle something and much less will it select how to assemble something. One needs guidance to select against natural tendencies like selecting velocity and position of material objects to put them in configurations that go against what is natural (whereby “natural” means ordinary expectation, not as in “natural vs. supernatural”). An illustration of a configuration that goes against what is natural (as in ordinary) and therefore needs guidance to make it happen:
You picked a house of cards as an illustration of guided evolution? 😀
It predicts none of these. If you want us to think otherwise, actually tell us how it predicts those. Or anything. Can you do other than point to things and say that they were designed, or that they predicted by design? It’s very tiresome and stupid for you to just chant the same nonsense over and over again.
.
They’re not “preserved,” they’ve evolved, generally being more different the further back the divergence was. How do you explain that by “design”?
Why would the “same genes” be substantially changed if a “designer” were out there doing it?
How do you explain “common genes” at all? And can the “common design” claptrap, you haven’t begun to show anything at all about things being “commonly designed.” You simply ignore the vast amount of data that indicate a lack of “common design” in characters that appeared after divergence.
You can’t tell us why birds and bats have “common design” as far as being tetrapods is involved, and lack “common design” in the adaptation of forelimbs to being wings and other later-evolved structures. That is what is expected of evolutionary mechanisms, not design mechanisms.
The problem is that you assert “problems” that you neither understand nor express clearly enough for us to understand how you’re so confused. The bigger problem is that you simply ignore the evidence of derivation and how organisms are not “commonly designed” past the point where derivation of characters becomes impossible (or at least highly unlikely).
Common design by humans means that the latest products may share the latest innovations, regardless of lineage. Common descent without design means that only the “innovations” prior to divergence are shared, with the latest “innovations” not appearing in unrelated lineages. It’s a huge difference, one that you avoid by merely restating your evidence-free design claims without acknowledging–or apparently, understanding–what the issue even is.
Glen Davidson
I admit that I felt a little bad about accusing keiths of failing to read for comprehension.
Jock:
[note the use of quotation marks — I am quoting keiths]
keiths
Jock:
[that’s English for “I don’t believe you”]
Jock quotes keiths thus:
[note emphasis on that phrase, present in Jock’s original quotation]
And asks:
[meaning: if you are not claiming that we are making this silly mistake, why did you mention it? ]
To which keiths replies
Oh dear.
No, keiths does not have any problem reading for comprehension.
So when keiths finishes his post
there’s no (situational) irony whatsoever.
When I pointed out to keiths that
I included in my comment four embedded links to help him out.
How does he respond?
He quotes his earlier comments, regurgitating his Rain Fairy argument-by-analogy.
keiths, I encourage you to go back and re-read this thread, open to the idea that other posters might have a point.
I admit that I was originally thinking of a guider who introduces specific mutations, and was only considering the goal-directed effort needed to destroy the ONH in that particular case, but, as Rumraket and Zachriel have pointed out, there are entire categories of guiders (matchmakers and cullers) who do not degrade the phylogenetic signal at all.
None of those add any explanatory power, they’re untestable, so we’re still left with good old plain evolution
That’s just you assuming your conclusion (that nature can’t do it on it’s own), unsurprisingly, nothing new under the sun.
The same vacuous negative argument rehashed over and over and over again.
Cut the crap and tell us how we can positively tell apart guided and unguided evolution, and while you’re at it, try common design once and for all.
We want actual explanations, something testable, no analogies or crap like that
Who’s we?
I’m pointing out that evolution is a process guided by the niche. If the universe is created by God, he created niches and he guided evolution (maybe even intelligently). What evidence disproves this hypothesis?
As I promised, I began working on an OP on trilobites and I just thought I’d site search for previous references to trilobites and I find Vincent Torley wrote an OP just nine months ago as a rebuttal to a post by Cornelius Hunter. Vincent concludes his OP with:
We have seen that there is excellent genetic and biochemical evidence for the evolution of all animals’ eyes from a common ancestor, 700 million years ago. We have also seen that there are plausible fossil precursors for trilobites, and several examples of trilobite evolution in the fossil record. Finally, we saw that the most sophisticated trilobite eye, which is confined to a single lineage, did not appear until 36 million years after the first trilobites emerged, and that it seems to have originated from a simpler trilobite eye via the process of paedomorphisis. Whatever one might think of the case for evolution, I do not think that trilobites constitute any special difficulty for the theory.
I’ve no excuse for saying I was unaware of the OP as I see I commented in the thread. I see he has already covered several points I planned to include in a new OP. I see you commented too, Bill, though the OP did not seem to generate much interest in trilobites amongst our members. It might be simpler to feature Vincent’s post rather than do a “remake”. I see he even mentioned Naraoia.
😀
keiths knows how. Ask keiths.