Biological Information and Intelligent Design: Evolving new information

[Billcole]

@gbrooks9

You keep forgetting that God is fully capable of handling the things that natural laws truly can’t accommodate…

You must have spent a very very long time disputing with Atheists, yes?

Yes George, I have spent lots of time debating with Atheists. They see evolution as an internal part of their worldview and are very uncomfortable what new genetic evidence is exposing.

The fact that God can handle the things that natural law truly cannot accommodate is beside the point.

What is the science telling us? How do we best describe what we are seeing in nature? We are seeing stages where massive amounts of new genetic information are infused into life. How do we describe this? IMHO universal common descent is a very poor description of what we are seeing.

[Billcole]

@Jonathan_Burke

Chris already understands the scientific method. He’s asking you to actually follow it. As Chris and I keep pointing out, you still don’t actually have a hypothesis or a method of testing the hypothesis. Instead of talking about the scientific method and how to write a hypothesis, you need to actually write a hypothesis, propose a method testing the hypothesis, and then actually test the hypothesis.

[quote]Test Your Hypothesis by Doing an Experiment: Your experiment tests whether your prediction is accurate and thus your hypothesis is supported or not. It is important for your experiment to be a fair test. You conduct a fair test by making sure that you change only one factor at a time while keeping all other conditions the same.
You should also repeat your experiments several times to make sure that the first results weren’t just an accident.[/quote]What experiment will Chris do to test the hypothesis that that all life shares a common ancestor by reproduction and genetic recombination? How will he repeat that test?

If you really think he has answered this then I think we need to agree to disagree.

[beaglelady]

Too funny!

[gbrooks9 (George Brooks)]

@Billcole

What is the science telling us? How do we best describe what we are seeing in nature? We are seeing stages where massive amounts of new genetic information are infused into life. How do we describe this? IMHO universal common descent is a very poor description of what we are seeing.

You are tilting at windmills again… you are asking what does [pure] Science tell us… But this is not my concern as a supporter of BioLogos.

BioLogos is an umbrella for those who look to the miraculous surrounded by science.

You don’t seem to have much sympathy for that combination…

I’m not sure how you function in the modern world we live in … but that is another matter.

NOTE: As I look at the animal kingdom around us … I see common descent EVERYWHERE.

[Jonathan_Burke (Jon)]

@Billcole

What experiment will Chris do to test the hypothesis that that all life shares a common ancestor by reproduction and genetic recombination?

Chris has already explained this, thus.

@Chris_Falter

You measure the genomic differences and similarities, apply the mutation/inheritance model, and infer (or disprove) common ancestry.

@Chris_Falter

Harshman’s analysis of paleognaths, volant tinamous, neognaths and crocodilians is based on the same principles and techniques that 23andme uses for human genetic analysis.

@Chris_Falter

I already explained how the genomic mathematical model works very powerfully with a known case (human lineage). Biologists apply this tested model to other creatures who reproduce in a similar manner.

As he pointed out, you already accepted this.

@Chris_Falter

You already accepted paleognath common descent based on the 8-bp indel in ALDOB, I thought.

[quote=“Chris_Falter, post:61, topic:16409”]
You already accepted my testable hypothesis that a shared mutation (such as the 8bp indel in ALDOB) found only in the population under study establishes common descent. Now may I ask: what is your testable hypothesis?[/quote]

This is what a real scientific hypothesis looks like, complete with a method for testing it empirically.

@Chris_Falter

My hypothesis is that if they share a common ancestor, the proximity of their genomes will be proportional to the number of generations back to the common ancestor. Proximity would be measured by DNA sequences of pseudogenes, endogeneous retroviruses, functional genes, and so forth–essentially using the same techniques (such as 23andme’s) used to determine the number of generations to a common ancestor between two humans.

See also:

• A formal test of the theory of universal common ancestry
• Testing for Universal Common Ancestry
• On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence
• Statistical evidence for common ancestry: New tests of universal ancestry

These articles show you what a real scientific hypothesis looks like.

[gbrooks9 (George Brooks)]

All of this fuss is unnecessary if you focus on how Geology and Physics confirms the age of the Earth, from a dozen different views, as millions of years older than 10,000 years…

[Chris_Falter]

Hi Bill,

I had always wondered how to do a science fair project. Don’t know how I missed that in my education. Thanks for helping me get to that level.

More seriously, you’re missing an extremely important class of scientific inquiry, which is inference to causation outside of laboratory conditions.

Even in science fair projects, the experimenter is inferring to causation. It’s impossible to do science without inferring to causation.

What makes much of biology, geology, and astronomy so interesting is that you can’t go into a lab and cause specific changes and report the results. Instead, you make certain observations, infer causation, and then make predictions about further observations you expect. Sixty years ago, the dominant frequentist school of statistical modeling argued that you couldn’t even use seismographs to determine the epicenter and depth of an earthquake. Where were the controls? Where were the valid known valid observations that you could use to test your predictions? How could you know what assumptions would allow you to understand what had really happened? It sounded a lot like a debate between ID proponents and evolutionary creationists.

Fortunately, the Bayesian school did not give up. They made reasonable Bayesian inferences to causation, then used those inferences to make further predictions. As the geologists’ models improved, the accuracy of their predictions (about the statistical profile of future seismographic observations) improved. The inferences became more accurate, which made future predictions more accurate.

It is still possible for an earthquake skeptic to say: “How do you know that the earthquake happened at X location at Y depth without assuming that your model is true?” Again, a lot like an ID argument.

But the geologists have pretty much settled the questions, and the earthquake model is consistent with observations about plate tectonics, crustal composition, and so forth. You can’t use the model(s) to predict when the next big one will strike San Francisco, but you can make accurate, probabilistic predictions about the distribution of quakes and their magnitudes over long periods of time and large geographical areas. The science is uncontroversial.

The science around evolution is similarly uncontroversial among the community of biologists. The theory of evolution dovetails nicely with the genetics, speciation, and lab experiments with bacteria that we observe, in the same way that earthquake models dovetail nicely with plate tectonics.

The same thing happens in astronomy, which like evolutionary biology is an entirely observational scientific discipline.

Hope you find this perspective helpful.

Blessings,
Chris Falter

[Billcole]

@Billcole

The hypothesis you are trying to set up is an inference argument with some supporting evidence. I will stipulate you can do that as I believe I can do the same thing for the design inference.

Hi Chris
Yes, I agree with your solid explanation.

I honestly am a little frustrated that I mentioned, as my quote above shows, the same thing you just eloquently explained three hours ago.

If you look above I agreed that I believe that you can form an inference argument for common descent. The design argument is also an inference argument. The argument that UCD is testable and the design inference is not is non sense. Both are evaluated by observing evidence and coming to a conclusion based on that evidence.

[Billcole]

@gbrooks9

NOTE: As I look at the animal kingdom around us … I see common descent EVERYWHERE.

I see the diversity of life everywhere. Common descent is an inference of how that diversity of life occurred. If you are convinced that common descent is how that diversity occurred I certainly respect that. If you say that common descent needed a little occasional Devine intervention I respect that also.

[gbrooks9 (George Brooks)]

@Billcole

The design argument is also an inference argument. The argument that UCD is testable and the design inference is not is non sense. Both are evaluated by observing evidence and coming to a conclusion based on that evidence.

How do you suppose to make Intelligent Design a TESTABLE scenario? It is inherently a non-scientific position. It is like testing for God.

[Billcole]

@gbrooks9

How do you suppose to make Intelligent Design a TESTABLE scenario? It is inherently a non-scientific position. It is like testing for God.

Good question. I honestly am not sure ID is the way to go at this point. As an inference it is testable the same way UCD is. By observing evidence and inferring design vs inferring UCD. Who the designer is, is not the argument. As Mike Behe said to me, an interesting question but not the argument. IMHO the UCD inference (with unassisted reproduction) does not really answer the question of how the massive amount of new genetic information (DNA sequences) came into existence.

Your idea of UCD with an occasional assist from the almighty may be the best idea.

This, however, is very similar to the design argument just a little more conjecture on how the design was implemented.

I think the idea that needs to be explored is how hard is it to come up with the DNA sequences of a new animal. This in my mind is an incredibly difficult problem and requires very precise design rules way beyond human capability. Maybe it was information generated outside space time and then downloaded to allow your concept of assisted UCD.

[gbrooks9 (George Brooks)]

@Billcole

As an inference it is testable the same way UCD is.

@Billcole

No… that really isn’t true. UCD is a scientifically accessible hypothesis.

There is no known scientific approach for TESTING miracles… and Intelligent Design scenarios that are being sought are those that either God or Aliens perform. And I’m pretty sure you will not accept the Alien scenario for your default position.

ID is the stuff of God.

[gbrooks9 (George Brooks)]

@Billcole

I think the idea that needs to be explored is how hard is it to come up with the DNA sequences of a new animal.

@Billcole

What is the definition of “new”?

In the theoretical evolutionary path of the emergence of Whales… at what point do you say… okay…THAT"s new? Thousands of years before it is a whale, right? But where?

Tigers and Lions are different right? But they can cross-breed. So what the heck is a KIND?

The genetic gradient is virtually without milestones… as much as you desire them. But they are not there.

[benkirk (Benjamin Kirk)]

@Billcole

While I agree that the 8 base pair deletion is evidence that supports common ancestry (except the ostrich), the cladogram simply sorts the data and arranges a tree and assumes ancestry based on closest DNA match.

Hello Bill,

The cladogram is simply a cladogram that illustrates the relatedness.

What’s YOUR interpretation of the cladogram?

[benkirk (Benjamin Kirk)]

@Billcole

Good question. I honestly am not sure ID is the way to go at this point. As an inference it is testable the same way UCD is. By observing evidence and inferring design vs inferring UCD.

Hello Bill,

You’re very, very mistaken. You don’t seem to understand the meaning of “testable,” which is about predicting what one will directly observe, not what we or anyone else might infer. The point is to overcome wishful thinking by baking in all inferences BEFORE we know the answers.

Common descent is testable because it makes empirical predictions about data we don’t have. It’s simply false to pretend that science is just about explaining existing data.

[Aceofspades25]

I realise this but you were doing this in reply to a comment about natural selection. This was not a comment about mutation.

Benkirk wrote: “Bill,Natural selection isn’t random.”

He is correct it is not the “random” or “unpredictable” part of evolution. Mutation is the unpredictable part of evolution. Natural selection filters out a lot of that unpredictability and is directed towards the goal of increasing fitness.

[Aceofspades25]

@Billcole

In the case of humans we can assume ancestry. Can you make an argument that this technique establishes common ancestry when it is not assumed?

Hi Bill, based on a previous comment you seem to have a misunderstanding of how this algorithm determines common ancestry. You wrote:

the cladogram simply sorts the data and arranges a tree and assumes ancestry based on closest DNA match.

It doesn’t simply group the data based on closest DNA match. It is a lot cleverer than that. It groups the species based on the number of shared common mutations. For example if three of the species have the same 6 nucleotide deletion then there is a good chance that that deletion happened once in a common ancestor. If another mutation is found to happen elsewhere as well with the same three members then it significantly increases the chance that they form a clade.

If another mutation is found that groups these three together with a fourth species then the chances are that the 4 members will form a parent clade to the one I just described.

So the algorithm is trying to construct clades based on shared nested mutations more than anything else. It doesn’t just look at overall DNA similarity.

[gbrooks9 (George Brooks)]

@Aceofspades25

He is correct it is not the “random” or “unpredictable” part of evolution. Mutation is the unpredictable part of evolution. Natural selection filters out a lot of that unpredictability and is directed towards the goal of increasing fitness.

@Aceofspades25

As long as we are agreeing that it is not random or unpredictable to God … I’m Good to Go!

[Aceofspades25]

@Billcole

but the reconciliation of 22 million fixed mutations and possible 30 to 40k splicing variations is equally a challenge on the other side of the argument.

Why is this a challenge? Mutations can become fixed all by themselves due to genetic drift. In fact given known equations from population genetics, known mutation rates (~100 mutations per generation) and divergence dates (~5 million years), we can calculate that we should expect there to be roughly 25 million fixed mutations.

Splicing variations aren’t an issue either. Many of these are spurious (accidental and non-functional). So how many functional splicing variants do you think there are in humans that Chimpanzees don’t share?

[gbrooks9 (George Brooks)]

@Billcole

If a new complex protein differentiated these animals I would be skeptical.

@Billcole

Your fixation on the idea that closely related animals cannot be differentiated by a complex protein is complete Bunk.

Your correspondents have explained why. It is you, sitting on God’s throne, deciding what can or can’t happen over millions of years … when you don’t even understand why “virtually speciated” phenotypes have sterile offspring.

On the Issue of Cross-Breeds:
It is the ability to pass on genetic traits that keep a gene pool unified. As soon as there is a drop in successful production of fertile offspring between two sub-groups/kinds, the genetic mix in either sub-group can continue to drift further and further away from the “Common” ancestral group.

Alternatively, sometimes animals diverge geographically more than their gene pools diverge… and in the process, the surrounding environment produces some distinctly different phenotypes … even though the two separated gene pools are still able to produce offspring (sometimes fertile sometimes not); this is why Tigers and Lions can breed, even though their phonotypes are now fairly distinct, and even dramatically different.