Another talk on evidence

Are you suggesting it’s evolution no matter what? If it was due to a design than within the code every adaptive process was coded to occur and not only that it would require the ability to evolve in new species over and over throughout time allowing each new life the same properties. The other possibility chance and necessity which has no creative power only destructive. 

When you refer to “natural” processes as if you are explaining what is going on, you are leaving out all the mechanisms that do the work without saying how did this come into being? Instructions don’t just happen without a cause capable of creating them.

Again, we already agree that the origin of these natural cellular processes, and the origin of cells themselves is problematic from a natural/materialistic view. However, once they exist....

So regardless of how such cellular processes came to be they're here now and cause evolutionary changes in genomes and organisms without the need for divine intervention. And these processes include the ability to do *natural genetic engineering* that results in random genetic changes in genomes and random gene shuffling and random transfers of different genes and mobile genetic elements within genomes, and between genomes, and between organisms in a controlled way that allows for natural variation and natural genetic "experiments" without lethal effects.

That is to say these random changes are not *accidents* but normal cellular processes that generate new genetic variation and evolutionary changes in genomes and organisms. In the same way that "crossing over" is a normal, natural process during cell division that results in new genetic variation and new *random* genetic combinations that are not *accidents* but a result of normal functioning of cells (*no divine intervention needed).

(Recombinant random genetic shuffling due to crossing-over)

*If you want to say an Intelligent Designer originally put this all together and created cells with the ability to naturally evolve, then you could say that if you want

I have no issues whatsoever saying a programmed process will run as programmed, and if it is a programmed design placed in nature that makes it a natural process. That said, we may agree on some pieces of this without difficulty, but the closer to the details we get the more issues we will have with one another's point of view, Nothing about this I think we disagree on.

If we agree that within life all that we see is due to instructional causes placed within life then everything is, that includes the ability to alter itself into some other form if a common ancestor is a real thing. That is an incredible amount of coding, to not only deal with a lifeform in the time it lives in, but also all subsequent life that would arise later.

Cool. Looks like we're largely on the same page. I think however this is where the computer coding analogy breaks down. That may require incredible amount of coding with computers, but with living things not so much. One of the amazing discoveries of the past 50 years is how large scale change and restructuring can result from just small scale genetic tinkering.

I beg to differ, biology is much more complex than our computer languages. As complex as our computers are, compared to the code directing life they are simple. It displays more computing power that a small tweak can accomplish different great things. That simply means that much is done in a little bit of biology's code, it is tremendously advanced to do much with little. When you compare what can be done directing the processes if done correctly, if done wrong can be most damaging, what can be done correctly is very small compared to all the things that could go wrong and doesn't.

The entire living, autopoietic cell system with sophisticated cybernetically directed information processing systems that integrate hardware and software and integrate linear digital genetic information processing with networked analog type enzyme catalyzed metabolic reactions that maintain far from equilibrium conditions to achieve the metagoal of replication and staying alive.....ABSOLUTELY! FAR MORE COMPLEX. But that's the origin of life. A GIGANTIC GULF separates life and non-life that most people don't comprehend the difficulty (some would say impossibility) of spanning.

But once you have those sophisticated autopoietic systems (i.e., living cells) in existence....it makes evolutionary change a breeze by comparison.

*Like (I think) I've said before: The discovery of these inbuilt evolvability mechanisms/processes in cells makes evolution easier than ever, but the origin of life far more difficult than ever.

YES, the initial "coding" (and a ton more!) has a complexity and sophistication no computer system can touch. But it's those sophisticated systems that enable dynamic change in genomes. And it only takes minor tinkering. To give you an example, the important genetic differences between say aquatic mammals like whales and dolphins vs. what are believed to be their four legged terrestrial ancestors involves a small handful of regulatory genes difference between the two. To give another example, a tiny tweak in a single gene can produce leg bones with musculature in fins.

This is a point I don't think you give enough thought to, nothing is ever really established, every cell activity can be a possible cancer event or something else can go wrong. It is not just run the code and away you go, maintaining a lifeform is as daunting a task as establishing one. The number of things that can affect it negatively can occur both internally and externally, it must handle and adapt to all of that while reproducing, error checking, and maintaining feedback responses so that everything is kept at the right thermal desired temperatures, all of the start-stop mechanisms are kept in running perfect order, don't clot the blood except where needed and only as long as it is needed. The really important part is also passing all of the instructions to do it again and again without screwing anything up. A healthy code may make it seem simple by comparison, but hardly.

And yet the amazing things is that's what we've been seeing in documented study after study after study over the past 50 years that is showing these normal, natural cellular processes like symbiogenesis, horizontal DNA transfer, hybrid speciation, and natural genetic engineering (especially the action of mobile DNA elements) causes major evolutionary changes with large scale genomic restructuring and physical changes in organisms. People still think of genomes as these static depositories of information, when the truth is they are dynamic systems where mobile genetic elements 'jump' from place to place within a chromosome between different chromosomes and between different organisms and between organisms of different species. It's a dynamic information highway of genetic material that gets shared and transferred and exchanged and modified and shuffled and recombined and not just vertically by inheritance but horizontally as well and not *accidentally* but as a result of normal cellular processes. 

Perhaps the only real way to convey the enormous scope of these dynamic genetic elements is to start a separate OP and start posting on all this research a little bit at a time...

Yes, code preforms in a remarkable way, just what is needed to keep life going just occurs, and when it doesn't something bad happens.

FYI: YECs/IDers often say they accept "small-scale" change and variation within "kinds," but don't accept "large-scale" changes like the "major" changes between animal phyla and classes. Like the "major" change between "fish and amphibians," reptiles to birds and mammals, and so on.

*But the truth is these "major" changes are miniscule in terms of genetic differences. It's hard for us to wrap our heads around this, because first we're inherently biased towards our own species and "larger" = "more complex" way of thinking vs "simple" = "small, single called life"; and second, because we're still conditioned by the old "Five Kingdoms of Life" way we were taught (which is still how it's taught!):

But phylogenomics has revolutionized our understanding. Phylogenetic relationships used to be constructed on the basis of physical characteristics, and then by molecular comparisons for a single protein or for a single gene. But today, we now compare entire genomes of an organism. And the results have completely transformed how we see the "Eukaryotes" (which by the old classification system consists of the four kingdoms: animals, plants, fungi and protists).

First, all life is now classified into domains, with eukaryotes making up a major domain.

The eukaryotes are then grouped into supergroups on the basis of whole genome comparisons. When we do this we see that all those supposedly "simple" single celled pond water protozoa like amoeba that make up Kingdom Protista is hands down the most genetically diverse group. So diverse you can't put them all in the same Kingdom Protista anymore, but have to divide them up into these different Supergroups.

The "Plant Kingdom" falls in the green colored Supergroup Archaeplastids....

while the blue-colored  Supergroup Opisthokonts down at the botton contains a diverse group that includes the "Animal Kingdom" and "Fungi Kingdom." 

And then somewhere in that are the "major" "difficult" to explain changes between reptiles and birds, and reptiles and mammals and such.

*So it's important to keep in mind that comparatively there's hardly any real genetic difference between a fish or amphibian or reptile or bird or mammal, and that the "major" genetic differences are actually found within the mind boggling diversity of "simple" single celled eukaryote "protozoa" we find in pond water scum.

It is important to realize that even repeating the task over and over without fail is a huge undertaking, monitoring it and making sure it occurs as needed. Small changes depending on what we are talking about may not seem like much but altering anything is a coin flip, will this harm or help? That question is not a 50/50 question we know the harmful ones outweigh the helpful possibilities in huge numbers, to change then build up a change to something new appears is gigantic I didn't think you can produce numbers looking at the possibilities of error versus success.

First, there's a difference between accidental "random chance," and biologically controlled "random chance" with natural genetic tinkering in non-essential and non-coding regions of the genome while protecting essential parts of the genome from such tinkering.

Second, the "harmful ones" don't "outweigh the helpful possibilities in huge numbers." You're still thinking in terms of old 20th century Neodarwinian selection theory ("random chance + natural selection") where most mutations were believed to be harmful, deleterious (Top Left Picture: "Selection theory": notice BLUE bar--"strictly deleterious" mutations--is the longest):

*The evidence to date shows this to be wrong. The evidence shows that most mutations are "neutral" (TAN bar) to "slightly deleterious" mutations (DARK GREEN bar) (Lower Left Picture). Not "harmful" enough to be selected against. Most genomic evolution does not occur by beneficial, "strictly advantageous" mutations (LIGHT GREEN bar), but by genetic "tinkering" that has little to no effect on fitness or survivability.

A biological random chance due to control isn't random, it is controlled. Chance and necessity if they play a part are quite different than a controlled change due to the coded restrictions upon what can and cannot be controlled.

Yes. To give an analogy, it’s the difference between a dealer accidentally tripping and sending a deck of cards flying that lands in a random mess vs. a dealer distributing random cards to players in a controlled manner according to a set of established rules and procedures. The results are still random. The "established rules and procedures" (i.e., normal cell function, cellular processes) make the random results possible, which occur in a restricted setting (confined to a dealer table; just like most genetic tinkering is confined to non-essential, non-coding regions in genomes and have neutral to slightly negative effects that don't harm an organism).

*Three other things to keep in mind include: (1) The ease with which organisms can transfer and acquire "new code" and incorporate it into their genomes. (2) New traits usually don't require additional "new code," but minor editing of code that already exists; we can also get new traits by the *loss* of code; and we can also get new traits without any modifications to code at all, but by simply switching different genes on and off, and changing the sequence in which they're switched on and off. And (3) there are many cases where if a random mutation does cause a harmful effect, the system can simply deactivate (switch off) that copy of the gene.

Odd that you throw in your (3) point, turning something off due to harm means that something is monitoring success and failure, which happens in a controlled designed system granted. The ease that something transferring code occurs is if they are compatible with one another, I could write code in the language of Perl, but that doesn't mean something that uses the code VBA can acquire it as is, they must be speaking the same language or have an interpreter. Any alteration in code, the adding to it or removal affects things, any computer that gets updated has this happen, but these things are done only with the greatest of care.

Well of course there's "monitoring." That's part of the cellular processes and normal functioning of a cell. Now again, I agree, how to get that cell in the first place seems impossible to do by purposeless, 'mindless' mass action chemistry.

But again....once you have it, evolutionary change becomes quite easy due to 'built in' evolvability mechanisms and processes in cells. 

And all life (plus viruses) is compatible and routinely "share" and "transfer" "code." That's the amazing part that no one thought possible 60 years ago. We used to think of genomes as static depositories of genetic information that do direct things from the "top-down." We now know this is all wrong. Genomes are dynamic, flexible, interactive, responsive, regulated systems that can readily transfer and aquire new genetic material. And most of the genome is a playground for natural genetic engineering and tinkering without any effect on an organism because most of this tinkering takes place in non-coding regions.

Once you have it, how did it get there? That answers all of the questions, top-down means it was deliberately put there, bottom-up means chance and necessity without foresight, what seems the reasonable explanation to you?

That's not what top-down and bottom-up mean in biology. And your other questions I've already answered multiple times here and in other posts.

It either started from a top-down programmed means or it started from the bottom-up from happenstance, chance, and necessity without being programmed, those are two choices, you have a third, if not it is binary.

I'm the one who introduced the terms top-down and bottom-up into the conversation and you're using them in a different way from what I said. You keep trying to go back to the origin of life (which we already agree on!). I wasn't talking about the origin of life, but the systems logic of a cell and how it is organized. That seems to be confusing you, so let's drop the terminology. 

We're not talking about the origin of the first cell (which we already agree on), but how cells work today