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.
Monday, October 24, 2005
Grand Canyon: Monument to Catastrophe Pt. 1
This is part one of a book review. I'm doing it in multiple parts for a few reasons:
- There's a whole lot of information in the book.
- It's taking me a while to go through the book, and I don't want the blog to go stale.
- It's a great book and worth the extra exposure.
I'm half-way through chapter four. So far, a few things have really stuck out that I like about the book:
- It can basically be used as an introduction to geology. It defines numerous terms, helps to read geological maps, and helps acquaint you with geological terminology. In fact, this is one of the reasons I started with this book. Geology is one of my worst subjects, but there have been a lot of geology articles in CRSQ lately.
- Austin is fair to those he disagrees with. Austin tries to give a good overview of the evidence used against the creation hypothesis, and while he provides rebuttals, he does so very respectfully, which is sometimes missing in creationist literature.
- The book is very well footnoted. Depending on what I find interesting, there are a whole lot of footnotes to research for further information. Chapter 3, for example, contains 121 footnotes, most of which are references to other work.
Since I'm supposed to be educating my readers about creationist research, I'll point out some of the experiments and research referenced in the first few chapters:
- In the Coconino sandstone, there are lots of footprints. Austin references an experiment that was performed to determine what kind of environment the footprints were laid down in. The experiment referenced observed the tracks of animals made on most sand, on dry sand, and underwater. The tracks observed in the Coconino sandstone match those made in the underwater environments.
- Austin himself has done research on nautiloid deposition in the redwall limestone. I'll probably report more on this later. He shows that the orientation of nautiloids along a northwest to southeast axis indicates water moving in a single direction with a significant current.
- Austin points to research done on investigating the relationship between water depth, water velocity, sand wave height, and depositional characteristics. He uses the work of Rubin and McColluch to show that some of the Grand Canyon sandstone was deposited at a depth of 180 feet, with a minimum velocity of three feet per second.
- Austin also points to grain-size research which indicate that Coconino sandstone was depositted under water.
This just scratches the surface of the information available in the book. Austin goes in to some detail about how interpretation of geological strata works, and many of the different types of unconformities, faults, and other structures important for interpretation, and what they point to.
Also, it has probably the best presentation I've seen of how interpretational frameworks shape they way that data is interpretted.
What's also interesting is that it seems that those outside creationism have been fairly impressed with this book, at least as far as they can be impressed with creationist literature.
Austin has done extensive research on catastrophic processes and has found that many geologic features once thought to require vast periods of time to form can in fact be replicated by short-term events. In his article "Uniformitarianism--a Doctrine that needs Rethinking" he outlines the misconceptions of founding geologist Charles Lyell and shows how uniformitarian thinking has become a misapplied dogma in many cases (the Channelled Scablands of Washington state being the most classic example). I concur with this analysis, as do many geologists. But Austin has swung to the opposite extreme such that he can't see long-term equilibrium even when it's staring him squarely in the face. His attempts to explain every geomorphic feature as a relic of past process leads to some rather humorous and incomprehensible logic.
Much more could be said about the ideas presented in this book, it being an easy target for critical analysis. Many readers may even consider it unworthy of a response. I disagree. For a young-earth creationist book it has reached a new level of scholarship, and as such it provides a new opportunity to evaluate an old idea. Although my review has been critical, I want to assure my readers that I've tried my level-headed best to see things through Austin's eyes in hopes of finding some spark of internal consistency and insight previously missed in a catastrophist model of earth history. But having made this attempt with no enlightenment, my childhood view of an old earth and long-term erosion seems more logical than ever.
Not a stunning endorsement, but nevertheless it seems almost like an endorsement when coming from the Skeptical Inquirer.
Anyone keeping up with the NCSE might be interested about what they had to say about the book. I haven't read this in detail, but probably will eventually as I read the book. But, interestingly, the NCSE has graciously allowed Steven Austin a rebuttal to their article.
Anyway, this has been a very interesting book, and I've learned a lot, especially from Chapter 3. I'll report more on the rest as I get into it.
Also, just a teaser for sometime in the near future, Austin did some great work in the RATE group about how the different methods of radioisotope dating not only differed from each other, but did so in a non-random, repeatable way.
Saturday, October 15, 2005
A good overview of creationist evolution
For those in need of something to chew on in the meantime, check out Chris Ashcraft's description of evolution in a creationist framework:
Evolution: God's greatest creation
And just for fun:
Gene Hijacking. This one points to the ability of organisms to trade genes within an environment. I think one thing that we can do as creationists is look at the biosphere as a cohesive machinery, and I think that gene transfer may eventually be a big part of that.
Thursday, October 13, 2005
Joshua's Long Day
The Long Day of Joshua
Wednesday, October 12, 2005
Features of Rapid Erosion -- Mt. St. Helens
Rapid Erosion at Mount Saint Helens
Also evident in Figure 3 is an elaborate dendritic pattern of rills and gullies on the sides of the pit that resembles badlands topography. Virtually all of these gullies and rills formed within the first five days after May 18 by the retrogressive slumping of the rim, not by water erosion. According to traditional interpretations, this topography might be assumed to require many centuries of rill and gully erosion if the rapid progress of its development had not been observed.
Sunday, October 09, 2005
BACKDATED: Water circulation during the genesis flood
However, Baumgardner and Barnette have used computer models to try to simulate this activity. Now, before giving you the results, lets be clear -- computer models are not a substitute for experiment, and should always be taken with a grain of salt. Perhaps a large grain. But in this case, there is literally no other way to examine it. All computer models are subject to modelling flaws and assumption flaws.
Anyway, having said all that, here's what Baumgardner discovered in his investigation. Basically, the currents accelerated over land. Even starting with an initially motionless ocean, the spin of the earth was enough to cause currents to start, which accelerated over land.
The calculations argue that strong currents spontaneously arise over flooded continents. They suggest that accurate observational data on the current directions in the Paleozoic and Mesozoic rocks coupled with careful numerical modeling could be extremely fruitful in understanding the origin of much of the earth's sedimentary record.
Numerical solution of the shallow water equations on a rotating sphere with parameters appropriate to the earth and flooded continental topography yields closed patterns of flow with velocities of 40 to 80 m/s and length scales typically 2500-5000 km above the flooded continental regions.
This is interesting combined with the fact that the paleozoic and mesozoic have continental-wide current indicator patterns.
The paper is here:
Patterns of Ocean Circulation over the Continents During Noah's Flood
Thursday, October 06, 2005
Foundations of Stratigraphy -- the Biblical creation and flood
Geological pioneer was a biblical creationist
I had thought he was a long-ager, but it seems at least from Walker's description that he was a diluvialist.
My favorite quote was this one:
Far astray, therefore, do they wander, who criticize the many errors in the writings of the ancients, because they find there various things inconsistent with the geography of today. I should be unwilling to put credence in the mythical accounts of the ancients; but there are in them also many things to which I would not gainsay belief. For in those accounts I find many things of which the falsity rather than the truth seems doubtful to me. Such are the separation of the Mediterranean Sea from the western ocean; the passage from the Mediterranean into the Red Sea; and the submersion of the island Atlantis. The description of various places in the journeys of Bacchus, Triptolemus, Ulysses, Aeneas, and of others, may be true, although it does not correspond with present day facts. Of the many changes which have taken place over the whole extent of Tuscany embraced between the Arno and Tiber, I shall adduce evident proofs in the Dissertation itself; and although the time, in which the individual changes occurred, cannot be determined, I shall nevertheless adduce those arguments from the history of Italy, in order that no doubt may be left in the mind of anyone.
Too often we dismiss the writings of the ancients because we don't see how it could have happened. But that is really irrelevant, given that much has changed, and we don't know what, specifically has changed. Dismissing them for being inconsistent with today's world is quite silly, for it presumes that we already know more now looking back than they did then looking around.
I also find it interesting that it seems the 1600s were a time dominated by Christian scientists -- Kepler, Newton, Steno and others. I've often wondered what happened in the 1700s to change that.
Philosophy of Science: The Scientific Status of Intelligent Design
The Scientific Status of Intelligent Design
Also this older one of Meyer's may be of interest to readers:
The Use and Abuse of Philosophy of Science:
A Response to Moreland