I just gave a quick look at the paper you quoted. I see many mechanisms mentioned which i do as well. But i dont find any that i do not mention. Can you point to which mechanisms that i did not include ?
Sy Garte
for what i remember, we had already a encounter on Facebook.
When i pointed out, what constraines macro evolution - i am not sure - but i think you didn’t like it, and unfriended me…
In embryonic development the transcriptional processes mediated by dGRNs are intrinsically insensitive to varying cis-regulatory input levels. No subcircuit functions are redundant with another, and that is why there is always an observable consequence if a dGRN subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.It is no surprise, from this point of view, that cell type re-specification by insertion of alternative differentiation drivers is changed only at the dGRN periphery, quite a different matter from altering body plan.
Hi Otangelo,
So here’s what I can ascertain about Minnich’s writings:
- Even before he gave his testimony at Kitzmiller, evolutionary pathways for many of the flagellar proteins had already been described in the scientific literature. His trial testimony, which I’ve read, ignored these findings. See also this subsequent publication (flagellum closely related to F-type ATPase).
- His testimony contained incorrect assertions about the irreducible number of proteins required in flagella (there are only 23, not the 40 he asserts) and the number of those proteins that do not have non-flagellar homologs (there are only 2, not the 30 he asserts). See this summary of Pallen & Matzke 2006, especially Table 1.
- The knockout experiments cited by Minnich (only some of which he himself performed) do not show what he says they show. The knockouts delete large sections of the genome at a time, but these are not the reverse of typical mutational pathways (transpositions, point mutations, copy-and-modify, etc.). The experiments do not in any way resemble real-world conditions. Since the knockout experiments do not, so to speak, run evolution backwards, they don’t show that a lack of a single evolutionary step leads to lack of functionality. Moreover, as a casual reading Table 1 from point 2 above shows, many of the knockouts do not result in substantial loss of functionality.
Otangelo, it’s clear that you’ve been reading a lot of literature written by ID proponents. I salute your hard work. However, you are perhaps not aware that much of the ID literature does not accurately represent the work done by the scientific community. Minnich’s testimony in Kitzmiller was certainly inaccurate with regard to the scientific literature at the time. Subsequent publications (see links above) have strongly refuted Minnich’s testimony.
Best regards,
Chris Falter
My point is that you won’t answer a simple question about a very important fact that’s not included on your web page.
Yes, we agree that peptidyl transferase is part of the ribosome, but that’s not my point.
Please fill in the blank: peptidyl transferase is a ___________. It’s extremely relevant to your pronouncements about the RNA World hypothesis.
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Chris
to be honest, i am not disposed right now to dig deeper into the subject of experiments made by Minnich, and if they are compelling or not. When oportune, i will do that .
What i know imho , is following: F-type ATPase had to emerge PRIOR life began.
The irreducibly complex ATP Synthase nanomachine, amazing evidence of design
Structural Biochemistry/The Evolution of Membranes
https://en.wikibooks.org/wiki/Structural_Biochemistry/The_Evolution_of_Membranes
F- and A/V- type ATPases are membrane-embedded proteins and were feasibly present in the LUCA (last universal common ancestor) due to their omnipresence in modern cellular life.
If ATP synthase was present at luca, it means it is strong evidence that it was present at the progenote, and was therefore not possible to emerge through evolution, since evolution depends on DNA replication.
Furthermore, at least five core units are irreducible.
At least five of the below mentioned parts are ESSENTIAL and IRREDUCIBLE. Take away one , and ATP synthase ceases to function. Neither could any of the sub parts simply be co-opted from anywhere else. That would be the same as to say, in order to make a motor function, and a cylinder is missing, go search and find any cylinder nearby , co-opt it, and solved is the problem. The thing is that cylinders come in all size, specification, materials etc. And there is no goal oriented search of parts that fit through evolution Evolution has no forsight. Furthermore, there must be the information how and when and where to mount the parts, at the exact place, in the right sequence. Thats a far fetch for a mindless tinkerer to be able to achieve.
1.The nucleotide binding stator subunits (“cylinders”) : The electrostatic interaction of these rotor and stator charges is essential for torque generation
2.The central stalk (“crankshaft”) : The torsional elasticity of the central stalk and the bending and stretching elasticity of the peripheral stalk create an elastic coupling between Fo and F1. Is is essential.
3, The A/V rotor subunit (“adapter”) ; It is not used in all ATP synthase motors, and can therefore be reduced.
4. The Rotor ring (“turbine”) ; A ring of 8–15 identical c-subunits is essential for ion-translocation by the rotary electromotor of the ubiquitous FOF1-
ATPase.
5.The Jon channel forming subunit ; Subunit a harbors the ion channel that provides access to the binding site on the c11 ring in the middle of the membrane from the periplasmic surface . The channel is essential for the operation of the enzyme, because mutants in which the channel is blocked are completely inactive in both the ATP synthesis and/or coupled ATP hydrolysis mode
6. The peripheral stalk (“pushrod”) ; The peripheral stalk of F-ATPases is an essential component of these enzymes. It extends from the membrane distal point of the F1 catalytic domain along the surface of the F1 domain with subunit a in the membrane domain.
7 - 11 do not exist in all atp synthase motors, and can therefore be reduced.
- Electrostatic interactions between rotor and stator in the bacterial flagellar motor - PMC
- Flexibility within the Rotor and Stators of the Vacuolar H+-ATPase - PMC
- Structure and Flexibility of the C-Ring in the Electromotor of Rotary FoF1-ATPase of Pea Chloroplasts
- http://onlinelibrary.wiley.com/doi/10.1046/j.1432-1033.2002.03264.x/pdf
- The peripheral stalk of the mitochondrial ATP synthase - PubMed
There are at least 5 subunit parts essential to mantain the basice function of the ATP synthase motor.
If the substrates like crude oil required to make gasoline are not provided at the correct refinery place at the Oil industrial plant, the refinery process cannot happen. Same happens inside the cell. In order for mitochondria to function, shuttling of ADP, ATP, phosphates and other substrates is essential. That process does not catch mutch attention, but is actually life essential for eukaryotic cells to function. We need the right charge of ADP and ATP, the electrochemical gradient inside the inner membrane, the ADP/ATP carrier proteins that drive the substrates around, and carrier proteins that shuttle the phosphate that is required along with ADP for ATP synthesis to the right place at atp synthase motors, ready to be used , to be added to ADP to make ATP. That seems a ingeniously precise orchestrated process requiring several indispensable parts. ATP synthase is a prime example of intelligent design, and should be able to convince even the most skeptic that intelligent design is the best explanation for its origin .
I think you misunderstood me. Let me try again. You included all of the EES mechanisms. I agree with that. What you seem to ignore, is the idea that evolutionary theory includes all of those mechanisms. So the questions is, if we forget about pure neo Darwinism, and focus on modern evolutionary theory that includes the EES, what is wrong with evolution?
Not quite. You joined the group Celebrating Creation by Natural Selection (where I am an admin) and were eventually booted from the group for not following the guidelines (by a different admin). I alluded to our past encounters earlier in this thread.
I looked for this fragment in the very long passage that you linked (I remember these interminable essays that you like to link to) and couldnt find it. By itself it goes against everything I know about GRNs (which is a lot), but I think it is out of context, and since I cant find it, I dont know what the context is. I did see some stuff about canalization, (which is the opposite of what this fragment says) but I dont have the time to go through 20 or 30 pages of text. Can you provide the citation for this fragment?
Hi Otangelo,
Again, you have done a lot of reading. However, I think you are missing the forest for the trees, so to speak. You make an argument that the fact that a protein requires 5 parts for its current function means that it could not have evolved. This is not a valid assumption. While knocking out one of the 5 “parts” means that F-type ATPase cannot perform its current function, there is no reason to think that an assembly of 4 of the parts could not perform some other biological function. Thus you have not proven that F-type ATPase is irreducibly complex.
You also make an argument about abiogenesis. Properly speaking, that is not an argument about evolution at all, since evolution starts with the assumption that there is an extremely primitive, reproducing form of life. Arguments over abiogenesis are interesting, and it seems that you are having a discussion with our friend @benkirk about it. But evolution could be true even if abiogenesis is not.
Best,
Chris Falter
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Its the fourth quote highlighted in red:
what is wrong with evolution?
Life depends far more on coded information than previously thought.
encoding, transmission, decoding, creations of codes, specially more robust and optimal amongst one million others ( the universal genetic code ) the creation of translation ( genetic cipher ) are best explained through intelligent design. The alternative isnt even evolution, but would be random chance. Life does not use only genetic, but mainly and specially epigenetic information…
The various codes in the cell
Another outstanding implication of the existence of organic codes in Nature comes from the fact that any code involves meaning and we need therefore to introduce in biology, with the standard methods of science, not only the concept of biological information but also that of biological meaning. The study on the organic codes, in conclusion, is bringing to light new mechanisms that operated in the history of life and new fundamental concepts. It is an entirely new field of research, the exploration of a vast and still largely unexplored dimension of the living world, the real new frontier of biology.
The Genetic Code
The Splicing Codes
The Metabolic Code
The Signal Transduction Codes
The Signal Integration Codes
The Histone Code
The Tubulin Code
The Sugar Code
The Glycomic Code
What can be asserted without evidence, can be dismissed witout evidence. You speak about evolution, but ATP synthase most probably had to exist prior dna replication began. So there was no evolution at this point. And secondly, you are not considering following:
For a working biological system to be built, the five following conditions would all have to be met:
C1: Availability. Among the parts available for recruitment to form the system, there would need to be ones capable of performing the highly specialized tasks of individual parts, even though all of these items serve some other function or no function.
C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.
C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.
C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a system are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.
C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if sub systems or parts are put together in the right order, they also need to interface correctly.
( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)
All of these operations are contained within the DNA and have to produce machines that are shape dependent and form fitting to the DNA and RNA transcript that comes from it.
Resumed : For the assembly of a biological system of multiple parts, following steps must be explained : the origin of the genome information to produce all subunits and assembly cofactors. Parts availability, synchronization, manufacturing and assembly coordination through genetic information, and interface compatibility. The individual parts must precisely fit together. All these steps are better explained through a super intelligent and powerful designer, rather than mindless natural processes by chance, or / and evolution, since we observe all the time minds capabilities producing machines and factories, producing machines and end products.
I think i made my point clear that i do not deny evolution in general. I refute common ancestry, and the blind watchmaker argument.
This principle undoes your argument, Otangelo. I have provided evidence that simpler protein assemblies with fewer components (i.e. f-type ATPase) can be functional, even as they form a potential precursor to a larger set of proteins (a flagellum). In other words proteins can be exapted.
You have made assertions to the contrary, but they are arguments from analogy.
There are countless other examples of exaptation besides the one I offered. Given that exaptation is so well-established in the scientific literature, I do not bear the burden of proof in this discussion.
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You are defining evolution quite idiosyncratically here. Evolution and common ancestry are inextricably bound together in the scientific community.
I do want to clarify that I believe strongly in an intelligent designer: the God of Abraham, Isaac, and Jacob. I do not believe that scientific methods can reveal His hand, however.
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i provided reasons why i do not think its that easy. For the assembly of a biological system of multiple parts, following steps must be explained : the origin of the genome information to produce all subunits and assembly cofactors. Parts availability, synchronization, manufacturing and assembly coordination through genetic information, and interface compatibility. The individual parts must precisely fit together. All these steps are better explained through a super intelligent and powerful designer, rather than mindless natural processes by chance, or / and evolution, since we observe all the time minds capabilities producing machines and factories, producing machines and end products.
ahm. Stephen C. Meyer is more of my gusto than the " scientific community " , whoever you mean with that.
Principal Meanings of Evolution in Biology Textbooks 1
What is fact :
- Change over time; history of nature; any sequence of events in nature
- Changes in the frequencies of alleles in the gene pool of a population
- Limited common descent: the idea that particular groups of organisms have descended from
a common ancestor. - The mechanisms responsible for the change required to produce limited descent with modification; chiefly natural selection acting on random variations or mutations
Non random mutations : How life changes itself: the Read-Write (RW) genome
What is not fact:
5. Universal common descent: the idea that all organisms have descended from a single common ancestor.
6. Blind watchmaker thesis: the idea that all organisms have descended from common ancestors through unguided, unintelligent, purposeless, material processes such as natural
selection acting on random variations or mutations; the idea that the Darwinian mechanism of natural selection acting on random variation, and other similarly naturalistic mechanisms, completely suffice to explain the origin of novel biological forms and the appearance of design in complex organisms.
Like I said, argument by analogy rather than by scientific evidence.
Since you seem to lean heavily on this rhetoric, I don’t see how we can make further progress. But I wish you every heavenly blessing as you continue your journey of faith.
Make sure you check out those links on Minnich for yourself. Also, do read Wiens’ paper for yourself. I would trust a Ph.D. physicist over a forum full of anonymous commentators any day.
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So you provide an article link that can’t be read without buying access. Is there an article that you could share that is less challenging to get to?
But let’s say that I’m delighted that you think Speciation is something that happens quickly via Evolution… this is certainly not the usual confession of folks we usually perceive as Young Earth Creationists.
So, do you think God used evolution to create the million Plus terrestrial life forms from the ones that survived on the Ark?
yes, absolutely. Non random mutations : How life changes itself: the Read-Write (RW) genome 2 3
And all available scientific evidence also indicates that evolution is an engineered process. In engineering and computer science, evolution never happens by accident. It’s always the result of a deliberate act. A program that can self-evolve is always considered an engineering marvel. 6
i said here already. I am biased towards YEC, but there are issues which are not settled for me, and where i put a question mark.
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Do you understand how many new life forms would have to be created all at once… or every year, for hundreds of years… for it to be called Evolution, there has to be multiple generations changing … I don’t think you grasp the ramifications of such a scenario…
Or do you think God just “poofed” a million creatures all into existence … which is pretty much a non-Evolutionary approach, right?
@Otangelo_Grasso1, well, that’s an honest answer.
So basically, you have no idea what you believe … BioLogos is certainly a good place to start when you are contemplating how God interacts with evolution to create the life forms he wants for the Earth …