Original Research--join In

[sfs]

sfs posted: "It's a fine example of scientists explaining patterns of genetic similarity"

Really? What were they "explaining" except how further story-telling is covering for prior story-telling? Read the actual article:

“Horizontal transfer (HT) is central to the evolution of prokaryotic species. Selfish and mobile genetic elements, such as phages, plasmids, and transposons, are the primary vehicles for HT among prokaryotes. In multicellular eukaryotes, the prevalence and evolutionary significance of HT remain unclear.”

You do realize that's from the introduction, right? It describes the existing state of knowledge. The paper then proceeds to describe a study of a specific case of HT in some detail, thereby explaining a particular pattern of genetic similarity.

So on the one hand, we have the scientific explanation for this segment of DNA that's in a bunch of distantly related organisms: a transposon that spread widely throughout tetrapods at a particular time in the past. Competing with that, we have the creationist explanation which is . . . what, exactly?

“Remains unclear” is an important phrase to dissect. Is there anything clear whatsoever about such mechanisms occurring in eukaryotes?

Yes, we know some of the mechanisms by which it occurs -- transposition from endosymbionts, infection with retroviruses. There remains much to learn about the mechanisms, however. That's why scientists still have jobs.

Has anyone seen it happen?

We've seen every step in the process, yes. We also see the result, e.g. some people with have transferred DNA inserted into their genomes that's lacking in others.

 

[WisdomSpy]

sfs posed: "Also, you refuse to say what happens to a mutation that truncates a crucial protein. Is it passed on or not? Why can't you answer this question?"

The Dystrophin gene is one classic example. By the data posted previously (Split Rock, I seem to recall), 2/3 of these individuals reproduce, thus passing along the defect. Now, I wonder how many millions of years supposed Natural Selection will take to eliminate this defect from the human genome. NS is not a magic genie, wizard or god. It has major limitations that keep getting glossed over by evolutionists.

 

[bhsmte]

sfs posed: "Also, you refuse to say what happens to a mutation that truncates a crucial protein. Is it passed on or not? Why can't you answer this question?"

The Dystrophin gene is one classic example. By the data posted previously (Split Rock, I seem to recall), 2/3 of these individuals reproduce, thus passing along the defect. Now, I wonder how many millions of years supposed Natural Selection will take to eliminate this defect from the human genome. NS is not a magic genie, wizard or god. It has major limitations that keep getting glossed over by evolutionists.

Still can't answer the question?

 

[WisdomSpy]

Loudmouth posted: "I am asking the people who keep claiming that the evidence points to a common designer. If they can't show why design would result in the observations we make, then they can't claim that the observations are evidence for a common designer. It is that simple."

It would be that simple if your presumed dichotomy were in fact true. Your error is so common to evolutionists--create a straw man by insisting that creationists don't accept any kind or degree of evolution--pose the question as if it has to be evolution versus creation. It's NOT one or the other!!! It's an argument which poses evolution alone against the proposition of creation, later affected by evolution. Why is this so difficult to deal with?

 

[WisdomSpy]

"HGT in eukaryotes is very limited and easily detectable, as demonstrated by the papers you have been alluding to."

You haven't separated the fact from fiction yet. "Detectable" infers that you could prove it occurring by direct laboratory experiments. The only thing being "detected" in the article is that their story-telling is matching their desired story. An equally valid story might be that a designer used common elements in different overall designs, like rubber is used in all automobiles. No lateral transfer necessary.

 

[Loudmouth]

I realize how easy it would be to download a sequence from a gene databank and claim that it was randomly generated.

If you are going to accuse me of lying, at least have the backbone to back it up.

Even if you actually did use a randomly-generated sequence, one trial is an anecdote only--I'm sure you realize that. I asked you several times to try that same thing multiple times and average the results. This is what I did, not only for random sequences but for simulated mutations upon existing genes... (mutations which disturb frame reading).

Let's use a random genome of 100,000 bases and see how many 300+ bp ORF's we get. A larger genome should balance out chance events. I want you to do this, and report your results as well.

Start with a random dna generator.

Random DNA Generator

Put 100000 in the box for the size of the sequence, and keep it at 50% GC content. Hit the generate button. Right click on the box with the results, select all, then copy.

Next, go to an open reading frame finder:

ORF Finder

Paste the random sequence into the box. Hit the button that says "OrfFind".

How many 300+ base pair open reading frams do you get in a 100,000 base genome? I got 25 of them. I added up the bases in the ORF's and got about 8,300 coding bases. 8k out of 100k is 8% which is even higher than the human genome.

If you don't believe me, do it yourself. I dare you.

 

[WisdomSpy]

"We've seen every step in the process, yes."

I don't think so. There is too much confusion of empiric science and the incredible speculation surrounding it.

 

[Loudmouth]

"HGT in eukaryotes is very limited and easily detectable, as demonstrated by the papers you have been alluding to."

You haven't separated the fact from fiction yet. "Detectable" infers that you could prove it occurring by direct laboratory experiments.

Here is a good paper on retroviral integration into the host genome:

Retroviral DNA integration: ASLV, HIV, and MLV show distinct target... - PubMed - NCBI

I really don't see why you find retroviral and transposon activity so controversial.

The only thing being "detected" in the article is that their story-telling is matching their desired story.

That accusation would hold a little weight if you showed any signs of understanding the science. The problem is that you don't understand the science, so your accusations are a bit silly.

An equally valid story might be that a designer used common elements in different overall designs, like rubber is used in all automobiles. No lateral transfer necessary.

That doesn't explain the nested hierarchy.

 

[Loudmouth]

"We've seen every step in the process, yes."

I don't think so. There is too much confusion of empiric science and the incredible speculation surrounding it.

What step do you think we don't understand?

 

[justlookinla]

I am asking the people who keep claiming that the evidence points to a common designer. If they can't show why design would result in the observations we make, then they can't claim that the observations are evidence for a common designer. It is that simple.

Common building blocks are evidence for a designer.

Why would common design look exactly like evolution when it doesn't have to?

The common building blocks used in the complex machines are not evidence for atheistic Darwinist creationism, in fact they're just the opposite. Now, before you go off on the phrase "atheistic Darwinist creationism", you must recognize that "evolution" isn't a monolithic term. When someone uses the term "evolution", one must explain what they mean by "evolution".

Why would a designer put so much unneeded effort into making genomes looke like they evolved from a common ancestor? Why not use the exact same cytochrome C sequence for all mammals instead of making a whole bunch of synonymous mutations that create the same phylogeny as that formed from morphology? Why make unnecessary changes to make it look like evolution?

Here you go again using the term "evolution" as if it's a monolithic term. Since you're unable to comprehend the tremendous complexity and variety of life, the question you're asking is one from ignorance. You don't have the slightest clue how to design and create the human body in it's complexity and you accuse the designer and creator of "unneeded effort"? You don't know what you're asking.

Of course birds always produce birds. That is exactly what evolution predicts we should see. Do you understand how cladistics works? I don't think you do.

The first alleged life form was a bird? If not, when did the first non-bird produce a bird?

If we use the oft cited "tree of life" analogy, do you think a new species breaks off of the branch it sprouted from, moves down the tree, and then attaches itself to the trunk? No, that is NOT how it works, and yet that is how you are describing evolution. At one time, "birds" were made up of just a single population of organisms, much like chihuahuas or goldfish. What happened over time is that the descendants of that original population were very successful, and what they produced was more and more species. However, they remained birds because their ancestors were birds. They also remained amniotes just as both birds and humans remain amniotes, and just as our common ancestor shared with birds was an amniote.

See question above.

Evolution is not random creation.

Here you go using "evolution" as a monolithic term again. In atheistic Darwinist creationism, the ONLY creative impetus is random/chance mutation. Nothing else, no other creative element.

Now you just want the inconvenient evidence to go away. That's not how science works.

What evidence?

 

[bhsmte]

"We've seen every step in the process, yes."

I don't think so. There is too much confusion of empiric science and the incredible speculation surrounding it.

Maybe you are confused, because you possess a personal faith belief, that is contradicted by well evidenced science.

Not unusual, by any means, we see it often on these boards.

 

[Loudmouth]

sfs posed: "Also, you refuse to say what happens to a mutation that truncates a crucial protein. Is it passed on or not? Why can't you answer this question?"

The Dystrophin gene is one classic example. By the data posted previously (Split Rock, I seem to recall), 2/3 of these individuals reproduce, thus passing along the defect. Now, I wonder how many millions of years supposed Natural Selection will take to eliminate this defect from the human genome. NS is not a magic genie, wizard or god. It has major limitations that keep getting glossed over by evolutionists.

What about the 1/3 who do not? How does this compare to the non-disease allele? Do 1/3 of the carriers of the non-disease allele die from having the non-disease allele? Why isn't the disease allele as common as the non-disease allele in the human population?

 

[Loudmouth]

Common building blocks are evidence for a designer.

A nested hierarchy is not evidence for a designer. It is evidence for evolution. If you think I am wrong, then explain why a designer would design life so that it fits into a nested hierarchy.

The common building blocks used in the complex machines are not evidence for atheistic Darwinist creationism, in fact they're just the opposite.

The nested hierarchy of common building blocks, and the fact that DNA phylogenies strongly correlate with morphological phylogenies, is evidence for evolution. As you have seen, no one can explain why design would result in these observations. Evolution does explain it.

Do you share features with your siblings and cousins because you were separately designed by the same designer, or because you share a common ancestor?

You don't have the slightest clue how to design and create the human body in it's complexity and you accuse the designer and creator of "unneeded effort"? You don't know what you're asking.

I have personally designed organisms. It is something that is easily done in many labs around the world. I was never forced to fit those designed organisms into a nested hierarchy.

I know EXACTLY what I am asking for. I know EXACTLY what I am talking about. You don't. All you know how to do is repeat the same things over and over and over without ever comprehending what they mean.

The first alleged life form was a bird? If not, when did the first non-bird produce a bird?

It would be no different than the first non-chihuahua producing a chihuahua.

 

[justlookinla]

A nested hierarchy is not evidence for a designer. It is evidence for evolution. If you think I am wrong, then explain why a designer would design life so that it fits into a nested hierarchy.

What kind of evolution...you're attempting to use it as a monolithic term again? You'd have to ask the designer. I doubt you'd understand though.

The nested hierarchy of common building blocks, and the fact that DNA phylogenies strongly correlate with morphological phylogenies, is evidence for evolution. As you have seen, no one can explain why design would result in these observations. Evolution does explain it.

"Evolution" isn't a monolithic term.

Do you share features with your siblings and cousins because you were separately designed by the same designer, or because you share a common ancestor?

Common building blocks.

I have personally designed organisms. It is something that is easily done in many labs around the world. I was never forced to fit those designed organisms into a nested hierarchy.

You've designed organisms? Do you even know what you're saying?

I know EXACTLY what I am asking for. I know EXACTLY what I am talking about. You don't. All you know how to do is repeat the same things over and over and over without ever comprehending what they mean.

Your, and my, ignorance concerning the design and construction of the human body cannot be measured.

It would be no different than the first non-chihuahua producing a chihuahua.

The 'birds will always produce birds' claim went south in a hurry, didn't it?

 

[Loudmouth]

What kind of evolution...you're attempting to use it as a monolithic term again? You'd have to ask the designer. I doubt you'd understand though.

Again with the semantics. You simply don't have the basic knowledge necessary to discuss the topic.

You've designed organisms? Do you even know what you're saying?

Yes. Do you?

Here is an explanation of how recombinant human insulin is made:

How did they make insulin from recombinant DNA?

They designed an E. coli strain with an exact copy of a human gene (i.e. the exons from the human gene). This is an obvious and clear violation of the nested hierarchy, and humans did it with ease. There is absolutely no reason why God would be more limited than humans are, so why would God be limited to a nested hierarchy when humans are not?

Your, and my, ignorance concerning the design and construction of the human body cannot be measured.

Are you ignorant of where babies come from? They don't come from a designer.

The 'birds will always produce birds' claim went south in a hurry, didn't it?

No, it didn't. The descendants of birds will always be birds.

The only thing going south is your understanding of cladistics.

 

[JacksBratt]

Not how science works, that is how the fundy mind works.

What's a "fundy"?

 

[Loudmouth]

What's a "fundy"?

Go grab an object with a large reflective surface . . .

 

[sfs]

sfs posed: "Also, you refuse to say what happens to a mutation that truncates a crucial protein. Is it passed on or not? Why can't you answer this question?"

The Dystrophin gene is one classic example. By the data posted previously (Split Rock, I seem to recall), 2/3 of these individuals reproduce, thus passing along the defect. Now, I wonder how many millions of years supposed Natural Selection will take to eliminate this defect from the human genome. NS is not a magic genie, wizard or god. It has major limitations that keep getting glossed over by evolutionists.

Yes, 2/3rds of those who have a defective copy of the dystrophin gene do reproduce: the 2/3rds that are women. What happens to those copies? Let's use a simple model: each woman has on average 1 son and 1 daughter (pretty close to accurate for most of human history, and not terribly bad even now). With 1 son and 1 daughter, there's a 25% chance the woman will not pass on the defective copy to either child, 25% chance the son gets it, 25% the daughter gets it and 25% both do. If the son gets it, he will die without reproducing. So 50% of the time, a defective gene in a woman goes no further. If the daughter does get the defective copy, she again has a 50% chance of passing it on to a daughter. The probability that the defective copy still exists in a woman declines by 50% every generation: 100%, 50%, 25%, 12.5%. The sum of the series 1 + 1/2 + 1/4 + 1/8... is 2. So on average, the defective gene persists in a reproductive individual for 2 generations.

Two generations takes a good deal less time than millions of years.

 

[WisdomSpy]

Loudmouth said: “How many 300+ base pair open reading frames do you get in a 100,000 base genome? I got 25 of them. I added up the bases in the ORF's and got about 8,300 coding bases. 8k out of 100k is 8% which is even higher than the human genome.”

O.K., the numbers I arrived at previously were somewhat similar. Your numbers showed that on average, around 4000 molecules would be used in order to produce one “gene” of 100 codons. My number was a bit over 6000. (Not worth quibbling about.) But your comparison to the human genome is completely illogical. Why? The average length of gene in humans is several orders of magnitude higher than this. You can’t even make a hemoglobin molecule with only 100 codons. Also, all evidence suggests that a free-living life form of any kind would need at least 1500-2000 genes in order to confer independence of metabolism and reproduction capacity.

Take the next step and see how many molecules would be used up, on average, when trying to generate a potential gene of 500 codons (1500bp)—a very average size for numerous ‘primitive’ cells.

 

[WisdomSpy]

sfs posted: "So on average, the defective gene [dystrophin] persists in a reproductive individual for 2 generations.

Any gene persists in a reproductive individual until they die. I think you must have meant that a defective gene persists in a given lineage... for two generations, if real life conformed to your calculations. Several problems exist: first, if she had nine children, which is quite common in undeveloped cultures, the math is off. Further, you are assuming a 100% selection pressure--i.e. that all boys die without reproducing. These boys frequently live to be 30y/o, sometimes more. The average age of sexual "debut" today is 14 and 1/2. I have seen a pregnant 9-year-old. Granted, the father was not likely to have been a 9-year-old, nor a DMD sufferer. It's not completely unthinkable, however.

The point you seem to be missing, related to this gene, is that it is outrageously long--something that cannot even be modeled without computers far advanced of what I own. The natural appearance of stop codons under any kind of modeling should have prevented this gene from ever coming into existence. And its huge length means that it is more prone to being damaged by random mutations--that's why is keeps showing up over and over again in human populations. This fact regarding its length should make everyone wonder about its origins. Every mutation of it that I am aware of effectively results in a shortened gene and product. It does not make sense to believe that this gene was created originally by random mutations.

Also, there are certainly many better examples of defective genes which are not associated with very high selection pressures, if any at all. Considering cancer rates observed in humans, it would seem rational to conclude that our genomes are gradually accumulating more and more defects rather than removing them by NS. This begs the question, then, of what the original genome may have looked like. The creationist paradigm would start with a "very good" (perhaps perfect or near-perfect) genome which has subsequently been acted upon by numerous mutations and sometimes by a degree of selection. Trying to look retrospectively and discern which areas are which is a very difficult proposition, however (especially if one is committed to purely evolutionary presuppositions).