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?
