Dr. Winston Ewert put forward his module hypothesis, but I put forward an alternate module hypothesis at the domain and motif level of proteins. It is based actually on papers by evolutionists who have pointed out that the problem of “Promiscuous Domains” remains an unsolved problem in evolutionary biology.
When I put Promiscuous Domains on the table in the Common Design vs. Common Descent thread, the TSZ Darwinists ignored the problem and then declared victory. I viewed their non-response as evidence they didn’t understand the problem and/or preferred to ignore it.
Perhaps pictures are worth ten thousand words. From the NIH, that great source inspiration for the Intelligent Design community, we have the CDART database viewer.
From the CDART viewer, I provide a few of the thousands of diagrams that show the promiscuity of protein domains. The diagrams below show the classical zinc finger ZF-C2H2 “ZF” domain and the Plextrin Homology “PH” domains. Note how the location of domains is “shuffled” to different locations in different proteins. It’s as if proteins are made by different lego-like parts in different order and position. My preliminary look into small 4-amino acid motifs that are the target of phosphorylating kinases suggests the the problem of promiscuity goes all the way down to small motif levels.
Such promiscuity is more consistent with common design than common descent.
Click to Enlarge Classical ZF-C2H2 Zinc Finger Page 5
Click to Enlarge Classical ZF-C2H2 Zinc Finger Page 157
Click to see all CDART Classical ZF-C2H2 Zinc Finger Architectures
Yes, they can. But organisms can also be arranged in a single non-arbitrary way, while the bible books can’t. There is no nested hierarchy of Genesis one.
Is there really any ambiguity here? “Discoverable” means something that really exists that we are capable of finding. I don’t know what you mean by “reality need not be tied in any way to human experience”, so I doubt I have contended any such thing.
Yes, true. But this is an invalid way of discovering nested hierarchy in data, as the hierarchy is wholly imposed by your particular choices. This is not true for phylogenetic data; nothing is imposed, only found.
That isn’t actually true. The introduction of non-heritable characters introduces noise and may end up making the hierarchy non-discoverable by that data set. But such a data set will not find an alternative hierarchy unless you carefully pick only those traits that fit your previously chosen hierarchy. There is only one discoverable hierarchy of life, and if you don’t pick data that are overcome by noise, you will find it.
No, we can do it using genetics. Do you know nothing of science?
The circularity is in your imagination.
Then you can demonstrate this by pointing to published work where it was done like that can you? Ever been wrong?
You need to define non-arbitrary. Are you saying that there is something in your chosen arrangement that is superior to the others in some demonstrable way. I love to heat that case
sure there is,
You have fish of the sea and the birds of the heavens and livestock and creeping things. Each of these separate groups nest into the group of things that man is to have dominion over. (Gen 1:26)
and you have separate groups labeled vegetation, plants yielding seed, and fruit trees. that nest into the larger group of plants placed in the garden. (Gen 1:11)
Doesn’t “finding” involve belief on your part? What exactly connects your belief to reality?
I disagree my hierarchy was found not imposed. I found that grey squirrels and grey foxes has lots of things in common. The similarities existed before I noticed them and would exist if I never noticed them.
When it comes to phylogenetic data there are times when accepted relationships are later abandoned.
Are you saying the incorrect relationships were “found” and later “lost”?
peace
what you call noise. Another person would call signal.
I did not have a previously chosen hierarchy when I grouped grey squirrels and grey foxes.
Instead I was thinking about the cool climbing habit of grey foxes and realized it had more in common with grey squirrels than red foxes.
what do you do when the hierarchy constructed with genetics does not match the one you constructed with phylogenetic data?
peace
I can point to a “published” comment by John Harshman in this very thread where he dismissed the climbing habit of grey squirrels and grey foxes as not sufficiently heritable. Coincidently of course, accepting that particular trait would put a monkey wrench in his chosen hierarchy
peace
I’m wrong all the time. I was wrong just this morning
I usually don’t comment here unless I’m pretty confident in the position I’m expressing.
peace
Sure. Please consider gray fur as a trait. That’s fine. However, when looking across all biological traits, a single nested hierarchy is evident. Even a cursory look at the biological characteristics of red wolves and gray wolves would find more similarities than of gray wolves and gray squirrels — even if they both climb trees.
The farther one strays from the original exposition of common descent, the more bizarre the arguments. Darwin’s best sources of evidence for common descent were plant and animal breeders, and known kinds and types of variation.
Not should be ,are.
Why, because things are discovered.
Darwin’s primary evidence for common descent was the nested hierarchy. Evidence from breeders and natural variation was support for natural selection.
How does the divine objective nested hierarchy place them? Grey wolves closer to squirrels or red wolves?
The very question reveals filth’s commitment to abject subjectivity. Someone who asks whether a worldview allows for something to be the case cannot complain about anybody else’s subjectivity.
The point is the nested hierarchy under consideration is not a bunch of abstract Venn diagrams.
It is genealogy.
It is an extension of a method now used by police to locate suspects when there are no witnesses. Find a bit of DNA and start looking through popular private DNA databases. Find a match and start looking at relatives.
This is a bit scary, but it works.
Opponents of common descent are applying the wrong standard. they are talking about proof where the correct standard is strong support.
The other leg of support is the kind of observation Darwin talked about. Direct observation of descent and variation.
Truer words were never spoken. All the time.
Ah, but does confidence correlate well with correctness?
You seem to understand very little. You assemble a nested hierarchy by picking one character, dividing based on that one, then picking another, further dividing based on that one. That’s not discoverable; that’s imposed. Or you pick a character you find interesting and then pick a second one specifically to support that first one. Again, not discoverable but imposed. A real nested hierarchy is forced by the data; data not specifically chosen for agreement still agree.
That Genesis 1 supposed hierarchy isn’t even a hierarchy. It’s a one-character division, and the characters considered even in pairs, don’t produce a hierarchy. Fruit trees are vegetation, and they yield seed. It’s not even an attempt at classification, much less a nested hierarchy.
I found this wonderful diagram on amino acids. Many domains are not defined by exact amino acids but amino acids of certain properties put in the right places. Here is a helpful diagram as some of the motifs (like the kinase targets) are by class of amino acid, not exact amino acid:
https://amit1b.files.wordpress.com/2012/09/venn-diagram.png
This will be helpful in doing feasibility of evolution calculations.
Actually you probably won’t be surprised to know that I think the actual objective nested hierarchy is somewhat close to the one that you get from phenotypic data.
What you are calling “discovering” I would characterize as general revelation. The difference would be my emphasis on God’s gracious condescension to allow us a glimpse into his mind on this subject. (thinking his thoughts after him)
peace
Data is not a person it can not force anything.
Rather we choose to weight certain data highly and designate other data as noise.
You are reading a modern botanical understanding into the text.
here is a commentary from the 19th century
quote:
Grass, herb yielding seed, fruit tree bearing fruit. – The plants now created are divided into three classes – grass, herb, and tree. In the first, the seed is not noticed, as not obvious to the eye; in the second, the seed is the striking characteristic; in the third, the fruit, “in which is its seed,” in which the seed is enclosed, forms the distinguishing mark. This division is simple and natural. It proceeds upon two concurrent marks – the structure and the seed. In the first, the green leaf or blade is prominent; in the second, the stalk; in the third, the woody texture. In the first, the seed is not conspicuous; in the second, it is conspicuous; in the third, it is enclosed in a fruit which is conspicuous. This division corresponds with certain classes in our present systems of botany. But it is much less complex than any of them, and is founded upon obvious characteristics. The plants that are on the margin of these great divisions may be arranged conveniently enough under one or another of them, according to their several orders or species.
end quote:
from here
https://biblehub.com/commentaries/genesis/1-11.htm
peace
OK so “discovery” is simply lucky accident in your worldview there is no reason we should expect it, correct?
How do we distinguish actual “discovery” from seeming
“discovery” based on misleading data or biased interpretation?
peace
“Strong support” requires an objective standard.
You need to be able to say the alternative to common decent is much less likely given the presence of the objective nested hierarchy.
I just don’t think that case can be convincingly made given your starting position.
It has been granted that there are no entailments that would distinguish common decent from it’s alternative special creation.
I would question the whole idea of “objective” given your worldview.
I am really interested in the new term discoverable. What exactly is discoverable and what is not?? How can tell the difference??
peace
Since you have shown (or at least claimed) that you understand the usages of metaphor, this can be nothing more than obfuscation on your part.
It isn’t a matter of weighting. The congruent signal will generally overcome the randomly distributed noise. Signal and noise are not determined in advance but recognized after the fact.
I’m reading the ordinary definitions of words into the text. Now what you have in your quote is merely special pleading, fitting the facts to the need. And, as I’ve pointed out before, it’s choosing to pay attention to at most two characteristics and ignoring all the others. That isn’t a real nested hierarchy even if we accept your definition of the categories. And hey, what’s coriander/cilantro? Is it an herb or a “plant bearing seeds”? What you have produced is a poor example of an artificial nested hierarchy, which we may contrast with the real nested hierarchy in which fruit-bearing trees, seed-bearing plants, and herbs will appear in the same families.
In practice, does this general revelation differ in any way from what we call discovering? How would we tell whether we were doing one or the other?
I imagine that FMM is going to say there is no such thing as discovering, it’s all revelation.
FMM is just Sal without the pretense of doing science. He’s got a set of pre-existing beliefs and will force everything into that shape. The idea that he’s wrong about the signal being imposed on the data rather then being discovered will never take root with him, why would you change your mind on something if you are utterly convinced you already know the answer?
Again you need to demonstrate a factual basis for the metaphor. You have not. Explain what you mean to say.
The signal is not a person it does not overcome anything.
It merely sits there waiting to be interpreted as significant or ignored as noise.
“recognized” by finite biased humans with preconceptions and agendas.
What you are calling “ordinary” in in fact 20th century Americanized modern botanical science influenced definitions of English interpretations of ancient Hebrew words.
This yet another example of why your naive understanding of “data” is woefully inadequate and misleading.
peace
I’m so glad you asked. When you are dependent on revelation you are humble and recognize that you may be misunderstanding the message and as a result you seek to compare what you think you know with other more certain revelation you have received.
This sort of knowledge is a comprehensive whole and can’t be atomized or reduced to a single data point. You recognize that your knowledge is fruit of a relationship rather than your own individual efforts in a particular area.
Think about the difference between “discovering” that your wife does not like Chinese food and your wife revealing to you that she does not like Chinese food.
Knowledge in the former case is dependent on you and your ability to adequately understand your wife’s likes and dislikes. There can be no guarantee that what you think is a discovery is not in fact your imagination. It’s possible you will live your entire life being wrong about what you think you know. It’s possible that your wife doesn’t even have a preference when it comes to food.
Knowledge in the latter case is relational, it depends on your wife’s ability to share her preferences with you. All that is necessary is that you be willing to listen when she speaks.
It’s possible that you might have misheard what she had to say on this particular occasion but you can compare your conclusion with everything you know about her even things seemingly unrelated to food
And you can trust that if it’s important she will eventually let you know if you got it wrong.
I hope you can see the difference.
peace
what you need to do is explain how “discovery” is different from “being imposed”. What does the difference look like?
For example look at the following number sequence
90820188675309
Ive placed a pattern in the data. How can you ever know that you have actually “discovered” it instead of imposing your own pattern?
peace
You might try simpler patterns.
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, …
Is there a pattern to this string of numbers? Can all reasonable observers agree that there is such a pattern?
What about this:
Well of course all scientific knowledge is provisional, so scientists display the sort of humility you refer to. We just lack any comparison with any more certain revelation, whatever you mean by that. What do you mean by that?
Completely opaque.
Which of these is similar to what we’re talking about here, which is God revealing through nature? How can you distinguish God revealing through nature from science learning about nature?
Any normal person would have realized what I meant to say and certainly would not have explained to me that a metaphor is not literally true. You’re still obfuscating.
Now, regarding justification, you would need to learn something about how phylogenetic analysis is done. Do you know anything about the subject already? Have you ever looked? I invite you to try one of my publications. Would you like a link?
I’d like you to show just how my finite bias, preconceptions, and agenda have influenced my analyses of data. Read anything I’ve published and show me where the bias lies. Now, when I say that the signal overcomes noise, I mean that when analyzed, the data produce a tree congruent with the signal, not with the noise. And “noise” is an a posteriori judgment, not something we decide to ignore. You, on the other hand, ignore almost everything when you put gray foxes and gray squirrels together.
And your interpretation is better because why?
Says the person who thinks his fox-squirrel group is just as good as any other.
How do we distinguish actual “discovery” from seeming
“discovery” based on misleading data or biased interpretation?
peace
Oops
The “basic” subset intersects with the “charged” subset, but the “acidic” subset does not. There are two amino acids that are “charged” but are neither “basic” nor “acidic”. How can this diagram be “helpful” when it is definitionally incoherent?
When it comes to the nested hierarchy I think John Harshman would say that if a consensus of folks who study phenotypic data agree that it’s an actual discovery and can duplicate the grouping then it qualifies as actual.
I think that this is circular reasoning and all it really does is establish that the supposed “discovery” is popular and has not been falsified as of yet.
I’m certainly willing to be proven wrong here so I will await to see if he has better criteria for making that determination.
peace
I’ll take a different view. The nested tree is an invention.
However, it is a very likely invention. It isn’t one of those inventions where it is hard to see how people came up with it.
That’s not all the way to how John describes it, but it is close enough.
No, that’s not at all what I would say. But newton wasn’t asking you what I would say. He was asking how you would tell. As usual, you dodge.
Like the first person to see the Grand Canyon, the discovery is popular and it has been replicated many times and it has not been falsified as of yet.
Are you asserting that saying the Grand Canyon exists is an example of circular reasoning?
Or am I misunderstanding your argument?
My worldview is I am not sure why the world “should” do anything except exist.
Lucky is relative, it would be luckier if we were lots smarter and didn’t forget things and had a better knee design. If whiskey was cheaper.
While omniscience might be ultimately boring ,it would be luckier than what we have now, lots of stuff your can do with omniscience.
Then again you might be asking are there any possible ,beneficial ,advantage for an organism if it is aware of its surroundings?
A organism who could not learn by experience seems like it would be at a disadvantage competing with one that can.
peace
I would not say a “discovery” is the equivalent of being aware of your surroundings. It seems to me to require a more big picture perspective.
There is a huge difference between knowing it’s cold outside and “discovering” that temperatures in Maunder Minimum were below the expected normal range due to 4 separate volcanic eruptions in the tropics.
Don’t you agree??
peace
I thought I had just explained that
Among other things I tell if a supposed revelation is genuine by checking to see if it corresponds to other more certain revelation.
That works for revelation from God or my wife.
peace
No,
I’m saying that declaring I know “objectively” or “I discovered” that the Grand cannon is the result of millions of years of slow erosion because it’s popular to say that that the Grand Cannon is the result of millions of years of slow erosion is circular reasoning.
If all you mean when you say that the grand cannon exists is that folks you know agree on a particular location name in northern Arizona that is a different matter entirely.
It’s not the same as I’m understanding John’s use of “discovery” here
peace
This would be close to my own view.
The difficulty arises when you then declare your “invention” to reflect objective reality because simply it’s likely given what you understand right now.
I think that is where John’s confidence goes too far.
peace
If you were to see a phylogenetic tree, and let’s suppose you think it might be a revelation from God, what more certain revelation would you check it against?
Why would some revelation be more certain, it is the receiver or the transmitter?
I would check it against scripture and against general revelation I see in everyday life.
For example one thing that would make me doubt the objective truth of the nested hierarchy would be if I saw genetic isolation in extant species.
Since I don’t see that it provides supporting evidence that the nested hierarchy you like reflects reality.
Evidence that the nested hierarchy you choose is not the final word would include the observation that you get a different slightly different result when you look at genetic data than you do for phenotypical data. and that the tree has changed slightly over time and there are still arguments about it in places.
The only thing that would make me certain that a particular nested hierarchy was “objective” reality would be the impossibility of the contrary.
peace
neither.
I’m more certain that my wife eats than I am that she likes Chinese food.
It’s not about me or her it’s about the nature of the revelation
peace
Was that criteria revealed through general, scriptural or special revelation?
It was revealed by both general and special revelation. It’s simply the understanding that God is faithful and consistent and if reality is to be comprehensible it must reflect God’s nature in that regard.
If reality contradicted itself all knowledge would be impossible.
peace
So the more specific the revelation the more uncertain it is? You have proposed the an omnipotent God can make the objective truth known to you despite your own finite ,biased nature.
Why don’t all revelations fall into this class, wouldn’t it remove any question of subjective bias creeping in?
Am I to suppose by “general revelation” you mean nothing more than “observation of the world”? But isn’t that how scientists work?
That seems like nothing more than agreement that all scientific results are provisional, approaching but never attaining absolute certainty and capable of being overturned by future data. Have you abandoned your claim that your “gray animal” group is as good as any other?
How do you define “impossibility”? How would we decide that the contrary was impossible in any particular case?
No the more certain a revelation is the more certain it is. It has nothing to do with specificity. For instance I am certain that God loves me individually and died in my place.
That is pretty specific
Off the top of my head I’d say because if all knowledge was certain for everyone communion with God and reliance on and trust in him would not be necessary and I would miss out on the greatest joy in my life.
peace