I’ve committed the unpardonable sin several times of criticizing other ID proponents publicly, but when I think claims or methods need to be challenged, I feel obligated to speak out because I find myself contesting certain ways the ID argument is presented when I make presentations about ID and/or special creation.
The conflicts are over the relevance of the 2nd Law of Thermodynamics, Information Theory, Specified Complexity, Conservation of Information, Framing Probability Arguments, and whether ID is science.
Many ID proponents and creationists privately concede the 2nd Law of Thermodynamics is not an argument against the evolution biological organization. If I asked sophomore chemistry, physics, and mechanical engineering students to use standard molar entropy tables, they can demonstrate a living human has MORE entropy than a frozen dead rat. Thus, it is silly to argue that somehow lowering entropy is a requirement for making complex biological systems. There are many cases the opposite is necessary! Nuff’ said…
AE Wilder-Smith in his famous debate with Richard Dawkins introduced the idea of chemicals plus information are necessary for the origin of life. Generations of ID proponents and creationists have equivocated, confused, and muddled the issue with conflicting definitions of information ever since Wilder-Smith, and the outcome has had mixed results.
Contrast Wilder-Smith’s arguments with how James Tour (620 peer-reviewed articles, 77,000+ citations) argues against natural origin of life. He doesn’t need information theory!
Worse, consider the following simple example of design in the arrangement of dominoes standing up. If I asked why is this arrangement of dominoes likely designed based on ID information theory arguments, Specified Complexity, Conservation of Information, one will quickly realize all ID information theory arguments confuse the issue at best. Simpler arguments based on expectation and law-of-large-numberESQUE arguments will suffice.
Ask yourself, if one can’t even apply Specified Complexity, Conservation of Information Arguments, to trivial designs like dominoes, how can these arguments be persuasive to much more involved designs like that in the Origin of Life, Zinc Fingers and Nuclear Localizations Signals in Eukaryotes? Eeesh! More mathematical theatrics does not make an argument better. Substance rather than theatrics is better.
The way to frame probability arguments so as to avoid the claims of after-the-fact-Texas sharpshooter fallacies needs to be addressed more. It can be done, but not enough has been done on this…
ID proponents do not serve their cause well, imho, by saying, “ID is science.” It ends up being a red herring, and opponents of ID would love ID proponents to make this claim because ID proponents will be taken to task for saying it. I get a lot of hatred from ID types for saying things like ID falsifiable, not science, not positive, not directly testable. But if I, as a card carrying creationist and card carrying Discovery Institute donor can see the problems of saying “ID is science,” how much more anyone else, especially those on the fence.
The best pro-ID talk I’ve ever heard was by someone who doesn’t even identify as an ID proponent, James Tour. His infamous talk at a Discovery Institute-sponsored event is the model that ID proponents should follow. [See the ironically titled article James Tour: Liar for Jesus]. The other model of arguing for ID AND special creation was by John Sanford at his infamous talk at the NIH. [see Famous Geneticist Tells NIH that Humans Are Going Extinct].
Sal,
Who’s claiming that proteins should have a single common ancestor?
No one I know of, but if there is not universal common ancestor for all proteins, then what is the need to assume universal common ancestor of organisms, we can just as well assume they don’t have universal common ancestors either.
But I pointed out, if we assume universal common ancestor of organsims (LUCA), but assume there is no Protein Universal Common Ancestor (PUCA, pronounced puke-ah), then for LUCA to be true, new protein architectures sort of just poof onto the scene for no good natural reason.
Hence Common Descent is in the un-enviable position of requiring the equivalent of miracles of special creation to make common descent feasible — evolutionary biologists just don’t want to advertise such problems.
I showed ZNF136 zinc finger protein. There is another zinc finger protein, CTCF which binds to 55,000 locations on the genome, and must be partnered in very specific ways to make extrusion loops for regulation. That would require something like miracles of special creation. More on that later….
But in brief, one of the children of ENCODE is 4D Nucleome. CTCF is critical part of 4D Nucleome…
I thought Scordova left TSZ?? Well glad he is back.
whats the point of this thread? A shot at ID?
id is not science rant again ? why from a iD dude?
ID is as sciency as anything in origin matters. godd grief . put a fork in it. Its over with that accusation.
If one has pet complaints about subjects then one should not use those to sample a whole population.
Everybody complains about everybody. don’t take it so deeply close to the soul.
ID thinkers have become famous, innovators, threat, and just starting. not that many! surely this is the evidence of a paradigm change SOON coming .
Card carrying creationists/ID thinkers should be on the team.
To get along, go along.
Please no inventing fractures., conflicts.
I didn’t say it wasn’t incoherent.
Sal:
keiths:
Sal:
Then your point is pointless.
Sal:
Evolutionary biologists don’t assume either of those. They base their conclusions on the evidence — a practice that is understandably alien to you, a creationist.
The conclusions are that organisms share a common ancestor, but proteins do not.
walto,
I know, but I’m wondering why van Inwagen thinks it isn’t.
They don’t go together Salvador. I’ve told you a million times, they don’t go together. They have no relationship with each other.
This is twisted thinking salvador. We don’t assume universal common ancestry, it was suggested, as a hypothesis, when two-and-two were put together to understand that species diverge into new species. Today there’s lots of evidence that there’s something pretty close if not universal common ancestry. We don’t assume universal common ancestry for proteins because it doesn’t make any sense (once we understand the relationship between DNA and protein sequences). To our credit, there’s also evidence for the recent evolution of some new proteins from non-coding regions of DNA, for example, so we don’t need to speculate or “assume,” as if we were too ignorant of the most basic biology, a “PUCA.”
Hence you have no idea what you’re talking about and you should stop and read for comprehension. Have some self-respect for once in your life.
No they don’t. What’s the evidence that Eukaryotes naturally emerge? No common descent unless a Eukaryote can emerge naturally.
I pointed out a simple problem with membrane bound organelles and the problem of localization.
Evolutionary biologists don’t know how this can happen in principle. Unlike the phylogenies I showed, at least those might happen in principle, but those mechanisms can’t be extrapolated to other problems, even though evolutionary biologist pretend it can be.
So like I said, common descent is like geocentrism, it is built on cherry picking data and pretending the solution to one problem (like the explanation of individual protein phylogenies), actually solves the problem of novel structures and substantially novel LIFE-CRITICAL proteins and facets of proteins.
So the tally here at TSZ regarding the Protein Universal Common Ancestor:
1. ENTROPY : doesn’t exist
2. Keiths: doesn’t exit
3. Allan Miller : unlikely to exit
4. Rumraket: IIRC, doesn’t exist
5. DNA_Jock: ….
6. Joe Felsenstein: …
7. John Harshman: IIRC, doesn’t exist
What is evident is mechanism that might explain phylogenies of individual proteins across species does not explain emergence of brand new architectures of proteins.
For example, it appears Prokaryotes don’t have any zinc finger domains at all, that it’s a Eukaryotic innovation. The DNA-binding variety of Zinc Finger proteins have tandem arrays of 3-42 zinc finger domains. It’s not exactly trivial for these to just pop up in a functional way.
Sure they do, because if one need miracles to make proteins with no ancestors, then common descent proceeds because of miracles of special creation, which really isn’t much of a common descent at all, but some sort of progressive creation.
There are plenty of miraculous proteins and pathways needed to emerge a Eukaryote. Apparently you trivialize the requisite transmembrane proteins and the localization signal peptides that require global reformatting of pre-existing proteins so they are localized to the right compartments at the right time.
One example of reformatted proteins with signal peptides for Eukaryotes are Ribosomal ones. How could that happen without a statistical miracle. Without proper localization, the would-be Eukaryote is Dead on Arrival (DOA).
The claim of common descent is premature at best, dead wrong at worst. If evolutionary biologists can’t suggest in principle how critical transitions such as the emergence of Eukaryotes can plausibly happen without killing the intermediates (for reasons I outlined), then they don’t know. But “we don’t know” is not a claim of fact.
The similarity of genes/proteins could be a miraculous coincidence, or that common descent was made possible by a miracle. To claim it happens by ordinary processes is not justified for the reasons I gave.
The hidden Markov models you swear by, don’t prove the requisite transmembrane proteins in Eukaryotes emerge naturally — it doesn’t provide one iota of proof, not to mention, you just admitted many proteins don’t have a universal common ancestor and hence, as a matter of principle, can’t be proven to arise by the same mechanisms that govern the variation of homologous proteins across species. In fact new architectures have to arise by radically different mechanisms as illustrated by the radically different architectures for Collagen Col1a1 and ZNF136.
The facts suggest miraculous origin of certain classes of architectures. The fact that homologous proteins with modest variation between species can be grouped together by hidden Markov models ( or even less sophisticated methods) does NOT explain how certain novel architectures can emerge naturally.
But even homologs shared between species, such as yeast and humans the variation may not be feasible naturally because the homologs may have species specific constraints that are improbable. I.e. human Toposiomarase Top2A and Top2B might work in yeast, but yeast Top2 will not function in as human Top2A nor Top2B. Human Top2B apparently had its special feature emerge with animals that had CTCF zinc finger proteins that implement gene regulation via extrusion loops (my diagram below).
So lets not naively assume that just become some proteins can tolerate lots of mutational variation without phenotypic consequence, that all proteins can.
Sal,
This has been explained to you over and over, including in this very thread, but I’ll do it yet again:
Common descent is a claim about phylogenetic relationships. It is not an explanation of the origin of features, and it’s not supposed to be.
Your complaint is akin to saying “This can opener is no good. I can’t drill holes with it.”
It’s the same mistake poor Granville makes when he tries to get the 2LoT to rule out evolution.
Sal,
We don’t need miracles to explain de novo proteins.
Sal, LUCA is based on empirical evidence: the universality of genetic code and the similarity of many basic processes and it has never been assumed. There are many people, including Craig Ventor who think we may one day find organisms from a separate origin.
As for proteins, its assumed that de novo proteins arose many times in early life. We see de novo proteins arising now from ncDNA in the complex streamline organisms of today so it should have been far easier when life was simpler. One lab ( I forgot whether was the Yonath or Tawfik lab) did a statistical analysis of protein domains and showed that most appear to be derived from simple repeat sequences of amino acids. As you may be aware, even very simple aa sequences of the form XYXYXYXYXYX can have function.
Would you acknowledge that present day eukaryotes are descended from a fermentative proto-eukaryote in which an alpha proteobacteria took up a symbiotic relationship with and became the mitochondrion?
He has a book on it. I wrote a paper criticizing his main argument many years ago, but I couldn’t get anybody to publish it. And van Inwagen–whom I’d met at some little upstate NY conference before he got famous on Plantinga’s bandwagon–refused to read it.
Hasty generalization, keiths, which is a logical fallacy.
That some can arise, doesn’t mean all can arise naturally. I pointed out a few cases, starting with transmembrane proteins and lack of zinc finger classes in prokaryotes.
No, but even if we say yes, for the sake of argument, but it doesn’t solve the problems I outlined with localization issues and transmembrane proteins that serve as gateways for membrane bound organelles.
Phylogenetic methods do not solve the mechanical issues I outlined.
The claim of LUCA is based on similarities, but similarities don’t explain the requisite miracles needed to make LUCA possible, starting with the problems of localization in Eukaryotes, transmembrane proteins, different initiation complexes, spliceosomal intron processing.
Here is one miracle that is necessary, for example that is pretty obvious. I start by describing the initiation complex in protein translation in Eukaryotes:
This is the corresponding initiation complex in prokaryotes. Intermediates would be DOA as a matter of principle. Phylogenetic methods do not give answers to the requisite mechanical changes of the intermediates, except as bald assertions without any systematic accounting for the actual mechanistic difficulties.
stcordova,
Read for fucking comprehension Salvador! If you don’t you just ridicule yourself!
Check this:
See the bolded part? That means that once you understand DNA->RNA->protein you pretty much can conclude that universal common ancestry of all proteins doesn’t make biochemical sense.
The issue is: it appears that you don’t understand that, otherwise you would not need a “poll”, you’d understand instead.
I know, maybe you think you need that piece of crappy thinking to pursue your “proteins have to be explained.” Well, don’t worry Salvador, you can improve your thinking and still ask that question. It doesn’t matter at all to your question. Not one bit. But you need to understand, otherwise you come across as a poor idiot talking out of deep ignorance of the most basic biology. How can you expect to advance your creationist ideas if you show off as an ignorant fool? If you found your ideas on nonsensical and unrelated premises?
Have some self-respect!
Thanks for the link, but that was mostly bald assertion, and not examination of mechanistic details. I could just well say trans membrane proteins unique to Eukaryotes just appeared and say they emerged de Novo.
Thanks anyway for the link, and thanks for the conversation.
Don’t misinterpret my disagreement as lack of understanding. You’re the one who is failing to make a defensible argument.
You can start trying to explain for the reader how different initiation complexes as depicted above arose naturally. I mean, the transitionals from a common ancestor would be DOA without a miracle. It’s rather obvious.
No? Then you’re either unaware of the evidence or you’re immune to evidence.
As for the other problems, I dont know if anyone has put work into the evolution of transmembrane proteins. I’ll just observe that all thats required for a transmembrane protein are ~50% hydrophobic α-helices. Almost all proteins have α-helices with some hydrophobic residues so it doenst seem like a stretch for a transition, but maybe they all evolved early on and all tmp share common descent
As for localization issues thats a no brainer. Most organelles have multiple targeting systems and they all have low complexity. Sometimes just 2 basic residues in a row at the NH2 end will do…and there can even be flexibility
Thats not true but maybe we can get to that later. You’re example brings up an interesting idea that I think is worth pursuing:
You wont be surprised to hear the eukaryotic IT is more complex than prokaryote. Can you speculate on why its so complex? What is the reason its complex? Does it need to be to function? Could you make an analogy with human inventions?
Thanks for your comment,
But if common descent requires miraculous origin of features, how is this fundamentally different than creationism?
The false insinuation is that because we can build nested hierarchical diagrams for proteins, that somehow this proves no miracles were needed for radically different new proteins architectures, or even global reformatting of existing proteins for proper localization in Eukaryotes. That’s a logical non-sequitur:
Thank you for the reply, but that issue is exactly the point, the problems are never critically examined from a feasibility standpoint.
The fact we can build phylogenetic trees for some proteins, doesn’t explain the mechanical problems such as initiation complex, transmembrane proteins, spliceosomal introns, and global reformatting of localization signals.
As a personal anecdote. Change Tan, an associate professor of cellular biology with a PhD in Physical Organic Chemistry at an Ivy League school used to accept evolution, but the problems I’m pointing out were part of her journey to becoming a creationist. What I’m describing is what this professor of cellular biology sees and what she knows hasn’t been adequately addressed, but rather swept under the rug via “phylogenetic methods.”
Am I correct in thinking that the eukaryotic translation initiation complex depicted is in fact not being used in mitochondria and plastids, and that the translation apparatus in plastids appears to be a lot more similar to the bacterial system then to the cytosolic one?
Am I correct in thinking that not all “prokaryotes” have the translation initiation complex depicted, but that archaea use a different one that shares certain features with eukaryotes not present in bacteria?
This horrible mess is optimized for scientific discovery …. how exactly?
Good questions, of which I don’t have answers. Now a substantive objection. Well done!
Nice to hear from you.
Corneel,
It’s ludicrous, isn’t it?
Worse still, it appears that the evidence is actually optimized for false discovery. After all, evolutionary biologists are overwhelmingly convinced by the evidence that a) common descent is true, and b) organelles such as mitochondria are explained by endosymbiosis. Both of which, according to Sal, are false.
So rather than optimizing things for scientific discovery, God has pulled off the ultimate snow job, convincing biologists of things that are utterly false. Excellent work, God.
But he didnt do a very good job at this snow job because he didnt fool Sal or the guys at the Discovery Institute.
Sal,
I can understand that you wouldnt want to take my challenge ( on the functionality of all that stuff in your diagram) …it would take some work and its not fair to ask you to write an essay….so I’ll just get to my point…..
Its a strange paradox but most of the complexity is not necessary for the basic function. We see this over and over, especially in eukaryotes- a kind of riotous useless complexity The illustration of this is the IRES sequence in virus mRNAs. An mRNA that has this can do without most of the proteins required for translation initiation. One of them, the Cricket Paralysis Virus IRES can do without ALL OF THEM.
This is very counter-intuitive even for people who accept evolution. It suggests there is a general ratcheting up in complexity for no other reason that it can happen. Later on, some parts of this complexity can become necessary for function or selected for improved or new function.
RodW,
Rube Golberg machines are designed, not for efficiency, but to showcase ingenuity of the Designer in getting something to work the hard way — that was the problem of Peackock’s tail for Darwin. It was soooo inefficient, something selection should not have evolved.
RodW,
Those guys, like the POTUS, are very stable geniuses. The rest of us can only aspire to such heights.
Not any more than God made the world look GeoCentric to those with primitive understanding of how things actually work. At the time, things like centrifugal and Corioliss forces, not to mention theories of gravity, were not well-formulated if at all.
As more knowledge was gained, the superficial understanding of the universe was dispensed with. Same goes for evolutionary theory for those willing to see common descent won’t work without miracles.
Sal,
You’re making my point for me. The world is clearly not optimized for scientific discovery.
If God was trying to do that, he screwed up.
Rube Goldberg machines aren’t optimized for scientific discovery.
You can’t have it both ways, Sal.
Sal,
We have been there before…
Do you remember when John Harshman acknowledged the need for a miraculous appearance of genes for endosymbiosis to be even considered as a possibility for common descent of eukaryotes from prokaryotes?
Doolittle humbly acknowledged:
“‘Many eukaryotic genes turn out to be unlike those of any known archaea or bacteria; they seem to have come from nowhere.’ (Doolittle, D.F., Uprooting the tree of life, Scientific American 282(2):72–77, 2000.).
So, people who ignore the evidence like the above, attribute god-like creative powers to sheer dumb luck, substituting one kind of faith for another.
Sure you can because they are God-made, not man made.
Grand slam!
Thanks a billion.
RodW, Corneel,
Thanks for the info on initiation complexes. Great stuff.
Sal
keiths:
Sal:
How does that help? They still aren’t optimized for scientific discovery. Complex systems are harder to understand than simple ones.
We don’t need to know the nitty-gritty details of every evolutionary transition in order to have evidence for common descent. If you don’t understand this, then you don’t understand the evidence.
There is no need to assume that. You keep portraying this as an assumption that is needed for something, but it’s an evidentially derived conclusion.
It is derived from the evidence that SOME proteins and SOME genes are universally conserved, exhibit significant levels of nesting hiearchical structure, and converge on a highly similar branching topology. That’s what makes them evidence for common descent.
Then further there is the fact of the molecular and functional roles of these genes, as the core components of the translation system. They are exact the sorts of components upon which almost everything else in modern cells depend, so if any gene could be said to be expected to be conserved over extremely long timescales, it would be genes like these carrying out the most central and crucial functions of known cellular life.
The fact that other genes are not conserved over such timescales is not evidence against universal common descent. It just means those particular genes not universally shared, can’t be used as evidence for universal common descent. They can still be used as evidence for common descent within the clades where they are shared, like all eukaryotes for example.
You are free to make all the assumptions you find pleasing, that’s just not how science or evolutionary biology works. The conclusion of common descent is not assumed, it is derived from evidence like I just explained.
Obviously for genes that are not universally conserved we shouldn’t just assume they are universally distributed anyway (that wouldn’t make sense), and nobody is claiming that genes that aren’t universally distributed are somehow still evidence for universal common descent.
Still not an assumption anyone makes.
However new proteins come to exist is actually irrelevant. Either there was common descent or there was not, and either there is evidence for this or there is not.
Now, there is good evidence that new proteins can in fact evolve de novo from non-coding DNA by mechanisms like mutation in non coding DNA and selection among low level spurious transcripts, so there are perfectly good “natural reasons” why across the tree of life we should see taxonomically restricted genes.
See for example this new review article:
Van Oss SB, Carvunis AR. De novo gene birth. PLoS Genet. 2019 May
23;15(5):e1008160. doi: 10.1371/journal.pgen.1008160.
Common descent makes no claims about how new genes come to exist, though we now know they often times evolve from non coding DNA. Your mindless insistence that this is miraculous is nothing more than that, a mindless insistence. It just means whatever it is that feed into your intution about how likely or feasible it should be for a novel protein coding gene to evolve is wrong.
An unbiased and rational person should change his mind in light of evidence that his intuitions are wrong, but instead you’re just stamping your feet and declaring with strenuous conviction that new genes evolving is miraculous.
My less educated reading is that traces of such histories can be erased by drift.
Software bloat.
Thank you for you comment.
Unlike other ID proponents and creaitonists, I agree genes can arise de novo, but they can’t be certain classes of genes. It’s brutally obvious anything life critical needing simultaneous highly specific binding/connection and mulitple connections won’t arise by such means.
Examples are TopoIsomerases, Helicases, Zinc Finger Proteins, Ribosomal Proteins, life critical Transmembrane proteins, etc.
Collagen, may look innocent enough, but it requires numerous post translational modification to work. Here is a more detailed collagen architecture with the domains, motifs, localization signals and PTMs laid out. I assembled the diagram myself from data on Post Translational Modifications and Domains.
I know but this, and other evidence, doesn’t matter when one has found a way around the evidence that contradicts the beliefs…
If you watched the documentary Behind the Curve, you will see this phenomenon first hand. Educated people design a very sophisticated experiment to disprove the curvature of the earth. When their own experiment proved the opposite, that the earth is curved, they ignored the results of their own experiment and looked for ways to continue to justify their beliefs…
The much deeper question is, why? Why would seemingly intelligent people continue to deceive themselves and others?
I already said SOME proteins can arise de novo easily, but life- critical integrated ones, not so easy. Proteins with homo or hetero quaternary structures must be able to geometrically adhere to each other.
Consider the homo-dimer quaternary structure of TopoIsomerase. Not only must the Topo be able to do the amazing job of uncoiling tangled supercoiled DNA, it has to first assemble it self by mating two copies of the Topo monomer/polypeptide. The interface/connection points of this cannot be trivially arrived at by random mutation and still have a working homodimer.
It’s absurd to think this can be evolved in steps. For one, Topo type II Cuts DNA and then stitches it back together. A half-formed topo that only cuts but doesn’t stitch will then make mincemeat of the genome in short order. Hence the creature would be DOA. Bwahaha!
Likewise for the other steps that can’t be evolved piecemeal.
The red is one Topo monomer/polypeptide the blue is the other identical copy. Look at all the connections necessary. Oh, that’s the other thing, it’s bad juju for the TopoMonomers to accidentally form complexes with other polypetides in ways it shouldn’t!!!!
So yeah, mindlessly made de novo proteins would have be trivially unsophisticated compared to more God-made sophisticated ones. And secondly, the sophisticated ones can’t be evolved piecemeal by natural selection for the reasons given.
Let’s imagine a scenario that scientists, Craig Venter for example, were able to re-create life by artificially assembling a bacterium, e-coli…
What would happen next? What would that mean for both theists and materialists?
For example: Would this achievement mean that blind, random processes were responsible for the origin of life?
Would scientists be able to re-create the endosymbiosis in the lab then which they can’t do now?
J-Mac,
This has been done according to Perry Marshal. The problem is this is before the first inning of explaining the origin of the eukaryotic cell.