Isn't it time to junk common descent?

Creationism, Evolution, and other science issues

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richic
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Isn't it time to junk common descent?

Post #1

Post by richic »

First a story: Two martians travel to the planet earth in the year 2300 to document what they find and report back to the mother ship.

They don’t find any living beings, but there are a number of freestanding structures grouped together with smaller free standing structures seemingly associated near them. We will call the larger structures homes, and the smaller structures garden sheds and dog houses.

“ok” the one says, all the structures have common attributes. We will document these traits and call them walls, roofs, windows, and doors. There is a myriad of complexity in the larger structures, whether it be color, square footage, window style, roof pitch, etc. but they are all very similar. The simpler structures don’t have this same complexity.

In my report I will say that we have found a world of many like structures and there must be a relationship between them since they are similar so we will hypothesize that the doghouse evolved into the home through an unknown process. We’ll call it mutation.

“Ok let’s get back on the ship. We’re out of here”

Meanwhile, his partner has been nosing around the house and he finds the front door key under the mat. He goes in the door, and sees that there’s a lot more complexity that on the outside. He goes into the garage and there’s a can of green paint. He thinks, “Hey wasn’t the window trim and the dog house the same color” Maybe it comes from this material. He opens a drawer and there’s a roll of paper, a blueprint, that shows several views of the house with detailed specifications for all the home’s attributes. And there’s a signature on the bottom.

He runs out the door to show it to his buddy who is busy cataloging the outside features of the garden shed. ‘Hey I thinks these structures were designed. I have a blueprint and materials common between the structures.”

His partner says, “Well my theory came first and on Mars we’ll never decipher the signature of who wrote that blueprint, so let’s go with the doghouse evolution theory”

Why is it that just because we don't know who the creator is that we deny the obvious evidence for creation?

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gluadys
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Post #21

Post by gluadys »

richic wrote: Here is a quote from the above link “As in other characteristics, we would expect those organisms with fewer differences in their protein amino-acid sequences to be derived from common ancestors more recently, and therefore to be more closely related. We can then use this molecular evidence to place organisms in their proper places in a cladogram”

I'm not sure how we can make that case without thoroughly understanding the underlying programming to create those proteins. It would seem to be the equivalent of equating the output of two computer programs based on the number of lines of code.
I think molecular biologists DO have a pretty thorough understanding of the process. I don't. But I know the basic outline. The base nucleotides of a DNA sequence are read in groups of three called codons. Each codon (and there are 64 altogether) signifies an amino acid, except for the three that mean "stop". Since only 20 amino acids are used to build proteins, there are two or more codons which signify each amino acid. RNA is used to transcribe the codon sequence and move it from the cell nucleus to the protein construction area. More RNA edits the message, which includes not only the sequence of amino acids but the proper folding of the protein into its 3-dimensional shape. Then the protein is built and goes off to do whatever it is supposed to do.

Cytochrome c is a protein. The various lists you see in those exercises are the amino acid sequences in the protein as it exists in different species. Even though it performs the same function in different species, it is made up of slightly different sequences of amino acids.

As an analogy, I think of proteins as being similar to baked goods. We all know what a pumpkin pie is. But when you look in a recipe book, or compare the way Aunt Tilly makes pumpkin pie to the way Uncle Dave does, you find although there are some basics, there are a zillion different recipes for pumpkin pie. In the same way a protein is defined by its basics, its function. It has certain recognizable characteristics. But there can be all sort of variations in the amino acid "recipe" for a protein.

And just as certain recipes for pumpkin pie are handed down in a family from generation to generation (with each generation tweaking it a bit till Aunt Tilly would never recognize the recipe with her name on it) so do the amino acid "recipes" for proteins get passed from generation to generation in the DNA, with the same sort of tweaking. That's how you end up with so many variations of what is essentially the same protein.

It is also possible (and this is what is done with old manuscripts, such as those of the bible) to trace when a certain variation (copying mistake) first occurred by seeing who "inherited" it. And, in biology, this tells us who is related to whom.

[quote
But we may be entering a period now through genomics where we can actually begin building a design theory that is predictive. I agree it must do this to be viable. Personally I think it's locked in the information stores of the respective species. Once that code is decrypted we should know what's really going on.[/quote]

Well, DNA is the information store, and we are decrypting it as fast as possible. If that permits ID to start making predictions, then it will get serious scientific attention.

IT seems like convergent evolution could be better explained by design.
Natural selection also explains it. Convergent designs (such as the streamlined fish shape or the ubiquity of the Fibonacci series in plant structure) tend to be efficient designs and natural selection tends to favour efficient designs.
I think of it something like the way we do 3D solid modeling. IF you are going to rapidly build a number of items you would use a common building block and then just tweak the programming code. You can then render the item, and move on to the next. Custom builds take a very long time. When it's a single designer he can also be highly efficient and reuse as many components as he can.
I don't see this as persuasive. Time is not significant to God. Custom building takes more time for humans; but then we also value the unique craftmanship of a custom built item more than the efficiently mass produced item too. But for God, time is not an element that needs to be factored in.

So it still comes down to design theory not predicting one or the other.
This is a very valid point, but I don't necessarily see the design process as taking the best of everything an putting it in one package.
ok. But then, if the designer is capable of taking the best of everything and putting it in one package, there needs to be an adequate reason why this was not done.

I saw a paper by Dembski on this to the effect that Intelligent Design need not be optimal design. It was very logical as long as the Designer could be thought of as having human qualities.

He essentially boiled down the reasons for less than optimum design as:
a) the designer is stupid and makes mistakes (e.g Edsel car)
b) the designer has an evil purpose (e.g. efficient torture chamber)
c) the designer is constrained by competing design specifications (e.g. it must be efficient, and lightweight, and inexpensive)

a) does not apply to most deities and certainly not to the God of the bible.
b) does not apply to the biblical God

so we are left with c). In that case, it should be possible to figure out what design constraints led to a less than optimum design. Granted that would be a long term project. I don't expect answers tomorrow.

Its just that natural selection does work under design constraints that we already understand in part. One being that it can only use what history has given it to work with.
It could be that a general family of like species are rendered successively, inheriting certain basic functions along the way until all the species have been rendered for that track. So we could end up with a flying mammal that is more mammal than bird. This design methodology would fit the nested hierarchies we see.
Well, you would need to turn your "could be" story into a testable hypothesis to give it scientific interest. Otherwise it is just an ad hoc conjecture.
I would be interested to see what "bird-like" genomic sequences we might find in the bat and compare that with the bird. IF we found some "re-used" sequencing I would consider it evidence for design since evolution has "decoupled" the two species. IF we had exact matches of sequences that would be even better. Do we have anything like this one way or the other?
None that we have found barring human genetic engineering. Sequences like the cytochrome c sequence show differences to be expected by the evolutionary history.

richic
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Post #22

Post by richic »

gluadys wrote: As an analogy, I think of proteins as being similar to baked goods. We all know what a pumpkin pie is. But when you look in a recipe book, or compare the way Aunt Tilly makes pumpkin pie to the way Uncle Dave does, you find although there are some basics, there are a zillion different recipes for pumpkin pie. In the same way a protein is defined by its basics, its function. It has certain recognizable characteristics. But there can be all sort of variations in the amino acid "recipe" for a protein.

And just as certain recipes for pumpkin pie are handed down in a family from generation to generation (with each generation tweaking it a bit till Aunt Tilly would never recognize the recipe with her name on it) so do the amino acid "recipes" for proteins get passed from generation to generation in the DNA, with the same sort of tweaking. That's how you end up with so many variations of what is essentially the same protein
I am definitely over my head on these issues, but please humor me if you don't mind.
I did a quick search on protein sequencing and see this Cytochorme-C example is pretty well documented. I had a quick look at this site:http://www.rtis.com/nat/user/elsberry/e ... uence.html
And this quote I found interesting:"Even without a fortuitous coupling of a neutral mutation with a selected-for trait, one can work out the math for reproduction in finite populations to find that, over time, it is likely that barring other mutations arising, a population will eventually come to have a reduced number of neutral alternate representations of the same genetic trait (alleles), and eventually only a single allele for the trait will be found in the population."

It would seem by your baking example that we may have different protein coding sequences for the same protein due to evolution in different species, but according to the article, within a species that sequence would be exactly the same(or near to).

I think it's interesting in terms of a design argument that evolution anticipates uniformity in the sequencing of the protein "within" the species. Also from what I understand, the genetic sequence does not contain 100% of the controlling information in the protein building process. There are other separate drivers within the cellular information bank that are part of the process.

In this same article, the author, shows the percentage genetic drift associated with cytochrome-c in various species. The numbers are interesting from both a design and common descent perspective. Clearly he's making a case for CD showing how the drift in features fits exactly the taxonomy. It all fits well except for one anomoly with mice and humans which he dismisses.

When I look at his progression, I immediately think of a mathematical algorithm that might be employed in a design theory. If species were rendered in a progression you would expect some controlling algorithm to be evident.

Unitl we know though how to account for the Cyto-C differences, you have to give this one to common descent.
gluadys wrote: Well, DNA is the information store, and we are decrypting it as fast as possible. If that permits ID to start making predictions, then it will get serious scientific attention.
I'm encouraged ID is looking forward which is where science should always be. New disciplines like bioinformatics together with data mining and cryptography can all be employed in the reverse engineering process. Isn't the fact we have this massive reverse engineering exercise going on occassionally make you wonder if it is engineered in the first place?
gluadys wrote: Natural selection also explains it. Convergent designs (such as the streamlined fish shape or the ubiquity of the Fibonacci series in plant structure) tend to be efficient designs and natural selection tends to favour efficient designs.
There's no debate on natural selection selecting better forms of a trait, but the issue is how a common feature can appear with no common ancestor? Isn't it improbable that the same mutation would occur in separate lineages and be so strikingly similar? I think the famous example is the photographic eye shared by the squid and human.
gluadys wrote:
I don't see this as persuasive. Time is not significant to God. Custom building takes more time for humans; but then we also value the unique craftmanship of a custom built item more than the efficiently mass produced item too. But for God, time is not an element that needs to be factored in.
As a Creator, I see God marrying the best design with the most efficient mass production process. We can only marvel at the biological craftsmanship that surrounds us and is within us. I think time is a constraint on the design process since we do have a finite number of species on earth. I view God as more of an engineer than model builder. My guess is he would have first designed a process for Creation then run the process over a very short period of time.
gluadys wrote:ok. But then, if the designer is capable of taking the best of everything and putting it in one package, there needs to be an adequate reason why this was not done.

In that case, it should be possible to figure out what design constraints led to a less than optimum design. Granted that would be a long term project. I don't expect answers tomorrow.
I will give you one design constraint that I think is highly probable: All species must co-exist. The interdependence of species is required to maintain life. In order for that to work, you must have a hierarchy, a food chain, and other interdependencies as well.

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gluadys
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Post #23

Post by gluadys »

richic wrote:I am definitely over my head on these issues, but please humor me if you don't mind.
I did a quick search on protein sequencing and see this Cytochorme-C example is pretty well documented. I had a quick look at this site:http://www.rtis.com/nat/user/elsberry/e ... uence.html
And this quote I found interesting:"Even without a fortuitous coupling of a neutral mutation with a selected-for trait, one can work out the math for reproduction in finite populations to find that, over time, it is likely that barring other mutations arising, a population will eventually come to have a reduced number of neutral alternate representations of the same genetic trait (alleles), and eventually only a single allele for the trait will be found in the population."
That's getting way above my head too. Clearly it would depend on the exact circumstances. The cytochrome c proteins are listed by species, as if there is one per species. On the other hand humans have hundreds of different alleles of the haemoglobin proteins. So some different factors must be at work.

But I am glad you gave me the reference. I have been trying to explain to someone else what is wrong with the way Michael Denton deals with this evidence in his book. Now I can show him it's not just me. Real scientists are making exactly the same criticism.

I think it's interesting in terms of a design argument that evolution anticipates uniformity in the sequencing of the protein "within" the species.
Don't extrapolate too far. That is a common failure of scientific laypersons. You must note every condition that was set out: "finite population", "barring other mutations". When those conditions fail, the consequence fails as well.
Also from what I understand, the genetic sequence does not contain 100% of the controlling information in the protein building process. There are other separate drivers within the cellular information bank that are part of the process.
Yep, that's true. But I'm at about a Biology 101 level, and that is more advanced stuff. I wouldn't begin to try and account for that type of factor. It's enough to be aware that genetics is not the be-all and end-all.

gluadys wrote: Natural selection also explains it. Convergent designs (such as the streamlined fish shape or the ubiquity of the Fibonacci series in plant structure) tend to be efficient designs and natural selection tends to favour efficient designs.
There's no debate on natural selection selecting better forms of a trait, but the issue is how a common feature can appear with no common ancestor? Isn't it improbable that the same mutation would occur in separate lineages and be so strikingly similar?
It's not the same mutation. That is why convergent features are called "analogous" rather than "homologous". Analogous features are those that are superficially alike and often serve a similar purpose, but whose origin does not depend on descent. The flipper of a whale is not formed from the same tissue or in the same manner as the fin of a fish. The development of the octopus eye is not directed by the same genetic influences as a human eye. Each convergence occurs independently as a result of different mutations in different lineages.

A good read on the multiple evolutions of the eye is found in Richard Dawkin's Climbing Mount Improbable.

Homologous features on the other hand are developmentally directed by homologous genes, derived from homologous embryonic tissue and display a deep uniformity even though they may be re-modeled in detail to have a significantly different appearance and function.

So human inner-ear bones have a different appearance and function than reptilian jaw hinge bones, but are genetically and developmentally homologous to them. And the transformation of the reptilian jaw hinge into the mammalian inner ear also happens to be exquisitly preserved in generations of therapsid mammal-like reptiles, so that the various stages of the transfomation are known.
As a Creator, I see God marrying the best design with the most efficient mass production process. We can only marvel at the biological craftsmanship that surrounds us and is within us. I think time is a constraint on the design process since we do have a finite number of species on earth. I view God as more of an engineer than model builder. My guess is he would have first designed a process for Creation then run the process over a very short period of time.
ok. You think so. I won't argue with that.

I also think the Creator designed a process for Creation. I think that process is evolution.
I will give you one design constraint that I think is highly probable: All species must co-exist. The interdependence of species is required to maintain life. In order for that to work, you must have a hierarchy, a food chain, and other interdependencies as well.
Isn't the interdependence of species a decision of the designer? Again you are assuming that what does is exist is what must exist. But you haven't demonstrated that your assumption is true.

richic
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Post #24

Post by richic »

gluadys wrote: Isn't the interdependence of species a decision of the designer? Again you are assuming that what does is exist is what must exist. But you haven't demonstrated that your assumption is true.
Species interdependence is a constraint imposed by the creator on the system design, so I would agree that the constraint is a decision by the designer. It's not imposed on the Creator.

When you begin any design from a blank slate you first need to build boundaries then fill in the detail. Constraints, in my view, just help better define the design and provide some rules to govern the design once it's implemented. I would put the physical laws(i.e. gravity) that we rely on into a similar bucket.

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