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
No worries. I understand how having your assumptions challenged from a different perspective can be difficult. Have a great day
peace
Ok, God forgives our sins. How does this follow” Any nested hierarchy that God produces will be an objective nested hierarchy by virtue of ( God forgives our sins)?
Actually it would need to be not illogical and support your assertion that God is limited in His creative choices to objective nested hierarchies.
peace
Your smug, passive-aggressive attitude is one of the reasons it’s impossible to talk to you. Not the only reason, but it’s up there. “Peace”, my ass.
And yet so many people keep trying. I wonder why that is?
.
I think it’s, paradoxically, an urge to pierce his armor of smug, passive-agressive attitude, even though we all realize deep down that it can’t be done.
I don’t need to. You do it for me each time you pretend to be an unreachable idiot.
1. It wasn’t an argument, it was an explanation.
2. That looks as if your imaginary friend does not have enough knowledge and enough power to help you out understanding some very simple metaphorical language. Therefore your god is imaginary.
Again? That insistence doesn’t look as if your imaginary friend has enough knowledge and enough power to help you out understanding some very simple metaphorical language. Therefore your god is imaginary.
Or how about this one?
1. The god described by every presuppositionalist I have exchanged words with is not worthy of worship. Therefore it is imaginary.
2. A god that cannot even help you out understanding some simple metaphorical language cannot be worthy of worship. Therefore your god is imaginary.
3. You willingness to ridicule your own beliefs by not even trying to understand some simple metaphorical language show that you don’t feel like your god is worthy of worship. Therefore your god is imaginary.
Then maybe you can use those enormous ears to gather all that bullshit you spread around and shovel it back up your ass where it belongs.
Peace.
I can can forgive someone who has wronged me as well. That does not make me worthy of worship.
God on the other hand is worthy of worship because (among other things) he is sinless.
In order to be sinless ones opinion must be impartial, unbiased, unprejudiced etc.
That is the sort of thing plus omniscience will necessarily lead to objectivity
peace
Confidence is not smugness but it might look that way at times.
As for passive-aggressive here is the definition
quote:
being, marked by, or displaying behavior characterized by the expression of negative feelings, resentment, and aggression in an unassertive passive way (as through procrastination and stubbornness)
end quote:
from here
https://www.merriam-webster.com/dictionary/passive-aggressive
I certainly don’t have any negative feelings,resentment or aggression to anyone here (except maybe Keiths).
So I’m not sure why you think I’m passive aggressive.
I do try to be extra polite here simply because I know that this sort of discussion often rapidly deteriorates into name calling and insults and I would not want to be the cause of that happening if I can help it.
check it out
peace
I think I am pretty good at understanding metaphorical language.
The problem is you haven’t provided any factual basis for the metaphor.
As I explained earlier data can not interpret itself. Biased subjective human beings interpret data.
Human interpretation of data can never be “objective”. It’s simply not possible
Therefore in this context to speak of data “talking” or “leading” is simply incorrect and highly misleading. (metaphorical or not)
My comments were an effort to illustrate that to you. Sorry you missed it.
peace
for what it’s worth
I think that we would all be happier if you didn’t try and change other people here and instead spent our time trying to focus on ideas and the assumptions that drive them.
peace
Harshman has nowhere to go…He is either banned or on ignore on most blogs…Why would anybody waste his time, other than Sal, on someone who can’t reflect on the evidence he has been presented against his beliefs for over 20 years?
I will briefly touch on Topoisomerase’s own “promiscuous domain” problem, but first consider how difficult it might be to evolve Topisomerase Class 1 and 2 enzymes.
There are some important components, but here is an overview of the function of Topisomerase. It poses chicken-and-egg paradoxes:
To get hundreds of hours of free-of-charge editorial review of ideas and works headed for publication. In fact, I almost put John in the acknowledgment section of a paper I submitted to some venue, but given that he complained about being put in the acknowledgement of my AM-NAT paper, he won’t be acknowledged.
I get that…No worries…
Don’t forget that quantum biology is coming… It can override this stuff…as you know very well…
Have you had a chance to review my ” Does embryo development process require ID” OP?
Many ID people I know didn’t like it…I’m not sure why…
John’s posts are much appreciated here — and by quite a few of those who post here. For that matter, his posts at “talk.origins” were much appreciated back in an era before online forums and blogs.
Yes, they are …but they have not evolved since forever…Why can’t he use the same evolutionary mechanism that he believes put him together to his posts?
Shouldn’t have his posts evolved by now?
There are proteins/systems that require more than one gene to make, or multiple copies of the same gene. This situation created a level of organization known as Quantenary Structure:
https://en.wikipedia.org/wiki/Protein_quaternary_structure
TopoIsomerase 2A proteins have a quantenary structure whereby 2 copye of Top2a are put together to make a functioning unit.
In contrast TopIsomerase 6 is composed of the products of two copies each of two genes!!!! Top6 requires two copies created by the Top6a gene and two copies created by the Top6b gene. On the plant Arabidopsis Thaliana, the two genes are on two separate chromosomes. How does random mutation and natural selection create such a contorted Rube Golbberg system to manufacture Topisomerase 6 in this way. This is an example of a promiscuous domain.
I think of systems like this, and evolving by random mutation and natural selection just seems silly. Common descent advocates are invited to explain how this came about, but if they require miracles of special creation to make it feasible, then to me this is little different from Intelligent Design.
If the creationist arguments were to evolve, then maybe John’s responses would appropriately evolve.
I asked Harshman to do some experiments to prove his theory…Why did he object my experiments? Is objection to scientific experiments now called evolving?
You have never asked anyone here anything, at least not sincerely. You, sir, are a troll.
As has been pointed out before, many times, “seems silly” is not an argument. Have you ever looked for any of the literature on protein evolution? You should at least try that before declaring that miracles are required.
The rest is obfuscation. Of course if miracles are required, that’s a form of ID. But I think that when you said “ID” then, you meant “separate creation of species”. As I have pointed out many times, miraculous mutations, if required, would still be a more parsimonious interpretation of the evidence than separate creation of species.
Also, what’s your explanation for these proteins? Is “god just created them that way” really an explanation?
Yes, mostly phylogeentic nonsense, not mechanistic explanations of how the organism doesn’t die or is not compromised in the process.
And one of the famous foundational papers on protein evolution I refuted right here at TSZ. Even you and Rumraket agreed with me.
I agree,
John is well read and reasonably pleasant fellow. We could do a lot worse.
My only criticism would be that he often seems to be jousting against a straw man rather than interacting with the actual position of his opponents.
I think he would be money ahead to slow down and listen more here.
It did bug me a little bit that he spent several days discussing that “Adam” paper with me only to assert that it was not worth wasting any time on.
but all in all I’m glad he is here.
peace
So you read the literature and dismiss it with a word. This is not how a real scientist behaves.
It’s not a foundational paper on protein evolution, but yes you did find some problems with it. Not relevant to anything we’re talking about now, though.
In your case, that’s because your actual position is opaque, as are the arguments you occasionally use to support it. One might speculate that the opacity is intentional, but it would be only speculation.
Ok, let’s take Topoisomerase. What happens to organisms that have malfunctioning topoisomerases, much less non-existent one topoisomerases? Well, we have some idea because anti-cancer CHEMOTHERAPY (by design) disrupts topoisomerases.
No disrespect intended to the patient below, but hopefully you get the picture of what evolutionary biologists don’t address, namely, how does the organism survive through the evolutionary process, like say evolving a topoisomerase before it exists, or modifying it via mutation?
Speaking of how scientists behave, you express little interest in the mechanistic challenges to evolution. You seem to accept phylogenies as an explanation or proof, but they don’t prove mechanistic feasibility. In contrast, I’m the one who seem to show interest in the functional details of biology, relative to you. Now why is that?
Yes, and mutations that disrupt topoisomerase activity will be selected against. Only mutations that don’t disrupt activity will (some of them) increase in frequency.
Actually, there are studies of protein evolution that do such things as reconstructing ancestral sequences, synthesizing them, and determining their functionality. Now a study of the initial appearance of a topoisomerase would have to reach way back in time, to the point where reconstructing the ancestor becomes difficult. But you can’t assume that, just because nobody has shown the exact evolutionary pathway plus a demonstration of function at each step, such a pathway is impossible.
It’s because I’m a systematist, and the tree of life is my main interest. Again, “mechanistic feasibility” is not relevant to common descent. Phylogenies are not an explanation of topoisomerase, though they do give us information on topoisomerase evolution. What makes you think that the intermediate states inferred from phylogenies are non-functional?
Of course you don’t show interest in the functional details. You only show interest in talking about how amazing and complex various things are, generally with lots of colors and arrows, but no real information on function. Your interest seems entirely in proving that evolution is impossible, a conclusion you came to in advance.
Ever hear of asking clarifying questions?
I would suggest that It’s always a good idea to make sure you understand a position fully before you
attack or dismiss it.
It makes for more productive dialogue.
You might try seeing if you can rephrase it in your own words.
peace
That is the jousting with a straw man thing that I’m talking about.
peace
The problem is there aren’t enough population resources for higher multicellular eukaryotes like humans to explore the sequence space of possibilities. There are waiting time problems.
Look how hard and how many generations Lenski’s bacteria had to go through to create new function, and that was at the cost of bacteria that would be unfit in real environments.
It’s simply not credible, unless one invokes statistical miracles as a mechanism rather than ordinary events as a mechanism. At some point statistical miracles are practically indistinguishable from miracles of God.
For the reader’s benefit, since John was questioning me on the “rkps” motif in Top2A, here is the link where “rkps” motif is stated:
http://www.pnas.org/highwire/filestream/596660/field_highwire_adjunct_files/4/SD5.xls
Here is what it looks like in the Excel spread sheet (where I circled the appropriate portion in RED):
Click to Enlarge
John asked if the “rkps” motif is conserved (like in other proteins).
The answer is a tenative “yes”. In fact, our very own Bill Cole brought up the issue and pointed out something interesting related to this NIH funded website. Go here:
https://www.phosphosite.org/psrSearchAction.action
And click “Sequence Search” and enter “rkps”. You’ll find a list that looks like:
This list
Rows with the red boxed “s” indicates experimentally confirmed phosphorylation events in that protein. Superficial examination of these with cross-species MEGA/CLUSTAL/MUSCLE alignments show these motifs were inserted in mammalian or animal lineages across several proteins.
I have to do more work to confirm the promiscuity of these motifs.
When I do, you don’t clarify. Problem.
I don’t believe you are capable of evaluating that question.
That doesn’t show it’s conserved. It just shows that it is present here and there. But any random four-residue sequence would also be present here and there.
What do you mean “inserted”? What’s your evidence that it got there by insertion?
Understatement.
You see, it’s remarks like this that demonstrate your incorrigibility on how biological evolution works. Individuals don’t evolve. Individuals contribute or don’t to the next generation and the collective gene pool is enriched or diminished in genotypes that are more or less successful at being passed on.
OT: how did the scallops work out?
Communication is a two way streak. I promise that I never purposely avoid clarifying.
I expect the gap you see is the result of the radically different perspectives we start from.
If I ask a question and am not satisfied with the answer I usually try and rephrase it or spend a little time trying to see if there is another way to get at the information I’m looking for.
Again the goal is always to be able to understand my opponents position before I attack or dismiss it.
peace
Granted though not sure why being objective or sinless make one worthy of worship either, it is not like He has any choice except to be those things by definition.
He does have the choice to forgive.
Are you you saying, one cannot be objective and sinless and still create things that do not fall into an objective nested hierarchy.
That God’s creative choices are determined by a human categorization just because both have the word “ objective “ as a characteristic?
Interesting belief.
peace
<
Interesting that your options do not include the possibility that you are in error and your opponents position is correct and that you should adopt it.
You sure that subconsciously you might not believe that is what you do?
What do you mean by “explore the sequence space of possibilities”? Nobody claims Eukaryotes have explored the totality of sequence space, but why believe that is even required?
You seem to have an assumption that the functions seen in eukaryotes could not have been discovered by eukaryotes in the available time. Please put some meat on that argument and pick a particular example.
Such as? Be specific.
What is a “new” function really? And why are the number of generations the function you think of indicative of a problem?
You make so many blanket statements with zero support or elaboration here. It’s the same thing we see from Bill Cole, once we start asking for support the whole thing collapses.
The flask environment is a real environment. It really does exist in physical reality, and the bacteria really do live there and continue to adapt to it. All adaptation that has ever happened has been at the cost of the loss of adaptation to an environment that is no longer manifest. You’ll notice how you’d make a pretty shitty fish, and whales don’t do so well when beached. This is the very essence of Darwin’s idea of natural selection. Organisms adapt to their current circumstance, they don’t adapt to all possible future circumstances and become super-organisms.
I still haven’t seen you make a case for something that we are required to posit must have emerged through a “statistical miracle”, nor have you even defined that concept yet.
Then one must assume that you are just very, very bad at it. The effect is the same.
So is it your current argument that objectivity is, by definition, only possible for God, and so humans are incapable of discovering one other than by having God directly pointing it out?
If so, where is the subjectivity in DNA sequences?
You are making the same mistake as Entropy. DNA is not a person it can not interpret itself.
Quickly off the top of my head as a layman I can thing of…..
Subjective humans need to make subjective choices as to the importance they will place on DNA compared to other things they observe.
Subjective humans will need to make choices as to the weight they give coding regions verses non-coding regions.
Subjective humans will need to calibrate and interpret the assays that tell them what DNA a particular sample has.
Subjective humans will need to choose what DNA in the sample belongs to the organism and what is contamination from the environment.
Subjective humans need to choose what of the various diverse DNA found in the different tissues and cells of the organism will count as that organisms DNA.
Subjective humans need to choose the amount of shared DNA that is necessary that is necessary to call a group of separate organisms the same species.
Subjective humans need to choose the threshold of DNA similarity beyond which organisms are considered different species
etc etc
I could go on and on. Some of my off the top of my head musings will undoubtedly be factually incorrect and my choices will also be subjective.
peace
I would be very interested if you would view anything whatsoever as worthy of worship.
It’s possible. That is why it’s important to test our ideas and assumptions for internal contradiction.
peace
I’m saying that anything that can be categorized will form an objective nested hierarchy.
I suppose it’s possible that God could create things that could not be categorized But I’m thinking that sort of absurdity would require a different sort of deity.
peace
Simply understanding your opponents position is not usually enough to make you adopt it. Most of the time you need to be convinced it’s better than the alternatives.
peace
Nobody, including Entropy, has made such a claim. You are not the first creationist to be unfamiliar with metaphor, and I always wonder why.
Not relevant if we are talking only about DNA, which was the subject.
Are you suggesting that there are no ways to be sure that these things have been done correctly, or perhaps that there is no real meaning of “correctly”?
“Species” are irrelevant to this discussion.
You could come up, I suppose, with equal objections if I were to tell you it’s objectively true that an object we were holding in your hand was an apple, not a tomato. I would have to choose to subjectiively look at certain characteristics, choose not to consider your hand part of the object, suppose that my eyesight was properly calibrated, etc. I could go on.
You are carrying subjectivity to new heights. Apparently you can know nothing unless God personally tells you it’s true, and that’s the only thing that saves you from complete intellectual nihilism. Is that correct?
Except that there are non-hierarchical classification schemes (e.g. soils may be best represented by non-hierarchical classification).
Also, in the case of the hierarchical classification of organisms, there is only one consistent hierarchical classification scheme, while with artifacts, there are usually many consistent classification schemes (e.g. library classification).
I apoligize to everyone else but it seems that Zac is late to the party
As I said before::::
Just because you can classify using a nested hierarchy doesn’t mean you have to.
Since you missed that comment I want to make sure you know that I don’t deny common decent and I don’t deny that organisms can be placed in an objective nested hierarchy.
I know Ive told you (Zac) that repeatedly in the past but you always seem to forget it
Hopefully that will minimize future misunderstandings.
Except you get different hierarchies depending on whether you classify acouriding to phenotype or genotype.
and the classification scheme that I presented earlier for organisms is different as well so is the one found in Genesis one. Each one of schemes these is internally consistent. You only see inconsistency when you chose to raise the importance of other characters.
peace
Fashionably late, perhaps.
Okay. But you said, “anything that can be categorized will form an objective nested hierarchy,” which is not the case. A simple example is a jar filled with red marbles, blue marbles, and green marbles. The classification of the marbles is non-hierarchical. You can form them into an arbitrary (non-objective) nested hierarchy, but any one such hierarchy is not objectively better than any other.
{red, {blue, green}}{blue, {red, green}}
{green, {red, blue}}
Phenotypes and genotypes form the same objective nested hierarchy, within the margins of error expected of any such classification. For instance, humans objectively group with other mammals, whether looking at phenotypes or genotypes.
That’s because you have different criteria as to what would count as a credible statistical miracle. This relates to the question, “what would count as evidence” of a miracle for you.
For me (not for you), the first level of miracle is between life and non life, that is the top of the hierarchy. The next level is the divide between Eukaryote and Prokaryote.
So if you say, “we just don’t have enough knowledge, but there is a natural solution,” well, ok, I respect that, but then if a miracle happened in the past, no matter how many improbability arguments you are presented with, unless you see the miracle with your own eyes, then you wouldn’t recognize the miracle even if it did happen and even if my inference was correct.
The problem is you will always appeal to some “other” mechanism. That’s fine, my “other” mechanism is the Christian God. I cited considerations from Quantum Mechanics that something like the Christian God must exist based on an essay in Nature 2005:
So, if hypothetically this scientifically inferred entity actually exists (note, this is not a theological concept alone, but proceeds from QM):, at what point do we invoke this entity (aka God, or Ultimate Observer, or Ultimate QM Wave collapser). I think the Origin of Life and the Eukaryote/Prokaryote divide are starting points.