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.
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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 Iâll point out that all this math is directly verifiable with simulation.
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Egg yolk genes in humans. Donât 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
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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 â Naturalis Historia.
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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:
- The vast majority of genetic changes are neutral and do not need to be specifically explained by evolution. They are âunspecified.â They are just noise. This makes evolution a much more believable story.
- It also means the positively selected mutations are vastly outnumbered by the neutral mutations, perhaps by a factor of 10,000 in mammalian systems. This means it is much harder (impossible?) to show a signal for design in DNA with the evidence we see that entirely supports CD.
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 âif lncRNA is not usually functional, than the ID case is weakerâ, so they argued like their life depended on their instinct that lncRNA is always function. This is transparently absurd.
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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 itâs related to a desire to make references âinfallibleâ.
A similar âauthoritarianâ infallibility sentiment seemed to have been at work when Phillip Johnson (author: âDarwin on Trialâ) 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 âHIV doesnât cause AIDSâ 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.
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Again thanks for your detailed response - I will be glad when I can agree with you and I can âcross offâ 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 âwork in progressâ 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 âadd thisâ 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:
. âGroups α and Îł 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 sticklebackâ-
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 didnât 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. Thatâs 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 âhowâ 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. Iâd point to Venemaâs 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. Iâd 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.
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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 weâve established that, does it really matter how many problems there are with the technical unknowns of Evolution?
Scientist like to get things right.
Hi George -
I pray you are enjoying the wonders of Godâs creation today.
I am extremely curious as to why you classify Alex Rosenbergâs philosophical musings as a scientific paper. Tracking down the provenance of your quote, I learned this from Wikipedia:
Alexander Rosenberg is an American philosopher, and the R. Taylor Cole Professor of Philosophy at Duke University. He is also a novelist.
His fellow philosopher Edward Feser provides a little more background on Rosenbergâs âEliminativism Without Tearsâ paper:
suppose you hold that what is real is only what science tells us is real. Then you are at least implicitly committed to denying that even human purposes or ends are real, and also to denying that the intentionality of thought and the semantic content of speech and writing are real. Scientism, in short, entails a radical eliminativism. Alex Rosenberg and I agree on that much
So I am just completely baffled as to how you would characterize Alex Rosenbergâs paper as a scientific paper.
The larger point that I, Swamidass, and many others have been making is that the theory of evolution, like any other scientific theory, is not inherently atheistic. It is true that many atheist philosophers like Rosenberg and Dennett cite evolution as evidence for atheism; they also cite biochemistry as evidence for manâs having no soul, and they cite astrophysics as evidence for the universe having no Creator. As Christians, we disagree; we believe that God established an orderly creation for us to thrive in. The scientific theories that emerge from our study of that creation, then, are evidence of His order.
Thus, If I can affirm that:
- The theories of biochemistry are valid, yet it is also true that God has given us immortal souls; and
- The theories of astrophysics are valid, yet it is also true that God created the universe;
then I can also affirm that the theory of evolution is true, yet God is the creator of life.
I dont think Billy Graham has written any Scriptures
Snowflakes are technologically advanced? Snowflakes are information rich systems? In what ways?
Once again, you put words into my mouth that I did not say. I believe that the evidence supports the special Creation of life that the Bible testifies to. Perhaps you can detail for me why you believe the evidence supports a purely naturalist origin and evolution of life?
[quote=âgbrooks9, post:385, topic:4944â]
This is why BioLogos throws open all the doors of possibilities by simply adding one key ingredient: God
[/quote]\
Thanks for your frank confession that believe in God is entirely independent of the believe in a purely naturalistic narrative for the phenomenon of life. Now it should be an easy step for you to recognize that the latter is a necessary foundational pillar of the atheist worldview.
Nope. What I am arguing is that it is a contradiction of the laws of logic to propose that it is possible to believe that both the TOE and the Bible are true.
even in this case we need to see a much more difference. if most of the mutations that get fixed are neutral- then most of the gene sequence can be change without make any problem. so we can expect negative selection for some small part of the gene, but not most of it.
the vit gene have some other functions then making yolk. so even if it is indeed a real vit pseudogene it cant be evidence for making yolk in the past. its s simple logic. more then that- humans have genes for feathers development. do we need to conclude that human evolved from birds?
so if we will found a gene that shared between far species but lack in the species between them, evolution will be in a big problem?
the problem is that zebrafish fossils isnt even close to the spliting time of fish and tetrapod (around 400 my). so its not fit with the fossil record.
but we never seen a complex trait evolved in the laboratory. only variations. so we cant say that we can test it by a scientific method.
actually the paper do talk about complexity:
âHere we extend on that work and, using data from a total of 1,627 prokaryotic and 153 eukaryotic complete and annotated genomes, show that the proportion of ncDNA per haploid genome is significantly positively correlated with a previously published proxy of biological complexity, the number of distinct cell types.â
about the onion test: again: we see a correlation in most of the species and not few here and there. so the onion is an abnormal. even in this case- we know that plants with a big genome grow very slowly. so it may have a function even in the onion case.
Hi Chris,
Thanks for your kind remarks and I hope you are well.
I realise that Rosenberg is a poor example of a scientific paper, as you correctly point out, he is not a scientist - my wording is poor. I used that as an extreme example of how atheists extend biological evolution into other areas, but mainly because he has said a great deal about evolution, science, and a general outlook of materialism. He wrote a book that I have quoted from, that is more or less Philosophy of Science, and in it, he has given an exposition of evolution, (and Darwinâs thinking re variation and natural selection) which I consider a thorough treatment of why atheists put such stock in TOE.
I happened to come across his book, and since my time and energy are limited, I consider his treatment as typical of atheistic evolution. I can spend time looking through other papers, if that is important, but I feel that for this discussion, this example should suffice, particularly since he devotes many pages discussing his take on evolution as being variation and natural selection.
On the more general point of any scientific theory not being inherently atheistic, I agree and I made a lengthy response to gbrooks, that presents my thinking on this point. Perhaps you may look through that and I would welcome any comments you have.
I commence with a dogmatic statement that God is Creator of all. Everything stems from this. I have spend some effort to develop a (hopefully) clear idea of what it means to formulate scientific theories and observations, and have concluded that in terms of my theological outlook, I am far more comfortable in dealing with established matters of science. For example, we may discuss the wave-nature of matter/energy, by starting with basic notions, such as wave maths and classical equations (conservation of matter and energy). All of this requires using constants that are essential for such work (I am sure you are familiar with this). Thus, why is it so? How can I, as a scientist, understand the world of objects, and must discover these constants (a simpler example is pi - I am fascinated at how we came to use pi).
To my mind, such contemplations avoid controversy and debate - from science. The only question that remains is on faith - I have stated my position dogmatically. I understand if an atheist made a contrary statement dogmatically - our positions are opposite, but both are understood.
When I look at TOE, I cannot come to the same point - thus I regard it as speculative for my faith-science outlook. This should not be taken as saying I think it is false, or the work of the devil, or such nonsense - it is imo inadequate for what I think is necessary re theology and faith-science harmony. I point out the historic conflict and angst that TOE has left, a trail that should cause us to look at it critically.
To avoid a charge of uncharitable comments on this matter, I will put a suppose - I would suppose that if biologists provided a robust theory of how life began, I would look at this seriously, and I would expect to consider this theory in the same way - i.e. there would be similar constants and equations (mathematical, chemical, biochemical, and so on), and these would also leave us with a sense of wonder and mystery. Perhaps when biologist achieve this, someone may come up with a constant D, and these things would be reported as so many Darwins (D) etc.
I am not sure I can add to this - my comments would not have a âyetâ about God. Instead, I affirm that God is the Creator, and I am privileged to study chemistry, a small portion of His creation, and physicists theirs, biologists theirs and so on. When we indulge in these discussions, we may endeavour to construct a mental concept of the entire creation - a big ask, but a wonderful thing all the same.
This is a wonderful articulation of how faith and science can, and should, work together. Thanks, George!