Chromatin Topology: the New (and Latest) Functional Complexity
| July 23, 2018 | Posted by PaV under Intelligent Design |
There’s a paper out in Nature Genetics discussing “chromatin topology.” Here’s the abstract:
A long-standing question in gene regulation is how remote enhancers communicate with their target promoters, and specifically how chromatin topology dynamically relates to gene activation. Here, we combine genome editing and multi-color live imaging to simultaneously visualize physical enhancer–promoter interaction and transcription at the single-cell level in Drosophila embryos. By examining transcriptional activation of a reporter by the endogenous even-skipped enhancers, which are located 150 kb away, we identify three distinct topological conformation states and measure their transition kinetics. We show that sustained proximity of the enhancer to its target is required for activation. Transcription in turn affects the three-dimensional topology as it enhances the temporal stability of the proximal conformation and is associated with further spatial compaction. Furthermore, the facilitated long-range activation results in transcriptional competition at the locus, causing corresponding developmental defects. Our approach offers quantitative insight into the spatial and temporal determinants of long-range gene regulation and their implications for cellular fates.
This is rather stunning stuff since what they are essentially saying is that the protein wrapping of DNA, the chromatin, is somehow functionally arranged, and that two distant sites on DNA (located 150,000 bases away from each other) NEED to come into contact for enhanced transcriptional activity. And, in the italicized section, they’re saying this comes about because the ‘needed’ conformation is somehow ‘stabilized,’ which means that the overall energy configuration of the local DNA molecule is lowered when put into this ‘conformation.’ (Oh how biochemists would love to be able to do such things!)
This only adds to the complexity of organisms to function properly and leaves in shambles the thought that all of these new layers of complexity came about by some “random” process.
I could post articles like this every day. I don’t because “News” does a good job of it, and over at Evolution and News, serious treatment of the more consequential articles routinely appear.
I cannot understand how any rational human being, aware of all this level of complexity, could possibly maintain a Darwinist, neo-Darwinist, or any other putative evolutionary (random) mechanism explains such orderliness and machine-like functioning.
We’re a long ways from thinking that ovum are just a bunch of goo. And yet . . . .
A related news item: Here.
241 Responses to Chromatin Topology: the New (and Latest) Functional Complexity
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My dear PaV. You have not demonstrated that it could not possibly have come about by numerous slight successive modifications.
Mung:
No one has demonstrated that it could possibly have come about by numerous slight successive modifications. Until then there is nothing to refute.
Of related note to topology in general, Reductive materialistic, i.e. Darwinian, explanations are grossly inadequate for trying to explain how any particular protein (or organism) might achieve its basic form:
This failure of reductive materialistic explanations occurs at a very low level, much lower than DNA and proteins, In the following article entitled ‘Quantum physics problem proved unsolvable’, which studied the derivation of macroscopic properties from a complete microscopic description, the researchers remark that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,, The researchers further commented that their findings challenge the reductionists’ point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description.”
I have a feeling that Gödel would be very pleased with the preceding result:
Mung:
I’ve come awfully close!
Andrew:
Evolutionists only need be able to convince themselves of its plausibility. Nothing more.
Like imagining how an eye might come about.
Darwin looked forward to the next generation of biologists/naturalists who, being young, would have great imaginations.
Personally, I can imagine myself circling the planet Jupiter, and then plunging to its innermost core.
I’m very creative, you see.
This theory started out with a logical fallacy.
Darwin:
A theory based on an argument from ignorance. What a con job.
I don’t think it’s possible for a rational, honest, intelligent human being to learn about that complexity and continue to maintain a blind-watchmaker evolutionary mechanism.
But, all of the evolutionists of the world will do just that.
Therefore … I can only conclude that they are either irrational, mentally-ill (I’m not making a joke of that), ignorant, unintelligent – or just plain dishonest. Or it’s some combination of those factors.
I think it’s mostly just dishonest. They’re just lying.
Dear Chuck,
You’ve presented an non-falsifiable proposition as justification in science, but don’t worry, I don’t think anyone cares. You’ll still get your holiday, and they’ll sell your dolls to the kids at Down House. In any case, when the first ever aaRS was successfully synthesized on earth, enabling biology to occur, how many of the other aaRS had to be in place?
Great stuff PaV,
Rules based instruction sets 🙂
Indeed! Rules-based systems or reference data allows modular code quick access frames. They see there are rules to follow, but doubt they equate it to Design. Even if they must use Design Language to explain what they’re accomplishing in reprogramming efforts to cure disease.
In order to “re-engineer the programs” they must have been designed to start.
One does not re-engineer blind, unguided matter – to solve problems with disease – because blind, unguided matter would not follow a rules based set of instructions – let alone create them to start with.
Stating the obvious is necessary sometimes.
Rules usually exist prior to access by programs, or can be modified and updated if required by extenuating circumstances of Epigenetic functions.
Rules are pre-planned, prescribed instruction sets that varying Modules can access, interpret and compare as necessary and ongoing response operations. Modules that carry out any number of specific processing routines.
And again, mutations cause disease, not enhancements to the regulatory code(s).
re: Rules,
In a post by Gpuccio and subsequent comments by Upright Biped, Dionisio and myself, a discussion of Rules was mentioned quite a few times in relation to the Ubiquitin Proteasome System(UPS) and regulatory functions.
As well as a review of Codes, language and rules Upright brought into the picture by Barbeiri and Pattee.
Here’s a comment on the Ubiquitin Post by Gpuccio I briefly made on Rules…
https://uncommondescent.com/intelligent-design/the-ubiquitin-system-functional-complexity-and-semiosis-joined-together/#comment-652201
Upright BiPed’s comment #94 provides excellent review on Rules and Language some 45 years ago by Pattee.
https://uncommondescent.com/intelligent-design/the-ubiquitin-system-functional-complexity-and-semiosis-joined-together/#comment-652105
PaV,
If you don’t want to post interesting articles like this daily, you could try at least weekly. I think you’ll have many readers here.
You wrote:
“I cannot understand how any rational human being, aware of all this level of complexity,…”
Who said they’re aware of all this level of complexity?
Maybe they aren’t? Perhaps they see it but the penny doesn’t drop?
As to PaV’s comment on thermodynamics
The information content that is found to be in a one cell bacterium, when working from the thermodynamic perspective, is found to be enormous,,, 10 to the 12 bits,,,
,,, Which is equivalent of 100 million pages of Encyclopedia Britannica. ‘In comparison,,, the largest libraries in the world,, have about 10 million volumes or 10^12 bits.”
In the following video, it is noted that the information to build a human infant, atom by atom, would take up the equivalent of enough thumb drives to fill the Titanic, multiplied by 2,000.
The following video states that “There are 10^28 atoms in the human body.,, The amount of data contained in the whole human,, is 3.02 x 10^32 gigabytes of information. Using a high bandwidth transfer, that data would take about 4.5 x 10^18 years to teleport 1 time. That is 350,000 times the age of the universe.”
Moreover, we now have fairly strong evidence indicating that this enormous amount of positional information, that is telling all the atoms of the developing embryo exactly where to be, is somehow coming into the developing embryo from outside the material realm.
For instance, at about the 41:00 minute mark of the following video, Dr. Wells, using a branch of mathematics called category theory, demonstrates that, during embryological development, information must somehow be added to the developing embryo, ‘from the outside’, by some ‘non-material’ method.
The following article adds weight to Dr Wells assessment and states: “the process of development should be thought of as being controlled by an “algebraic structure outside space-time itself””
To provide further evidence for information coming into the developing embryo from ‘outside space-time itself’, it is also important to note that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,,,
And these quantum correlations which somehow arise from outside spacetime, are now found in molecular biology on a massive scale. In every DNA and Protein molecule,,, For instance,
In fact, quantum criticality is now found in a wide range of important biomolecules,,,
It is important to note that quantum entanglement is a physical resource, which can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems.
In regards to information in general, in direct contradiction to Darwinian claims that hold information is merely a metaphor, information is now shown to be a physically real entity that is separate from matter and energy. A physical real entity that has, of all things, a quote unquote ‘thermodynamic content’
Of related note to information now being shown to have a ‘thermodynamic content’, in the following paper, Dr Andy C. McIntosh, who is professor of thermodynamics and combustion theory at the University of Leeds, holds that it must be non-material information that is constraining biological life to be so far out of thermodynamic equilibrium. Moreover, Dr. McIntosh holds that regarding information as independent of energy and matter ‘resolves the thermodynamic issues and invokes the correct paradigm for understanding the vital area of thermodynamic/organisational interactions’.
Moreover, in quantum mechanics it is information that is primarily conserved, not necessarily matter and energy that are primarily conserved, as matter and energy are primarily conserved in classical mechanics. As the following article states, ‘In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed.’
Moreover, classical ‘digital’ information has now been found to be a subset of ‘non-local’, (beyond space and time), quantum information by the following method:
Of final note, besides quantum information providing direct empirical falsification of neo-Darwinian claims that say information is emergent from a material basis, the implication of finding ‘non-local’, beyond space and time, and ‘conserved’, quantum information in molecular biology on such a massive scale, is fairly, and pleasantly, obvious.
That pleasant implication, or course, being the fact that we now have direct physical evidence strongly indicating that we do indeed have an eternal soul that is capable of living beyond the death of our material bodies.
As Stuart Hameroff notes in this following video, “the quantum information,, isn’t destroyed. It can’t be destroyed.,,, it’s possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul.”
Verses:
DATCG
I think I’d change ‘usually’ there to ‘always’ – or are you thinking of an exception to that?
Any sort of blind, random-based processes are reactions only to the immediate circumstances. They cannot create a set of rules for later use. A gradualist, natural selection scenario also could not create rules which have to govern the processes that supposedly created them and which have to be consistent before being functional.
Rules are like language but even more complex. Language is a third-party which joins the two organisms. But rules are much more precise and functional because rules govern the activity and responses of the two (or multiple parties).
So, evolution of any of the ‘governed’ cannot account for the rules which exist at a higher level of order.
To me, a rules-based scenario is one of the most obvious evidences of Design. Rules are top-down, functional and independent – complex and precise. An unintelligent, blind output is in direct contradiction to that.
#10 Upright BiPed:
“…when the first ever aaRS was successfully synthesized on earth, enabling biology to occur, how many of the other aaRS had to be in place?”
Very intriguing question. Thanks.
Can you elaborate on it?
BA77:
Here’s two papers you might find fascinating.
First
Second
The first was just published in Physical Review Letters.
The first relies on the ‘second’ paper; and I think you’ll find the thermodynamic angle quite interesting. From my very brief view of the abstract and introduction, it looks like it could, and should, be of use when dealing with DNA conformations/configurations.
And the ‘first’ paper’s conclusion that ‘information’ is ‘physical’, like heat and energy, is also very fascinating.
Hope you enjoy the read.
Thanks PaV, here are a few more references that are a bit more digestible for the average readers:
There was a time here at UD, when a certain number of evolutionists would actually try to defend their theory in the face of an article like this (and many others).
They never had an argument – just a lot of huffing and puffing, wishful thinking and snide attacks to change the topic.
I’m very glad they’re gone. They obviously have nothing to say.
Research like this is not even a close-case where an imaginary scenario could be plausible. From what I saw the researchers themselves do not even attempt to fit evolution into the findings. There’s no confirmation of evolutionary predictions – it’s all just observational. “Wow, look at this complexity of function.”
Evolution contributed nothing to it.
@bornagain77 post 19
“…shows that information is a physical thing…”
Are you suggesting that information has a physical existence independent of any substrate?
To my knowledge, information is just a meaningful (to someone) arrangement of other physical matter or energy.
Deputy Dog, I am not suggesting anything, the evidence itself now establishes the fact that ‘information is physical’. i.e. it is no longer merely a suggestion but a scientifically established fact.
See post 15, 18, 19 and this video:
Also see quantum teleportation:
The simplest way for demonstrating that immaterial information is its own distinct physical entity, separate from matter and energy, is Quantum Teleportation:
@bornagain77 post 22
So, how would you go about preparing a container that contains pure information without any physical substrate?
And how would one read and interpret that information?
Whatever DD, I don’t do trolls.
Chromatin: A ubiquitin crowbar opens chromatin (PDF available)
@bornagain77 post 22
That youtube video is about as cranky as it gets.
Here is a better source:
http://cqi.inf.usi.ch/qic/64_L.....mation.pdf
Quote from the paper”
“Information is not a disembodied abstract entity; it
is always tied to a physical representation. It is represented
by engraving on a stone tablet, a spin, a charge,
a hole in a punched card, a mark on paper, or some
other equivalent. This ties the handling of information
to all the possibilities and restrictions of our real
physical word, its laws of physics and its storehouse
of available parts.
“
Bornagain77:
“The simplest way for demonstrating that immaterial information is its own distinct physical entity, separate from matter and energy, is Quantum Teleportation:
Quantum Teleportation Enters the Real World – September 19, 2016
Excerpt: Two separate teams of scientists have taken quantum teleportation from the lab into the real world.
Researchers working in Calgary, Canada and Hefei, China, used existing fiber optics networks to transmit small units of information across cities via quantum entanglement — Einstein’s “spooky action at a distance.”,,,
This isn’t teleportation in the “Star Trek” sense — the photons aren’t disappearing from one place and appearing in another. Instead, it’s the information that’s being teleported through quantum entanglement.,,,
,,, it is only the information that gets teleported from one place to another.
http://blogs.discovermagazine……-HqWNEoDtR”
If you want to understand quantum entanglement, ask a physicist. From medium.com:
“So now to Olivier’s question: could we use this property?—?quantum entanglement?—?to communicate from a distant star system to our own? The answer to that is yes, if you consider making a measurement at a distant location a form of communication. But when you say communicate, typically you want to know something about your destination. You could, for example, keep an entangled particle in an indeterminate state, send it aboard a spacecraft bound for the nearest star, and tell it to look for signs of a rocky planet in that star’s habitable zone. If you see one, make a measurement that forces the particle you have to be in the +1 state, and if you don’t see one, make a measurement that forces the particle you have to be in the -1 state.
Therefore, you reason, the particle you have back on Earth will then either be in the -1 state when you measure it, telling you that your spacecraft found a rocky planet in the habitable zone, or it will be in the +1 state, telling you that it didn’t find one. If you know the measurement has been made, you should then be able to make your own measurement, and instantly know the state of the other particle, even if it’s many light years away.
It’s a brilliant plan, but there’s a problem: entanglement only works if you ask a particle, “what state are you in?” If you force an entangled particle into a particular state, you break the entanglement, and the measurement you make on Earth is completely independent of the measurement at the distant star. If you had simply measured the distant particle to be +1 or -1, then your measurement, here on Earth, of either -1 or +1 (respectively) would give you information about the particle located light years away. But by forcing that distant particle to be +1 or -1, that means, no matter the outcome, your particle here on Earth has a 50/50 shot of being +1 or -1, with no bearing on the particle so many light years distant.”
Information states seem to have become a modern form of ouija boards, at least for some of the religiously inclined.
1
Funny, DD quotes Landauer’s ‘information is physical’ paper, and yet Landauer’s materialistic version of information is precisely what was refuted in the video that he, in typical trollish fashion, denigrated. Specifically,,,
Because of such an elementary mistake on DD’s part, I smell a toll instead of honest inquiry. If this type of behavior continues I will file a complaint.
Then timothya chimes in and states from this article (which he did not link)
These following claims from the article are far too broad in their scope and thus fail to be rigorously true:
The reason these ‘broad’ claims fail to be rigorously true is because of what is termed ‘past-future entanglement’
As Professor Crull states in the following article “entanglement can occur across two quantum systems that never coexisted,,, it implies that the measurements carried out by your eye upon starlight falling through your telescope this winter somehow dictated the polarity of photons more than 9 billion years old.”
It is also interesting to point out that this experiment for ‘quantum entanglement in time’ is very friendly to Dr. Michael Egnor’s (Theistic) contention (via Aristotle) that “Perception at a distance is no more inconceivable than action at a distance.”
And that this ‘entanglement in time’ finding from quantum mechanics also refutes Dr Vincent Torley’s objection against Dr Egnor that perception cannot possibly occur ‘at a distance’. For example, Dr. Torely held that perception cannot possibly be at a Supernova which “ceased to exist nearly 200 millennia ago, long before the dawn of human history.”
Yet, despite Dr. Torley’s objection that the supernova no longer exists, and to repeat the earlier paper I cited, quantum entanglement in time “implies that the measurements carried out by your eye upon starlight falling through your telescope this winter somehow dictated the polarity of photons more than 9 billion years old.”
Of related interest to this, in the following article Dr. Egnor points out that Aristotle anticipated Quantum Mechanics thousands of years before quantum mechanics was discovered.
Since timothya suggested “If you want to understand quantum entanglement, ask a physicist” it is interesting to point out that the great physicist Einstein himself, (who developed EPR in the first place), was refuted by quantum mechanics and thus apparently did not completely ‘understand’ entanglement.
also of related note:
Bornagain77:
“Then timothya chimes in and states, from this article (which he did not link)
“It’s a brilliant plan, but there’s a problem: entanglement only works if you ask a particle, “what state are you in?” If you force an entangled particle into a particular state, you break the entanglement, and the measurement you make on Earth is completely independent of the measurement at the distant star. . If you had simply measured the distant particle to be +1 or -1, then your measurement, here on Earth, of either -1 or +1 (respectively) would give you information about the particle located light years away. But by forcing that distant particle to be +1 or -1, that means, no matter the outcome, your particle here on Earth has a 50/50 shot of being +1 or -1, with no bearing on the particle so many light years distant.”
https://www.forbes.com/sites/startswithabang/2016/04/30/ask-ethan-can-we-use-quantum-entanglement-to-communicate-faster-than-light/#29b0b39bfbcd
These following claims from the article are far too broad in their scope and thus fail to be rigorously true:”
Here’s why Bornagain77’s quantum entanglement ouija board can’t possibly work.
1. Entangle two particles (demonstrably possible)
2. Separate the two particles by some arbitrary distance (also demonstrably possible, so let’s make it several light-years).
3. Step 2 will require the use of a condensed-matter system to move the remote particle to its target location, which means its carriage will be subject to the limit of light-speed motion applying to “classical” objects. In other words, it will take several million years to get the remote entangled particle to a location several light-years away.
4. Now we want to ask the remote particle what state it is in (in order to answer some question we happen to be interested in – for example, Ethan’s question about whether the particle is on a rocky exoplanet in a remote star’s Goldilocks zone). Let’s forestall an objection by assuming that the question, and the way to interrogate the entangled particle, is already encoded in the interstellar probe (remember that the classical/quantumly entangled remote system has taken a million years to reach its target).
5. So now (a million years later) the remote system is in place and is ready to answer its encoded question. The system automatically presses its button, the remote particle uses its accompanying classical system to sense its surrounding environment and sets its spin to either +1 (rocky and Goldilocks) or -1 (not rocky or not Goldilocks)
6. Instantly, the Earthbound particle will change state to match the state of the remote entangled particle and we will know the answer
7. But it will still be a million years after we sent it on its way.
That is why Bornagain77’s ouija board can’t work (it’s the million years, stupid).
Information is mediated by condensed physical matter that is subject to the rules of General and Special Relativity (unless Bornagain77 has found some way around them).
timothya, you misunderstand my claim. I am not claiming that full scale communication for humans is possible via entanglement alone. I am well aware of the speed of light caveat for full scale communication for humans via entanglement. The ‘modest’ claim I am making, a claim that is backed up by ample experimental evidence, is that, via quantum teleportation, information can be transferred between particles completely independent of the material particles themselves physically interacting (quantum computing itself would not be possible if this were not so!):
i.e. Information is independent of the material particles. This ‘modest’ finding directly refutes the reductive materialistic claim that says immaterial information is merely a metaphor and/or emergent property of some material substrate.
Of related note:
Bornagain77:
“timothya, you misunderstand my claim. I am not claiming that full scale communication is possible via entanglement alone. I am well aware of the speed of light caveat for full scale communication. The modest claim, a claim that is backed up by ample experimental evidence, is that, via quantum teleportation, information can be transferred between particles completely independent of the material particles themselves physically interacting:”
No, I do not misunderstand your claim. Here is why.
1. As soon as a remote (classical) system interrogates a quantumly entangled particle about its state, the entanglement is broken.
2. The corresponding state of the local particle after the remote interrogation is then no better than 50 per cent likely to correspond to the state of the remote particle.
3. This is a result predicted by a well-attested mathematical theorem
Do you have any evidence that the theorem is wrong?
timothya so what? The important thing is that the state of the entangled particle(s) is instantaneously determined without recourse to any possible materialistic explanation.
You flippantly stated: “it’s the million years, stupid”
Yet quantum mechanics could care less about time,,,, “For instance, space and time are two of the most fundamental classical concepts, but according to quantum mechanics they are secondary. The entanglements are primary. They interconnect quantum systems without reference to space and time. If there were a dividing line between the quantum and the classical worlds, we could use the space and time of the classical world to provide a framework for describing quantum processes. But without such a dividing line—and, indeed, without a truly classical world—we lose this framework. We must explain space and time (4D space-time) as somehow emerging from fundamentally spaceless and timeless physics.”
Simply put, Quantum Mechanics simply destroys any purely reductive materialistic conception of nature:
Bornagain77:
“timothya so what? The important thing is that the state of the entangled particle(s) is instantaneously determined without recourse to any possible materialistic explanation.”
I’ve given you a “materialistic explanation” of why your ouija board can’t work. It is now up to you to provide a scientifically plausible reason to abandon the current state of physical understanding. Go to it.
You’ve done no such thing. You either misstated something or else you do not understand entanglement (or both)
Bornagain77:
“You’ve done no such thing. You either misstated something or else you do not understand entanglement (or both)”
Heh.
You will have to be a bit more specific or else the onlookers might assume you can’t make good on your claim that information flows faster than light. Both the experimental evidence and the theorems suggest you are wrong.
Silver Asiatic @16,
Thanks. No, I was thinking(operative word) what you clarified, but had a glitch in the system 😉 Great summary too by you.
Was in a hurry and flipped an “and/or” thought about modifications into “usually” for some odd reason.
So much for mutations making sense 😉
OLV @25,
Nice find with Ubiquitin post-modifications.
Cross-posted your link to Gpuccio’s article on The Ubiquitin System: Functional Complexity and Semiosis…
https://uncommondescent.com/intelligent-design/the-ubiquitin-system-functional-complexity-and-semiosis-joined-together/#comment-662072
Whatever timothya, I have confidence that unbiased readers can easily judge who is being fair to the evidence from quantum teleportation and who is trying to blow smoke.
PaV:
You are too modest.
Just because information “is always tied to a physical representation,” it does not follow that it “is not a disembodied abstract entity.”
Over at TSZ keiths argues that disembodied things, things that don’t even exist, are tied to a physical representation.
BA77 @ 41: Indeed we can.
bornagain77
Truth Will Set You Free said it correctly at #44.
Keep posting your interesting comments. Don’t let the surrounding noise (there’s a lot of it) distract you.
@bornagain77 #29
You provided the link:
https://phys.org/news/2011-01-scientists-erase-energy.html
This research proposes a way to erase information without a heat energy cost. It in no way disproves the fact that a physical substrate is required to encode the information in the first place, which was my original point.
DD, Landauer specifically held that ‘information is physical’ precisely because he believed it always took energy to erase it. He was proven wrong in that assumption and therefore his supposed experimental proof that ‘information is physical’ collapses in on itself.
A little background,,,
I was surprised to learn that, counter-intuitive to materialistic thought (and to every kid who has ever taken a math exam), a computer does not consume energy during actual computation but will only consume energy when information is erased from it,,, such as what happens when a computer’s memory is cleared or with the merging of two computation paths where you put in two bits into a logical operation, and you get one bit out. This counter-intuitive fact of energy expenditure during erasure is formally known as Landauer’s Principle.
When I first realized that it took energy to erase information from a computer, and yet no energy was consumed during computation itself, then that implied, for me at least, that information must be physically real and independent of matter and energy since it took energy to erase information from the computer. After all, if you want to move a car you need to supply energy. And thus, why should any energy be expended at all by the computer unless real work is being performed on a real entity when it erases information?
Yet, even though it was a counter-intuitive surprise for me to learn that a computer will not consume energy while it is supposedly ‘working’ during its computation, but will only consume energy during the erasure of its information, it should be noted that Rolf Landauer himself maintained that the information in a computer is ‘physical’.
When I first heard that Landauer said ‘Information is Physical’, I first thought that Landauer was directly implying that information is physically real and therefore independent of matter and energy. Yet on closer examination I found out that my first impression of what Landauer meant by his statement ‘Information is Physical’ was wrong. Landauer was actually implying that information is physical because it is inevitably inscribed in a physical medium.
In fact Landauer said that Roger Penrose’s contention that information has an existence independent of matter and energy was a quote unquote ‘quaint notion’.
That Landauer would hold that information does not exist apart from its representation in a physical medium was surprising for me. Did the late Landauer really believe that the number 4 completely disappears from reality when he erases a representation of the number 4 from a computer?
Apparently he did believe just that since he derided Penrose for his ‘quaint notion’ of information’s independent existence apart from matter and energy.
Yet contrary to what Landauer and other atheistic materialists may believe, there is much evidence for the physical reality of immaterial information which is independent of matter and energy.
In fact, the entire field of mathematics presupposes the physical reality of the immaterial Platonic realm of information which is independent of matter and energy.
In fact, the physical reality of the immaterial information of mathematics, (as well as the physical reality of the immaterial mind), is abundantly testified to by the very existence of modern technology:
If immaterial information (and the immaterial mind) was not objectively real in some meaningful sense, apart from its encoding on material substrates, then the ‘miracle’ of modern technology simply would never have been possible.
Moreover, Landauer’s supposed experimental proof that information does not exist apart from its representation on a material substrate was that it supposedly always took energy to erase it from the computer. But that supposed ironclad experimental proof of Landauer’s was overturned. To repeat:
In fact, as also referenced previously, information can be transferred between particles completely independent of the material particles themselves physically interacting:
In fact. quantum computation itself is dependent on the physical reality of some type of immaterial ‘platonic’ realm:
In fact, as also already referenced, in the quantum world it is immaterial information that is primarily conserved. Not matter and energy that are primarily conserved. . As the following article states, ‘In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed.’
In fact, not too long ago there was a fairly big debate in physics about ‘conserved’ information possibly being erased in black holes .
Then there is also the fact, as was referenced in post 15, that work is being accopmplished with immaterial information:
Thus DD, you and other atheistic/materialistic trolls can stamp your feet all you want that information does not really exist apart from its material representation, but that does not change the fact one bit that there is abundant empirical evidence now confirming the fact that immaterial information has a VERY pronounced effect on material substrates that would simply be impossible were it not for the objective existence of some type of “Platonic realm” of immaterial information. An objective existence completely apart from its representation on material substrates.
@ba77 #47
You said:
“Landauer was actually implying that information is physical because it is inevitably inscribed in a physical medium.”
Yes. That is what he meant, and he is right. Nothing in your “wall of quotes” refutes that.
All you need to do to refute it is to send me a container full of pure information with no matter or energy involved.
DD, I did not list my ‘wall of quotes’ for your benefit (in fact I consider you a troll who should be banned from UD), but I listed them for the benefit of unbiased readers. On that score I am more than satisfied that I have made my point about the physical reality of immaterial information abundantly clear.
Deputy Dog @ 23
Perfectly good questions, I would say. Telling me that information is neither matter nor energy nor any variant thereof, tells me what it isn’t, it doesn’t tell me what it is. Perhaps it is a misconception to think of it as some sort of third domain of existence, a reification of the abstract.
As for the problem of reconciling quantum teleportation with relativity, perhaps we are not thinking far enough outside of the box.
I was musing about of how two-dimensional beings living in a 2D universe would perceive a 3D sphere that passed through their world. I imagined them seeing it as starting as a point that extended in both directions to form a line which then contracted back to a point and then disappeared. As 2D beings they would have no conception of a 3D sphere. For them it would be an extending and contracting line.
Now, suppose our two entangled but separate quantum particles are actually two manifestations of a single entity that exists in one or more dimensions beyond the four that we experience. Perhaps, when we change the value of one of the particles properties and observe a corresponding change in the remote particle, we are actually performing one operation on a single entity which is manifest in two separate locations in our 4D world. We cannot conceive of what awareness of additional dimensions would actually reveal, any more than the inhabitants of the 2D universe could envisage a 3D sphere.
Just a thought.
Seversky, better watch it, such ‘musings’ about higher dimensions is dangerously close to ‘musing’ about a eternal heavenly dimension above this temporal dimension, (which Christians have ‘musing’ about for a few thousand years now):
A few notes to that effect:
Of related note to ‘musing’ about higher dimensional objects interacting with a 2-dimensional plane, a three-dimensional hologram appears on the 2-dimensional surface of the Shroud of Turin:
All in all, I find our very best ‘higher dimensional’ mathematics behind our very best scientific theories to be extremely comforting to overall Christian presuppositions:
Verse:
The methods in this paper seem pretty interesting, but I don’t think the requirement of promoter-enhancer proximity for full gene activation is anything new or “stunning.” It’s just a fact of how enhancers work, and the resulting transcription in turn reinforces the close proximity between promoter and enhancer through protein interactions.
Nothing in this paper “leaves in shambles” any current evolutionary ideas.
Seversky
“Telling me that information is neither matter nor energy nor any variant thereof, tells me what it isn’t, it doesn’t tell me what it is.”
Excuse my interference. This apophasis applies not only to information, but also to time, space, energy, mass or anything else we think we know about.
@Seversky #51
Interesting thoughts.
I tend to think that it is often necessary to start with what a thing is NOT, in order to eventually arrive at what it IS.
Reductio ad absurdum is a powerful tool for eliminating nonsense.
As for entangled particles being a manifestation of one unseen entity, isn’t that the basis for the “hidden variable theory” of quantum mechanics?
https://en.wikipedia.org/wiki/Hidden_variable_theory
Deputy Dog:
Neither matter nor energy would exist without information.
@ET #56
ET:
As a cause, or as a side-effect?
Deputy Dog @ 57
As a cause
GC
Yes, it’s just observations and explanations. Evolution did not enter into the discussion. Evolution contributes nothing to it.
I don’t want to sound glib but that only tells me that evolution was already in shambles before this paper.
@ET #58
That implies information can exist on its own.
So…. do YOU want to fill the container, to prove your hypothesis?
as to the materialistic conjecture of hidden variables. That conjecture is now experimentally falsified.,,, A few notes to that effect:
And, despite the ill-founded hope of Einstein and other materialists, that hidden variables between particles might someday explain away the instantaneous ‘spooky action at a distance’ found in quantum mechanics,,
,,,despite that ill-founded hope of materialists,,, The fact of the matter is that multiple mathematical theorems have all but proven that hidden variables between particles cannot explain away the instantaneous ‘spooky action at a distance’ that is seen in quantum mechanics.
Besides these multiple mathematical theorems that have all but proven that hidden variables between particles do not exist, it has now, as previously mentioned, also been experimentally confirmed that “entangled objects do not cause each other to behave the way they do.”
Simply put, with the refutation of hidden variables, there is no cause within spacetime that materialists can appeal to in order to ‘explain away’ this instantaneous ‘spooky action at distance’ witnessed in quantum mechanics. As the following article states, “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,”
Whereas, on the other hand, I, as a Christian, presently have, and have always had, a beyond space and time cause that I can readily appeal to in order to explain quantum entanglement:
Here is a bit more background on just how badly Quantum Mechanics has now refuted Einstein’s materialistic preconceptions about the universe,,, as well as his materialistic preconceptions about how the universe should operate:
Deputy Dog:
Does it? Well information is neither matter nor energy so there you have it.
The container wouldn’t exist without information. The matter and energy it took to make the container would not exist without information.
At 48, ba writes that it is basically confirmed that there is,
This is the fundamental philosophical difference between dualists and monists: to ba and others abstractions have an independent existence in some Platonic sense.
Others don’t believe this, and certainly don’t believe it is a confirmed fact.
Obviously, Christians who believe that “in the beginning was the word” are such dualists, FWIW.
So Deputy Dog, for instance believes, as do I, that information must come in some physical form: it doesn’t exist by itself, Platonically.
This is matter of metaphysical perspective, in my opinion, not a matter than can be empirically investigated, much less settled.
Silver Asiatic @59:
In reference to George Castillo @53, the Darwinian theory is its own worst enemy. This paper does not affect its miserable state which seems getting worse by day. It’s a matter of time.
DD @ 49
It may be true that information requires a physical medium. But from that it does not follow that information, therefore, is necessarily physical itself.
You’re requesting that matter and energy be involved, but information may be an immaterial entity that acts upon matter and energy (“inscribed in a physical medium” as someone said). Matter and energy may necessarily be “involved” but not necessarily a component part of information.
It may be true that the only way we can make information “visible” is through its effects on physical things – but that does not mean that information is necessarily physical.
A thought can cause a human being to move, but that does not mean that the thought is necessarily a physical thing.
jdk
You made a good point that monism is a philosophical/metaphysical conclusion.
But isn’t it a problem for monism to assert that everything is reducible to matter, but at the same time accept that we cannot reduce information to a material source?
Because if we could do that, the question of the monistic nature of information would not be a philosophical question. There would be evidence that information is a physical substance and therefore it could be evaluated by empirical evidence. Correct?
Geroge Castillo @53:
What you’ve written is correct. But that’s not the central finding of their study. Instead, they find that not only is “promoter-enhancer proximity for full gene activation,” but that the chromatin stabilizes this proximate positioning.
Here, again, is the critical text (which is bold-faced in the OP):
So, the focus should be on this stablization brought about within the ‘chromatin.’ This stablization of chromatin means that there is an ordered structure operating within the chromatin—it’s not just ‘shielding.’
Your assessment is this:
Here’s what I said:
We’re finding, day after day, layers upon layers of orderliness. All of this integrated orderliness is explained by darwinists as happening at “random.” We’ve reached mind-boggling proportions of order—i.e., complex, specified information, and this compounding of ‘order’ now means the exponential growth of order. It is this exponential growth of order which has now caused Darwinism to lay in “shambles.” Intellectual honesty demands it.
But, you know, lots of people are not intellectually honest. And, depending on our own personal investment in a particular point of view, it can be very hard to do so.
As Max Planck, the discoverer of the ‘quanta’ said, “A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”
Of course, this is precisely why Darwinists won’t allow anything dealing with ID to be published, nor anything like it to be taught in schools—because this will only draw nearer the day when Darwinism disappers.
(P.S. I’ve been sick in bed, and am not sure if I can stay up and running)
PaV:
Very good thoughts! And I hope you can be wll quickly. 🙂
Here is a quote from the beginning of the paper, just to try to understand how important and complex is the role of enhancers:
That’s something, indeed. 200000 – 1000000 enhancers, each of them something between 50 – 1500 bp. Junk DNA! 🙂
And these are only part of the cis regulators. Add to that the plethora of trans regulators, many of which are derived from non coding DNA too, for example lncRNAs, which we have recently debated in some detail here.
https://uncommondescent.com/intelligent-design/breaking-a-junk-dna-jumping-gene-is-critical-for-embryo-cell-development/
Shambles over shambles…
jdk, when I made the statement that you highlighted, I was probably, too charitably on my part, trying to make the argument for higher dimensional information palatable for atheistic materialists.
I could just as easily have extended the argument for the immaterial ‘Platonic realm’ with Godel’s incompleteness theorem and thus brought the argument for the so called ‘Platonic realm’ full circle to the necessity of postulating John 1:1-4
A few notes to that effect:
@Silver Asiatic #65
I agree with what you said in #65, with the caveat that the term “physical” is really making this conversation difficult !
Let’s talk in terms of patterns.
When I put pen to paper, I encode information in the pattern of ink atoms on the paper, forming characters and words. You can read the ink patterns, and it translates to concepts in your mind that are hopefully close to what I was trying to convey. Paper and ink are the media.
But if you burn the paper before anyone reads it, the information goes away. It only existed as patterns. The atoms still exist, but they are scrambled. Those patterns had no meaning unless someone could read and match those patterns to known patterns they had learned previously.
Patterns have existence only as arrangements of matter or energy, and they only have meaning if the creator and interpreter of the pattern have an a-priori shared understanding of the patterns.
The patterns in DNA only have meaning in the context of the biochemicals of a cell, where the cell “knows” how to transcribe the DNA and perform life-related activity. Scramble the DNA irrecoverably and the information goes away. The DNA is the media.
As far as I know, all patterns require a media.
As jdk notes in #63, I am not aware of any evidence of a “platonic realm” that can hold patterns independent of matter/energy.
It’s fine to talk about higher dimensions, or other universes, but they would need to have their own form of matter or energy to encode patterns, based on what we observe in our universe.
DD is either purposely, or ignorantly, trying to be confusing about the issue,
,,, to remind everyone once again, in the classical world information can be created or destroyed,,, however in the quantum world information is conserved
Moreover, to also remind everyone once gain, classical information is now known to be a subset of ‘conserved’ quantum information:
According to the conservation of quantum information, and the fact that classical information is a subset of it, just because you erase something does not mean that the information you erased completely ceases to exist from reality. According to the conservation of information in quantum mechanics, it still must necessarily exist somewhere.
It is also interesting to note that Christians should have expected this ‘conservation’ of information, despite erasure, to be true beforehand.
Verse:
Chromatin: cracking the chemical code
#70 Deputy Dog:
“When I put pen to paper, I encode information in the pattern of ink atoms on the paper, forming characters and words.”
Help me to understand your point.
What information do you encode? Can you give an example?
You say that “chromatin stabilizes this proximate positioning”, but then the quote says that “transcription…enhances the temporal stability of the proximal conformation”
So, it’s not the chromatin doing something, but the transcriptional complexes/processes.
The “ordered structure operating within the chromatin” is reinforced by active transcription and is most likely driven by the protein factors involved.
Repetitive recruitment and associations of protein factors driving changes to the 3D shape of chromatin and driving some level of “orderliness” is not really that complicated and hardly “random,” I doubt any scientist would say so.
This is in fact a good example of evolution taking advantage of two simple processes (protein interactions and promoter-enhancer contacts) in order to bring about a more complex and important cellular event: gene activation.
Deputy Dog @ 70
Agreed that the term physical is causing some confusion. But you lost me with the analogy – not sure where you were going with it.
Yes, shapes or blotches of ink are patterns. The paper is media.
Well, the pen and ink are not the source of the information. In your analogy here, information is clearly independent of the physical media. The same information could be inscribed on any media. Also, of course, whoever created the words retains those words in memory. If someone had read the words, and then the paper was burned just after – then two minds would possess the information. There would be no paper but the information would be retained. So, the information is retained and can be communicated – even when the patterns do not exist any more. So, I think this is an example of how information is not bound to the physical media (the paper in this case). Yes, some will say that the brain is just “inscribing the same patterns”, so now the brain is the media. We don’t have evidence that information in the brain is physical patterns of molecules – for example, that every word we read is an independent configuration in the brain (every memory, etc).
This is true of patterns, yes – but we haven’t reduced information to physical patterns. Obviously, information can be transmitted from human to human through hearing, touch, sight, non-verbal cues – and even suggestion. In that case, a certain movement can “say” more than the movement itself (rolling your eyes at a comment, for example).
The key word you put in quotes, but it’s essential. It’s the “knowing”. If your point is that without intelligence that can know the meaning of symbols and patterns then there is no information – yes, agreed.
Yes, but I don’t think you showed that information is reducible to the pattern. As said, whatever was written with the pen and ink can be written with other instruments on other media. It can be done in different languages or even in coded language – the same information. So, it’s not the pattern or the media. It’s the intelligence that places meaning into the symbols and another intelligence that interprets the meaning. This seems to be a process that is independent of any media or even any particular pattern.
Well, something has to hold the meaning. It’s not the patterns, it is the meaning. It’s the “knowing” that assigns and interprets meaning in patterns. Yes, you wouldn’t find this platonic realm through empirical science, as jdk noted. But I think we do see that information is something independent.
The media, since it can be of a variety of types for exactly the same information, seems to be irrelevant to what information really is.
Chemical chromatin ubiquitylation
George C:
When you say that evolution “took advantage of two simple processes,” you’re using anthropological language to describe a supposedly ‘random’ process.
A senseless, random process that works through elimination is now to be considered as having some forethought. Does ‘evolution’ say to itself: “Aha. Now if only I combine process A with process B, I can generate something that I otherwise couldn’t do.”
In a nutshell, this is the problem.
To get a robotic arm to pick up a nickel and stack it onto a pile of nickels requires computer chips working in sync with one another, all linked to the machinery involved in bringing about its movement.
Now picking up a coin is a “simple process,” and stacking one coin atop another is another “simple process,” so shouldn’t it be ‘easy’ to combine the two? Well, not exactly. Intelligent thought and engineering is required.
How can some kind of random process bring this about?
What does the configuration space of all possible permutations of small section of a genome look like?
How does one part of a genome, separated by 150,000 base pairs “know” how to get close to the other part of the genome?
Who told it to do this? I could go on and on.
When you consider the incredible complexity involved, it staggers the mind to think that some unintelligent process is responsible.
This should be self-evident truth.
I see you don’t actually want to talk about the paper you originally posted on, ok.
And forgive me for anthropomorphizing, I was merely trying to describe some thing in a way simple enough for you to understand.
The fact remains that two very simple processes can bring about order and also plays an important role in a complex event such as gene expression.
This event is extremely different from your absurd robot arm example and you would understand this if you were familiar with biochemistry.
As I have said, no scientist would say this is a random process, and almost nothing is truly random anyways, especially when it comes to biology.
First off we live in the Quantum World, not a classical world,,,
dealing with conservation of information in a quantum world:
Also of related note, besides everything in the universe, even the universe itself, having a wave function, quantum entanglement itself is ubiquitous within the universe and quantum entanglement is actually the process by which decoherence is achieved:
Simply put, Decoherence is actually a quantum process not a classical process as materialists often try to imply.
Bottom line, we live in a thoroughly non-classical, quantum, universe, and as such, conservation of quantum information applies to everything in the universe.
Supplemental quote:
EugeneS @54:
“we think we know about”
Good point. Thanks.
George Castillo @78:
“almost nothing is truly random”
Please, can you elaborate on that? Thanks.
@Silver Asiatic #75
I agree that the media is not the source, and there can be multiple copies in different media, including brains.
But there IS evidence that brains store information as action potentials among neurons – a media involving both matter and electrical energy.
More patterns sent and received by human brains and transmitted by photons.
Sure, although there are plants and animals that instinctively react to chemical signals like pheromones that could be considered information, where the word “knowing” would be a bit strong.
I mostly agree with your comments, and to summarize what I think you are getting at: For us to call something “information”, it has to have meaning to someone somewhere, otherwise it is just a pattern. All information is patterns, but not all patterns are information. I know that it “feels” like the information is independent of the media, since it can be copied to various media and translated to various kinds of representations, but it could not exist without having some media on which to reside. Can software exist without computer memory, or hard drive or SSD on which to reside? Bits need bit-holders.
@PeterA #73
If I write my wife a note to let her know I have gone to the store, I encode (translate) that idea into a string of characters in the English language, by writing "gone to store".
Deputy Dog @ 82
There is evidence of something. But I think, for your point to hold up, we need to see – directly – all of the information inscribed on the medium. So, every word, every image in imagination, every dream. Plus, every new idea that is generated. That is how information is generated, by the intention of the mind. It’s not the medium, as you said.
So, when we talk about the patterns which are information – it is not the patterns, but the mind and intelligence that make them into information. Information exists in the mind and the mind is independent of matter. That’s a reasonable view of it, as I see it.
The ideas and programming for the software can exist in the mind before it is encoded on software. Mozart wrote sonatas that existed as music in his mind. Was the information ‘inscribed’ in the brain before it was created? Is the individual consciousness just looking at neutrons that are already formed as words in the brain?
I think it’s more reasonable to believe that the conscious, intelligent person creates information that is independent of neutrons – and the process of creating thoughts (adjusting, comparing, evaluating) is the ‘inscribing’ of the information into the mental pathways.
This is how we experience the generation of novel information. We do not have an experience of “looking at some pre-existing thoughts in our brain”. Instead, we experience the actual generation of thoughts, by our own will and intention.
Now, you could say that the final result of that willful “arrangement of the brain” to create information is your very point — that the information could not exist unless the brain was configured for those words, images, sounds. I think it’s far from conclusive that every word, every letter – every bit of information and knowledge we have is a physical configuration in the brain – but even if it was, none of those brain patterns are information until the conscious-person freely decides that it has meaning.
Yes, we do not think it’s a conscious awareness from plants or insects for example, but it is a less-strong aspect of “knowing”. When birds communicate, for example, there is an intentionality. There is intelligence at work that separates information from noise and which derives meaning from the information. That is different from a rain drop falling from a cloud. The water moves by gravity and hits the ground. There’s no communication (that we know of) between cloud, water and soil. It’s an entirely determined process. That is the difference with an information loop – where there is a creation of information, a sender, a translation process, and then a receiver – and then action that comes from it all.
The “knowing” aspect is essential to what we call information. Otherwise, it is just patterns – it does not communicate anything.
Geroge C:
I believe you would admit that it’s hard to “talk about the paper” when (1) the paper is not linked in the OP, because (2) I do not have access to the paper since its behind a paywall.
That said, the main point of the post comes directly from the “abstract” (not the ‘paper’), where the opening sentence indicates the purpose of their study:
The authors seem intent on the connection between chromatin and the juxtapositioning of segments of DNA. The critical finding is that there are three conformational structures that the chromatin can take, and that this structure is affected by transcriptional activity.
Hence, one can no longer presume that chromatin structure is passive and inert, but now must assume that it “dynamically” interacts with DNA processes. IOW, a new level of complexity is now in view—the whole point of the post.
As to what I know, or do not know, about biochemistry, I took biochemistry in college years ago. Most of it is about metabolic pathways and activation energies. Is this rocket science?
The authors imply that different energy levels are involved, and this, of course, takes place at the quantum/chemical level.
But you miss the point, and the robotic arm makes the point—namely, that it is not trivial matter to hook up two biochemcial processes when these processes are driven by quantum effects.
You say no one would say this happens randomly; but, that’s not the point. If they did act randomly, no one would have noticed. It would have been background noise.
What matters is that evolutionary biologists claim that life arose through random processes, and each time a new level of complexity and order is discovered—which implies some kind of dynamical interplay, then this only adds to the absurdity of their claim.
Either you see this, or you don’t. And if you can’t, then I can’t help you with this, nor can hours and hours of back-and-forth advance the discussion.
From Science Daily:
I find it remarkable, too. And the “chromatin topology” has some role in all of this.
George @ 78
You can refer to PaV @85 where you’ve been missing the point. We’re talking about the origin of the process, not the process itself.
Mutations are analyzed statistically as if they are truly random. The only source for innovating a complex function of that sort, that evolution gives us, is random mutations. If you’re saying that mutations are not random, then what is causing that to be the case?
Regarding the dynamic response of Chromatin – that is beyond just ordered-complexity. It’s a dynamic relationship.
Of course, it’s not random. In fact, the less random a function is, the more impossible it is for random mutations and selection to create it.
@Silver Asiatic #84
The nature of consciousness is that it SEEMS to arise out of nothing, so it FEELS to be the source of our thoughts. This is what Nasim Taleb calls the “problem of hidden evidence”.
If we could directly sense all the neuronal activity that leads up to a thought or decision, it would be obvious that dualism is false.
Why don’t we sense this activity? Because the firing of billions of neurons would drive us INSANE, that’s why. Selection would have long ago eliminated anything brain that behaved like that.
So we have to resort to other ways of detecting it:
https://www.wired.com/2008/04/mind-decision/
https://www.sciencealert.com/harvard-scientists-think-they-ve-pinpointed-the-neural-source-of-consciousness
“the paper is not linked in the OP”
The first line of the post contains a link to the paper… am I missing something?
Not having access and not willing to pay for something are two different things.
“one can no longer presume that chromatin structure is passive and inert”
On it’s own, it is. It’s not until transcription factors and other proteins act on the chromatin that it is shuffled around the nucleus, driven by successive protein binding interactions that reinforce topological arrangement, as shown in this paper, and bring about distinct nodes of active transcription.
The “new level of complexity” in chromatin organization that you keep harping on about is driven by the downstream product, “gene expression” in this case.
You demonstrate a critical misunderstanding of the report or maybe even biology in general.
What’s happening is not “the chromatin stabilizes this proximate positioning” as you stated in comment 67, but it is the act of transcription. It is a self-reinforcing system which, I might add, is a beautifully simple solution found by evolution in order to drive a complex process (gene expression) through more simple processes, as I said before.
Am I anthropomorphizing again? Sorry!
Also,
“it is remarkable that enhancers can reach the exact target at the right time for that gene to become active”,
I’m sure you are misunderstanding the researcher here, as these events are causal.
The enhancer reaches the promoter and drives the activation of the gene.
“If you’re saying that mutations are not random, then what is causing that to be the case?”
There are numerous reasons why mutations are not random, depending on how you wish to look at it.
There are numerous ways that DNA can be damaged, different regions of the genome are more susceptible to mutations, certain mutations are more easily detected than others, different types of mutations are repaired by different pathways and each of those is pathways is carried out by a variety of enzymes, each with their own biases.
Take your pick.
GS
I think all of those are examples of random effects.
Random outputs can be more or less predictable due to bias or external influences but it is still a stochastic event.
If you’re saying that everything in biology is non-random, deterministic and as predictable as the effect of gravity, for example, I don’t think that’s the case.
Deputy Dog @87
That may, indeed, be one key reason why we do not detect it – yes. But it also may be that thoughts are not directly and precisely represented in neuronal activity. You point here to why we can’t sense our own brain activity – but what about observations of another’s brain? That wouldn’t drive us insane. But we haven’t seen it.
The reports you posted regard correlations of thought and roughly defined sectors of the brain. But not only is this just a relationship, but it does not show that each of our individual thoughts is inscribed in molecules like a pen writing on paper.
From an evolutionary perspective, it does not seem reasonable that we evolved billions of neurons that actually create information like that. I don’t know why selection removed brains that were able to observe their own function, or when those brains existed – but it just doesn’t seem like a workable answer to the origin of the human mind as I see it.
George Castillo and Silver Asiatic:
I don’t want to intrude, but this is an old issue which always generates confusion, so I would like to propose my view.
If we exclude quantum events, randomness in the macroscopic world of classical physics is not intrinsic randomness. It’s just a way we describe a system.
IOWs, all systems in classical physics can be considered deterministic (I am not considering here the possibility of free will intervention). That means that even if we choose the most classic random system, tossing a coin, it is still a deterministic system. The individual results are certainly determined by the laws of classical mechanics.
But of course we cannot really describe the system in a deterministic way, IOWs we cannot really know in advance the sequence of heads and tails that will really take place in the system, because there are too many variables that we cannot measure or anticipate with precision.
So, we could say nothing about a system where a fair coin is repeatedly tossed, because we cannot describe it in a necessity way, even if the system is in reality deterministic.
But that is not really true, because we can say something about that system, and that something is relevant and useful. We can apply to the system a probability distribution, a mathemathical object which really describes some important properties of the system, even if it cannot ever give us any certainty about any specific result. In this case, for some specific number of tosses, the binomial distribution will give us reliable probabilities for a specific outcome, for example the probability of getting 5 heads in 20 tosses is 1.478577e-02. With great numbers, that probability will be the best description we can have of how the system behaves.
So, the definition is quite simple: a system is a random system if the best description we can give of its behaviour is by some appropriate probability distribution.
In that sense, biological mutations are certainly a random system. Some believe that a system is random only if an uniform distribution can be applied. That is completely wrong.
GC says, for example:
“different regions of the genome are more susceptible to mutations”.
And so? That does not make the system less random. Of course, different regions will have different probabilities of mutation. But we cannot anticipate which region will be subject to mutation at a certain moment, therefore the system is random.
Quantum probability, of course, is all another matter. And so is any design intervention.
George C @88:
The first line of the post contains a link to the paper… am I missing something?
When you work for a university that pays for access to Nature’s journals, yes, you click and it opens up. But not if you’re sitting at home at your desk.
“one can no longer presume that chromatin structure is passive and inert”
On it’s own, it is. It’s not until transcription factors and other proteins act on the chromatin that it is shuffled around the nucleus, driven by successive protein binding interactions that reinforce topological arrangement, as shown in this paper, and bring about distinct nodes of active transcription.
There’s a certain blindness, or inattention, to the dynamics involved. It seems that you presume everything that happens happens because of the DNA. But isn’t it true that the DNA is actually passive when it comes to the chromatin structure? After all, it is the Chromatin structure that enables a huge length of DNA to be compartamentalized within the nucleus of the cell.
It is this dynamics I’m pointing to. (Dynamics presumes two systems interacting) If one portion of DNA is ‘brought close to’ another section quite distantly located, why would you think that this is brought about by the DNA itself? If I understand you correctly, you’re saying that for the chromatin to “operate” transcriptional factors are required. So this already shows that the chromatin is being acted upon by the DNA once the enhancer is near the target gene.
However, it seems to me that it is simply a conjecture to assume that the DNA is responsible for ‘driving’ the enhancer towards the target gene. It seems to me it is much more reasonable to assume that the ‘chromatin’ itself has some kind of active potential of its own, a kind of inner logic separate from the DNA itself, which has the ability to work harmoniously with the demands of transcription. It’s this likely ‘independence’ that the chromatin structure has on its own that I’ve been pointing to all along. (I presume that at this point in time, whole portions of chromatin activity/activation/etc. is hidden. This paper is an attempt to move beyond this. I feel that logically, some such hidden potency must exist, and will eventually be discovered)
The authors seem to agree with this as you remember. They said: Given that there can be numerous genes between the enhancer and its target, it is remarkable that enhancers can reach the exact target at the right time for that gene to become active.
They’re saying: “How does this come about by chance.” I’m saying the same thing.
What’s happening is not “the chromatin stabilizes this proximate positioning” as you stated in comment 67, but it is the act of transcription. It is a self-reinforcing system which, I might add, is a beautifully simple solution found by evolution in order to drive a complex process (gene expression) through more simple processes, as I said before.
However you want to slice it, the stablilization involves the chromatin “topology.” This was the very question they were asking themselves.
Again the opening sentence of the abstract:
A long-standing question in gene regulation is how remote enhancers communicate with their target promoters, and specifically how chromatin topology dynamically relates to gene activation.
From this one sentence it should be clear that these researchers consider the “communication” taking place between the “remote enhancer” and this “target promoters” as involving in some manner the “chromatin topology.” That the “act of transcription” is what affects the chromatin so as to “stabilize” it only points out the dynamical relationship between DNA strands and chromatin structure that must underlie the transcriptional mechanism. This needs explaining.
When you say this, “It is a self-reinforcing system which, I might add, is a beautifully simple solution found by evolution in order to drive a complex process (gene expression) through more simple processes, as I said before”, here’s what I see:
(1) You’re admitting that what we see is a dynamic “self-reinforcing system.”
Well, “system” is a charged word. Where in the natural order do we see such incredibly precise “systems” at work? Scientists now labor to accomplish just a bit of what we’re seeing take place within the cell. This kind of nanotechnology is the only comparable analogy to what we see happening in the cell. Well, how did “nature” master what humankind at its intellectual peak can only stumble around with?
Which leads to (2) How can you say that “evolution found” this solution when, in fact, if this “solution” weren’t already in place, then eukaryotic life would cease. Hence, this “system” had to be in place before ‘evolution’ could ever have laid a hand on it.
These are severe logical difficulties. This was the point of the post.
I simply have not your faith in ‘evolution.’ I see ‘design’ instead. And I don’t need to know Who the Designer is; all I need to know is how His logic operates. [Little by little, scientists around the globe are making this more and more understandable; actually the word is not ‘understandable,’ but evident.]
#83 Deputy Dog:
OK, thanks.
Now, let’s suppose you have a dog, a cat, a fireplace, and a standing fan. Let’s say that the dog barks up to the cat, the cat runs away and jumps, landing on the base of the standing fan, right on top of the button to turn the fan on, then the wind blows your note into the fireplace and the flame devours your note. Gone. C’est fini. Your wife won’t get the information that was encoded in the note. Sorry for that.
But what about the original information? Does it still exist? Where is it?
Now, let’s assume that your wife was talking to somebody on the phone when you went to the store. Being such a nice guy, you did not want to interrupt her important conversation, hence you wrote the note and left it on the table.
After finishing her conversation on the phone, your wife looks for you to no avail. Then she calls you and asks “honey, where are you?”
Probable you will respond: “I left a note for you with the information about me, didn’t you see it on the table?”
“Oh, no” your wife may respond.
Could you repeat the information that was written in the note that got consumed by the flames in the fireplace? At least the main idea?
Is it too late? Oh, no!
Note this is in reference to #70.
Thanks.
Saw this on KGOV.com:
RSR: Good Mutations Occurring On Demand
Blyth Institute Research on Mutation By Design: Bob Enyart interviews Jonathan Bartlett, the layman who founded the Blyth Institute (.org) after spending years researching the nature of mutations to understand the genetic disease that tragically took the lives of his two young children. It turns out that while many mutations are random and apparently neutral or often harmful, our body itself intentionally induces a large percentage of mutations and targets them often at miniscule segments of the DNA with beneficial and needed results.
Soooo…the body takes the neutral & harmful mutations and uses them for BENEFITS?
Just throwing this out there. I would appreciate some good feedback on this. Small video at the website by Jonathan Bartlett.
Buzulak:
I think there are two completely different processes that are discussed in the video by johnnyb.
When you say:
“our body itself intentionally induces a large percentage of mutations and targets them often at minuscule segments of the DNA with beneficial and needed results”
you are probably referring to the process of antibody affinity maturation, which I have discussed in some detail here:
https://uncommondescent.com/intelligent-design/antibody-affinity-maturation-as-an-engineering-process-and-other-things/
This is an algorithmic process embedded in organisms, especially mammals, and it is very complex and highly engineered. The mutations in that process are highly controlled, but they are implemented by specific proteins (in particular Activation-induced cytidine deaminase) in a process called somatic hypermutation. These mutations, even if essentially random, are very different from the “usual” random mutations that take place in normal DNA duplication.
A second process referenced by Bartlett is instead the interesting possibility that some mutations that happen in the course of evolutionary history are guided and beneficial. Transposons could be a special tool for that kind of process. I absolutely agree with that idea, which is of course a typically ID model. I don’t agree that guided mutations are the rule, and random detrimental mutations an exception, as Bartlett seems to say. I would say the opposite is true. But the general idea is certainly correct.
@PeterA #94
Sure, I still have the information in my head and can reproduce it. So what? That doesn’t mean it can exist without a substrate.
If a meteorite falls to earth and vaporizes my head, no one would ever be able to recover the information, because all substrates upon which it was written are gone.
#97 Deputy Dog:
Well, that’s not necessarily true. Unless you can prove it.
It’s just your personal opinion. That’s all.
The hypothetical event you describe may kill the body but not the soul.
At this point, our discussion has hit a wall, hence it must stop.
It’s just your belief vs. mine. Not worth discussing it.
Besides, this seems like digression from the OP topic.
@PeterA #98
Oh NO ! Discussing BELIEFS ! Must STOP !
Peter, meet UncommonDescent.
#99 Deputy Dog:
“meet UncommonDescent”
Please explain what you meant. The penny didn’t drop in my mind. Thanks.
That is the exact opposite of what I was saying, PaV. It’s clear that your lack of knowledge is going to hinder any further conversation about this paper. For our purposes DNA/chromatin are interchangeable. In the nucleus virtually all DNA exists as chromatin, which is DNA wrapped around a histone every ~200 bases.
DNA/chromatin is passive, it does not have some “inner logic”. What it has is a variety of sequences that are binding sites for proteins, these proteins are driving the 3D organization/topology of the DNA/chromatin.
George Castillo (and Pav):
How does the chromatin get assembled?
Does it come in the cell package?
How does the cell arise?
I have more questions, but let’s start with the simpler ones.
Thanks.
PeterA,
Those are rhetorical questions, aren’t they?
You should know by now that those guys don’t have even a clue about what you’re asking
Paolo Verspi,
My questions are valid.
You better go back to the philosophical discussion threads and stay away from serious scientific discussions.
Peter,
Chill out
Paolo,
Take it easy buddy. Leave Peter alone. His questions are valid. They were not addressed to you. Just move on.
Transcriptional Regulation by Chromatin and RNA Polymerase II
new chromatin regulatory mechanism?
Peter, it is unclear what you are asking in all 3 of those questions.
George Castillo,
Perhaps it’s unclear to you because you lack something basic that is required to understand those questions.
There’s no much I can do to help you. Sorry.
George Castillo,
Maybe OLV can give you a hand. He’s more technical (nerdy) than I am.
Definitely refrain from engaging in any discussion with Paolo V.
He could sweep and mop the floor with your best ideas, though he is merciful at times. ????
Peter,
Please, leave me out of your unproductive discussions with folks who are not interested in discussing anything seriously.
I don’t have time to squander. Ok?
Peter,
I agree with Paolo. Better think twice before getting in a situation where you might end up throwing pearls before swines.
BTW, thanks for calling me “nerd”. 😉
Oscar Luis,
I don’t understand your position on this.
First you say my questions were valid but later you backtrack?
Can’t you make your mind?
🙂
Eukaryotic genomes are stored in the form of chromatin. The fundamental building block of this polymeric structure is the nucleosome in which the DNA is tightly associated with an octameric assembly of the highly basic histone proteins, H2A, H2B, H3, and H4.
In eukaryotic cells, genetic information stored in DNA is present in a highly organized chromatin structure. The nucleosome, the basic unit of chromatin, is composed of two copies of each core histone, H2A, H2B, H3 and H4, wrapped by about two turns of DNA.
Peter,
Did you scare away your interlocutor ?
Paolo,
Peter just provided hints. However, his interlocutor hasn’t come back, but we don’t know why. Peter will have to wait patiently. If the discussion gets technical, which I doubt, I may jump in too. But don’t hold your breath waiting for that to happen. The comment at #109 seems to indicate that the guy is not too serious about this.
Oscar Luis,
The discussion has been technical from the start.
Several folks have posted very interesting comments in this thread.
But in any case, you don’t have to wait for the discussion to get more technical. If you have something to contribute with, go ahead and post it. I’d enjoy it.
Peter,
thanks for the invitation to contribute.
I’ll keep it in mind.
Here’s a paper that I think was posted earlier in this thread, but it won’t hurt to repost it:
Unlocking the chromatin code by deciphering protein–DNA interactions
Gene-regulatory interactions in embryonic stem cells represent cell-type specific gene regulatory programs
Oscar Luis,
Interesting articles. Thanks.
BTW, I think Paolo found his turf to hang around in. Did you see his post in another thread? Good for him. 🙂
No, either the questions asked are so broad that it’s unclear exactly what is being asked, or they flat-out don’t make sense.
If you want answers, try asking more precise questions.
Complex systems biology
George Castillo,
PeterA posted this in #115:
and this in #116:
Do not elaborate. At this point just answer yes or no. Thanks.
Do you know how the genetic information is stored in prokaryotes?
Do you know how the eukaryotes got this chromatin structure?
Some folks here claim it was designed and they back it with a rational explanation.
Do you have a different explanation?
Do you require more precise questions?
Do these questions make sense to you?
Yes.
Yes, plausible evolutionary pathways have been shown.
Yes.
Yes.
Yes, for the most part.
Complex systems biology
George Castillo,
Thank you for answering the questions.
To this question:
“Do you know how the eukaryotes got this chromatin structure?”
you responded:
“Yes, plausible evolutionary pathways have been shown.”
Can you point to the most serious (credible, comprehensive, coherent) literature that shows those plausible evolutionary pathways? Let’s review it together here.
Thanks.
PS. as gpuccio has said in this website, the appearance of the eukaryote cells is as amazing as the origin of the most simple cells. I think he’s completely right on that. Actually, he has elaborated his arguments very extensively -mainly at the protein level- in various articles he has posted here. You may want to review them for your information.
Here’s what a 5 minute search on pubmed gets me.
Did you really need me to do that for you?
Phylogenomics of the nucleosome.
Nat Struct Biol. 2003 Nov;10(11):882-91.
Histone variants–ancient wrap artists of the epigenome.
Nat Rev Mol Cell Biol. 2010 Apr;11(4):264-75. doi: 10.1038/nrm2861. Epub 2010 Mar 3.
Archaeal histone selection of nucleosome positioning sequences and the procaryotic origin of histone-dependent genome evolution.
J Mol Biol. 2000 Oct 13;303(1):25-34.
Phylogenetic analysis of the core histones H2A, H2B, H3, and H4.
Nucleic Acids Res. 1994 Jan 25;22(2):174-9.
Evolution of histone H3: emergence of variants and conservation of post-translational modification sites.
Biochem Cell Biol. 2012 Feb;90(1):79-95. doi: 10.1139/o11-036. Epub 2011 Sep 12.
DNA repeats and archaeal nucleosome positioning.
Res Microbiol. 1999 Nov-Dec;150(9-10):701-9.
Structure and functional relationships of archaeal and eukaryal histones and nucleosomes.
Arch Microbiol. 2000 Mar;173(3):165-9.
Histones and nucleosomes in Archaea and Eukarya: a comparative analysis.
Extremophiles. 1998 Aug;2(3):141-8.
The evolutionary history of histone H3 suggests a deep eukaryotic root of chromatin modifying mechanisms.
BMC Evol Biol. 2010 Aug 25;10:259. doi: 10.1186/1471-2148-10-259.
Evolution of histone 2A for chromatin compaction in eukaryotes.
Elife. 2014 Jun 17;3. doi: 10.7554/eLife.02792.
Archaeal histones: structures, stability and DNA binding.
Biochem Soc Trans. 2004 Apr;32(Pt 2):227-30.
Rapid divergence of histones in Hydrozoa (Cnidaria) and evolution of a novel histone involved in DNA damage response in hydra.
Zoology (Jena). 2017 Aug;123:53-63. doi: 10.1016/j.zool.2017.06.005. Epub 2017 Jun 15.
Bacterial histone-like proteins: roles in stress resistance.
Curr Genet. 2015 Nov;61(4):489-92. doi: 10.1007/s00294-015-0478-x. Epub 2015 Feb 13.
A histone-like protein of Helicobacter pylori protects DNA from stress damage and aids host colonization.
DNA Repair (Amst). 2012 Sep 1;11(9):733-40. doi: 10.1016/j.dnarep.2012.06.006. Epub 2012 Jul 8.
OLV,
I’m back. Will join you to review the papers George Castillo has listed.
Let’s see what we find in there.
George Castillo,
Thanks gor listing those papers.
Let’s review them to see what they say on the discussed issue.
George Castillo,
Thanks for the information.
I could have done that too, but wouldn’t.
Let’s see what is in there.
Peter,
Look for the (comprehensive, coherent) explanation of the underlying mechanism(s) to go from the prokaryote to the eukaryote chromatin structure. Thanks.
This oughta be good.
OLV,
Ok, will do.
George Castillo,
@128 OLV wrote to you:
“let’s review it together”
referring to the literature you would list.
Did you see if the papers you listed show how to get the chromatin structured in the eukaryotes starting from the prokaryotes?
I think that’s what OLV is looking for. Maybe that’s why he asked you “how” @128.
George Castillo,
Yes, agree with what you wrote @134.
I’m sure OLV coincides with us on that too.
🙂
George Castillo,
They should give you credit for activating the discussion in this technical thread. Maybe gpuccio, DATCG, ET, Upright Biped and the thread author PaV will join in too?
I’m watching from the sideline. This is too technical for me. I’m sure Oscar Luis and Peter are enjoying this friendly debate.
PaoloV,
Yes, it would be interesting to see PaV, gpuccio, DATCG, and other frequent contributors coming back to this discussion. They could contribute with their usual insightful comments.
At this point the ball is in PeterA’s and OLV’s court. Let’s not put pressure on them now, but they better come back and keep this interesting discussion going.
I assume they are reviewing the papers George Castillo posted @129. BTW, I agree with what he wrote @134: “This oughta be good.”
jawa,
do you have any idea what they could be looking for in those papers?
I doubt they even know what they’re looking for.
Paolo,
Obviously, according to what OLV wrote @128, it seems like they are looking for a comprehensive (i.e. all the bells and whistles, the whole enchilada) and coherent (i.e. rationally, physically, chemically, logically, mathematically consistent) explanation of the spatiotemporal mechanisms that led to the appearance of the functionally complex chromatin structure in eukaryotes. Keep in mind that some of those papers seem to be behind a paywall and we don’t know how much access those guys have to that kind of restricted literature.
BTW, in a sense they are doing the work their dissenting interlocutor should have done. But that’s fine. The rest of us appreciate their effort.
I look forward with much anticipation to reading their comments when they come back to continue the discussion.
These papers are not in the list @129, but they seem interesting too:
Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates
From dynamic chromatin architecture to DNA damage repair and back
A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage
Here’s the list posted @129 but chronologically sorted:
I quickly looked at the three most recent papers in the list and did not find what OLV and PeterA must be looking at. If the most recent papers don’t mention it, why would an older paper do it? However, they might, hence it would not hurt to look at them too.
It seems like George Castillo should start looking for more recent papers to see if his argument can stay afloat. But let’s not rush to draw premature conclusions. Better let’s wait for OLV and PeterA to see if they find something relevant in the full text of the paywall papers.
12. 2014 Jun
Evolution of histone 2A for chromatin compaction in eukaryotes
13. 2015 Nov (paywall)
Bacterial histone-like proteins: roles in stress resistance
14. 2017 Aug (paywall)
Rapid divergence of histones in Hydrozoa (Cnidaria) and evolution of a novel histone involved in DNA damage response in hydra
jawa,
Note that this discussion thread is now the most popular the last 30 days in this website.
I didn’t expect so many nerdy readers visited this website.
Paolo,
would you have preferred to see a more philosophical / less scientific thread to be the most popular?
I was asked for papers on evolutionary pathways of histones and their usage.
I provided them.
Obviously there was never any intention to read and discuss the papers, just posturing and subterfuge.
I guess I shouldn’t really be surprised.
George Castillo,
You’re completely off target, buddy. Sorry to tell you this.
OLV wrote to you @128:
You have failed to point to the text within those (or other) papers where the spatiotemporal mechanism(s) that made the chromatin appear in the eukaryotes are explained clearly and coherently.
Perhaps PeterA and OLV are trying to find such explanations. They probably are having problems obtaining the full text of some of the papers that you referenced which are paywall.
In my opinion PeterA, OLV and maybe even jawa are wasting their time looking for something that doesn’t exist. Your answers to OLV’s questions were simply misleading as if trying to hide your own realization that such mechanisms haven’t been explained yet.
The biological systems are designed. No unguided mechanisms can explain the functional complexity observed by the researchers.
Wake up and smell the coffee! It’s time for you to realize that you’re on the losing side of this debate.
“Can you point to the most serious…literature”
Is what was asked of me.
That is exactly what I did.
And no one cares what your opinion on the matter is because you’ve already admitted in comment 138 that “This is too technical for me”
George Castillo,
There’s no such a known mechanism underlying the appearance of the chromatin in the eukaryotes. And there can’t be any because the functionally complex chromatin as well as the rest of the cell is designed.
One doesn’t need any technical expertise to know that. It suffices to look at the evidences.
I may be out of my turf here, but I’m sure PaV, DATCG, gpuccio, Upright Biped, Dionisio, PeterA, OLV, Jawa, and other folks I’ve seen posting insightful comments here, could sweep and mop the floor with the expertise of any experts out there.
Bottom line, neither the papers you indicated not any other paper you may point to could explain how the chromatin appeared in the eukaryotes.
They might speculate on many things, but nothing worth consideration.
You lost before the game started.
You sure are saying a whole lot for someone who’s already admitted the topic is too technical for them.
Unfortunately it’s a whole lot of nothin.
George Castillo,
Perhaps this science topic is too technical for Paolo, who seems more attracted to philosophical/theological discussions. However, what he wrote could be valid. I looked only at the 3 most recent papers among the 14 names you posted. I did not find any explanation of the mechanism(s) underlying the appearance of the functionally complex chromatin in the eukaryote cells. I have to admit that some of the papers in your list are hidden behind a paywall. We could assume that PeterA and OLV are trying to review the full text of all the papers, hence they have to obtain access to the “paywall” ones. That could take some time.
From the little I saw, nobody seems to present a comprehensive/coherent explanation for the appearance of chromatin in the eukaryote cells.
You two geniuses must have missed the fact that each one of those papers presents evidence for the evolution of histone proteins. (which is exactly what I was asked to provide)
Why don’t we just start with this:
I believe this conversation began with Peter and OLV harping on the fact that eukaryotes have histones and a complex genome organization, while prokaryotes do not have histones. (see #125)
What they didn’t know is that there are proteins in bacteria that have similarities to histones in both structure and function, they have even been called histone-like proteins.
Now that they know this, it seems they have run for the hills.
Now, what do you think about these proteins?
Do you think it’s just a coincidence that bacteria have proteins similar to histones… what some may call “potential precursors” to histones?
George Castillo,
Please, do me a favor:
Open this website https://uncommondescent.com/ in a separate tab of your internet browser. Then slowly scroll down the front web page. What is the first reference to this current discussion thread that you see? What does it say? What does it mean to you? Thanks.
Paolo,
Now you lost me. Can you stick to the discussion topic? Please?
Thanks.
Paolo,
Never mind. You may disregard my previous comment.
It was a knee-jerk reaction to your weird comment @154.
Better stay away from this discussion thread.
Here we are discussing Biology, not philosophy.
OK?
George Castillo has presented an interesting point @153.
If you want to contribute to this discussion, respond to his comment. Don’t digress to another unrelated issue, that in this case seems completely irrelevant.
I don’t think PeterA and OLV have run for the hills. I would like to see them back here, but I realize that it takes time to review all those papers well, specially considering that some of them are hidden behind a paywall.
However, George Castillo raised an interesting point in his comment @153.
Your philosophical comments won’t help us to understand and get to the bottom of what we are discussing here.
Please, don’t take me wrong. This is a friendly advice.
Thanks.
George Castillo:
I have been away, so I can only now join the discussion.
You say:
“What they didn’t know is that there are proteins in bacteria that have similarities to histones in both structure and function, they have even been called histone-like proteins.”
OK, I am not sure that is really true for bacteria. This is from one of your quoted papers:
Bacterial histone-like proteins: roles in stress resistance
And this is from another paper you quote:
Archaeal histones: structures, stability and DNA binding.
Things are different for Archea. Again from the second paper:
And:
So, I can agree that some form of histone fold is already present in some Archaea, and that some DNA regulation is performed by these archaeal histones which is partially related to the eucharyotic function, while still being very different.
That is one more point to believe that the eukaryotic common ancestor derives many structures from Archaea.
I would suggest this further paper:
Structure of Histone-based Chromatin in Archaea
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5747315/
But that is no explanation for the complex and highly fine tuned regulation of chromatin structure in eukaryotes.
Firts of all, these histone like structures in some Archaea (but not in Bacteria) have structural and functional similarities to eukaryotic histones, but lack most of their highly specific functions, especially post-translational modifications and therefore the comnplex histone code which is the foundation for chromatin regulation in eukaryotes.
Second, the complex and dynamic chromatin structure in eukaryotes is cetainly not only realized by histones. There are many different layers of regulation that make chromatin structure a dynamic, complex and still very incompletely understood issue. Followinf yo0ur example, I will give a brief list of recent papers:
Chromatin structure and its chemical modifications regulate the ubiquitin ligase substrate selectivity of UHRF1.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5747315/
The State of Long Non-Coding RNA Biology.
https://www.ncbi.nlm.nih.gov/pubmed/30103474
Roles of NIPBL in maintenance of genome stability.
https://www.ncbi.nlm.nih.gov/pubmed/30096364
By the way, NIPBL is a 2804 AAs long protein which exhibits an information jump of 2124 bits in human conserved information in bony fish.
Protein phosphatases in chromatin structure and function.
https://www.ncbi.nlm.nih.gov/pubmed/30036566
The simple fact is: chromatin regulation and regulatory functions in eukaryotes are much. much more complex than you seem to believe. And there is no convincing explanation for that functional comnplexity. Except design, of course.
I’m glad you agree that there are proteins in bacteria having “marginal similarities with the eukaryotic histones” and also that there are proteins in archaea that are even more similar to eukaryotic histones, gpuccio.
Were you trying to make an argument against me?
I’m a little confused.
George Castillo,
If you’re confused then go back and read carefully gpuccio’s comment again. You may read it as many times as necessary until the penny finally drops and you get the point.
Gpuccio has written a clear (as usual) explanation that makes a very strong case for intelligent design.
He summarized his comment with this excellent paragraph:
“The simple fact is: chromatin regulation and regulatory functions in eukaryotes are much. much more complex than you seem to believe. And there is no convincing explanation for that functional comnplexity. Except design, of course.”
Cars, trucks, buses, trains, airplanes, all of them have wheels and windows.
By design.
However, each of them is a completely separate class of transportation machines.
Uh, no.
Gpuccio himself copied and pasted from a paper stating that bacteria have proteins containing “marginal similarities with the eukaryotic histones” and he then agreed that there are proteins in archaea that are even more similar to eukaryotic histones.
But, despite having just admitted all this, gpuccio then (in typical Uncommon Descent-fashion) went on to claim that the only possible explanation is design.
George, you do realize that these are synthesized proteins, requiring memory right? They are not the products of dynamics, but the products of control — semiosis, not dynamics alone.
The design inference is firmly on the table.
Anything could be on the table when you have the same aversion to evidence that gpuccio apparently has.
You clearly have no idea the detail that GP is accustomed to dealing with. You’ll probably need to sharpen your arguments to keep his interest. Your #162 isn’t likely going to cut it.
Since you brought up the subject of aversion to evidence, can you answer a quick question: We know that aminoacyl synthetases are the finite set of complex proteins that establish the genetic code. Their task in the cell is to perform a double-recognition and bind a particular amino acid to a particular tRNA adapter prior to the act of translation. We can all conceive of their significance to the system.
They are synthesized from nucleic memory, and it stands to reason that there was once a time in earth’s history that none of the set of aaRS had ever been synthesized from that memory. Here is my question: Regardless of what anyone thinks preceded that time, at the point in earth’s history that the first ever aaRS was successfully synthesized from memory, how many of the other aaRS had to be in place?
If by “dealing with” you mean “ignoring” the details, then I’d have to agree, based on what I’ve seen so far.
Anyways, if you’re asking me how the translation system we see today was established, I don’t know the answer.
What I can tell you, is that assuming the system we see today looks anything like it did as it first arose is…well…a bad assumption.
I didn’t ask you how the translation system came into being, nor did I ask you what it looked like.
I asked you “Regardless of what anyone thinks preceded that time, at the point in earth’s history that the first ever aaRS was successfully synthesized from memory, how many of the other aaRS had to be in place?”
You avoided the question.
When the first aaRS, as we know it today, was synthesized from memory, none of the other aaRS, as we know them today were in place.
As I said, assuming the system that we see today is the same as it was when it came about is a bad assumption.
George Castillo:
Do you have any evidence for a different system that could evolve into the one we know observe? Or is that just an assumption based on dire need?
George Castillo:
Today’s bacteria and archaea. Assuming the bacteria and archaea of today are the genetic identical to those of millions/ billions of years ago is a bad assumption.
#166
In your attempt to avoid the issue, I believe you’ve unintentionally mis-spoken here.
In any case, the argument you’re attempting to make is that at the point in time that the first aaRS was successfully synthesized, it may have been (along with other aaRS) an entirely different sequence than it is today. The problem is that your argument is fundamentally irrelevant. The aaRS is not defined by its sequence, but by the very specific role it must fulfill in the process of biological organization. If that critical role is not fulfilled, then the system could not describe itself from memory. It therefore could not achieve semantic closure (autonomous self-reference) and extant biological organization would not be possible.
I’d ask you if you’d like to try again, but I am getting the sense that you don’t actually understand the system well enough to recognize the problems with your arguments.
George Castillo,
You may want to read what PaoloV and I were talking about you publicly in another discussion thread.
Check this out.
Upright BiPed,
It seems like George Castillo doesn’t understand much of what is being discussed here.
Upright BiPed, jawa,
The superficial way he reacted to gpuccio’s and other comments here seems to indicate some lack of seriousness.
George Castillo:
I am happy thgat I got your attention. Mybe not a really careful attention, however.
You say:
“Were you trying to make an argument against me?”
I never try to make an argument against anyone, I just try to argue for what I think is true.
So, I will try to make my points more clear.
Let’s go in order.
In your comment #74 you make some really strange statements:
“Repetitive recruitment and associations of protein factors driving changes to the 3D shape of chromatin and driving some level of “orderliness” is not really that complicated and hardly “random,””
Well, random certainly it is not, but complicated certainly it is. You really seem to misunderstand how complex, and still poorly understood, those processes are. Chromatin states change continuosly, in highly functiobnal and specific configurations, and a number of different parallel levels of regulations are involved in the control of those states, and therefore of gene transcription. How you can believe that this is “not really that complicated” is a mystery to me.
But it gets worse. You say:
“This is in fact a good example of evolution taking advantage of two simple processes (protein interactions and promoter-enhancer contacts)”
How can you think that protein interactions and promoter-enhancer contacts are “simnple processes”?
TFs constantly interact in groups, in highly complex combinatorial patterns, and with DNA loci, to generate those contacts in a dynamic and always functional way. There is nothing simple in that. Just look at this recent paper about the circadian changes in chramatin conformation:
A day in the life of chromatin: how enhancer–promoter loops shape daily behavior
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5900705/
Or look at this:
Recent evidence that TADs and chromatin loops are dynamic structures.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5990973/
There is nothing simple here.
In your comment #88, you make another strange statement. You declare that chromatin is, on its own, “passive and inert”, and that:
“It’s not until transcription factors and other proteins act on the chromatin that it is shuffled around the nucleus, driven by successive protein binding interactions that reinforce topological arrangement, as shown in this paper, and bring about distinct nodes of active transcription.”
But of course chromatin is never “on its own”, and the processes you metion are interactions between the DNA sequence, the dynamic chromatin structure, and the factors interacting with those levels.
Chromatin is not the DNA sequence. It is a highly dynamic structure, continuosly interacting with proteins and other factors. While the DNA sequence remaisn stable (but certainly contributes to all the processes already mentioned), chromatin structure is continuosly changing: nucleosomes are not fixed structures, they change, and histones continuosly undergo PTMs, TFs create dynamic loops, non coding RNAs are important players, and so on.
Nothing passive, nothing inert, and certainly nothing simple.
In your comment #101. again you are coinfused about what chromatin really is. You say:
“That is the exact opposite of what I was saying, PaV. It’s clear that your lack of knowledge is going to hinder any further conversation about this paper. For our purposes DNA/chromatin are interchangeable. In the nucleus virtually all DNA exists as chromatin, which is DNA wrapped around a histone every ~200 bases.
DNA/chromatin is passive, it does not have some “inner logic”. What it has is a variety of sequences that are binding sites for proteins, these proteins are driving the 3D organization/topology of the DNA/chromatin.”
Again, chromatin is not DNA. And it is not just “DNA wrapped around a histone every ~200 bases”. If, for your purposes, DNA and chromatin are interchangeable, then your purposes are really wrong.
For reference, just look at the definition of chromatin in the relevant Wikipedia page:
More in next post.
Hi UB,
You have mail.
George Castillo:
That said, I will now state again my points, and try to clarify them better:
1) The proteins found in bacteria are not credible ancestors for eukaryotic histones. This is not my personal opinion,m but what emerges from the papers you quoted. They may habe some DNA regulating role that has some generic affinity with what histones do, but they have no sequenc or structure affinity with histones.
2) The histone like proteins found in some archaea are probably related to eukaryotic histones, not so much at sequence level, but at structure level. They can be ancestors of eukaryotic histones, but they are still very different from them. At sequence level, only a few positions are shared with eukaryotic histones, and the sequences involved in PTMs are lacking.
So, even if the histone fold as implemented in archaea is partially re-used in eukaryotes, eukaryotic histones are completely re-engineered at sequence level. Moreover, that specific eukaryotic sequence is one of the most conserved sequences in eukaryotes, as you certainly know.
So my point is, even if the histone fold is already found in archaea, the eukaryotic histone is a new and original structure, with completely different functional features.
3) The third point, again, is very simple. Histones are only a small part of the whole. Chromatin structure is probably the main functional node in eukaryotes and in transcriptional regulation, and it is the final result od many different and very complex processes (they seem to be simple only for you). This complex process is still poorly understood, and is probably the real feature that allows ordered and functional transcription to take place. And it is essentially an eukaryotic meta-process, depending on many essentially eukaryotic levels of specific regulation, form DNA sequences to PTMs to TFs. And certainly many other things.
I think gpuccio’s explanations @173 & 175 qualify as high level biology textbook material for graduate or postgraduate coursework
George Castillo,
Did you read PaoloV’s comment @ 154?
jawa,
don’t hold your breath while waiting for George Castillo to do what PaoloV kindly asked @154.
Note that @153 George Castillo wrote that it seems OLV and I had run for the hills, but now, after gpuccio posted his excellent (as usual) explanations, it seems like George Castillo has run for the hills.
Still, George Castillo should get credit for keeping this discussion a little longer. 🙂
BTW, I saw Paolo’s good observation about George Castillo distorting what OLV ad I wrote. Well done, Paolo!
PeterA,
gpuccio saved us many hours of reviewing papers.
We appreciate it.
Someone else had to run for the hills.
I like Paolo’s sharp observation about George Castillo distorting our message.
Is that reading comprehension?
OLV,
Yes, agree. gpuccio has made someone run for the hills.
Also, Upright BiPed @163, 165 & 169 has had a tremendous effect on chasing the nonsense proponents away from this discussion.
We couldn’t have done it as well as gpuccio and Upright BiPed have.
Other folks have posted sharp comments that kept the nonsense off this discussion too.
We appreciate all their effective contributions.
guys, forget what George Castillo wrote, which is totally irrelevant.
Contribute with more references to papers that provide additional evidences, like gpuccio and DATCG often do.
Oh boy. Where to even begin.
For starters, gpuccio, chromatin certainly is DNA wrapped around histones.
It is the base unit of our genomic storage and how the vast majority of our DNA is packaged.
99.999% of our genome at any given moment is wrapped around histones in the 10 nanometer beads-on-a-string.
Nothing beyond that has been shown to exist in vivo (during interphase).
Also, if you have to copy and paste from wikipedia, no one with an actual science background is going to take you seriously.
“The proteins found in bacteria are not credible ancestors for eukaryotic histones. This is not my personal opinion…”
It is, in fact, your opinion and your opinion happens to disagree with the actual science (no surprise there).
Here are the facts:
1. There are proteins in bacteria that carry out very similar functions as eukaryotic histones
2. These bacterial proteins do have some simple structural similarities to histones, such as being positively charged
3. These proteins have a an affinity for AT-rich stretches of DNA, as do histones
4. Sequence similarity has been found between these bacterial proteins and eukaryotic histones (albeit rare)
5. The canonical histone fold is found in archaea and is virtually identical to that of eukarya
6. There is a high degree of structural similarity between various archaeal and eukaryotic histones
Saying that there is no credible bacterial ancestor for eukarytoic histones is flat-out wrong.
Upright, for the last time, assuming that this system is the same as when it first came about is a terrible assumption.
Your assumption relies on proteins having a “very specific role” with each role having to be “fulfilled,” and fulfilled perfectly, for the system to function.
That’s not how evolution happens.
But hey, keep beating that horse.
This is perhaps the only part of your response that makes any sense at all. You are attempting to shrug off 150 years of logic, prediction, and experiment (Peirce, Shannon, Turing, Von Neumann, Crick, Zamecnik, Hoagland, Nirenberg, Pattee) all in an effort to avoid a very straightforward question. It makes perfect strategic sense on your part to exit the conversation before you get trapped by the details.
As I’ve already said, you don’t understand the system well enough to recognize the problems in your argument, even after they are explained to you.
George Castillo:
You say:
“For starters, gpuccio, chromatin certainly is DNA wrapped around histones.
It is the base unit of our genomic storage and how the vast majority of our DNA is packaged.
99.999% of our genome at any given moment is wrapped around histones in the 10 nanometer beads-on-a-string.
Nothing beyond that has been shown to exist in vivo (during interphase)
Also, if you have to copy and paste from wikipedia, no one with an actual science background is going to take you seriously.”
I quote Wikipedia for simplicity, when I need a very brief summary of what is well known.
You don’t like that?
Look at this:
Chromatin states and nuclear organization in development — a view from the nuclear lamina
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4549078/
(Emphasis mine)
And so on. Read it.
Are you still convinced that “wrapped around histones in the 10 nanometer beads-on-a-string” is the only thing that “has been shown to exist in vivo (during interphase)”?
Of course, both Wikipedia and the scientific literature must be wrong. You are certainly the only reliable source of knowledge.
Regarding ancestors, bacterial proteins have no significant sequence or structure similarity to eukaryotic histones. Nobody would seriously consider them as credible ancestors of them.
Archeal proteins, as I have always said, have limited sequence similarity and good structure similarity to eukaryotic histones, and can be considered credible possible ancestors of them. Again, as I have always said.
But archaea are not bacteria (believe me, I have read it on Wikipedia! 🙂 ).
So, if your points number 5 and 6 about archaea (the only ones that make sense in your list) are intended as a demonstration that my statement:
“The proteins found in bacteria are not credible ancestors for eukaryotic histones.”
is wrong, then there is something that does not work properly in your logic.
Maybe reading Wikipedia more often (and with more attention) could help!
Reading wikipedia and thinking you have credible knowledge of biology is what you do gpuccio, not me.
It’s why you have only a surface-understanding of, and are confusing terms such as chromatin with much higher-order nuclear structures.
Anyways, each of my six points in comment 182 are 100% accurate and come from either the papers I initially listed or a Nature review by Dillon & Dorman (2010).
In that paper, bacterial proteins similar to eukaryotic histones are mentioned, although they are rare (as I already stated). Specifically, the most well known is Hlp in species of Mycobacterium which consists of an N-terminus domain similar to Hu from E.coli and a C-terminus domain similar to eukaryotic histone H1. They state, and I quote,
“This is a rare example of a bacterial NAP that is truly histone-like in its amino acid sequence.”
As, always, your opinion is at odds with the actual science.
But luckily for you, you can just keep ignoring the science.
George Castillo:
That the bacteria of TODAY have it does not mean the bacteria of illions of generations past had it. There still isn’t a mechanism capable of producing eukaryotes given starting populations of prokaryotes.
Assuming the bacteria and archaea of today are the genetic identical to those of millions/ billions of years ago is a bad assumption.
There isn’t even a credible bacterial ancestor for eukaryotes.
Allow me to repeat the question you will avoid answering at all costs.
”Regardless of what anyone thinks preceded that time, at the point in earth’s history that the first ever aaRS was successfully synthesized from memory, how many of the other aaRS had to be in place?”
You’ve deliberately avoided it three times thus far.
Just because you don’t like how I answered the question, Upright, doesn’t mean that I haven’t answered it.
Yes, it does, I’m afraid. This has nothing to do with liking or not liking your answer. Notice the bolded text above? You did just the opposite in order to avoid the question.
You are now up to four times, by the way.
GC, It was ill-advised for you to project ignorance to GP as just caught my eye. If you were to survey his contributions and comments on ID-related matters over the years, you would learn that he first contributed here to strengthen his English by participating in a forum on a matter of his interest. You would also learn of his strong medical background and of the level of thought and even outright research he has contributed, including through significant statistical studies. I suggest you walk back from the dismissive remarks above, when he says he uses the humble summary at Wikipedia as a handy way to make a point, he has read it with a very knowing eye first. KF
Fully agree with kairosfocus.
GC could learn a few important scientific concepts related to advanced biology just from reading GP’s numerous contributions in this website.
kf, jawa:
Thank you for the kind words! 🙂
George Castillo at #185:
“Reading wikipedia and thinking you have credible knowledge of biology is what you do gpuccio, not me.”
It’s really frustrating to debate with someone who has not even the least understanding of some form of simple irony.
Regarding your 6 points, I did not say that they were not accurate, I just sayes that only points 5 and 6 (those about archaea) made sense, because they point to a possible role of the archaeal proteins as ancestors of the eukaryotic histone. The other points (those about bacteria) make no sense in that context, because, however accurate they may be, they are irrelevant in establishing a credible role as ancestors.
The Nature review by Dillon and Dorman tat you quote says it clearly:
Proteins that alter the shape of the DNA to make it more compact and that have the potential to influence transcription have been identified in all three kingdoms of life. In eukaryotes these proteins are known as histones, and their ability to influence chromatin structure and transcription is understood in considerable detail. Initially, this depth of understanding influenced our appreciation of those proteins that carry out analogous tasks in bacteria, leading them to be referred to as ‘histone-like’ proteins1,2. However, this term is becoming less appropriate as the distinct nature of these bacterial proteins is revealed. They are now collectively referred to as nucleoid-associated proteins (NAPs), which more accurately reflects their cellular location without implying that they have any structural similarity to histones.
Emphasis mine.
Now, to support your hypothesis that bacterial NAPs could be ancestors of eukaryotic histones, you rely only on this statement in the same paper:
So your theory is based on a rather vague statement about one domain found in one type of bacteria. Let’s see if it is credible.
My first, strong objection, is that, even if that “similarity” were really true (see later), it would, of course, be irrelevant to your thesis. Such an isolated example is no good foundation to hypothesize a bacterial ancestry for eukaryotic histones, as anyone with some understanding of these problems would recognize. It is obviously too little, and the main objection is that even that supposed “similarity” can be well explained, if real, by HGT. Which is a very good explanation for isolated anomaluous cases like that, especially in the bacteri-archaea kingdom, where it happens all the time.
That said, let’s see how real that “similarity” is. The quoted review supports the statement with one reference, reference 38.
Here it is:
Identification of an immunogenic histone-like protein (HLPMt) ofMycobacterium tuberculosis
https://www.sciencedirect.com/science/article/pii/S0962847998900041
To make it brief, the alignments with a few eukaryotic histone molecules are in Fig. 6. The C terminal domain aligns reasonably well with the corresponding parts of the eukaryiotic molecules, 4 in all. The most relevant are the first two, which are from two carieties of sea urchin. As you can see, significant the homology starts at AA 116 of the HLP sequence, and is generated essentially by numerous tetraptide repeats (PAAK, PAKK,
PKAK and KAAK).
Well, the simple fact is that that part of the sequence has nothing to do with the histone domain in those two sea urchin molecules.
You can check that easily. Go to Uniprot (not Wikipedia, this time!) (Beware, that was ironi 🙂 ), and check the two proteins:
Lytechinus pictus (Painted sea urchin)
Protein P06144 (Late histone H1). The sequence is exactly the one shown in the paper as LYTPT.
Strongylocentrotus purpuratus (Purple sea urchin)
Protein P07796 (Histone H1-gamma, late). Again, the sequence is exactly the one shown in the paper as GSTRPV.
Now, if you look in Unprot the section “Family and Domains” for both proteins, you will see that the hisotne domain is in the first part of the protein, in both molecules.
More precisely, at AAs 17-91 for both proteins. And if you look at Fig. 6 of the paper, there is only scarse homology in that part of the sequences, essentially random and not significant.
IOWs, the homology that starts at AA 116 of the HLP sequence, and is generated essentially by numerous tetraptide repeats (PAAK, PAKK, PKAK and KAAK), has nothing to do with the histone domain.
So, the conclusion in the paper, reported passively by the Nature review, is simply wrong.
More in next post about chromatin states.
George Castillo at #185:
So, let’s go on.
You say:
“It’s why you have only a surface-understanding of, and are confusing terms such as chromatin with much higher-order nuclear structures.”
You are still obstinately embarassing yourself.
“Much higher order nuclear strictures”? Really?
What we are debating here are chramtin states. The way chromatin is configured in the nucleus. What other “nuclear structures” are you talking of?
The only other nuclear structure that contributes to chrmatin configurations is the nuclear lamina, as I have already pointed out in the paper quoted at #184:
Chromatin states and nuclear organization in development — a view from the nuclear lamina
The title of the OP we are debating is:
Chromatin Topology: the New (and Latest) Functional Complexity
Can you understand what “topology” means?
Chromatin topology, or chromatin conformation, or chromatin states, are all terms that indicate the different configurations chromatin assume in space, in the nucleus. And, of course, their functional consequences in transcription regulation.
Look at this:
Multiscale Topology of Chromatin Folding
https://arxiv.org/pdf/1511.01426.pdf
How can you reconcile that with your obtuse statement:
“For starters, gpuccio, chromatin certainly is DNA wrapped around histones.
It is the base unit of our genomic storage and how the vast majority of our DNA is packaged.
99.999% of our genome at any given moment is wrapped around histones in the 10 nanometer beads-on-a-string.
Nothing beyond that has been shown to exist in vivo (during interphase).”
Emphasis mine.
Now just look at Fig. 1 in the above quoted paper:
Now, let’s have a look at more sophisticated classifications of chromatin states, based on epigenetic markers.
For example, look at this presentation:
Learning Chromatin States from ChIP-seq data
https://www.encodeproject.org/documents/049704a4-5c58-4631-acf1-4ef152bdb3ef/@@download/attachment/Learning_Chromatin_States_from_ChIP-seq_data.pdf
Slide #9:
“Chromatin states are defined based on different combinations of histone modifications and correspond to different functional regions”
As you can see in the slide, they are defining here 15 different chromatin states, and heterochromatin is only one of them. So much for “DNA wrapped around histones in the 10 nanometer beads-on-a-string” being the only thing “that has been shown to exist in vivo (during interphase)”!
In this page:
https://egg2.wustl.edu/roadmap/web_portal/chr_state_learning.html
you will find resources for different models of chromatin states, a simpler 15-state model, a 18-state model, and a more complex 50-state model.
This paper:
Multi-scale chromatin state annotation using a hierarchical hidden Markov model
uses a 30-state model (see Figure 2).
And this is really, really recent (August 2, 2018):
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
Look in particular at Figure 2:
“Clustering of Single-Cell Chromatin Accessibility Identifies Diverse Cell Types”
They used t-distributed stochastic neighbor embedding, a nonlinear dimensionality reduction technique, to identify 30 major clusters of cells, that were then further detailed to 85. Beautiful.
OK, I could go on forever, but that’s enough. Of course, you will be always certain that all these things are non existent, pure ignorance, and denial of reality. Good for you.
It must be exhaustingly frustrating to try discussing anything with someone who isn’t interested at all.
gpuccio seems to be well trained to deal with such folks
It’s sad to see someone trying to debate gpuccio without understanding his clear textbook-style explanations.
ES,
I seems apparent to me that we are not getting each other’s mail. I have no idea why.
The insightful comments # 194 and 195 are excellent.
Those two comments alone could open a whole serious discussion.
Why doesn’t that happen here?
OLV,
I agree with your assessment of gpuccio’s explanations @ 194-195.
That’s why discussions on the topic of proteins are so interesting here, because gpuccio doesn’t seem to leave any detail out of his analysis.
Perhaps that’s a reason why his stubborn opponents eventually run for the door. It’s hard to keep debating unless you’re serious about finding the true evidences.
Hi guys!
I realized that I forgot to give the links for the last two papers mentioned at #195. I apologize.
Here they are:
Multi-scale chromatin state annotation using a hierarchical hidden Markov model
https://www.nature.com/articles/ncomms15011
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
https://www.cell.com/cell/fulltext/S0092-8674(18)30855-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867418308559%3Fshowall%3Dtrue
I am trying to write an OP about transcription and its regulation. Let’s see how it goes! 🙂
gpuccio:
That settles it! Clearly you are wrong and tried to fool us. Or so George would have us believe…
Thank you for your contributions!
ET,
I agree. gpuccio hid the contents of those papers away from us so that we couldn’t see that George Castillo’s arguments were based on real evidences.
😉
Peter,
Jokes aside, most papers gpuccio references here are very interesting.
But the news that he’s working on a new OP about transcription and its regulation is very exciting.
Pater and jawa, while we await gpuccio’s next OP, let’s have some appetizers:
Epigenetics: the first 25 centuries
UB #199
Yes, it is strange.
Guys,
I have raised this many times now. Could anyone able to influence decision making on this blog please persuade those who run it to create an index by author. It would be a GREAT feature indeed! Readers won’t have to worry about bookmarking interesting stuff for reading later.
I have already lost count of gpuccio’s contributions 🙂 I do not want to miss anything he posts here but I cannot follow it in real time. There are some other key contributors I want to follow as well.
I guess other readers will vote for this too.
Eugene S,
You may count my vote for your your idea.
I vote for Eugene S’ request too.
Please, add my vote too. Thanks.
jawa,
You repeated a word in your statement in #210.
Paolo,
The repeated word reinforces its meaning. 🙂
What about your opinion on the suggestion made by Eugene S?
Do you support it?
Friends:
Maybe you have already seen that I have posted my new OP about these issues. You are warmly invited to the discussion! 🙂
I’m glad that you agree that the “N-terminal exhibits significant homology to the bacterial HU proteins particularly in those amino acid residues implicated in DNA interaction, while its C-terminal segment displays homology to eukaryotic H1 histones,” Gpuccio.
That is also exactly what the original researchers found as I just quoted.
It’s unfortunate that you have to try to sweep this conserved homology under the rug in an effort to support your worldview, though.
And just FYI, this bacterial protein was never claimed by anyone to have homology in the histone domain, it was at the N and C termini that there was homology to bacterial and eukaryotic proteins, respectively.
You can check comment 185 again if you’d like.
Maybe it is you who lacks careful attention, or maybe it’s just a lack of knowledge in biology. Probably both.
Bottom line is, there are bacterial proteins that are credible ancestors to histones They have similarites in structure and sequence that span the major kingdoms of life.
This is true no matter how much you stomp your feet.
George Castillo:
Don’t embarass yourself any more.
The fact that the C-terminal sequence of one bacterila protein has homology with 4 eukaryotic repetitive sequences found in 4 particolars eukaryotic proteins (and only in them) which are labeled as “histones” because a different part of the sequence has homology to the histone domain does not mean, in any possible way, that such homology of a repetitive sequence has anything to do with “being ancestor to histones”.
To be ancestor to histones, some bacterial protein should, of course, have homology to histone-specific sequences (the histone domain), or at least to histone specific structures (the histone fold).
Even a child would understand that.
Moreover, wherever did I “agree” that:
“the C-terminal segment displays homology to eukaryotic H1 histones”?
Read again my comment #194. I just quote that statment from the paper, and then I give very good evidence that it is not true. That’s all.
You are beyond any hope, you know?
However, you are welcome to read, and if you like comment upon, my new OP about transcritpion regulation.
After all, you contributed to motivate me to write it (sigh).
George, perhaps your situational awareness has failed you in this instance. To have any meaningful impact on GP’s comments you’ll have to actually address the details of what he says. That’s usually how it works.
Oh boy.
It’s quite sad to watch you claim that a small amount of homology maintained over billions of years is meaningless, and then post about the importance of “jumps” of homology representing function because they’ve been maintained over millions of years.
I guess that’s what I should expect from UD.
“Moreover, wherever did I “agree” that: ‘the C-terminal segment displays homology to eukaryotic H1 histones’?”
Let me refresh your dwindling memory; in comment 194 you said:
“To make it brief, the alignments with a few eukaryotic histone molecules are in Fig. 6. The C terminal domain aligns reasonably well with the corresponding parts of the eukaryiotic molecules”
At this point I’m questioning whether you even know what you’re saying.
Anyways, as I’ve said, there are credible bacterial ancestors to eukaryotic histones, at both the sequence and structural level.
No obfuscation on your part will change that.
George Castillo:
Why am I wasting my time with you?
You can’t even understand English. Or you son’t want to understand.
In Fig. 6 of the paper, the C termoinal somain does align reasonably well with the corresponding parts of the 4 eukaryiotic molecules shown there.
What a pity that the aligned sequence has nothing to do with histones!
Good luck to you.
What are the eukaryotic proteins that align reasonably well in figure 6?
No response gpuccio?
Let me jog your memory, the 4 eukaryotic molecules with corresponding parts that align reasonably well with the NAP C-terminal domain are eukaryotic HISTONES.
So when you say “the aligned sequence has nothing to do with histones” you are completely wrong.
And when you deny that there are credible ancestors to histones in bacteria, you are also completely wrong.
Denying evidence, ignoring evidence, and being flat out wrong…the UD trifecta!
George Castillo:
Oh my, you are dense. Just because the bacteria of today have it does not mean the ancient bacteria had it.
Clearly you have no clue at all
@220 gpuccio posed an interesting question that we have asked before.
It took gpuccio much longer than me to ask such a question regarding the clueless and stubborn discussant he has dealt with so well. I’m sure other folks here (including myself) wouldn’t have kept that discussion that long.
You might want to keep in mind that we live on a rotating planet.
Allow me to repeat the question: ”Regardless of what anyone thinks preceded that time, at the point in earth’s history that the first ever aaRS was successfully synthesized from memory, how many of the other aaRS had to be in place?”
jawa,
Don’t go so fast. Note that George Castillo has pointed to very specific problems in gpuccio’s affirmations. I think gpuccio should clarify this with more details. It’s human to err. He should admit any mistake in his statements, so that his credibility remains intact or even increases.
Peter,
Please, don’t take a few statements or comments out of the context of their discussion.
As far as I understand, the main point gpuccio is trying to make here is that the chromatin is functionally dynamic in vivo, which apparently is something that George Castillo strongly denied from the beginning of his discussion with gpuccio.
Also I think gpuccio is trying to make the point that the functional complexity of the eukaryotic chromatin is designed, because it shows a tremendous jump in functional information anyway you look at it. A few similarities here and there don’t make a dent in gpuccio’s point. Not even a scratch.
The issues George Castillo is trying to raise seem like digression from the main point to avoid it. Typical red herrings. Nothing new. We’ve seen this before here.
Bikes, cars, trucks, buses, airplanes, trains, all have wheels. But there are major functional differences that were engineered (i.e. intelligently designed).
Keep in mind the main point of the discussion lest you draw premature conclusions.
George Castillo (and others):
Excuse me for being late in answering, but I needed to make further research to understand well what was happening, and at the same time I was fully absorbed by my new OP (to which you are still invited to participate.
So, to be really sure of the matter, I made further inquiries, and I found what follows:
a) I was wrong about one thing. The N terminal domain you speak of is really a part of a specific histone protein, histone H1 (sometimes existing in a different form as histone H5).
b) Histone H5 is not one of the gour histones that make the nucleosome strucure. However, it helps satbilize it, and has probably other roles, many of them still not understood.
c) Differently from other histones, the H1 family is made of longer molecules, and it has a definite histone domain at the N terminal, and another repetitive sequence at the C terminal. That’s exactly the sequence that aligns with the protein found in Mycobacterium tuberculosis. The bacterial protein, instead, has no significant alignment with the histone domain of the histone H1 family.
d) So I apologize for my error: I believed that the C terminal sequence was some accessory sequence restricted to those 4 proteins, but that is not the case: it can be found in all H1 hostones C terminal sequences.
e) Part of the reason for my error was that, strangely, the blast algorithm does not recognize and align that C terminal sequence in histone H1 proteins (and therefore not even in the mycobacteium tuberculosis protein). I have blasted many times different H1 histone one against the other, and no alignment is found for the C terminal sequence, while a hit is always shown for the histone domain at the N terminal sequence. I had to align the sequences with Mega to visualize the homologies in the C terminal sequence. I think that the reason for that is probably that it is a highly repetitive sequence, made of 4 AAs repetitions, and the blast algorithm has special rules for these “low informational” sequences.
f) That said, I apologize again for the error.
g) Error apart, what does that mean?
h) It means that the protein in mycobacterium tubercolosis really has a detectable homology with a sequence found in the H1 family of eukaryotic histones, which is not the histone domain of the H1 family, and is not marked as a specific domain at Uniprot.
i) However, as far as I can see, it has no homologies with the histone domain in the H1 family, or with the other histone families.
j) The fact remains that that kind of homology does not qualify as an explanation for all the other basic histone sequences, domains and structures, which show no homology with the protein found in mycobacterium tuberculosis.
k) The fact remains that, as far as I know and as far as can be understood by the papers you quoted, the protein in mycobacterium tuberculosis is an isolated case. Homologies or not, it does not qualify as a foundation for a credible ancestry of eukaryotic histones, because the best explanation for isolated cases remains, IMO, HGT.
l) That said, I still cannot understand your insistence on a single finding in a single bacterial protein. As I have admitted just from the beginning that archeal proteins do show a structural similarity with eukaryotic histones, the only credible hypothesis is that eukaryotic histones may derive from archeal proteins, and not from bacterial ones that seem not to exist (whatever exception the mt protein may be).
That’s all.
Just a final human note. It took you more than six days to answer my comments #194 and 195 (August 22 , 2 pm) with your comment #216 (August 28, 7.50 pm). Indeed, you never answered my #195.
So, why were you taking offense that I needed some time (a few hours) to answer your last comments? “No response gpuccio?”
Still invited to contribute to my new OP about transcription regulation. It is, indeed, an expansion of my comment #195 here.
At no point did I argue that this bacterial NAP explains the existence of all eukaryotic histone sequences.
Gpuccio, you have posted about the importance of conserved homology many times and yet here you brush it aside simply because it disagrees with your opinion.
Do you really expect anyone to take you seriously when you do things like that?
How do you propose HGT combined a bacterial histone-like protein with a segment of a eukaryotic histone?
gpuccio’s response @228 is very professional, totally acceptable and very clear. The ball is back in George Castillo’s court, which hasn’t responded previous comments.
Peter,
I agree with you. George Castillo still hasn’t addressed gpuccio’s main points in their discussion. Judging by George Castillo’s last comment, it doesn’t seem like he’s ready to continue this discussion. He should go back and read all gpuccio’s comments to see if he can finally understand the bottom line. Better, we all should accept gpuccio’s invitation to move to his new discussion thread.
George Castillo:
I have never said anything against “the importance of conserved homology”, of course. Homology is always important.
I don’t want to demonstrate that HGT is the explanation for the observed homology. I simply don’t know.
But I think that nobody would seriouslky build and defend any evolutionary hypothesis based only on one observed homology of one sub-sequence in one protein of one bacterial species according to one old paper.
Frankly, I am not so interested in this repetitive sequence found in mycobacterium tuberculosis and which has some homology with the C terminal domain of eukaryotic histone H1 family. Nor seems the scientific literature interested in it, or at least I am not aware of any follow-up to that observation.
I am not even sure that the repetitive sequence is found only in that species, and not elsewhere in bacteria. I have no way to check that personally, because as explained that sequence eludes the blast algorithm.
If someone will show that the sequence is well represented in bacteria, I will be happy to admit that it could be a reasonable ancestor for the eukaryotic C terminal domain of the histone H1 family (and only for that). Exactly as I have happily recognized, just from the beginning, that archaeal proteins could be reasonable ancestors of the eukaryotic histone fold, because the evidence for that was rather good.
But in the absence of that kind of good evidence for bacterial sequences, I am not interested in hypotheses based on one single protein in one single species, and apparently lacking in all the rest of the bacterial world.
That’s all.
George Castillo:
You can’t even argue that it explains anything with respect to eukaryotes. You don’t have a mechanism capable of producing eukaryotes given populations of prokaryotes and archaea.
So that would be a problem, George
Common design, not HGT
You’re “not interested” in this homology because it goes against your personal opinions.
And yet you make numerous posts about the importance of homology…
And based on the nature review, it’s not just “one bacterial species” as you say, but actually Mycobacterium spp.; which refers to, I believe, well over 100 species of the genus Mycobacteria.
But of course, no matter what I say, this example of homology is unimportant to you and you will just continue to ignore any evidence that doesn’t support your worldview.
I guess I really shouldn’t be surprised.
That’s all.
Once again, allow me to repeat: ”Regardless of what anyone thinks preceded that time, at the point in earth’s history that the first ever aaRS was successfully synthesized from memory, how many of the other aaRS had to be in place?”
When (or if) you return to tiptoe and dismiss the question once again, it will now be either the sixth or seventh instance on this thread alone where you’ve avoided material that doesn’t support your worldview. Perhaps your zingers have lost all their sting.
It’s funny that you have to switch the word “evidence” to “material,” upright.
I guess it does actually suit you and your comedy act better.
That was your seventh time in this thread alone.
Join us, George.
Somebody fix that broken record!
Ok, I’ll play.
Will George Castillo ever say something substantial that is worth reading?
jawa,
maybe someday he will.