Re: The Tuatara, a Still-Evolving Original - NYTimes.com

Hey Brandon,

Can’t quite figure out what this article is trying to say.  It describes the traits of the tuatara—straightforward and factual.  

It also asserts that “ a few regions of tuatara DNA appear to be evolving at hyperspeed <http://www.cell.com/trends/genetics/abstract/S0168-9525%2808%2900003-6> , possibly the fastest mutation rate yet clocked in a vertebrate genome.”  And, “The quick-changing sequences are limited to so-called neutral regions of the tuatara’s DNA, affecting filler codes, rather than the molecular blueprints for how to build a tuatara.”  This is where things get a little vague and nonspecific.  What do they mean by evolving at hyperspeed?  What are neutral regions?  It almost sounds as if they’re referring to ‘junk’ DNA.  And, since the tuatara hasn’t changed for ‘hundreds of millions of years’, what would be the evolutionary significance of  these regions evolving at hyperspeed?  The creatures are still tuataras.  Are the authors trying to imply that the tuatara is getting ready to evolve into a higher, more complex kind of organism?  Do the authors see the mutations as being good or deleterious?  

Unfortunately, I don’t have easy access to the full study linked to in the NYT article—perhaps it would answer some of my questions. The NYT article itself doesn’t seem to be much more than an interesting description of an unusual animal, with an obligatory reference to evolution thrown in.

http://jvi.asm.org/cgi/content/abstract/81/23/12979
This study found no beneficial mutations at all.

http://www.nature.com/nature/journal/v467/n7315/abs/nature09352.html
Study of fruit flies over 600+ generations finds a resistance to change.  The fruit flies remained fruit flies.

Susan

The Tuatara, a Still-Evolving Original - NYTimes.com

Why haven't we made little robots that kill unwanted animal and plant species yet?

-b

http://www.nytimes.com/2010/11/23/science/23angier.html?pagewanted=2&_r=1&src=fbmain

Fwd: only slightly creepy biology

From: Ben
Date: November 10, 2010 2:12:18 PM PST
To: Brandon
Subject: only slightly creepy biology

http://arstechnica.com/science/news/2010/11/an-array-of-body-neurons-helps-larvae-see-light.ars

Loss of amphibian population

Hey Brandon,

Neither the fish in the Royal Society article nor the development of bacterial resistance support Darwinian evolution—they’re both examples of adaptation to environmental conditions.  For example, some bacteria carry latent genes that code for antibiotic resistance; these genes become active in the presence of certain antibiotics.  In other bacteria, mutations lead to resistance to certain types of antibiotic, but the resistance comes with a cost, such as slower growth rate or decreased resistance to other antibiotics—when these bacteria are in natural conditions (with no antibiotics), they aren’t able to compete with the faster growing non-mutated bacteria.   

Here are several related articles...  

The agents of divergent selection are extrinsic and can include abiotic and biotic factors such as food resources, climate, habitat, and interspecies interactions such as disease, competition, and behavioral interference.

This comes from Evidence for Ecological Speciation and Its Alternative, Dolph Schluter, in Science Magazine ( http://www.sciencemag.org/cgi/content/full/323/5915/737?ijkey=57JzKGxEe.F.Q&keytype=ref&siteid=sci ).  This sounds good when you’re promoting Darwinian evolution.

Potential causes [of worldwide decrease in amphibian population] include habitat degradation, pollution, acid rain, ultraviolet irradiation, pesticides, predators, competition from introduced species, climate changes, and disease.

From Holt, W. V. et al, eds. 2003. Reproductive Science and Integrated Conservation. Cambridge, UK: Cambridge University Press, 360.  (You can look this page up online at amazon.com.)  This sounds good when you’re talking about protecting the environment.

So, what we have here are scientists with very different perspectives based on different fields of study.   One says that climate, habitat, and so on, drive evolutionary change and development of new species and classes of organisms, and Dawkins would agree with this.  The other suggests that these same factors lead to population degradation and loss of many  species.  Apparently the factors that are said to have driven Darwinian evolution (with its development of increasingly complex species) in the past, and supposedly continue to do so now, also lead to species degeneration and loss.  How do the same factors manage to lead to both increase and decrease of species (and concomitant  genetic information)?

According to the second reference, a decrease in amphibian population over time has been observed by scientists—that part is something we can know for sure.  What isn’t known for sure is the cause for the decrease in population.  It doesn’t make sense that the same factors would drive both the increase of complexity/genetic information and the decrease of complexity/genetic information.  If climate, habitat, and so on do drive Darwinian evolution, why are amphibians not evolving into something else rather than disappearing?  

As previously reported from allozyme analyses, A. japonicus exhibits little genetic differentiation, in strong contrast to salamanders of the genus Hynobius with which their distributions overlap. This reduced genetic variability in A. japonicus is attributable to a unique mating system of polygyny, delayed sexual maturity, notable longevity, life in a stable aquatic environment, and gigantism, as well as bottleneck effects following habitat fragmentation and extinction of local populations during Quaternary glaciations. The species is thus susceptible to extinction by potential environmental fluctuations, and requires extensive conservation measures. Matsui, M., et al. 2008. Reduced genetic variation in the Japanese giant salamander, Andrias japonicas (Amphibia: Caudata). Molecular Phylogenetics and Evolution. 49 (1): 318-326. linkinghub.elsevier.com/retrieve/pii/S1055790308003795

According to this study, A. japonicus (the Japanese giant salamander) has reduced genetic variability (genetic differentiation).  Organisms that have insufficient genetic variability are less able to adapt to environmental changes.  Because of this, the giant salamander is susceptible to extinction due to environmental fluctuations. This reduced genetic differentiation would be expected with genetic entropy.  If Darwinian evolution were taking place, one would expect environmental fluctuations to be driving further evolutionary development of new genetic information in order to help the amphibians adapt—but this doesn’t seem to be taking place.  Overall, we readily observe extinctions, but no one has ever observed the development of life from non-life or of a new class of organism with greater complexity from one with lesser complexity, such as a eukaryote from bacteria.  We readily observe adaptations within a kind, such as the above bacteria and fish, but we don’t observe one kind developing into another, more complex kind.  

Susan

Fwd: evolution article

From: ben
Date: November 8, 2010 1:13:30 PM PST
To: Brandon Meredith <mathcadd@gmail.com>
Subject: evolution article

A cool example of artificial selection, kind of like antibiotic resistant bacteria, but on an animal:
http://rsbl.royalsocietypublishing.org/content/early/2010/09/06/rsbl.2010.0663.full?sid=b26a2194-7a63-4bfc-acdd-b62460fffa9a

Re: Evolving altitude aptitude

Hey Brandon,

Well, it would make sense for either Adam or Eve to have carried this particular gene, although it doesn’t mean that the gene was necessarily active in either one of them. People carry the genes for many different traits which they don’t have themselves.  Even though I have green eyes, I probably carry the genes for blue, brown, and/or other eye colors.   I’ve seen families with red-headed kids who whose closest red-headed relatives were several generations back.  Adam and Eve would have had the genetic material for all the possible traits, and then various populations, as they spread out and became more isolated, would have lost some traits because of less genetic material available to pull from.

I do find it much more logical and scientifically sound to believe that a Creator God created everything than to believe that living organisms came from non-living material, then developed complex genetic information through mutation and natural selection, and without any intelligent guidance.  I suppose this will continue to be a bone of contention for us.  Perhaps you could find research showing how Darwinian evolution handles handedness, entropy, and the other problems I’ve mentioned?  

Also, if I could find one stretch of human DNA that had three beneficial configurations, wouldn't that disprove your logic?  

I’m not sure what you’re trying to say here—perhaps you could rephrase?

Susan

Fwd: Evolving altitude aptitude

Hey Susan,

I absolutely detest having to talk about what you base your ideas on, but I see no way around it in this case. You say that this special stretch of DNA in the Tibetans has always been around, presumably placed there by a god for the precise reason of making a happy population on a mountain  but if you also believe that all of humankind came from one man and one woman, then you believe that either Adam or Eve had this special stretch of DNA that the Tibetans now have. Is that what you really believe?

Also, if I could find one stretch of human DNA that had three beneficial configurations, wouldn't that disprove your logic?

-Brandon