While they introduce themselves at the start, I will also mention some of my personal interactions with the debaters:
A few years ago, I came in contact with Jackson Wheat and since then I have helped him with writing and fact-checking the scripts for his videos on his youtube channel.
Regarding Otangelo, he is a young earth creationist who (from my experience) suddenly popped up in internet communities which I often interact with. I found his blog “reason and science”, which he mentioned during his introduction, where he posts long threads. The bulk of his blog simply copy pasted paragraphs from other sources, supplemented with his commentary sprinkled in between. Very often, it is difficult to tell from which source the paragraph is copy pasted from. Sometimes it is even difficult to tell wether a paragraph is his own commentary or a copy pasted section. Sometimes the personal commentary text is in a different colour, but the delineation is not consistent. The blog is just a big mess, even just looking at the formatting alone.
Otangelo’s most used arguments are: 1) the appeal to personal incredulity and 2) argument from analogy. With the incredulity arguments, he mentions some biological complex process or structure, emphasising how amazingly complex it is as verbose as he possibly can, and then conclude that it just too complex for it to have evolved. Ergo, design is the only reasonable explanation. Regarding the argument from analogy, he will draw comparisons between biology and things that know are designed. E.g: DNA is a blue print. Sometimes he will just assert that these are not analogies… which is absurd. I als had a few interactions with him, often followed by deep disappointment. When I point out the fallaciousness of his arguments and that the conclusions simply don’t follow, he says things like:
OTANGELO: “incredulity is justified by the most basic logical principles. randomness does not select materials. intelligence does. you are unable to think even like a 10 year old.”
I guess if Otangelo is following his own advice to think like a 10 year old, that would explain a lot. In a recent interaction in a youtube live chat he asked me:
OTANGELO “how can you have synthesis of iron sulfur clusters, without the membrane import channels for iron and sulfur, and chelate of iron? and non-ribosomal peptide synthetase (NRPS)?”
I provided this paper [Spontaneous assembly of redox-active iron-sulfur clusters at low concentrations of cysteine | Nature Communications]. This paper shows that the Fe-clusters, which are vitally important for many fundamental enzymes that are involved in core metabolism, can be produced from inorganic Fe2+/Fe3+ and S2− in the presence of the amino acid cysteine in water at alkaline pH. I was rather astonished by Otangelo’s response.
OTANGELO “u believe everything when it says: scientists say ?
there are many different FE-Sulfur clusters with different compositions. Each protein has a specific one. So you believe in pseudo science, because its [sic] from nature magazine. Awesome
i am warranted to be skeptical towards just so stories, like in that "science"paper. Synthesis of iron sulfur clusters is VERY complex !!”
How incredulous can someone be? I don’t have to believe what the scientists say. The paper is open access and you can read the methods and results for yourself. He claims that he is “warranted to be skeptical”, so I asked him if he actually read the paper in question. The next question would be to ask what part of the paper he actually thinks is unsubstantiated. However, he responded as such:
OTANGELO “have you read it? Or did you just google it right now ?”
Since he simply firing the question back at me, a classic way to avoid the question. I think it is safe to say that Otangelo did not read the paper at all. The problem here is that Otangelo has an assumed conclusion - that Fe-clusters are just ooooh sooo complicated, they can’t possibly form without the complex proteins - and when a paper comes along that contradicts him, he simply dismisses it outright. This is not skepticism… this is wilful ignorance. This is further exemplified when he says the following:
OTANGELO “well, they talk about protocells, and protometabolism. The problem is, thats just made up stuff. Nobody knows that a protocell is supposed to be.”
But the paper makes it clear what protocells are and how they can form, all while providing citations to previous work:
JORDAN ET AL. 2021 “Previous experimental work shows that hydrothermal Fischer-Tropsch-type syntheses can also form long-chain 1-alkanols and fatty acids55, which spontaneously assemble into protocells under alkaline hydrothermal conditions56,57. Amino acid synthesis from pyruvate has also been demonstrated under similar conditions58. However, the polymerisation of amino acids and nucleotides in water remains elusive, suggesting that the earliest stages in the emergence of life might have taken place in a monomer world17. Thus, protocells formed from combinations of monomeric molecules such as fatty acids were arguably the earliest units of selection at the origin of life16,59,60.”
He also commits psychological projection, saying that I haven’t read the paper. That I just googled it on the spot and gave it to him without looking what the paper says. He said it again later (in a different live chat):
OTANGELO “and everything indicates that YOU did not read the paper that you claim you did read. You just quickly googled it, and then though; Gotch ya”
While I obviously can’t show that I did read the paper, I can show that I did not quickly googled it on the spot. I was in fact aware of this paper for over 2 months. I follow ‘NatureEcoEvo’ on twitter and they tweeted about the paper in November 2021 on “Iron sulfur clusters: the first metal cofactors?”. I retweeted this, and look who is responding to my retweet?? None other than Otangelo himself… If Otangelo read the article that I retweeted back in November, he would have known about the paper before I provided to him again to answer his question about Fe-clusters… and he would’ve known better than to flatly assert that I “just quickly googled the paper”. However, it is clear that Otangelo is not someone who carefully considers the positions of those who he disagrees with, nor is he above making baseless accusations just to get himself out of a difficult situation.
So that is enough about my personal interactions with him. My apologies for starting the thread like this… these interactions occurred while I was writing this, and I just had to include it.
Moving on. IMO, the debate was not something special. The conversation was cordial and polite, but before the debate I knew that the choice of topic was problematic. “Evolution vs. creationism”. That is so unspecific that the debate can become unfocused, and that is exactly what happened. Otangelo and Jackson prepared to talk about very different subjects. Also, while I have previously said a lot of negative things about Otangelo, it should be stated that he is rather good in having descent conversations and debates. That doesn’t mean his arguments are good… they are not. I won’t go over every argument he makes. Certainly not every argument that are included in his slides (many of which are not even mentioned verbally). Just the ones that stood out to me, and keeping this as brief as possible.
@ 7:00 Otangelo intends to disprove universal common ancestry and that evolution explains the origins of complex life forms. First he cites paper by Koonin from 2007 “The Biological Big Bang model for the major transitions in evolution” reading the abstract verbatim about the six major transitions for which Koonin thinks requires a “biological big bang” which is described as a rapid phase of evolution involving extensive horizontal gene transfer, and thus would differ with a simple tree-like evolutionary process. While I do think that horizontal gene transfer was and still is important in the evolution of single celled life, I don’t think that was a particularly relevant to things like the eukaryotic supergroups and especially not to the animal phyla of the Cambrian explosion. Koonin claims that the difficulty to resolve the relationships between the eukaryotic souper groups and the relationships between animal phyla hint do a biological big bang. However, we actually understand these relationships quite well, even better today. These don’t show evidence of excessive horizontal gene transfer. Furthermore, difficult to resolve phylogenetic relationships is not necessarily the result of explosive horizontal gene transfer. There can also be more “mundane” explanations such as incomplete lineage sorting that explains such situations. I also find him drawing the analogy to the ‘cosmological big bang’ rather far fetched to put it mildly, even regarding instances where horizontal gene transfer was likely prevalent. Koonin also seems to misunderstand punctuated equilibrium. For more, see Moran’s comments on Sandwalk:
Having said that, even taking this paper for granted, I don’t see any way how this can fit in a young earth creation model. Does Otangelo think that the eukaryotic supergroups and animal Phyla exchanged genes at some point in their phylogenetic history? Otangelo doesn’t even believe in them having a phylogenetic history. When responding to William Martin (one of the review commentators) Koonin also makes it clear that his hypothesis does not help ID proponents, and Koonin is rather prophetic about how ID proponents like Otangelo will abuse his work:
KOONIN 2007 “I changed “ready-made” to “abruptly”, to avoid any ID allusions and added clarifications but, beyond that, there is little I can do because this is an important sentence that accurately and clearly portrays a crucial and, to the very best of my understanding, real feature of evolutionary transitions. Will this be used by the ID camp? Perhaps – if they read that far into the paper. However, I am afraid that, if our goal as evolutionary biologists is to avoid providing any grist for the ID mill, we should simply claim that Darwin, “in principle”, solved all the problems of the origin of biological complexity in his eye story, and only minor details remain to be filled in. Actually, I think the position of some ultra-darwinists is pretty close to that. However, I believe that this is totally counter-productive and such a notion is outright false. And, the ID folks are clever in their own perverse way, they see through such false simplicity and seize on it. I think we (students of evolution) should openly admit that emergence of new levels of complexity is a complex problem and should try to work out solutions some of which could be distinctly non-orthodox; ID, however, does not happen to be a viable solution to any problem. I think this is my approach here and elsewhere.”
@ 12:13 Otangelo is dismissing all the paleontological evidence supporting evolution and common ancestry. On what basis you may ask? Because Michael Behe says so. No really, that’s it. Otangelo also says that Behe popularised the concept of irreducible complexity and interdependence in biology. I would say that the credit should go to H. J. Muller who came up with the exact same concept by a different name “interlocking complexity” 70 years ago, but reached the very opposite conclusion. That such systems are expected to evolve by a few simple steps: 1) a redundant part, 2) make it neccesary.
@ 14:17 Here he begins to talk about nitrogen fixation, which is one of the things I really wanted to get into. Otangelo says that cyanobacteria rely on other bacteria with complementary metabolisms. And he also says that without all these completing the nitrogen cycle, fixed nitrogen wouldn’t be available and life could not start. That is not accurate. While it is true that many other bacteria produce reduced nitrogen and make it available to other life, such as cyanobacteria, many cyanobacteria are able to fix nitrogen gas (N2) directly to ammonia themselves, without any other help. Also, ammonia can be produced without life, so it was available before life even existed.
@ 16:02 Otangelo shows a screenshot of the abstract of this paper telling us that “uncertainty remains about the origins of the earths’ early nitrogen cycle”. However, he has left out the part where it summarises the findings of this research, which says:
YANG ET AL. 2019 “Our data reveal a dominantly anaerobic marine nitrogen cycle in which ammonium-replete ferruginous waters underlay an ephemeral oxygen oasis. Driven by the emergence of oxygenic photosynthesis, increased primary productivity could have periodically strengthened export production, which allowed for the accumulation of ammonium in the water column during organic matter degradation. Restricted oxygen availability could have allowed the upwelling ammonium to reach the photic zone to provide ample nitrogen to fuel a prolific Late Archaean biosphere.”
Quote mining is not a good look Otangelo!
@ 16:29 Next Otangelo mentions Weiss et al. 2016 which conclude that LUCA possessed (among other things) nitrogenase. Otangelo claims that this conclusion was reached because:
OTANGELO “Nature magazine came up with a genius ad hoc idea. They simply claimed that nitrogenase, the enzyme in Cyanobacterias [sic], responsible for the chemical reaction that transforms nitrogen to ammonia was already extant in LUCA, the last universal common ancestor”
This is just flat out wrong. Firstly, cyanobacteria aren’t the only organisms that possess nitrogenases. Secondly, NO!! They didn’t “simply” make this claim as an “ad hoc” solution. They used statistical methodology to test which of the 286,514 protein clusters were likely present in LUCA. Other researchers have disagreed with this conclusion. I have read other papers that proposed that nitrogenase originated in Archaea, specifically methanogens, and later the nif operon from these spread around other lineages via horizontal gene transfer. Koirala & Brozel 2021, Mus et al. 2019, Boyd et al. 2011, Boyd et al. 2011 and Raymond et al. 2004.
Koirala & Brozel 2021
So there are legitimate disagreements to be had, but Otangelo expresses his disagreements by outright misrepresentation.
About nitrogenase, Otangelo is mostly right about his description. The nitrogenase enzyme fixes N2 to ammonia in the following reaction:
N2 + 8 H+ + 16 MgATP + 8 e− → 2 NH3 + H2 + 16 MgADP + 16 Pi
Since N2 contains a strong triple covalent bond, nitrogen fixation has a high metabolic cost, as you can that the hydrolysis of 16 ATP is required for reducing just one molecule of N2. The enzyme itself is composed of 2 main units.
Oldroyd & Dixon
- The reductase: A homo-dimeric complex which includes an 4Fe-2S cluster, encoded by NifH
- The nitrogenase: A hetero-tetradimeric complex, including 2 P-clusters between the a and b subunits, and two FeMoco clusters in the a subunit. Subunit a and b are encoded by NifD and NifK respectively.
Many other genes are also involved. Most importantly are those that encode for proteins involved in producing the FeMoco cluster. These are:
- NifB: a SAM-dependent protein, which adds a carbon atom to the 4Fe4S cluster to produce the NiB-co intermediate.
- NifE and NifN, together forming a hetero-tetradimeric complex that forms a scaffold for the ‘maturation’ of the cluster from NiB-co to VK cluster, and then finally FeMoco.
- The P-cluster is produced by reduction of 2 4Fe4S clusters by NifH.
Otangelo concludes on nitrogenase by questioning how this could evolve? All these genes/proteins and cofactors all have to be together, otherwise they have no use. He later makes the conclusion that since this is so mysterious, design is the only option. That good old appeal to ignorance again. Do you really need all these proteins and cofactors all together, unless they have no function on their own? Let’s see.
The minimal gene set for nitrogen fixation includes the aforementioned six Nif genes: HDK (catalysis) and ENB (FeMoco cofactor assembly). There are quite a few more gene associated in many diazotrophs (nitrogen eaters).
Vincente & Dean 2017
NifF and NifJ supply electrons. There are also other genes involved in cofactor assembly. NifS takes sulfur from cysteine and supplies it to NifU, which is a scaffold for the synthesis the 4Fe4S clusters (the starting point of FeMo-o and P cluster biosynthesis, as well as providing the 4Fe4S for the NifH reductase). NifQ and NifV supplies molybdenum and homocitrate respectively needed to mature NiB-co into MoFeco. NifX and NifY shuttle NiB-co (from NifB to NifEN) and FeMoco (from NifEN to nitrogenase NifDK) respectively. NifM and NifW functions to allow NifH to fold properly and acquire its 4Fe4S cluster. Transcription regulators NifA, NifL. Hu & Ribbe 2016
However, these don’t appear to be always necessary. NifF/J can be functionally substituted by other promiscuous reducing agents such as ferredoxin. The shuttle proteins NifX/Y can be simply be skipped by transferring the compounds directly from NifB-to-EN and from NifEN-to-DK. Furthermore, NifS/U, NifQ and NifV aren’t needed because what they provide can be accomplished by other means. Molybdenum can be incorporated directly. Homocitrate is also a product of lysine biosynthesis, and 4Fe4S cluster synthesis can be done by other genes, since 4Fe4S clusters function in many other systems. These ‘housekeeping’ genes that can substitute for these Nif genes are also often homologous, which indicates that these accessory Nif genes evolved by recruiting housekeeping genes and were specialised specifically for nitrogen fixation. Vicente & Dean 2017, Larrea-Alvarez & Purton 2021, Buren et al. 2020 and Li & Chen 2020. It is also interesting to note that these accessory nif genes are mostly present within (facultative) aerobic lineages, but absent in anaerobes. Which would indicate that the simpler system evolved first in anaerobes (consistent with the oxygen sensitivity of nitrogenase) and the accessory genes are correlated with the adaptation to aerobic metabolism. Mus et al. 2019 and Boyd et al. 2015.
But what about the indispensible genes? NifDKH (catalysis) and NifENB (MoFeco assembly)? Surely these proteins and their cofactors all need to be together, otherwise they would be useless? Well…
Vedalankar & Tripathy 2018
The NifDKH nitrogenase complex is related to other enzymes. Hu & Ribbe 2020. Particularly, Light-independent protochlorophyllide reductase (DPOR), which convert protochlorophyllide to chlorophyllide a. It is also homologous to the enzyme Chlorophyllide a reductase (COR) that catalyses the reaction that changes chlorophyllide a to bacteriochlorophyllide a (in anoxic phototrophic bacteria). The enzymes have the same basic structure; subunits corresponding to NifH, NifK, and NifD in nitrogenase are homologous to ChlL/BchL, ChlN/BchN, and ChlB/BchB in DPOR; and BchX, BchY and BchZ in COR respectively. Another curious similarity is that they are also similarly sensitive to oxygen. In oxygenic phototrophs, the DPOR enzyme was supplemented by a light dependent DOR (LDOR). In angiosperms, the DPOR has been lost entirely. Also note that these enzymes share FeS clusters, but DPOR and COR don’t have FeMoco or P-clusters. They only have 4Fe4S clusters in the corresponding place for the P-clusters, and nothing in the corresponding place for FeMoco, except that this is the substrate binding sites in DPOR and COR. Hence, these enzymes are simpler than nitrogenase (lacking 2 of these unique cofactors), and yet… somehow… they are still functional. But we can go even further.
Moser & Layer 2018
It turns out the subunits D and K, which form the hetero-tetradimer of nitrogenase, are homologous to each other. This is similar to our haemoglobin, which also a hetero-tetradimer. It consists of two subunits, 2 alpha and 2 beta subunits, which are also related by gene duplication and haemoglobin likely evolved from a homodimer (produced by the original protein before the duplication event) Pillai et al. 2020. So, a straightforward evolutionary scenario for nitrogenase (as well as DPOR and COR) is that the tetradimer similarly evolved from a homodimer. Indeed, there is yet another nitrogenase-like enzyme CfbC/D (full name to long to put here). Subunit C is homologous to NifH and D is homologous to both NifD and NifK. However, instead of forming a tetramer, the D subunit forms a homo-dimer. This enzyme is involved in the biosynthesis of coenzyme F430, which is similar to chlorophylls and precursors. F430 is essential for methanogens, the same organisms wherein nitrogenase might have originated. Ghebreamlak et al. 2020
Carcia et al. 2022
But what about the the FeMoco cofactor assembly proteins? NifE/N and NifB? Well, NifE and NifN are also homologs of NifD and NifK respectively. That is right. The enzyme that makes the cofactor is homologous to the enzyme that uses it to reduce nitrogen. This is why it is proposed that the common ancestor of NifD/K and NifE/N perhaps did both functions, or was enzymatically promiscuous. Even modern nitrogenases and NifEN enzymes are rather promiscuous, catalysing various different reactions, not just nitrogen reduction. North et al. 2020, Hu & Ribbe 2016. Lastly, NifB is part of the radical SAM enzyme superfamily, which are involve din various processes. NASA 2010. This is similarly true for NifH, which appears to be part of a very ancient protein super family. Lahiri et al. 2008, Lutkenhaus 2012 and Thakur et al. 2013.
In short, Nitrogenase is not all or nothing. As revealed by its various homologs, many components and simpler precursors can still be functional. Furthermore, the evolutionary origins is also indicated from these homologs, as well as its own structure.
(due to word limit, the thread is continued in next post)