What is the Evidence of Mutations and New Information

[one.opinion]

2 hours ago, shiloh357 said:

What evolutionists need, but cannot provide is actual evidence that mutations provide entirely new information that leads to an entirely new species evolved from the old.  The issue of mutations is not friendly to the Theory of Evolution.

This is the abstract from the last link I provided in my most-recent post:

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The origin of new genes is extremely important to evolutionary innovation. Most new genes arise from existing genes through duplication or recombination. The origin of new genes from noncoding DNA is extremely rare, and very few eukaryotic examples are known. We present evidence for the de novo origin of at least three human protein-coding genes since the divergence with chimp. Each of these genes has no protein-coding homologs in any other genome, but is supported by evidence from expression and, importantly, proteomics data. The absence of these genes in chimp and macaque cannot be explained by sequencing gaps or annotation error. High-quality sequence data indicate that these loci are noncoding DNA in other primates. Furthermore, chimp, gorilla, gibbon, and macaque share the same disabling sequence difference, supporting the inference that the ancestral sequence was noncoding over the alternative possibility of parallel gene inactivation in multiple primate lineages. The genes are not well characterized, but interestingly, one of them was first identified as an up-regulated gene in chronic lymphocytic leukemia. This is the first evidence for entirely novel human-specific protein-coding genes originating from ancestrally noncoding sequences. We estimate that 0.075% of human genes may have originated through this mechanism leading to a total expectation of 18 such cases in a genome of 24,000 protein-coding genes.

It is true that evolution (hypothetically) occurs by changing what is already present. But there is also some solid data supporting the idea that some genes (a pretty small percentage, as you can see) in the human genome have originated from "non-gene" DNA sequences. Granted, these genes are not hypothesized to be responsible for the speciation of Homo sapiens, but these genes to represent the "entirely new information" that is claimed not to exist.

There are also examples of genomic alterations that have led directly to speciation. Here is an abstract from another paper:

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Speciation by polyploidy is rare in animals, yet, in vertebrates, there is a disproportionate concentration of polyploid species in anuran amphibians. Sequences from the cytochrome b gene of the mitochondrial DNA (mtDNA) were used to determine phylogenetic relationships among 37 populations of the diploid-tetraploid species pair of gray treefrogs, Hyla chrysoscelis and Hyla versicolor. The diploid species, H. chrysoscelis, consists of an eastern and a western lineage that have 2.3% sequence divergence between them. The tetraploid species, H. versicolor, had at least three separate, independent origins. Two of the tetraploid lineages are more closely related to one or the other of the diploid lineages (0.18%-1.4% sequence divergence) than they are to each other (1.9%-3.4% sequence divergence). The maternal ancestor of the third tetraploid lineage is unknown. The phylogenetic relationships between the two species and among lineages within each species support the hypothesis of multiple origins of the tetraploid lineages.

(https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1994.tb01370.x)

3 hours ago, shiloh357 said:

The Theory of Evolution was first introduced BEFORE there was any evidence to support it.

I think it would be more fair to say that the theory was introduced before there was an explanatory mechanism. Darwin published On the Origin of Species in 1859, obviously prior to the discovery of the role of DNA in living organisms (Mendel didn't publish until 1866). But Darwin gathered A LOT of evidence supporting his theory through his very extensive and careful observations of plant and animal life during his voyage on the HMS Beagle.  Here is a pretty good (and short) summary regarding Darwin's voyage and the evidence that he used to formulate his hypothesis. (click here)

[Guest shiloh357]

7 minutes ago, one.opinion said:

 

It is true that evolution (hypothetically) occurs by changing what is already present. 

 

There is nothing "hypothetical" about it.  Evolution NEEDS new, and previously non-existent information in order for something to occur like dinosaurs evolving into birds.

I am not talking about speciation.  I am talking about way more than that.  Evolutionists try to move the goal posts on this and try to prove macro-evolution through things like speciation and it really isn't going to work.

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I think it would be more fair to say that the theory was introduced before there was an explanatory mechanism.

Wrong.  There was no evidence of Evolution  to explain and Darwin admitted he had no evidence and the only evidence that can vindicate  Evolution is the fossil record and the Evolutionist camp has a really bad track record of knowingly faking "evidence" in order to score points, only to be embarrassed later on.  There is simply nothing in the fossil record that prove the theory because it is not a theory. 

Ordinarily evidence leads to a hypothesis that is tested over and over and over and only then after the results are examined is a theory formulated.  Evolution is assumed correct and now people are trying to dig up "evidence" to support that assumption.  It is simply not science.  It's the cart before the horse.

[one.opinion]

1 hour ago, shiloh357 said:

Evolution NEEDS new, and previously non-existent information in order for something to occur like dinosaurs evolving into birds.

There is fossil evidence of feathered dinosaurs. Todd Wood is an outlier, but he is a PhD YEC biologist that admits what the evidence tells us in this case.

http://toddcwood.blogspot.com/2016/12/god-made-dinosaurs-with-beautiful.html

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For some reason, feathered dinosaurs have become a touchy subject among creationists.  As far as I'm aware, the major creationist organizations still do not accept the existence of feathered dinosaurs.  Either the fossils are not really dinosaurs and have real bird feathers, or the fossils are real dinosaurs but the feathers aren't really feathers, or it's all just a hoax.  There is certainly precedent for being suspicious of feathered dinosaur fossils.  Back in 1999, National Geographic ended up with egg on its face after it put Archaeoraptor on its front cover.  Turns out, Archaeoraptor was a fraud, two different fossils stuck together by shady fossil dealers. On the other hand, there are many, many other feathered dinosaur fossils that have been discovered since then.  I had the opportunity to see one up close and personal at the Carnegie Museum of Natural History back in 2013.  Now, you can't really see much in a museum exhibit, but it was still pretty cool seeing one in person.  I have no problem whatsoever with feathered dinosaurs.  If God wanted feathered dinosaurs, He could make feathered dinosaurs!

 

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I think it would be more fair to say that the theory was introduced before there was an explanatory mechanism.

1 hour ago, shiloh357 said:

Wrong.

Why is the fossil record not evidence? Yes, there have been some rather famous examples of hoaxes, but there are millions of other fossils that corroborate Darwin's original hypothesis.

Young Earth Creationists have a terrible time trying to explain why fossils exhibit such layering. Here is an excerpt from a page at the AiG website (https://answersingenesis.org/fossils/fossil-record/doesnt-order-of-fossils-in-rock-favor-long-ages/?

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The vast majority by number of fossils preserved in the strata record of the Flood are the remains of shallow-water marine invertebrates (brachiopods, bivalves, gastropods, corals, graptolites, echinoderms, crustaceans, etc.).8 In the lowermost fossiliferous strata (Cambrian, Ordovician, Silurian, and Devonian), the contained fossils are almost exclusively shallow-water marine invertebrates, with fish and amphibian fossils only appearing in progressively greater numbers in the higher strata.9 The first fish fossils are found in Ordovician strata, and in Devonian strata are found amphibians and the first evidence of continentaltype flora. It is not until the Carboniferous (Mississippian and Pennsylvanian) and Permian strata higher in the geologic record that the first traces of land animals are encountered.

Because the Flood began in the ocean basins with the breaking up of the fountains of the great deep, strong and destructive ocean currents were generated by the upheavals and moved swiftly landward, scouring the sediments on the ocean floor and carrying them and the organisms living in, on, and near them. These currents and sediments reached the shallower continental shelves, where the shallow-water marine invertebrates lived in all their prolific diversity. Unable to escape, these organisms would have been swept away and buried in the sediment layers as they were dumped where the waters crashed onto the land surfaces being progressively inundated farther inland. As well as burying these shallow-water marine invertebrates, the sediments washed shoreward from the ocean basins would have progressively buried fish, then amphibians and reptiles living in lowland, swampy habitats, before eventually sweeping away the dinosaurs and burying them next, and finally at the highest elevations destroying and burying birds, mammals, and angiosperms.

 

The author admits that the fossil record is clearly layered, but instead of selecting the most obvious explanation (organisms were fossilized at different times) he offers a very interesting reason for this layering. The tremendously violent hydrological forces of the global flood washed all marine organisms onto land but at the same time selectively and neatly organized these marine organisms into neat layers based on their respective swimming abilities.

 

1 hour ago, shiloh357 said:

Ordinarily evidence leads to a hypothesis that is tested over and over and over and only then after the results are examined is a theory formulated.  Evolution is assumed correct and now people are trying to dig up "evidence" to support that assumption.

The hypothesis has been tested over and over. In the last few decades, scientists have been able to assemble molecular data that frequently support Darwin's original hypothesis, but have also led to significant refinement of the theory over time. Current evolutionary theory is substantially different from Darwin's version due to molecular evidence (see link).

 

[Guest shiloh357]

13 minutes ago, one.opinion said:

There is fossil evidence of feathered dinosaurs. Todd Wood is an outlier, but he is a PhD YEC biologist that admits what the evidence tells us in this case.

http://toddcwood.blogspot.com/2016/12/god-made-dinosaurs-with-beautiful.html

Feathers on a dinosaur is not really evidence of evolution.  It simply means that a dinosaur had something resembling feathers. 

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Why is the fossil record not evidence?

The fossil record doesn't vindicate the claims of evolutionists and evolutionists are using fossil record to support an assumption, and thus they filter the fossil record in a manner through that assumption.  Again, it is the cart before the horse when it comes to evolution.   It's like saying, "here is a crime; now, go make that man guilty of it."

 

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Yes, there have been some rather famous examples of hoaxes, but there are millions of other fossils that corroborate Darwin's original hypothesis.

That's not how science works.  A hypothesis is built upon evidence; not the other way around.   You don't form a hypothesis and then go looking for evidence.  All you're doing is interpreting the fossil record in a manner that supports what you want to be true. And that is not science.

 

 

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The hypothesis has been tested over and over. In the last few decades, scientists have been able to assemble molecular data that frequently support Darwin's original hypothesis, but have also led to significant refinement of the theory over time. Current evolutionary theory is substantially different from Darwin's version due to molecular evidence (see link).

That only accounts for micro-evolution and variations.  It lends nothing to macro-evolution.

[one.opinion]

1 minute ago, shiloh357 said:

Feathers on a dinosaur is not really evidence of evolution.

No, but it certainly lends credence to the hypothesis that birds are closely related to dinosaurs.

 

2 minutes ago, shiloh357 said:

That's not how science works.  A hypothesis is built upon evidence; not the other way around.   You don't form a hypothesis and then go looking for evidence.

Generally, yes. But of course this requires a different approach because science has to be used to figure out what no one experimented on at the time!  Sure, it is problematic, but it is the only avenue for research on the development of life forms. But it is unfair to simply claim it isn't scientific when the science just has to be done differently. Tens of thousands of actual scientists would disagree with you on this point.

 

6 minutes ago, shiloh357 said:

It lends nothing to macro-evolution.

That's where the fossil record and biogeography come in (again, Darwin DID have evidence!).

[Guest shiloh357]

1 minute ago, one.opinion said:

No, but it certainly lends credence to the hypothesis that birds are closely related to dinosaurs.

No, it doesn't.  In fact,  no one has proven that what is being interpreted as "feathers" were actually feathers.

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Generally, yes. But of course this requires a different approach because science has to be used to figure out what no one experimented on at the time!  Sure, it is problematic, but it is the only avenue for research on the development of life forms. But it is unfair to simply claim it isn't scientific when the science just has to be done differently.

It is not unfair.   There is no scenario where good science begins with a hypothesis and is followed a subjective interpretation of alleged "evidence."  That isn't science by any stretch of the imagination.   Evidence always comes before the hypothesis.

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Tens of thousands of actual scientists would disagree with you on this point.

Doesn't matter.  Science is not a democracy.  Something isn't true because of who believes it or how many believe it.   Geocentrism would not be true if tens of thousands of scientists believed it to be true.  If only two  scientists in the world believed in Heliocentrism, they would be right and everyone else would be wrong.  

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That's where the fossil record and biogeography come in (again, Darwin DID have evidence!).

Micro-evolution doesn't help macro-evolution and Darwin didn't have evidence of macro-evolution.  He hoped the fossil record would vindicate him and it hasn't. 

[one.opinion]

37 minutes ago, shiloh357 said:

Doesn't matter.  Science is not a democracy.

You are correct, science is not a democracy. My point is this (but I wanted to put it nicer) - real scientists know more about real science than you do.

Science is self-correcting. That why geocentricism was overturned. Scientific discovery has changed a lot regarding Darwin's original hypothesis. It has not discarded it altogether, though.

 

Edited August 22, 2018 by one.opinion

[Guest shiloh357]

Just now, one.opinion said:

You are correct, science is not a democracy. My point is this (but I wanted to put it nicer) - real scientists know more about real science than you do.

I know enough about science to know how the scientific process works and Evolution as a hypothesis predated any available evidence and I know that is not how scientific theories work.   I have had to study under evolutionist professors and they have readily admitted (off record) that the fossil record is inconclusive.

And I know that science isn't based on how many scientists believe something to be true, so appealing to tens of thousands of scientists is really a very unimportant and pointless line of argumentation.

[one.opinion]

2 hours ago, shiloh357 said:

And I know that science isn't based on how many scientists believe something to be true, so appealing to tens of thousands of scientists is really a very unimportant and pointless line of argumentation.

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.

[one.opinion]

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.