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.
stcordova,
I’m afraid I don’t quite get the logic of taking genomes that are (say) 95% similar, and saying that the 5% ‘orphan’ difference proves they weren’t commonly descended. You can’t even spot the differences if you can’t find areas of alignment. I realise I may have missed something.
You are not alone sir. Nothing Salvador has written undermines common descent.
Whoops. Where did the chloroplasts go? What do creationists have against plants, I wonder?
Doofus
http://www.vendian.org/envelope/TemporaryURL/what_is_oom.html
Doofus squared
https://www.merriam-webster.com/dictionary/order%20of%20magnitude
Sal, the questions was “Why is there a nested hierarchy of life?”, not “Why don’t you believe in naturalistic evolution?” Try again. When I respond to your posts, it’s a critique of what you said. You have to respond to that critique, and just repeating what you said before is not a response. Nothing you say below is a response.
Yes it is. If you want to claim that feature X couldn’t happen naturally, the logical position would be to adopt the Behe position and claim that god stuffs the occasional innovation into a lineage. That explains the nested hierarchy and the various Xs, while your idea only explains the Xs and leave the hierarchy inexplicable. (Probably should have put “explains” in quotes.) The cause of new features is not relevant to the nested hierarchy of those features.
No, that isn’t why. Phylogeneticists rightly don’t care about the engineering difficulties because they are irrelevant to inferring phylogeny. You could as well say that phylogeneticists don’t appreciate the reason that birds have feathers. That reason is irrelevant to phylogenetic analysis, but the presence of feathers does help us discern that birds are theropods.
I do not understand what, if anything, this statement means, or is supposed to be responding to, or has to do with common design as an explanation.
No, that explains nothing. Why should a pre-defined plan follow a nested hierarchy, either within the taxon covered by the plan or outside it? (Did Owen really mean “plan”, as something determined by an intelligent being, or just an archetype, not necessarily designed? And why should we care what Own thought anyway?)
That’s because you have never explained what the problem is.
That, incidentally, seems like word salad to me.
What “orphan systems” do any of these have? You have mentioned some candidates for eukaryotes, but what about the rest? Why are these systems arranged in a nested hierarchy, with mammals, trees, and birds all eukaryotes? Why are there apparently plans within plans?
Incidentally, “tree” isn’t a taxonomic term at all. It’s a habit (and that is the technical term) adopted by many separate lineages in different families and phyla of plants. I say this to point out your gross ignorance of biology.
Does it? What is a “kind”? Are birds a kind? Are eukaryotes a kind? Please explain what you mean. Are there kinds within kinds? If not, what can this possibly have to do with the question of common descent vs. common design?
But of course a bird does follow a fish plan, only we call it a vertebrate plan or perhaps a gnathostome or osteichthyan plan. Neil Shubin has a whole book about that, Your Inner Fish, which you might want to read.
Forcefitting? I thought we were all agreed that there was in fact a nested hierarchy of life and merely disagreed on the explanation. Are you walking that back now? Are you claiming that giraffes are not eukaryotes? Are you claiming that elephants are not vertebrates? The jumble is all in your head. You seem stuck at the kindergarten level of taxonomy (“doggie!”, “kitty”, “froggie”) and seem to know nothing about modern taxonomy, let alone phylogenetics.
Common design doesn’t define nested hierarchies. You have not in fact said anything about nested hierarchies. You have not said anything about orphan systems either, other than a few vague mentions, one of which was chromatin (and I assume you have not yet taken the hint about archaeal chromatin), nor were even 19th Century taxonomies based on orphan systems. And phylogeny isn’t a jumbled mess.
None of that post had anything to do with common design. You start by attacking the adequacy of natural processes, add a few snide comments about phylogenetics, and wave your hand in the direction of unspecified “taxonomic hierarchies” and “orphan systems”. We are left with the original question, which you haven’t addressed at all: why is there a nested hierarchy of life?
It explains, most conveniently.
Just-so perfectly.
Glen Davidson
10x Doofus!
Poor phoodoo writes:
Any bets on how long it will take before phoodoo realizes that he just shot himself in the foot?
Alan, to Sal:
You haven’t received the gift of the Holy Spirit, by which anything, no matter how irrational, will seem to make sense.
Any bets on how long it will take before phoodoo realizes that he just shot himself in the foot?
keiths thinks a range means a field where buffalo roam.
keiths:
phoodoo:
phoodoo, dear, a number within that range is of the same order of magnitude as the original.
You wrote:
If the two numbers are of the same order of magnitude, then the second one is not off by an order of magnitude. Obviously.
Now do you see why there’s blood coming out of your foot?
keiths,
No keiths, and I just gave you an even more clear explanation that an order of magnitude CAN be used to mean 10x a value but it can also be used to mean 2x a value. Or 3…
No, even then it still makes no sense.
phoodoo,
The definition that you supplied:
And of course, that is the definition that scientists and engineers use, which is why people laughed when you wrote:
Swallow your pride, phoodoo. You made a mistake. We corrected you. It’s happened many times before, and it will no doubt happen many times in the future.
keiths,
You didn’t understand this? It doesn’t have to mean 10x keiths. An order of magnitude is a very imprecise term, for the exact reason that we are involved with a wide range of numbers in which we don’t know the exact number. A range.
THAT is the whole point. We have NO IDEA how old humans are. We can be 2x off, we can be 3x off, we know nothing. That is what I was writing. It wasn’t about an exact number, it was about the fact that we can be so wrong, as to have zero meaning about what our guess is.
Epistemic probabilities to the rescue!
stcordova,
Depends what you mean by ‘chromatin’. They don’t have histones. There are DNA binding proteins, but they are different from those in nuclear chromatin. But TFAM, for example, has homologs in … well, bacteria. And …
http://cshperspectives.cshlp.org/content/5/5/a012641.full
phoodoo,
That’s why people laughed at you. You used “off by an order of magnitude” to mean “way off”, when we knew that it had a technical meaning to which you were oblivious and which did not fit the situation you were describing.
Not to mention the fact that being off by a factor of two does not amount to knowing nothing or having NO IDEA of how old humans are. Obviously.
It’s not even a factor of two anyway. 200K vs 300-350K
Phoodoo will have us believe he understood orders of magnitude all along. No dice. He just spent weeks trying to find something that might make him look less stupid. No dice
dazz,
Or maybe 3x or 4x..but not 6x times right? Or sure, why not.
Dude, you’re fucking retarded, deal with it
one of the errors of evolutionism and its acceptance so easily WAS the lack of imagination to have other options.
Seeing likeness in biology convinced too quickly folks about a common origin after it was proposed.
The option of likeness in biology from a common design would do the trick. with details.
Never does one need see common descent as the only option for likeness in biology.
Its a line of reasoning and likeness in biology is not evidence for common descent. Just a line of reasoning. Other lines are here and another reason why evolutionism is losing and will lose soon enough.
What do you have against retarded people?
Mung,
At least I am not blind; although Alan probably does have a heightened sense of touch.
phoodoo,
But have no fear, Lizzie will be storming in on her white horse any day…
Wait, this just in, sad news, her horse contracted Equine encephalitis. But don’t worry, SHE WILL GET ANOTHER ONE! Just hang in there Alan, help is on the way soon.
An army marches on its stomach.
I predict she doesn’t show up and stick around. Maybe another 8 months before another fly-by.
Perhaps if we start spewing anti-muslim hate speech Alan will complain again. For now hate-speech is ok, unless it’s racist. LoL.
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ETA
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Reminder to readers: Alan doesn’t follow the rules.
Because it was designed that way. This is like asking why there is a house of cards somewhere. A house of cards is built for the designers amusement many times. For all we know the nested hierarchy was built so that evolutionists could make fools of themselves and God could laugh at their willful ignorance of problems with evolutionary theory like spliceosomes and spliceosomal introns. Maybe he’s entertained when evolutionary biologists glory in their belief they are related to monkeys.
Common descent fails as an explanation unless you add miraculous transformations along the way.
I said it in another thread, to maintain a tidy phylogenetic explanation of genes, you have to overlook the poof of splicesomal introns.
Let X represent and exon and i represent a comparable size section of intron. The supposed common ancestor of a prokaryotic and eukaryotic gene looks like:
XXXXXXXXX
but the eukaryotic gene looks like
iiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiii
That’s a poof, and a non-trivial one to boot, because it require special machinery like splicesomes composed of over 300 proteins to make this possible. How does phylogeny explain the origin of such complexity. It doesn’t, it is a non-sequitur to assert this.
You think I’m just complaining, Gerd Muller has this to say:
Common descent requires poof, to argue otherwise is to just assert blind faith belief something as complex as a spliceosome is an ordinary expectation over time.
I think you should stop assertig phylogenetics methods solve the problem of common descent. It doesn’t because the problems of common descent involve the formation of orphan systems, and phylogeny can’t explain such orphan system because their is no trace of their ancestors.
If their is no evidence of ancestor, and the feature is fairly complex, that is evidence against ordinary evolution. At what point is something extraordinary deemed statistically miraculous? If you refuse to admit the possibility of the miraculous, then well, even if a miracle did take place, you’re epistemology guarantees you’ll be on the wrong side of truth.
So what is the cure for the problem? You’ll insist unless you see a miracle with your own eyes, unless you see the Creator with your own eyes, you won’t believe in miracles. Fair enough, but then at that point you’re admitting your at the Creator’s mercy and assuming he really wants to help you along on YOUR terms. For all we know, God might be content to make fools of people who keep insulting his ingenious designs which also reveal his wrath, and he won’t show up until judgement day after they’ve spent their lives chasing after theories that are demonstrably at variance with the problem of complexity.
And it is revealed in the form of the cruel designs in nature:
This is a picture of what Darwin was speaking of:
https://youtu.be/ziUdOdHKpk8
These are the pictures of designed cruelty which Jesus alluded to:
“‘where the worms never die and the fire never goes out” Mark 9:48
If God is the designer, he can design worms like the one Darwin was so horrified by, and he can design worms to torment people for eternity.
That is the design of biology. It reveals ingenuity and the wrath and power of God. It’s also designed to let people who want to believe in evolution just enough rope to hang themselves. But don’t complain on judgement day you weren’t given clues common descent was wrong. You have such evidence in things like spliceosomes. You’re wanting the Designer to prove himself to you, whereas it could be the Designer is demanding you prove yourself to Him, that you are willing to accept His mercy and consider that maybe the world is designed and that wrath is upon creation.
But if you want to believe in universal common ancestry, that’s is your God- given choice, but you can’t say on judgement day that problems such as spliceosome weren’t pointed out to you.
Splicesomes and spliceosomal introns and other complex orphan systems are part of a nested hierarchy not consistent with ordinary common descent.
I refer readers to this video showing the two systems of replication especially the one processing the Okazaki fragments.
Common descent doesn’t explain this. Where is the mechanistically feasible ancestor of the Okazaki fragment processing system? One might cite Rolling Circle Replication (RCR) but then to the extent RCR uses Okazaki-like fragments, one is stuck with the same problem.
Because God wanted to provide a framework, a background, against which evolution could be tested, so that people would be able to see that evolution is false.
Can someone explain to me what Sal is going on about Okazaki fragments for? Are they new to eukaryotes and not found in other forms of single-celled life?
Must not question authority, might be punished
Funny thing is you seem to think God wants you to be ignorant.
He created monkeys too So humans come from the same designer and with common design. Sounds like you are just an another version of monkey design
Cordova gallop.
Poor God, if this is what His believers think of Him.
That’s all you have? Even you must realize that that “explanation” is worth nothing.
You repeat yourself, and it seems you are becoming a bit testy, as the God you apparently make in your image also seems a bit testy.
Agreeing for the sake of argument, why then don’t you accept common descent with occasional miracles?
Yes, you said it. But why should anyone believe it?
It isn’t clear what you mean by “the problem of common descent”, but I think you actually mean “the problem of particular innovations”. Nobody said phylogenetic methods solve the problem of particular innovations. They just tell us that common descent happened. But they can help solve the problem of particular innovations too, as long as some intermediate forms are preserved.
Again, all that is irrelevant to the evidence for common descent. So we’re back to the original question, which you still have never made a serious attempt to answer: Why is there a nested hierarchy of life?
No argument there, but what does that say about his character? Is he not evil? Don’t you worship an evil god? Are you perhaps suffering from Stockholm syndrome?
No, Okazaki fragments were first discovered in bacteria (E. coli). Don’t know what his point is.
Because I think there are too many orphan systems, so we’d have to accept many miracles, but then that looks like special creation.
If rea evolution is reductive, and not constructive, then that would strengthen the claim of special creation.
Next, the MRCA (most recent common ancestor) of each species lines is also too recent. Can you name one species where the molecular clock on its genes says its a billion years old? No. How about a half a billion? Not that I know of.
Next, I was impressed by Jeason’s work on speciation. I want to read up on that more.
stcordova,
By implication, you accept that the molecular clock is accurate.
But special creation doesn’t explain the nested hierarchy of life, remember? You need a hypothesis that explains all the data, and common descent with tweaking by Jesus explains (to the extent that miracles explain anything) all the orphan systems (which I have allowed for the sake of argument) as well as the nested hierarchy.
What do you mean by “rea evolution”? What does it have to do with the miracles we’re positing to account for the putative orphan systems?
So coalescence is another bit of evolution you don’t understand. I’m not surprised. You must understand that drift alone removes variation from a species, and selection can speed that up considerably. Both of these forces conspire to make the MRCA of any given gene much more recent, on average, than “billions of years”, or even the time of origin of the species itself. The main exception would be selection favoring diversity, which can maintain variation for quite a long time, as for example in the HLA alleles shared by humans and chimps.
I have no idea what you’re talking about there. Cite something and/or explain.
Really? How does that happen if individuals of the species are isolated geographically? 🙂
This is getting more and more interesting 🙂
I have no idea what you’re trying to hint at there. Please explain. And could you please start using the “reply” buttons?
John Harshman,
Then you’re the one who doesn’t understand. Not me. 🙂
stcordova,
deliberately?
It could be more than one . It might be you don’t understand what you are talking about and John might not understand what you are talking about either.
So replication happens on the leading strand and the lagging strand. Do you think the first creatures duplicated only the leading strand. If yes, then how did the lagging strand processing emerge with Okazaki fragments (or Okazaki-like fragments in Rolling Circle Replication).
If the Okazaki fragment processing (or Okazaki-like processing) happened after evolution of the leading strand replication, then one is faced with a bit of a functional gap as to how it arose. It would be common descent made possible by a miracle.
If no, then one is assuming both leading and lagging strand replication came into place simultaneously. Well, that’s also kind of miraculous too.
Phylogenetic methods then become a formal way to ignore problems with common descent, which makes it kind of flimsy since it is a proof of common descent via willful avoidance of mechanistic problems.
Oh, and another thing, we have creatures with Rolling Circle Replication, and then others with the replication shown in the video I provided. How do phylogenetic methods explain the emergence of one from the other or their independent origins without implicit appeal to some sort of miracle?
No it does not, if individuals of the species are reproductively isolated. Agree or disagree.
Of course I can’t see how you’d disagree because if two groups of creatures were reproductively isolated, we wouldn’t expect the two groups to be identical after umpteen generations due to drift would we?
The problem I was alluding to is that as I scanned some data on species we presume to be ancient, each time the researchers were astonished the MRCA (most recent common ancestor) of the species was a lot younger than they thought. There wasn’t enough INTRA-species divergence.
This is a message I circulated two years ago in creationist circles, but which I couldn’t pursue further:
Yes, I don’t understand. What are you trying to say? The polite thing to do would be to explain.