Joshua
Thanks - we speak with much the same voice, I think. My own “bruising” experience, you’ll perhaps appreciate, has been several years long.
Just one thought in closing:
Might it be that this is one reason you’ve just had a brusing blog war (which I’ve followed with interest, by the way)?
Thanks Joshua, this is probably the most articulate presentation of a position on evolution I have seen on a web site.
I will add that my area of expertise is not in any area of the biological sciences, so I rely on papers I come across and reviews, along with papers that are more in keeping with philosophy of science. I am aware that debates rage amongst a number of groups, and also things such as the third way - so as one viewing from the outside, my impression is one of disputes, changes in overall outlook, and on-going debates. Within this context, I regard this area as NOT settled, and so I hope that at some future date, we may have a well accepted TOE, and people such as myself, may include this within a general view of science and faith.
On common descent, I confess that my outlook has been influenced by debates during my years as a student, where we as college “know-it-all” students debated (fiercely) common descent. The other side was so dogmatic about it (those were the days of the missing link) that I concluded their position was one of dogmatic-atheistic, and not science. I have regarded common descent since then with suspicion and have made a couple of comments on population modelling and bottlenecks, which imo seems to assume a lot as given - but that is for another discussion.
can you give a specific example? thanks.[quote=“Swamidass, post:492, topic:4944”]
If it was true, all the ID math we have seen falls apart.
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how actually?
WOW. Haven’t I and just about everyone else made it clear that we don’t EXPECT or DEPEND upon
You are working yourself up to a frazzle over this? You GOTTA be kidding …
I invoke God’s involvement in the evolution of Earth’s life OUT OF THE INTERSECTION
of FAITH IN GOD …
AND…
of MY OBSERVATION that the Earth cannot be less than 6000 years old.
I have no choice in the matter.
Science DENIES me a plausible way of accepting an Earth of 5000 years in age … with a GLOBAL FLOOD in the middle of Egypt’s 4th or 5th Dynasty. It never happened. That part of the Bible is wrong.
Now let’s turn our attention to YOU, GJDS:
Tell us, exactly, how YOU THINK we should be looking to a SCIENTIFIC PAPER about God.
This should be FASCINATING.
And in this, @GJDS, we are in virtual, if not perfect, agreement.
I do not rely on Science to inspire my thoughts that God was involved in evolution. It is my faith in the necessity for God that provides the inspiration.
I look forward to the day when such faith and inspiration doesn’t OFFEND YOU to the bone.
I agree with Josh that CD is the heart of evolution historically, including for Darwin, who did not limit the mechanisms to natural selection alone, even though NS was the most important for him. Prior to Darwin, “transmutation” (the word used by French evolutionists and adopted by the English with no changes in spelling or meaning) was about CD, and it was still about CD for Darwin, who actually never used the word “evolution” in the first edition of Origin of Species, which ends with the final word “evolved,” which is the only use of that word in the whole book.
For a couple of generations after Darwin, many biologists accepted evolution (in the sense of CD) but not “Darwinian” evolution (where NS was the main driver). Peter Bowler refers to this period as "the eclipse of Darwinism,’ but CD was not under attack in the scientific community.
Not to distract from the good discussion… The notion that most of the human genome is functional or that every bit of DNA in genome has a functional role is, ironically, both a common ID/Creationist and an ultra-selectionist viewpoint. Some of the strongest selectionists can be creationists (i.e. those taking the positions that mutations are overwhelmingly harmful, or that there is no ‘junk’ in our genome). I’m sure Joshua encountered those positions in his recent exchange on other blogs.
I understand the background here. This is how it was for me during high school too.
However, in 2000 and 2005 everything changed with the publication of the human and chimpanzee genomes. It could not be more clear. If God created us de novo for some reason He created us to look like we share an ancestor with the chimpanzees. Of course, God can do anything, but this presents a serious question to any holdout caring to communicate with our world. God could have made us with genomes that were obviously different than apes, at least more different than mice are from rats. He did not. Why not?
This, ultimately, is the question that lead me to realize (1) disproving evolution was not one of God’s design goals, (2) therefore, it probably shouldn’t be one of my goals, and (3) it was idolatorous (for me) to look outside of Jesus for scientific proof for God. As I left ID, I found a more Jesus-centered confidence, and cam to see a profound beauty in evolution. As @Kathryn_Applegate would say, “endless forms are most beautiful.” For me, the journey from ID to theistic evolution was a journey out of idolatry.
So I can help here. There is a portion of the evolution that is settled, and not under debate in any meaningful way. And there is a portion that is not settled. Of course you can dispute this, but this is how mainstream science shakes out now.
SETTLED:
NOT-SETTLED:
To be clear, this doesn’t mean that CD is TRUE. It is possible that God created the world to look like we all evolved from a common ancestor. God can do anything. However, this does mean that science is very clear right now, and any one who disputes it should devote some time to the theology to explain how this could be. I’m willing ton consider the possibility that evolution did not happen, but I would need to know why God made a world that looks evolved.
Moroever, it is a common strategy to conflate about the unsettled details with debate about the settled theory. Do not be fooled. The settled details really are settled. The evidence is so strong in its favor it is hard to imagine anything that could disprove it at this point. It’s not that CD isn’t falsifiable (it is), rather an ocean of different types of evidence has failed to falsify it.
My first exposure to evolution came in college. The same is true for others. Your simplistic caricature of legitimate science based opposition to the TOE may allow you to keep your blinders on, but it is not rooted in reality.
This article gives a great review of the math behind neutral theory, with several of the experiments used to validate it over neo-Darwinianism (positive-selection) http://inference-review.com/article/the-neutral-theory-of-evolution. The math here is very well founded. Another helpful overview is here: Genetic drift - Wikipedia. Also, remember that drift happens in parallel (not sequentially) with all mutations across the genome fixing at the same time. Therefore the fixation rate EQUALS the mutation rate. And I’ll point out that all this math is directly verifiable with simulation.
Egg yolk genes in humans. Don’t forget to look at the mathematical simulations in this study. You will see a host of patterns in the data that are all explained by CD + neutral theory, with a small amount of positive selection: Loss of egg yolk genes in mammals and the origin of lactation and placentation - PubMed
This is one of the most profound experimental results in evolution I have recently seen. Genome-wide patterns and properties of de novo mutations in humans | Nature Genetics, look at Figure 4. We see that de novo mutation rate + recombination rate ENTIRELY explains variation in divergence across the genome. This is analogous how the rate of continental drift predicted by radiometric dating exactly predicts the measured rate by GPS Smoking Gun Evidence of an Ancient Earth: GPS Data Confirms Radiometric Dating – Naturalis Historia.
So this is another paper showing experimental validation. It has been long hypothesized (based on looking at genomic comparisons) that the splice reaction can be reversed to add introns into genes, splitting a single exon into two. This is a 1 out of trillion event that was recently observed in the laboratory: Rare Evolutionary Event Detected in University of Texas Lab - UT News and http://www.pnas.org/content/113/23/6514.abstract. This is a great example of evolutionary theory making a prediction about how biological systems behaive that we can directly observe, but would otherwise not be predicted.
I could go on and on. There is also literally thousands of papers just like these that experimentally test the claims of evolution. But this gives you a good sense.
And how does this make ID math fall apart?
Basically, if neutral theory is true, there are two consequences:
Therefore, ID people fight tooth and nail against neutral theory. If it is true (as it looks to be) it seems to foreclose any hope of proving ID scientifically with mathematical rigor. All they are left with are lawyerly arguments. And we know how far that gets you in science.
Given this data, right now, in ID you have to hold an alternate view of how nearly the whole of biology works. This is the only way that the ID arguments are plausible.
PS: I just had the absurd experience of having random non-experts instantly form very emotionally strong opinions about whether or not most lncRNA is functional. Most of them had never heard of lncRNA before, and did not even know what it meant. All they knew was “if lncRNA is not usually functional, than the ID case is weaker”, so they argued like their life depended on their instinct that lncRNA is always function. This is transparently absurd.
Thank you for your posts. It goes without saying that you are a skilled communicator, and explain things in such a way that those of us on the periphery of science can understand, rather than getting bogged down in jargon.
Perhaps in part because William Dembski and Jonathan Wells have supported the position that ID implies DNA should be functional. However, those claims imply either hyperselection such that most changes are severely deleterious or that a creator actively put almost every base in place for a functional reason when it formed a species. However, there is no inherent conclusion implied by ID that junk DNA cannot exist. So perhaps it’s related to a desire to make references ‘infallible’.
A similar ‘authoritarian’ infallibility sentiment seemed to have been at work when Phillip Johnson (author: ‘Darwin on Trial’) started dabbling with those like Peter Duesberg in promoting the idea that HIV was not involved in AIDS. Jonathan Wells also supported that position. At about the same time, many ID supporters in the various discussion boards also embraced the “HIV doesn’t cause AIDS” position. This was at a time after it was long clear that HIV had causal role in AIDS and that antiviral treatments against the virus demonstrated efficacy against AIDS.
Again thanks for your detailed response - I will be glad when I can agree with you and I can “cross off” reading papers and texts on biology 
As I have indicated elsewhere, I have approached the faith-science aspect decades ago by considering the physical sciences and relevant philosophical arguments, and I had concluded that there is harmony between faith and science, and not conflict. Biological evolution did not seem to fit within this framework, so I have placed it in a separate “work in progress” category. I have read many papers in the bio-area over the past tow or three years, just to keep abreast of things, and not to display expert insights - the work on genetics has been impressive. I also read with interest, " MAPPING THE FUTURE OF BIOLOGY EVOLVING CONCEPTS AND THEORIES Editors ANOUK BARBEROUSSE MICHEL MORANGE THOMAS PRADEU" Perhaps you may be familiar with this review. My impression (from these sources) is that aspects such as natural selection (and other ideas) are still considered central by prominent bio-scientists. From your remarks, it appears that you do not share this outlook. In any event, I for one will applaud if a coherent and comprehensive theory of biology were to emerge in the near future - as I said before, I would then be in a position to “add this” to my contemplations of faith-science. From your remarks, I think it unlikely that a settled theory would make a significant difference to my faith-science outlook, and I cannot imagine any great changes to orthodox theology.
I also feel that the differences between atheists and theists will continue, and it is likely that any TOE (once settled and coherent) would still be appropriated by anti-theists for ideological purposes. Perhaps it may be wise if Christians took the trouble to consider the fundamentals of the physical sciences, and then see if we can work through the complexities of theoretical aspects of the bio-sciences.
I close my comments with the suggestion that I cannot see great validity in ID, TE, EC. YEC, OEC, etc., because I cannot accept a view the bible is a scientific text book. So I maintain my position that productive effort should be directed to the harmony that is, in my view, in faith and science - this is reasonable, can motivate good science, may indeed strengthen our faith, make us better appreciate the creation, and is an approach that avoids angst and conflicts, especially in matters pertaining to the Christian faith and orthodox theology.
Dr. Swamidass,
I do not disagree with what you have written about the study of genetic change. That aspect of evolution checks out.
However, evolution requires two processes to work together to bring evolutionary change. One is Variation, which is the genetic side, and as I have said, checks out. The other process is Natural Selection, which traditionally has been based on Malthusian survival of the fittest population theory that has not been scientifically verified. That for me is serious problem, because it allows people like Dawkins to make statements about evolution which are not true.
I have been advocating a view of Natural Selection based on ecological selection. I am seeing signs that this view is gaining popularity, but not being a scientist myself it is hard to gauge what is going on the scientific world. Maybe you can help me in this respect. This is not a new idea, but to me it is important to many reasons.
Yours,
Roger .
hi dr joshua.
about point 1) even if neutral theory is true- i dont see how it have any conection to falsified id model. also it may have some problems. for example: according to evolution fly and mosquito split off about 250 my ago. fly generation is about less than one month. so even if one generation mean only 1 new mutation we will need only 10^8 month to change his entire genome. or about less than 10^7 years. so fly and mosquito are suppose to be different in about their entire genomes from each other. far from reality. so maybe most of the mutations in the coding region arent neutral.
about 2) even if its a real vit pseudogene, it cant be evidence for a commondenscent. for example: some fish (like the stickle back) also have or pseudogenes for land senses. but the problem is that fish never have a land ancestor:
. “Groups α and γ of type 1, which are present in amphibians, reptiles, birds and mammals and absent in fish except for one intact gene in zebrafish and a few pseudogenes in medaka and stickleback”-
so now we need to conclude that those fish evolved from a land species?
about 3 and 4)i dont see how an intron gain\loss\variation events are evidence for evolution.
5)what about the corelation between the species complexity and the anoumt of junk in this species?
Good point. Once we start dealing with very distant species, neutral change wipes out all the neutral similarities. What we are left with are the critical pieces that are preserved by negative selection. This is why we still see similarity between drosophila, humans, and mosquito: negative selection. This of course, does not disprove neutral theory. Remember, I said most (but not all) change is due to neutral mutations. You are just pointing out an edge case where this is important to explicitly consider.
If you only looked at protein similarities for these two species, you might conclude common designer. However, this is where synteny (the order of genes) still leaves a strong signal, even after 250mya. This paper gets into the details: http://genome.cshlp.org/content/12/1/57.long. I didn’t see a whole genome comparison here, and this might be because of lack of data or very poor alignment (as would be expected) in most non-coding regions.
To be clear, after even more time, even these similarities would probably be erased. Eventually the wind blows away all the footprints in the sand. Genome similarity is more clear in the 50mya range. Before that, things get progressively blurrier, just as we can mathematically model too.
Thanks for bring up this example. This is just another example to add to the pile of cases that are explained by CD.
Just be clear. I believe God designed us. So none of this falsifies design per se. However, it does make detecting design very difficult. That’s all.
This is a nonsequitur. VITG1 is absolutely evidence for common descent. Changing the topic to another piece of evidence does not detract in any way for the strong evidence it gives for common descent.
And your statement about pseudogenes misreads the data.
This is just evidence that this class of smell receptors was present in the common ancestor between fish and land animals. This is also a very very distant relationships. If, on the other hand, we were consistently seeing (for example) distinctly HUMAN proteins randomly showing up out of place in nature, that would be a significant problem. This, however, is not what we see in genomes.
These are actually pretty important. If common descent is true, it makes predictions about the behavior of biological systems. Specifically, it makes claims about “how” they change from one generation to the next, at a time scale that we can observe in the laboratory. These points validate two of these predictions, demonstrating them to be correct. This just demonstrates how evolution actually is testable science.
Great question. I’d point to Venema’s excellent posts on Junk DNA. This explains much of this. The simple answer is that this specific study only finds a very low-level correlation that we already know. In fact, many of the graphs are quite misleading, just showing correlation between coding and non-coding length (not complexity). Regardless, I woudl point you also the onion test: The onion test. | Genomicron.
Aside from the things you will find online, I will also point out that one reason complex organisms might have more Junk DNA is that they are (1) less tuned to reduce genome size (because it has less impact on fitness), and (2) are tuned so most mutations are in regulatory regions (because this is safer and more likely to be beneficial). This (especially #1) is a pretty strong reason why most biologists are not very worried about being shown wrong about this.
Hope that helps. Have fun reading more.
I should also add that many in the ID community agree with me in this analysis. I’d point you to VJ Torley, Denton, and Behe.
Sorry to belabor this.But did you read the paper you quoted to me?
It explains in full detail how this data is consistent with common descent.
Disputing the INS and OUTS of evolution is a red herring. It can be tremendously murky.
The question is much clearer on the side of GEOLOGY and PHYSICS.
How old is Earth? Even before Darwin, Geologists could tell us the Earth was at least MILLIONS of years old.
Once we’ve established that, does it really matter how many problems there are with the technical unknowns of Evolution?
Scientist like to get things right.
“Let your conversation be always full of grace, seasoned with salt, so that you may know how to answer everyone.” -Colossians 4:6
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