Wednesday, March 22, 2006
Creation, Ecological Diversification, and Symbiosis
Some Creationists have thought that the genome and traits are essentially unchanging, and that inheritance is almost entirely Mendellian in nature. However, this is usually a holdover from atelic assumptions about the nature of how genomic change can occur. However, there are a number of evidences that genomes can change in specific, adaptable ways, which I have touched on from time to time on this blog.
The great diversifications after the flood involved numerous speciation events. Here I am going to hypothesize one (of many) methods by which this speciation occurs, which I will call "Ecological Diversification". If anyone knows of an existing term which matches this, please post it in the comments.
Previously, I posted a review of a paper on ecological developmental biology. To recap, some of the ideas presented there included:
- During development, environmental factors can shape the developmental pathways an organism takes, and thus its resulting phenotype.
- Species can detect predators during development through kairomones and develop adaptively to help them against the predator.
- Many generations of exposure to an environmental influencer on developmental pathways can cause the change to be permanent, and continue on even in the absence of the environmental inducers. In other words, the inducers have become internalized. The term for this is genetic assimilation, though that does not necessarily mean it is a genetic change.
I would propose, therefore, that a major impetus for speciation is the organism detecting its environment, and then its offspring developing in specific ways to adapt to the environment. These adaptations are precoded for certain types of environmental inducers. Some of the inducers I would propose might be:
- Other organisms, both friend and enemy
- Available vegetation
- Landscape (there is nothing limitting the visual cortex of the parent from inducing change any more than any other organ)
So, let's say you have fours species, A, B, C, and D, and environments X, Y, and Z. My speculation is that if you were to put A, B, and C in environment X; B, C, and D in environment Y, and A and D in environment Z, all organisms would, in a relatively short amount of time become recognizably different species. And, accordingly, I would propose that if the same environment were reproduced for the same sets of species, the results would be the same. However, this would be difficult to determine because of the number of factors involved.
Taking this idea further, let's look at symbioses. Symbioses have always fascinated me. Some of the elaborate symbioses have long been used to demonstrated the wonderful beauty and integration of Creation. And yet, I am almost entirely certain that many if not most symbioses are recent, not permanent. This may sound like a contradictory view, but it is not. Some people mistakenly think that "irreducible complexity" and similar ideas mean that a given feature cannot have evolved. That is not entirely true. What it means is that it cannot have evolved purely by stochastic means (i.e. Darwinism). It means that the evolution of the feature must be guided by some other mechanism. In other words, the "evolution" of the feature must be pre-coded, or at least semi-pre-coded. In the same way, I think that organisms have the ability to evolve specific types of symbioses. Then, the types and morphologies of the other flora and fauna in their environment will trigger a change in the organisms, which will induce an appropriate symbiosis with one or more creatures in the area.
One class of such symbioses which have been studied are the Type III Secretory Systems of bacteria. These systems appear to be made to help bacteria develop symbiotic relationships with eukaryotic hosts. While reading the research, it was difficult to separate the fact from evolutionary speculation, so it would be interesting to see a Creationist look at this. It seems that at least some symbioses are apparently a one-way transformation. Here is an interesting paper on an endosymbiont that uses such a system to invade the cell.
[short rant] It would be much more interesting if these papers spent more time discussing functional aspects of the relationships than try to guess phylogenies [end short rant]
Also, Type III Secretory Systems are often the cause of pathogenicity of microbes. As we have noticed in previous entries, it seems logical that these pathogenic systems are due to a breakdown of symbiotic mechanisms that make them pathogenic. Unfortunately, most of the research seems to be on pathogens rather than symbiotes.
Anyway, this seems to be a very fertile area for Creationist research.
For those interested in reviews covering aspects of such secretory systems, you might see this genomic analysis of the systems and this description of the protein transport process.
Tuesday, March 21, 2006
- The copying mechanism for cells is excellent, but not perfect
- The double-helix is likewise good at maintaining integrity, but not perfect
- The distribution of these random (as opposed to adaptive) mutations are well-known
- Natural selection is good at removing bad codes, but not degraded or neutral codes
- Therefore, the genome will slowly degrade and lose information over time
There are several sources on this subject, and I have not had time to read all of all of them. Jerry Bergman gave an excellent overview of this subject in Darwinism and the Deterioration of the Genome (membership to CRS required, if you don't have a membership, the abstract is here). Todd Wood gave a good overview of a specific instance in Genome Decay in the Mycoplasmas, where he hypothesized that pathogenicity in many instances is the result of the loss of regulatory genes. This study (summarized here and pointed out to me by MikeGene) indicates that a disruption of a single gene can cause a relationship to go from symbiotic to parasitic. John Sanford wrote a whole book on this (which I have not yet had the opportunity to read) called Genetic Entropy & the Mystery of the Genome.
This post is mostly a summary of Bergman's paper. The rest will likely be dealt with at greater length as I have time.
Bergman starts by pointing out that in neo-Darwinistic theory, the only source of real biological novelty is in random mutation. Minor variation can be explained through sexual recombination, but the real stuff of evolution is in the mutations.
Note that Bergman uses slightly different definitions than what are standard. He uses "mutation" to refer to genomic change which is not specific responses to stress. In papers where he is discussing genomic changes which are in response to specific stresses, he uses the term "recombination". I think that is a much better terminology than the standard usage of "mutation" for both directed and undirected change.
Bergman's first point, however, is that mutations are not random -- they show several distinct biases. Such biases over long periods, even balanced by natural selection, would produce a genome that was dominated by a few amino acids -- serine, arginine, leucine, valine, proline, threonine, alanine, and glycine. However, the patterns found in the genome are in opposition to what would be expected from mutation. This is even more striking when we examine DNA that has no known function. This indicates that mutation has only had a small effect in producing the modern genome.
Bergman also discusses mutational hotspots, showing that the locations where mutations are likely to occur are limitted. Personally, I think he did not do a good enough job explaining the difference between a mutational hotspot and a hotspot that is the result of adaptive recombination, and perhaps even a hotspot that is the result of a now-failing, disfunctional recombination system (genome deterioration will also bring about a deterioration in adaptive mechanisms).
He surveyed the beneficial mutation literature, and found almost all of them to be loss of function mutations. I.e. -- it was an instance of genome degredation, but one which happened to be useful to a certain degree. This supports, not negates, the hypothesis of genome degredation.
Bergman has an excellent table listing the biases of mutations, and perhaps I will see if I can reproduce it here.
My main criticisms are Bergman are these:
- He fails to mention recombination as a source of genetic variation
- He fails to note that many previously identified "mutations" wound up being just more recombinational activity
- He uses genome decay as more of a criticism of Darwinism than as a useful step towards understanding Creation. For instance -- what can we expect the genome to look like 100 years down the road? How does genome decay in certain parts of the genome affect different systems? How is the adaptive recombination systems in the genome affected by genome decay?
We really need to stop focusing on taking down Darwinism (honestly, this is already complete -- it will just take a generation for the old guard to step down), and start work on positive models of creation.
Anyway, the paper is much better than I could do it justice for here. The Creation model of an initially very good creation which has suffered from the fall works well with the concept of genome decay. Wood has pointed out that the decrease in speed of adaptation since after the flood could be the result of the decay of adaptation mechanisms.
Saturday, March 18, 2006
Stasis of the Baramin, Purpose, and Inheritance Mechanisms
Ultimately, Williams was trying to describe the issue faced by Creationists with regard to inheritance. That is, of the ultimate stasis of the baramin, but the incredible diversity available within baramins. He quotes from Gould, who states:
Paleontologists have always recognized the longterm stability of most species.
The lines of evidence he draws from are these:
- Genes can be developed by the organism in some circumstances. Humans can produce new antibodies as needed. Microbes can often develope new digestion enzymes. Mutation patterns in these areas seem to be controlled by the cell to some extent. (read the blog archives for other examples and ideas as to the mechanisms for this change)
- Early zygote development/differentiation is base solely on cytoplasmic factors, with the genome not even being in use until a certain stage (the cell relies on existing RNA material to produce new proteins).
- Some organisms seem to have more available diversity in their baramins than do others. Orchids and beetles each have thousands of named species, while humans only have a few named species.
- In chimeras, one baramin will always take over development, and be "in the driver's seat". Examples of mouse/human and pig/human chimeras exist, and in every case where the embryo survives, one baramin becomes dominant and takes control of development. The cells of the other baramin function fine within such a context, but they function essentially as members of the other baramin.
- We do not know the effects of cross-baramin genome transfers, or if they are even possible. The closest one is an experiment with a carp genome and a goldfish recipient (carp and goldfish are in different genuses, but they readily hybridize, though, so it isn't a cross-baramin example). Interestingly, while most cell features were that of the carp, the number of vertebrate matched that of the goldfish, indicating that cytoplasmic factors are involved in inheritance.
So what can we conclude from this?
Williams thinks that all of these data points make sense when looked at from the apobetic level of information (apobetics is the purposive part, see the above link for more information, or see an overview of Gitt information theory, specifically the section on "levels of information"). The huge variety of beetles and plants reflect that their purpose is to make the earth habitable in all sorts of ecological/geological conditions. They provide the substrate, and therefore, must be able to easily change to fit the conditions of the ecology and make it habitable. On the other hand, humans are supposed to reflect the image of God, and therefore, the there is much more stasis in the human baramin. As Williams states, "apobetics, not statistics, controls information change". In my earlier commentary on Williams, I criticized him for his assignment of Gitt categories, and I will do it again. While apobetics is where the source of variability and stasis lies, the implementation of the apobetics is in the semantics and pragmatics.
Williams also thinks that the primary baraminic information is inherited through the cell's cytoplasm, with the more configurable aspects inherited through the genome. This is interesting if thought about in conjunction with Sternberg's hypothesis of teleomorphic recursivity, which I won't go into, but you can read about. However, he does note that some parts of the genome are very well conserved, and a lot of cell machinery goes towards maintaining stasis in the genome, so it is likely that some of the baraminically-defining portions are in the genome as well.
Williams says that there is a two-level view of inheritance. The first level is "after their kind" stasis, and the second level is designed to diversify, adapt, and fill the earth. He says "the most obvious experimental correlates with this two-level system are the cell and chromosomes" but that
The existence of multilevel error correction and error avoidance mechanisms also points to stasis in the chromosomes. Perhaps both cell and chromosomes together control stasis. Indeed, so much of the structure of life is devoted to information conservation that there is very little room left for random variation.
So, perhaps the stasis is encoded in both places? While Williams thinks that the variation is entirely localized in the chromosomes, I think that it is more likely that both the variation and stasis will be in both places, though I do think that the relative distribution of the stasis and variation will favor cytoplasm for the stasis and the chromosomes for the variation.
One interesting quote that he made that I will leave you with is this:
How much of the error correction machinery is aimed at function and how much is aimed at maintaining integrity of the baramin? Or perhaps the two aims are in fact one -- are baramins functional peaks in an otherwise 'flatland' of non-functionality?
A very good question indeed. If so, it would make structuralism and creationism a lot closer to each other, and perhaps indicate a reason for homologies (i.e. they reliably create functional peaks).
Anyway, a fabulous paper, interesting hypotheses, and good things to think on.
Monday, March 13, 2006
Dinosaurs and Man
Dinosaurs are the icons of deep time, and any creation model will need to address their existance. Biblically, they would have been created on the sixth day with the land animals. But what happened after that? There are two lines of thought. The first is that they were all killed in the flood. That seems to be the position of the Geoscience Research Institute.
I take another view, which I think is the majority view among Creationists. That is, most dinosaurs were with Noah. Most of them have died out by now, but there are a few species still extant in various parts of the world.
You might wonder -- if Dinosaurs have been with man, why don't civilizations know about Dinosaurs? Well, in fact they do. Only they were called dragons. The modern conception of dragons is really a chimera of many dragon reports throughout the world. No dragon contained all of the elements of the modern "dragon" conception, and, if you look at the reports individually, many of them match the characteristics of well-known dinosaurs.
John of Damascus, in the 700s wrote a treatise on dragons (sorry, no primary source -- there is no English translation). In it, his purpose is to dispel the myths about dragons as mystical creatures, and instead describes their biology and ecology so that people will know the truth about them. In this book, he describes a report by a Roman historian where the Romans encountered a dragon during a battle.
Several historical reports of dragons in the UK are here.
There are drawings/images of Dinosaurs throughout the world. In South America, the Ica Burial Stones have etchings of several types of dinosaurs (for a defence of their authenticity, see here). Several other pieces of Dinosaur art can be found here.
Bill Cooper gives several dinosaur reports from the Anglo-Saxon records. None of these are legendary -- most are just simple news reports. Here is a report from 1793:
In the end of November and beginning of December last, many of the country people observed dragons appearing in the north and flying rapidly towards the east; from which they concluded, and their conjectures were right, that...boisterous weather would follow
Bill Cooper also has an interesting theory on Beowulf. It seems possible to me that the heroes of old did in fact fight dragons. Like so many creatures in earth history, the presence of man caused them to go extinct.
A large number of accounts, both recent and old, of interactions of man with dinosaurs and other strange creatures, can be found in William Gibbons' book Missionaries and Monsters. He primarily documents accounts from missionaries and priests.
Gibbons himself is searching for Dinos. Specifically, there are reports of a Saurapod dinosaur called Mokele Mbembe which he is organizing an expedition to search for.
Some depictions of the American Indian Thunderbird resemble a Pterosaur.
Many dinosaur bones have been found unfossilized or only partly fossilized.
To be sure, there have been false leads along the way, but I think the historical evidence gives us sufficient reason to keep on searching, and to not be overly-skeptical of new finds.
Two additional sources of information which I found while researching but haven't had time to look through yet are here and here. Also the out-of-place artifacts collection has more information on the subject. Also here is an AiG article on the subject.
There is lots of evidence for the co-existance of man and dinosaurs in recent times. But it seems that man has killed off most of the evidence. However, I think that a little persistence will turn up hard proof of living dinosaurs in the near-recent future.