Tuesday, October 10, 2017

Under Construction

I am making some adjustments to the templates and layout of the blog. Feel free to comment if this makes the blog easier or harder for you to read (no promises that I will respond accordingly).


DDeden said...

Just 2 notes:

Indonesian article: https://academic.oup.com/mbe/article/doi/10.1093/molbev/msx196/3952785/Complex-patterns-of-admixture-across-the

Indonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly undercharacterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea, and Oceania, notably including previously unsampled islands across the Indonesian archipelago.

Question: Does genetic evolution operate within one's lifetime?
MtDNA - No,
Nuclear - No,
GI Microbiome - Yes.

andrew said...

"Question: Does genetic evolution operate within one's lifetime?
MtDNA - No,
Nuclear - No,
GI Microbiome - Yes.

Usually, but not quite always. Retroviruses can change a the DNA of a living person (usually nuclear DNA) and there are indeed examples of that happening. Also, pregnancy can cause a woman to develop mosiac DNA with some cells having DNA from a child (or fetus even if not born). Fraternal twins can also sometimes have mosiac DNA.

Also, DNA can mutate or evolve in the course of cell production in some but not all cells. Two common examples are older men's sperm and cancer. Some environmental circumstances can make this more common.

A third issue not directly addressed in your question is that your epigenome can change during life and sometimes lifetime epigenomic changes arising in life are passed on to descendants for a generation or two. The epigenome is the biochemical way that the body regulates gene expression, for example, telling a particular cell's DNA to produce lung tissue rather than bone tissue, or imprinting a particular kind of gene expression in response to cocaine. The paradigmatic, although not the only part of the epigenome is mythelation.

DDeden said...

Thanks. I guess also radiation altering cells would also be an example.

But I was thinking more in terms of multiple generations of microbiota evolving within a single generation of the host human, and 'domesticating/breeding' them to influence pancreatic insulin or gluten or lactose or alcohol metabolizing. There are other ways to treat these, but GI biogenome breeding might be advantageous in some ways. (Just a floating thought.)

andrew said...

Gut bacteria really is useful and underutilized because the main remedy (digesting bacterially active poop) sounds gross.

The appendix, once thought to be useless, has since been determined to be an organ that reboots the body's gut bacteria after being wiped out, for example, by poison or a parasitic infection. It keeps a feeder stock of gut bacteria out of the GI battlefield ready to rebuild if necessary.

We're really only scratched the surface of the microbiome and active efforts are underway to better document what it is and what it does. This is a cutting edge area of medical and biological research.

It is also true that what you eat influences what microbiome evolves within you in relation to that diet, mostly in the form of balancing selection, more of this and less of that within a pre-existing range of variation.

The immune system isn't normally conceptualized as part of the microbiome, but functionally it behaves quite similarly and can also evolve through exposure to pathogens and imitation pathogens which we know as vaccines. One exciting potential near future vaccine makes you immune to most forms of tooth decay.

Phages in lieu of antibiotics is another hot area of microbial ecology manipulation which is basically analogous to introducing a non-native species of predator into an ecosystem to shut down a pest.

Also, there is a lot of hot research on manipulating the epigenome, for example, to allow a one time administration of a drug to turn off cocaine receptors in the body and instantly end a cocaine addiction.

DDeden said...

Yes, agree. Also saw this today regarding teeth: http://www.thisisinsider.com/dental-fillings-cavities-alzheimers-disease-tideglusib-2017-10?utm_content=buffer828ae&utm_medium=social&utm_source=facebook.com&utm_campaign=buffer-insider-science

andrew said...

On point re viral gene transfer. https://www.nytimes.com/2017/10/04/science/ancient-viruses-dna-genome.html

DDeden said...

Yes, the virome embedded within us. Some places I dare not dig, the virome is one; someone else will figure it out, not me! Viruses are like robotic alien life forms to me.
I'm now looking at Goyet Cave Belgium and Tianyuan cave China; human and dog may have come from Phu Quoc island (my dog domestication source hypothesis), very intriguing around 30ka - 40ka.

DDeden said...

Andrew, I'm very interested in the possible link of these 3 stories, in reference to my hypothesis that dog domestication began on Phu Quoc island around 45ka. with first deliberate breeding for pulling coracles and sleds (a long shot, of course). [I match Quoc to Kuon@Greek & quan@Chinese and kutaka/gudaga/dog@Mbabaram-Queensland.] Any thoughts on the articles?

A new study in Current Biology analyzed the entire genome of the Tianyuan man who was found near Beijing, China and lived around 40,000 years ago. The Tianyuan man’s genome marks the earliest ancient DNA from East Asia, but this is not the first time we have studied Tianyuan’s genes.
In 2013 paper in PNAS, the same group that published the Current Biology paper showed there is a closer relationship of Tianyuan to present-day Asians, based off his genes, than to present-day Europeans. At that time it was suggested that present-day Asian history has a deep lineage as far back as 40,000 years ago.
An international team of scientists has just identified what they believe is the world's first known dog, which was a large and toothy canine that lived 31,700 years ago and subsisted on a diet of horse, musk ox and reindeer, according to a new study.
DD ~ David ~ Da'ud ~ Diode ~ ∆^¥°∆

andrew said...

There are lots of contradictory studies on dog domestication that put it all sorts of places.

I touch on Tianyuan man in a footnote to my latest post, although I'm not convinced that I believe the conclusions reached with regard to Paleo-Asian ancestry in South American indigenous populations which is at odds with a prior study on the same subject.