This analogy can only be described as a strawman. This is nothing at all like how real genetics works. I’m astonished that you could be seriously advancing this. Beneficial and deleterious mutations are nothing like binary switches that function independently.
Do any of the other scientists that we engaged with (e.g. @swamidass , @glipsnort , @Joe_Felsenstein , @Mercer) want to sign their names in agreement with what Stern Cardinale has written here? Seems like a repeated rehashing of statements that have already been addressed.
You’re confusing two completely different discussions. Namely, the discussion of nucleotide ratios vs. the discussion of the DFE of mutations. There is an equilibrium for the nucleotide ratios–and life is NOT there. There is NO equilibrium for mutational effects. They are always mostly deleterious, because it’s always much easier to cause damage to something functional than it is to improve upon it.
Mutation–selection balance is an equilibrium in the number of deleterious alleles in a population that occurs when the rate at which deleterious alleles are created by mutation equals the rate at which deleterious alleles are eliminated by selection.[1][2][3][4]
Crow, James F.; Kimura, Motoo (1970). An Introduction to Population Genetics Theory ([Reprint] ed.). New Jersey: Blackburn Press. ISBN9781932846126.
Me! Ooh me! (Insistently raises hand hoping the teacher will notice).
A slightly better analogy would be when the light have a higher probability of being green than red, say that after becoming green they have a somewhat smaller chance of changing to red each second, than they do of changing to green if they are currently red. If all start red, more and more of them become green until finally Prob(being green) x Prob(this copy changes to red next second | it is now green) = Prob(being red) x Prob(this copy changes to green next second | it is now red) where “|” means “given”. And then the numbers fluctuate around an equilibrium which has more greens than reds.
At the expected equilibrium frequencies of Red and Green, the rates of green mutations per red copy will not necessarily equal the rates of red mutations per green copy, but the total numbers of to-green mutations will be expected to equal the total numbers of to-red mutations. More properly, if we have natural selection slightly favoring green, the events should be not mutations but substitutions, the probability of which is the product of the probability of a mutation times the probability that it substitutes.
The genome is not a pile of independent nucleotides that are either green (beneficial) or red (deleterious). That’s a massive oversimplification to the point of being worse than useless–in fact entirely misleading.
This is pretty much how Sanford describes the genome. Fixed fitness effects for each individual locus, independent of genetic or ecological context. The vast majority having small but harmful effects, none truly neutral.
It is worse than useless. It is entirely misleading.
That’s why Sanford is wrong.
It would seem that our disagreement is now over specifically what Sanford’s assumptions are. Want to bet against my characterization of his argument? Want to double down on me not actually reading his book?
If much of the DNA is simply “spacer” DNA whose sequence is irrelevant, then there will
be a far smaller mutational load. But notice that the sequence must be truly irrelevant,
not just of unknown function. If the “extra” DNA has regulatory or chromosome-pairing
function requiring it to have a specific base sequence, then mutations in that sequence
will still cause a mutational load, even if these loci are not producing polypeptide chains.
Thus the mutational load argument seems to give weight to the notion that this DNA is
nonspecific in sequence. That is now believed to be the case, and the mutational load
must give pause to anyone who proposes to find important functions for most of the
DNA in eukaryotic genomes, especially functions that constrain its sequence.
Putting the cart before the horse? “DNA can’t be functional, because otherwise we would all be dead by now from mutational load”. Or… deep time is false. There’s the hidden unquestioned premise.
The mutational load calculation continues to be relevant to understanding whether
most eukaryotic DNA has any function that is visible to natural selection. Recent announcements (Encode Project Consortium, 2012) that 80% of human DNA is “functional”, based on finding some transcription or binding of transcription factors in it, are very misleading. Junk DNA is still junk DNA, however often its demise has been announced.
OR, Sanford is right AND the Bible is right. You’re admitting here that your assumptions about deep time are forcing you to assume that most DNA must be junk; because you know that mutations are mostly deleterious, and the mutational load would be an insurmountable problem unless you write off most of the genome as meaningless. If ENCODE is right, evolution is wrong.
Sorry but life existing over deep time isn’t an assumption. It’s as well established a scientific fact as any in the realm of science. Don’t you think you should do at least a tiny bit of research before always making these embarrassingly wrong proclamations? I suppose if you ever did any research on actual science you wouldn’t be a YEC.
PDPrice’s statements totally fail to take into account that populations have overlapping generations in time, fluctations of weather and of the prevalence of predators, diseases, and availability of resources, finite population size, fluctuating finite population size, geographic structure, variations in ploidy, hybridization, meteor impacts, glaciation, shortages of one or the other sex owing to accidents of sampling, chromosome inversions, and so on. And I’m shocked, shocked to see that gambling is going on in this establishment …
How is any of that relevant to what I said? Actually all of that stuff you mentioned is taken into account by Sanford, and much of it is what we would call “noise”. Noise makes the problem of nearly neutral mutations worse. It makes the threshold of selection higher. More mutations will be effectively neutral, because the signal needs to be strong in order to override these confounding factors.
I’m working from the 3rd edition of “Genetic Entropy and the Mystery of the Genome”.
Page 16:
it can very reasonably be argued that random mutations are never good.
Page 21:
Just as there are really no truly neutral letters in an encyclopedia, there are probably no truly neutral nucleotide sites in the genome. Therefore there is no way to change any given site, without some biological effect no matter how subtle. Therefore, while most sites are probably “nearly neutral”, very few, if any, should be absolutely neutral.
Page 34:
Even if we were to accept the lowest estimate (100 mutations), and further assumed that 97% of the genome is perfectly neutral junk, this would still mean that at least 3 additional deleterious mutations are occurring per person per generation. So every one of us is a mutant, many times over! What type of selection scheme could possibly stop this type of loss of information? As we will see given these numbers, there is no realistic method to halt genomic degeneration.Since the portion of the genome that is recognized as being truly functional is rapidly increasing, the number of mutations recognized as being actually deleterious is also rapidly increasing. If all the genome proves functional, then every one of these 100 mutations per person is actually deleterious.
Page 39:
It is becoming increasingly clear that most, or all, of the genome is functional. Therefore, most, or all, mutations in the genome must be deleterious.
Tell me again how I’m misrepresenting Sanford’s argument.
Yes exactly. Completely unrelated fields. If the evidence from genetics contradicts deep time, then it doesn’t matter what the astronomers or geologists say. You’re letting the other fields dictate how you do your genetics. Tsk tsk!
The Fall was polemic against the Nehushtan serpent/seraph in the temple, which was later replaced by cherubim (hence the ending of The Fall with cherubim guarding the way to the tree of life).
Noah’s Flood itself was an insertion
As I have remarked in previous articles, it is fairly well-understood that the story of the Flood was a later insertion into a patriarchal foundation story that didn’t have it. (For a recent paper on this, see Derschowitz 2016.)…
According to research by Old Testament scholar Ronald Hendel among others (Hendel 2012), the insertion of the flood story in Noah’s day created a problem that later scribes couldn’t overlook: if you did the math, the long-lived patriarchs Jared, Methuselah, and Lamech all survived for many years past the Flood, even though the Flood story made it clear that all outside the Ark had perished.
The editors of the LXX, SP, and MT had basically two ways to solve the problem: either delay the year of the Flood by delaying the age at which the patriarchs begat sons, or have the patriarchs in question die sooner. Here’s what each of them did:
The LXX’s editor methodically added 100 years to the age at which each patriarch begat his son. Adam begat Seth at age 230 instead of 130, and so on. This had the result of postponing the date of the Flood by 900 years without affecting the patriarchs’ lifespans, which he possibly felt were too important to alter. Remarkably, however, the editor failed to account for Methuselah’s exceptional longevity, so old Methuselah still ends up dying 14 years after the Flood in the LXX. (Whoops!)
The editor of the SP adopted a simpler method. He just altered the lifespans of the three patriarchs that posed a problem. Adjusting their ages as little as possible, he had them die in the same year as the Flood.
The editor of the MT chose to keep the lifespans untouched (like the LXX), and he altered the age of begetting only for the three patriarchs affected, pushing back the Flood date as a result. He first added 100 years to Jared’s begetting, and then 120 years to Methuselah’s. This reduced the overlap to 94 years. By adding 94 to Lamech’s begetting, he completed the fix, placing Methuselah’s year of death in the year of the Flood.
…because you’re imputing your “red and green” analogy to Sanford. But he would never agree with it. Because the genome is information, and encoded information is context-specific. We explained this in our joint article, and you’ve ignored it. Now I’m being forced to rehash. See: HOUSEHOLD v. HOUTNHELDE explanation.
