Original Research--join In

[Loudmouth]

Oh my!.....

I wasn't sure what to say . . .

 

[Loudmouth]

Just so we are clear on definitions, let me give an example:
Craig Venter "created" what he called "the first artificial cell" by stringing together DNA of one million molecules and inserting it into a cell which he had previously evacuated most or all of the native DNA. (google it) Now, suppose this cell undergoes numerous mutations during future years. Then, suppose a new researcher discovers this cell and inspects its DNA. Could he come to a correct conclusion about the origin of this cell? What would you say is the true origin of the cell?

This is an interesting question, and one that sheds some light on how you view genetics and how real geneticists view genetics.

What Dr. Venter and company did was to exactly copy, or nearly so, the genome of a living bacterium. What they did was to try and mimic the natural process of reproduction. They made a copy.

Is that what intelligent design is? No. For intelligent design, you need NEW genomes and NEW organisms, not exact copies of already existing life. That is where artificiality can be detected, in how those new genomes are put together. What we look for is designs that nature would not produce. In fact, humans have been doing this for a while.

One example is the Glofish. This is a vertebrate, ray finned fish that can be raised in anyone's aquarium. If you install a UV light in the top of your tank these fish will fluoresce in many different colors, depending ont the strain. Why do they do this? They carry a copy of a jellyfish gene that produces a fluorescent protein. In fact, they carry an exact copy of a jellyfish gene.

Evolution has no way of evolving the exact same DNA sequence in such divergent genomes and divergent species. It simply can not do this. Design can. If design were true, then we would expect every genome to be littered with clear and obvious signs of tampering between species. That evidence just isn't there. Instead, we see the nested hierarchy that we would expect to see from evolution.

 

[Loudmouth]

Let’s be clear: various constructions of creationism are essentially opinions based upon evidence from scripture and nature. Granted, various evidences are given different weights based upon prepositional biases or worldviews. Yet, to imagine that evolutionism does not exercise bias and presupposition and weighting of evidence, is simply not honest.

It is dishonest to accuse an entire field of scientists of bias, and then not substantiate such an accusation. Where is your evidence of bias?

It is also not honest to say that creationists don’t do any real research.

Then show us the research.

I don’t want to waste my time, so if 5 people or more would simply respond by agreeing to follow this through, I will walk you through the steps, which are not really hard to do. If you understand the basic concepts of DNA, the genetic code, mutations, and how DNA is “read” in order to turn its code into proteins/enzymes, then you should be able to keep up. All of these basic things can be gleaned from wiki and other easily-found web sources. If you are with me, just respond “yes”.

I am more than willing to participate, although this has the feel of letting a 5 year old attempt to drive the family car.

 

[JacksBratt]

An understanding of nature is not required for teaching righteousness. The bible is about theology, not science.




None of this indicates God dictated scripture concerning anything about nature. At best, it may indicate that prophecies were directed from God... not science.

I like that description, "directed from God". That is a much better description than the way I was trying to say it.

However, you stated that the scripture doesn't support it and the scripture that I quoted clearly supports it. Not just the prophesies either. ALL scripture.

If you cannot accept this then Christianity pretty much falls apart or is a buffet christianity. That is, all the truth is on the table and you pick what you want and leave the rest

 

[Loudmouth]

SFS posted: "the mechanism you're modeling has nothing to do with the actual processes thought to produce new genes.

You mean; thought by evolutionists... who just happen to have enormous presuppositions. The operative word is "thought", which actually means speculate here. And that speculation specifically fails to account for the stop codons and for the amount of molecular resources required to fund the search for lengthy genes, whether during presumed abiogenesis or in any/all major presumed "transitions" thereafter.

We don't presume that genetic recombination exists. We have directly observed genetic recombination. It is a very real mechanism. We have also found that novel genes can be made up of sub-units of different genes which is entirely consistent with genetic recombination.

One interesting example is T-urf13 which is a very functional protein that resulted from the recombination of several different genes:

On the evolution of Irreducible Complexity - The Panda's Thumb

You can't ask us to show examples of new genes evolving, and then ignore the evolutionary mechanisms that give rise to new genes. It's as if you want to know who painted the Mona Lisa, and anyone who says da Vinci is automatically wrong . . . just because.

 

[Loudmouth]

I like that description, "directed from God". That is a much better description than the way I was trying to say it.

However, you stated that the scripture doesn't support it and the scripture that I quoted clearly supports it. Not just the prophesies either. ALL scripture.

If you cannot accept this then Christianity pretty much falls apart or is a buffet christianity. That is, all the truth is on the table and you pick what you want and leave the rest

When it comes to science, christians have been at the buffet since Galileo. Why stop now? Or are you a Geocentrist as scripture demands?

 

[Loudmouth]

IOW, Genesis "kinds", such as a dog group, allows for the idea that over the years many different varieties of dogs had the same ancestor, whose genome contained all the information to produce the varieties.

What is stopping dogs and humans from being two varieties of the mammal kind?

What is stopping fish and humans from being two varieties of the vertebrate kind?

The research I spoke of when I started this thread is very applicable here. Mutations of existing genes have a high likelihood of creating premature stop codons and thus, tons of meaningless junk to clutter up cells.

I would love to see your math on this one. At first blush, it would seem to me that most substitutions result in a change in the protein sequence instead of a stop codon. Substitutions are about 7 times more common than indels, so if you are talking about "most mutations" you are going to be talking about substitutions.

Undirected processes simply cannot create a meaningful cadre of new and uniquely useful genes which could turn one genome--say of a dog--into a substantially different one--say of a cat.

That is why evolution predicts that a living species will not evolve into another already living species. Instead, the descendants of dogs will diverge from cats (i.e. become less and less like cats) and be modified versions of their ancestors.

Responsible evolutionists should take the cell biochemistry seriously and conduct step-by-step simulations, as I have done, accounting for molecular resources necessarily used during the steps.

This is a bit like a 5 year old telling a policeman that he should take crime seriously. In case you didn't know, geneticists already take these things very seriously.

Here's a fairly simple example: during any kind of random assemblage of sequences of nucleotides (something that MUST be accounted for during presumed abiogenesis), how many molecules would be used up, on average, in the search to produce genes that are only 100 codons long (with a stop codon only at the last position)? Venture a guess or do some practical research using the random DNA sequence generator site (google it).

You assume too much. Why would DNA even be needed, much less codons? RNA already has the properties of both DNA and proteins.

 

[Split Rock]

I like that description, "directed from God". That is a much better description than the way I was trying to say it.

However, you stated that the scripture doesn't support it and the scripture that I quoted clearly supports it. Not just the prophesies either. ALL scripture.

If you cannot accept this then Christianity pretty much falls apart or is a buffet christianity. That is, all the truth is on the table and you pick what you want and leave the rest

The truth you are ignoring is that the bible is a Work of Man. Now maybe it was inspired by God and if we take the bible at face value, maybe even the prophecies in it are directly attributable to God. The fact remains it is a work of man, and is thus limited by what the authors knew and did not know at the time.

 

[Loudmouth]

I am not aware of any online resource that counts the results of a single substitution in a given open readin frame. Anyone know of one? Just looking at a single codon off the top of my head:

CCA

Mutations include GCA, TCA, ACA, CTA, CAA, CGA, CCT, CCG, CCC

Not one of those is a stop codon. If you have a codon that starts with T it would seem that you have a better chance of getting a stop codon.

TTG

mutations: CTG, ATG, GTG, TAG*, TGG, TCG, TTA, TTC, TTT

You have a much better chance if the codon starts with a TA, it would seem. I just don't see how the claims made by WisdomSpy can pan out. A majority of mutations in genes will produce a change in amino acid sequence, but not a stop codon.

 

[Non sequitur]

Oh my!.....

You guys are so darn smart; it's like a mental panty-dropper.

 

[Zosimus]

Are Ford's and Toyota's living creatures, that can reproduce?

Relevance?

 

[Zosimus]

Yes.


That is only part of my argument. It is also the PATTERN of similarities that points to common ancestry and evolution. That pattern is a nested hierarchy. My position is that the observed similarities and the pattern that the similarities fall into are are all consistent with what we would expect from evolution. That is why these observations are evidence for evolution.

On the other hand, there is absolutely no reason why a designer would need to put designs in a nested hierarchy. The designer of different car models would not be forced to use a specific radio in a car if a specific tire rim is used. These are two independent design elements that can be mixed and matched however the designer sees fit. However, with life we do see independent adaptations that are always found with each other, such as middle ear bones and mammary glands.

If you want to claim that the similarities found between different species is evidence for a designer, then you need to explain why a designer would go to such lengths to make it look just like evolution.



No, I wouldn't. Automobiles do not fall into an objective nested hierarchy like life does. This is one of the big clues that automobiles did not evolve through Darwinian mechanisms from a common ancestor through vertical inheritance like complex life did.

tRNA is not a reason. It's an adapter molecule composed of RNA, typically 76 to 90 nucleotides in length, that serves as the physical link between the nucleotide sequence of nucleic acids (DNA and RNA) and the amino acid sequence of proteins.

Your "nested hierarchy" argument is BS until or unless you address the points raised by the person who put up the shark vs. human link, something you have never done or even attempted. You don't get to insist that things share common ancestors by just ignoring people who try to provide counter examples.

 

[Split Rock]

I am not aware of any online resource that counts the results of a single substitution in a given open readin frame. Anyone know of one? Just looking at a single codon off the top of my head:

CCA

Mutations include GCA, TCA, ACA, CTA, CAA, CGA, CCT, CCG, CCC

Not one of those is a stop codon. If you have a codon that starts with T it would seem that you have a better chance of getting a stop codon.

TTG

mutations: CTG, ATG, GTG, TAG*, TGG, TCG, TTA, TTC, TTT

You have a much better chance if the codon starts with a TA, it would seem. I just don't see how the claims made by WisdomSpy can pan out. A majority of mutations in genes will produce a change in amino acid sequence, but not a stop codon.

I believe that Wisdom's ideas are kind of murky and based on intuition (most mutations are bad because they're mutations) and not actually based on a well-founded understanding of genetics.

 

[WisdomSpy]

Loudmouth posted: "That's easy. Thousands of substitution events and indels that are multiples of 3 would not produce frameshift mutations and their accompanying stop codons. Challenge met."

Every casino on earth is hoping you will come play their games! You, like so many evolutionists are failing to apply the law of averages. Why don't you do something original and spend time with the online random DNA sequence generator. See how long it takes you to generate a 100 codon sequence (300 nucleotides) which fortuitously lacks internal stop codons. More importantly than time, calculate how many nucleotides would be needed, ON AVERAGE, to fund the search for such a "gene" and honestly recon with the fact that under abiogenesis, this number would have to occur, ON AVERAGE, for each new gene originated. And then, figure out how a "protocell" or a cell could possibly function in the presence of such overwhelming junk. Only after this exercise are you ready to credibly address the Dystrophin gene.

 

[sfs]

Loudmouth posted: "That's easy. Thousands of substitution events and indels that are multiples of 3 would not produce frameshift mutations and their accompanying stop codons. Challenge met."

Every casino on earth is hoping you will come play their games! You, like so many evolutionists are failing to apply the law of averages. Why don't you do something original and spend time with the online random DNA sequence generator. See how long it takes you to generate a 100 codon sequence (300 nucleotides) which fortuitously lacks internal stop codons. More importantly than time, calculate how many nucleotides would be needed, ON AVERAGE, to fund the search for such a "gene" and honestly recon with the fact that under abiogenesis, this number would have to occur, ON AVERAGE, for each new gene originated. And then, figure out how a "protocell" or a cell could possibly function in the presence of such overwhelming junk. Only after this exercise are you ready to credibly address the Dystrophin gene.

You started the thread by saying that you wanted to talk about evolution, not the origins of life. Which is it?

As for generating novel open reading frames -- does your random sequence generator model the production of large amounts of low complexity sequence? See here for why that might be relevant.

 

[Loudmouth]

tRNA is not a reason. It's an adapter molecule composed of RNA, typically 76 to 90 nucleotides in length, that serves as the physical link between the nucleotide sequence of nucleic acids (DNA and RNA) and the amino acid sequence of proteins.

Why does being an "adaptor molecule" disqualify tRNA's as evidence for common ancestry?

The reason that I list tRNA's as evidence is because the anti-codon and amino acid are independent. There is no physical law that requires a tRNA molecule to have a methionine if the anticodon is UAC. None. So why do human and bacterial tRNA's have the same relationship between anticodon and amino acid?

A designer could could mix and match as the designer sees fit. A designer does not explain why all life shares the same codon usage, and why tRNA sequences fall into a nested hierarchy. Why would a designer be forced to make the sequence of tRNA more similar between whale and human than it is between human and fish? Why would a designer be forced to make fish tRNA equidistant between whale and human tRNA? Design answers none of this. Evolution does. That is why this is evidence for evolution.

Your "nested hierarchy" argument is BS until or unless you address the points raised by the person who put up the shark vs. human link, something you have never done or even attempted.

Until someone shows how the peer reviewed paper falsifies evolution, there is nothing to address. I can't address an argument that has never been made. Perhaps you could tell us how the data falsifies evolution?

You don't get to insist that things share common ancestors by just ignoring people who try to provide counter examples.

There is nothing to ignore. Bare links are not an argument.

 

[Loudmouth]

You, like so many evolutionists are failing to apply the law of averages. Why don't you do something original and spend time with the online random DNA sequence generator.

That's not how evolution works. Evolution modifies non-random sequence. For example, the vast majority of differences between humans and chimps is due to differences in shared genes. It is not due to the emergence of brand new genes from random sequence.

Like so many creationists, you don't know how to model evolution.

See how long it takes you to generate a 100 codon sequence (300 nucleotides) which fortuitously lacks internal stop codons.

If we start with the common ancestor of humans and chimps, we already have 30,000 open reading frames.

More importantly than time, calculate how many nucleotides would be needed, ON AVERAGE, to fund the search for such a "gene" and honestly recon with the fact that under abiogenesis, this number would have to occur, ON AVERAGE, for each new gene originated.

Abiogenesis? I thought we were discussing evolution. You need to pick one.

As to abiogenesis, the first life may not even have had DNA or modern stop codons, so your model is way off to begin with.

 

[WisdomSpy]

Important clarification: I do not contend with the statement that most mutations are base substitutions. You apparently missed the rest of the discussion. A thousand base substitutions can NEVER turn the hemoglobin gene into the Dystrophin gene. My meaning, if I failed to be entirely clear, is that most TYPES of mutations run a high risk of causing frame shifts and hence stop codons, hence junk. Are you going to presume that insertions and deletions and splicing events etc. magically avoid the "wrong" places and only "select" the small percentage that won't disturb the pre-existing frame reading?

 

[WisdomSpy]

Loudmouth posted:
"If design were true, then we would expect every genome to be littered with clear and obvious signs of tampering between species."

I totally agree... however, we would need to be examining the genomes right after the original creation, not thousands or more years afterwards. Evolution has added way too much confusing stuff since then. And who says that genetic recombination would not be the intent of the designer--a designer who loves diversity--a designer who knows the value of variation and adaptation? Quit making a straw man of the design/creation paradigm.

 

[Loudmouth]

A thousand base substitutions can NEVER turn the hemoglobin gene into the Dystrophin gene.

I wasn't aware that anyone was claiming that it could, or that the dystrophin gene evolved from an ancestral hemoglobin gene.

My meaning, if I failed to be entirely clear, is that most TYPES of mutations run a high risk of causing frame shifts and hence stop codons, hence junk.

The truth of the matter is that most mutations do not result in a stop codon, so your point is moot.

Are you going to presume that insertions and deletions and splicing events etc. magically avoid the "wrong" places and only "select" the small percentage that won't disturb the pre-existing frame reading?

I have made no such presumption. I fully accept that deleterious mutations are a very real thing. What you refuse to accept is the process of negative selection.