The active iron centre in hemoglobin is fascinating. The site is situated in such a way that a “space” is created on a stereochemical site of iron, that favours the binding of a particular molecule (eg O2). The chemistry is such that an internal electron transfer takes place that “drives” the associated biochemistry (itself an extraordinary process that I as a chemist do not fathom at a molecular level). This fascinating structure also shows why carbon monoxide will prove fatal, as the CO molecule is similar in size to dioxygen, so it can be accommodated in the “space” above the iron centre, but binds more firmly to the iron centre and prevents dioxygen from becoming involved.
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I don’t find your reference to “no selective pressure” to be quite accurate. Frequently some hidden potential of genetics is revealed only when the average organisms begin to die off because of a change in the environment!
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I’d certainly consider the Na+/K+ pump as a basic function, but the rhodopsin is rather specialized. In any case, I’m sure there are some examples of genes (basic function or otherwise) that scientists are unable to trace back to prokaryotes, but these two examples are indeed traceable. An internet search would bring a lot more information, but here is an article regarding the pump, and a different one here regarding rhodopsin and bacteriorhodopsin.
One of the really interesting things I saw regarding the hemoglobin evolution is that the bacterial forms often bind NO, rather than O2. It seems that it is an important feature to have a protein that can bind a small gas, and once that is established, the gene and encoded protein can adapt to binding different small gases.
I think what you are getting at (correct me if I’m wrong) is the question of where the tremendous variety of prokaryotic genes come from. This is a good question and if my perception is accurate (again, I’d welcome the input of professional scientists here) we are much shorter on answers. I think someone resurrected a thread recently regarding the “minimal genome” which consisted of 473 genes as of March 2016 (I don’t know if this number has been pared down any), but the specific details of how that minimal genome would have come into being is still rather speculative. As an evolutionary creationist, I can comfortably say that I believe God set up conditions that would lead to those stages necessary for evolution to work (or maybe even created the first cells intact?), but there are still many details that need to be filled in.
Well, what I’m getting at really is where any particular protein (or its corresponding gene) with a unique, previously non-existent function can arise / come from initially, if it were not benefiting from natural selective processes. At some point, every novel function had to just (poof) appear just to get the process of mutation/natural selection started. Before that point, you had simply a random string of AAs that were accomplishing nothing (or if something, still not the new function), and thus natural selection was utterly powerless to get the sequence that far. Once the function, however rudimentary, appeared, natural selection then had something to work with to improve the process, but until then, it is just random. The fact that there are 473 separate required functions, if I understood correctly, merely compounds that problem exponentially.
Quickly, one clarification, to make sure I understand your position::
[quote]I can comfortably say that I believe God set up conditions that would lead to those stages necessary for evolution to work (or maybe even created the first cells intact?), but there are still many details that need to be filled in.
[/quote]
Do I understand this to mean you believe
A) that God set up the initial, non-organic, non-living, basic laws of chemistry and physics (essentially no differently than we have at our disposal) and that this was sufficient for evolution (or abiogenesis?) to work and therefore produce the first functional prokaryotes…
B) that God (in whatever manner- direct/supernatural or via strictly natural means) set up not only the basic core laws of chemistry and physics, but also set up the particular arrangement, formulae, particular conditions (e.g., atmosphere, environment, reagents, energy sources, etc.), which were necessary for evolution/abiogenesis to work and produce the first functional prokaryotes… or
C) that the first functional prokaryote[s], with its designed, functioning genes, was the “initial condition” necessary for subsequent evolution to work.
(Or did I miss you completely, and you meant something else entirely? 
)
So there is bacteriorhodopsin. It is used for light-based energy generation.
And all this time I was under the impression that prokaryotes were simple organisms…!
Thanks for the additional insight. Thus you have me curious, are there in fact any animal / mammalian proteins (or of another kingdom for that matter) that have a novel function not shared with prokaryotes?
It all depends how you define “function.”
On a biochemical level, I’m pretty sure single-celled organisms (not just prokaryotes) have way more functional classes than mammals. Mammals are not mammals because they have a host of new biochemical functions, but because they “put them together” to build something more complex.
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Yes! Prokaryotes are often regarded as simple because they lack some of the features of eukaryotic organisms, but they are fascinating little creatures! Just think about this little factoid… E. coli possesses a much broader array of functional metabolic enzymes than we do!
Back to your question of A, B, or C – my answer is “yes”. I’m going to diverge a bit from mainstream scientists, but I think all 3 scenarios are possibilities. Questions like these make me very excited for the day when I am no longer “seeing through a glass darkly”!
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Or a random string of ribonucleotides! Most scientists buy into the concept of the “RNA world” (read about it here) in which the first molecules with enzymatic function were RNA, and not protein. This probably isn’t exceptionally pertinent, but fascinating to consider.
Huh… so you use the meme of “poof” to assault molecular biology? Of the billions of individual life forms that teem on this planet, every new cell, every new generation, makes billions of replication mistakes … billions of replication mistakes is not a trivial number.
And I assure you, it is not a “poof” process. In contrast, however, when God says he made Adam from clay, do you think God patiently sat on a ridge somewhere, carving away at the clay with an artisan’s tool? Or do you think he went “poof” !?
Ultimately, God is capable of doing his finest work by using Evolution as his artisan’s tool - - where the process of Evolution allows him to choose any number of specific replication events to get exactly what his purposes require.
George,
First, “poof” refers to the fact that, at some point, any new function had to appear completely randomly, with no guidance or selection process (natural or otherwise) whatsoever. it would be akin to breaking into a computer by trying numerous passwords completely at random, with no feedback telling me how close I came with any particular attempt. At some point, if I broke in, it would happen “poof” by random chance. This is not a critique or assault on molecular biology, it is simply a way of observing the reality. until some function - even in the most rudimentary form - actually begins, there is nothing for natural selection to work on to get it to appear.
Secondly, let’s consider the math you mentioned: I grant the billions upon billions of replication mistakes (and hence “attempts” to find combinations that accomplish these new functions). However, if I understand Curtis correctly, most of these random “discoveries” of new protein functions happened during the timeframe between the first self-replicating “life” (~4.3 bn years ago) and the appearance of eukaryotes (~1.8 bn years ago), giving roughly 2.5 billion years of time for the billions upon billions of replication variations to come up with these functions, which I assume can be accomplished by perhaps billions of variations of any particular polypeptide. That used to sound impressive and convincing to me. I heard creationists use the line about “the odds of putting one functional protein together…”, but I remained unconvinced for the very reason that we were talking about billions upon billions of opportunities over billions of years to find potentially billions of possible combinations. Until one day I actually did the math…
Let’s assume, given the probable spread of life on early earth, 100 trillion variations (replication mistakes) in the genes happen, worldwide, every second over that 2.5 billion years. That sounds generously reasonable to me, but let me know if that number should be higher. That is 100 trillion x 60 (to calculate total variations per minute) x 60 (variations per hour) x 24 (per day) x 365 (per year) x 2,500,000,000 (variations over 2.5 billion years) = 7.88 x 10^30 total variations (attempts to crack the “code”) in that time. Now let’s recognize that not just one sequence will work for any particular function, but let’s grant 100 quadrillion (10^17) different variations would work. (someone who knows the science can tell me if this is a fair estimate or not). This gives 7.88x10^47 opportunities to attempt a “winning” sequence combination that will start the function…
But if we are talking about a protein that needs, say 100 amino acids minimum to function (which to my understanding seems a reasonable starting point for many functions), the number of possible combintations that actually exist are 20^100, or 1.26x10^130 (if for the sake of simplicity we are limiting the math to only variations of 100). Therefore the odds of this random variation process achieving a particular required function for life as we know it, given the billions upon trillions of chances to find even one of the quadrillion possible sequences over 2.5 billion years is…
1 in 10^81. I understand that is roughly the number of atoms in the observable universe. So let’s try a game: I’m thinking of one particular atom in the observable universe. You have to guess it. You get one guess.
Now, to clarify, I recognize of course that are lots of other factors involved which contribute to our understanding of protein function development. That is not my point here: I put all that above just to clarify one point in particular, and that is simply that “billions upon billions upon trillions upon quadrillions upon quintillions of replication mistakes” is in fact a very, very, very trivial number when you actually do the math and recognize what is really required. Hence, simply, why the claim that “but there are billions of replication mistakes,” which I hear far too often, remains singularly unimpressive to me.
Sir, certainly, I recognize that our proteins share many if not most of their functions with the proteins of the simplest organisms (reaction catalysis, structure, etc.). I had just been under the impression that many functions mammals like us have were also the result of proteins that are completely unique (in biochemical function). I had assumed (mistakenly) that light detection and O2 transport were in such a category. Now I just find myself curious if all basic functions of proteins that are used by even the most advanced animals and plants are also shared with Prokaryotes. That is a fascinating observation or inquiry to me.
You are describing the preconditions that Atheists hold to.
We have God in the BioLogos metaphysics. All things are possible with the Father.
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Sure, but either God used 1) natural processes, the same we can detect and experiment with in labs today, or he 2) intervened in some kind of direct/supernatural/miraculous manner that is outside of what “natural processes” in operation today as we see them are able to accomplish.
If you lean toward the second, then I think we could both describe this as a “poof” of sorts. If the first, then all the limitations of natural processes are rightly able to be critiqued as we explore how those natural processes that God ordained accomplished such a feat without retreating to the “Goddidit” that so many atheists accuse us (I think rightly) as using as a cop out.
I’ve omitted some too. In addition to:
- starting with a temperature-sensitive mutant instead of the wild-type enzyme, there’s
- using life and death as a proxy for enzymatic activity instead of simply doing the assays, and
- there’s a pathetically tiny amount of actual work in the paper–an average student could have done this in a month, and a star student or postdoc could have done it in a week while doing other projects!
Any of those three massive methodological issues would get the paper rejected by any reasonable journal, irrespective of the hypothesis and conclusions.
What on earth gave you such an impression, Daniel?
Do you realize that you have inadvertently offered empirical predictions of a scientific ID hypothesis that you now must realize is false?
Making mistakes is how we learn.
That depends entirely on how you define “function,” as Swamidass told you. That’s why you learn more when you test the empirical predictions of hypotheses, even if others have already done so.
Here’s something that may impress you, then: for diploids like you and me, what drives evolution is not new mutations, but already-existing, directly measurable variation (polymorphism). The ratio is between 1/100000 and 1/1000000.
I’m fine with that. When God uses a natural law … sometimes you can hear Quantum space making squeaky stretching sounds.
But when God uses the miraculous to accomplish something, there is a definite “poof” sound !
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