After going through some of the recommended articles, here’s a few observations (my comments in are in bold letters):
Article: There are still quite a few gray areas in the figure where either the higher plant sequences have not been determined or they are known but the gene phylogeny is insufficiently clear (in our view) to make a statement on the origin of the plant nuclear genes. Chloroplastic and cytosolic pyruvate kinases are a good example of sequenced genes with an evolutionary history that is so intriguingly complex (Hattori et al., 1995) that one cannot yet tell where the plant nuclear genes come from. Furthermore, cases are also known in which the compartmentation of individual gene products can change in different lineages over evolutionary time, such that Figure 2, if prepared for Chlamydomonas or Euglena rather than spinach, would reveal different patterns of origins and compartmentation for the enzymes of the same pathways in those organisms (for an overview, see Martin and Schnarrenberger, 1997).
1) Complexity: The scientists are unable to work out some of the aspects of gene phylogeny in their labs. How could these develop randomly, spontaneously and unaided?
Article: Further work is in progress to determine the mechanism and consequences of the sams gene switching in amoeba/X-bacteria symbiosis. The switch in gene expression in amoebae is not only an example of genetic alterations caused by host-symbiont interactions but also may serve as a good model to study interactions between hosts and infective agents such as Mycobacterium, Legionella, Toxoplasma, Salmonella, and others.
2)
Amoebal Immunity: This is a simple immunity mechanism integral to Amoebae,
similar to our more complicated immune response. This is not a random process and
cannot develop spontaneously. It has been designed that way. In addition, there’s a huge chasm between Amoebal
immunity and mammalian immunity, as I remarked earlier.
Article: Various strains of Human Papilloma Virus (HPV) have recently been found to play an important role in the development of cervical cancer. The HPV oncogenes E6 and E7 that these viruses possess have been shown to immortalise some human cells and thus promote cancer development. Although these strains of HPV have not been found in all cervical cancers, they have been found to be the cause in roughly 70% of cases. The study of these viruses and their role in the development of various cancers is still continuing, however a vaccine has been developed that can prevent infection of certain HPV strains, and thus prevent those HPV strains from causing cervical cancer, and possibly other cancers as well.
3) Human cancer cells remain human even though their nuclear material had been altered (not a new species)
Article: As shown by our study on the growth rates of amoebae, xD amoebae are more sensitive to exogenous AdoMet than are D amoebae. It is not known why xD amoebae are more sensitive to AdoMet, but it seems to be related to the fragility of the plasmalemma of xD amoebae. It is known that xD amoebae are more sensitive to overfeeding, starvation, microsurgical operations and elevated culture temperature (Jeon, 1995).
4) Natural selection: Interestingly, the xD amoebae have not been improved. Their chances of survival have been considerably reduced. No super or improved organism with the proses of endosymbiosis, I’m afraid.
Article: Genome sequences reveal that a deluge of DNA from organelles has constantly been bombarding the nucleus since the origin of organelles. Recent experiments have shown that DNA is transferred from organelles to the nucleus at frequencies that were previously unimaginable. Endosymbiotic gene transfer is a ubiquitous, continuing and natural process that pervades nuclear DNA dynamics. This relentless influx of organelle DNA has abolished organelle autonomy and increased nuclear complexity.
5)
Theoretically then, super or improved organisms should result from the following processes, even in the lab. We
see, this is not the case.
Article: The bacterial recA gene and its eukaryotic homolog RAD51 are important for DNA repair, homologous recombination, and genome stability. Members of the recA/RAD51 family have functions that have differentiated during evolution. However, the evolutionary history and relationships of these members remains unclear. Homolog searches in prokaryotes and eukaryotes indicated that most eubacteria contain only one recA. However, many archaeal species have two recA/RAD51 homologs (RADA and RADB), and eukaryotes possess multiple members (RAD51, RAD51B, RAD51C, RAD51D, DMC1, XRCC2, XRCC3, andrecA). Phylogenetic analyses indicated that the recA/RAD51 family can be divided into three subfamilies: (i)RADα, with highly conserved functions; (ii) RADβ, with relatively divergent functions; and (iii) recA, functioning in eubacteria and eukaryotic organelles. The RADα and RADβ subfamilies each contain archaeal and eukaryotic members, suggesting that a gene duplication occurred before the archaea/eukaryote split. In the RADα subfamily, eukaryotic RAD51 and DMC1 genes formed two separate monophyletic groups when archaeal RADA genes were used as an outgroup. This result suggests that another duplication event occurred in the early stage of eukaryotic evolution, producing the DMC1 clade with meiosis-specific genes. The RADβ subfamily has a basal archaeal clade and five eukaryotic clades, suggesting that four eukaryotic duplication events occurred before animals and plants diverged. The eukaryotic recA genes were detected in plants and protists and showed strikingly high levels of sequence similarity to recA genes from proteobacteria or cyanobacteria. These results suggest that endosymbiotic transfer of recA genes occurred from mitochondria and chloroplasts to nuclear genomes of ancestral eukaryotes.
6) The sentence reads: "Members of the recA/RAD51 family have functions that have differentiated during evolution." The next sentence reads: "However, the evolutionary history and relationships of these members remains unclear." Isn't that accepting things at face value without evidence?
Article: Chloroplasts arose >1.2 billion years ago (1) when a free-living cyanobacterium became an endosymbiont in a eukaryotic host. Since that time, chloroplast genomes have undergone severe reduction, because chloroplast genomes encode between 50 and 200 proteins, whereas cyanobacterial genomes encode several thousand. Accordingly, endosymbiotic theories have always assumed that the cyanobacterial ancestor of plastids relinquished much of its genetic autonomy: “it is not surprising that chloroplasts lost their ability to live independently long ago,” as Mereschkowsky put it in 1905 (2). In today's terms, that means that during the course of evolution, genes must have been transferred from the ancestral chloroplast to the nucleus, where they acquired the proper expression and targeting signals to allow the encoded proteins to be synthesized on cytosolic ribosomes and reimported into the organelle with the help of a transit peptide. This process, a special kind of lateral gene transfer called endosymbiotic gene transfer (3), appears to be very widespread in nature: ≈18% of the nuclear genes in Arabidopsis seem to come from cyanobacteria (4), and obvious remnants of the chloroplast DNA have been found in higher plant nuclear chromosomes (5). Evolutionary biologists have long been able to infer endosymbiotic gene transfer from evolutionary sequence comparisons but have not been able to watch it happen in the lab until now. In this issue of PNAS, Stegemann et al. (6) report gene transfer from the tobacco chloroplast genome to nuclear chromosomes under laboratory conditions. Their findings, together with other recent developments, open up new chapters in our understanding of organelle–nuclear DNA dynamics and have far-reaching evolutionary implications.
7)
Mitochondria and Chloroplasts: If things took place randomly and spontaneously, Why did chloroplasts not find their way into the
animal and human genome?
Article: Photosynthetic eukaryotes, particularly unicellular forms, possess a fossil record that is either wrought with gaps or difficult to interpret, or both. Attempts to reconstruct their evolution have focused on plastid phylogeny, but were limited by the amount and type of phylogenetic information contained within single genes1, 2, 3, 4, 5. Among the 210 different protein-coding genes contained in the completely sequenced chloroplast genomes from a glaucocystophyte, a rhodophyte, a diatom, a euglenophyte and five land plants, we have now identified the set of 45 common to each and to a cyanobacterial outgroup genome. Phylogenetic inference with an alignment of 11,039 amino-acid positions per genome indicates that this information is sufficient — but just barely so — to identify the rooted nine-taxon topology. We mapped the process of gene loss from chloroplast genomes across the inferred tree and found that, surprisingly, independent parallel gene losses in multiple lineages outnumber phylogenetically unique losses by more than 4:1. We identified homologues of 44 different plastid-encoded proteins as functional nuclear genes of chloroplast origin, providing evidence for endosymbiotic gene transfer to the nucleus in plants.
8) Again, the fossil record is full of gaps and do not support symbiogenesis as the principal mechanism of developing life forms.
Article: The experimental design used by Stegemann et al. (6) was simple and effective. Using a technology called chloroplast transformation (7), they introduced a cassette containing two foreign genes into tobacco chloroplast DNA. The first one encoded spectinomycin resistance (aad) under the control of a chloroplast-specific promoter; the second one encoded kanamycin resistance (npt) under the control of a nuclear-specific promoter. They took advantage of the fact that whole tobacco plants can be regenerated from single cells. By subjecting transformed tobacco tissues to several rounds of selection on medium containing spectinomycin, they were able to obtain tobacco plants that were homoplastomic for aad and npt; that is, all copies of the chloroplast DNA in all plastids in those plants contained the new cassette. By placing small sections of leaves from those aad/npt homoplastomic lines on kanamycin-containing medium, they initiated selection for strong expression of the npt gene under the control of the nuclear-specific promoter. That was the key step, because on kanamycin medium, only such tobacco cells will survive whose nuclear DNA has incorporated a segment of the genetically modified chloroplast DNA containing the new npt gene.
9)
Unnatural Gene Manipulation by Researchers: If it was an open, random,
spontaneous process to begin with, why is it now a closed process that can
only be manipulated with the help of the genetic engineers?
