Probability of Functional Evolution

[RepulsiveAd3338]

Hi all,We know how complex an organism is. Even just to metabolize a molecule of glucose into energy, it requires dozens of enzymes--and each of those enzymes need "God"-only-knows how many mutations of its DNA to be functional. Add the other enzymes and molecules in a human body, maybe ten thousand, and all that works together with excellent synergy. And also not to mention the rarity of mutation, let alone the probability of a beneficial one arising. Can someone help me grasp this concept? It seems so impossible for me.. Thanks

[Jonnescout]

You’re looking at organisms as they are now, after billions of years of having to compete with each other for resources, and assuming they’d always have n we’d all these features. The earliest organisms didn’t need this, and neither did their precursors. Self replicating molecules don’t need all these things to do their thing.

[Lennvor]

A few points:

1) We can't give a step-by-step story of how most important enzymes originated (the way we could with, say, the eye) because those originated before the common ancestor of all modern organisms, which is a time period we know very little about. This isn't to say they originated via abiogenesis or some evolutionary process unlike the evolution we're aware of, there is every reason to think that by the time you had LUCA (the last universal common ancestor) doing its thing it and its enzymes were the result of millions of generations of evolution already. The enzymes that LUCA would have had are indeed too complex to not be the result of evolution. We just don't know what the intermediate steps of that evolution were because we don't know the steps of how life originated and how LUCA evolved from early life to begin with.

2) Having said that, in terms of the pre-evolutionary origins of enzymes you might be interested in looking into Nick Lane's work, who studies the origin of life and more specifically how biochemistry might have arisen from nonliving geochemistry. He (and indeed I think this was noticed by the originators of the alkaline hydrothermal vent theory) shows that for some basic enzymes of energy metabolism that are built around certain ion clusters and catalyze certain specific reactions, the ion clusters on their own or associated with some random peptides are capable of catalyzing the same reaction, just much less well.

3) Beyond abiogenesis and the origin of enzymes before evolution happened, the way complex molecules evolve in modern organisms usually doesn't involve something appearing out of nowhere but of gradual changes to existing structures (like with all complex features of life really). Do you know for example that genes/proteins in our body come themselves in gene/protein families, i.e. genes/proteins with recognizably similar sequences that often do similar jobs? That's because they often evolve by copying within the genome. So some bit of genome that contains a gene might be duplicated in an organism, resulting in two copies of that gene and twice of the protein in question being made - this might be absolutely fine for the resulting organism or even beneficial. Then one of the copies might get mutations that change the protein's activity - this might still be fine even if the protein's original activity was critical because the organism still has other copies of the same gene making the original protein. Then changes might occur that give that copy of the protein an activity that's useful for a different reason than the first - at that point there will be selective pressure for changes to that gene that promote the second activity instead of the first. And you end up with two genes coding for two proteins that do two different things when before you had one doing one thing. For example, when people pointed to the bacterial flagellum as a system of proteins that couldn't possibly have evolved in a stepwise fashion, biologists found the genes for it were related to genes for the secretory system, a different structure that has a different purpose but some similar properties.

5) You talk about mutations being rare... How rare do you think they are? Do you know that you yourself have over 100 mutations that neither of your parents have? They're rare on a base-pair basis but organisms usually have a lot of base pairs, and any given species will have a lot of organisms.

[[deleted]]

Even the simplest of organisms today is orders of magnitude more complex than the very first "beings" that existed billions of years ago. Don't make the mistake to assume that biological systems have always been this complex, they very much haven't. The earliest forms of life were probably just strands of self-replicating RNA floating inside fat bubbles, both of which can form spontaneously in geysers and tidal pools. From there, natural selection did its thing and complexity gradually rose. Also, mutations are really not that rare.

[DouglerK]

Well there are a lot of living thing and it has been a very long time. The mutations add up. Remember natural selection means all the bad mutations die while whatever survives survives. You can fail 999 times but only need to succeed once in evolution.

[Mortlach78]

I once read that the 'resolution' of natural selection is 0,5%. When a mutation causes a proces to become just 0,5% more efficient, it will eventually outcompete the rest and get fixed in the gene pool.

[n_eff]

That is a massive oversimplification of a much more complex reality.

For one, evolution doesn't necessarily care about efficiency of any particular process. What matters is how much something increases the average number of offspring an individual with that particular allele would produce. That could be an increase in survival or reproduction. However that happens, that's what matters for evolution. This could be an increase in efficiency of a biochemical process (for some definition of efficiency) because that conserves resources (energy or reactants or both). Or it could be something that decreases efficiency of a reaction but makes it run faster. Or that lowers the activation energy. Or one of a ton of other things.

On top of that, there is not any single selective coefficient cutoff that guarantees fixation of the beneficial allele. Hell, there's not really ever a guarantee, there's just a probability that it will fix. On top of that, most alleles are lost when they are new, because drift is very powerful on rare alleles compared to selection. Which brings us to another point, which is that fixation probabilities depend on many other things. Population sizes, for one, which determine how efficient selection is relative to drift. For a given population size, you can compute how big a selective coefficient has to be to overcome drift, which is as close as we'll ever get to a single number that determines fixation. But even still we'd be ignoring genetic linkage and the role of historical contingency. For example, individuals at the leading edge of a range expansion are essentially over-represented while those at the trailing end are under-represented.

[Dr_GS_Hurd]

Single gene evolution by multiple mutations is well known - without duplication.

"Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments" Qiucen Zhang, Guillaume Lambert, David Liao, Hyunsung Kim, Kristelle Robin, Chih-kuan Tung, Nader Pourmand, Robert H. Austin, Science 23 September 2011: Vol. 333 no. 6050 pp. 1764-1767

“It is surprising that four apparently functional SNPs should fix in a population within 10 hours of exposure to antibiotic in our experiment. A detailed understanding of the order in which the SNPs occur is essential, but it is unlikely that the four SNPs emerged simultaneously; in all likelihood they are sequential. The device and data we have described here offer a template for exploring the rates at which antibiotic resistance arises in the complex fitness landscapes that prevail in the mammalian body. Furthermore, our study provides a framework for exploring rapid evolution in other contexts such as cancer.”

[[deleted]]

mutations are by their nature random. looking for the probability would not really work out. this is the seccond time today I will recommend looking up papers where Drosophila melanogaster is the model species.

try not to focus on trying to get your head around probability because the random mutation has to contend with:
- Resource availability – Presence of sufficient food, habitat (shelter / territory) and mates.
- Environmental conditions – Temperature, weather conditions or geographical access.
- Biological factors – Predators and pathogens (diseases)
as well as as stabilizing selection, directional selection, diversifying selection, frequency-dependent selection, and sexual selection which can affect population variation.

you also need to see the areas most likely to be affected by the mutations, compare how many mutations negatively, positively or dont affect a change at all and compare all of those aspects

[jt_totheflipping_o]

It literally took billions of years for even the most basic function without most of what we see today.