God and natural selection

Epigenetics. It is an exploding field which has to do with just what you said -- there is a lot more than chromosomes involved in our heredity. One of the first known examples I know of regarding anything was by Franklin in Way of a Cell -- the shape of the E.coli bacteria is NOT determined by its genetic components. So why is it the shape that it is? </font>[/QUOTE]This adds a whole new level of difficulty to the whole proposition of genetic evolution, huh?

 

from Helen...

"Just one note here, Phillip: the bacteria were already antibiotic resistant, or they wouldn't have been able to resist the antibacterial agent and thus would have died. It's nothing we did; it's a natural variation which appears in various individuals of a colony by virtue of 'hot spot' mutations -- a sort of back and forth mutation which never goes forward and forward and forward, but only back and forth. Some of these hot spot mutations, or combinations, yield natural antibiotic resistance. When there is an antibiotic present, these individuals are, of course, favored to survive. In a wild population, however, they are the minority and actually the weaker of the bacteria and do not gain dominence."

In a previous discussion, you made the same claim. I answered as followed to which yu never responded.

So their VanA elements were different from the original gene by a new insert, a point mutation, and a deletion. How does this fit into you hotspot idea? My understanding was that the hotspots were locations where point mutations were more favorable. This is significantly more involved than that.</font>[/QUOTE]For background, here is how the cascade involved in vancomycin resistence works. This sounds like a good example of the modern evolution of an IC system.

Again, quoting myself.

 

"I was hearing this so often that I asked, on another board, for examples of mutations that were considered beneficial by the poster who made that claim. I did request they be in the animal kingdom and did not try to define any terms, so that the field could be as wide open as possible."

You recently asked me a similar question. I gave a very short list of examples. (You don't like my long lists of examples it seems.) The response I got was just something along the lines of "That's interesting.

Anyhow, here was my short list. You'll notice that in the three items you also see three different mechanisms for generating that new information some some like to say is not possible.

"Selective sweep of a newly evolved sperm-specific gene in Drosophila," Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL, Nature. 1998 Dec 10;396(6711):572-5.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9859991&dopt=Abstract

You have two genes that are beside each other. They get duplicated. In one of the copies, some of the sequence between the two genes gets deleted. This allows the genes to combine into one chimeric gene. You have the two original genes intact and you have a new gene.


"Adaptive evolution after gene duplication," Hughes AL, Trends Genetics, 2002 Sep.18(9):433-4.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12175796&dopt=Abstract

In this case a gene, RNASE1, was duplicated such that we had a new gene, RNASE1B. These genes occur in the colobine monkey, douc langur and make pancreatic ribonuclease. Through a change in diet, the conditions within the digestive tract of the monkey were altered. Through delective pressure, the B copy of the gene mutated until it was adapted to digest single stranded bacterial RNA.

Again, we have new information. The original gene still exists to perform its original function. The gene was duplicated. When the copy mutated, then there was information that was not there previously, namely the new DNA sequence. The second copy eventually mutated until it performed a new digestive process.


"Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis," Mi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, LaVallie E, Tang XY, Edouard P, Howes S, Keith JC Jr, McCoy JM, Nature 2000 Feb 17;403(6771):785-9.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=20155476&dopt=Abstract

In this case, a retrovirus inserted a section of DNA into the genome. In this case, humans have co-opted the gene to serve an important role in the area of human placental morphogenesis. The purpose of the original gene was as the envelope gene of the virus. So humans gained a gene and a function which they previously did not have. The information of the human genome was thus increased.

 

There are also numerous examples that show how the genomes of organisms show the evidence of having been produced through evolutionary processes. For example, here is one from humans and shows how duplication and subsequent mutation can make new and useful genes.

It is often claimed by YEers that all mutations cause harm or decrease "specificity" or something else asserting that a series of mutations could not build up the life that we see. One of the common answers is that duplication and mutation are powerful means of creating new genes which can be used to evolve new features. I think Petrel actually gave you some links that discussed this very thing.

Now I want to give one example here. I am doing this from memory, so please forgive any errors. But I think the general gist is correct.

The hemoglobin that carries oxygen in your blood is made up of four globins, two are called alpha globins and two are called beta globins. The alpha globins are made by two genes from a group of 7 genes called the alpha cluster. The betas are in a cluster of 6.

Each cluster also contains about 4 other copies of similar genes that are not functional because of mutations. The seventh alpha is called zeta and is used in the fetus only.

Now an individual gene is generally broken into pieces. The pieces are called exons and must be connected to one another to make the final gene. The bits inbetween are called introns, these must be spliced out. When looking at the clusters, it becomes obvious that the various genes were made by duplicating an existing DNA segment.

(Please note that this next bit is something I might have looked up first to confirm, but it is late. It is what I remember. Someone will correct me if I get it wrong.) How do we know they were made by duplication? Well, close examination will show that each individual gene in each cluster is broken into exons in the same way and that the introns, or bits of junk seperating them, are mostly the same. One original alpha was copied and copied, eventually making 7 individual genes.

Now these copies were able to mutate. A couple became useful enough to be the ones actually incorporated into hemoglobin. Others mutated themselves into uselessness. But the pattern shows that the most likely explanation is that the useful genes of today were created through a process of duplication and mutations.

YEers are free to step in here and tell us why, instead, we have this pattern. Surely we were not created with defective and unused genes. Surely we did not once have all of them working in some unusual system and we have all lost the same functional genes in the same manner through time.

Let's take this a step further. If you look around, life can be grouped in a hierarchal manner into larger and larger groups. Evolutionarily, you would expect that members of a goups would be likely to share a common ancestor.

Now if you look around at other apes, you will see that they share the same division of alpha and beta globins. So do primates. So do all mammals. So so all tetrapods (mammals, reptiles, birds, amphibians). So do most fish. You have to move to larger and larger groups before you find that the grouping that would include lampreys and hagfish with the rest of the animals mentioned above before you find animals without the division into alpha and beta globins. They have only one.

This allows you to tie down with some confidence where in the past the duplication that gave us the alpha and beta genes happened. You may have already made the connection back to our other topics. By comparing many different genes and their patterns in the genomes of life, you can use such techniques to tie down many different relationships.

If you take a look, you will also see what I have described here repeated over and over. Most genes have been found to belong to so called gene families where members of each family appear to have been made through repeated duplication events.

You will also see another recurring theme if you dig. If I remember correctly, the globins that we use for oxygen transport are very similar to proteins that some more primitive organisms use to bind to NO (nitrous oxide). Evolution has a habit of often reusing old parts for new functions and of rarely requiring true novelty.

 

Here is one more example of such. Well, the same idea of evolutionary history being written in the genes at least. But this is a totally different process. This is an insertion that eventually leads to a new gene.

There are segments of DNA called retroposons which are easily duplicated and inserted into the genome at diverse places. In humans and other primates there is a particular family of these called Alu sequences. There are very, very many Alu insertions in the human genome. It is possible for these Alu inserts to mutate until they present the proper genetic sequence to mark them as an exon. They can then be spliced into genes potentially making novel and useful genes.

The paper here discusses a particular Alu insertion that occurred all the way back in the basal ancestor of anthropoid primates. The changes that happened to the Alu sequence through time is then charted by looking at the same sequence in various descendents. Eventually mutation caused the sequence to become an exon which was then used in a novel gene p75TNFR in the ancestor of old world monkeys and apes.

This case is of particular problem for YEers because we see a useless insert spread throughout the primates and as various lineages split off, we can trace its change to something useful.

Singer SS, Mannel DN, Hehlgans T, Brosius J, Schmitz J., From "junk" to gene: curriculum vitae of a primate receptor isoform gene, J Mol Biol. 2004 Aug 20;341(4):883-6.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15328599&query_hl=1

 

Again overstating the evidence?

Here are examples of explanations of observations that if true are consistent with evolution... but that isn't really surprising since they were derived while considering evolution an established truth.

 

Or far more likely, you can trace its origin to somethng useful.

 

Thanks Helen for taking my question seriously. I would say the division between variation and mutation is difficult if not impossible to define genetically.

 

In response to the assertion that denial of evolution is done by denying the evidence:

Sorry, regardless of whether one accepts or denies naturalism in one's view, we now have evidence for evolution. In order to deny evolution, you have to deny that evidence. For example, you must say hey, that isn't really a vestigal hip bone, and then you are left with the question of explaining away the whole fossil whale record that shows those legs dwindling away - and the leg muscles that still form inside whale bodies as well!

And there are so many many things you must deny and cannot find a corresponding reasonable explanation for them.

Flightless wings on ostriches, for example - why bother making them at all?

Bats without hollow flight bones - how come birds get them and bats don't?

the list goes on and on.

Go ahead, keep denying, but what you are denying is - evidence.

 

God called his original creation "good"... and man wasn't dying. That is a plenty enough unusual system for me.

 

Sorry, regardless of whether one accepts or denies naturalism in one's view, we now have evidence for evolution.</font>[/QUOTE] No Paul. We have evidence successfully explained by evolution. There is a very, very significant difference. A plausible explanation may or may not be true. For something to be evidence in favor of one particular concept, it must lead to that conclusion and only that conclusion... or a very reasonable approximation thereof.

Nope. You simply have to have an alternate, plausible explanation. If you accept naturalism then you lose that perspective. If you accept supernaturalism as your premise for approaching science (the study of natural phenomenon) then you gain a whole new spectrum.

I have read accounts of this "record". It is extraordinarily poor. Animals have been force fitted into the gaps for nothing other than sheer convenience. The actual fossils supporting this particular tale are not convincing. The major part of the series is necessary conjecture.

Thanks to UTE for actually guiding me to that discovery.

That presumes that God made the ostrich as a separate species exactly as it appears in nature now. There is no contradiction between the ostrich's wings and the concept that the originally created, pristine order of Genesis "kinds" speciated into animals with less adaptability.

Because birds and bats didn't descend from the same kind perhaps.

Yes I know. You have blinded yourself to your presuppositions and thus your earlier post where you admit that evolution has become a fact in your "mind". IOW's, your paradigm no longer allows you to seriously, critically consider anything that might overturn that faith.

Nope. Just the explanations given by evolutionists whose sum equal a contradiction to what God said He did in the scriptures.

 

BTW, UTE thanks. Before you argued that I had no proof for my claim of highly variable, pristine original kinds... your hemoglobin discussion provides a very promising potential proof.

 

Thanks Helen for taking my question seriously. I would say the division between variation and mutation is difficult if not impossible to define genetically. </font>[/QUOTE]You're welcome. It is a question I have brought up before myself. However I don't think it is that difficult to DEFINE, but it is to pin down, even when you have the definition. That's because you have to have some kind of access to at least the ancestral type if not the original type in order to determine which was a mutation (a change in the genetic structure) and which was a variation (the results of combining genetic structures in sexual reproduction, for the purposes of this illustration/argument).

I tend to take the conservative side and figure that, unless we can find a genetic cause, and unless there is an obvious deformity or disability involved, simple body variations are simply that -- variations. Others seem to think that any variation they have not previously been aware of, and maybe them, too, are all the products of some kind of mutation. Although each side would like to be right, the truth is probably somewhere in the middle.

 

For you evolutionists out there, this might nterest you:
http://www.bio.psu.edu/People/Faculty/Nei/Lab/2005-glazko-etal.pdf

Eighty percent of proteins are different between humans and chimpanzees

Here are the conclusions of the article:

(1) Although nucleotide sequence identity between
humans and chimpanzees is very high, only 20% of
proteins are identical between the two species, and
80% of proteins are different.
(2) Even the 80% protein differences appear to be too
small to explain the phenotypic differences. It seems
that the phenotypic differences are controlled by a
small proportion of genes, either by regulatory genes
or by major effect genes.
(3) A larger number of genes than ours need to be studied to
understand the genetic basis of phenotypic differences.

 

OK Lets look at some alternative plausible explanations and see how they fare.

Lets take the alternative explanation of seperate creation of kinds by an omnipotent and omniscient being, for example.

Whales, then, would be created independently, by this omniscient being, Who would be free to make them any way He wanted. For example, He would be free to make the tails horizontal instead of vertical.

But then you have to consider the fact that whales have those hip bones left floating in there. Some whales don't have them, you know, so we can't say they are essential. What kind of omnipotence adds scraps of bones that cannot possibly be required?

Another blow to the theory of independent creation by an omnipotent creator is delivered by consideration of the vitamin c situation.

Primates in general have a defective gene for making vitamin C. It has been identified, the same defect is shared by us all. Defects in genes happen randomly, not systematically, so it is no use saying they all got that way after the fall due to the curse; the damage is too uniform, to much exactly the same between species. Something else caused the same damage over the whole primate class. Evolution explains it by common descent from a single defective gene in the common ancestor.

Vitamin c gene damage has occurred independently in guinae pigs and in fruit bats, and the gene damage has been shown to be of a different kind in those cases.

The hypothesis of inpendent creation could be rescued by assuming defective blueprints at the time of creation. The "creator" using a common blueprints for the chemical subroutine in the creature could put it together with those defective blueprints and make the same mistake over and over for a while - while working on the primates, say . . .

This does not square with my theology of God as being omniscient.

But it is a nice rescue interpretation for that particular issue. In your desire to avoid accepting evolution, are you willing to go that far?

 

thank you for the interesting article.

For the lurkers, if a protein has the following sequence

aaababbbacaaabaac
and another has this sequence
aaababbbacaaabaad

they would be considered different in the method used in this article. That accounts for why the genomes can be so much alike yet the proteins have so many that are different.

 

Paul, you are accepting the definition of those tiny bones as 'hip bones.' There is no indication they were ever hip bones. What we do know is that they have a purpose -- they anchor internal organs. There is no reason to suppose they ever did anything else in whales. You are swallowing the evolution stuff hook line and sinker without even thinking about the idea that God might know how to communicate in Genesis!

"Defective blueprints at the time of creation"? You are judging God.

Consider that the exposure to the first radioactive material at the time of the Flood might easily have caused the same genetic damage in the few humans as in the few primates who survived.

Now, about those primates and humans -- what excuse for evolution do you have for that 80% difference in proteins?

 

Small differences in proteins yield enormous differences in the organism. It is not something you can slide out of that easily, Paul, especially when you are claiming evidence from the vitamin c mutation...

 

OK Lets look at some alternative plausible explanations and see how they fare.

Lets take the alternative explanation of seperate creation of kinds by an omnipotent and omniscient being, for example.

Whales, then, would be created independently, by this omniscient being, Who would be free to make them any way He wanted. For example, He would be free to make the tails horizontal instead of vertical.

But then you have to consider the fact that whales have those hip bones left floating in there. Some whales don't have them, you know, so we can't say they are essential. What kind of omnipotence adds scraps of bones that cannot possibly be required? </font>[/QUOTE] Three fallacies to answer here. First, just because you don't know the function doesn't mean there is none. Could these be useful in reproduction or something else? Maybe.

Two, I didn't say that God did create it that way. Maybe He did or maybe whales did in fact have rear appendages at some point and lost them due to a radical deletion... which provides no help to your idea of the ascension of species.

Third, your rhetorical question at the end implies a metaphysical proposition about God. God is sovereign. He can create a whale any way He chooses for any purpose He chooses. Your question is dealt with at length in the book I suggested. It was the idea that "God wouldn't have done it that way" that largely gave rise to evolution in the first place.

The problem with this is that statistically the mutation is just as likely to happen twice as it is to happen once. Seeing that similar genetic design was used for humans, apes, and monkeys only makes it far more likely to have occurred under the right environmental conditions. Before you scream foul... consider that evolutionists believe that evolution accounts for the eye... via 12 lines of convergent evolution whose boundaries aren't always as distinct as would be expected. Further, they believe that Tasmanian wolves and a few other species developed by convergently because they have a marsupial reproductive system... yet otherwise they belong with others of their type.

If you want a speculation, I would offer that a plague among primates before they were well dispersed wiped out the ones who didn't have this mutation.

I am not confused about the fact that guinea pigs and bats are far more different from humans than apes and monkeys... Are you?

Nope. Very effective blueprints actually.

God created it perfectly and sin has deteriorated it since the fall. Had the blueprints been the least bit defective, all life would have ceased. Instead, it simply began to die.

BTW, I caught something very interesting in UTE's last post concerning the origins of exons and introns. He even said the latter was once active but is now "junk". That sounds to me like genetic complexity, order, flexibility, and code that was lost in the past. IOW's, the answer to your question lies in the current construction of the gene itself. It isn't the same. It isn't as good perhaps. But it still functions.

Again assuming what God could or couldn't do and for what reasons huh?

It very well should if you can swallow a camel so large that you would believe that He could originally spark the universe, leave everything else to chance combinations of natural events, and still accomplish the universe and creation that He intended 5 billion years later.

You believe God could omnisciently create something apparently very simple... but would struggle with creating perfect kinds capable of surviving the corruption brought by the fall?

No. It is a nasty little straw man typical of folks who really don't want to deal with the key points of another side's arguments.

 

No, it couldn't! That is patently ridiculous! Radiation would cause random damage throughout the genome, it would not target this specific sequence! I must go soothe my nerves with a cup of tea--that proposition was quite jarring.

Why would evolution need an excuse? It would predict this variation. In fact, I have repeatedly used the variation among homologous proteins and their capacity to replace native proteins when placed in a different organism as evidence that mutation is not necessarily detrimental.

It's interesting that the creationists commonly seem to habitually deny explanations that would favor evolution and then attempt to use that same explanation in the service of YE creationism. For instance, "Mutations are rare and invariable detrimental, except when they're resulting in the formation of thousands of new species in the 4000 years following the Flood."