For Christians (or anyone else) who deny Darwinian evolution.

[Simon Moon]

It simply isn't necessary to posit anything beyond the natural order to explain the existence of our bodies or our minds.

Go ahead...as long as you realize you crossed from science into philosophy when you do. Theories (that contain gaps in our knowledge) don't magically become facts because that's how you decided to approach the problem.

Every single murder investigation, trial and conviction has gaps in knowledge. Let's free all the convicted murderers then, since they have been imprisoned based on philosophy.

Wonder how we ever convict anyone of murder?

[I_am_not_mafia]

I've snipped the crap about definitions of evolution and what one person believes. It's a typical religionist tactic to get the conversation bogged down in irrelevant definitions so people are faced with a wall of text and no one making any progress. It makes it look like the debate is equal when it is not.

Irreducible complexity is flawed. It is understood quite well how complexity develops over time. You are the one claiming that complex organs and traits evolved without any survival benefit until they were complete. No evolutionary scientist claims that, only creationists making strawman debates.

I asked for an example of a partially formed non-functioning ability found in nature. Clearly the current theories indicate there should be some. Isn't that the hallmark of a good theory: predicting?

Learn to read.

Again only creationists claim that there is a glaring lack of fossil records / intermediate forms and they will always claim that no matter how many are found. Very few fossils are made. If we find a missing link then this creates two other missing links that they can claim are a glaring lack. We have plenty of evidence from the fossil records.

Is the theory of Punctuated Equilibrium (developed to explain the lack of transitional forms in the fossil record) true? 

That's not why the understanding of Punctuated Equilibrium came about. Punctuated equilibrium comes about because the evolutionary process is not a steady, linear improvement over time.

The evolutionary process can be considered much like hill walking in fog with the landscape being a fitness landscape. The higher up the population the fitter its members are. But it's a blind ascent which means that a population can get stuck on a local maxima, or a plateau. Note, this is not to insinuate that evolution is a deliberate process, it is something that happens as a form of self organisation.

When a population spreads out randomly on a plateau with each member roughly as fit as each other, the population is effectively exploring that part of the fitness landscape. If there is a way off then the plateau that leads to much higher up on the fitness landscape then this leads to punctuated equilibrium.

A species cannot be considered in isolation though. It is part of a larger ecosystem or environment, and this may suddenly change. So what was once a local maxima or plateau may no longer be that because the fitness landscape changes. The classic example being the peppered moth which evolved from white to black and back to white again because of the industrial revolution.

It just so happens that punctuated equilibrium also explains why some transitional fossils are much harder to find, because they occurred during stages of rapid evolutionary progress.

And before you say that this is not observable or testable, it's a feature of genetic algorithms. We see it happening all the time. I myself have one experiment that I need to wait for roughly two days of processing before it comes across the right solution and the fitness shoots up.

Junk DNA does not disprove the theory of evolution. The neutral gene theory explains that actually junk DNA opens up new areas of search space and can allow for complexity to develop over time. Also see point f.

Because there is no benefit in getting rid of those traits and no cost to keeping them so they hang around, like with junk DNA.

Wait, that explains why we still have them. How did we get them? 

Because they were useful once. I explained above that the environment changes, not least because of speciation.

LOL. We do not have evidence of the mechanisms that would generate complexity from simplicity and that all life has a common ancestor. If you think we do, provide them.

If all you're asking for is complexity from simplicity then that's easy. Self organisation does that. We see it all the time with crystalisation. Or do you think that each snowflake is designed?

If you're specifically asking for the increase in complexity over time from simpler life then the neutral gene explains that which I referred to early. There is also duplication where part of the genotype gets duplicated. If this does not lower the fitness of a member of the species then, as with junk DNA, it can hang around. The important thing is though it opens up a whole new area of search space whereby the duplicated part can be mutated. This increases complexity over time.

I actively use this in my evolutionary algorithms when developing AI.

  Our evidence is that we see life as it is now and we see fossils so we know life existed before and all life is coded in DNA. 

Evidence also includes using the evolutionary process as a form of computation.

I will respond with more in another post. If you could explain why you say that Sean Carroll says that DNA doesn't support the "tree of life" then I can respond to that as well.

[SteveII]

Go ahead...as long as you realize you crossed from science into philosophy when you do. Theories (that contain gaps in our knowledge) don't magically become facts because that's how you decided to approach the problem.

Every single murder investigation, trial and conviction has gaps in knowledge. Let's free all the convicted murderers then, since they have been imprisoned based on philosophy.  

Wonder how we ever convict anyone of murder?

Actually, they were imprisoned based on philosophy. Reasoning is thinking about something in a logically ordered way. Logic is a branch of philosophy. What a murder trial is NOT is a scientific experiment.

[Crossless2.0]

Every single murder investigation, trial and conviction has gaps in knowledge. Let's free all the convicted murderers then, since they have been imprisoned based on philosophy.  

Wonder how we ever convict anyone of murder?

Actually, they were imprisoned based on philosophy. Reasoning is thinking about something in a logically ordered way. Logic is a branch of philosophy. What a murder trial is NOT is a scientific experiment.

Sometimes they're imprisoned based on mistaken or untruthful witnesses.

I suppose that falls under the theological branch of jurisprudence.

[Jehanne]

Every single murder investigation, trial and conviction has gaps in knowledge. Let's free all the convicted murderers then, since they have been imprisoned based on philosophy.  

Wonder how we ever convict anyone of murder?

Actually, they were imprisoned based on philosophy. Reasoning is thinking about something in a logically ordered way. Logic is a branch of philosophy. What a murder trial is NOT is a scientific experiment.

DNA testing, when done properly with the proper controls, IS science.  It is absolute.

[SteveII]

Actually, they were imprisoned based on philosophy. Reasoning is thinking about something in a logically ordered way. Logic is a branch of philosophy. What a murder trial is NOT is a scientific experiment.

DNA testing, when done properly with the proper controls, IS science.  It is absolute.

It's applied to the case using reasoning, so that does not help this very poor analogy.

[Jehanne]

DNA testing, when done properly with the proper controls, IS science.  It is absolute.

It's applied to the case using reasoning, so that does not help this very poor analogy.

That's just bullshit; with enough samples (parents, siblings, cousins, etc.), an analyst can establish things like paternity with near-absolute confidence.  Replication will remove any doubts about the methodology.

[I_am_not_mafia]

So? The theory of evolution is not a belief. It is an explanation for the evidence. The truth of a description of reality does not depend on who believes in that description. What matters is whether the explanation matches the evidence, whether it is falsifable, reproducible and can be tested. Reality does not change depending on how much people understand.

Wrong. It is a belief as to what the evidence indicates.

But unlike other beliefs, like in a sky pixie, or intelligent design, the theory of evolution by natural selection is useful. This is what is meant by explanatory power. Intelligent design does not explain why the flu virus keeps mutating, or why antibiotic resistance keeps occurring. The theory of evolution does, to the point where we can even start making predictions. For example the flu vaccine is based on predictions of how the virus will evolve. Not just flu though, there are many other viruses that we have to be aware of in case they turn into a major pandemic. And there have been a few close calls already. As mentioned earlier we use evolutionary algorithms in computers for evolving designs of new products, like aerofoils for example. This understanding also helps with conserving endangered species. Zone fossils were useful for dating geology before more accurate technologies were developed.

The theory of evolution is more than a belief. It is more than a theory that fits the evidence, it is useful.

[Gawdzilla Sama]

The theory of evolution is more than a belief. It is more than a theory that fits the evidence, it is useful.

Yep. Scientists use it to predict what the next season's flu strain will be like. That allows them to develop vaccines to help people avoid getting the flu.

[Cod]

Every single murder investigation, trial and conviction has gaps in knowledge. Let's free all the convicted murderers then, since they have been imprisoned based on philosophy.  

Wonder how we ever convict anyone of murder?

 What a murder trial is NOT is a scientific experiment.

That sentence makes no sense. Logic is logic not philosophy, philosophy looks at logic and tries to make sense of it, logically speaking philosophy has no logical grounding philosophically.