Darwin re-visited

[Galapagos]

Originally Posted by Biochemist

What?????? No role??????

What is a mutation???????? How likely is any individual mutation???

Mutation Rates

[Turtle]

Originally Posted by Biochemist

What?????? No role??????

What is a mutation???????? How likely is any individual mutation???

It doesn't matter how likely it is. The simple fact is, that it is, and it is what scientists have defined it as. A mutation by any other name....

[Galapagos]

Prepare to witness the impossible!!!

Copley, S. D. (2000). “Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach.” Trends Biochem Sci 25(6): 261-265. PubMed

Harding, M. M., Anderberg, P. I. and Haymet, A. D. (2003). “‘Antifreeze’ glycoproteins from polar fish.” Eur J Biochem 270(7): 1381-1392. PubMed

Johnson, G. R., Jain, R. K. and Spain, J. C. (2002). “Origins of the 2,4-dinitrotoluene pathway.” J Bacteriol 184(15): 4219-4232. PubMed

Long, M., Betran, E., Thornton, K. and Wang, W. (2003). “The origin of new genes: glimpses from the young and old.” Nat Rev Genet 4(11): 865-875. PubMed

Nurminsky, D., Aguiar, D. D., Bustamante, C. D. and Hartl, D. L. (2001). “Chromosomal effects of rapid gene evolution in Drosophila melanogaster.” Science 291(5501): 128-130. PubMed

Patthy, L. (2003). “Modular assembly of genes and the evolution of new functions.” Genetica 118(2-3): 217-231. PubMed

Prijambada I. D., Negoro S., Yomo T., Urabe I. (1995). “Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution.” Appl Environ Microbiol. 61(5):2020-2. PubMed

Ranz, J. M., Ponce, A. R., Hartl, D. L. and Nurminsky, D. (2003). “Origin and evolution of a new gene expressed in the Drosophila sperm axoneme.” Genetica 118(2-3): 233-244. PubMed

Seffernick, J. L. and Wackett, L. P. (2001). “Rapid evolution of bacterial catabolic enzymes: a case study with atrazine chlorohydrolase.” Biochemistry 40(43): 12747-12753. PubMed

Source: The Panda's Thumb: Meyer's Hopeless Monster

[Galapagos]

Originally Posted by Biochemist

Post # 463 was my first material post here.

Your calculations are nonsense. I now quote from John Wilkins' page on abiogenesis from TO:
Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations

Originally Posted by John Wilkins

Every so often, someone comes up with the statement "the formation of any enzyme by chance is nearly impossible, therefore abiogenesis is impossible". Often they cite an impressive looking calculation from the astrophysicist Fred Hoyle, or trot out something called "Borel's Law" to prove that life is statistically impossible. These people, including Fred, have committed one or more of the following errors.

Problems with the creationists' "it's so improbable" calculations

1) They calculate the probability of the formation of a "modern" protein, or even a complete bacterium with all "modern" proteins, by random events. This is not the abiogenesis theory at all.

2) They assume that there is a fixed number of proteins, with fixed sequences for each protein, that are required for life.

3) They calculate the probability of sequential trials, rather than simultaneous trials.

4) They misunderstand what is meant by a probability calculation.

5) They seriously underestimate the number of functional enzymes/ribozymes present in a group of random sequences.

I will try and walk people through these various errors, and show why it is not possible to do a "probability of abiogenesis" calculation in any meaningful way.

You didn't address any of these problems with your model before.
Wilkins continues:

Originally Posted by Wilkins

A primordial protoplasmic globule

So the calculation goes that the probability of forming a given 300 amino acid long protein (say an enzyme like carboxypeptidase) randomly is (1/20)300 or 1 chance in 2.04 x 10390, which is astoundingly, mind-beggaringly improbable. This is then cranked up by adding on the probabilities of generating 400 or so similar enzymes until a figure is reached that is so huge that merely contemplating it causes your brain to dribble out your ears. This gives the impression that the formation of even the smallest organism seems totally impossible. However, this is completely incorrect.

Compare this to your calculation:

Originally Posted by Biochemist

To get a functional protein by mutation: you would need at least 200 specific amino acids in specific sequence out of 300 in the protein (it is actually more like 260 on average, but I am making it simpler). This would be randomly 1 in 20^200, or about 1 in 10^260. Heck. To be conservative, let's make it a couple of trillion trillion trillion trillion times more likely, and make it 1 in 10^200.

Wilkins continues:

Originally Posted by Wilkins

Firstly, the formation of biological polymers from monomers is a function of the laws of chemistry and biochemistry, and these are decidedly not random.

Secondly, the entire premise is incorrect to start off with, because in modern abiogenesis theories the first "living things" would be much simpler, not even a protobacteria, or a preprotobacteria (what Oparin called a protobiont [8] and Woese calls a progenote [4]), but one or more simple molecules probably not more than 30-40 subunits long. These simple molecules then slowly evolved into more cooperative self-replicating systems, then finally into simple organisms [2, 5, 10, 15, 28]. An illustration comparing a hypothetical protobiont and a modern bacteria is given below.

Modern enyzyme systems did not spring into existence. Nobody is claiming this except for creationists:


This is as much of his paper I am going to directly quote here. If you really want to, you can address each of his points head on(I mean with scientific citation and a full response to it, do not just quote his five points above and spit out some more unsupported nonsense). If you want to discuss it further with him personally, I'm sure he'd love to hear from an ID advocate over on his blog(linked above).

[Biochemist]

Originally Posted by Galapagos

Mutation Rates

Thanks, Gala. That attachment is a nice little monograph.

I assume you recognize that I was befuddled by T's assertion that genetics had nothing to to with probability.

I should also mention that the mutation rate discussion in your attachment supports my view that the vast majority of genomic changes should be spontaneous, rather than induced. The issue (as alluded to in your attachment) is that some genomic changes are much more likely than others (referred to as hot spot and cold spots).

I think these sorts of discussion would seem less biased to me if we referred to "genomic changes" as just that rather than "mutations". The higher the likelihood of a particular genomic change, the less applicable the notion of "mutation" applies.

"Mutation" certainly applies (for example) when we hit DNA with UV. But where spontaneous genomic change occurs at a fixed rate in a random population, we should not assume it is a mutation. It could well be a propensity.

[Galapagos]

Originally Posted by Biochemist

Thanks, Gala. That attachment is a nice little monograph.

I assume you recognize that I was befuddled by T's assertion that genetics had nothing to to with probability.

I should also mention that the mutation rate discussion in your attachment supports my view that the vast majority of genomic changes should be spontaneous, rather than induced. The issue (as alluded to in your attachment) is that some genomic changes are much more likely than others (referred to as hot spot and cold spots).

I think these sorts of discussion would seem less biased to me if we referred to "genomic changes" as just that rather than "mutations". The higher the likelihood of a particular genomic change, the less applicable the notion of "mutation" applies.

"Mutation" certainly applies (for example) when we hit DNA with UV. But where spontaneous genomic change occurs at a fixed rate in a random population, we should not assume it is a mutation. It could well be a propensity.

No, I think that page shows you have no idea what you are talking about with your assertions and calculations(I mean beyond the fact that you are claiming something to be impossible that occurs regularly).

There are many kinds of mutations:
Mutation - Wikipedia, the free encyclopedia

See the section on causes of mutation:
Mutation - Causes - Wikipedia, the free encyclopedia

The burden of proof is on you if you want to rewrite the biology textbooks. What is wrong with any of the above on the wiki page(one issue at a time, be specific)?

[Biochemist]

Originally Posted by Galapagos

Your calculations are nonsense. ...You didn't address any of these problems with your model before.

Really interesting. Given that I did not discuss abiogenesis at all, or that i did not make any of the above mistakes, it is odd that you would include it. This is also that vague "oh those guys underestimate..." argument, and yet there is no counterpoint that is quantitative. The author gives the point that many protein sequences are viable, not just a specific one, and "we" underestimate that. But that number is actually reasonably small compard to the problem. If we assume that a 100 billion different species each have 100,000 uniquely different proteins (which pretty high, given the acceptance of common descent) that only gives us 10^16 total unique proteins. This barely scratches the surface of the probabilities, when we are discussing likelihoods on the order of 1 in 10^1000. Nice to get down to 1 in 10^984, but I don't feel a lot better.

Originally Posted by Gala

Modern enyzyme systems did not spring into existence.

Never said they did. In fact, i started my analysis assuming that DNA and the related replication machinery was already in place. The largest problems occur once the lysosomes arrive. These little machines are highly effective at eradicating cytoplasmic protiens that are foreign. The moment that the evolutionary tree gave lysosomes to eukaryotes, it significantly cranked up the inhibitor to expressing a genomic change unless it was recognized as non-foreign by the lysosomes.

Originally Posted by Gala

If you want to discuss it further with him personally, I'm sure he'd love to hear from an ID advocate over on his blog(linked above).

I wish you guys would get off this horse.

Maybe we should discuss a narrower problem: How does any "mutation" that involves more than a single protein get past a lysosome?

[Biochemist]

Originally Posted by Galapagos

What is wrong with any of the above on the wiki page(one issue at a time, be specific)?

Nothing, but it might help describe (what might be) a semantic problem I am having.

Originally Posted by From Wiki

In biology, mutations are changes to the nucleotide sequence of the genetic material of an organism. Mutations can be caused by copying errors in the genetic material during cell division, by exposure to ultraviolet or ionizing radiation, chemical mutagens, or viruses, or can be induced by the organism, itself, by cellular processes such as hypermutation. In multicellular organisms with dedicated reproductive cells, mutations can be subdivided into germ line mutations, which can be passed on to descendants through the reproductive cells, and somatic mutations, which involve cells outside the dedicated reproductive group and which are not usually transmitted to descendants.

In this definition, any change to a nucleotide sequence is a mutation. By this definition, all changes to species are due to mutation.

You have defined away the problem, not solved it.

My suggestion is that some genomic changes (e.g., UV light damage to DNA) truly are mutations. Other genomic changes that are highly likely based on the extant state of the genome should not be called mutations. They a code-based changes.

[Turtle]

Originally Posted by Biochemist

.. If we assume that a 100 billion different species each have 100,000 uniquely different proteins (which pretty high, given the acceptance of common descent) that only gives us 10^16 total unique proteins. This barely scratches the surface of the probabilities, when we are discussing likelihoods on the order of 1 in 10^1000. Nice to get down to 1 in 10^984, but I don't feel a lot better. Never said they did. In fact, i started my analysis assuming that DNA and the related replication machinery was already in place.
...
Maybe we should discuss a narrower problem: How does any "mutation" that involves more than a single protein get past a lysosome?

No; we are not changing the topic yet again. Your assumptions, your "pretty highs", your "barely", your yada, yada, yada, probability ad nauseum is invalid. Period.

[Biochemist]

Originally Posted by Turtle

No; we are not changing the topic yet again. Your assumptions, your "pretty highs", your "barely", your yada, yada, yada, probability ad nauseum is invalid. Period.

This is a narrower slice of the same problem. Since you seem to want to accept by faith that this "just happened somehow", let's focus on the lysosome problem.

Bio