Potential falsifications of the theory of evolution

Just to re-emphasize your point. . .

You received the answers we pretty much expected you would. We were pretty sure his responses would use the term non-random in the same misleading way as in his other writings.

He considers increasing the random mutation rate in times of stress to be a sentient reaction. Interesting, but I personally wouldn't call it sentient.

Darwin knew nothing of horizontal transfer, whole genome doublings or natural genetic engineering capabilities and neglected symbiosis. His ideas were based strictly on vertical inheritance, and he insisted on gradualism.

This is more assertion than fact. I see no problem with mutation and selection accounting for the evolution of antibiotic resistance across the board. Once such mutation has occurred in a bacteria then it can pass it on by HGL, but the mutation and selection are still at work in cases without HGL.

Darwin new nothing about genetics, apparently not even aware of Mendel's work. He did however know that traits were inherited and that this allowed natural selection to work on populations.Darwin did not "insist" on gradualism, in fact he discussed changes in rates of evolution as entirely possible. He was just of the opinion that gradualism was more likely.

he does clarify that by saying rather emphatically that it is not deterministic, which is shadow71's interpretation.

Has NATURAL GENETIC ENGINEERING changed the modern Darwinian theory of evolution as we know it today?Of course. Going from random accidents to regulated biochemical systems as the source of genetic variation is a fundamental change. It allows us to understand how outside events can trigger change (see table in my 2006 "Genome Informatics" article), makes it clear how combinatorial change can occur using established adaptive components (e.g. protein domains, regulatory modules), and provides a way to investigate what kind of heuristic guidance may be operating in genome change.

Do you all disagree with his assertion that Natural Genetic Engineering has changed the modern Darwinian theory? Not necessarily falisfied it, but changed it?

I am still trying to understand what is meant by random mutation. Although it may not be determistic, it seems that the alternatives to random mutation may be so limited that it is really not random, but allows such a small choice that it may not be as imortant as stated by the modern theory.

That cell sentience may be more important than random mutation.

I am still trying to understand what is meant by random mutation.

That cell sentience may be more important than random mutation.

If some outside influence (stress, a chemical, UV, etc.) initiates an SOS response in an E. coli (note: an SOS response is one of the many biochemical systems Shapiro considers NGE) it amps up the mutation rate.What mutations occur (e.g. if base substitutions, which base A/C/T/G will change) is RANDOM.
Where the mutations occur in the genome is RANDOM.
Thus, the mutations are RANDOM with respect to fitness.The SOS response is the same every time. But it produces different results.The SOS response can produce beneficial, neutral or deleterious mutations. It's random. There's no pre-determined endpoint

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome
Although TEs are a major component of all studied plant genomes, and are the most significant contributors to genome structure and evolution in almost all eukaryotes that have been investigated, their properties and reasons for existence are not well understood in any eukaryotic genome. In order to begin a comprehensive study of TE contributions to the structure, function, and evolution of both genes and genomes, we first identified all of the TEs in maize and then investigated whether there were non-random patterns in their dispersal. We used homology and TE structure criteria in an effort to discover all of the retroelements in the recently sequenced genome from maize inbred B73. We found that the retroelements are incredibly diverse in maize, with many hundreds of families that show different insertion and/or retention specificities across the maize chromosomes. Most of these element families are present in low copy numbers and had been missed by previous searches that relied on a high-copy-number criterion. Different element families exhibited very different biases for accumulation across the chromosomes, indicating that they can detect and utilize many different chromatin environments.Article Metrics Related Content Comments: 1 To add a note, highlight some text. Hide notes
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Regina S. Baucom1#, James C. Estill2#, Cristian Chaparro3, Naadira Upshaw1, Ansuya Jogi1, Jean-Marc Deragon3, Richard P. Westerman4, Phillip J. SanMiguel4, Jeffrey L. Bennetzen1*1 Department of Genetics, University of Georgia, Athens, Georgia, United States of America, 2 Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America, 3 Universit de Perpignan, Via Domitia, CNRS UMR5096 LGDP, Perpignan, France, 4 Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of AmericaAbstract Top
Recent comprehensive sequence analysis of the 1maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and ~35,000 copies, respectively, or a combined ~1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity.Author Summary Top
Although TEs are a major component of all studied plant genomes, and are the most significant contributors to genome structure and evolution in almost all eukaryotes that have been investigated, their properties and reasons for existence are not well understood in any eukaryotic genome. In order to begin a comprehensive study of TE contributions to the structure, function, and evolution of both genes and genomes, we first identified all of the TEs in maize and then investigated whether there were non-random patterns in their dispersal. We used homology and TE structure criteria in an effort to discover all of the retroelements in the recently sequenced genome from maize inbred B73. We found that the retroelements are incredibly diverse in maize, with many hundreds of families that show different insertion and/or retention specificities across the maize chromosomes. Most of these element families are present in low copy numbers and had been missed by previous searches that relied on a high-copy-number criterion. Different element families exhibited very different biases for accumulation across the chromosomes, indicating that they can detect and utilize many different chromatin environments.Citation: Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A, et al. (2009) Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome. PLoS Genet 5(11): e1000732. doi:10.1371/journal.pgen.1000732

This paper talks of Non-Random Distribution of TEs, where the TEs non-randomly occur in what appears to be selected sites.

However, as mentioned above and observed previously (reviewed in [44]), LINEs, SINEs and some LTR retrotransposon families accumulate preferentially in areas that are near genes.

Overall, LTR retrotransposons are found to be most abundant in pericentromeric heterochromatin and least abundant in the more gene-rich arms on all chromosomes.

), LINEs, SINEs and some LTR retrotransposon families accumulate preferentially in areas that are near genes.

A nonrandom distribution, shadow. Near genes.
The paper doesn't say near WHICH genes.

preference noun \ˈpre-fərn(t)s, ˈpre-f(ə-)rən(t)s\
Definition of PREFERENCE
1a : the act of preferring : the state of being preferred b : the power or opportunity of choosing
2: one that is preferred

Viewed from the standpoint of the TE, much of the diversity in TE populations and their arrangement takes on a new and informative light. A previous model proposed that low-copy-number TEs must insert near or into genes so that they have a reasonable chance of expression and activity in subsequent generations, while highly repetitive TEs need to avoid insertions that disrupt genes in most cases because 1000 or 10,000 such insertions would lead to a dead host [44]. Hence, abundant TEs rely on their abundance per se to guarantee transmission and the opportunity for activity in future generations. The data for LTR retrotransposon abundance versus copy number shown here agrees with this model, as does the fact that (to date) none of the high-copy-number LTR retrotransposons have been shown to cause a de novo mutation, while low-copy-number LTR retrotransposons (e.g., Bs1, Tnt1, Tos17) that make up a relatively small part of their genomes have caused many new mutations [47]—[49],[53]. The analysis of the maize genome suggests that the copy number for this transition is fairly low, 10—100 intact copies per genome (Figure 4), for this change in lifestyle. LTR retrotransposon families with copy numbers less than ten were usually found to preferentially accumulate in genic regions, while most LTR retrotransposon families with copy numbers higher than 100 were found to be enriched in gene-poor regions like pericentromeric heterochromatin.The insertion preferences of LTR retrotransposons can contribute to their potential for more than just transcriptional activity. Elements that land in recombination-rich regions have a greater chance of inter-element unequal events that can create novel LTR retrotransposons with possible new properties [38]. Insertion into an LTR provides the opportunity to acquire the gene regulatory properties of the target LTR retrotransposon. Moreover, insertion of an LTR retrotransposon into an LTR retrotransposon would usually eliminate the target element as a potential competitor for future amplification.

shadow71 writes:Molbiogirl writes; Preferentially does not seem randdom to me. The TEs are in some way prefering to locate in preferred areas.

Of the 1991 SINEs discovered, 1174 were found in the introns or UTRs (untranslated regions) of genes and 21 in putative coding exons (data not shown).