Forum Poll :Evolution Re:Majority of Americans reject theory of evolution (doh!)

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I have a dim view of evolution mostly because I have a dim view of (macro)biology. Macrobiology is little better than a pastiche of fashionable prejudice held together by bones and duct tape, and nearly as unscientific a discipline as Freudian psychoanalysis.

I recall angus saying that some biology book he was reading didn't contain a single equation (i.e., a quantifiable observation), so he got bored and just put it aside.

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I have a dim view of evolution mostly because I have a dim view of (macro)biology. Macrobiology is little better than a pastiche of fashionable prejudice held together by bones and duct tape, and nearly as unscientific a discipline as Freudian psychoanalysis.

I recall angus saying that some biology book he was reading didn't contain a single equation (i.e., a quantifiable observation), so he got bored and just put it aside.

There are plenty of quantifiable things with genetics. You can find books on biological Markov chains.

Did you know that 16 million people are a direct male desendent of Ghengis Khan (or maybe one of his not so distant ancestors)? They have a Y-chromosome, and from genetic mutations you can figure out about how long ago their common ancestor lived.

Don't tell me that biology has nothing quantifiable just because you're reading the wrong book.

See, now you're confusing microbiology, which I have no problems with (as it is based on the detection of mutations in DNA structure or protein strands, both quantifiable by techniques like NMR, GPC, etc.), and, the larger, "grander" macroevolution, a brief run through can be seen here. And even there, I had to filter out a lot of polemic  nonsense just to find that one fact-based page.

In short, I find the connection between the first method, based on proven chemistry, and macroevolution, tenuous.

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Hmm. You quote one of the many sources that I threw out of my initial search.

From the Paleo 21 discussion on macroevolution from the Natural History Museum :

1. Macroevolution can be defined simply as evolution above the species level

2. One striking macroevolutionary pattern that has emerged from the fossil record is that major groups and evolutionary novelties have not originated randomly in time and space ... mechanisms underlying the origins of novelties remain poorly understood.

3. Much macroevolutionary research was triggered by the realization that many species appeared to be almost static morphologically after their first appearance in the fossil record rather than evolving continuously. This led to the hypothesis of punctuated equilibrium, which holds that most evolutionary change accrues at the branchpoints of species' histories rather than over the duration of established species. ... Still unclear is whether these different evolutionary tempos and modes are distributed unevenly among taxa, habitats, regions, or ecological categories.

My comment: So, evolution occurs, until it doesn't?

4. Mathematical models have also been used to good effect. The most extensively explored methods to date have been models of taxonomic diversification, in which the dynamics of clades or entire faunas are modeled with simple equations to explore the effects of variations in extinction, origination, and the strengths of interaction among and within groups

Yes, this is a start, but it's a poor start. Like a prof told me when I showed interest in chaotic dynamics, "Unless the models you make can be observed, then it's only speculation and not science" (I of course paraphrase).

In fact, modeling phenomenon using chaotic (nonlinear) has become something of a past-time among applied mathemeticians. Not that mathematicians shouldn't find new ways of being able to solve systems of  nonlinear differential equations without recourse to FORTRAN and supercomputer number-crunching, but so far, mathematical applications to biology, particularly biology that attempts to explain more than population shifts and such, seems far-fetched.

In fact, the professors of this symposium seem intuitively to feel the same way, as most of the interdisciplinary focus involves areas outside of, say, physical sciences:

5. ...electronic databases will play an important role, but targets should expand beyond the synoptic taxonomic databases that have dominated the field, to include morphological, ecological, phylogenetic and biogeographic information; collecting and standardizing such data will be a major challenge in many instances.

I guess the very best I can say about this theory is that it is now about the same level as astronomy was during the age of Brahe, but before Kepler -- a mass of data that no one has yet to systemise.

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Hmm. You quote one of the many sources that I threw out of my initial search.

Why did you throw it out?

...Rest of thread...

The quality of a source is nearly as important as the source itself, so I throw out every web site search result that (1) is not written by someone with credentials in the field (2) poorly referenced (i.e. no peer reviewed journals) or not referenced at all (3) has a polemic or apologetic nature.

The source you found came from a Usenet discussion group, so out it went. I don't bother citing cranks, whether the crank support my argument or not. The data do that for themselves.

So, following my own criteria, I found a delightful little page from your university that couples statistical algorithms to the mutations of DNA. They even wrote a PostScript book on the subject that I've downloaded. Wild stuff.

However, in the PostScript book, the models they derive are applied to point mutations in specific creatures, namely Drosophilia. Yes, the models describe mutation rates of DNA over generations of one creature (well-characterized by biochemical methods), but they don't describe mutation rates in populations of the same creature, which is the basis of macroevolution.

To be truthful, I'm curious about the direction that research will take, so I will suspend my judgement until those computational biologists create theorems that can describe mutation rates in statistical ensembles of genomes.   

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Hmm. You quote one of the many sources that I threw out of my initial search.

Why did you throw it out?

...Rest of thread...

The quality of a source is nearly as important as the source itself, so I throw out every web site search result that (1) is not written by someone with credentials in the field (2) poorly referenced (i.e. no peer reviewed journals) or not referenced at all (3) has a polemic or apologetic nature.

The source you found came from a Usenet discussion group, so out it went. I don't bother citing cranks, whether the crank support my argument or not. The data do that for themselves.

So, following my own criteria, I found a delightful little page from your university that couples statistical algorithms to the mutations of DNA. They even wrote a PostScript book on the subject that I've downloaded. Wild stuff.

However, in the PostScript book, the models they derive are applied to point mutations in specific creatures, namely Drosophilia. Yes, the models describe mutation rates of DNA over generations of one creature (well-characterized by biochemical methods), but they don't describe mutation rates in populations of the same creature, which is the basis of macroevolution.

To be truthful, I'm curious about the direction that research will take, so I will suspend my judgement until those computational biologists create theorems that can describe mutation rates in statistical ensembles of genomes.   

I already told you, movement of a population's genes as a whole varies on how genetically fit they are relative to those of smallish changes. Some things seem to be more able to evolve that others. If their genes are a local optimum of genetic fitness, you will see less evolution. One problem is that what genetically fit means changes with outside pressures. You really can't state a theorm here, the system is too complicated. The best you could do is compare different populations and how fast they seem to evolve, and come up with a statistical distribution.

Have you ever heard of genetic algorithms? They do something similiar but with computer algorithms, FPGA, or walking robots.

As for your your criticism of talkorigins,

1. How do you know they don't have credentials?
2. You missed the very long reference list at the bottom.
3. What do you expect when they're refuting ID?

From the Questions and Answers page of Talkorigins:

Isn't the Talk.Origins Archive just some website that has no particular credibility? Those FAQs and essays aren't peer-reviewed, and many are written by interested laymen rather than specialists, so they can be ignored, right?

   We encourage readers not to take our word on the issues, but rather to look at the primary literature and evaluate the evidence. While materials on the Archive have not necessarily been subjected to formal peer-review, many have been subjected to several cycles of commentary in the newsgroup prior to being added to the Archive. Most of our materials provide links and/or bibliographic references to enable the reader to evaluate the evidence for themselves. While anyone can decide to ignore our materials, the Archive has been recognized as a valuable online resource by many well-known groups, magazines, and individuals. Further, a number of college courses have chosen to use materials from the Archive in their coursework. See: Awards, Honors, and Favorable Notices for The Talk.Origins Archive.

I don't take them on their word, and found independent literature on the the topic, exactly as the site recommends.

And from a site on Genetic Algorithms

Genetic Algorithms (GAs) are adaptive heuristic search algorithm premised on the evolutionary ideas of natural selection and genetic. The basic concept of GAs is designed to simulate processes in natural system necessary for evolution, specifically those that follow the principles first laid down by Charles Darwin of survival of the fittest. As such they represent an intelligent exploitation of a random search within a defined search space to solve a problem.

I could be a deep cynic like the authors of the physics textbook I'm studying and claim, "when a physicist speaks of a heuristic solution he is apologizing in advance for a sloppy and nonrigorous one," but because I am a chemist, I already know that plenty of science is already sloppy and nonrigorous.

Indeed, the GA site states:

GAs were introduced as a computational analogy of adaptive systems. They are modelled loosely on the principles of the evolution via natural selection, employing a population of individuals that undergo selection in the presence of variation-inducing operators such as mutation and recombination (crossover). A fitness function is used to evaluate individuals, and reproductive success varies with fitness.

The Algorithms

1. Randomly generate an initial population M(0)
2. Compute and save the fitness u(m) for each individual m in the current population M(t)
3. Define selection probabilities p(m) for each individual m in M(t) so that p(m) is proportional to u(m)
4. Generate M(t+1) by probabilistically selecting individuals from M(t) to produce offspring via genetic operators
5. Repeat step 2 until satisfying solution is obtained.

The paradigm of GAs descibed above is usually the one applied to solving most of the problems presented to GAs. Though it might not find the best solution. more often than not, it would come up with a partially optimal solution.

So, in general, you could design an algorithm that would sample all outcomes given some set of parameters, leaving the researcher the alternative to pick the outcome that most supports his theory? Of course, that would be unethical, but, then again...

I think I found the reason why evolutionary biologists find microevolution, which is indisputable, so pallid in comparison to macroevolution:

The attractiveness of macroevolution reflects the exhaustive documentation of large-scale patterns which reveal a richness to evolution unexplained by microevolution. If the goal of evolutionary biology is to understand the history of life, rather than simply document experimental analysis of evolution, studies from paleontology, phylogenetics, developmental biology, and other fields demand the deeper view provided by macroevolution.

http://www.blackwell-synergy.com/doi/full/10.1046/j.1525-142x.2000.00045.x

Dr Erwin states in his article:

...discontinuities have been documented at a variety of scales, from the punctuated nature of much speciation, to patterns of community overturn, the sorting of species within clades by differential speciation and extinction, and finally mass extinctions. These discontinuities impart a hierarchical structure to evolution, a structure which impedes, obstructs, and even neutralizes the effects of microevolution.

That phrase "hierarchichal structure to evolution" contradicts your view of "...movement of a population's genes as a whole varies on how genetically fit they are relative to those of smallish changes." .. in fact, Erwin spends seven pages arguing against your conclusion.

My problem with both is the ad hoc explanations of those hierarchical structures.