Evolution/Creation on Trial

[Loudmouth]

"If ENCODE is right then Evolution is Wrong."

Why can't ENCODE be right and Evolution be right?

Let's break this down. ENCODE says that 80% of the human genome has some sort of biological activity, which you are calling "function". Evolution says that about 10% of the human genome has DNA sequence specific function which impacts human fitness. So can parts of the genome have biological activity but not impact human fitness in a sequence dependent manner?

The answer is yes. A section of junk DNA can have biological activity in the form of low copy transcription. That biological activity can also have no impact on human fitness with respect to the sequence of those RNA molecules.

In other words, both ENCODE and evolution can be right since they are not talking about the same thing.

 

[Smidlee]

Why can't ENCODE be right and Evolution be right?

Lol. Ask Graur that.

 

[bhsmte]

Lol. Ask Graur that.

Why ask only him?

 

[Smidlee]

It misses so many obvious points it's comical. It then presupposes that what did happen didn't. And never offers an alternative.

Why do you need an alternative to compete nonsense?

Why ask only him?

What do you think I was referring to?

 

[Loudmouth]

because your faith is greater than mine. You have no evidence at all . . .

I just showed you the evidence. It is a nested hierarchy of shared and derived features.

Oh, so those similar appearances means related, but similar appearance of design is just illusion?

Nope. That's not it at all. If you were to find multiple fossil or living species that had derived features from both mammals and birds, then I would conclude that it is evidence against evolution. It isn't the mere fact of shared features that evidences evolution.

Want to try again? I will give you a hint. It starts with a p . . . and ends with hylogeny.

Then why so eager to list all those things that are similar as separate things? Shared and derived features you share with every human being. The rest is just illusions.

We are talking about shared and derived features shared between different species.

Yes you do have a lot of ERV's. ERV's which are one and all foreign to the host (us, monkeys, every animal) and which carry foreign genomes across species lines.

You haven't produced a single reference showing how ERV's take host DNA from one species and put it into another species.

"But all agree that the exchange of genetic information across species lines — which is how we will define LGT in this primer — is far more pervasive and more radical in its consequences than we could have guessed just a decade ago."
http://www.cell.com/current-biology/abstract/S0960-9822(11)00101-1?_returnURL=http://linkinghub.elsevier.com/retrieve/pii/S0960982211001011?showall=true

ERV's aren't even mentioned in that article, and none of what you describe disqualifies ERV's as valid genetic markers for determining common ancestry.

I have explained this time and again, and you never respond to them. Perhaps this time you will?

So do you actually expect me to believe that a retrovirus that forms a defense against specific genetic sites, would not pass those defenses to its offspring, and those offspring would not seek out sites to which they already have a defensive mechanism against? Of course they attach at the same sites - they have defenses for those sites already in place.

That is word salad. Do you even understand what a retrovirus is? A retrovirus is an RNA based virus that reverse transcribes (i.e. retro-) the RNA viral genome into DNA. It then inserts that DNA randomly within the host genome. ERV's are the remnants of those insertions. Since the insertion happens randomly among billions of bases, the chances of two different insertion events happening at the same base are very low. Therefore, when you find the same ERV at the same base in two genomes, the best explanation is that the insertion happened once in a common ancestor.

 

[The Cadet]

ENCODE did use a "different" definition for function.

Yes, a definition of function that makes very little sense.

Another thing ENCODE did was go in without an a priori evolutionary mindset. They went into it with no preconceived evolutionary concepts. Thus, the reason for many Scientists to dismiss what they had to present.

without addressing the issue of gene conservation (a matter of natural selection at the micro level, which I think not even you would deny), calling 80% of the genes "functional" is nonsensical. A gene which is not well-conserved is necessarily a gene which did not fulfill any significant non-redundant function. This is why we talk about evolution being the current paradigm in biology. It's like if you try to study the epidemiology with AIDS without having an a priori germ theory mindset - you're going to come up with some nonsensical results and miss some very important points. Science builds on what we already understand.

The biggest problem with ENCODE (scientists worked very hard on this project) was that they were part of a circus designed to garner great interest in BiG Science. [...] The Media circus caused a great deal more controversy than should have occurred and it ultimately will hurt the small research arenas that garner great advances in Science.

I can definitely agree on that one.

Actually it is not 55 million years which has always been considered the required amount of time according to materialists for this evolution to occur. However, you must be unfamiliar with the discovery of fossil evidence that drops that 55 million down to around 3 to 5 million years. Which sounds like a lot of time but considering the evolutionary models it is hardly a blink of an eye.
http://news.nationalgeographic.com/...tica-whales-oldest-evolution-animals-science/

Based on 53-million-year-old fossils of whale-like, semi-aquatic mammals, scientists had thought mammals gave rise to whales in a process that took 15 million years. The new find suggests it took just 4 million years. (See a prehistoric time line.)

Okay, my mistake, I did not know the research. So 3-5 million years. I repeat my previous question - is there any published research making the case that this somehow cannot happen? I don't mean some video by a creationist, I mean actual published research indicating that this is somehow unlikely or impossible.

But only someone blinding themselves to the truth could ignore that clear hierarchy in each distinct class of cars all the way back to the first.

You say that only a blind man could ignore the hierarchy. But see, the nice thing about modern phylogenetics is that it's not subjective - you could demonstrate this even to a blind man. You find a set of criteria by which to measure phylogeny. These criteria should be points where various samples on your tree share similarities and difference - for example, in anatomy, some good traits might be the shape of the skull, whether the organism is bilateral or not, whether the organism exhibits a spinal column or not, whether the organism's blood carries oxygen via hemoglobin or hemocyanin, et cetera. Then you start building your cladogram based on which traits the organisms exhibit and which don't. How close any given organism is to another is not some "take a guess" issue, it can be calculated, and once we include DNA in the mix (obviously not an option with cars), we have robust mathematical models to determine the most parsimonious sequence of vertical gene transfer, horizontal gene transfer, and mutation.

But back to cars. Unfortunately, I could not find a tool for building automatic phylogenies that worked off of taxonomic traits; however, it should be pretty simple to construct your own parsimonious cladogram for automobiles showing this structure. With that in mind: please provide this hierarchy. You hold this up as something trivial, so clearly you understand the issue better than I do (and in case you feel like you need to brush up on it, here's an excellent resource on the subject). So show your work. Show how the Camaro line of cars forms a nested hierarchy.

I don't consider it in any way "obvious", and given that your picture displays the outside of a series of designed objects that may be completely and utterly different on the inside, it seems to be a fairly disingenuous example.

I'll save you the trouble. You cannot form a consistent cladogram with automobiles. Whether a car has power steering has no relation to whether or not it has air conditioning, or leather seats, or takes diesel or unleaded, or is a V4, V6, or V8, or has a fin sticking out the back, or has the gas cap on the left or the right, whether it has a turbo drive, whether it has anti-lock brakes... Almost nothing that makes up a car has any correlation to anything else beyond the core structure. Meanwhile, if you find an animal that lactates, you will for some reason find that it always exhibits, at least vestigially, the following traits:

• Warm blood
• Body Hair
• Live birth of young
• Bifurcated at the spinal column
• Internal skeleton
• Red blood
• Four limbs

Furthermore, it will never exhibit any of the following traits:

• Avian feathers
• Cold blood
• Radial symmetry
• An exoskeleton
• Hollow bones

With cars, we see something completely different: features shoved here and there all over the place, with absolutely no consistency. If I tell you "My car has a bit of its motor sticking out of the top", what can you tell me about my car? Can you even determine what company made it, or exclude any company? And that's a relatively specific trait! Never mind things like "has a CD player" or "has FWD", which don't line up with anything, and are randomly present or missing all over the cladogram in a way that totally skews any attempt at parsimony.

"If ENCODE is right then Evolution is Wrong." Now he didn't prove the evidence was wrong

...Did you watch the slideshow or just ignore it?

 

[Smidlee]

...Did you watch the slideshow or just ignore it?

I already knew he reject the evidence and goes against the majority of molecular biologist. You know how much evolutionist love to be in the majority.

He doesn't accept the data to determine what is functional but his own bias.

By the way James Shapiro was one who doesn't support ID yet rejected Junk DNA ten years ago. ENCORE results were exactly what he predicted.

 

[Justatruthseeker]

Yes, a definition of function that makes very little sense.

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? A code that if mutated would become useless? Or another strand of disabled DNA so that it does not undergo mutation and can be compared to, to complete the DNA repair process? That junk DNA is about as junk as are the backup programs for reinstalling when the system becomes corrupted by those viruses.

without addressing the issue of gene conservation (a matter of natural selection at the micro level, which I think not even you would deny), calling 80% of the genes "functional" is nonsensical. A gene which is not well-conserved is necessarily a gene which did not fulfill any significant non-redundant function. This is why we talk about evolution being the current paradigm in biology. It's like if you try to study the epidemiology with AIDS without having an a priori germ theory mindset - you're going to come up with some nonsensical results and miss some very important points. Science builds on what we already understand.

Who denies breed mating with breed producing new breeds by the recombination of genes and new dominant and recessive traits except evolutionist's? And then pretend they see evolution by mutation and species changing into other species in the fossil record.

You say that only a blind man could ignore the hierarchy. But see, the nice thing about modern phylogenetics is that it's not subjective - you could demonstrate this even to a blind man. You find a set of criteria by which to measure phylogeny. These criteria should be points where various samples on your tree share similarities and difference - for example, in anatomy, some good traits might be the shape of the skull, whether the organism is bilateral or not, whether the organism exhibits a spinal column or not, whether the organism's blood carries oxygen via hemoglobin or hemocyanin, et cetera. Then you start building your cladogram based on which traits the organisms exhibit and which don't. How close any given organism is to another is not some "take a guess" issue, it can be calculated, and once we include DNA in the mix (obviously not an option with cars), we have robust mathematical models to determine the most parsimonious sequence of vertical gene transfer, horizontal gene transfer, and mutation.

Such as say similarities in breeds within each species, be they Husky and Mastiff or Asian and African shall we say? Or similarities with Finches that all interbreed as well? Are these the similarities you are discussing? Or were you discussing similarities in design with that bilateral symmetry. Or were you discussing bacteria that match their billion year old cousins that have never evolved in all this time? Similar to E. coli experiments where even after billions of forced mutations - most of which killed them, they finally ended up with guess what, E. coli.

Are those the similarities you meant?

You can't form those claims with living matter - without adding Fairie Dust. I'm still waiting on one single example of the creatures that split into both pathways on whatever tree you choose to use for whichever species you care to name. You can show me different breeds of one species or another, extinct or not and call them transitional all you want and mix up where they belong, but you will never find the claimed species where the claimed lineage split. Because it never did.

From the youngest T-Rex to the oldest T-Rex fossil - all T-Rex. From the oldest Husky bones to the youngest Husky bones - all Husky. From the oldest Asian bones - to the youngest Asian bones - still Asian. Only when breed mates with breed and the genome is recombined into new dominant and recessive traits (becomes one again) - does anything new appear in the record.

No one is ignoring the empirical observations but those that claim evolution.

 

[Justatruthseeker]

With cars, we see something completely different: features shoved here and there all over the place, with absolutely no consistency. If I tell you "My car has a bit of its motor sticking out of the top", what can you tell me about my car?

I can tell you more than likely its a blower - and still of the same make and model, even though you claim it's a separate make and model now that it has a blower on top. So even if you know it's the same make and model, you've chosen to describe the new occurrence as a separate make and model. I can also tell you none of those parts were a random addition - but all put in place in a specific order to function as a whole. Or it wouldn't be a car would it.

You see - when things are actually of a different make and model - parts don't fit from one to the other. Just as an Asian can still interact with an African and produce an Afro-Asian - because they are all of the same make and model, just add-ons in some places and other things moved to the background (dominance and recessive). All working with more precision than any car ever made.

 

[The Cadet]

I don't know why I bothered trying. Of course you're not going to actually do the legwork and prove what you were saying right. Of course you're not going to apply the well-established scientific methods to demonstrate that automobiles fall into a nested hierarchy. Of course you're just going to repeat your assertions without providing any evidence. Look, I'm sorry, but we have well-established methods for determining whether things fall into parsimonious nested hierarchies in relation to their morphology. These methods should be very straightforward to adopt to automobiles.

And no, even if I tell you my car has a blower, you still cannot tell me very much about the rest of the car, because blowers have been produced by virtually all the major car companies, because they've been put in various completely different forms of cars for completely different reasons (cosmetics vs. utility) and the other features those cars had were almost completely non-dependent, whereas in the nested hierarchy of life, the features found in organisms are completely interdependent. You will never find a mammal without red blood or bilateral symmetry. This parsimonious pattern of similarities and differences is a dead ringer for descent with modification, but makes no sense when we compare it to designed objects. You disagree? Make a cladogram for those camaros. I told you exactly how to prove me wrong (in such a way that should be very trivial if your claims are true) and your response was to completely ignore the challenge.

 

[Smidlee]

And no, even if I tell you my car has a blower, you still cannot tell me very much about the rest of the car, because blowers have been produced by virtually all the major car companies, because they've been put in various completely different forms of cars for completely different reasons (cosmetics vs. utility) and the other features those cars had were almost completely non-dependent, whereas in the nested hierarchy of life, the features found in organisms are completely interdependent. You will never find a mammal without red blood or bilateral symmetry. This parsimonious pattern of similarities and differences is a dead ringer for descent with modification, but makes no sense when we compare it to designed objects. You disagree? .

This is an argument from ignorance as the articles I being referring to by Howard Glicksman reveals "real numbers have real consequences." Again there is no reason for evolution to produce nested hierarchy as Denton points out the line between fish, reptile and mammals are too good it someone expects "random mutation plus natural selection" to be true. The whale and dolphin according to evolutionist did some serious changes but magically kept their mammal features so we could easily classify them. Evolutionist can no more explain (or predict) why "evolution" would produce the nested hierarchy as why evolution would cause a caterpillar to transform into a butterfly.

 

[The Cadet]

This is an argument from ignorance as the articles I being referring to by Howard Glicksman reveals "real numbers have real consequences." Again there is no reason for evolution to produce nested hierarchy as Denton points out the line between fish, reptile and mammals are too good it someone expects "random mutation plus natural selection" to be true. The whale and dolphin according to evolutionist did some serious changes but magically kept their mammal features so we could easily classify them. Evolutionist can no more explain (or predict) why "evolution" would produce the nested hierarchy as why evolution would cause a caterpillar to transform into a butterfly.

None of this is cited, I have no idea where you get these claims from, and the last claim, that we doesn't know why evolution produces a clear nested hierarchy is completely false, as even a very simple evolutionary algorithm followed by parsimonious cladogram formation can demonstrate:

Indeed, not only does evolution predict a parsimonious nested hierarchy, it would predict that you could form hierarchies like this fractally - the nested hierarchy for an organism's morphology should line up with the nested hierarchy for any given gene, any given structure, and indeed the entire genome. And it does. This makes no sense in intelligent design. There's simply no reason why intelligent design would show this kind of pattern. But evolution explains it perfectly.

 

[Loudmouth]

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?

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.

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?

A code that if mutated would become useless?

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?

Who denies breed mating with breed producing new breeds by the recombination of genes and new dominant and recessive traits except evolutionist's? And then pretend they see evolution by mutation and species changing into other species in the fossil record.

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

Such as say similarities in breeds within each species, be they Husky and Mastiff or Asian and African shall we say?

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

I'm still waiting on one single example of the creatures that split into both pathways on whatever tree you choose to use for whichever species you care to name.

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.

From the youngest T-Rex to the oldest T-Rex fossil - all T-Rex.

H. erectus is not H. sapiens.

From the oldest Husky bones to the youngest Husky bones - all Husky.

Where did the huskies come from?

 

[Loudmouth]

I can tell you more than likely its a blower -

Could we find a blower on a '67 Camaro and a '10 Camaro? Could we find an absence of a blower on another '67 Camaro? If so, this would put a blown '67 and '10 on the same branch and the other '67 Camaro models on another branch, completely contrary to what you were describing before.

As you can see, cars don't fall into a nested hierarchy.

So even if you know it's the same make and model, you've chosen to describe the new occurrence as a separate make and model.

What we have shown is that two cars from separate makes and models share a same feature that other cars within the same make and model do not share. That would be a clear and obvious violation of a nested hierarchy. Cars don't fall into a nested hierarchy.

We can find several more violations very easily if you are saying that cars should be divided by manufacturer, make, model, and year.

I can also tell you none of those parts were a random addition - but all put in place in a specific order to function as a whole. Or it wouldn't be a car would it.

All you are doing is agreeing with us that intelligent design does not produce a nested hierarchy.

You see - when things are actually of a different make and model - parts don't fit from one to the other.

Yes, they do. You can find the same rims and tires on a Ford and Chevy car, but two different sets of tires and rims on the same model of Chevy car. You can find the same radio in a Dodge and Buick car, but two different radios in two cars of the same Buick model. You can swap tons of different parts all over the place with no restrictions set by a nested hierarchy.

 

[Loudmouth]

Again there is no reason for evolution to produce nested hierarchy . . .

We OBSERVE that evolution produces a nested hierarchy.

"Inbred mouse strains have been maintained for more than 100 years, and they are thought to be a mixture of four different mouse subspecies. Although genealogies have been established, female inbred mouse phylogenies remain unexplored. By a phylogenetic analysis of newly generated complete mitochondrial DNA sequence data in 16 strains, we show here that all common inbred strains descend from the same Mus musculus domesticus female wild ancestor, and suggest that they present a different mitochondrial evolutionary process than their wild relatives with a faster accumulation of replacement substitutions."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800920/

These are mice with a known heritage, and an examination of their DNA produces the expected nested hierarchy. We know that evolution would produce a nested hierarchy because we observe evolutionary mechanisms producing a nested hierarchy.

If you disagree, then please tell us how evolution could take adaptations from mammals and give it to birds.

The whale and dolphin according to evolutionist did some serious changes but magically kept their mammal features so we could easily classify them.

There is nothing magical about inheritance.

 

[Smidlee]

Indeed, not only does evolution predict a parsimonious nested hierarchy, it would predict that you could form hierarchies like this fractally - the nested hierarchy for an organism's morphology should line up with the nested hierarchy for any given gene, any given structure, and indeed the entire genome. And it does. This makes no sense in intelligent design. There's simply no reason why intelligent design would show this kind of pattern. But evolution explains it perfectly.

Notice your video assumes most mutation are completely random but what if, as even James Shapiro pointed out, they are not random at all. You obviously believe in the central dogma which even many biologist now questions. You believe in DNA-R-US belief that genes alone is what make us human.
You also don't explain why evolution would produce the nested hierarchy you only assume it. Why would evolution allow boobs only evolve once while eyes at least 40 times.

 

[Loudmouth]

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

Shapiro fails to demonstrate that mutations are non-random with respect to fitness. What he does is focus on just the beneficial mutations and ignores the neutral and detrimental mutations that those same mechanisms produce.

You obviously believe in the central dogma which even many biologist now questions. You believe in DNA-R-US belief that genes alone is what make us human.

The Central Dogma is DNA to RNA to Protein, and even then biologists accept that retroviruses reverse this order. If you don't believe that the differences between species are explained by differences in DNA sequence within their genome, then I would love to hear what you think are causing those differences.

 

[Smidlee]

Shapiro fails to demonstrate that mutations are non-random with respect to fitness. What he does is focus on just the beneficial mutations and ignores the neutral and detrimental mutations that those same mechanisms produce.

Then you got the problem of how to get weed out all those bad mutations without throwing out the few beneficial ones. Shapiro is not a creationist but at least he trying to make evolution makes sense which you seem to disagree.

Shapiro is not fan of Noe-Darwinism , random mutation plus NS.

The Central Dogma is DNA to RNA to Protein, and even then biologists accept that retroviruses reverse this order. If you don't believe that the differences between species are explained by differences in DNA sequence within their genome, then I would love to hear what you think are causing those differences.

There are already examples that show the central dogma is false.

 

[klutedavid]

Shapiro fails to demonstrate that mutations are non-random with respect to fitness. What he does is focus on just the beneficial mutations and ignores the neutral and detrimental mutations that those same mechanisms produce.



The Central Dogma is DNA to RNA to Protein, and even then biologists accept that retroviruses reverse this order. If you don't believe that the differences between species are explained by differences in DNA sequence within their genome, then I would love to hear what you think are causing those differences.

Hello all.

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

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

 

[Loudmouth]

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

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

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

Shapiro is not a creationist but at least he trying to make evolution makes sense which you seem to disagree.

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?

There are already examples that show the central dogma is false.

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