Genome complexity: variation within species (Introduction)

by dhw, Saturday, December 10, 2016, 12:15 (2906 days ago) @ David Turell

Thank you for these three posts, which I am combining since they all relate to the same subject.

DAVID (under "genome complexity”): Cells are constantly reproducing themselves as daughters. DNA must be constantly monitored against mistakes, and it is:
http://www.businessinsider.com/breakthrough-prize-winner-dna-research-2016-12

SELECTED QUOTES (my bold):
"That DNA tells our cells what to do. When they divide, that information is copied from one cell to another."

"It's only thanks to a mechanism in our cells that can recognize when something has gone wrong that we aren't all riddled with cancer."

"That mechanism, known as the DNA damage response, functions like an individual intelligent agent, able to monitor when things are going wrong and then try to come up with a way to deal with them."

"'One of the remarkable properties of nature’s most remarkable molecule, DNA, is self-awareness: it can detect information about its own integrity and transmit that information back to itself,"

"When this response detects damaged DNA, it can respond in several ways.”

David’s comment: There is no way life could have continued with a DNA code controlling it, unless such a defense mechanism against mistakes was present at all times. Only a saltation could have produced this result. Not by chance.

As always, a powerful case for design. But design of what? A microcosm within a macrocosm? “DNA tells our cells what to do…a mechanism that can recognize…like an individual intelligent agent…try to come up with a way…self-awareness…respond in several ways…” So many of the actions and attributes we associate with intelligence – and yet we are not even aware of them. It’s as if we are inhabited by a colony of ants, each with their own particular role to play, but constantly communicating, adapting, making decisions in the world that is you or me. It’s what some scientists call cellular intelligence.
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QUOTE (re the killifish): "The team's genetic analysis suggests that the Atlantic killifish's genetic diversity make them unusually well positioned to adapt to survive in radically altered habitats. At the genetic level, the tolerant populations evolved in highly similar ways. This suggests that these fish already carried the genetic variation that allowed them to adapt before the sites were polluted, and that there may be only a few evolutionary solutions to pollution.

David’s comment: It is becoming recognized that alternate metabolic pathways may be present in many species, as I noted in our previous discussions about bacteria responding to antibiotics (can't find the reference). The species is still one species. It is not a new evolutionary process as the articles headline proclaim.

May I suggest that if the killifish is able to cope so quickly with different pollutants, what it carries before the sites are polluted is not an alternative metabolic pathway anticipating whatever might happen next, but the ability to process new information and change its genome accordingly – which means it can construct a new metabolic pathway to cope with each new threat. And I would suggest that this applies to all processes of adaptation, though different organisms will have different capacities for change. You are quite right: this is not the same as innovation. It is simply confirmation that the genome can be changed when an organism experiences new conditions. We don’t know how far the ability for change can extend. Or do you still think your God put each alternative metabolic pathway for all eventualities into the first cells to pass on to the killifish a few thousand million years later?
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QUOTE: "Over the past 10 years, large-scale sequencing projects have revealed startling levels of individual genomic variation across the tree of life, challenging the value of the modern reference genome—as well as the very notion of a species. To better capture the genetic makeup of any given taxon, many researchers now argue that the field of genomics should adopt a pangenomic framework in which diversity is central, rather than incidental, to our view of species.”

Nobody has yet solved the problem of defining species (Darwin devotes a whole section to it), which is why I usually put “broad sense” in parentheses, since it is the borderlines that are blurred. Nobody would claim they can’t distinguish between, say, elephant species and butterfly species. But what is really interesting is the variability between individuals. This would explain how common descent works. Changes can only take place in individuals, and individuals are different. So some will respond to environmental change and others won’t. So far we only know of adaptation and non-adaptation (those that can’t respond will die). But it is conceivable that the variation will also apply to innovation. Some organisms may have the wherewithal to invent. In much the same way as some humans are creative, and some are not.