Evolution observed in bacteria?

[David Blacklock]

Hi Kurieuo,

Thanx for your thoughtful reply. In answer to >>is there even one example where a hox gene mutation resulted in something really new and beneficial? I don't recall coming across any such examples, but would be interested in them<<

The hox genes, being core genes, are unlikely to change. The DNA segments on either side of any active (core) gene contain genetic switches. They decide when to turn the various core genes on and off and they are very susceptible to non-lethal mutation. Most of the changes in mammals would not be fast enough to observe within someone's generation, or even ten generations, but whenever an example is found, it is mentioned in current books and journals. A common one nowadays is the stickleback fish, which has changed its body armour. Molecular geneticists have identified areas of DNA close to the core genes that are responsible.

Here is a website: After Sewage Spill Cleanup, Fish in Lake Washington Evolving in Reverse ...
Now that the sewage spill in Lake Washington has been cleaned up, the threespine sticklefish has devolved back to its armored former state to protect itself.
earthfirst.com/after-sewage-spill-cleanup-fish-in-lake-washington-e.

To get this site, I googled stickleback fish. There are several sites that have info:

Kingsley, who is also an associate investigator with the Howard Hughes Medical Institute, said the debate over how limbs evolve has been stymied because most animals that evolved to have fewer or altered limbs also have a host of other genetic changes, making it hard for scientists to tease out the number and location of genetic changes most important for altering the limb. Sticklebacks, with their recent divergence into many distinct populations, present an opportunity to study recent limb evolution.

The marine stickleback (top) has a large pelvic hind fin but other stickleback populations that evolved in freshwater locations have lost this pelvic fin (bottom). Tracing the evolutionary shift, researchers have discovered that changes in the hind fin skeleton are controlled by alterations in activity of the Pitx1 gene. Photo: Mike Shapiro

Sorry the photo didn't paste through, but these sites are easy to find.

DB

[Kurieuo]

Hi Kurieuo,

Thanx for your thoughtful reply. In answer to >>is there even one example where a hox gene mutation resulted in something really new and beneficial? I don't recall coming across any such examples, but would be interested in them<<

The hox genes, being core genes, are unlikely to change. The DNA segments on either side of any active (core) gene contain genetic switches. They decide when to turn the various core genes on and off and they are very susceptible to non-lethal mutation. Most of the changes in mammals would not be fast enough to observe within someone's generation, or even ten generations, but whenever an example is found, it is mentioned in current books and journals. A common one nowadays is the stickleback fish, which has changed its body armour. Molecular geneticists have identified areas of DNA close to the core genes that are responsible.

The stickleback fish is an interesting case, however I think I need to clarify the type of example I was looking for.

I previously wrote that "I can accept hox genes with mutation as a possible natural vehicle for macro-evolutionary change." A hox gene mutation on its own can only account for what I consider to be microevolutionary changes. This is because hox genes are simply switches to activate (or de-activate) pre-existing biological code. While a biological change happens, no new biological code segments are produced. As such, the stickleblack fish and its armour is for me not a case of macroevolution, but rather microevolution.

For illustrative purposes of what I am looking for with regards to "a hox gene mutation resulting in something really new." Say a hox gene mutation caused the pre-existing biological code for an arm to appear below a torso. This lower torso arm then somehow underwent changes to the point that the DNA code itself no longer represented that of an arm, but rather resembled a fully functioning and unique leg. Hox genes combined with mutations would here I believe account for macroevolution. That is the kind of example I am looking for. Hox genes could be the vehicle to "copying and pasting" pre-existing code, but another vehicle is required to transform that code into something new and meaningful.

[David Blacklock]

The stickleback is the best example I know of where a part changed in a short period of time. A fin didn't become a leg, but give it a million or 10 million years. A big change like sticklebacks have is pretty impressive for only a few decades.

The ear is a remarkable Rube Goldberg apparatus. There is a beautiful transitional series from reptiles to mammals showing that the malleus and the incus of mammals' middle ears evolved from bones set in the back of the jaws of reptiles. But it doesn't stop there. Genes responsible for our ears can be traced back to jellyfish.

Our fish to human framework is so strongly supported scientists no longer try to marshall evidence for it. The exercise is like peeling an onion, exposing layer after layer of history. The pattern of descent with modification is deeply etched inside our bodies, and is matched by the geological record. The jerry-rigging from being forced to use remanufactured parts has resulted in a less than perfect product - hiccups, hernias, back pain, joints that don't last long enough, and sleep apnea - to name a few.

DB

[godslanguage]

David said:

Genes responsible for our ears can be traced back to jellyfish.

Our fish to human framework is so strongly supported scientists no longer try to marshall evidence for it.

Hi David, personally I don't care much for similarities between species, but here is a indirect reply (that you don't necessarily have to respond too since I'm quoting Bornagain77 from uncommondescent)

"Naturalists always try to establish scientific validity for evolution by pointing to suggestive similarities while ignoring the foundational principle of science (genetic entropy) that contradicts their preconceived philosophical bias. For example, naturalists say that evolution is proven true when we look at the 98.8% similarity between certain segments of the DNA in a Chimpanzee and compare them with the same segments of DNA of a Human. Yet that similarity is not nearly good enough to be considered “conclusive” scientific proof. For starters, preliminary comparisons of the complete genome of chimps and the complete genome of man yield a similarity of only 96%. Dr. Hugh Ross states the similarity may actually be closer to 85% to 90%. Secondarily, at the protein level only 29% of genes code for the exact same amino acid sequences in chimps and humans (Nature, 2005). As well, our DNA is 92% similar to mice as well as 92% similar to zebrafish (Simmons PhD., Billions of Missing Links). So are we 92% mouse or are we 92% zebrafish? Our DNA is 70% similar to a fruit fly; So are we therefore 70% fruit fly? Our DNA is 75% similar to a worm; So are we 75% worm? No, of course not!! This type of reasoning is simple minded in its approach and clearly flawed in establishing a solid scientific foundation on which to draw valid inferences from! Clearly, we must find if the DNA is flexible enough to accommodate any type of mutations happening to it in the first place. This one point of evidence, (The actual flexibility of DNA to any random mutations), must be firmly established, first and foremost, before we can draw any meaningful inferences from the genetic data we gather from organisms!! Fortunately we, through the miracle of science, can now establish this crucial point of DNA flexibility. The primary thing that is crushing to the evolutionary theory is this fact. Of the random mutations that do occur, and have manifested traits in organisms that can be measured, at least 999,999 out of 1,000,000 (99.9999%) of these mutations to the DNA have been found to produce traits in organisms that are harmful and/or to the life-form having the mutation (Gerrish and Lenski, 1998)! Professional evolutionary biologists are hard-pressed to cite even one clear-cut example of evolution through a beneficial mutation to DNA that would violate the principle of genetic entropy. Although evolutionists try to claim the lactase persistence mutation as a lonely example of a beneficial mutation in humans, lactase persistence is actually a loss of a instruction in the genome to turn the lactase enzyme off, so the mutation clearly does not violate genetic entropy. Yet at the same time, the evidence for the detrimental nature of mutations in humans is clearly overwhelming, for doctors have already cited over 3500 mutational disorders (Dr. Gary Parker)."

[David Blacklock]

Hi GL and thanx for your reply.

I agree the percentages of DNA similarities in similar and non-similar species seem to be thrown around quite frivolously.

This statement from your offering seems a little out of line:

Of the random mutations that do occur, and have manifested traits in organisms that can be measured, at least 999,999 out of 1,000,000 (99.9999%) of these mutations to the DNA have been found to produce traits in organisms that are harmful and/or to the life-form having the mutation (Gerrish and Lenski, 1998)! Professional evolutionary biologists are hard-pressed to cite even one clear-cut example of evolution through a beneficial mutation to DNA that would violate the principle of genetic entropy.

I think I found the article from Gerrish and Lenski, 1998. Parts of the data from that article data appear to be cherry-picked and taken out of context. The authors were most certainly not suggesting evolution has not happened.

Rather than focus on what evolutionary naysayers have come up with (instead of doing any real research), consider this: First, maybe forget about the mechanism. Forget about natural selection, microevolution, macroevolution, genetics, DNA, or any other explanations as to how this occurred. Instead, consider the evidence that concludes common descent HAS occurred.

Talkorigins.org
"Relics of Eden"
"Your Inner Fish"

DB

[godslanguage]

Hi David,

Thanks for the tips and I'm sorry you feel that its such a simple consideration. Common descent is only one piece of the puzzle, I'm really less interested in that than I am about the process and mechanism. When you make wild claims, you have to back those up. Even if I do accept common descent, I don't accept the chance and luck happy one, rendering it uncommon descent.

[David Blacklock]

>>Thanks for the tips and I'm sorry you feel that its such a simple consideration. Common descent is only one piece of the puzzle, I'm really less interested in that than I am about the process and mechanism. When you make wild claims, you have to back those up. Even if I do accept common descent, I don't accept the chance and luck happy one, rendering it uncommon descent<<

Thanx for the reply, GL. So you accept common descent? Over a period of hundreds of million of years? Good, so do I. And I have no problem with a designing God. I guess we're in agreement. Finally!

DB

[11diesej]

Can someone please tell me why, if all earthly organisms do not share a common ancester, they all share the same four nitrogen bases in their DNA. Adenine, cytosine , guanine and thymine are found in all organisms, experiments have also been conducted transplanting DNA from one species to another, and the recipient organism has showed characteristics associated with the DNA donor.

[zoegirl]

Can someone please tell me why, if all earthly organisms do not share a common ancester, they all share the same four nitrogen bases in their DNA. Adenine, cytosine , guanine and thymine are found in all organisms, experiments have also been conducted transplanting DNA from one species to another, and the recipient organism has showed characteristics associated with the DNA donor.

But this not not exclude the presence of a creator who used the same materials throughout His creation. Why in the world would you be surprised by an artist using the same paints, the same techniques, the same brushstrokes throughout his artwork? Why would you be surprised at God using the same chemicals in the organisms?

Having said that, I don't disagree with God using the organisms early in the creation to cvreate the ones later and as such these common elements would have come up.

[Kurieuo]

Can someone please tell me why, if all earthly organisms do not share a common ancester, they all share the same four nitrogen bases in their DNA. Adenine, cytosine , guanine and thymine are found in all organisms, experiments have also been conducted transplanting DNA from one species to another, and the recipient organism has showed characteristics associated with the DNA donor.

Because such code forms a basis of biological language. Why, if all computer programs do not share a common ancestor, they are all ultimately reduced to binary code? Because binary code forms the basis of computer language.

How such languages came to be are more interesting questions.

[godslanguage]

I went back to read the first page of the thread....

Micro evolution is nothing like Macro Evolution. Why? Because there is no such thing as Macro evolution. There simply is or isn't evolution. The only place Macro Evolution exists is in a place called philosophy. Micro evolution is observable, stick with the observable, don't add millions or billions of years to micro evolution, call it macro and then call it science. Sorry, this kind of garbage does not hold grounds. This is inline with how they speak about continental drift, as though both are telling the same tale. Change does occur, but the problem that must be faced is what kind of change it is (what is changing), what mechanism drives x change etc...its not so simple.

A biological system is the most complex piece of technology on the planet, I think the Darwinists had better start treating it as such else they're going to be bombed with more arguments against they're fairytale and then they're going to complain that the creationists and/or ID'st are preventing them from doing science.

[godslanguage]

Can someone please tell me why, if all earthly organisms do not share a common ancester, they all share the same four nitrogen bases in their DNA. Adenine, cytosine , guanine and thymine are found in all organisms, experiments have also been conducted transplanting DNA from one species to another, and the recipient organism has showed characteristics associated with the DNA donor.

So cars, boats, skyscrapers and airplanes must all be related because each use screws and fasteners as they're building blocks. I'm not saying they aren't, but I'm not saying they are either.

If screws and fasteners are a good way to put things together then perhaps its good to use screws and fasteners for many purposes, don't you think?

On the other hand, you are right. DNA does tell us a lot. It tells us that the source of information is best explainable by an intelligent cause. Codes are like that, they tend to have origins other then mud or goo.

Whether we share 92% of our DNA with Zebrafish and mice at the same instance, this tells us nothing about how we have come to share that similarity or non-similarity. It tells us nothing about where DNA itself originated, how it came to form the first living cell and how the rest of it came out. Thus, again the emphasis is always the mechanism.

To keep the note to self records up to date, loss of function, similarities in function, don't tell us how that function came about in the first place. You can only draw sloppy conclusions from that, Darwinian Evolution is an example of a sloppy conclusion. Or did I already know that....

[David Blacklock]

Science doesn't know how as much as it would like, but the trail of evidence left by the DNA of life leaves (almost )incontrovertible evidence that common descent happened. I added "almost" because there is always the possibility that God did it some other way and then left this trail as a trick to mislead us - not a strong possibility, IMHO.

From RationalWiki:

Irrefutable evidence for common descent:

Endogenous retroviral insertions - These are inactivated viral genes that were inserted by ancient retroviruses. In order for a retrovirus to be inherited in all members of a species many highly improbable events must happen. The virus must insert into a gamete cell, it must mutate so it is inactive, that gamete cell must be used to make an embryo that lives to reproduce and whose genome fixates into the population. This is a very rare event, and ERVs are usually species specific and insert themselves nearly randomly into the genome of the host. The fact that we share ERVs with simians is proof we share a common genome. Even more than that, phylogenetic trees can be constructed based on the pattern of ERVS, humans share more ERVs with chimps than either share with gorillas. This is absolute proof of common descent.

Pseudogenes - Shared errors are a powerful argument for a common source. If two text books describe the same event in similar language it's [doubtful, but] possible they just both converged on the same wording. But if they both share the same grammar or spelling errors it becomes impossible to say they did not derive from a common source. There are genes that no longer code for a protein due to a mutation or error. Species often share the same pseudogene, with the same inactivating mutation. A famous example of this is the L-gulonolactone oxidase which synthesizes vitamin C. All simians including humans share this pseudogene, but the guinea pig which also has an inactivated L-gulonolactone oxidase gene has a different mutation.

Embryology - The pharyngula stage of embryonic development appears to be highly conserved over time. At this stage it is difficult to tell the difference between various vertebrate species. This conserved state screams common ancestry, and the field of evolutionary development, which is highlighting the role of such things as HOX genes, has expanded our knowledge of embryo ontogeny to amazing new levels of detail. All thanks to acknowledging the fact of common descent.

Chromosome fusion - Chimpanzees have one more chromosome than humans do. If it is true we share a common ancestor we should be able to figure out what happened to that chromosome. Researchers have found it. Chromosome 2 in humans is actually the fusion of two chromosomes that have remained separate in the chimpanzee line. At the end of each chromosome is a marker called a telomere which usually appears only on the ends. But in human chromosome 2 it also appears in the center, marking where the two ends fused. Another knock down win for common descent.

Convergence - The phylogenetic trees constructed using anatomical homology, DNA homology, pseudogenes, endogenous retroviral insertions, and many other methods all converge on a similar looking tree. There are slight differences but the general relationships of the trees are intact. If all of these methods were flawed you would not expect each of them to converge on the same tree.

DB

[Byblos]

Science doesn't know how as much as it would like, but the trail of evidence left by the DNA of life leaves (almost )incontrovertible evidence that common descent happened. I added "almost" because there is always the possibility that God did it some other way and then left this trail as a trick to mislead us - not a strong possibility, IMHO.

It's a little more than 'almost' DB.

From RationalWiki:

Irrefutable evidence for common descent:

Let's see how irrefutable it is:

Endogenous retroviral insertions - These are inactivated viral genes that were inserted by ancient retroviruses. In order for a retrovirus to be inherited in all members of a species many highly improbable events must happen. The virus must insert into a gamete cell, it must mutate so it is inactive, that gamete cell must be used to make an embryo that lives to reproduce and whose genome fixates into the population. This is a very rare event, and ERVs are usually species specific and insert themselves nearly randomly into the genome of the host. The fact that we share ERVs with simians is proof we share a common genome. Even more than that, phylogenetic trees can be constructed based on the pattern of ERVS, humans share more ERVs with chimps than either share with gorillas. This is absolute proof of common descent.

We've discussed ERVs at length some time ago; I'll try to find the link.

In the mean time 2 questions:

1. How can you tell an ERV is an ERV when you see one? One would have to have a frame of reference for comparison but alas we have none. ERVs could simply be part of junk DNA and as much evidence of common design as it is of common descent (which I;m not totally against on principal, just that we don't have enough evidence of it as science would tend to suggest).

2. The argument for common descent is strongest when discussing not only the identical so-called ERVs but also their insertion points. The argument is such that, out of millions of possible base pairs, for ERVs to be inserted in the same exact spots in both humans and chimps is evidence of common descent. On the surface it's a great argument if one assumes that the insertion is completely arbitrary. But is it? Are you aware of recent discoveries of a particular protein that directs the HIV virus to be inserted in specific spots in the DNA? If ERVs were truly viruses one then cannot exclude the possibility that 2 distinct species with the same director proteins were infected with the same virus. This will render ERVs as evidence of common descent inconclusive at best.

Pseudogenes - Shared errors are a powerful argument for a common source. If two text books describe the same event in similar language it's [doubtful, but] possible they just both converged on the same wording. But if they both share the same grammar or spelling errors it becomes impossible to say they did not derive from a common source. There are genes that no longer code for a protein due to a mutation or error. Species often share the same pseudogene, with the same inactivating mutation. A famous example of this is the L-gulonolactone oxidase which synthesizes vitamin C. All simians including humans share this pseudogene, but the guinea pig which also has an inactivated L-gulonolactone oxidase gene has a different mutation.

Pseudogenes MIGHT be explained by common descent but they certain are NOT the ONLY explanation there is. Junk DNA is more and more being found not to be junk at all. It has definite functions and in some cases can regain its coding capacity. The conclusion is that if junk DNA does have a function, then one would also expect their location to be the same in similar species. Again evidence of common design as much as it is of common descent.

Embryology - The pharyngula stage of embryonic development appears to be highly conserved over time. At this stage it is difficult to tell the difference between various vertebrate species. This conserved state screams common ancestry, and the field of evolutionary development, which is highlighting the role of such things as HOX genes, has expanded our knowledge of embryo ontogeny to amazing new levels of detail. All thanks to acknowledging the fact of common descent.

It could just as well scream common design. Although last I checked screaming is not one of the more commonly recognized scientific steps.

Chromosome fusion - Chimpanzees have one more chromosome than humans do. If it is true we share a common ancestor we should be able to figure out what happened to that chromosome. Researchers have found it. Chromosome 2 in humans is actually the fusion of two chromosomes that have remained separate in the chimpanzee line. At the end of each chromosome is a marker called a telomere which usually appears only on the ends. But in human chromosome 2 it also appears in the center, marking where the two ends fused. Another knock down win for common descent.

Genetic similarities may or may not be rooted in common descent. Why is it so hard to comprehend that it is by no means a foregone conclusion? In almost every bit of scientific discussion on the subject, common descent is assumed a priori to the exclusion of any other possibility. That's not science, it's revisionist placation.

Convergence - The phylogenetic trees constructed using anatomical homology, DNA homology, pseudogenes, endogenous retroviral insertions, and many other methods all converge on a similar looking tree. There are slight differences but the general relationships of the trees are intact. If all of these methods were flawed you would not expect each of them to converge on the same tree.

Now that's circular reasoning if I ever saw one. So ERVs and pseudogenes are evidence of common descent because they seem to point to common decent?

[godslanguage]

David, first you say:

1)

Irrefutable evidence for common descent:

then you say:

2)

This is absolute proof of common descent.

While I think ERV's, pseudogenes etc... are examples supporting common descent, they are in no way 2).