Can natural selection create: Part 1? (See Figure 1—Genes; Figure 2—Irreducibly complex)
BQ: Based on the independent research of Haldane, Gabriel, Tishkoff, Verrelli, Crow, Kimura, ReMine, and other scientists, I'd like to start a deeper look at natural selection’s ability to create useful information. We'll start off with the question, "can natural selection create even a single useful gene?" Furthermore, we'll work our way slowly, recalling past research and questions, and give ourselves a favorable scenario to create an "origin of species."
Let's take a look at defining our first desirable mutation by asking, "is any particular nucleotide more valuable than any other?"
A: By itself, no nucleotide (A, T, C, G) has any more value than any other, in the same way that no letter in the English alphabet has any particular value outside of the letters around it. That is, a letter's value is defined by the context we find it in, and so are nucleotides. A change to a single letter in this sentence can only be evaluated by the surrounding letters.
From this, we see an example of irreducible complexity. Irreducible complexity presents a problem for evolutionary thought, though circularly many try to arm-wave it away with the all-powerful, "natural selection." By irreducible complexity, we mean, "a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition non-functional.’ (Behe)
If we look at the problem with creating these sentences (the DNA of this BQ), we'll see we have a very basic bit of irreducible complexity. To create new information, we need to select for our first beneficial mutation, but...we can only define the value of the nucleotide/mutation as compared to its nucleotide neighbors. By changing the nucleotide, we inherently also change the overall meaning of the neighbors; we have therefore created a circular paradox as we keep destroying the context on which we are trying to build.
Tomorrow, we'll start off from here and look at the problem of fundamental inter-relationships of nucleotides, known as "epistasis." If you have any questions at this point, shoot me a message and I'll be glad to explain it better. :)
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Figure 1—Genes
Figure 2—Irreducibly complex
Can natural selection create: Part 2. (See Figure 3—Epistasis)
BQ: We are considering the question, "Can natural selection create even a single useful gene?" We are giving ourselves a massive advantage by assuming that we have no negative mutations ever (IRL, the neg/pos ratio of mutations is pretty much "vast-to-none"). Yesterday we learned that no nucleotide (DNA building block) is more useful than another by itself. We also learned that they are only useful in the context of the other "building blocks" around them, and that any mutation inherently affects context. Therefore, we inherently have irreducibly complex DNA.
Today we need some background information clarified, so we're going to look at epistasis. Epistasis is a problem with the fundamental inter-relationship between nucleotides. Essentially, this inter-relationship between nucleotides is infinitely complex. When we define epistasis, we say that, "Different mutations that affect the same trait often interact, so a harmful mutation may be much more or less harmful depending on the absence or presence of other mutations." This "noise" in the DNA makes natural selection of genetic benefits almost impossible, like trying to get only internet with Comcast, yet having to buy a bundle with overpriced phone and TV. Genomes are a package deal; we can't just take that nice internet deal for super cheap.
Genetic language, like any language, is not a product of chance. Having letters randomly fall into meaningful places is not statistically feasible (in fact, as we saw before, it exceeds the probabilistic resources of the entire universe), and the same can be said for our genetic language. We know from computational models than strings of nucleotides (and just dozens of them, not billions as found in our DNA) cannot randomly fall into place, but we're going to look and see if we could accomplish this one nucleotide at a time, giving ourselves another advantage.
With this background information out of the way, tomorrow we'll examine the timespan we'd have to have for our first mutation within human evolution to become "fixed," and we're going to give ourselves the benefit of having no "package" deal with mutations, though epistatically we know that we would HAVE to have many bad mutations attached to any "improvement mutation." We'll use the assumed population model proposed by evolutionary theory and see how long it'd take us if everything was perfectly in our favor.
Attached is a picture I made to help you visualize what we're talking about when we say "epistasis."
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Figure 3 —Epistasis
Can natural selection create: Part 3, The waiting game. (See Figure 4—Extrinsic Factors.)
BQ: We now know what the concept of irreducible complexity is as well as the tough problem of epistasis. We continue to move forward with our question, "can natural selection create even a single useful gene?" Today, we're assuming no harmful mutations exist or would exist, and that we have a pristine human population to pull from, using the evolutionarily accepted figure of about 10,000 individuals.
The mutation rate for any given nucleotide is about 1 chance in 30,000,000. So if we assume 100 mutations per person per generation, we need about 3000 generations, or 60,000 years, to expect a specific nucleotide within our population of 10,000 to mutate. About 66% of the time, it will mutate into the "wrong" building block. So for a specific site to get a beneficial mutation, it'll take about 3x as long, or 120,000 years. Once we do get it, we need to "fix" it—that is, make sure that all individuals will have two copies.
Our challenge is then genetic drift. That is, a mutation needs to be exceedingly noticeable and beneficial to counteract the extrinsic factors and genetic noise. In other words, it's hard to "keep the mutation ball rolling," because most reproduction will not be based upon this one beneficial mutation, but rather other aspects. So perhaps the mutation gives our individual nice abs, but because of the way he was "raised," he is obnoxious and no other individual mates with him to produce offspring which might pass the mutation on. According to population geneticists, the new mutation has 1 chance in 20,000 (total number of non-mutant, location-specific nucleotides present in the population) of not being lost via this genetic drift.
At least 99% of the time, even a good beneficial mutation will be lost via drift. So even a BENEFICIAL mutation needs to happen about 100 times before it "sticks around." On average, then, we would need 120,000 years times 100, or 12,000,000 years to stabilize a first desired genetic mutation. But remember, this is ONE nucleotide segment, and we need MANY of these to build just one desired mutational gene. It supposedly took us 6,000,000 years to evolve from ape-like creatures, but we can see that we can only realistically expect to fix one good mutation in twice that long, and that's without harmful mutations thrown in.
Next, we'll look at the wait for other mutations in building our gene, because one nucleotide base pair does not a gene make.
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Figure 4—Extrinsic Factors