Absorbing DNA

[Resha Caner]

Though it's an engineered solution, it does appear processes are being found that significantly shrink the time scales: Accelerated Evolution. [edit] ... and involve increasingly longer sequences: Construction of long DNA molecules.

 

[Loudmouth]

How is it known to be HGT? Is it that the same sequences were found in different species or is there some other indicator?

They detected HGT through phylogenetic methods. Genes trees that were very different from the species trees were tagged as candidates for HGT. In other words, they use a phylogenetic method to differentiate between vertical transfer and horizontal transfer. If it is vertical transfer, then the gene tree should match the species tree.

To use a made up example, if we found an exact copy of a mouse gene in the chimp genome but not in the genomes of other primates, then this would be a strong candidate for an HGT event.

Finding an example in nature would be preferable, but I don't think it's absolutely necessary. One could argue that engineered solutions are natural - that we and what we do are part of nature. However, if the engineering is too extreme, that could be a problem.

I have always disliked the categories of natural and artificial as well. However, it is sometimes best to use bad terminology when your audience has adopted that bad terminology. It is better to be understood than to be right.

That's what I would expect. I wasn't looking for "willy nilly" HGT. I would expect that most of the time HGT events are low, but conditions may arise occasionally (such as during adaptive radiation time periods) that increase the frequency of HGT events.

In what ways do you think adaptive radiations increase HGT?

 

[Loudmouth]

Though it's an engineered solution, it does appear processes are being found that significantly shrink the time scales: Accelerated Evolution. [edit] ... and involve increasingly longer sequences: Construction of long DNA molecules.

It is definitely an exciting time to be involved in molecular biology. In the last 20 years I have seen the maturation of many really cool technologies and techniques. Sequencing a bacterial genome used to be an entire graduate project. Now people are sequencing a bacterial genome in a single day. CRISPR/Cas9 technology is a really exciting new tool for genome editing. Real time PCR and DNA/RNA array technology has revolutionized how we look at transcriptomes, and omics in general. Mass spectrophotometry has become a new powerful tool in the last 10 years, especially in the field of proteomics.

The real movement is towards speed, scalability, and parallel workflows. Do it fast, in large volume, and do a lot of them at the same time. It isn't enough to sequence one genome. You need to be sequencing 20 genomes at once. It isn't enough to measure one protein in a serum sample. You want to be able to measure all the proteins in a serum sample in under 5 minutes for 10 patients at once. Like I said, fun times.

 

[PsychoSarah]

It would appear that the mutation rate isn't even the same for all populations of E. coli. One of the E. coli populations in Lenski's study had a much higher mutation rate. I think we can all agree that population genetics is a complicated subject.

As to viruses, it would be problematic if viruses mutated more quickly than they do. If a new strain appeared every 2 weeks it would be quite difficult to keep up.

Hence why an effective vaccine for HIV is unlikely, given that it has an excessively high rate of mutation.

Then there is the flu, which we need a yearly vaccine for, and chicken pox, which people only need to get more shots for every 5 years because acquired immunity isn't retained indefinitely, not because the virus itself has changed to the point that the vaccine is ineffective.

 

[Resha Caner]

In what ways do you think adaptive radiations increase HGT?

I meant it the other way round - not that adaptive radiations cause HGT, but rather that there may have been periodic events that created conditions promoting increased HGT. Adaptive radiations just seem a good candidate for a place to look as in this case: Adaptive radiation by waves of gene transfer.

My pet idea at the moment is that increased volcanic activity leading to widespread conditions similar to hydrothermal vents might be the cause: Hydrothermal Vent Ecosystems.

I have always disliked the categories of natural and artificial as well.

And as you well know, I'm not opposed to the idea that biological developments in the distant past were directed by an intelligent agent. I just don't expect to be able to prove that.

 

[Loudmouth]

I meant it the other way round - not that adaptive radiations cause HGT, but rather that there may have been periodic events that created conditions promoting increased HGT. Adaptive radiations just seem a good candidate for a place to look as in this case: Adaptive radiation by waves of gene transfer.

My pet idea at the moment is that increased volcanic activity leading to widespread conditions similar to hydrothermal vents might be the cause: Hydrothermal Vent Ecosystems.

I am a bit confused. Are you saying that volcanic activity caused increased HGT?

And as you well know, I'm not opposed to the idea that biological developments in the distant past were directed by an intelligent agent. I just don't expect to be able to prove that.

I am aware, and I have always found our conversations interesting and well worth the time.

 

[Resha Caner]

I am a bit confused. Are you saying that volcanic activity caused increased HGT?

It's a possibility. A link between genetics and geology has been suspected for quite some time - both with respect to genesis and change.

I am aware, and I have always found our conversations interesting and well worth the time.

The same for me, though we probably take away different conclusions.