Evolution/Creation on Trial

[Smidlee]

It's called genetic recombination, and it is the reason why sex is an advantageous strategy.

https://en.wikipedia.org/wiki/Genetic_recombination



He is trying to sell an idea without having the evidence to back it up. What exactly do you think "makes more sense" with respect to the mechanisms that Shapiro has proposed?

That's pretty normal for evolutionist. They come up with nonsense all the time without evidence. Genetic recombination doesn't automatcially remove the bad mutations.

Are you still referring to the central dogma of DNA->RNA->Protein?

including the "Selfish Gene" idea as well as DNA-R-US.

 

[Loudmouth]

Hello all.

A random event, how do we know there can be such a thing as a random event, in the first place?

For mutations, this was already answered by two experiments done back in the 50's and 60's.

https://en.wikipedia.org/wiki/Luria–Delbrück_experiment

http://home.earthlink.net/~dayvdanls/replica_plating.htm

They found that beneficial mutations occurred in the absence of the environment where they would be beneficial. For example, they found that mutations that conferred antibiotic resistance occurred in cultures that didn't have antibiotics.

Since then, we have a much better understanding of the mechanisms that cause mutations. As the earlier experiments demonstrated, there is no mechanism whereby a specific mutation is produced in response to a specific stimuli. At best, organisms can increase the rate at which they produce random mutations in hopes of finding a beneficial mutation. To use an analogy, the lottery is still random even if poor people buy more tickets than rich people.

Not sure if we know enough at all, to be able to specify that any event whatsoever, could be a random event.

We do. We can even look at the interaction of DNA and the proteins that copy DNA.

Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15803-8. Epub 2005 Oct 25.

Probing the active site tightness of DNA polymerase in subangstrom increments.

Kim TW, Delaney JC, Essigmann JM, Kool ET.

We describe the use of a series of gradually expanded thymine nucleobase analogs in probing steric effects in DNA polymerase efficiency and fidelity. In these nonpolar compounds, the base size was increased incrementally over a 1.0-A range by use of variably sized atoms (H, F, Cl, Br, and I) to replace the oxygen molecules of thymine. Kinetics studies with DNA Pol I (Klenow fragment, exonuclease-deficient) in vitro showed that replication efficiency opposite adenine increased through the series, reaching a peak at the chlorinated compound. Efficiency then dropped markedly as a steric tightness limit was apparently reached. Importantly, fidelity also followed this trend, with the fidelity maximum at dichlorotoluene, the largest compound that fits without apparent repulsion. The fidelity at this point approached that of wild-type thymine. Surprisingly, the maximum fidelity and efficiency was found at a base pair size significantly larger than the natural size. Parallel bypass and mutagenesis experiments were then carried out in vivo with a bacterial assay for replication. The cellular results were virtually the same as those seen in solution. The results provide direct evidence for the importance of a tight steric fit on DNA replication fidelity. In addition, the results suggest that even high-fidelity replicative enzymes have more steric room than necessary, possibly to allow for an evolutionarily advantageous mutation rate.
http://www.ncbi.nlm.nih.gov/pubmed/16249340​

What that all means is that mutations are caused by a loose fit between the active site of the proteins that copy DNA and the bases that are used to make new strands of DNA. We have the experiments to back it up. We also understand the types of physical damage that DNA takes from things such as chemical carcinogens and ionizing radiation.

An incoming UV photon doesn't know which mutation an individual organism needs in order to adapt to a given environment, so how could this mechanism be non-random?

 

[Loudmouth]

That's pretty normal for evolutionist. They come up with nonsense all the time without evidence. Genetic recombination doesn't automatcially remove the bad mutations.

It is part of the process. Genetic recombination is able to separate the bad mutations from the good mutations, and allows bad mutations to be selected against independently of the good mutations. It does exactly what you were asking for.

including the "Selfish Gene" idea as well as DNA-R-US.

Then please explain why humans and chimps look different if it isn't due to differences in the sequence of our genomes.

 

[Astrophile]

Speaking of light speed, it is only constant in a vacuum. Space is not even close to a perfect vacuum.

It is a great deal closer than anything that can be produced on Earth; most of the volume of the interstellar medium contains only 1000 hydrogen ions per cubic metre, which implies a density of about 2E-24 kg/m³. What are your reasons for thinking that the speed of light in the interstellar medium differs significantly from the speed of light in a perfect vacuum, and how close to a perfect vacuum do you want space to be?

 

[Smidlee]

It is part of the process. Genetic recombination is able to separate the bad mutations from the good mutations, and allows bad mutations to be selected against independently of the good mutations. It does exactly what you were asking for.

Sex doesn't work in evolution favor even in the lab. They did experiment a few years on fruit flies and genetic recombination (sex) reveal resistance to change.

Then please explain why humans and chimps look different if it isn't due to differences in the sequence of our genomes.

Caterpillar looks different from a butterfly and it's uses the same DNA.

 

[Loudmouth]

Sex doesn't work in evolution favor even in the lab. They did experiment a few years on fruit flies and genetic recombination (sex) reveal resistance to change.

Sex does exactly what you were asking for. This is the challenge you put forward:

"Then you got the problem of how to get weed out all those bad mutations without throwing out the few beneficial ones."

The solution is genetic recombination which separates the bad mutations from the good mutations by putting them in different halves of the diploid genome during meiosis. With meiosis and sex, you can pass on good mutations without passing bad mutations that were previously linked on the same chromosome. This allows for selection against the bad mutations without also selecting against the good mutations. It solves the very problem you brought up.

Caterpillar looks different from a butterfly and it's uses the same DNA.

Caterpillars and butterflies are not different species. Different species of caterpillars look different. Why? Different species of butterfly look different. Why?

 

[Smidlee]

Sex does exactly what you were asking for. This is the challenge you put forward:

"Then you got the problem of how to get weed out all those bad mutations without throwing out the few beneficial ones."

The solution is genetic recombination which separates the bad mutations from the good mutations by putting them in different halves of the diploid genome during meiosis. With meiosis and sex, you can pass on good mutations without passing bad mutations that were previously linked on the same chromosome. This allows for selection against the bad mutations without also selecting against the good mutations. It solves the very problem you brought up.

You do realize that you inherit and pass on both good mutations and bad. It's the same a brown eye person can have the blue mutation and can even pass it on to have a blue eye baby.

Caterpillars and butterflies are not different species. Different species of caterpillars look different. Why? Different species of butterfly look different. Why?

Of course we know that because they are living today. So two different body plans can be produced by the same DNA.

 

[Loudmouth]

You do realize that you inherit and pass on both good mutations and bad. It's the same a brown eye person can have the blue mutation and can even pass it on to have a blue eye baby.

You aren't comparing a bad allele for one gene to a good allele for a different gene.

Let's say blue eyes were bad, and type A blood is good. You are arguing that if someone has both blue eyes and type A blood that you can't select against blue eyes without also getting rid of type A blood. This isn't true. Due to shuffling during meiosis, it is possible to get blue eyes and type B blood on a single strand of DNA where they can both be selected against while putting brown eyes and type A blood on the same strand of DNA where they can be positively selected.

Of course we know that because they are living today. So two different body plans can be produced by the same DNA.

They are both bilaterian body plans. Is a fetus a different body plan than an adult human? Is an acorn a different plant than an oak tree?

What you still don't have is an explanation for the differences observed between adult members of two different species.

 

[Smidlee]

You aren't comparing a bad allele for one gene to a good allele for a different gene.

Let's say blue eyes were bad, and type A blood is good. You are arguing that if someone has both blue eyes and type A blood that you can't select against blue eyes without also getting rid of type A blood. This isn't true. Due to shuffling during meiosis, it is possible to get blue eyes and type B blood on a single strand of DNA where they can both be selected against while putting brown eyes and type A blood on the same strand of DNA where they can be positively selected.

Of course in this situation you have bad/good mutations at 50% which is unrealisitc.

They are both bilaterian body plans. Is a fetus a different body plan than an adult human? Is an acorn a different plant than an oak tree?

What you still don't have is an explanation for the differences observed between adult members of two different species.

Again we know this because we can study them alive. A caterpillar transforming into a butterfly is not like an acorn become a tree. We have evidence of different body plans can come from the same DNA. If chimps DNA were 100% identical to man's it wouldn't automatically mean the chimp would be a scientist.

 

[Justatruthseeker]

I know of no DNA repair mechanisms that take DNA elsewhere in the genome and use it as a template for duplicating DNA in another part of the genome. Many repair mechanisms don't even require a template. Of those that do use template, they use the complementary base on the other strand, the one directly across from it.

Who said anything about taking DNA from one spot to another except you in your strawman?

Apparently you are unaware of what compare to means? Instead you want me to believe that a repair mechanism is supposed to use it's own damaged DNA to know how to repair itself? Or is that Junk DNA merely blueprints - in which to compare against when repairing the damaged strand. Last I checked experts use repair manuals when repairing complicated things.

They don't have a clue as to what's going on. The one directly across from it is not an exact copy - or have you forgotten that one strand is from the female - and the other from the male? I mean really, is this what you believe or want people to believe - that the other strand is a copy in which the repair mechanism compares one side to the other??

Name one that doesn't use a template and prove it.

None of this has anything to do with ENCODE's definition of functional. If a stretch of DNA is transcribed to RNA at low levels, what does that have to do with DNA repair? How does being transcribed indicate that the RNA molecule does anything that impacts the fitness of the individual?

"The problem comes from the fact that ENCODE looked for chemically active parts in the DNA and called those parts "functional." Not all of that activity is necessarily important for human life, however. For example, ENCODE scientists looked for DNA regions that bind to proteins, because such binding is essential to opening, reading and bookmarking DNA. But a region can also bind proteins without affecting human health. The human genome is full of DNA picked up from viruses in our evolutionary past. Sequences that don't harm or help their hosts may still contain regions that bind to proteins or do other things without affecting cell function."

And they may not too, correct? The real truth is NO ONE KNOWS.

If that were true, then why don't we see a signal of sequence conservation in junk DNA? Why is 90% of the human genome accumulating mutations at a rate consistent with neutral drift?

What, you think the human genome is going to remain the same when breed mates with breed producing new breed by the recombination of genes and new dominant and recessive traits? They ain't mutations - they are the normal transcription process when two genes are joined. You can tell when mutation occurs.

You deny the evidence demonstrating that humans and chimps share a common ancestor.

What evidence, incorrectly labeled fossils?

At one time there were just wolves. Now there are wolves and huskies. Where did the huskies come from?

From those several breeds of wolves that existed. Breed mates with breed. Before that back to the original two wolves which contained every genetic combination that exists today within their genes - half in one - half in the other.

"As of May 2015, genetic analyses indicate that the Taymry wolf diverged from the ancestor of the dog/modern gray wolf 40,000 years ago, with the Taymry wolf being classified as Canis lupus because it was found to be substantially closer to modern gray wolves than it was to coyotes. Shortly after, the dog/modern gray wolf ancestor diverged into 2 sister clades formed by the ancestral dog and the ancestral modern gray wolf."

"Dogs arrived with the first humans to the New World within this timeframe. Some Arctic dog breeds show a genetic relationship to the Taymry wolf, indicating admixture before the Taymry wolf became extinct".

So before the Taymry wolf became extinct, it mated with other breeds of the same species, or else admixture could not have occurred. They did not magically evolve.

Those creatures would be humans and chimps. We share a common ancestor. I have given you the genetic evidence. We also have the transitional fossils.

You showed me ERV's which are one and all foreign to the host and are known to carry genes across species lines. You just ignore the fact they are known to do this, because you don't want it to be true.

You have shown me incorrectly classified fossils you claim are transitory. I claim they are either separate species completely, and in some cases merely just a different breed - not a different species.

You have again ignored man's eagerness to get his name in the books as a discoverer of a new species - so they named everything a new species. When all you got is different breeds of one species. I asked you all before to first correct the problems in classification. Until you remove those half-dozen from the books, there is no sense talking about what's fact and what isn't.

http://www.theguardian.com/science/2013/oct/17/skull-homo-erectus-human-evolution

H. erectus is not H. sapiens.

Of course they are not the same breeds, just like a Husky isn't a Mastiff and an Asian isn't an African.

Where did the huskies come from?

you were told that above if you read.

""some Arctic dog breeds show a genetic relationship to the Taymry wolf, indicating admixture before the Taymry wolf became extinct"."

So before the Taymry wolf became extinct, it mated with other breeds of the same species, or else admixture could not have occurred. They did not magically evolve.

 

[Loudmouth]

Of course in this situation you have bad/good mutations at 50% which is unrealisitc.

I didn't give any such values.

Again we know this because we can study them alive. A caterpillar transforming into a butterfly is not like an acorn become a tree. We have evidence of different body plans can come from the same DNA. If chimps DNA were 100% identical to man's it wouldn't automatically mean the chimp would be a scientist.

Why are butterflies different from each other?

 

[Smidlee]

I didn't give any such values.



Why are butterflies different from each other?

Why are human being different from each other?

 

[klutedavid]

Hello Loudmouth.

You made a claim in response to my initial question.

Your claim that a random event is possible, was based on the following information.

The Luria–Delbrück experiment (1943) (also called the Fluctuation Test) demonstrates that in
bacteria, genetic mutations arise in the absence of selection, rather than being a response
to selection. Therefore, Darwin's theory of natural selection acting on random mutations...
Wikipedia

Well there appears to be an assumption in this article.

The assumption is of course, that the mutations of bacteria can be random events.

Just because a mutation that occurs and is not a selection event, in no way implies, that
mutation events are random events.

The word 'random', infers no specific pattern, purpose, or objective.

There may very well be a pattern, a purpose and an objective, in every single mutation.

Just because we observe no pattern in some mutations, does not mean there is no insitu
pattern.

Once again, how do we ultimately know whether any event is a random event?

 

[bhsmte]

Why are human being different from each other?

Can't answer his question?

 

[Smidlee]

Can't answer his question?

Can't answer mine?

 

[justlookinla]

Can't answer mine?

They don't have an answer.

 

[Loudmouth]

Who said anything about taking DNA from one spot to another except you in your strawman?

You did.

"You mean a definition that makes the most sense. You just fail to realize backup programs when you see them. To what does the DNA repair mechanism use to repair DNA?"--Justatruthseeker

Instead you want me to believe that a repair mechanism is supposed to use it's own damaged DNA to know how to repair itself? Or is that Junk DNA merely blueprints - in which to compare against when repairing the damaged strand. Last I checked experts use repair manuals when repairing complicated things.

And there it is again.

Junk DNA is not used as a template for DNA repair.

I mean really, is this what you believe or want people to believe - that the other strand is a copy in which the repair mechanism compares one side to the other??

"Translesion synthesis (TLS) is a DNA damage tolerance process that allows the DNA replication machinery to replicate past DNA lesions such as thymine dimers or AP sites.[31] It involves switching out regular DNA polymerases for specialized translesion polymerases (i.e. DNA polymerase IV or V, from the Y Polymerase family), often with larger active sites that can facilitate the insertion of bases opposite damaged nucleotides."
https://en.wikipedia.org/wiki/DNA_repair#Translesion_synthesis

Name one that doesn't use a template and prove it.

"Cells are known to eliminate three types of damage to their DNA by chemically reversing it. These mechanisms do not require a template, since the types of damage they counteract can occur in only one of the four bases."
https://en.wikipedia.org/wiki/DNA_repair#Direct_reversal

And they may not too, correct? The real truth is NO ONE KNOWS.

We do know that functional DNA should show sequence conservation because of detrimental mutations. Only 10% of the human genome shows evidence of sequence conservation.

What, you think the human genome is going to remain the same when breed mates with breed producing new breed by the recombination of genes and new dominant and recessive traits? They ain't mutations - they are the normal transcription process when two genes are joined. You can tell when mutation occurs.

That's word salad. Perhaps you could try including some real science?

What evidence, incorrectly labeled fossils?

Where did you show that any H. erectus fossil was incorrectly labeled as transitional?

From those several breeds of wolves that existed.

Where did those breeds come from?

Before that back to the original two wolves which contained every genetic combination that exists today within their genes - half in one - half in the other.

Evidence?

"As of May 2015, genetic analyses indicate that the Taymry wolf diverged from the ancestor of the dog/modern gray wolf 40,000 years ago, with the Taymry wolf being classified as Canis lupus because it was found to be substantially closer to modern gray wolves than it was to coyotes. Shortly after, the dog/modern gray wolf ancestor diverged into 2 sister clades formed by the ancestral dog and the ancestral modern gray wolf."

There you go. The Taymry wolf evolved from the gray wolf, not because of two breed mates producing them.

You showed me ERV's which are one and all foreign to the host and are known to carry genes across species lines.

You have never shown that they carry host genes across species lines.

You have shown me incorrectly classified fossils you claim are transitory.

Why did they stop being transitional when they were correctly classified as H. erectus?

You have again ignored man's eagerness to get his name in the books as a discoverer of a new species - so they named everything a new species. When all you got is different breeds of one species. I asked you all before to first correct the problems in classification. Until you remove those half-dozen from the books, there is no sense talking about what's fact and what isn't.

Why does being part of the same species stop fossils from being transitional?

 

[whois]

finally, could someone answer the question about how the first life could have got started all on its own without any divine intervention. In particular, where all the information came from to start life and build the first self-reproducing cell and how the problem of chirality could have been overcome in such a process.

koonin sums this up quite nicely with the following:
The origin of life is one of the hardest problems in all of science, but it is also one of the most important. Origin-of-live research has evolved into a lively, interdisciplinary field, but other scientists often view it with skepticism and even derision. This attitude is understandable and, in a sense, perhaps justified, given the “dirty” rarely mentioned secret: Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the ultimate goal, the origin of life field is a failure – we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth. Certainly, this is due not to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle.

- Eugene V. Koonin, molecular biologist, The Logic of Chance: The Nature and Origin of Biological Evolution (Upper Saddle River, NJ: FT Press, 2011), 391

 

[The Cadet]

Notice your video assumes most mutation are completely random but what if, as even James Shapiro pointed out, they are not random at all.

If you are going to cite research, please actually cite it. Don't just vaguely assert "Scientist X sez" and make me do all the legwork. I couldn't find the peer-reviewed paper where Shapiro claimed that mutations are non-random; what I did find was numerous people pointing out that he's kind of a crank. The idea that mutations are fundamentally non-random is unsupported and makes no sense given the paradigm of how mutations are formed, and there are numerous experiments (such as bacteria gaining antibiotic resistance genes through mutation despite no exposure to that antibiotic) that show just how random it is.

But even if the mutations weren't completely random, it should still form a nested hierarchy fairly consistently. And hey - the methods for this are all really easy. There's a ton of cladogram programs online (the video cited one, and others are a quick google search away), and you can play around with making X% of the mutations non-random to see where the threshold is. Would be an interesting (if rather pointless) experiment. I strongly encourage you to actually do the legwork to back up your claims, rather than to just throw them out apropos of nothing.

You also don't explain why evolution would produce the nested hierarchy you only assume it.

The explanation is that descent with modification necessarily leads to a single natural cladogram which is the most parsimonious that will line up with the descent. We have the mathematical models to prove this, as detailed in the video. This is not some assumption, this is a proven mathematical theorem.

 

[bhsmte]

Can't answer mine?

Usually and I don't know about you, but when one person asks a question first, that would be the first question to be answered. If you are not willing to answer a simple question, why would you expect anyone to answer yours?