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2016 September 23

Evolution of caffeine

Filed under: Uncategorized — gasstationwithoutpumps @ 13:07
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PZ Myers has a nice discussion of the convergent evolution of the synthesis of caffeine (separately evolved at least 5 times!), based on the paper from PNAS, Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes, by Huang, O’Donnell, Barboline, and Barkman.

Biologists used to think that there was one canonical pathway for caffeine synthesis, from xanthosine through 7-methylxanthine and theobromine to caffeine.  The paper shows that some plants use a different pathway (through 3-methylxanthine and theophylline) and that the enzymes used even on the common pathways are different.

The evolutionary model that best explains the data is that ancestral enzymes were promiscuous (which means that they had several different functions, not that they were sexual) and were eventually duplicated and specialized for caffeine production.  The researchers reconstructed some of the ancestral enzymes from the modern descendants and confirmed that this hypothesis was reasonable, as only single amino-acid substitutions were necessary to confer the two different specificities of the modern enzymes from the ancestral ones.

2012 July 4

Evolving a tune

Filed under: Uncategorized — gasstationwithoutpumps @ 17:42
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The site DarwinTunes | Survival of the funkiest provides an example of crowd-sourced artificial evolution.  They are attempting to evolve a piece of music by having many people listen to and rate clips from a population generated by a genetic algorithm.  The selection pressure from the user ratings is supposed to result in gradually more pleasant clips.

It is a somewhat interesting idea, but note that they are only evolving a single piece of music or a small population, not a program for generating music or rules distinguishing music users like from music users don’t like.  So even after running their experiment for a long time, they only end up with a small amount of music.

They have examples sampled about every 150 generations up to 6000 generations.  I find even the latest generation quite difficult to listen to for more than a minute or so.  Composers need not fear being replaced by this technique any time soon.

2012 January 19

Bogus story in Science Times

Filed under: Uncategorized — gasstationwithoutpumps @ 14:14
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In this week’s Science Times (a section of Tuesday’s NY Times, and the only reason we buy a newspaper on Tuesdays), Carl Zimmer wrote and article Yeast Reveals How Fast a Cell Can Form a Body, which reports claims from William Ratcliff to have evolved a primitive form of multi-cellularity in yeast.

I think that Mr. Zimmer may have been fooled.  The process described in the article, of yeast cells clumping together is known as flocculation and it a natural property of yeast that evolved (most likely) millions of years ago.  It has been well studied as it is critically important for beer brewers (even Wikipedia has an article  on yeast flocculation). Standard lab strains often have a disabling mutation in one of the flocculation genes (for instance, strain S288C has a mutation in FLO8), since lab strains have been selected for non-flocculation. Some of these mutations are frame shifts and  it is generally very easy to restore flocculation to yeast by having a compensating mutation that restores the correct reading frame to the disabled gene.

Of course, Mr. Zimmer may have left out some crucial information from the paper. The article itself is

William C. Ratcliff, R. Ford Denison, Mark Borrelloand Michael Travisano
Experimental evolution of multicellularity

PNAS 2012 ; published ahead of print January 17, 2012, doi:10.1073/pnas.1115323109

and is open-access, so anyone can read it.

The authors claim that their “snowflake” phenotype differs from the flocs of flocculent strains of yeast:

During this time each cell was seen to give rise to a new snowflake-type cluster, whereas aggregation was never seen, demonstrating that clusters arise via post-division adhesion and not by aggregation of previously separate cells [as would be the case for flocs].

They also distinguished their phenotype from another way yeast cells are known to cluster:

The snowflake clusters are distinct from S. cerevisiae pseudohyphal phenotypes, which have filamentous elongate cells and arise under conditions of nutrient stress. Clustering in snowflake-phenotype yeast is independent of pseudohyphal growth, as the snowflake phenotype is stable under both high- and low-nutrient conditions. Individual cells within clusters retain the ancestral ability to form pseudohyphae when starved, but remain oval (not elongate) during standard culture conditions

So they do seem to have observed a new phenotype for yeast, but it is it a new evolution (as they claim) or simply a new observation of something that evolved a long time ago? They do “evolution” but do not then look to see what has changed in the genome—probably because they know that they have just turned on a pre-existing gene and don’t want to spoil their fantasy of “evolving multicellularity”.

I’d need a lot more data to show that multicellularity had evolved within 60 days, as they claim.  It is so much more likely that they turned on a pre-existing pathway that is not normally on in the yeast strains people study.  If I had been refereeing this paper, I would have made them tone down their claims for having evolved something new—given that all replications resulted in the same phenotype, it was almost certainly a pre-existing possibility in the genome.  (I fault PNAS, which has such a crummy refereeing process that I refuse to referee for them.)

Disclaimer: I’m not a yeast biologist.  If the “snowflake” phenotype really is a new evolution, I’d like to hear about it from someone who is an expert on yeast, and what the evidence is that it is really newly evolved.

 

2011 November 2

Microbe DNA Swaps

Filed under: Uncategorized — gasstationwithoutpumps @ 02:00
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Science News has just reported on a new, but unsurprising result: that bacteria are more like to swap DNA with other organisms in the same environment [Nearness Key In Microbe DNA Swaps].

The paper they are reporting on

Ecology drives a global network of gene exchange connecting the human microbiome
Chris S. Smillie
, Mark B. Smith,Jonathan Friedman,Otto X. Cordero,Lawrence A. David, & Eric J. Alm
Nature (2011) doi:10.1038/nature10571

identified recently transferred genes as those having “blocks of nearly identical DNA (more than 500 nucleotides, more than 99% identity) in distantly related genomes (less than 97% 16S rRNA similarity)”.  Given the fairly rapid drift of protein-coding genes in the “wobble bases” (the third base of codons, changing which often does not change the amino acid coded for), which is about 25 times faster than the changes to 16S ribosomal RNA, this definition of recently transferred genes seems reasonable.  There will be a few false positives, but not too many—they estimate that about 99% of their putative horizontal transfers are genuine.  About 27% of their predicted transfers include known mobile elements (phages, plasmids, transposons), but most of the transferred genes (87%) seem to be other genes not associated with the mechanism of transfer.

The observed “most gene exchange occurring between isolates from ecologically similar, but geographically separated, environments.”  Of course, they observed the most exchange between human-associated bacteria, and people move around so much that “geographically separated” does not have much meaning for the bacteria they carry.  The mere fact that the samples could be collected indicates recent contact chains that could spread bacteria and allow DNA interchange between them.  Soil bacteria have slower transport, so it is not surprising that less DNA interchange was found there.

Because most of the DNA transport was found in human-associated bacteria and particularly between pathogenic bacteria, most of the study focused on those bacteria.  It is not clear to me whether these bacteria have more DNA exchange, or if the greater numbers of transfers is just due to the much heavier sampling of human-associated bacteria.  We might well find the similar rates of DNA transfer in other bacteria, if we had similarly large databases of their genomes, with as thorough coverage of the ecological niches. The authors claim to have corrected for this effect and still seen a 25-fold greater exchange rate among human-associated bacteria, but I’m not sure that a good correction can be made without more data on soil bacteria. Soil bacteria for sequencing have been deliberately chosen to get maximum phylogenetic diversity, which is not an easily corrected bias—just looking at raw numbers of genomes when one group is chosen for similarity (disease-causing bacteria) and another selected for diversity (soil bacteria) will underestimate the sampling bias.  As is common in Nature papers, the Methods section of the paper is completely inadequate for determining what the authors actually did.

The conventional wisdom about gene transfer is that phylogeny matters most (because many of the horizontal transfers use viruses, plasmids, and other fairly host-specific mechanisms) and geography next (because of observed geographic patterns of antibiotic resistance and disease strains).  Others have observed that there have been massive exchanges between archaeal and bacterial hyperthermophiles, which inhabit similar niches but are very far apart phylogenetically and spatially. [Aravind, L., Tatusov, R. L., Wolf, Y. I., Walker, D. R. & Koonin, E. V. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14, 442–444 (1998) http://dx.doi.org/10.1016/S0168-9525(98)01553-4].

I know that David Bernick has observed that two hyperthermophile archaeal species collected on opposite sides of the world (Pyrobaculum oguniense and Pyrobaculum arsentaticum) are very similar genetically (so much so that one even has CRISPR immune sequences protecting it from a virus that infects the other), despite not being able to live in the intervening environment and despite somewhat different metabolic requirements (one is a strict anærobe, the other can live in ærobic conditions).  If hyperthermophiles can have genetic exchange between hot springs separated by 1000s of kilometers (probably on a time scale of 10s of years or less, based on the CRISPR evidence), then exchanges between mesophilic bacteria carried around by humans should be much quicker.

So the new claim that environment matters most is hardly surprising, but some of the consequences are important.  For example, there is a large horizontal gene transfer between organisms in the guts of animals and those in the guts of humans, even if the bacteria themselves do not live in multiple hosts.  That means that antibiotic resistance genes that are strongly selected for in cattle fed antibiotics can easily transfer to human pathogens, spreading antibiotic resistance much more rapidly than previously assumed.  This looks to me like strong evidence that we should immediately prohibit the use of antibiotics in animal feed for any purpose other than the treatment of existing disease, just as we restrict antibiotics for human use.

 

2011 October 11

Optimal defocus estimation—possible explanation for evolution of astigmatism

Filed under: Uncategorized — gasstationwithoutpumps @ 14:46
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I found this article, Optimal defocus estimation in individual natural images, rather interesting, despite being well outside my current field.

The basic idea is a simple one: compute the effect on Fourier transforms of images of defocusing by various amounts, and use modern machine learning techniques to learn filters for detecting the defocusing.  One can get a lot of extra information about the defocus if the lens system is not perfect, using astigmatism and chromatic aberration to get more precise defocus estimates. This paper gave me some insight into why astigmatism has not been eliminated by natural selection.  I had always assumed that it was either not a serious enough defect to have strong selection or that it was linked to other, desirable traits that kept it around in the population.  This paper points out a possible selective advantage to astigmatism, allowing faster focusing in low-light conditions (when the chromatic aberration signal may not be available).

The paper did not go so far as to provide fast algorithms for autofocus using the new technique, but it looks like it might be feasible.  It would be nice to have an autofocus algorithm for digital cameras that did not do so much slow movement of lenses as the current ones use.

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