Originally published at: http://peacefulscience.org/cancer-evolution/
This important article was written after my first Nature Genetics paper. It was original published at elsewhere in January 2017, where it had become one of the most viewed forum topics. Since then, this contribution has highlighted cancer as one of the Icons of Evolution, and its true. Cancer is only possible because life evolves. Cancer biology…
Originally published at: http://peacefulscience.org/cancer-evolution/
The original forum post is here: Cancer and Evolutionary Theory - Scientific Evidence - The BioLogos Forum, and copied below.
So I am please to announce my first Nature Genetics paper:
The real reason I am posting here is to reopen the conversation about the usefulness of evolutionary theory. It turns out that evolutionary theory is indispensable to understanding cancer. The link I offered above leverages evolution for just this purpose. Though I am hardly unique. See for example this article aimed a wide audience…
And several article from the literature…
From this body of work, we can see the evolution of new functions (new information!), neutral theory, and the effectiveness of obtuse metrics like Ks/Ka ratios. It would hard to imagine rejecting evolution of species without somehow forgetting everything we have learned about the evolution of cancer.
I’m happy to answers questions about this work. =)
For the curious, here are some of the responses from ID:
I appreciate their engagement on this work. Certainly there are disagreements, but I do think this has moved the conversation forward. One value of looking at cancer is that is serves as a good theological “control.” If we see a new feature arise in evolution of species, we can always wonder if God directly inspired some mutations to make that possible. Maybe He did, but I’m not sure how to prove that one way or another, though others think they can. Cancer, however, is different. No one (as far as I know) thinks God is intervening in cancer evolution to enable cancer cells to innovate.
For this reason, among others, cancer might be among the best places to look to understand what unaided evolution can and cannot do. The good news, also, is that we are getting just a massive amount of data on cancer. This is what is going to map out the true strengths and weaknesses of evolution.
Well congratulations on the paper. It would take me hours of study to even ask intelligent questions on it. I do think that those who have not met you in person will think Runjon is you and that his name should probably go on that header pic right under his chin.
10 posts were split to a new topic: @GBrooks9’s View On God’s Engagement
Thank you for this. I learned a lot. And thank you for working on Cancer. Hopefully, the generation and future generations will see more progress in fighting cancer.
7 posts were split to a new topic: Cancer and the Problem of Evil
I think this is an important article, especially because our current best hope for cancer, right now, might be immunotherapy, where immune cells evolve to clear the cancer.
Would you pass this article around your networks? I imagine the man from the Church of the Spaghetti Monster might like this.
For many cancers, agreed. Need to improve specificity and manage the ‘off target’ effects, however. That could be very tricky. But if we could better modulate immune system functions, we could address a large number of autoimmune diseases as well.
I gotta say, it’s the interconnectedness of biology that attracted me to the field. Pull a string here… and someone apparently distant moves. Cool!
Quick question, Joshua.
How much of your modelling work do you run on university clusters or lab clusters versus how much do you run on ‘contract’ services like Amazon’s? Just wondering how academic computing is evolving…
This article from @Wayne_Rossiter is worth quoting in detail. He exhumes some really important quotes from the forum discussion that are important to understand my position. Though he does disagree with me, I’m thankful he did that:
Specifically, the individual argued,
[The Theory of Evolution (TOE)] is a semantic statement, and the only paradigm in the sciences that cannot be derived from first principles (mathematical rigor), nor can we perform straightforward experimental verification of its fundamentals (which by definition ought to be equated with first principles).
In that context, Swamidass responded,
I must respectfully and forcefully disagree on several points. This may come as a surprise, but there is a very solid mathematical foundation to evolution, and a very strong experimental grounding. This doesn’t make it ‘True’ (because science does not make truth claims), but evolution is very compelling in science.
And some important quotes from me, which I still stand by:
There are several other theories that are derived in a very similar way as evolution, and are not verifiable by straightforward experimentation. A great example is inflation and the Big Bang. Also black holes, the age of the earth, the Higgs Boson, and many many more things. Even things that are ‘testable’ were often settled upon long before their truly seminal experiment (e.g. heliocentricity, general relativity, and many more). Moreover, there are whole fields of science focused on ‘emergent’ properties that are not derivable from ‘first principles,’ thinks like protein function (because we cannot derive protein structure from sequence) and (e.g. action of psychiatric drugs) medicine are great examples.
And this surprise about Darwinism (repeated in the blog post):
Rather, if specific mechanisms of evolution are true, they make testable predictions about how biological systems behave today. We can test these predictions in biological systems experimentally, and there is an immense body of work that does just this, finding that predictions from some mechanisms are wrong (e.g. neo-Darwinian positive-selection dominated change) and of others are correct (e.g. neutral theory and common descent). This [is] one of the big reasons that I (as a biologist) say there is very strong evidence for evolution.”
Whoa! What!?!? Science has demonstrated that the neo-Darwinian theory of evolution has failed, and it has validated neutral theory and common descent? Call the Royal Society, the National Academy of Sciences, and the publisher of every general biology textbook on the market.
If there is any doubt, in the 1960’s Kimura and Haldane demonstrated that positive-selection dominated change does not explain most of DNA. This is well known in biology. So arguing against scientific “Darwinism” is anachronistic if we mean anything but atheism.
It seems that @Wayne_Rossiter does agree, despite his surprise:
My point is, as Swamidass offers,
Positive selection is important, but it is not necessarily the most important mechanism.
And correctly quotes my definition of evolution, which I think really should be the default definition:
Defining evolution correctly as just common descent is really helpful. There is nothing intrinsically atheistic about it. CD [common descent] is also the most historically and scientifically consistent and correct definition. To be clear, also, I am not adding to this definition abiogenesis (origin of life) or universal common descent. These things are up for debate in the scientific community, and not part of evolution proper. One group of scientists thinks that life arose multiple times (so they do not believe in universal common descent). Another group of scientists severely doubts any natural mechanism for abiogenesis could ever be found. Regardless, evolution is just common descent of all life to a few (or one) ancestor.
Put plainly, for Swamidass, “evolution” is just the evidence for universal common descent. Here acknowledges much that no other evolutionary biologist (or theistic evolutionist) would admit: Darwin’s mechanism is not the dominate force in evolution, there is serious debate about the origins of life, and universal common ancestry might be false.
To be clear, I am not actually saying something surprising to scientists here. The fact that positive-selection dominated change does not explain DNA is well known among competent biologists. I’ve always argued that the fundamentally most important and difficult part of evolution is the “common descent of man,” not whether bacteria all share a common ancestor.
Human evolution has always been where the conflict lies, even for Christians that affirm evolution. That is why my work focused there, and why the progress we have made has a chance to really reorder the debate.
What are Science's Limits?
I don’t agree cancer hows evolutionism to be true.
its all working within a type or kind of think.
I guess your big point is that new information is created.
Well is it new? i agree that after the flood , upon migration, people changed thier colours to deal with the environment. It was a sudden instant change for the whole population so all had the advantage.
it would look like new information but its just something still within the blueprint.
Though a novice I don’t see why these mutations is very surprising even if selected on.
Indeed are mutations mutations? Could mutations be a program in biology? not accidents.
Its not the purpose of biology to stay the same but to survive.
Its still cells working with cells.
I see these areas as very atomic or not well understood as to what is really going on.
mutationism changing real species into very different species is very unlikely.
It is likely at cell centres in biology.
its interesting anyways.
(1) “Instant change”? Are you saying that one morning everybody woke up and they had all changed to the same skin color? Seriously?
(2) How do you know this?
(3) Are you saying that it was a miraculous change, that God simply ordered all DNA to change simultaneously to start expressing the already-existing alleles?
If it was such a Divine miracle, then we are not in the realm of science and there’s not much to discuss. (Of course, if you are claiming that this is Bible theology issue, then you can cite the Bible passages which form the basis of your claim.)
How do you know that the mutations were already within the code/blueprint?
If you can tell us where the mutations are stored (and how), then scientists could verify your claim.
Upon needs thresholds being crossed human bodies would change instantly to colours etc etc to help out.
They did change. its reasonable God knew we needed to change and so gave us the ability to change. Like creatures.
Then its obvious colour etc change had to be instant. Any intermediate stages would not have a need to change more.
You must allow our glorious genetic beings to be able to change in these minor ways.
Like those sea creatures that change instantly. No big deal in nature.
These mutations, I suggest, are only special cases of mutations gone wild. Mutations are possible a natural normal part of biology. Or rather not really mutations. Speculation but better then evolutionism.