How New Genes Arise (yes they do)

sayak83 · Apr 15, 2017

It has been claimed several times by evolution deniers here that evolutionary theory has yet to provide any theory or evidence for the arising of new genes through mutation and natural selection. This, of course, is completely false. In this first post, I will discuss the experimental and observational evidence for a mechanism by which genes with novel functions arise. It is one of many mechanisms that scientists have validated.

The mechanism is called Innovation-Amplification-Divergence (IAD) model of arising of new genes by gene duplication. Duplication of stretches of DNA including genes by the DNA replication mechanism during cell division is quite a common occurrence in all types of life. These duplication often have no effect and hence are quickly lost. However in a sizeable number of cases, these copies of existing genes become the sites where mutation and natural selection act in concert to create new genes with new functions.

(i) Genes code for proteins and enzymes that are used in cells for various reactions and processes vital to life. Often it is the case that a mutation arises in the gene that slightly alters the protein such that the new variant is able to either initiate or participate in a new process to some extent along with its primary process. In such cases the gene gains a secondary functionality along with its primary function. This is the Innovation through mutation phase.

(ii) In such cases, if the proteins are manufactured in greater numbers, the secondary activity gains a boost out of greater protein or enzyme concentration. When genes are duplicated multiple times, each copy of the gene serves as another additional command to make more of the protein or enzyme. Hence natural selection over the secondary function helps in maintenance and fixation of multiple copies of the gene in the genome when these genes are duplicated during cell replication process. This is the Amplification through duplication phase.

(iii) The increased number of copies provide multiple targets where mutations can occur. Some of the copies undergo beneficial mutations that increase their efficacy with respect to the secondary function. Any loss of activity of the primary function in these copies is compensated by the presence of the original parent or other copies where the primary function is retained. During continuous evolution under conditions that select both for the primary and the secondary functions, beneficial mutations that enhance the efficacy of some copies for primary and some copies for the secondary function gain a fitness advantage and these copies become predominant in the population. This cause divergence between the gene copies in terms of sequence structure as well as the protein they code for.

(iv) Any improved copy can be further amplified whereas less functional copies can be lost.

(v) Eventual it leads to one group of closely related genes that code for the primary function only and another group of closely related genes that code for the secondary function only.

Thus a new gene with novel function is created through duplication, mutation and selection process.

In the next post, I will present experimental and observational evidence for this mechanism of origin of novel genes in organisms.

sayak83 · Apr 15, 2017

Experiment demonstrating the arising of new Genes

In 2012 a group of researchers used a bacterial strain of Salmonella to demonstrate the evolution of a new gene by the mechanism described in the first post. Below is a short description, the key results and the link to the paper:-

1) Salmonella bacteria, like all of life, requires two essential amino acids Histidine and Tryptophan in order to grow and divide.
Histidine - Wikipedia
Tryptophan - Wikipedia

2) Several strains of Salmonella exist, some that can synthesize both histidine and tryptophan by themselves from sugar and others that can synthesize only one and rely on ingesting the other from the environment.

3) Salmonella that can synthesize Histidine, has a specific gene that manufactures an enzyme called HisA which is critical to the synthesis of Histidine from sugar. Similarly for Salmonella that can synthesize Tryptophan, has a gene that manufactures a specific enzyme TrpF that is critical for the synthesis of Tryptophan from sugars.

4) First, the researchers took a strain of Salmonella that only has the HisA making gene and hence can only synthesize Histidine and needs to ingest Tryptophan from the environment. Thus the original bacteria had the ability to make:-

Sugar→Histadine with reaction rate k=0.6
But no Sugar → Tryptophan reactivity.

5) They then cultured it for several generations in a solution that was poor in Tryptophan but rich in Histidine. This created a selection pressure on the bacteria since Tryptophan was in short supply. Soon enough a strain emerged among the descendants that had a mutation in the HisA gene (consisting of the internal duplication of base pair numbers 13-15 of the gene) that gave the mutant a weak ability to make TripF (and hence synthesize Tryptophan) but this resulted in the complete loss of any HisA making ability.

This mutant strain had Sugar → Tryptophan with reactivity k = 0.2 but no sugar to histadine activity.

6)After this mutant strain had proliferated in the Tryptophan rich solution, it was then introduced in another solution that was rich in Tryptophan, but was poor in Histadine. This created a selection pressure on the bacteria and after several generations of growing in this medium, another mutant strain emerged with a DNA letter substitution in the 10th base pair of the gene that made the mutant hisA gene capable of moderate ability to synthesize histamineA enzyme again while retaining its ability to synthesize Tryptophan.

Thus the new mutant hisA gene with both internal duplication and base letter substitution has the ability to make

Sugar → Tryptophan at k=0.2 and the ability to make Sugar → Histadine at k=0.3

So far all this is happening in one gene, and what was seen was the Innovation stage of the gene duplication mechanism where a gene for a single function (making histadine) gained a secondary ability (making tryptophan) due to environmental selection pressure.

In the next post, I will look at how the researchers went further and demonstrated the other steps of the process.

sayak83 · Apr 15, 2017

In the last post one saw how, a bacterial gene that could only catalyze the synthesis of histamine evolved through accumulation of beneficial mutation under natural selection to evolve the secondary ability to synthesize tryptophan as well. However, the ability of the gene to synthesize both histamine and tryptophan, essential to growth were low to moderate.

Thus the mutant strain required an average 5 hours to replicate in a medium that had only sugar but lacked histamine or tryptophan while it took the strain only 1.5 hours to replicate when both the amino acids were present in the medium.

So, now, the researchers cultured several independent lineages of of this mutant strain of Salmonella in a glycerol medium lacking both amino acids. Thus the lineages were under continuous selection pressure for a) Improved growth rates b) Increased ability to synthesize histamine and c) Increased ability to synthesize tryptophan.

1) Within a few hundred generations, the growth rate of most lineages had increased from 5hrs per cell division to 1.9-2.5 hrs per cell division. Simultaneously multiple duplication events had increased the expression of the bifunctional gene (and hence the associated enzyme) in a stepwise fashion to over 20-fold its original value through repeated duplication events. Variants with greater number of gene copies could make more of the HistA and TrpF enzymes and hence could synthesize the amino acids faster and hence could reproduce faster, becoming predominant in the population. This increase in fitness by gene duplication was the experimental evidence of Amplification process described in the first post.

2) After 3000 generations of culture, the genetic copies in all the lineages had acquired novel mutations that resulted in increased efficiency for the synthesis of HistA or TripF enzymes. In most lineages, different copies of the gene had acquired different mutations changing what enzyme they were producing, how and at what rate. This was the validation of the diversification stage that was proposed as the final stage of the arising of new genes. From the 8 lineages which originally had the same mutant bifunctional gene, 22 distinct types of descendant genes were isolated after 3000 generations. Their function and rate of activity was measured and it was found that

a) Seven of these descendant genes have become histamine specialist only catalyzing histamine production:-
Sugar → Histamine at reaction rates 0.4<k<0.65
b) Seven of these descendant genes have become Tryptofan specialist with
Sugar → Tryptophan at 0.5<k<0.65 reaction rates
c) 8 of these genes have improved bifunctionality catalyzing both reactions such that
Sugar → Histamine at reaction rates 0.4<k<0.7
AND
Sugar → Tryptophan at 0.2<k<0.5 reaction rates

The same cell often contained several of these variants at once greatly increasing the efficiency of amino acid production.

Thus I have provided an unambiguous experimental evidence of the arising of
1) A novel function in genes through mutation and natural selection in real time
2) Arising of 22 novel genes in just 3000 generations from one variant through the Innovation-Amplification-Duplication process

The scientific paper is linked (2012, Science, Nasvall et al):-
Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence

Finally to allay any doubts that such a mechanism of new gene formation does not arise in animals, here is unambiguous observational evidence that the same process led to the creation of anti-freeze genes in fish that live in frigid waters of Antarctica

Antifreeze proteins: How one gene becomes two (with different functions)

Polymath257 · Apr 15, 2017

But they were still bacteria, right?

j/k

Sonofason · May 15, 2017

sayak83 said:
Experiment demonstrating the arising of new Genes

In 2012 a group of researchers used a bacterial strain of Salmonella to demonstrate the evolution of a new gene by the mechanism described in the first post. Below is a short description, the key results and the link to the paper:-

1) Salmonella bacteria, like all of life, requires two essential amino acids Histidine and Tryptophan in order to grow and divide.
Histidine - Wikipedia
Tryptophan - Wikipedia

2) Several strains of Salmonella exist, some that can synthesize both histidine and tryptophan by themselves from sugar and others that can synthesize only one and rely on ingesting the other from the environment.

3) Salmonella that can synthesize Histidine, has a specific gene that manufactures an enzyme called HisA which is critical to the synthesis of Histidine from sugar. Similarly for Salmonella that can synthesize Tryptophan, has a gene that manufactures a specific enzyme TrpF that is critical for the synthesis of Tryptophan from sugars.

4) First, the researchers took a strain of Salmonella that only has the HisA making gene and hence can only synthesize Histidine and needs to ingest Tryptophan from the environment. Thus the original bacteria had the ability to make:-

Sugar→Histadine with reaction rate k=0.6
But no Sugar → Tryptophan reactivity.

5) They then cultured it for several generations in a solution that was poor in Tryptophan but rich in Histidine. This created a selection pressure on the bacteria since Tryptophan was in short supply. Soon enough a strain emerged among the descendants that had a mutation in the HisA gene (consisting of the internal duplication of base pair numbers 13-15 of the gene) that gave the mutant a weak ability to make TripF (and hence synthesize Tryptophan) but this resulted in the complete loss of any HisA making ability.

This mutant strain had Sugar → Tryptophan with reactivity k = 0.2 but no sugar to histadine activity.

6)After this mutant strain had proliferated in the Tryptophan rich solution, it was then introduced in another solution that was rich in Tryptophan, but was poor in Histadine. This created a selection pressure on the bacteria and after several generations of growing in this medium, another mutant strain emerged with a DNA letter substitution in the 10th base pair of the gene that made the mutant hisA gene capable of moderate ability to synthesize histamineA enzyme again while retaining its ability to synthesize Tryptophan.

Thus the new mutant hisA gene with both internal duplication and base letter substitution has the ability to make

Sugar → Tryptophan at k=0.2 and the ability to make Sugar → Histadine at k=0.3

So far all this is happening in one gene, and what was seen was the Innovation stage of the gene duplication mechanism where a gene for a single function (making histadine) gained a secondary ability (making tryptophan) due to environmental selection pressure.

In the next post, I will look at how the researchers went further and demonstrated the other steps of the process.

Okay well done. You are the first person to provide evidence. This particular post may not be certain evidence of evolution, but it surely indicates a process that supports evolutionary processes that would support the theory of evolution, assuming of course that the results are accurate and true. I have no reason to doubt that they are accurate and true.

sayak83 · May 15, 2017

Sonofason said:
Okay well done. You are the first person to provide evidence. This particular post may not be certain evidence of evolution, but it surely indicates a process that supports evolutionary processes that would support the theory of evolution, assuming of course that the results are accurate and true. I have no reason to doubt that they are accurate and true.

Thanks. I am happy that you have an open mind. Also feel free to read the rest of the links in the other thread at leisure. I have tried hard to make them understandable and readable within the limitations of a forum post.

Sonofason · May 15, 2017

sayak83 said:
Thanks. I am happy that you have an open mind. Also feel free to read the rest of the links in the other thread at leisure. I have tried hard to make them understandable and readable within the limitations of a forum post.

Thanks. I honestly have no trouble with evolution. I have a problem with people believing it without the ability to show the evidence they claim exists. I know it took some work for you to do that, and I appreciate that.

Valjean · May 15, 2017

Sonofason said:
Okay well done. You are the first person to provide evidence. This particular post may not be certain evidence of evolution, but it surely indicates a process that supports evolutionary processes that would support the theory of evolution, assuming of course that the results are accurate and true. I have no reason to doubt that they are accurate and true.

Technical journals report processes like this in every issue. Textbooks are full of examples like this illustrating the various processes of evolution.
I'm still baffled as to how anyone manages to get through school without learning this.

Sonofason · May 15, 2017

Valjean said:
Technical journals report processes like this in every issue. Textbooks are full of examples like this illustrating the various processes of evolution.
I'm still baffled as to how anyone manages to get through school without learning this.

Me too. You will note that I never, not ever did I say evolution does not occur.

Deeje · Jun 4, 2017

Sonofason said:
Me too. You will note that I never, not ever did I say evolution does not occur.

I'll say it.

LOL

What is described in these posts is adaptation, not anything that proves macro-evolution.
This was done artificially in a lab.....not naturally in the bacteria's normal environment. What is seen when creatures are taken out of their natural environment and are forced to subsist on foods they would not normally eat, they adapt to the new food source or change of environment because if they don't, the species will die out. Its a survival mechanism, brilliantly designed to ensure the survival of that species. It never turns them into something else.

No one can deny adaptation....we see it clearly in many species.....like the Peppered Moth, which is used as a prime example of "evolution".....it isn't. It's an example of adaptation, and the fact that the moths returned to their original color after the pollution problem was rectified, proves it.

Show us where any species that was forced to adapt because of environmental factors ever became something other than their original taxonomic "family" description. As someone has already said....they are still bacteria.

What have you proved, really :shrug:

idav · Jun 4, 2017

Deeje said:
What have you proved, really

That unique mutations can and do occur.

Are you asking for evidence of the hulk?

ArtieE · Jun 4, 2017

Deeje said:
Show us where any species that was forced to adapt because of environmental factors ever became something other than their original taxonomic "family" description. As someone has already said....they are still bacteria. What have you proved, really

That gene duplication and mutation naturally produces new genes with new functions. And when genomes continually and naturally add on new genes with new functions you'll eventually end up with more and more complicated genomes including the human genome.

Deeje · Jun 4, 2017

idav said:
That unique mutations can and do occur.

Are you asking for evidence of the hulk?

No.....fictitious creatures are already rife enough in the evolution story.

There is no proof that adaptation leads to anything but minor changes in any organism. It never takes them outside of their taxonomic family description. If you have proof of that I would like to see it.

Lets take horse evolution as an example.....we're talking about this from this...right?

And this is what evolution advocates propose as the line of decent or the chain of creatures morphing (evolving) into the modern horse....

Apparently, Eohippus was a small deer like creature and if you do some research, it becomes clear that very little is clear about many of these so-called 'ancestors' of the modern horse.....not to mention the fact that they all have four legs, a tail, and fur. (according to the artist's impression) So even assuming that this line of decent is true and these varieties of horse adapted to different environments...they all appear to be still within their taxonomic family.

One source said....

"There's a similar amount of confusion about whether Eohippus and/or Hyracotherium actually deserve to be called the "first horse." When you go back in the fossil record 50 million years or so, it can be difficult, verging on impossible, to identify the ancestral forms of any given extant species.
Eohippus....seems to deserve a place more firmly in the equid than the palaeothere family tree, though of course this is still up for debate!....

As with many such evolutionary precursors, Eohippus didn't look much like a horse, with its slender, deerlike, 50-pound body and three- and four-toed feet; also, to judge by the shape of its teeth, Eohippus munched on low-lying leaves rather than grass."

Eohippus Facts

Nothing precise about the musings of evolutionists it seems.

Oft quoted Paleontologist David Raup wrote:

"Darwin's theory of natural selection has always been closely linked to evidence from fossils, and probably most people assume that the fossils provide a very important part of the general argument that is made in favor of Darwinian interpretations of the history of life. Unfortunately this is not strictly true. .... The evidence we find in the geologic record is not nearly as compatible with Darwinian natural selection as we would like it to be. Darwin was completely aware of this. He was embarrassed by the fossil record, because it didn't look the way he predicted it would, and, as a result, he devoted a long section of The Origin of the Speciesto an attempt to explain and rationalize the differences...Darwin's general solution to the incompatibility of fossil evidence and his theory was to say the fossil record was a very incomplete one...Well we are now about 120 year after Darwin, and the knowledge of the fossil record has been greatly expanded. We now have a quarter million fossil species, but the situation hasn't changed much. The record of evolution is surprisingly jerky, and ironically, we have fewer examples of evolutionary transition [changes over time of species] than we had in Darwin's time. By this I mean that some of the classic cases of Darwinian change in the fossil record, such as the evolution of the horse, in North America, have had to be discarded or modified as a result of more detailed information-that what appeared to be a nice simple progression when relatively few data were available now appears to be more complex and much less gradualistic. So Darwin's problem has not been alleviated in the last 120 years and we still have a record which does show change but one that can hardly be looked upon as the most reasonable consequence of natural selection."

Many believe that Raup is quoted out of context by creationists to demonstrate that he wasn't supporting evolution....that is not true, as he was definitely an evolutionist......but he was at least honest enough to report the theory's many shortcomings.

Looks can be deceiving.....If you were to compare an otter and a beaver for example, would you assume that they are related because of their many physical similarities?

"On the surface, at first glance, there may not seem like much of a difference between otters and beavers. Yet they are vastly different animals, and even come from different orders."

Difference Between Otters and Beavers | Difference Between

The thing is...if those in the same scientific field cannot agree on what the "evidence" suggests in many areas, then how are we (the mere public) to ascertain the truth about any of it? :shrug:

Deeje · Jun 4, 2017

ArtieE said:
That gene duplication and mutation naturally produces new genes with new functions. And when genomes continually and naturally add on new genes with new functions you'll eventually end up with more and more complicated genomes including the human genome.

But you never end up with an entirely different creature....that is the point. All remain within their biological classification. There is no proof at all that creatures ever morphed into other creatures. That is evolution's fantasy. Unproven and unprovable.

Valjean · Jun 4, 2017

The fossil record shows a clear evolution of numerous species, if you'd care to look.
Denying "macroevolution" is like acknowledging inches but denying feet or yards. Small changes + time accumulate into big changes.

Thief · Jun 4, 2017

sayak83 said:
It has been claimed several times by evolution deniers here that evolutionary theory has yet to provide any theory or evidence for the arising of new genes through mutation and natural selection. This, of course, is completely false. In this first post, I will discuss the experimental and observational evidence for a mechanism by which genes with novel functions arise. It is one of many mechanisms that scientists have validated.

The mechanism is called Innovation-Amplification-Divergence (IAD) model of arising of new genes by gene duplication. Duplication of stretches of DNA including genes by the DNA replication mechanism during cell division is quite a common occurrence in all types of life. These duplication often have no effect and hence are quickly lost. However in a sizeable number of cases, these copies of existing genes become the sites where mutation and natural selection act in concert to create new genes with new functions.

(i) Genes code for proteins and enzymes that are used in cells for various reactions and processes vital to life. Often it is the case that a mutation arises in the gene that slightly alters the protein such that the new variant is able to either initiate or participate in a new process to some extent along with its primary process. In such cases the gene gains a secondary functionality along with its primary function. This is the Innovation through mutation phase.

(ii) In such cases, if the proteins are manufactured in greater numbers, the secondary activity gains a boost out of greater protein or enzyme concentration. When genes are duplicated multiple times, each copy of the gene serves as another additional command to make more of the protein or enzyme. Hence natural selection over the secondary function helps in maintenance and fixation of multiple copies of the gene in the genome when these genes are duplicated during cell replication process. This is the Amplification through duplication phase.

(iii) The increased number of copies provide multiple targets where mutations can occur. Some of the copies undergo beneficial mutations that increase their efficacy with respect to the secondary function. Any loss of activity of the primary function in these copies is compensated by the presence of the original parent or other copies where the primary function is retained. During continuous evolution under conditions that select both for the primary and the secondary functions, beneficial mutations that enhance the efficacy of some copies for primary and some copies for the secondary function gain a fitness advantage and these copies become predominant in the population. This cause divergence between the gene copies in terms of sequence structure as well as the protein they code for.

(iv) Any improved copy can be further amplified whereas less functional copies can be lost.

(v) Eventual it leads to one group of closely related genes that code for the primary function only and another group of closely related genes that code for the secondary function only.

Thus a new gene with novel function is created through duplication, mutation and selection process.

In the next post, I will present experimental and observational evidence for this mechanism of origin of novel genes in organisms.

novel genes....as in the genetics of the Tasmanian Devil?

a radio report just last week ....
the species is being devastated by a cancer
the discussion went to genetics

sayak83 · Jun 4, 2017

Do not feed the troll. Is @Deeje presented any arguments that refute the evidence shown in the OP that novel genes can and does arise through evolution? No? Then he has said nothing relevant regarding thread topic.

sayak83 · Jun 4, 2017

Thief said:
novel genes....as in the genetics of the Tasmanian Devil?

a radio report just last week ....
the species is being devastated by a cancer
the discussion went to genetics

I have never understood what half of your posts mean. This is one of them. Sorry.

Thief · Jun 4, 2017

sayak83 said:
I have never understood what half of your posts mean. This is one of them. Sorry.

the radio report was as short of words as I am

genetics as a means of evolution?.....of course
the mechanism must change for the species to change

unfortunately for the Tasmanian Devil....the marker has gone sour
AND can be transferred from one individual to another

the cancer is contagious

Skwim · Jun 4, 2017

Sonofason said:
Thanks. I honestly have no trouble with evolution. I have a problem with people believing it without the ability to show the evidence they claim exists.

Thing is, many people wanting evidence for evolution don't really know what they're looking for, and when it's presented they often don't understand it or refuse to. As far as an inability to show evidence, this is not unlike many other subjects people take on their faith in experts. I would have a difficult time assembling convincing evidence that there's probably a huge supermassive black hole lurking in the middle of our galaxy; however, I am willing to accept its probability on the faith I have in the abilities of cosmologists. So, I have no problem believing that there's probably a huge supermassive black hole in the middle of our galaxy despite my inability to produce understandable evidence.

.

How New Genes Arise (yes they do)

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