The Common Ancestry Thread

by cantleave 271 Replies latest members adult

• 

  PSacramento

  It seems that there is some evidence of non-random mutation rates:

  http://www.nature.com/nature/journal/v485/n7396/full/nature10995.html

  A central tenet in evolutionary theory is that mutations occur randomly with respect to their value to an organism; selection then governs whether they are fixed in a population. This principle has been challenged by long-standing theoretical models predicting that selection could modulate the rate of mutation itself 1, 2 . However, our understanding of how the mutation rate varies between different sites within a genome has been hindered by technical difficulties in measuring it. Here we present a study that overcomes previous limitations by combining phylogenetic and population genetic techniques. Upon comparing 34 Escherichia coli genomes, we observe that the neutral mutation rate varies by more than an order of magnitude across 2,659 genes, with mutational hot and cold spots spanning several kilobases. Importantly, the variation is not random: we detect a lower rate in highly expressed genes and in those undergoing stronger purifying selection. Our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations. Current knowledge of factors influencing the mutation rate—including transcription-coupled repair and context-dependent mutagenesis—do not explain these observations, indicating that additional mechanisms must be involved. The findings have important implications for our understanding of evolution and the control of mutations.
• 

  PSacramento

  http://nar.oxfordjournals.org/content/38/5/1515.full

  Exerpt:

  Throughout evolution, eukaryotic genomes have been invaded by transposable elements (TEs). Little is known about the factors leading to genomic proliferation of TEs, their preferred integration sites and the molecular mechanisms underlying their insertion. We analyzed hundreds of thousands nested TEs in the human genome, i.e. insertions of TEs into existing ones. We first discovered that most TEs insert within specific ‘hotspots’ along the targeted TE. In particular, retrotransposed Alu elements contain a non-canonical single nucleotide hotspot for insertion of other Alu sequences. We next devised a method for identification of integration sequence motifs of inserted TEs that are conserved within the targeted TEs. This method revealed novel sequences motifs characterizing insertions of various important TE families: Alu, hAT, ERV1 and MaLR. Finally, we performed a global assessment to determine the extent to which young TEs tend to nest within older transposed elements and identified a 4-fold higher tendency of TEs to insert into existing TEs than to insert within non-TE intergenic regions. Our analysis demonstrates that TEs are highly biased to insert within certain TEs, in specific orientations and within specific targeted TE positions. TE nesting events also reveal new characteristics of the molecular mechanisms underlying transposition...

  To conclude, our analysis shows that although TEs are usually inserted randomly in intergenic regions, there are hundreds of exceptions to this rule. These exceptions have a strong tendency to be overrepresented rather than under-represented, meaning that some new TEs tend to insert within older TEs. We provide examples for TE types that are enriched or depleted within other TE types. Insertion orientation also plays an important role in dictating whether a TE will insert into another.
• 

  PSacramento

  A view on the inverted retina of the eye:

  http://prl.aps.org/abstract/PRL/v104/i15/e158102

  Retinal Glial Cells Enhance Human Vision Acuity

  A. M. Labin and E. N. Ribak
  Physics Department, Technion–Israel Institute of Technology, Haifa 32000, Israel

  Received 11 January 2010; published 16 April 2010

  We construct a light-guiding model of the retina outside the fovea, in which an array of glial (Muller) cells permeates the depth of the retina down to the photoreceptors. Based on measured refractive indices, we propagate light to obtain a significant increase of the intensity at the photoreceptors. For pupils up to 6 mm width, the coupling between neighboring cells is only a few percent. Low cross talk over the whole visible spectrum also explains the insensitivity to chromatic aberrations of the eye. The retina is revealed as an optimal structure designed for improving the sharpness of images.
• 

  cofty

  Psac - Lots of us have taken hours to describe complex stuff in our own words to help others understand the evidence for evolution. We can do that because we really understand the topics we are posting about and we are familiar with the evidence and the objections to the evidence.

  Do you think its reasonable to google search key words and copy-paste stuff you clearly don't understand?

  You posted about evo-devo as if it contradicted the randomness of mutations. It didn't.

  Now you post a reference to a paper about the non-random loci of mutations as if it contradicts what we have said about the random nature of mutations. It doesn't.

  If you do some more research you will find that T-T bonds are also more prone to copying errors.

  Why not take time to study the articles you want to refer to and explain the point in your own words with a link for further reading?
• 

  tornapart

  CL: So what is convincing about the supernatural explanation?

  Touché LOL
• 

  still thinking

  Actually, neither evolved to chase and kill ( or run and not get killed) according to what you wrote previously.

  Accoring to that, they happened to get "fast" and use that speed to either run and kill or runaway and n ot get killed.

  It seems what is being said is that mutations just happen ( either by radiation or certain environment factors) and then the animal USES those the natural selection as shown to be most benefitial for it.

  Is that the jist of the theory?..psac

  Sorry, I know I'm not explaining myself very well. I am also learning about evolution myself, so what I write I am more than happy to have corrected. So that I can correct the way I explain. That helps me to learn and understand.

  You are correct. I worded that porely. They didn't evolve TO chase and kill. They developed speed through natural selection because it benefitted them. The slower animals were eaten which enabled the faster animals to breed and pass on those genes. Likewise in the predator. If it wasn't fast enough to catch prey, it didn't eat. Only the successful managed to pass on their genes to the next generation. They took advantage of mutations that benefitted them. But the two are linked, prey and predator. If the prey was not being chased and eaten, it would probably evolve differently.

  I also picked up on another error in my explanation. I called them 'good and bad genetic changes' there aren't good and bad. There are only beneficial and not beneficial. Depending on what helps the animal survive at the time. What might be useful now. might not be useful in the future.
• 

  cantleave

  Depending on what helps the animal survive at the time. What might be useful now. might not be useful in the future.

  Absolutely. Interestingly a trait may only be beneficial for a short period of time.

  The peppered moth is an well known example of how a trait that is beneficial in one environment is disadvantageous in another. The melanic strain provided an advantage in terms of camouflage on the soot polluted surface found post Industrial revolution until the clean air acts, and the population increased dramatically in this period. Once the clean air act came into force the pale variety once again became dominant in the poulation.
• 

  PSacramento

  Why not take time to study the articles you want to refer to and explain the point in your own words with a link for further reading?

  You are assuming Cffty and you shouldn't assume.

  None of what I posted contridicts that random mutations are the main (overwhelmeing) way mutations accure.

  That some mutations are being found to be NOT as random as others is a fact and all I wanted to point out.

  It was mentioned that the inverted retina is a flawed design, I posted the view that it may not be as flawed as some thing.

  I recall that you said:

  I don't know what you have been reading but it wasn't written by a scientist.

  In regards to what I suggesated that perhaps some mutations ( I don't think I said "some" in the original post) may be influenced but outside sources ( other than pure random chance).

  I simply note two artciles that mention the possibility that some mutation is not as random as others.

  My point is that, while I agree about the core premesis of evolution ( and by such commen ancestry) as I stated above, I am also opne to the possibility that science may discover that mutations may not be as random and purposeless as we may think them to be right now.

  At least give me the possibility that 20, 50, 100 years from now we may have a different understanding of how evolution works.
• 

  cofty

  Psac Im not assuming that you are pasting stuff with zero input from yourself in response to a lot of effort from us. That is obvious.

  The fact that some locations in the genome are more prone to mutations changes nothing. We already knew that.

  Imagine a sequence of letters that is read in threes. Take one letter out and the whole frameset changes in a totally unpredictable way.

  Mutations and their effects are 100% random even if there is a bias in where they occur. This will still be true in 100 years time. You think your citations are relevant because you dont yet understand the basics.
• 

  PSacramento

  It's your thread dude.

  I have a degree in business and Mech.Eng, not in biology and I am trying to understand ALL sides of the argument as best I can, while keeping an open mind to the very real fact that our understanding of evolution is still evolving and that what we know for a FACT today, may not be the case tommorrow.

  That you view the links I posted as simply cut-n pastes with no input from myself speaks volumes in regards to your opinion of me.

  Good luck with this thread, hope it goes the way you want it.

  Later.