@PeterWaller, what would say your main evidences are after hashing a few things out regarding ‘natural processes are insufficient, therefore divine detection is in order?’ Also if I’ve got that idea wrong, feel free to help me to understand you better.
Thanks for the question. I thought of four types of evidence: timing, complexity, feasibility, and need.
Timing
The first evidence for animal life in the fossil record begins approximately 60 million years prior to the first vertebrate, Haikouichthys, 580 Ma. From what I can ascertain from Figure 2, it appears that amphioxus appears approximately 60 million years after the origin of bilateria, if that is the meaning of the cephalochordate - vertebrate split in Figure 2. There is mounting DNA and morphological evidence that chordates were derived from extant cephalochordates, with their full sequence of 14 Hox genes in the single cluster, gene expression, and many of organs and structures (Marlataz et al., 2018). This indicates to me that cephalochordates existed in a state that is somewhat close to their present condition at the time of the cephalochordate-vertebrate split, which would take place after approximately 60 million years. The alternative seems to be that bilateria would evolve for 250 to 300 million years of the Neoproterozoic, for which there is no evidence.
Marletaz, Ferdinand, Panos N. Firbas, Ignacio Maeso, Juan J. Tena, Ozren Bogdanovic, Malcolm Perry, Christopher DR Wyatt et al. “Amphioxus functional genomics and the origins of vertebrate gene regulation.” Nature 564, no. 7734 (2018): 64.
Complexity
First, let me say that I am not one to just say that something complex must have been created, but I would like to say that the list of vertebrate characteristics that began this thread does not do justice to the complexity of the organs, structures, and nervous system in vertebrates. For example, the olfactory bulb has 10 million neurons and a series of mechanisms that pass the information to the brain. Just the enteric nervous system in humans has 500 million neurons. The adaptive immune system is amazing. Endothelium and myelin sheaths are amazing. The lamprey fish in the Cambrian had smaller system, but they were fully functioning vertebrate systems. The complexity of these systems makes the sudden appearance of the vertebrates in the Cambrian seem even more unnatural.
Feasibility.
Although God can do anything, I think that there would need to be some sort of explanation for how God might have changed one thing into another. The neural crest cells that form next to the neural tube in vertebrates form most of the vertebrate organs, nerves, and structures other than the central nervous system (spine and brain). Thus, it seems feasible that God could add the neural crest cells to an extant cephalochordate and add vertebrate complexity. God could also work with the neural tube and concentration of thousands of neurons at the anterior end of amphioxus to form a much more complex central nervous system.
Need
I think that God only acted when necessary and otherwise allowed natural processes to form our world. Could a vertebrate, which would eventually become human, have evolved on its own? Would the kidney, essential for life on land, have formed in the sea? Would a strong hydroxyapatite internal skeleton, essential for large animals on land, have formed in the sea? Would blood vessels lined with endothelium or the DNA for myelin have formed on its own? Would the adaptive immune system have formed on its own? They did not form in any other phyla.
Hi Stephen. Thanks for the clarification. I found information on the effect of including and deemphasizing the effect of the vertebrate genome on molecular clock analysis of the origin of metazoa.
In 1996, Wray estimated divergence times based on gnathostome vertebrates, “with the addition of mollusks and echinoderms for 18S rRNA.” Wray et al. estimated that invertebrates diverged from chordates, one billion years ago (1 Ga). In 2004, Peterson et al. compared the DNA of vertebrates with drosophila (arthropod flies) and estimated that vertebrates split from dipterans (Drosophila) 900 Ma. In 2011 and 2015, Erwin calculated divergence times of metazoa, basing their estimates primarily on divergences across the many metazoan phyla and deemphasized the vertebrate genome.
“The study included 24 different calibration points distributed across the tree, in contrast to the dominantly vertebrate calibration points used in previous studies, and employed a relaxed clock analysis.”
Erwin’s neglect of vertebrate DNA resulted in an estimate of the origin and appearance of animals that agreed with the fossil record.
“First, the results suggest an origin of Metazoa during the Cryogenian, approximately 780–800 Ma, the LCA of cnidarians and bilaterians at approximately 700 Ma and of bilaterians approximately 688 Ma (all estimates have analytical uncertainties discussed in detail in reference [1]). Because so many taxa were included we were able to estimate the ages of the crown groups for the larger clades, and these largely fell during the late Ediacaran and Cambrian. The congruence between these estimates for the origin of the crown group and the actual appearances of the crown group in the fossil record provides additional confidence in these results.”
Erwin’s model showed that the divergence of bilaterian phyla took place 670 Ma rather than 1 billion or 900 Ma as the previous studies estimated that were constrained by vertebrate DNA. Thus, there is a 300 to 400 million year difference between molecular clocks based on vertebrate DNA and those that are not based on vertebrate DNA.
Looking at environmental factors, Erwin stated that the origin of animals prior to 800 Ma would not have occurred because oxygen levels were too low.
“The results from geochemical proxies suggest an emerging model of redox condition through the late Neoproterozoic, with atmospheric oxygen levels less than 0.1% PAL O2 before approximately 800 Ma and partially oxygenated oceans from approximately 750 to 580 Ma with levels of approximately 1–3% PAL O2”
In summary, the origin of vertebrate DNA does not agree with the fossil record or molecular clock analysis while all other phyla line up well with the fossil record and molecular clock analysis. This is evidence that vertebrate DNA is not natural. Vertebrates should have been evolving for 400-500 million years prior to their appearance in the fossil record. Yet, they appear suddenly, with all of the uniquely vertebrate characteristics appearing at once in the Chengjiang Lagerstatten. In addition, there is no possibility that the animals could have begun evolving prior to the time that oxygen concentration rose 800 Ma. Yet, just the divergence of vertebrates from other bilaterians is estimated as taking place 100 to 200 million years prior to that time. These facts indicate that the natural evolution of vertebrates is extremely unlikely.
Wray, Gregory A., Jeffrey S. Levinton, and Leo H. Shapiro. "Molecular evidence for deep Precambrian divergences among metazoan phyla." Science 274, no. 5287 (1996): 568-573.
Peterson, Kevin J., Jessica B. Lyons, Kristin S. Nowak, Carter M. Takacs, Matthew J. Wargo, and Mark A. McPeek. "Estimating metazoan divergence times with a molecular clock." Proceedings of the National Academy of Sciences 101, no. 17 (2004): 6536-6541.
Erwin, Douglas H., Marc Laflamme, Sarah M. Tweedt, Erik A. Sperling, Davide Pisani, and Kevin J. Peterson. "The Cambrian conundrum: early divergence and later ecological success in the early history of animals." science 334, no. 6059 (2011): 1091-1097.
Erwin, Douglas H. "Early metazoan life: divergence, environment and ecology." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1684 (2015): 20150036.
When you wrote “neglect” you revealed that you either did not understand the 2015 paper or that you chose to mislead others about what it says. It is about metazoan divergence. Overemphasis on vertebrate lineages is a basic sampling error, which Erwin and others corrected by sampling across the tree. You quoted him saying that, then called it neglect. That’s wrong.
This paragraph is a train wreck. “Constrained by vertebrate DNA” is wrong, as is “based on vertebrate DNA.”
I think that probably explains why you are struggling to understand the topic of early animal evolution; you probably aren’t trying to understand it, but are seeking holes for god or the supernatural to fill. This is an impulse I will never understand.
You can have the last word. I don’t think we can discuss evolution without a more solid mutual commitment to facts and reasonable logical thought.
You’re doing it again! As I mentioned several months ago, “Posts of skeptics are nitpicked for details or language.”
And leveraging off your own comment, when you posted this, you either did not understand or chose to mislead others about what PeterWaller is saying. Why do this?
As an atheist, I know your belief system requires naturalist processes alone to be adequate. And the entire thrust of this thread violates your “religion” so you respond with verbal abuse.
Someone once said something like, “When a man understands, he is happy to explain and learn. When he doesn’t, he sits back with his arms folded and criticizes those who are talking.” @PeterWaller looks here like the first guy, you, the second.
And BTW if you don’t like the word “religion” applied to your belief system, then stop acting like a middle ages cleric trying to silence honest questioners.
And yet again, nitpicking. Since you don’t understand what the author is saying, maybe you should ask. I understand what he is saying.
Perhaps more correctly, your projection of your own approach to this topic onto others explains exactly why you don’t understand his point. Maybe you should try.
@PeterWaller - Thank you for your posts here and how thoughtfully you have put them together. These forums can be a mixed bag. You need to ignore the abuse in these forums sometimes doled out by some of the atheists. When they are not in their stinky self-righteous mode, they can provide interesting dialog.
I have a further question/perspective. One point not addressed by molecular clocks is the need for many coordinated mutations to produce new function. Even if molecular clocks could account for the gross amount of change, mutations don’t self-coordinate. This is an area difficult to assess but which would exponentially increase the time demand.
Have you read Behe’s Edge of Evolution? Not the best book ever written, but he does an effective mathematical analysis of mutation rates and waiting times from something we do know, and applies it to binding sites in proteins, which also require multiple coordinated mutations. He comes to the same conclusion as you: there isn’t enough time for natural processes to do this on their own.
Have you given any thought to “multiple coordinated mutations” versus simple molecular clock analysis?
Thank you Marty, but I still had some errors in the last post, which is why I welcome critiques. They encourage me to take another look. I think I am closer to the correct understanding in the following:
DNA molecular clock studies use rates of DNA mutation that are based on differences in known genomes of existing animals and the time that they diverged in the fossil record. In 1996, Wray et al. estimated divergence rates based on DNA differences in gnathostome vertebrates. Based on these rates, Wray estimated that vertebrates diverged from all invertebrates one billion years ago (1 Ga) and from arthropods 1.2 Ga. Other studies calculated similar origination times for vertebrates. Peterson et al. evaluated the rate of change of DNA for vertebrates by comparing the DNA sequences for Osteichthyes (bony fish) and other vertebrates. As with other studies, he found that vertebrate rate of DNA change is approximately half that of drosophila and other invertebrates. These calculated rates of change lead to the same ancient divergence times as that calculated by Wray and others. However, molecular clocks based on the rate of divergence of invertebrate DNA led to much more recent last common ancestor calculations. Peterson proposed that the rate of vertebrate DNA change may have slowed, and that if it was half as fast as the observed rate of change, then it would be in agreement with the rate of change or origin of the animal kingdom predicted by invertebrate DNA.
In 2011 and 2015, Erwin et al. (including Peterson) calculated divergence times based on genes across the many metazoan phyla, which meant that weight of vertebrate divergence in the calculation was only a small fraction (1/24?) in the calculated rate of divergence of the animal kingdom as a whole.
“The study included 24 different calibration points distributed across the tree, in contrast to the dominantly vertebrate calibration points used in previous studies, and employed a relaxed clock analysis.”
Based on his research, Erwin stated the following.
“First, the results suggest an origin of Metazoa during the Cryogenian, approximately 780–800 Ma, the LCA of cnidarians and bilaterians at approximately 700 Ma and of bilaterians approximately 688 Ma (all estimates have analytical uncertainties discussed in detail in reference [1]). Because so many taxa were included we were able to estimate the ages of the crown groups for the larger clades, and these largely fell during the late Ediacaran and Cambrian. The congruence between these estimates for the origin of the crown group and the actual appearances of the crown group in the fossil record provides additional confidence in these results.”
Erwin’s research, with vertebrate rate of change of DNA weighted as a small fraction, showed that the divergence of bilaterian phyla began 670 Ma rather than the one-billion-year estimates by molecular clock analyses with dominantly vertebrate calibration points. Thus, there is a huge difference between molecular clocks that are based on the vertebrate rate of change and molecular clocks with calibration points distributed evenly across the tree of all animal phyla. These calculations with divergences primarily based on invertebrate DNA agreed with the fossil record; thus, the natural processes that led to invertebrate evolution from microbes have not changed. The same cannot be said for vertebrate evolution.
Looking at environmental factors, Erwin stated that the origin of animals prior to 800 Ma would not have occurred because oxygen levels were too low.
“The results from geochemical proxies suggest an emerging model of redox condition through the late Neoproterozoic, with atmospheric oxygen levels less than 0.1% PAL O2 before approximately 800 Ma and partially oxygenated oceans from approximately 750 to 580 Ma with levels of approximately 1–3% PAL O2”
The lack of oxygen prior to 800 Ma means that vertebrate animals could not diverged from other bilateria 1 Ga, and the animal kingdom could not have originated before that, as calculated with the rate of vertebrate change in DNA observed in the last 400 million years by several studies. Yet, there is no evidence that the rate of change of vertebrate DNA has changed.
Wray, Gregory A., Jeffrey S. Levinton, and Leo H. Shapiro. "Molecular evidence for deep Precambrian divergences among metazoan phyla." Science 274, no. 5287 (1996): 568-573.
Peterson, Kevin J., Jessica B. Lyons, Kristin S. Nowak, Carter M. Takacs, Matthew J. Wargo, and Mark A. McPeek. "Estimating metazoan divergence times with a molecular clock." Proceedings of the National Academy of Sciences 101, no. 17 (2004): 6536-6541.
Erwin, Douglas H., Marc Laflamme, Sarah M. Tweedt, Erik A. Sperling, Davide Pisani, and Kevin J. Peterson. "The Cambrian conundrum: early divergence and later ecological success in the early history of animals." science 334, no. 6059 (2011): 1091-1097.
Erwin, Douglas H. "Early metazoan life: divergence, environment and ecology." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1684 (2015): 20150036.
@pevaquark
[musing on the Figure 2 you posted above]
IIRR, there are simply not a whole lot of layers of rock before the Precambrian period, or they are damaged by metamorphic processes. Of course, there are a few layers that can be found from some 3 G years ago, but they are rare. There are also banded iron formations from about 2 G years ago. Still, it is difficult to argue from fossils alone what the course of history was unless we find those fossils. From the Cambrian onward, we have a reasonable number of fossils to make some valid assessment, but before that time, if I am not mistaken, there is not a whole lot of information, so we are in the twilight zone of understanding.
Also, many of the organisms may have been shell-less, making such organisms very difficult to detect as fossils.
So I wonder to some extent if the “Cambrian explosion” has as much to do with the lack of information we have available before that time as it has to do with some (possible) rapid shift in the rate of diversification.
As a matter of my faith, I can accept that God was somehow involved (with all the vague qualifications), but as a matter of science, I think that would be very difficult to show. It’s our own tendency to put a flag on some spot, but God is supposed to have created the universe. God is not petty like we are. [… well, some may differ particularly in citing the OT, but at any rate, the NT does have a bit more of a “sacrificing his own life to save us” rather than the meddlesome butt-kicking God of the Exodus, and there is a clear evolution of thought in the OT understanding of God in the voice of the prophets as well in the NT.] I think we are given a choice and if we come to love God, we will also try to discern and follow. But wanting to post a flag on the ground of science (assuming it could even be done) would mean that we don’t need faith anymore.
Of course, it is human nature to want to have a club to beat others over the head with, it is certainly evident in the response of the people of the old testament and it seems often the case of many people in the new testament age. Following Jesus in the real world is hard.
by Grace we proceed
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I have not read the Edges of Evolution, but it is possible that the timing of the appearance of vertebrate characteristics presents a greater difficulty for philosophical naturalism than irreducible complexity. Reading the literature, it appears that the primary focus in the irreducible complexity debate is the blood clotting cascade, which is found in complete form in all vertebrates and is not found in invertebrates. The blood clotting mechanism is amazingly complex and involves 10,000 genes (wrong, 26 proteins). In a paper arguing against irreducible complexity, Aird argued that the cell and protein clotting mechanism in higher invertebrates could have evolved into the vertebrate blood clotting cascade; however, he thought that the timing of the formation of the cascade was a greater problem.
“A second, more interesting aspect of the coagulation mechanism that has attracted the attention of the creationists relates to the time frame of evolution. Studies of the most primitive extant vertebrate, the jawless fish, have revealed a well‐developed coagulation cascade. In contrast, there is no ancestral form of the vertebrate clotting cascade in invertebrate animals (the serine protease cascade of the horseshoe crab evolved independently and is an example of convergent evolution). These observations suggest that the coagulation mechanism was assembled over a period of only 50 million years and then remained relatively unchanged for the next 450 million years.”
Aird, William C. "Hemostasis and irreducible complexity." Journal of Thrombosis and Haemostasis 1, no. 2 (2003): 227-230.
Aird allocates 50 million years to vertebrate evolution and states that vertebrates appeared 450 Ma. Possibly, he was not aware of the Chengjiang Lagerstatten, which was discovered at approximately that time. The 10,000 genes (wrong, 26 proteins) of the blood clotting mechanism and the coordination of so many proteins makes the sudden appearance of vertebrate characteristics in the Chengjiang Lagerstatten seem even more unnatural.
No, that’s just one failed case study of IC. The more famous one is the bacterial flagellum.
The actual number of proteins involved in vertebrate coagulation is about 26. If your claim were true, about half the human coding genome would be devoted to clotting. I admit I’m curious about where you got the preposterous number you cite.
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Thanks, I read 10,000 somewhere. My bad
I don’t have a problem with evolution of the bacterial flagellum because I think microbial life evolved from chemicals.
I only have vague recollection of reading about the process of clotting from long enough ago that even if I did remember the details, they would probably be quite out of date. What probably remains true, I’m sure is how complicated that deceptively simple sounding process actually is. Even with “just” 26 genes involved (thanks for keeping us straight about those numbers, @sfmatheson), I understand there is quite a lot of variation in size of genes themselves. There is undoubtedly much intricacy left to marvel over even in what scientists have come to understand. And that progress too is something I marvel over.
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I am not sure where I read it, but the 10,000 number possibly refers to the total number of unique vertebrate genes. I will do my best to summarize the following paper although I am not claiming that the 10,000 number is there. However, 10,000 is in the range of uniquely vertebrate genes or gene copies.
Prachumwat, Anuphap, and Wen-Hsiung Li. “Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes.” Genome research 18, no. 2 (2008): 221-232.
70% of vertebrate genes are found in invertebrate genomes with “standard homology search criteria. (VMCL)” An additional 6% are found with “relaxed search criteria.” An additional 2% are found in fungal and bacterial genomes. 22% cannot be found in nonvertebrate genomes (Vertebrate only or Vonly). Vonly genes are singletons while the majority of other genes belong to gene families. Vonly proteins evolve faster than VMCL proteins. There is discussion about family sizes and types that I do not understand (help), but the Vonly genes are different than the VMCL genes with respect to family sizes and types.
Table 1 in the paper states that the number of Vonly gene types shared by >= 2 vertebrate genomes is 2,881 and the number of Vonly gene types restricted to only a single vertebrate genome is 10,157. The number of Vonly gene copies shared by >= 2 vertebrate genomes is 24,068 and the number of Vonly gene copies found in only a single vertebrate genome is 11,375.
These are the potentially vertebrate-specific genes. They discuss (reasonably) annotation errors in the Discussion, and note that these genes are evolving faster than the ones that are not specific (presumably new) to the vertebrate lineages. The number is about 6200 genes and 4700 gene types, in humans. Table 2 is the relevant source.
This is not relevant to blood clotting. Perhaps more central to what I gather are your goals, the origins of these new genes are not well known but there are many plausible hypotheses, some discussed in the paper.
So this is for present day genomes? Are you trying to get at the difference is far too large and then when superimposing present the differences up on the time frames that you began this post with the the rate is much too fast and hence God did something?
Do you think that it is fair to compare human genome is to what vertebrates and invertebrates genomes would’ve look like 500 million years ago? Interesting stuff, but I’m not sure that your approach is anything more than playing around inside of error bats and uncertainties. Feel free to help clarify to be how this is not the case.
As Stephen correctly pointed out, the size of the genome, number of genes, and complexity of the animal are not part of the molecular clock calculations. I looked more carefully at the papers by Wray, Erwin, etc… and the molecular clock of the vertebrates is based on the observed rate of change of vertebrate genomes over the last 400 million years. Vertebrate genome rate of change is about half that of invertebrate genome rates of change. This is why molecular clocks based on vertebrate genomes predict an origin of bilaterian animals at about 1 Ga (billion years) while molecular clocks based on invertebrate genomes agree with the fossil record.
I made a mistake with the 10,000 genes. If I had thought about it, I wouldn’t have put down 10,000 genes as part of the blood clotting mechanism. Then, I tried to figure out why I put down 10,000 genes, and I realized that I probably looked at a reference to the total number of vertebrate genes that are unique and not found in invertebrates. Whether looking at human genes or lamprey genes, I think we are talking about thousands of genes that are unique and not found in invertebrates. This number would not be part of the rate of change of the genome calculation. Also, I am not concerned about the number or percentage of unique genes. My understanding is that many genes in amphioxus were adapted to different purposes in vertebrates.
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