Friday, October 28, 2005
Thus, when we look at life, we should not be surprised that even many of the "dangerous" things have, at least at one point, contributed to the benefit of life.
Often times we look at microscopic life as dangerous. Part of that may be fear of what we can't see, and some of it may be a lack of understanding, and some of it is legitimate. However, ultimately, without bacteria, viruses, and the rest, the ecosystem would fail.
Anyway, I'm going to point out a few review articles dealing with viruses and their positive effects.
The first, on regular viruses, is a review article from TJ by Jerry Bergman, Did God Make Pathogenic Viruses? The main point is this:
The view now emerging of the normal relationship between viruses and genes is not so much a host/invader relationship, but a relationship more akin to bees carrying pollen from flower to flower, thus causing cross-fertilisation. Viruses carry not only their own genes, but also those of other creatures as well, especially those of bacteria. Although bacteria pass genetic information to each other using several processes such as pili transfer (see below), viral transfer is now known to be critically important.
A critical role that viruses play relates to the fact that bacteria contain a constant, stable genetic system (the large replicon), but they function in the world by acquiring and exchanging a diverse set of variable genetic systems (several small replicons, including plasmids, viruses, and so forth). The small replicons are physically separated from the major bacterial DNA, called the genophore. New DNA can be inserted into the genophore; and it usually divides synchronously with it, but some is able to start self-replicating autonomously (Figure 5).
Several mechanisms for this are discussed.
Then the origin of pathogenic viruses are discussed:
As long as the HIV lentivirus lived in monkeys, it was not a threat for humans. HIV in monkeys (called SIV), ‘appears not to cause disease in most of its natural hosts’, and ‘bacteria and viruses that cause disease today may not always have done so’. The same situation also is true of syphilis (apparently from sheep) and many other infectious diseases. Baboons resist being adversely infected by HIV, and for years researchers have been exposing certain animals to the virus without infecting them.
This supports the argument that viruses normally do not, and should not, cause disease. Only if something goes wrong, such as a mutation or accidental inappropriate movement of genes, do they cause problems. Dr Charles Stiles recognised this many years ago when he concluded that ‘germs were not created as they are today, but they later evolved into germs … those germs were originally created in some form other than as disease germs.’ Stiles claimed that germs developed as a result of the devolution that has occurred since creation.
This idea is expounded on, and is quite interesting.
Another review article is from a secular source, called Beneficial Role of Human Endogenous Retroviruses: Facts and Hypotheses. It covers the beneficial effects of what used to be (and still is to a degree) a very mysterious kind of virus -- the endogenous retroviruses. These viruses are RNA-based, and use reverse transcriptase to insert DNA into the host genome.
This article mentions the use of retroviruses to modulate gene expression:
The large number of solitary LTRs and complete HERVs may benefit the host genome by contributing regulatory enhancer sequences to genes in their vicinity. At present five human genes have been shown to be transcriptionally regulated by HERV LTRs (reviewed in 1). These are the salivary amylase, ZNF80, cytochrome c1, Krüppel-like H-plk and phospholipase A2-L (PLA2L) genes. The potential for beneficial effects provided by these LTRs could represent a fine functional balance for specific gene regulation in the host genome. Moreover, accumulated changes in gene regulation are likely to be important factors in the process of speciation.
In placental animals, retroviruses play a role in development:
The function of ERVs, particularly ERV3, in the placenta has been linked to several ERV activities:
(1) provision of immunological protection of the embryo and the fetus;
(2) regulation of trophoblast cell growth;
(3) protection of the fetus from unwanted maternal material, and
(4) protection against infection by a related exogenous retrovirus, i.e. 'germline vaccination'.
Anyway, it makes for a good read.
One other article which is of interest is form PLOS: Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences. This adds to the theory that these elements are part of a planned system -- they have distinct preference for specific site attachments. While this article deals with pathogenic viruses, there is no reason to think that other retroviruses have similar site-specificity. Previously, retroviruses were thought to insert themselves somewhat randomly in the genome. It has a nice bibliography at the end as well, which should make interesting reading sometime. The final results are this:
Integration by HIV vectors, analyzed in two primary cell types and several cell lines, strongly favored active genes. An analysis of the effects of tissue-specific transcription showed that it resulted in tissue-specific integration targeting by HIV, though the effect was quantitatively modest. Chromosomal regions rich in expressed genes were favored for HIV integration, but these regions were found to be interleaved with unfavorable regions at CpG islands. MLV vectors showed a strong bias in favor of integration near transcription start sites, as reported previously. ASLV vectors showed only a weak preference for active genes and no preference for transcription start regions. Thus, each of the three retroviruses studied showed unique integration site preferences, suggesting that virus-specific binding of integration complexes to chromatin features likely guides site selection
Anyway, I hope your understanding of viruses and how they fit in creation is a little more enahnced. And, for those of you who are real virus buffs, I give you The Big Picture Book of Viruses.
The most usual effect of these elements is neutral or harmful like other mutations. This is confirmed by the fact that most ERV copies in the human genome are decaying indicating they are neutral, and these elements have been involved in the duplication/deletion/disruption of genes that causes disease.
The expressed placental gene (syncytin) only consists of the envelope (env) gene of the virus but the locus also contains remnants of the other genes (gag, pol) that would have existed in the intact virus - this is exactly what you would expect if the gene were the product of evolution. Is it your contention that the syncytin) hominoids (humans and the other apes) were created without this (currently) essential gene but with the possibility that it might evolve?
The fungus Neurospora Crassa has evolved a system (Repeat-induced point mutation) that has eliminated or inactivated by mutation all mobile elements in it’s genome - odd if they were a designed part of the genome/ecosystem.
Also many mobile elements have a clear evolutionary origin - usually from previously existing RNA encoding genes. For example alu elements evolved from a mutated copy of 7SL RNA and ID elements found in rodents derived from the BC1 RNA gene. So were organisms created without these potentially useful (and harmful/neutral) elements but just with the precursors to them in the hope that they would happen to evolve?
A giant biofeedback system delivering genes to the creatures that need them? Yes!
"The most usual effect of these elements is neutral or harmful like other mutations."
It is true that creation has deteriorated since the fall, and the specificity with which it used to operate is not as good as it used to be. This is expected from the effects of the curse.
"This is confirmed by the fact that most ERV copies in the human genome are decaying indicating they are neutral"
It could also be that they are only currently neutral, but at one point had a purpose.
"these elements have been involved in the duplication/deletion/disruption of genes that causes disease."
Just about everything has been involved in causing disease. Disease is simply when the "normal" system breaks down. Your throat always has strep, but if the strep gets out of control, problems happen. Likewise, when viruses lose their specificity or their internal limitting systems, they start causing problems.
"The expressed placental gene (syncytin) only consists of the envelope (env) gene of the virus but the locus also contains remnants of the other genes (gag, pol) that would have existed in the intact virus - this is exactly what you would expect if the gene were the product of evolution."
I think the problem is that you are viewing "creationism" means "no change". It does not. Look back through the early entries of the blog for creationist ideas of change. The fact that you have viruses which are designed to insert beneficial genes into genomes is very evident of purposeful arrangement.
"Is it your contention that the syncytin) hominoids (humans and the other apes) were created without this (currently) essential gene but with the possibility that it might evolve?"
It is very possible. Evolutionists seem to think that the creationist position is that there is no change within species. I know of no serious creationist who believes this. The YEC position is that the original "created kinds" generally fall within the family level of taxa, indicating that there has been a large amount of diversification since then. While traditionally this has mostly been assigned to heterozygous fractionation, there is nothing about creation that prevents genomes from actively reconfiguring themselves, or for environmental biofeedback mechanisms. What is objected to by creationists is the idea of information creating itself from nothing, not the use of information in the cell or outside for a cell to engineer solutions to its own problems, or for the environment to cooperate in establishing helpful equilibriums. This is why many creationists usually talk about _Darwinian_ evolution, as opposed to evolution in general. Natural Genetic Engineering, and many other aspects of biological self-organization and structuralism, are very compatible with creationist beliefs.
"The fungus Neurospora Crassa has evolved a system (Repeat-induced point mutation) that has eliminated or inactivated by mutation all mobile elements in it’s genome - odd if they were a designed part of the genome/ecosystem."
It would only be surprising if it stays alive very long like that. Todd Wood's specific assertion in his view of transposons and other mobile elements is that their adaptive power has decayed through time because of point mutations.
"Also many mobile elements have a clear evolutionary origin"
How is this clear? Similarity does not mean a direct evolutionary relationship. I have not heard of the things you are speaking of, but would appeciate if you linked me to a pubmed (or other) article/book I could check into.