What is the Evidence of Mutations and New Information

[RockyMidnight]

2 hours ago, one.opinion said:

I just ran across an article that is relevant to the conversation. You can link to it (here).

Theodosius Dobzhansky, an Eastern Orthodox Christian and scientist, famously wrote in 1973 that “nothing in biology makes sense except in the light of evolution.” He was talking specifically about fossils, the diversity and geography of life, and the sequence similarities between proteins. We now know he could also add cancer to his list. Our understanding of both cancer and evolution are intertwined.

Evolutionary theory “makes sense” of cancer, giving us critical insight into how it works.

This has become particularly clear in recent years. Now, we can sequence all the genes in a patient’s cancer, and see how they change over time as cancer evolves. Cancer evolves with the same evolutionary mechanisms¹ that drive the evolution of new species. Like breadcrumbs marking a path through a forest, cancer evolution leaves information in cellular genomes that evolutionary theory can decode.

Going the other direction, cancer makes sense of evolution too. Cancer itself is not evolution at the species level. However, it validates the mathematical framework underlying modern evolutionary theory. Cancer cells evolve multiple new functions in an evolutionary process, creating precise genetic signatures of common descent. At both a genetic and functional level, cancer follows patterns explained by evolutionary theory.

Skeptics of evolution often doubt we know enough about how genomes change over time, or how new functions arise, to correctly infer common ancestry from patterns in genetic data. They sometimes argue that “historical science” cannot be trusted, since it is making claims about the distant past. In cancer, however, we can directly verify that evolutionary theory correctly reconstructs a cancer’s history, including its ancestry. We see all the same patterns in cancer evolution that we do in the evolution of species: neutral drift, nested clades, novel functions, and positive selection. The same math, software, and theory that is used to study the evolution of species works for cancer too.

If evolutionary theory is wrong about the origin of species, why does it work so well for cancer?

What is Cancer?

On a human level, we are all affected by cancer. Many of us will die from it. Almost of all of us will be close to someone who dies from it. Cancer is a tragedy. Scientists want to understand how cancer works so we can intervene and reduce human suffering.

From a biological point of view, it is now clear that cancer is an evolutionary disease. Cancer biologists use evolutionary theory because it is useful and accurate, not because they are pushing an “evolutionary agenda.” In cancer, cells evolve a set of new functions. These functions are beneficial to the cancer cell, but ultimately lethal to their host. And cancer must do much more than just grow quickly. It must also…

1. ignore signals to die,
2. evade immune defenses,
3. grow blood vessels to obtain nutrients,
4. invade surrounding tissue,
5. survive in the bloodstream,
6. establish new colonies throughout the body,
7. and even resist treatment.

Not every cancer acquires all these functions. Nonetheless, in all cases, more than just rapid growth is required for cancer to develop. Several new functions are required. Ultimately, many cancers will acquire more than ten beneficial (to the cancer cell) mutations that enable these new functions.

One incorrect metaphor for cancer (and a misguided way of dismissing evolution) is that cancer is just cells “breaking down” or “gunk in the machine.” Superficially, the “breaking down” metaphor explains some changes in cancer. For example, some cells acquire the ability to divide uncontrollably by truncating, or “breaking,” specific proteins that normally control cell division.

The “breaking down” metaphor, however, is not adequate. When our technology breaks down, it never produces anything resembling cancer. Old cars, laptops, and watches do not grow tumors as they break down. In this way, cancer reminds us that biology is unlike any human design. Cancer is unique to biological systems, and we are afflicted with it because we are intrinsically capable of evolving.

Evolution, it turns out, is a much more useful framework for understanding cancer. From the cell’s point of view, cancer is evolving new functions in the environment of the host’s body. It evolves these functions in an evolutionary process. Cancer exists only because biological systems, including humans, have the intrinsic ability to evolve.

Does Cancer Evolve New Species?

Of course, cancer does not evolve new species. At least not usually…

In biology, there are exceptions to almost every rule, including this one. As it turns out, cancer occasionally produces new species. The two most interesting examples of this are a parasite that infects dogs, and another that infects Tasmanian devils. In these cases, a cancer evolved specific new functions: genetic stability and infectivity. Then, because of its location and the behavior of its host, it spread to others. A new species of parasite is born.

New species arise from cancer only very rarely; this isn’t the rule. Still, sometimes, they do. The evolution of new species from cancer is an important reminder that biology is surprising. It does not work according to our intuitions. In biology, there are always exceptions to the rules, and the improbable flukes are important.

Moreover, cancer still demonstrates how evolution works at a genetic level. Instead of millions of years, the time scale of cancer’s evolution is just years. So, cancer enables us to repeatedly study evolution in a system that matches our own biology. We see several important patterns: signatures of evolution. Evolution leaves information in our genomes from which we can reconstruct the past.

“Neutral” Processes Dominate Evolution

A common misconception about evolution is that it is dominated by natural selection acting on beneficial mutations (this is often what is meant by “Darwinian” mechanism). However, brilliant mathematical work and genetic experiments in the 1960s and 1970s by scientists like Haldane and Kimura demonstrated that evolution, at the genetic level, is usually dominated, instead, by the drift of neutral or near-neutral mutations. So most of the genetic differences between different lineages were either non-functional or not beneficial enough for natural selection. Only a few of the differences were fixed by natural selection. This is one reason biologists say that Darwinian evolution² is quantitatively less important than non-Darwinian evolution (e.g. neutral drift, neutral draft,³ and other mechanisms) in explaining the complexity in genetic differences between species.

Cancer evolution independently confirms that neutral theory is correct. We see the same patterns here, but the terminology is different.

In place of beneficial and neutral mutations, Cancer biologists often talk about “driver” and “passenger” mutations. The driver mutations are the ones that cause cancer, by conferring new abilities on the cancer cells. The passengers have no strongly selectable function: they are neutral. Rather than by natural selection, these neutral mutations are fixed by other mechanisms, like neutral drift. Any individual cancer cell will have tens, hundreds, or even thousands of mutations. But only a few⁴ of the mutations are drivers that are selected by natural selection. We know this fact from direct experimentation; only a small handful of mutations (of the thousands we observe) can actually induce cancer.

This is exactly what we expect from neutral evolutionary theory: drivers are vastly outnumbered by passengers. This is true for cancer, and it is also true for the evolution of new species. For example, the vast majority of genetic differences between humans and chimpanzees are neutral, and were fixed by neutral mechanisms like drift and draft. Over the last 6 million years, our ancestors explored hundreds of billions of mutations,⁵ tens of millions of these mutations were neutral and drifted into our genomes, and perhaps just a few thousand mutations were functionally important enough to be selected by natural selection.

Genetic Information and Common Descent

Most of the information in cancer genomes is a record of history. Genomes record the origins and evolution of every cancer cell, and their relationships to one another. Using evolutionary theory, we can read this history out of genetic data.

The specific part of evolutionary theory that reads history from genetic data is “phylogenetics.” Phylogenetics is foundational to modern evolutionary theory, with deep roots in information theory, population genetics, and neutral theory. It bears repeating, the exact same math, software, and theory that so accurately reconstructs a cancer’s history, is also used to reconstruct the evolutionary history of species.

Phylogenetics is powerful because there is so much historical information in genetic data. This information traces the ancestry of cancer cells. For example, one study used phylogenetics to map the ancestry of cells in a colon with a large tumor.⁶ This analysis showed that the cancer arose from a mutated original cell that also gave rise to neighboring regions of the colon and nearby polyps. The genetic mutations in the colon are in a “nested clade” pattern, exactly as evolution predicts.

Phylogenetics can identify exceptions to the normal rules of biology; it can reconstruct surprising and unexpected events. For example, we usually assume that cancer descends from a single cell in the host patient, but this is not always the case. Evolutionary analysis of genetic data (based on neutral theory), is how scientists demonstrated that the parasitic cancer in dogs is not a normal cancer, but an infectious parasite. Phylogenetically, parasitic tumors from different dogs shared most recent common ancestry with each other, rather than with the cells of the dogs. In the distant past, a single dog’s cancer evolved into an infectious parasite. This cancer is the common ancestor of all the parasitic cancer tumors we see today in dogs. As surprising as this is, we see the story recorded in the genetic information.

Phylogenetics also detects exceptions to common descent from a single Tree of Life, an overly simplified model of evolution. For example, many cancers are partly caused by “horizontal gene transfer.” In these cases, viruses transfer new genes into normal cells. Famously, the human papilloma (HPV) virus causes cervical cancer in this way. It transfers genes into the cells it infects. The newly transferred HPV genes give our cells some of the new functions needed for cancer.

In the same way, phylogenetics detects horizontal transfer of genes in the evolution of species. For example, an important protein in human placentas looks and functions like a viral protein that transferred to our ancestors in the same way HPV transfers its genes to enable cancer evolution.

Convergence and Multiple Solutions

What about the drivers? What patterns do we see in how cancer evolves new functions? Two key patterns emerge. On one hand, we see cancer evolution “converge” to the same solutions. On the other hand, cancers are incredibly diverse, demonstrating that there are multiple ways to evolve the same function.

Cancer demonstrates “convergent evolution.” We see this at both a genetic and a functional level. For example, specific driver mutations are often “recurrent”: they appear independently in different patients. In other common cases, different mutations in the same genes have very similar overall effects. Similarly, proteins in the specific pathways are often independently mutated in different patients. Functionally, cancers usually evolve new functions in a predictable sequence. So, cancer demonstrates convergent evolution in multiple ways.

We see convergent evolution of species too. At a functional level, bat and bird wings are a type of structural and functional convergence. So are the wide variety of eyes we find in nature, where we frequently observe structural and functional convergence. Evolution sometimes shows convergence on a molecular level as well. In these cases, the same mechanisms, pathways, and mutations occur independently in multiple lineages. For example, different mammals evolved similar placentas by horizontal gene transfers from different viruses (a convergent mechanism and genetic change). Then, as placentas became more effective at nourishing embryos, egg yolk became obsolete. Then, each line of mammals began to independently lose their yolk genes (a convergent genetic change).

On the other hand, cancer demonstrates there are thousands of possible mutations that could evolve the same functions. There are a very large number of ways to solve the problem. This makes evolution more likely, because no single specific set of mutations is required to generate a new function. Instead, evolution has only to find one of the many solutions. This makes it much easier for new functions to arise.

We see multiple solutions in the evolution of species too. A large number of mutations can all have the same functional effect. There are multiple ways to solve the same functional problem. In fact, convergence at one level is usually accomplished with totally different solutions at other levels.

For example, there are multiple ways to lose a gene, so there is divergence in the specific inactivation histories of yolk genes in each mammalian line. A similar example: bats and birds both have wings (convergence), but their wings are also different and make use of many different genes and structures (divergence). Evolution makes coherent sense of these patterns of convergence and divergence. And this feature of biology, that there are multiple ways of solving the same problem, makes the evolution of new functions much more likely.

Some see convergence as evidence against evolution. Cancer, however, empirically demonstrates that evolutionary processes do converge to similar solutions. Likewise, most mathematical arguments against evolution assume that specific mutations are required to evolve new functions. Cancer, however, empirically demonstrates that the same function can evolve from a very large number of different mutations.

Cancer’s Testimony of Evolution

We have some understanding of cancer evolution, but we are learning more all the time. Currently, we have the genomes of over 10,000 tumors, covering dozens of different types of cancer, and this number is going to exponentially grow in coming years. Repeated observations of the same evolutionary process gives us unprecedented understanding of how life evolves.

In the end, cancer does not (usually) demonstrate evolution of new species. It does not demonstrate that humans arose from a common ancestor with the great apes. It does not demonstrate the full story of evolution. To tell that story, we need information from the genomes from multiple species and the fossil record. Encouragingly, the same evolutionary theory that reconstructs cancer’s history works here too.

Even before engaging the larger story, a detailed look at cancer leaves us with some important conclusions; without doubt, evolution makes sense of cancer. Whether or not we agree with the full evolutionary story, cancer demonstrates that evolutionary theory itself is useful. Going a small step farther, understanding evolution is centrally important in medical research. Fundamentally, cancer is an evolutionary disease. It only arises because life evolves.

 

 

1.  We see both Darwinian and non-Darwinian mechanisms in cancer. The “Darwinian” mechanism is the most commonly understood mechanism of evolution: positive selection acting on random mutations. While this mechanism of evolution is important, is not the only mechanism of evolution. Evolution also works by several “non-Darwinian” mechanisms in addition to strict Darwinism. For example, neutral drift and negative selection (sometimes called purifying selection) are also necessary to understand evolution at a genetic level. This fact makes A Scientific Dissent From Darwinism very strange. Biologist do not think “random mutation and natural selection” can fully “account for the complexity of life;” for example, we need non-Darwinian mechanisms too. Moreover, the precise mechanisms of evolution are an active area of continued “examination” in science.
2.  In this sentence, Darwinism does not refer to the modern understanding of evolution, but the definition of Darwinism in A Scientific Dissent From Darwinism: exclusively random mutation and natural selection.
3. Genetic “draft” is subtly different than neutral drift, but also a mechanism by which neutral mutations are fixed. In this case, they are fixed because they are nearby beneficial mutations in the genome. They “hitchhike” on the selective force generated by the drivers. In principle, “passenger” mutations can be fixed by either drift or draft, though sometimes the distinction is not clarified when “passengers” are referred to as “hitchiker” mutations. Either way, these mutations are selectively neutral, are the most common mutations in cancer, and are not fixed by positive selection acting on their beneficial.
4. Estimates range from three to about seven rate limiting mutations, and perhaps ten or so more likely mutations too. The seminal work by Armitage-Doll in 1954 is a brilliant study of this point, well ahead of its time.
5. A low estimate of the number of mutations explored by our ancestors over the last 6 million years is 400 billion mutations. The human genome is only 3 billion bases long, so every possible point mutation could have been explored more than one hundred times.his estimate is computed assuming 10,000 individuals, 100 new mutations per individual, and a generation time of 15 years (10,000 * 100 * 6 million / 15). Remember, this is a very low estimate that ignores the upward contributions of population growth, individuals that die before reproducing, and variations in mutation rate. In this simplified model, we expect about 40 million mutations to be fixed by neutral drift (100 * 6 million / 15) and for there to be about 80 million point differences between chimps and humans (or 1.3% difference). This very rough calculation is reasonably close to the observed differences human and chimpanzee genomes (about 2% different). These are very rough estimates with simplified formulas and imprecise data, so some discrepancy is expected. As we improve the models and the data, the discrepancies reduce and neutral drift still accounts for the vast majority of genetic differences between us and our common ancestors with apes. Only a small number of differences, perhaps just a few thousand mutations, were beneficial enough to be fixed by natural selection. The rest were fixed by neutral processes (like drift and draft). Moreover, the rough formula is often a good approximation: mutation rate multiplied by divergence time approximately equals the observed divergence divided by two.
6. In the linked figure (warning: graphic image of internal organ), because of the low mobility of colon cells, we also see the clades in a geographical distribution that matches their ancestry. The spatial pattern of biogeography was one of the earliest clues to the evolution of species, and we see it in cancer too. We also see convergence, as multiple polyps (a convergent function) develop independently in different lineages. Moreover, phylogenetics has become a critical tool in studying colon cancer specifically, other cancers too, and also cancer metastasis.

Did you miss this one? 

http://peacefulscience.org/peace-be-with-you/

Cheers One.Opinion!!! 

[one.opinion]

25 minutes ago, RockyMidnight said:

Did you miss this one? 

http://peacefulscience.org/peace-be-with-you/

Cheers One.Opinion!!! 

No, I love, love, love that one! Glad you found it!

[Guest shiloh357]

10 hours ago, one.opinion said:

No, absolutely not. Good data should always trump (no pun intended) consensus opinion. However, I will appeal to the opinions of professionals in their field versus an amateur opinion any day. To discount the rigor of the intellectual pursuit required to become a successful professional scientist would be foolhardy.

This is not about opinions.   It is about being willing to overlook the scientific method when its convenient to do so.    Hypotheses are based on observable evidence.   You don't draw up a hypothesis about evidence you have never seen yet.    Yet, that is how Evolution started.   No evidence was present when Darwin drew up his idea about Evolution.   There is no fossil evidence that that he, or we have that demonstrates how one organism, over millions of years, evolved into some thing that did not originally exist (molecules to man).  No evidence that mutations provide the kind of new information needed for macro-Evolution to occur.  

The problem here is that we are supposed to look at things like finches and moths and bacterial strains that change and adapt as proof of macro-evolution. All scientists can produce is examples of adaptation within groups of birds and bugs or other organisms and that is the best evidence that they have, which is no evidence at all. They even tried to manufacture evidence.  If macro-Evolution were true, there would have been no need to fabricate evidence for years.   If macro-evolution were true, the earth would be pregnant with a fossil record of layers and layers and layers of billions of fossils and we would have billions of transitional fossils, more than the museums could house.  But that is not the case.

So Evolution must be accepted because these scientists are professionals. Even if they have no evidence, I am just supposed to accept their claims that Evolution is true? We are suppose to just accept something because being a "scientist" apparently means that one has donned the mantle of infallibility.    It's a logical fallacy. 

[Guest shiloh357]

10 hours ago, one.opinion said:

I just ran across an article that is relevant to the conversation. You can link to it (here).

Theodosius Dobzhansky, an Eastern Orthodox Christian and scientist, famously wrote in 1973 that “nothing in biology makes sense except in the light of evolution.” He was talking specifically about fossils, the diversity and geography of life, and the sequence similarities between proteins. We now know he could also add cancer to his list. Our understanding of both cancer and evolution are intertwined.

Evolutionary theory “makes sense” of cancer, giving us critical insight into how it works.

This has become particularly clear in recent years. Now, we can sequence all the genes in a patient’s cancer, and see how they change over time as cancer evolves. Cancer evolves with the same evolutionary mechanisms¹ that drive the evolution of new species. Like breadcrumbs marking a path through a forest, cancer evolution leaves information in cellular genomes that evolutionary theory can decode.

Going the other direction, cancer makes sense of evolution too. Cancer itself is not evolution at the species level. However, it validates the mathematical framework underlying modern evolutionary theory. Cancer cells evolve multiple new functions in an evolutionary process, creating precise genetic signatures of common descent. At both a genetic and functional level, cancer follows patterns explained by evolutionary theory.

Skeptics of evolution often doubt we know enough about how genomes change over time, or how new functions arise, to correctly infer common ancestry from patterns in genetic data. They sometimes argue that “historical science” cannot be trusted, since it is making claims about the distant past. In cancer, however, we can directly verify that evolutionary theory correctly reconstructs a cancer’s history, including its ancestry. We see all the same patterns in cancer evolution that we do in the evolution of species: neutral drift, nested clades, novel functions, and positive selection. The same math, software, and theory that is used to study the evolution of species works for cancer too.

If evolutionary theory is wrong about the origin of species, why does it work so well for cancer?

What is Cancer?

On a human level, we are all affected by cancer. Many of us will die from it. Almost of all of us will be close to someone who dies from it. Cancer is a tragedy. Scientists want to understand how cancer works so we can intervene and reduce human suffering.

From a biological point of view, it is now clear that cancer is an evolutionary disease. Cancer biologists use evolutionary theory because it is useful and accurate, not because they are pushing an “evolutionary agenda.” In cancer, cells evolve a set of new functions. These functions are beneficial to the cancer cell, but ultimately lethal to their host. And cancer must do much more than just grow quickly. It must also…

1. ignore signals to die,
2. evade immune defenses,
3. grow blood vessels to obtain nutrients,
4. invade surrounding tissue,
5. survive in the bloodstream,
6. establish new colonies throughout the body,
7. and even resist treatment.

Not every cancer acquires all these functions. Nonetheless, in all cases, more than just rapid growth is required for cancer to develop. Several new functions are required. Ultimately, many cancers will acquire more than ten beneficial (to the cancer cell) mutations that enable these new functions.

One incorrect metaphor for cancer (and a misguided way of dismissing evolution) is that cancer is just cells “breaking down” or “gunk in the machine.” Superficially, the “breaking down” metaphor explains some changes in cancer. For example, some cells acquire the ability to divide uncontrollably by truncating, or “breaking,” specific proteins that normally control cell division.

The “breaking down” metaphor, however, is not adequate. When our technology breaks down, it never produces anything resembling cancer. Old cars, laptops, and watches do not grow tumors as they break down. In this way, cancer reminds us that biology is unlike any human design. Cancer is unique to biological systems, and we are afflicted with it because we are intrinsically capable of evolving.

Evolution, it turns out, is a much more useful framework for understanding cancer. From the cell’s point of view, cancer is evolving new functions in the environment of the host’s body. It evolves these functions in an evolutionary process. Cancer exists only because biological systems, including humans, have the intrinsic ability to evolve.

Does Cancer Evolve New Species?

Of course, cancer does not evolve new species. At least not usually…

In biology, there are exceptions to almost every rule, including this one. As it turns out, cancer occasionally produces new species. The two most interesting examples of this are a parasite that infects dogs, and another that infects Tasmanian devils. In these cases, a cancer evolved specific new functions: genetic stability and infectivity. Then, because of its location and the behavior of its host, it spread to others. A new species of parasite is born.

New species arise from cancer only very rarely; this isn’t the rule. Still, sometimes, they do. The evolution of new species from cancer is an important reminder that biology is surprising. It does not work according to our intuitions. In biology, there are always exceptions to the rules, and the improbable flukes are important.

Moreover, cancer still demonstrates how evolution works at a genetic level. Instead of millions of years, the time scale of cancer’s evolution is just years. So, cancer enables us to repeatedly study evolution in a system that matches our own biology. We see several important patterns: signatures of evolution. Evolution leaves information in our genomes from which we can reconstruct the past.

“Neutral” Processes Dominate Evolution

A common misconception about evolution is that it is dominated by natural selection acting on beneficial mutations (this is often what is meant by “Darwinian” mechanism). However, brilliant mathematical work and genetic experiments in the 1960s and 1970s by scientists like Haldane and Kimura demonstrated that evolution, at the genetic level, is usually dominated, instead, by the drift of neutral or near-neutral mutations. So most of the genetic differences between different lineages were either non-functional or not beneficial enough for natural selection. Only a few of the differences were fixed by natural selection. This is one reason biologists say that Darwinian evolution² is quantitatively less important than non-Darwinian evolution (e.g. neutral drift, neutral draft,³ and other mechanisms) in explaining the complexity in genetic differences between species.

Cancer evolution independently confirms that neutral theory is correct. We see the same patterns here, but the terminology is different.

In place of beneficial and neutral mutations, Cancer biologists often talk about “driver” and “passenger” mutations. The driver mutations are the ones that cause cancer, by conferring new abilities on the cancer cells. The passengers have no strongly selectable function: they are neutral. Rather than by natural selection, these neutral mutations are fixed by other mechanisms, like neutral drift. Any individual cancer cell will have tens, hundreds, or even thousands of mutations. But only a few⁴ of the mutations are drivers that are selected by natural selection. We know this fact from direct experimentation; only a small handful of mutations (of the thousands we observe) can actually induce cancer.

This is exactly what we expect from neutral evolutionary theory: drivers are vastly outnumbered by passengers. This is true for cancer, and it is also true for the evolution of new species. For example, the vast majority of genetic differences between humans and chimpanzees are neutral, and were fixed by neutral mechanisms like drift and draft. Over the last 6 million years, our ancestors explored hundreds of billions of mutations,⁵ tens of millions of these mutations were neutral and drifted into our genomes, and perhaps just a few thousand mutations were functionally important enough to be selected by natural selection.

Genetic Information and Common Descent

Most of the information in cancer genomes is a record of history. Genomes record the origins and evolution of every cancer cell, and their relationships to one another. Using evolutionary theory, we can read this history out of genetic data.

The specific part of evolutionary theory that reads history from genetic data is “phylogenetics.” Phylogenetics is foundational to modern evolutionary theory, with deep roots in information theory, population genetics, and neutral theory. It bears repeating, the exact same math, software, and theory that so accurately reconstructs a cancer’s history, is also used to reconstruct the evolutionary history of species.

Phylogenetics is powerful because there is so much historical information in genetic data. This information traces the ancestry of cancer cells. For example, one study used phylogenetics to map the ancestry of cells in a colon with a large tumor.⁶ This analysis showed that the cancer arose from a mutated original cell that also gave rise to neighboring regions of the colon and nearby polyps. The genetic mutations in the colon are in a “nested clade” pattern, exactly as evolution predicts.

Phylogenetics can identify exceptions to the normal rules of biology; it can reconstruct surprising and unexpected events. For example, we usually assume that cancer descends from a single cell in the host patient, but this is not always the case. Evolutionary analysis of genetic data (based on neutral theory), is how scientists demonstrated that the parasitic cancer in dogs is not a normal cancer, but an infectious parasite. Phylogenetically, parasitic tumors from different dogs shared most recent common ancestry with each other, rather than with the cells of the dogs. In the distant past, a single dog’s cancer evolved into an infectious parasite. This cancer is the common ancestor of all the parasitic cancer tumors we see today in dogs. As surprising as this is, we see the story recorded in the genetic information.

Phylogenetics also detects exceptions to common descent from a single Tree of Life, an overly simplified model of evolution. For example, many cancers are partly caused by “horizontal gene transfer.” In these cases, viruses transfer new genes into normal cells. Famously, the human papilloma (HPV) virus causes cervical cancer in this way. It transfers genes into the cells it infects. The newly transferred HPV genes give our cells some of the new functions needed for cancer.

In the same way, phylogenetics detects horizontal transfer of genes in the evolution of species. For example, an important protein in human placentas looks and functions like a viral protein that transferred to our ancestors in the same way HPV transfers its genes to enable cancer evolution.

Convergence and Multiple Solutions

What about the drivers? What patterns do we see in how cancer evolves new functions? Two key patterns emerge. On one hand, we see cancer evolution “converge” to the same solutions. On the other hand, cancers are incredibly diverse, demonstrating that there are multiple ways to evolve the same function.

Cancer demonstrates “convergent evolution.” We see this at both a genetic and a functional level. For example, specific driver mutations are often “recurrent”: they appear independently in different patients. In other common cases, different mutations in the same genes have very similar overall effects. Similarly, proteins in the specific pathways are often independently mutated in different patients. Functionally, cancers usually evolve new functions in a predictable sequence. So, cancer demonstrates convergent evolution in multiple ways.

We see convergent evolution of species too. At a functional level, bat and bird wings are a type of structural and functional convergence. So are the wide variety of eyes we find in nature, where we frequently observe structural and functional convergence. Evolution sometimes shows convergence on a molecular level as well. In these cases, the same mechanisms, pathways, and mutations occur independently in multiple lineages. For example, different mammals evolved similar placentas by horizontal gene transfers from different viruses (a convergent mechanism and genetic change). Then, as placentas became more effective at nourishing embryos, egg yolk became obsolete. Then, each line of mammals began to independently lose their yolk genes (a convergent genetic change).

On the other hand, cancer demonstrates there are thousands of possible mutations that could evolve the same functions. There are a very large number of ways to solve the problem. This makes evolution more likely, because no single specific set of mutations is required to generate a new function. Instead, evolution has only to find one of the many solutions. This makes it much easier for new functions to arise.

We see multiple solutions in the evolution of species too. A large number of mutations can all have the same functional effect. There are multiple ways to solve the same functional problem. In fact, convergence at one level is usually accomplished with totally different solutions at other levels.

For example, there are multiple ways to lose a gene, so there is divergence in the specific inactivation histories of yolk genes in each mammalian line. A similar example: bats and birds both have wings (convergence), but their wings are also different and make use of many different genes and structures (divergence). Evolution makes coherent sense of these patterns of convergence and divergence. And this feature of biology, that there are multiple ways of solving the same problem, makes the evolution of new functions much more likely.

Some see convergence as evidence against evolution. Cancer, however, empirically demonstrates that evolutionary processes do converge to similar solutions. Likewise, most mathematical arguments against evolution assume that specific mutations are required to evolve new functions. Cancer, however, empirically demonstrates that the same function can evolve from a very large number of different mutations.

Cancer’s Testimony of Evolution

We have some understanding of cancer evolution, but we are learning more all the time. Currently, we have the genomes of over 10,000 tumors, covering dozens of different types of cancer, and this number is going to exponentially grow in coming years. Repeated observations of the same evolutionary process gives us unprecedented understanding of how life evolves.

In the end, cancer does not (usually) demonstrate evolution of new species. It does not demonstrate that humans arose from a common ancestor with the great apes. It does not demonstrate the full story of evolution. To tell that story, we need information from the genomes from multiple species and the fossil record. Encouragingly, the same evolutionary theory that reconstructs cancer’s history works here too.

Even before engaging the larger story, a detailed look at cancer leaves us with some important conclusions; without doubt, evolution makes sense of cancer. Whether or not we agree with the full evolutionary story, cancer demonstrates that evolutionary theory itself is useful. Going a small step farther, understanding evolution is centrally important in medical research. Fundamentally, cancer is an evolutionary disease. It only arises because life evolves.

 

 

1.  We see both Darwinian and non-Darwinian mechanisms in cancer. The “Darwinian” mechanism is the most commonly understood mechanism of evolution: positive selection acting on random mutations. While this mechanism of evolution is important, is not the only mechanism of evolution. Evolution also works by several “non-Darwinian” mechanisms in addition to strict Darwinism. For example, neutral drift and negative selection (sometimes called purifying selection) are also necessary to understand evolution at a genetic level. This fact makes A Scientific Dissent From Darwinism very strange. Biologist do not think “random mutation and natural selection” can fully “account for the complexity of life;” for example, we need non-Darwinian mechanisms too. Moreover, the precise mechanisms of evolution are an active area of continued “examination” in science.
2.  In this sentence, Darwinism does not refer to the modern understanding of evolution, but the definition of Darwinism in A Scientific Dissent From Darwinism: exclusively random mutation and natural selection.
3. Genetic “draft” is subtly different than neutral drift, but also a mechanism by which neutral mutations are fixed. In this case, they are fixed because they are nearby beneficial mutations in the genome. They “hitchhike” on the selective force generated by the drivers. In principle, “passenger” mutations can be fixed by either drift or draft, though sometimes the distinction is not clarified when “passengers” are referred to as “hitchiker” mutations. Either way, these mutations are selectively neutral, are the most common mutations in cancer, and are not fixed by positive selection acting on their beneficial.
4. Estimates range from three to about seven rate limiting mutations, and perhaps ten or so more likely mutations too. The seminal work by Armitage-Doll in 1954 is a brilliant study of this point, well ahead of its time.
5. A low estimate of the number of mutations explored by our ancestors over the last 6 million years is 400 billion mutations. The human genome is only 3 billion bases long, so every possible point mutation could have been explored more than one hundred times.his estimate is computed assuming 10,000 individuals, 100 new mutations per individual, and a generation time of 15 years (10,000 * 100 * 6 million / 15). Remember, this is a very low estimate that ignores the upward contributions of population growth, individuals that die before reproducing, and variations in mutation rate. In this simplified model, we expect about 40 million mutations to be fixed by neutral drift (100 * 6 million / 15) and for there to be about 80 million point differences between chimps and humans (or 1.3% difference). This very rough calculation is reasonably close to the observed differences human and chimpanzee genomes (about 2% different). These are very rough estimates with simplified formulas and imprecise data, so some discrepancy is expected. As we improve the models and the data, the discrepancies reduce and neutral drift still accounts for the vast majority of genetic differences between us and our common ancestors with apes. Only a small number of differences, perhaps just a few thousand mutations, were beneficial enough to be fixed by natural selection. The rest were fixed by neutral processes (like drift and draft). Moreover, the rough formula is often a good approximation: mutation rate multiplied by divergence time approximately equals the observed divergence divided by two.
6. In the linked figure (warning: graphic image of internal organ), because of the low mobility of colon cells, we also see the clades in a geographical distribution that matches their ancestry. The spatial pattern of biogeography was one of the earliest clues to the evolution of species, and we see it in cancer too. We also see convergence, as multiple polyps (a convergent function) develop independently in different lineages. Moreover, phylogenetics has become a critical tool in studying colon cancer specifically, other cancers too, and also cancer metastasis.

Yeah, that still does not prove Darwinian macro-evolution.   You keep trying to throw up examples of how something can change and evolve into different versions of what already exists.   That is not the kind of Evolution I am speaking of in the OP.  I am talking about mutations that create brand new, not previously existing information that causes organisms to evolve over time into a  new organism that never existed before.

[one.opinion]

2 hours ago, shiloh357 said:

Yeah, that still does not prove Darwinian macro-evolution.   You keep trying to throw up examples of how something can change and evolve into different versions of what already exists.   That is not the kind of Evolution I am speaking of in the OP.  I am talking about mutations that create brand new, not previously existing information that causes organisms to evolve over time into a  new organism that never existed before.

This is probably a good time to revisit the OP.

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If Evolution is true, and birds came from dinosaurs, then what is the evidence that mutations create brand new information in the genes of living organisms causing them to evolve into a completely different species?

I went on to show you exactly what you asked for. I showed you examples of mutations creating brand new information. I showed you genetic changes leading to completely different species. When I gave examples of your questions being answered, your response is "But these aren't what I'm talking about". If you are looking for examples of brand new classes or phyla of organisms that have come into being in the last 150 years (since the publication of "Origin of Species"), then I cannot provide an example. The time scale in which we are confined is just too narrow to directly observe the changes that would be convincing to you. That's why the fossil record is used as indirect evidence. We cannot directly observe what happened 6,000 years ago or 4.5 billion years ago, so scientists must use the available data. There are numerous aspects of evolution that can be tested directly. There is no scientific reason to suggest that what we can observe directly about evolution could not work on a larger scale in a larger time frame. Evolution is the best scientific explanation available.

3 hours ago, shiloh357 said:

So Evolution must be accepted because these scientists are professionals. Even if they have no evidence, I am just supposed to accept their claims that Evolution is true? We are suppose to just accept something because being a "scientist" apparently means that one has donned the mantle of infallibility.    It's a logical fallacy. 

Data > Trained and Expert Consensus >>>>> layman opinion

Let me throw a hypothetical situation that is rather similar to what you are claiming. If there is a hostage situation in Iraq and a Seal Team is called in to plan and execute a rescue mission. A team of data analysts and special operations officers meet for hours to draw up a plan of action. After much debate and discussion, the team arrives at an executable plan. I'm standing out in the hall and when they exit, I loudly proclaim "Look guys, I know you are highly-trained for what you do. I know you have a tremendous amount of experience. I know you have access to data that I don't and probably wouldn't understand if I did, but I did take a history class in college and we talked some about World War 2. Relying on your consensus opinion is a logical fallacy! Here, let me tell you how to do it better."

If you have some scientific data that contradicts the Trained and Expert Consensus, I would be very happy to read it and discuss it.

[Guest shiloh357]

6 hours ago, one.opinion said:

This is probably a good time to revisit the OP.
I went on to show you exactly what you asked for. I showed you examples of mutations creating brand new information. I showed you genetic changes leading to completely different species.

No, you didn't give me what I asked for.  New species of existing creatures isn't macro-Evolution.  The kind of mutations required to produce and entirely new organism that didn't exist before is what I am asking for . You have not provided that.

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When I gave examples of your questions being answered, your response is "But these aren't what I'm talking about". If you are looking for examples of brand new classes or phyla of organisms that have come into being in the last 150 years (since the publication of "Origin of Species"), then I cannot provide an example. The time scale in which we are confined is just too narrow to directly observe the changes that would be convincing to you. That's why the fossil record is used as indirect evidence. We cannot directly observe what happened 6,000 years ago or 4.5 billion years ago, so scientists must use the available data. There are numerous aspects of evolution that can be tested directly. 

The point is that not only do not mutations not create new organisms and never have, you don't have anything in the fossil record to support it. You should have millions of animal species and billions of transitional fossils in every strata going back millions if not billions of years.   That's what we would expect to see if Evolution had any truth it at all.  The fossil record, should give direct evidence if Evolution is true.   So far, all we get from evolutionists are excuses as to why what should be their strongest evidence is really no evidence at all.

Right now, as far as evidence is concerned, Evolution is an intellectual farce; a fool's errand.

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Data > Trained and Expert Consensus >>>>> layman opinion

The logical fallacy is that their alleged "expertise" puts them above critical scrutiny.   It's an appeal to the authority and that often disappoints.

 

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Let me throw a hypothetical situation that is rather similar to what you are claiming. If there is a hostage situation in Iraq and a Seal Team is called in to plan and execute a rescue mission. A team of data analysts and special operations officers meet for hours to draw up a plan of action. After much debate and discussion, the team arrives at an executable plan. I'm standing out in the hall and when they exit, I loudly proclaim "Look guys, I know you are highly-trained for what you do. I know you have a tremendous amount of experience. I know you have access to data that I don't and probably wouldn't understand if I did, but I did take a history class in college and we talked some about World War 2. Relying on your consensus opinion is a logical fallacy! Here, let me tell you how to do it better."

That's not analogous to this at all.  I am simply noting that the Evolution was popularized (as an alternative to the Bible) before there was any actual evidence for it.  And there is still no solid evidence for Darwinian evolution.  But more to the point, I am challenging the abandonment of the scientific method.

We are told evolution is science, but science is based on evidence.  Evolution came BEFORE any evidence for it, which precludes it from being scientific at the outset.  What scientists are doing is actually backwards to the scientific method.    Evidence>> Hypothesis>>Testing>>Formulate Theory.  In Evolution it's:   Theory>>Find Evidence

 

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If you have some scientific data that contradicts the Trained and Expert Consensus, I would be very happy to read it and discuss it.

No, I am asking you for evidence and so far you can't produce it. I don't have to produce the scientific data, as I have made no scientific claims that need to proved.

[one.opinion]

52 minutes ago, shiloh357 said:

The point is that not only do not mutations not create new organisms and never have, you don't have anything in the fossil record to support it.

The Smithsonian website has a great series of pages on transitional hominid fossils. (http://humanorigins.si.edu/evidence/human-fossils/fossils)

If you are looking for transitional fossils between fish and terrestrial vertebrates, you can look here (https://link.springer.com/article/10.1007/s12052-009-0119-2).

You can read about whale evolution here (https://evolution.berkeley.edu/evolibrary/article/evograms_03).

You can read about horse evolution here (https://www.amnh.org/exhibitions/horse/the-evolution-of-horses/).

If you disagree with the scientific interpretation, do you have any data that will support your position?

56 minutes ago, shiloh357 said:

No, I am asking you for evidence and so far you can't produce it. I don't have to produce the scientific data, as I have made no scientific claims that need to proved.

I've given you examples of mutations producing new information. You asked for mutations producing new information that would produce completely different species. If I recall correctly, I gave you one example (although there are more) of mutations causing completely new species. You decided that you didn't want just new species anymore, you wanted a completely different phylum or class - which cannot happen on time scales you expect. You set an impossible standard and judge evolution as fiction if it can't produce what you think it should produce.

You claim Darwin had no evidence. When I attempted to help you reformulate your statement into something accurate, you doubled down and insisted that Darwin had no evidence, despite his obvious use of the fossil record and biogeography. I understand that you don't think this is evidence, but actual experts in the field find this very important evidence. Loudly proclaiming evidence is not actually evidence does not alter the fact.

[Guest shiloh357]

5 hours ago, one.opinion said:

The Smithsonian website has a great series of pages on transitional hominid fossils. (http://humanorigins.si.edu/evidence/human-fossils/fossils)

If you are looking for transitional fossils between fish and terrestrial vertebrates, you can look here (https://link.springer.com/article/10.1007/s12052-009-0119-2).

You can read about whale evolution here (https://evolution.berkeley.edu/evolibrary/article/evograms_03).

You can read about horse evolution here (https://www.amnh.org/exhibitions/horse/the-evolution-of-horses/).

If you disagree with the scientific interpretation, do you have any data that will support your position?

Again, you're not really grasping what I am  talking about.  I am talking about Evolution from one organism to another over billions of years.  I am asking for fossil evidence that shows a successive line of transition from start to modern times.  Neither you nor the Smithsonian can provide that.

You are showing animals that evolve into different versions of the same thing.   

Not only that  but some these these are assumed to be transition due to an assumption that Evolution is true.   The fact is that when God sent the world-wide flood, a lot of animals were destroyed, both land, air and sea life.   God destroyed it all except for Noah and his family and the animals on the ark. 

That means that countless species of animal life were destroyed that we have never seen alive.  It means that many animals we have today were descendants of the animals that were on the ark.   We assume that the animals we see today always existed from time immemorial, but that may not be the case. 

Noah didn't take every species of every animal group on the ark.   He didn't take every species of dog.  He just took two dogs.  He didn't take two of every species of cats.  He just too, two cats. Same with other animals as well.    

That means that there were animals of all kinds that went extinct because of the flood and many of the animals we see today, may look much different than what was on the ark and so what many are calling "transitional" may not be, but simply extinct animals that existed before the flood.

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I've given you examples of mutations producing new information. You asked for mutations producing new information that would produce completely different species. If I recall correctly, I gave you one example (although there are more) of mutations causing completely new species. You decided that you didn't want just new species anymore, you wanted a completely different phylum or class - which cannot happen on time scales you expect. You set an impossible standard and judge evolution as fiction if it can't produce what you think it should produce.

No, what happened is that I began to realize that I was using the wrong terminology to express what I was asking for.  So I altered the question to clarify what I was asking for.   I am familiar with new information occurring within a given species.  None of that is in dispute. 

What I am asking for is evidence that new information sufficient to evolve one organism into a completely different organism.  Again, those kinds of mutations are not observed.  And you don't have evidence for those kinds of mutations in the fossil record.

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You claim Darwin had no evidence. When I attempted to help you reformulate your statement into something accurate, you doubled down and insisted that Darwin had no evidence, despite his obvious use of the fossil record and biogeography. I understand that you don't think this is evidence, but actual experts in the field find this very important evidence. Loudly proclaiming evidence is not actually evidence does not alter the fact.

The only real evidence that matters is the fossil record and Darwin admitted that he had nothing to support his notion of Evolution and thought it would be vindicated later.   Again, that is not science.  I am not a PhD in science, but I know enough that I can't be snowed and I know how to think critically about this stuff.  What's expected of people like me is that we be compliant sheeple and just accept what the scientists say without question.

I never said evidence is not evidence.   I am saying that the evidence only affirms that mutations occur within species, and that such is not disputed by anyone.   I said that there is no evidence for macro-evolution.    What I have found over and over and over is that when asked for evidence of Evolution, the evolutionists offer up micro-evolution, thus moving the goal posts because they understand what we are asking for, but put up the smoke screen of micro-evolution.

[one.opinion]

24 minutes ago, shiloh357 said:

The only real evidence that matters is the fossil record and Darwin admitted that he had nothing to support his notion of Evolution and thought it would be vindicated later.

He had some of the fossil record available, but not enough to suit his liking. If he really admitted he had “nothing” in the fossil record, I’d like to see evidence. It is true that he expected more than paleontologists have yet been able to discover.

[one.opinion]

27 minutes ago, shiloh357 said:

What I have found over and over and over is that when asked for evidence of Evolution, the evolutionists offer up micro-evolution, thus moving the goal posts because they understand what we are asking for, but put up the smoke screen of micro-evolution.

Scientists do not see a distinction in process between micro-evolution and macro-evolution, only in time scale. You keep asking and I keep giving you the same answer - it is completely unrealistic to expect to see a gradual process that takes millions of years to occur in 150. This is a completely immaculate depiction of what evolution is predicted, expected, and hypothesized to do. You want new phyla to appear before your eyes because of a misconception of the science. It will not happen. Let’s actually take a different angle and let me ask you a question.

What scientific evidence is there to support some type of physical barrier between micro and macro varieties of evolution?