In “Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution” (PLOS Genetics, November 3, 2011 ) Matteo Fumagalli et al argue,
Previous genome-wide scans of positive natural selection in humans have identified a number of non-neutrally evolving genes that play important roles in skin pigmentation, metabolism, or immune function. Recent studies have also shown that a genome-wide pattern of local adaptation can be detected by identifying correlations between patterns of allele frequencies and environmental variables. Despite these observations, the degree to which natural selection is primarily driven by adaptation to local environments, and the role of pathogens or other ecological factors as selective agents, is still under debate.
To address this issue, we correlated the spatial allele frequency distribution of a large sample of SNPs from 55 distinct human populations to a set of environmental factors that describe local geographical features such as climate, diet regimes, and pathogen loads. In concordance with previous studies, we detected a significant enrichment of genic SNPs, and particularly non-synonymous SNPs associated with local adaptation.
Furthermore, we show that the diversity of the local pathogenic environment is the predominant driver of local adaptation, and that climate, at least as measured here, only plays a relatively minor role. While background demography by far makes the strongest contribution in explaining the genetic variance among populations, we detected about 100 genes which show an unexpectedly strong correlation between allele frequencies and pathogenic environment, after correcting for demography. Conversely, for diet regimes and climatic conditions, no genes show a similar correlation between the environmental factor and allele frequencies.
This result is validated using low-coverage sequencing data for multiple populations. Among the loci targeted by pathogen-driven selection, we found an enrichment of genes associated to autoimmune diseases, such as celiac disease, type 1 diabetes, and multiples sclerosis, which lends credence to the hypothesis that some susceptibility alleles for autoimmune diseases may be maintained in human population due to past selective processes.
Do they mean it wasn’t cooking or shoes or fluid societies or anything? We’ve heard all those and hundreds more … Stay tuned.
This clearly sounds like epigenetically driven adaptation to local environments, rather than any ‘random micro-evolution’, despite the mandatory homage paid to Uncle Charley at the beginning and end of the article;
No. It doesn’t. Epigenetics would study the DNA methylation or histone codes that regulate DNA transcription. Epi-genetic means on top of the genome. They studied genes at the sequence level. That is this part: “spatial allele frequency distribution of a large sample of SNPs”
Nice article News. Should be an interesting read.
Nothing like a plague wiping out half a population to select for some resistance alleles!
DrREC you state:
Yet I seem to recall Shapiro stating:
Also of interest from the preceding paper, on page 22, is a simplified list of the ‘epigentic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis model) of neo-Darwinism.
Read the list of epigenetic mechanisms. Are any of them mutational? No.
You’re conflating these epigenetic mechanisms with the notion of “directed genetic engineering” which is a bit more dubious, especially in animals, with a few exceptions like the immune system.
DrREC you state:
That is exactly the point DrREC!!! And this ‘non-mutational’ process helps you establish ‘random mutations’ for neo-Darwinism how??? Clearly DrREC, this is not helpful to neo-Darwinian presuppositions!
This paper measured coding genetic changes. Coding genetic changes aren’t epigenetic. This paper doesn’t study epigenetics.
Mutational changes, such as studied in this paper, is the “random variation” of evolution.
Epigenetics marks aren’t, and aren’t thought to persist long enough to impact evolution.
DrREC you state:
Yet I have reason to believe that they are:
i.e. Giving the staggering level of information processing in the cell DrREC, I simply find it a stretch, to put it mildly, to claim randomness for the process when you yourself admitted “This paper doesn’t study epigenetics”;
Of related interest:
“DrREC you state:
Coding genetic changes aren’t epigenetic.
Yet I have reason to believe that they are:”
This is just a simple definition. Genetic vs. EPIgenetic. See the “EPI” It has meaning. Increased mutation rate in bacteria in stress conditions (where the paper is taking about the human genome) is interesting, but irrelevant.
BA…
seriously.
We have no problem admitting that selective pressures exist and do affect allele frequencies. Read The Edge of Evolution. Behe’s entire thesis is based on the demonstration that Darwinian processes not only exist, but that they can be measured.
tragic, I didn’t say otherwise, I just disagreed with the a priori conviction that the change in alleles was caused by purely random processes as is required for a neo-Darwinian interpretation in the first place!
correction: I just disagreed with the a priori conviction that the change in alleles, in this particular instance cited by the OP, was caused by purely random processes.
In fact, considering the stunning level of information processing going on in the cell, which we have just the barest glimpse of so far, I would have to say that, aside from induced mutations, it would be extremely difficult for a atheist to find examples of ‘purely’ random mutations, in these ‘local adaptations, so as to make his case with.
You do realize that SNP means “Single Nucleotide Polymorphism,” placing these mutations within Behe’s limit, right?
tragic, I’m not even questioning that (indeed would not a priori expect Behe’s limit to be violated even with the epigentic programming of the cell adjusting the nucleotide sequences), I am just pointing out that the atheists have not established that the changes were truly random. That is all! It is a simple point, yet it is still crushing to neo-Darwinism since neo-Darwinism is required, scientifically, to establish that the changes are truly random!
tragic, of humorous note; here is a experiment, I posted a while back, that would satisfy the empirical requirement, on neo-Darwinism, to establish that purely random processes can create all life:
Blackholes- The neo-Darwinians ultimate ‘god of randomness’ which can create all things
Being the helpful guy I am, always trying to help atheists out when I get a chance, I’ve been trying to piece together a experiment that would prove once and for all, for everyone to see, that RANDOM variation plus undirected natural selection can produce functional proteins just as atheists adamantly claim (even though no one has ever seen RANDOM processes do this). Now I just about got the RANDOM part of the experiment down for the atheists! I’ve searched for the maximum source of RANDOMNESS that I could find in the universe, (since the ‘god of randomness’ is who atheists claim for their creator), and I think I’ve found it for them;
First:
Thus, the more entropy a system has the more randomness it will generate for our experiment to find a RANDOM functional protein. And if we ask, ‘what is the maximum source of entropy, i.e. RANDOMNESS, in the universe?’, we find this:
Plus for a added bonus for atheists, being the helpful guy that I am, I found that if we find a really supermassive blackhole we might just start to overcome the homochirality problem, which is a huge problem against finding functional proteins, as well:
But of course there is the problem with actually getting the atheists to the super-massive blackholes to actually do the experiments, so that they may try to RANDOMLY generate a functional protein. Not to mention the problem of someone trying to survive being stretched into as a piece of spaghetti, by the extreme warping of space-time, near the blackhole. But what the hey, it is just a little sacrifice for ‘science’ right!?! At least atheists will have a maximum source of randomness to work with in their experiments!!! But there is another problem I probably need to tell atheists about before they pack up and go off to the super-massive blackholes in order to prove to the world that their ‘god of randomness’ can create all things,
But what the hey, atheists haven’t needed any stinking equations to prove their theory so far have they!?!
I even have a inspirational quote for their future experiment;
And even a song for their experiment;
lol.
Anyway, randomness cannot be proven as a cause, and neither can God for that matter. There is only faith in one or the other.
I have no particular problem granting that some things can be random, including certain random SNPs happening to provide some advantage relative to the environment, such as disabling most of the production of melanin in the first Europeans. There’s no need to be defensive. We are winning. 😉
Tragic Well,,, actually I disagree with you and think it is very important to hold Darwinists strictly accountable to their theoretical presuppositions!,,, and I disagree with you on your other statement of deducing sufficient warrant of ‘proof’ as to source of causality.