Our primitive architectural descriptions of buildings and parts when applied to individual biomolecules and their folding may not be so helpful or even accurate sometimes, but to talk about an RNA structure that has parts that function like “beams” (very stiff) and parts that function like “hinges” (highly flexible) and other types of parts and all highly dependent on this complex interdependent interaction, I am still forced to use a general word “scaffold” for the stiff-well-defined-structural parts whether you approve of it in your domain or not.
Additionally, even when talking about the structure you cite above (STE5), when we break it down into how each of the pieces operates, we are still forced to talk on the nanometer scale about units of structure that are like beams or blocks and flexible parts that work like hinges. One also sees that whereas you have a complex architecture in this protein (with 700+ aa), it is not composed of multibranch loops, it is the standard combinations of alpha helices and beta strands separated by several large regions of flexible, functional semi-non-structured (when not binding a target) features.
My view of a real scaffolding protein is something like NS1 that wraps up influenza A viral RNA segments. That is really functioning purely as a “scaffold” in the most literal sense of our human-derived word. For STE5, I would still have chosen a word like “processing protein”. Scaffold wholistically implies that the STE5 is simply a dumb passive filing cabinet rather than a highly complex interacting piece of machinery.
It is not exactly an answer, but Newton had to assume that there is this gravity even though he could not offer a “mechanism” to explain it. Although that did eventually yield to an explanation, we’ve had to accept the “speed limit” on the speed of light for a long time. Perhaps the whatever-you-call-it-that-makes-up-“stuff” likes 1/137 (with minor corrections). From a science point of view, we cannot say “because God made it that way”, but we can still go on doing physics and just say “because it is”. In that way, we go on like Newton had to go on. Euclidian geometry assumes some axioms, maybe we have to also.
One of the intriguing observations is that life appeared quite early (geologically speaking) on in Earth’s history. This has led some to propose that abiogenesis happens quite easily in places where biomolecules can form, but I think that requires a rather large leap in logic.
What will be interesting is if we can visit planets that are capable of producing biomolecules or did produce molecules for an extended period in the past, places like Mars and Europa. If we find life or signs of life there and they happen to use different genetic pathways than life on Earth, then I think we can start to move in the direction of abiogenesis happening easily, albeit very cautiously. At the same time, negative results can still cause us to come up with tons of valid and invalid reasons why there isn’t life on those other planets.
One thing is for sure, biochemists are a bit jealous of physicists because their experiments are a little more straightforward. It’s not as if biochemists can spend billions of dollars on a tunnel under Switzerland and have the answers to abiogenesis pop out a few years later.
From my reading, the attractiveness of the RNA World hypothesis is that the RNA can serve as an enzyme and as a genetic molecule (i.e. a template for reproduction).
Indeed, proteins are really bad at replicating themselves. I recall that there are attempts to make RNA able to replicate itself. As always, it is a really hard experiment with mostly humiliating results, but with all the help in the world, a few bases were replicated. There would be the advantage that there was no “competition” in the beginning. I should add that something like a SAM riboswitch could select out amino acids in reagent grade form. So RNA does have many merits.
I certainly don’t say that the RNA world cannot be so. However, there is something curiously appealing in the fact that RNA is replicated by a protein. All these things seem difficult to sustain as long-term stable, but supposing that a primitive form of RNA polymerase somehow “appeared” on the scene (like the old Far Side “and a miracle happens …” with equations), this would be one way to get replication to move forward without the tedium of some RNA enzyme. Of course, we still have to get the reagent grade RNA and this miraculous RNA polymerase, but … well … … … like grace, it is not something we can earn, it is all about what Jesus has done.
Agreed. We could spend billions of dollars and still find ourselves no closer to a viable answer and only be more keenly aware of how little we know and how much more ground needs to be covered. I don’t think it would be a waste of money to invest some effort in this direction because we would discover some useful innovations in chemical synthesis along the way that could potentially change the way we do a lot of chemistry. It would be a really hard sell, but that is almost certainly true.
Actually, if I read between the lines on what Vouthon (Colin Cooper) is saying correctly, the nagging question would be whether having a bigger collider would change these conclusions. Ironically, I think SSC was originally planned to be more powerful, but we should also remember that the human genome project has generated sequencing innovations, so maybe that was a better direction.
What I usually learn from a research project is (1) what I should have done at the beginning, (2) one problem solved introduced 10 new problems, and (3) how infinitely much more we have left to learn.
There is also the Metabolism First model where metabolism precedes genetics. The main attractions of this model is that it begins with simple reactions involving simple molecules like acetate. It is also capable of solving the chirality problem for amino acids and nucleotides.
It is also a question of how you approach the problem. Do you focus on what molecules can form in the absence of life, or do you focus on which molecules would have to form in order for life to emerge? Suffice it to say, I think it would be much more difficult to answer both questions at the same time.
We need to look at the whole and not the parts. Black holes do exist and are part of God’s system that produces life.
That God fine tunes for both, but the anthropic view says that God created a universe that is rationally intelligible. Why should time exist if it is known only to God or no one.
Does the universe have meaning, or in other words have a purpose? The answer seems to be yes, and life and human life seems to be the purpose.
Evolution created humans because intelligence gave them an evolutionary advantage. This can only be if nature is rationally structured.
It seems like you may be working a bit more diligently on this problem of abiogenesis. I think about it some of the time, particularly in terms of what I have learned about the folding of biopolymers, and some of that is quite interesting and encouraging. However, solving the question of “the beginning” seems far too difficult; I don’t have any really solid ideas that seem worth investing the time and energy that would be needed.
What is your general impression about the most promising direction presently, if any?
The extent of my knowledge of abiogenesis is pretty poor, so I’m not really sure. The Metabolism First idea certainly seems worth pursuing at the moment, but I have no idea if it is the best option. Scientists have also put forward PNA as a possibility which is an intriguing chimera of peptides and nucleic acids. Perhaps the largest problem is the lack of a focused solution to the problem.
Yeah, “fire” (i.e., metabolism) also seems a reasonable prospect.
It may not be so bad that we don’t have a focused solution – though admittedly it makes it very tough from the point of view of getting sustained funding and one can spend their life learning many things but get nowhere with the main question. This is not a project like building a rocket (a technology that we already had) to carry three people to the moon and back. That required technology and creativity, but the engineering fundamentals were already there at least, and the target well defined.
For example, what concerns me to some extent with the cosmology side is that so much emphasis when into string theory at the expense of other ideas. It has not helped that funding was constantly being cut back in the sciences so that real blue sky projects that didn’t have a solid guarantee of a good result could not be funded. We somehow forget that real discoveries take 20~30 years to make. Darwin poked at his idea for some 20+ years. Though Wallace stumbling on the same concept gave him a reason to publish, that long “aging/digestion process” is partly what makes “Origin of the Species” such a persuasive and well-written work. The current system demands “progress” on comparatively short-term timetables, which means lots of overhyped publications and a general movement toward short-term thinking – just long enough to grasp at the next grant. From the administrative standpoint, this is a very efficient and justifiable process, but “administration” invariably tends to kill creativity. As a result, it was basically string theory or forget academia.
With many of these new fundamental questions including abiogenesis and cosmology, we don’t have any clue which way to go, so it is like the middle ages in mathematics where people were trying to solve roots of cubic polynomials. It probably is just something we have to take a stab at when we have the time.
Another area of this that interests me is the idea of clay minerals; they can form very complex structures and might, if designed correctly, serve as a catalyst for some of the steps of making (and maybe even assembling) these basic molecules. It kind of reminds me of iron-sulfur proteins that basically have an inorganic “capacitor” buried in the protein; it is that earth, fire, water and air image that gets us back to the Greeks, in a circuitous way. They did leave out sunshine.
First off, I believe Universe/God is determinstic cause and effect. We just cannot see/find/discover or quantize all of multitude of ultra-micro phenomena ex gravity and dark energy.
Fine tune Universe/God exists. End of story.
The other thing I wanted to mention, was this lady scientist who took some carbon based molecules put them in a capsule and fired them into some sand in the lab to reproduce the environment of early Earth the pressures produced by metorite if it struck the Earth.
Much to her surprise, instead of less complex chaotic mess, when she opened the capsule she found the molecules had become more complex peptides and some other stuff.
If were to extrapolate this scenario to higher and higher pressures we might expect even more complex molecules to be created.
So the highest pressures we know of in Universe/God is with black hole phenomena.
We dont know what goes on inside black holes but Jacob Bekenstien discovered that what occurs inside a black hole is expressed on its event horizon surface. This was later confirmed/validated by S Hawling. Jacob Bekenstein then went onto create some holographic scenarios based on those findings.
I can conceive of some scenarios that involve the coding for most complex biological life --humans-- existing inside black holes.
I have considered “programming” within the atoms and molecules themselves (maybe a kind of epi-phenomena) – though there does not appear to be a strong tendency for complex molecules to assemble properly naturally, or we probably would have already observed it.
I am a little lost on what exactly you are saying. … how does programming inside a black hole accomplish anything useful outside the event horizon?
