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
I’m not sure what “baby-killing” has to do with common decent.
But you certainly get a gold star in well poisoning.
😉
peace
I don’t claim that ID is a mechanistic theory like evolutionary biology falsely claims evolutionary theory is a mechanistic theory. “It just happened” isn’t a mechanistic theory. “God did it” isn’t a mechanistic theory either. However, the falsehood is representing evolutionary theory as a mechanistic theory consistent with ordinary expectation.
Have you not been paying attention.
It’s much more obvious to link those animals if you place a higher value on color and climbing habit than on anatomical measurements.
Actually I did mention habitat previously. You just focused on color.
I could include other characteristics as well like the fact that grey squirrels bark like grey foxes and grey foxes don’t tend to howl like red foxes are known to do as far as I know.
Diet is also something to consider grey foxes generally eat more vegetable matter than other foxes and grey squirrels are generally more carnivorous than fox squirrels.
Then there is the fact that grey squirrels and are more likely to be crepuscular than “fox” squirrels. (interesting name is it not)
I also mentioned the fact that grey foxes are liable to be harassed by the larger red foxes and grey squirrels are liable to be harassed by the larger “fox” squirrels.
Then there is observation that grey foxes are more likely to den in hollow trees and even in the canopy while red foxes almost always den below ground.
I’m sure there are other similarities as well If I thought for a little bit.
It’s all about how you weight the data.
Noise is in the eye of the beholder. Give a characteristic a weighting of 90 and it’s signal give it a weighting of .9 and it’s noise.
I’m suggesting they be classified together when it comes to the characteristics I’m talking about and I have observed them in the wild. In fact it was while observing a grey fox climbing that it occurred to me that it moved a lot like a squirrel.
Now of course I would group them differently if I was weighting other characteristics more highly. It’s just that possibility that lets me know that all these sorts of groupings by humans are ultimately subjective.
Think about it for a minute. Folks have been observing animals closely for thousands of years
If your chosen groupings were objective we would expect that it would have been conceived of long before Carolus Linnaeus did it in 1735, and it would have been instantly accepted at that time .
Instead what we find is a messy process where the new classification system was opposed by folks like comte de buffon who thought that putting together a nested hierarchy was the wrong approach altogether.
peace
Bet that gave you a warm, tingly feeling too. I see you ignored the part about baby-murder and such.
I don’t think a clear reading of the text can support that interpretation. Did you get it from revelation? And Aslan isn’t really a lion, you know. He only looks like a lion in Narnia. Really, he’s Jesus. I can’t believe we’re talking about hermeneutics of the Narnia books.
It has more to do with common decency than common decent.
Until I have a conference with my colleague who is a Topisomerase researcher, I will for the time being slow down posting the Top2 PTM, metal binding, active site diagrams until I can resolve the cross linking issue.
This will give me an opportunity to analyze zinc finger domains in KRAB containing ZNF proteins.
That’s not what you actually said. I will not accuse you of dishonesty.
I think you’re confusing habitat with habit. You had mentioned the latter previously.
Note that you are choosing character specifically to fit a pre-conceived classification. That’s why it’s not a real nested hierarchy. Also, have you heard of a thing called “paragraphs”?
Notice that you’re the only person talking about weighting. I’m not proposing different weights for characters at all.
Doubling down?
Think about it for a minute. Folks have been observing animals closely for thousands of years
If your chosen groupings were objective we would expect that it would have been conceived of long before Carolus Linnaeus did it in 1735, and it would have been instantly accepted at that time .
“Objective” doesn’t mean “obvious”. And of course foxes were grouped separately from squirrels many thousands of years ago. That’s why we have a single word for each.
Not familiar with Buffon’s views on classification. Why are they relevant?
Look an elephant!!!
Thought the divine created objective nested hierarchies, could they be the wrong approach altogether?
So nothing is better than something that might not meet somebody’s ordinary expectations? Weird.
The thing is at some point the divine would have to create / manipulate matter,organisms exist in the material world , at that point intrusive design is a mechanistic theory.
It would be like saying , everything that comes between the blueprints and the finished building is irrelevant to how the building came to be.
I think I’ve made it clear that I tentatively think that current approach is the best one.
The deference between John Harshman and I is the difference between “tentatively concluded” and “objectively discovered”
peace
I’m not sure how given your worldview you are in a position to make blanket statements about what constitutes common decency.
Are you bothered by the fact that there are 125,000 abortions per day in the USA? Between 40 and 50 million a year in the world
What exactly have you done to prevent them?
peace
Precisely right. Of course Intelligent Design needs to deal with the mechanistic aspects at some point. So far ID proponents have merely put off that task or tried to shift the burden of proof to its opponents.
Certainly.
I challenge you to explain to Sal that, if its proponents aspire ID / common design to be a superior explanation, they need to deal with the mechanistic aspects of biological design, and not contend themselves with “Godiddit-And-I-Don’t-Care-How”.
A level of uncertainty? That seems like a dramatic deviation from your usual black-and-white universe. Wouldn’t you, to be consistent, have to argue that all things that aren’t completely certain are equally uncertain? After all, they are mutually exclusive terms. You can’t be 80% certain and 20% uncertain. Any smidgen of uncertainty undermines complete certainty, right?
But you laugh at your cartoon of evolutionary theory, yet you happily accept the bullshit of ID. So, even if your misconceptions about evolution were correct, your rejection of one for the other would still be a double standard.
Of course not. Fortunately, that’s not what evolutionary theory is about. But if it was, I would not be right there with you accepting something as ludicrous and hypocritical as ID.
You’ve got that one right. It’s not a scientific position either. It’s wishful thinking at best.
The falsehood is representing ID as if it was about science, when it’s a mere attempt to disguise your religious beliefs behind smoke and mirrors. Pretending it to be science. Your double standards are worse than merely rejection of evolution based on your lack of reading comprehension abilities, and accepting ID on no basis other than your religious beliefs. You also reject evolution because you describe it as a false claim, yet you agree with the hypocritical presentation of your religious beliefs as if they were scientific. You’re part of the hypocritical movement yourself.
I’d explain the mechanistic aspects of evolutionary theory, but it would be too much to expect if you read the second sentence of this comment. Besides, they’ve been explained to you a thousand times. I’d also explain that no scientists has ever said that evolution is consistent with ordinary expectations. If it was, there would be no research on evolutionary histories and mechanisms. But, again, I doubt you can read, let alone sustain some level of reading comprehension beyond “oh, this is so complex!”
The following is an alignment of 13 zinc fingers in the human ZNF136 KRAB protein.
https://www.uniprot.org/uniprot/P52737
Note that each finger is 23 residues in length. In fact on the protein the fingers are spaced apart by exactly 8 residues each time.
Such precise repeat of a motif arising by chance point mutations on a pre-existing strand are very remote. At best maybe some sort of duplication, maybe tandem repeat, but then the problem arises of duplicating the zinc finger according to proper boundaries of the domain, and note, zinc fingers appear in tandem in lots of places, so why a propensity for tandem zinc finger repeats at the correct zincfinger boundaries?
And note, they aren’t exactly tandem repeats, however the Zinc Figner structure where the 2 Cs and 2Hs are beautifully preserved in the right location.
As mentioned before, the multiple zinc fingers create a structure that conceptually looks like a comb that attaches to specific locations on DNA. In the diagram below, the bubble with the comb marked “KRAB-ZFP” has mutliple zinc fingers that are conceptually shown like a comb structure.
What has God done to prevent them? That’s more to the point.
You have hit on the correct explanation. So why repeats only at the correct boundaries? Simple: other duplications happened, but they weren’t favored by selection. Or suppose a duplication of a 3-finger sequence produced 2 1/2 more fingers happened and was favored by selection, but the extra 1/2 finger gradually degraded by small deletions until it was gone. Your inability to imagine that sort of thing is not a fatal blow to evolutionary biology.
It looks like 6 residues to me, but you’re the genius here.
Which is why nobody has ever proposed such a scenario.
Not at best. That’s the only way. Tandem duplications. These, by the way, are all natural phenomena that produce diversity, which is part and parcel with evolutionary theory.
Or maybe it’s enough if one pair duplicating at the right points for them to work together well in DNA recognition, and thus get naturally selected from the fact of producing some phenotypic effect. After just one pair, producing tandem duplications at the “right length” is but a question of replication slippage, which will happen at the right positions for no other reason than DNA/DNA base complementarity. This is, actually, the reason why our genomes gain and lose loads and loads of repeated pieces even within a single individual. All very well documented phenomena.
Because those at the incorrect zinc finger boundaries would be selected against (purifying selection), rather than selected for (positive selection).
You said the opposite above. I think that what you mean to say is that they’re not exact copies of each other.
Of course. Otherwise they would be selected against (purifying selection), rather than selected for (positive selection).
Fucking simple.
Most molecular evolution is neutral. You can’t just ad hoc invoke it. By that same logic the Alu repeats were selected for, for that matter the tons of tandem and dispersed repeats throughout the genome!
A few years ago I posted this OP on DNA as a Random Access Memory.
Below is a diagram of the changes in the RAM during embryogenesis. Each box shows the pattern of bits being flipped on an off. The it turns out the KRAB-Zinc Finger proteins are important to changing the pattern of bits.
The TSZ Darwinists here criticized me for calling the epigenetic marks RAM, until I, yes me who is supposedly illiterate and ignorant according to my detractors, pointed out in the stem cells handbook of 2013, that other researchers call it RAM!
It appears the Zinc Fingers are architected to make this possible. Now it may be easy to assume the Zinc Fingers are bind exclusively to DNA, but wiki says zinc fingers can bind RNA and proteins as well!
So what is the evolutionary conundrum here. DNA changes, but this entails a correpsonding coordinated change within the zinc fingers! That doesn’t sound like random mutation.
Furthermore, as Salthe pointed out:
So, that’s why I mostly dismiss Entropy’s “explanations” that invoke selection as an explanation since Salthe rightly pointed out the problem of making variation on traits under selection.
Entropy is left to saying “please read what I [Entropy] write.” I don’t have much time for reading such drivel, so I mostly ignore what he says unless he states something I actually don’t already know.
You really should take more care when you type. I can’t tell what “it” I “can’t just ad hoc invoke”, but I think you might mean selection. Do you understand that protein-coding exons are more constrained by selection than are junk sequences? This is not a far-fetched notion. As for Alu repeats, you will note that they tend to happen in junk DNA, and that the mechanism of replication and insertion tends to produce a fair proportion of fragmentary repeats. Your objection, if it can even be understood, is nonsensical.
stcordova,
Argument by pretty colors again.
Yes, and if they are constrained by selection, they are less evolvable, according to Salthe. If proteins are constrained by selection, then why would you expect random tandem repeats to emerge. For the tandem repeat to be selected FOR, such as a new duplicated zinc finger, the zinc finger needs a target to make a system functionally advantageous.
The alternative is to invoke a neutral walk, which then has the problems of accounting for coordinated function.
I think your proposed solution hasn’t been carefully thought out. I am providing pretty pictures and specific case studies to show some of the standard evolutionary talking points and “explanations” lack mechanistic validity if one is invoking ordinary processes.
Only if they’re under purifying selection. But copies of the genes coding for those proteins would not be under purifying selection. Thus more evolvable.
Because it’s not those emerging random repeats that are under purifying selection.
Eukaryotic genomes are pretty large. thus, potential targets are not that hard to be found. Also, zinc fingers bind small DNA sequences, which would make them easy to evolve.
Not a problem, since there can be plenty of neutral places to bind, and useful places to bind
More like you cannot think of positive scenarios, yet those exist, and are easy to understand. Your problems with them are religious in nature, not scientific.
Where ordinary processes are those you are willing to accept, rather than those that scientists have observed to occur.
Nope by habitat I mean forest as apposed to grass land or savanna.
No I’m not, I am noticing similarities in character and choosing a grouping based on that. I certainly did not come into the process with a preconceived classification.
We are spending a lot of time with my particular grouping but a similar one could be done with killer wales and great white sharks or with bats an nightjars. You find these sorts of obvious non-Linnaean groupings everywhere in nature.
For you to simply dismiss them all as special pleading rings very hollow
peace
First of all the decreasing uncertainty that I’m talking about in relationships is in the overall picture and not in individual facts.
I begin a relationship being uncertain about 100 things and after a while I’m uncertain in 85 things.
That seems to me to be just another way of describing the process of getting to know someone.
Secondly I think that you are confusing uncertainty with objectivity they are not synonymous.
Something could be objective while at the same time being uncertain all that is required is a lack of bias.
Also something can be certain while at the same time being subjective. I can be certain that tomatoes taste better than artichokes but that would just be my subjective opinion.
You can’t be is a 80% biased and 20% objective. It’s not logically possible. But I can be 80% certain about something
Do you see the difference now?
peace
fifthmonarchyman,
Fyi
It was very early this morning on the way to the office and I misquoted the article on abortions
I said “This corresponds to approximately 125,000 abortions per day in the USA.” but that figure was for the entire globe.
In the USA it’s more like 3,000 abortions per day
sorry if I misled anyone.
peace
What would you have him do exactly?
Remove free will?
Turn up the fear of hell a few notches?
Place his law on the hearts of humanity so that they know killing is wrong?
Do you complain that God has not done enough when you haven’t done anything.
People who claim to be atheists and then complain that objective evil exists in the world really crack me up.
The fact that they can’t see the obvious self defeating nature of their argument is simply priceless.
peace
Sorry that I’ve been trying to explain things to you. I didn’t know you cared so little. After all, you’re posting in a public forum, then pretending to give “answers” that came only to show that you didn’t read the explanations, or worse, that you lack the literacy to understand them. I will let you ridicule yourself from now on. No advice against it any more.
Now, saying that you already know about selection seems rather odd, since you keep going for “random versus magical-being-in-the-sky.” It also looks like you don’t know that there’s different kinds of selection, and that your excuse to forget about selection is some quotation that ignores that evolutionary paths occur regardless of whether some genes are “stuck” in some function, since organisms have more than just one gene (interesting that you wouldn’t know this), and plenty of genes are less constrained than, say, essential genes (interesting that you didn’t know this either). Even constrained genes have margins of variability (interesting that you didn’t know this either), that allow for further functions to evolve, and, if they didn’t, copies of genes would be more evolvable (interesting that you didn’t know this either). Plenty of options.
So that guy you quote convinced you because you have a narrow view of what’s available for an organism’s evolution. And that narrow view is due to your ignorance and inability to reason, not on scientific grounds.
So, as you wish, keep ridiculing yourself by making those amazingly stupid displays of ignorance and illiteracy. As for me, I won’t give you the benefit of the doubt again. I’ll remain perplexed at your willingness to ridicule yourself, at your hypocrisy and illiteracy. But that’s ok. It’s your choice to be such an exemplar for ID-creationism. The most illiterate, irrational, and uneducable you look the better.
Existing would be a start.
😉
Aha. So you were not talking about decreasing the level of uncertainty but about decreasing the number of things you are completely uncertain of. Sort of like a quantum theory of certainty. That statement is more consistent with the previous stuff you said allright.
Yes. So you are for example 100% certain that your left foot has five toes, but you don’t know this objectively, because you aren’t 100% certain what independent observers mean by “toes”.
I think this is crystal clear and not even a bit kooky in the slightest.
Unfortunately your replacement “explanation” is simply that god did it. What is it that you expect to happen next? Shall the biology textbooks be re-written with the single line “god did it”?
FMM,
You made a comment asking does anybody have any challenges to what Sal is claiming?
Perhaps it would be illustrative (for you) if you restate in your own words what you think Sal has demonstrated, and therefore what it is that people should be addressing?
FMM,
Given the rate of advance of medical technology it’s likely that death and sickness will be “cured” fairly soon. And as our understanding of physics increases perhaps in the very long term even the heat death of the universe won’t be a challenge (e.g. in theory an infinite number of thoughts can still be thought over ever extended periods of time in that phase) to life.
Following your logic, we’ve then become god.
There are trees that seem to have no cap on their longevity, and some other organisms too. Presumably those are more god-like then others then.
What a crock of shit.
I have seen arguments that when a single celled organism splits, the original dies. I don’t find that to be coherent.
Life is all kin, all descendant from early promiscuous life. Cells die, but life does not.
Eventually, yes. But not yet witnessed.
The challenge is to get Salvador to understand that his “challenges” are no such thing.
HAHAHAHA!!!!!!!!!!!!!!!!!!!!!!!!
Now who is believing in imaginary things?
Well, yeah we have “immortalized” cells in test tubes like the HeLa line, but that was a cancer cell. That’s not much of a life, imho.
https://en.wikipedia.org/wiki/HeLa
Well, if the Lord returns soon, then death will be cured for those whom He has forgiven. But I don’t think you were referring to that possibility.
Now I did some paper research on immortalized embryonic stems cells which weren’t cancerous.
But an immortal creatures is a long way from an immortal stem cell.
The number of toes on my left foot are an extreme example but you can get the idea even there.
It really is about perspective.
What qualifies as a toe as apposed to a nub or a claw or a protrusion. I have a perspective but I’m definitely biased. For example I would not say my toes are categorically the same as the digits on a bears lower appendage.
I might think that my first digit qualifies as a toe but I think it’s really quite different than the rest as is my smallest digit. Are they all the same thing??
Then there is the question of what makes a foot. Does an ape have a foot or a paw? What about a bear? Does he have four feet or two feet and two hands.
We can do the same thing with numbers. My smaller digits very rarely function as separate entities. Are they four separate toes or simply a singular but lobed forward extension of my foot.
Again it’s all about perspective. Everyone sees the world in slightly different ways. There is simply no way for a finite individual to step completely out of his personal perspective to see the world in a privileged God like way.
We in the twenty first century west might understand our feet and toes one way can we really say that every person that has ever existed or may every exist see them in the same exact way? If not can we really say that ours is the objective perspective while there is not??
Your understated sarcasm is my favorite part about your particular biased perspective on the world. 😉
peace
And it’s the Christians who supposedly have an irrational faith.
peace
Given his rate of acceleration from a standing start it’s likely that Usain Bolt will surpass the speed of light fairly soon and go back in time.
peace
I don’t think that Sal has demonstrated anything. he has made claims that are being dismissed rather than addressed
He is arguing that certain phenomena make more sense from a perspective of common design rather than common decent.
It seems to me he is saying in effect that “lego like” proteins make sense if you want the ability to build many very different kinds structures efficiently.
On the other hand there is no compelling reason to start with legos if you are only interested in passing on the most useful randomly arising feature to the next generation.
peace
That is not in dispute. The problem lies in you using that as an excuse to equate all viewpoints; everything is equally uncertain and equaly subjective to you, whereas there are degrees of certainty and degrees of subjectivity. Zack and John covered that stuff already, so I have no interest in rehashing it, but I did feel the need to seize the rare grayshaded bloom in the black-and-white desert. Too bad you trampled it again.
And your ability to appreciate that looks good on you. Cheers, Fifth.
You are asking yourself evolutionary (even, for you, revolutionary) questions here.
Shame you can’t make that final connection as to how paws and hands (and pandas’ thumbs) might have similarities that hint* at a hierarchy of relatedness.
*I’m toning it down from “scream”. 🙂
Pentadactyl limb.
Funny how Noah can live for nearly 1000 years and yet when I suggest that technology can ultimately extend lifespan near indefinitely that’s vastly amusing.
I’m going to guess FMM has never wondered where the name for that site comes from: https://archive.nytimes.com/www.nytimes.com/books/97/11/09/home/gould-panda.html
As I warned you FMM, the longer you talk to people who know what they are talking about the more you will learn. Despite yourself.
You are. OMagain was just a tad optimistic.
See? It’s you who believes in imaginary things. Though sometimes I doubt that you really believe this, since you’re so quick to ridicule yourself while pretending to represent the view from someone who believes in this supposed “Lord.” A Lord of charlatans maybe.
Yet you did “some paper research” on the latter rather than the former.
Haaaaaaaahahahahahahaaaaaaaa!!
At least you didn’t say he was out of his mind.
That really gets Alan’s ire.
phoodoo,
He doesn’t have a mind to be out of (or in) in the first place.
Other people use RAM metaphor! I is smart as other people! I is no ignorant. I is no illiterate!
Should I point out that “less likely to evolve” is not a synonym to “it will never ever evolve”? Should I point out that there’s more than one gene in an organism? That not all genes are under the very same degree of purifying selection? That genes get copied and copies have more freedom for changes to occur? That tandem duplications happen all too easily? That evolution is not just about point mutations? Of course I should not need to, unless, of course, the person who’s making claims against selection as a mechanism was showing signs of, ahem, ignorance and illiteracy.