Wednesday, July 26, 2006
WARNING: This blog may make sudden stops
I've got a few posts I'm working on that I will hopefully get done before seminary starts in September, but just remember if you don't hear from me for a while, it's because I'm preparing for ministry.
Sadly, the seminary is doing a "special topics" course on evolution and theology this summer, which is before I officially enroll, so I'll miss it :( It would have been an interesting discussion. There were several books on the reading list I had wanted to read.
Anyway, I'm not done blogging. I just probably won't do it so often.
Thursday, July 20, 2006
What is Baraminology?
In my mind, there's two meanings to baraminology -- the strict, technical definition, and then the worldview it entails.
The strict definition of baraminology is that it is a method of taxonomy based on Biblical ideas. "baramin" comes from the Hebrew words "bara" and "min" which are the words used for creating after their kind in Genesis. Baraminology reclassifies the world into baramins -- originally created kinds. Note that a baramin is not the equivalent with a species. A good first approximation of a baramin is often the "family" level of standard taxonomy. For example, the entire "cat" family (felidae) is considered a baramin. Lions, tigers, and the house cat are thought to be all of the same created kind. Dogs, wolves, and coyotes are all thought to be of another created kind. However, because standard taxonomy neither cares about nor believes in "created kinds", this approximation is not always reliable. For example, recently chimps and other non-human primates have been moved into family hominidae in the standard taxonomy, but chimps and humans are not from the same created kind.
Baraminology is a holistic view of taxonomy. Because baraminologists believe that baramins were created holistically, it is thought that this is the best way to classify it as well. It is usually based on morphology and ecology as opposed to molecular (gene sequence) evidence.
Baraminology as a classification system recognizes both continuities and discontinuities as real. Traditional taxonomy considers only continuities as real, and considers discontinuities as being simply the result of incomplete information. While certainly incomplete information may create the appearance of discontinuity when it is only an illusion, baraminologists believe that in general the observed continuity and discontinuity are both real.
The Baraminology Philosophy
In relation to the larger Creation/Evolution divide, baraminologists are almost exclusively Young-Earth or Young Age Creationists. However, while traditionally Creationists have focused on proving the Bible true or beating the evolutionists, Baraminology takes a different approach. The goal of Baraminology is to develop a Creationist model of biology, based on the Bible and Biblical principles. Note that this means, since baraminologists are using the Bible as a starting assumption, baraminology cannot, even in principle, be used to argue for Creationism. This is not the intention. The intention is to simply perform research within the context of Christianity. This does not mean that baraminologists do not engage in such debates -- many do (including me). However, this is separate from the practice of baraminology itself, because, as mentioned above, baraminology itself does not lend itself to such arguments since it assumes the Bible as a starting point.
If you want to do biology research from a Christian perspective, baraminology is for you.
For more information, you can go to the Creation Biology Study Group website, read Todd Wood's book, Understanding the Pattern of Life, which explains the basics and research methodology of baraminology, or also, stay tuned to this blog.
This blog tries to maintain the spirit of baraminology, by viewing research done by both Creationists and non-Creationists within the light of a Christian worldview, to see what we can learn about God's world through study. I try to avoid denigrating other positions and focus on constructive research and ideas. I certainly value very highly the work done by non-Creationists in biology (including many aspects of evolutionary biology), and I try to incorporate as much as possible in my thinking. But ultimately, scripture is authoritive in the matters of beginnings, and I trust what it says (my question -- why would someone trust the Bible as a source of salvation and not trust it regarding the question of origins?) An excellent essay on this is contained in the "Introduction" section (page 3) of last years BSG Conference Proceedings by Todd Wood (don't worry, it's not technical at all).
Is it possible to do science like this? Honestly, I don't really care. If you don't want to call it science -- don't. Names are meaningless. The question is, what is the truth about life? This is what I'm interested in. Personally, I think that this is compatible with science, and if you're interested I explain why I think so here. But if you don't disagree, I won't complain much. (However, just be aware that by most demarcation arguments, you have to either exclude both Creationism and Evolution or include both Creationism and evolution -- for a short essay see here).
Anyway, if you have questions, please post them below! Also, if I get too technical in my posts, please feel free to ask questions. I really have no idea who my readership is, so if you need me to re-explain something from the ground up, I'd certainly be glad to!
Some of the more interesting posts on this blog have been:
- The influence of ecology on development
- Gene mutation is a directed, regulated process
- The role of chance happenings in genetic mutation
- The meaning of Behe's "Irreducible Complexity"
- The relationship between Creationism and Intelligent Design
- Stasis and change within baramins, according to purpose
- Genome Reconfiguration
- The role of symbionts in ecology and creating new species
- Discussing biological similarity from a Creation perspective
Wednesday, July 19, 2006
I apologize for all gullibility I engaged in by actually even bothering to read the popular press, much less attempt to use it as the basis of anything else (and to think that some people vote based on what they read in the popular press).
The article I am referring to is this one. From the article, it sounded like a regular fish had grown human-like teeth. But in fact it wasn't the case. It's just a fish with teeth. Not human-like teeth, just teeth. Here is a page about pacu, the type of fish that was caught.
Basically, the headline was Texas Man Catches Fish With Human-Like Teeth when in reality it should have simply been titled South-American Fish Caught in Texas.
Friday, July 14, 2006
How to Be a Scientist -- Look at Your Fish!
Most unorthodox of all, and crucial as time would tell, was his manner of teaching. He intended, he said, to teach students to see -- to observe and compare -- and he intended to put the burden of study on them. Probably he never said what he is best known for, "Study nature, not books," or not in those exact words. But such certainly was the essence of his creed, and for his students the idea was firmly implanted by what they would afterward refer to as "the incident of the fish."
His initial interview at an end, Agassiz would ask the student when he would like to begin. If the answer was now, the student was immediately presented with a dead fish -- usually a very long dead, pickled, evil-smellling specimen -- personally selected by "the master" from one of the wide-mouthed jars that lined his shelves. The fish was placed before the student in a tinpan. He was to look at the fish, the student was told, wherupon Agassiz would leave, not to return until later in the day, if at all.
Samuel Scudder, one of the many from the school who would go on to do important work of their own (his in entomology), described the experience as one of life's turning points.
In ten minutes I had seen all that could be seen in that fish....Half an hour passed -- an hour -- another hour; the fish began to look loathsome. I turned it over and around; looked at it in the face -- ghastly; from behind, beneath, above, sideways, at three-quarters view -- just as ghastly. I was in despair.
I might not use a magnifying glass; instruments of all kinds were interdicted. My two hands, my two eyes, and the fish: it seemed a most limited field. I pushed my finger down its throat to feel how sharp the teeth were. I began to count the scales in the different rows, until I was convinced that that was nonsense. At last a happy thought struck me -- I would draw the fish, and now with surprise I began to discover new features in the creature.
When Agassiz returned later and listened to Scudder recount what he had observed, his only comment was that the young man must look again.
I was piqued; I was mortified. Still more of that wretched fish! But now I set myself to my task with a will, and discovered one new thing after another....The afternoon passed quickly; and when, toward its close, the professor inquired: "Do you see it yet?"
"No," I replied. "I am certain I do not, but I see how little I saw before."
The day following, having thought of the fish through most of the night, Scudder had a brainstorm. The fish, he announced to Agassiz, had symmetrical sides with paired organs.
"Of course, of course!" Agassiz said, obviously pleased. Scudder asked what he might do next, and Agassiz replied, "Oh, look at your fish!"
In Scudder's case the lesson lasted a full three days. "Look, look, look," was the repeated injunction and the best lesson he ever had, Scudder recalled, "a legacy the professor has left to me, as he has left it to many others, of inestimable value, which we could not buy, with which we cannot part."
The incident of the fish marked the end of the student's novitiate. As once Agassiz became more communicative, his manner that of a friend or colleague, now that the real work could begin.
The way to all learning, "the backbone of education," was to know something well. "A smattering of everything is worth little," he would insist in the heavy French accent that he was never to lose. "Facts are stupid things, until brought into conjunction with some general law." It was a great and common fallacy to suppose that an encyclopedic mind is desirable. The mind was made strong not through much learning but by "the thorough possession of something." In other words, "Look at your fish."
And so I encourage all of you who wish to engage in Creation research. Be prepared for hard, thorough, original research, with or without support of anyone else. It's not who has the best lab, best equipment, or even any equipment at all. It's about learning a subject deeply and thoroughly. It's about looking at your fish.
Friday, July 07, 2006
The Organosubstrate and the Symbiotic Planet
I once asked the eloquent and personable paleontologist Niles Eldredge whether he knew of any case in which the formation of a new species had been documented. I told him I'd be satisfied if his example were drawn from the laboratory, from the field, or from observations from the fossil record. He could muster only one good example. Theodosius Dobzhansky's experiments with Drosophila, the fruit fly. In this fascinating experiment, populations of fruit flies, bred at progressively hotter temperatures, became genetically separated. After two years or so the hot-bred ones bould no longer produce fertile offspring with their cold-breeding brethren. "But," Eldredge quickly added, "that turned out to have something to do with a parasite!" Indeed, it was later discovered that the hot-breeding flies lacked an intracellular symbiotic bacterium found in the cold breeders. Eldredge dismissed this case as an observation of speciation because it entailed a microbial symbiosis! He had been taught, as we all have, that microbes are germs, and when you have germs, you have a disease, not a new species. And he had been taught that evolution through natural selection occurs by the gradual accumulation, over eons, of single gene mutations... From the long view of geological time, symbioses are like flashes of evolutionary lightning. To me symbioses as a source of evolutionary novelty helps explain the observation of "punctuated equilibrium," of discontinuities in the fossil record. [Margulis, Symbiotic Planet 7-8]
At the last ICC, Joe Francis submitted a paper describing what he called the organosubstrate -- the microbes and viruses which act as the link between the inert physical world and the higher organisms. According to Francis, "microbes and viruses could also be thought of as a single, complex, massive, multicellular, multitaxon organism with incredible and powerful life supporting properties."
Francis argues that the design of the organosubstrate is evident from the reproductive efficiencies and the adaptability of its members. The ability to adapt to a variety of environments, efficiently extract nutrients needed by macro-organisms, and establish a variety of symbioses is what allows it to function as the organosubstrate. Many members of the organosubstrate also have dispersal mechanisms that allow them to get to remote environments.
Most interesting to me, however, is the ability of microbes to form symbioses. Francis gives numerous examples of very interesting, highly intricate symbioses that microbes can form, some of which are so integrated as to suggest properties of multicellular organisms. But they can form symbioses with not only other microbes, but with macro-organisms as well. Digestive systems are the most obvious.
Interestingly, the concept of the organosubstrate has a number of similarities with the Gaia hypothesis as proposed by Lynn Margulis. First of all, please don't confuse Margulis's Gaia hypothesis with the New Age ideas of similar names. Margulis's hypothesis is simply that the earth behaves in a systems fashion. In fact, Margulis's book shares numerous similarities with Francis's hypothesis. [Note that Margulis's hypothesis also carries with it a lot of old-Earth, atelic baggage as well, but as a current, operational view they are largely similar]
However, Francis goes even further with a very interesting hypothesis about the creation of symbioses with macro-organisms. Francis speculates:
Further investigation into the symbiotic relationships between microbes and mammals may also lead to insight into the originally created purpose of the immune system. For instance, among microbes phagocytosis can function as a non-destructive mechanism to acquire symbionts and is common among unicellular and multicellular pond organisms. In contrast, phagocytosis in macro-organisms is an immune response that participates in destruction of pathogens. I predict that future investigation of this phenomenon will lead to a hypothesis that the immune system may have been originally created as an environmental sensing device that received data about the environment through the phagocytosis of beneficial microbes. Indeed the mammalian immune system possesses very specific and complex mechanisms that interact with microbes, often causing inflammation and tissue-destructive autoimmune responses and therefore appear to make little sense in the context of evolutionary biology. [emphasis mine]
In Francis's recent talk at the 2006 BSG meeting, he discussed a particular symbiosis with
Furthermore, Vibrio fischeri (a bacterium similar to V. cholera) also uses virulence factors, similar to several found in V. cholera and other pathogens, to establish a beneficial symbiotic relationship with the Bobtail squid (Euprymna scolopes). In this symbiotic relationship, virulence factors are involved in tissue remodeling and morphogenesis of an elaborate light-producing organ. Interestingly, not only do these bacteria appear to be more fit for their beneficial ecological roles, but inflammation, tissue degradation and toxin production that cause pathogenesis in some ecological settings play beneficial roles in other ecological settings.
Francis discussed the fact that the inflammation response of the squid was used to isolate the specific microbe that it wanted to establish a symbiosis with.
As the Margulis quote indicated above, perhaps the genes are not the primary originating factors of speciation, but instead symbioses and ecological factors. Indeed it appears that the largest-scale changes that have been observed to take place revolve around symbioses. In a personal conversation, Francis related another symbiosis in which the organisms literally changed form in the presence or absence of the symbionts.
An interesting Creationist research possibility would be to attempt to catalog and systematize the types of symbioses available and the methods by which they are established. I hypothesize, as I believe does Francis, that we will find specific mechanisms that act to sense the available organisms in the environment, what sort of symbioses would be available, and can decide whether and how to establish that relationship.
Historically, I think Creationists have assumed that complex symbioses must have been original creations. However, as has been pointed out here repeatedly, complex interrelated processes need not be originally established, but can have the ability to assume those processes pre-coded for later activation. Therefore, we need not balk at the idea of the development of complex symbioses through time. Using an informationally-driven model we can see both the origination of the symbiosis as occuring post-flood, but also that the ability to form it was established as a part of the organism. Because of the short time span needed to establish a symbiosis, it can help explain the rate at which intrabaraminic diversification took place.
I think that a systematic researching of symbiosis could be a place where a Creationist could persue work that is both Creationist as well as usable (and possibly fundable) by non-Creationists. This is a wide-open field, especially with researchers such as Margulis concentrating so much on the origin-of-life/origin-of-eukaryote issues, the really interesting parts (systematic study of speciation through symbiosis) remains largely untouched (if this is in error, I would love to know of a good reference for a systematic treatment of mechanisms of symbioses -- please post in the comments).
Francis, J. 2003. The Organosubstrate of Life: A Creationist Perspective of Microbes and Viruses. Proceedings of the Fifth International Conference on Creationism.
Franics, J. 2006. The Role of Virulence Factors in the Establishment of Beneficial Ecological Relationships of Vibrio cholera and Vibrio fischeri. OPBSG 8:14-15.
Margulis, L. 1998. Symbiotic Planet: A New View of Evolution. Basic Books.
We've talked about this subject a little bit before. I thought I'd link to the other posts we've done on the topic:
Creation, Ecological Diversification, and Symbioses
Stasis of the Baramin, Purpose, and Inheritance Mechanisms
The New Science of Eco-Devo