For genomes devoided of junk DNA, no.
The human genome is mostly junk as evidenced by the lack of sequence conservation in more than 80% of the genome. Bacterial genomes are mostly functional. Don’t you have to take these things into consideration?
My logic is spelled out here:
Please note that my exchanges with @RonSewell was about differential genetic entropy in bacteria vs RNA viruses, two type of organisms devoided of junk DNA.
What positive correlation between virulence and fitness? Do you have some sort of systematic review where such a correlation is established as a general principle in virus evolution?
You there?
Thanks. So in your scenario, the virus was around in the european population for a long time without going extinct, but continually deteriorating. Eventually the european population developed a high level of immunity to it and carried it around. The virus still persisted without going extinct despite it’s huge mutation rate. The europeans made their way to the americas and then this much-deteriorated virus suddenly had a huge increase in virulence (which “positively correlates with fitness”, aka it must have evolved higher fitness?).
Or maybe in this very deteriorated state in europeans, it was still highly functional and had high fitness against a new population (so it hadn’t deteriorated after all?). Or did it manage to hide in some “natural reservoir”(a host where it was passed on as a retrovirus), then suddenly mutated back into functionality and high fitness and then started infecting native americans?
2 Likes
You just repeated the same statement I was responding to.
Like, seriously?
Aristotle: It is impossible to hold (suppose) the same thing to be [virulent] and not to be [virulent].
Aritotle: It is impossible to hold (suppose) the same thing to be [fit] and not to be [fit].
Yes. True. Absolutely. That is the point. That is why virulence is useless as a proxy for fitness of any sort. It matters not if you are talking of the proper biological meaning of fitness or have redefined fitness to mean Greek god viruses who work out and watch their diet.
Here are some publications that support the idea that virulence is generally positively correlated with fitness:
https://www.pnas.org/content/104/16/6806
https://jvi.asm.org/content/85/8/3959
https://www.sciencedirect.com/science/article/pii/S0042682211002789
Do you not understand the term “general”?
On a quick skimming of those papers it appears they’re not all talking about the same measures of overall viral fitness(for example the first one appears to be only about replicative fitness, which I understand to defined by the number of viral particles produced by a successful infection). It is not difficult to see how a virus could have overall lower fitness but higher replicative fitness, because it could have a hard time producing successful infections(hence have low virulence) despite each successful infection producing huge quantities of viral particles. And just to be clear I’m no expert on viral fitness, yet it’s pretty clear these relationships are anything but simple.
And they’re specific examples as opposed to demonstrations of an overall systematic relationship.
1 Like
Your thoughts, @Giltil?
The correlation between fitness and virulence is not perfect of course, but overall, the trend is there and can be explained as follow:
- within host replication has a large impact on fitness, meaning higher within host replication is associated with higher fitness.
- viral replication takes place at the expense of host resources. As a result, faster replication and higher viral loads tend to produce more severe disease and higher mortality rates.
Some in this discussion, who will constantly say something to the effect regarding problems in evolution, “we’re working on it” with little evidence that the problem will actually be solve will simultaneously dismiss the possibility of large scale integration and function of the human genome. The difference between evolutionary theory and the discovery of function in junkDNA is that we actually keep finding more and more function and more and more possibilities. I’ve listed some regarding 4D nucleome, Origami Code, RNA epitranscriptome, Alu elements. I could list even more for Line-1 elements, ERVs, poly-functional DNAs, micro RNAs, linc/lncRNAs, etc. etc.
And on top of that, this recent study that suggests DNA stores information in 3-dimensions, not just two. This is supported by the Origami code and the 4D Nucleome project:
https://advances.sciencemag.org/content/advances/6/2/eaay4055.full.pdf
Physical and data structure of 3D genome
With the textbook view of chromatin folding based on the 30-nm fiber being challenged, it has been proposed that interphase DNA has an irregular 10-nm nucleosome polymer structure whose folding philosophy is unknown. Nevertheless, experimental advances suggest that this irregular packing is associated with many nontrivial physical properties that are puzzling from a polymer physics point of view. Here, we show that the reconciliation of these exotic properties necessitates modularizing three-dimensional genome into tree data structures on top of, and in striking contrast to, the linear topology of DNA double helix. These functional modules need to be connected and isolated by an open backbone that results in porous and heterogeneous packing in a quasi–self-similar manner, as revealed by our electron and optical imaging. Our multiscale theoretical and experimental results suggest the existence of higher-order universal folding principles for a disordered chromatin fiber to avoid entanglement and fulfill its biological functions.
This suggests there is a 3D Data Structure which humans could not easily build something this complex, much less random mutation and natural selection. Personally, these are reasons I think God did it, but independent of that, it suggests more function for the genome, and it supports the ENCODE viewpoint, even though ENCODE may have arrived at the right conclusion independent of whether their reasoning is right or not.
Even if ENCODE is half right, that’s about 40 per individual. Using the bonkers formula, that implies each human female would need to bear on the order of 10^40 kids, just to have a eugenically clean baby, and even then this is not sufficient as one would have to assume some serious truncation selection which isn’t in evidence.
HT: my good friend Paul Nelson who pointed me to the above paper
Classic Creationist argument from ignorance and personal incredulity. Humans can’t recreate in the lab what natural evolution took 3.5+ billion years and a whole planet to produce, therefore My Personal Deity Of Choice did it.
You have demonstrated no such trend.
1 Like
That isn’t true. The estimated amount of functional DNA in the human genome has hung around the 5-10% mark for decades now, and nothing ENCODE published changes that figure.
Finding a handful of ERV’s that have function does not mean all ERV’s have function. Finding function for untranslated RNA does not mean that all transcribed RNA has function. Finding transposons that have function does not mean that all transposons have function. See a trend here?
Guess what we see with functional RNA sequences? Sequence conservation. Guess what we don’t see in ~90% of the human genome? Sequence conservation.
This has been known for a long time. Is the function in that DNA dependent on the sequence of bases? How much of the genome is made up of these sequences? How do you explain the difference in sequence conservation between exons and any other DNA that you deem to be functional?
Have you forgotten this very important publication…
…as well as his lecture at the NIH titled « Net Genetic Loss in Humans, in Bacteria, and in Virus »?
https://www.reddit.com/r/DebateEvolution/comments/9j4lrj/john_c_sanford_author_of_genetic_entropy_is/?utm_source=amp&utm_medium=&utm_content=post_body
You mean Sanford’s latest brain fart which has been virtually universally rejected by evolutionary biologists and population geneticists? The only people who seem to think it is “very important” are ID-Creationists who are desperate for any sciencey-sounding woo to use as ammo.