Responding to "Motor Proteins Paradox!" by Finding Truth @Ahmed_AbdelSattar

Another day, another paradox.

Here Ahmed has found another topic he thinks poses paradoxes to evolution.

Of course Ahmed starts out by drawing tight comparisons between designed things and these motor proteins and the cytoskeleton. The first thing I would like to address is the commonly used comparisons between motor proteins and machines. ID/creationists often like to make this argument that these proteins are not just “like” motors, they ARE motors, and that is a sign of design. Not only that, even non-creationists often describe these as motors. However, it’s not just an analogy, it’s a highly flawed analogy. These proteins don’t work like motors at all. An example of push back against the common approach of viewing the cell and its processes as machines comes from Daniel Nicholson. He has published many papers where he goes into great detail. See here and here.

One of his basic points is that at the cellular scale, the physical conditions are drastically different compared to our scale and that of motors. This may seem obvious, but it means that proteins CANNOT possibly work in the way motors do. For example, the animation that is shown with the kinesin walking on the microtubulin pulling the cargo along with it. Ahmed says it’s walking like a little robot. It’s actually not. When we (or robots) walk the major forces that are at play are gravity and inertia with little friction. But at the cellular scale, the effect of friction dwarfs everything and water becomes highly viscous. Swimming at that scale is like swimming through molasses, or walking in a hurricane. At the scale of proteins, water molecules are like a never ending hail storm, constantly bombarding the proteins causing it to move about via Brownian motion. There is simply no way for a kinesin to “walk” like a bipedal robot. The way these proteins actually work is, instead of having a specified motion and fighting against stochastic forces, they make use of it. By consuming energy, the proteins bias motion towards a direction like a Brownian ratchet. This is fundamentally different to how machines or motors work. This might seem as nitpicking, but this puts a nail in the coffin to many arguments from analogy with machines that ID/creatoinists often use. The cell is not a machine.

Now, Ahmed has mentioned a lot of structures regarding the eukaryotic cytoskeleton and motor proteins. To give a complete list, these include:

  • Cytoskeleton: Actin (microfilaments), IF proteins (intermediate filaments) and Tubulin (microtubules)
  • Motor [Brownian Ratchet] Proteins: Kinesin, Dynein and Myosin

He also mentioned kinetochore involved in pulling apart the chromosomes and segregating them during cell division, which is a complex that include some of the aforementioned proteins.

Ahmed makes the argument that no reasonable person can believe that something so complicated can have evolved. Yes, the old argument from personal incredulity.

Evolution cannot explain [insert complex structure here] therefore design wins by default.

In any case, can evolution explain this? Ahmed is right that this system is ancestral to all eukaryotes. Some of them may have lost some of these proteins, but the common ancestor almost certainly had them. Today, it is widely accepted that eukaryotes originated by the endosymbiosis between bacteria and archeae. So if these cytoskeleton and motor proteins evolved, we would expect that the prokaryotes possesses proteins that are homologous to some or all of these. Ahmed says here that prokaryotes don’t have these proteins. Well…as it turns out…they actually do!

The proteins in question (along with many others) are called Eukaryotic signature proteins (ESPs), because they are involved in key eukaryotic processes and conserved among eukaryotes. Recently, there has been a lot of research on a specific group of Archaea called the “Asgard” (some subgroups are named after the Norse gods as well, not kidding). Although other Archaea also possesses some ESPs, these Asgardians specifically possesses a large portion of them, including homologs to Cytoskeletal proteins.

One Tubulin-like protein in prokaryotes is FtsZ, which functions in prokaryotic cytokineses by forming a “ring” [see image below] in the middle of the cell that causes the cell to divide. Recently, CetZ was discorved in Archaea that controls cell shape. So, not only are they similar with regard to protein structure, they are also similar in function to tubulin. For more on tubulin, see here.

Actin-like porkaryotic proteins include MreB, FtsA, ParM, MamK and Crenactin. MreB forms dynamical shapes, often assembling into spirals [see image below] and regulate cell shape (often found in rod shaped bacteria). ParM is part of the ParMCR systems that some plasmids use to partition themselves during cell division ensuring that each daughter cell inherits one copy. It’s basically chromosomal segregation, but for plasmids. As the name suggest, the ParMCR system is composed of three parts: An centromere-like binding site, a motor protein that is responsible for the segregation and an adaptor protein connecting the two. ParM is the motor protein. Anyone else got deja vu, or is it just me? The archaean Crenactin is (at least as far as I am aware of) the most similar to actin, forming almost identical assemblies.

both form parallel, double-stranded filaments with a similar helical arrangement, and the individual subunits in a crenactin filament interact like those in an actin filament.

Even profilins (proteins that regulate the actin cytoskeleton) are found in archaea. See more on actin here and here.

Regarding IFs of intermediate filaments, it’s actually important to note that IFs are actually only present animals. So they likely weren’t there at the origin of eukaryotes. There has been some comparisons made with the prokaryotic protein CreS, but that not very certain. CreS is also only known from one species, so if CreS is related to IFs, it might be an example of horizontal gene transfer. Sources here and here.


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Here below more images (from this source) of the tubulin-superfamily (top) and actin-superfamily (bottom). An eukaryotic representative protein and corresponding assembly is shown on the left on each image, which prokaryotic homologs on the right.

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So a lot of these prokaryotic proteins are involved in controlling cell shape, sometimes specifically causing the cell to split, and sometimes actively segregating DNA as well. It even turns out that the ESCRT complex that is vital to Membrane abscission (cleaving the cell membrane into seperate daughter cells) in eukaryotes is also found in Archaea. See here and here.

But what about the kinetochore? This complex is composed of different modules. For some of these, there are homologous proteins present in prokaryotes. For others, they show hallmarks of evolution by gene duplication from eukaryotic genes that had other functions (evidence of co-option).

Mosaic origin of the eukaryotic kinetochore. Overview of the eukaryotic and prokaryotic close(st) homologs of LECA kinetochore proteins, which play roles in a wide variety of cellular processes, signifying the mosaic origin of the eukaryotic kinetochore. Relevant eukaryotic and prokaryotic homologs (hexagons) of LECA kinetochore proteins are colored based on the presence of a common domain ( Bottom Left : overview of kinetochore parts), and projected onto the location(s) in the eukaryotic cell at which they operate ( SI Appendix , Table S1). The hexagons of homologs are lined with different colors indicate a LECA kinetochore protein with a nonkinetochore function (green), the closest homolog to a LECA kinetochore protein (blue), and other close homologs of LECA kinetochore proteins (black). In addition, distantly related homologs of TBP-like, histones, UBC/RWD, and HORMA domain-containing kinetochore proteins were already present in prokaryotes ( Top Right ). ( Bottom Left ) Overview of the different number and types of domains in the LECA kinetochore. The Mis12/NANO and Ska domains are kinetochore-specific and thus are not found in other systems. The dotted lines indicate a potential intrakinetochore duplication during eukaryogenesis leading to the formation of various heteromeric (sub)complexes within the kinetochore. ( Bottom Right ) summary of the evolutionary links between the kinetochore and selected prokaryotic/eukaryotic molecular systems.

See source.

About motor proteins, Myosin, Kinesin and Dynein. These are a bit more mysterious than the ones previously discussed, but that doesn’t mean we can’t tell anything from them. The first two are likely related to each other, both belonging to P-loop NTPases, an ancient protein class.

Myosin and kinesin are related to each other, and moreover, all are classified to the P-loop NTPases. Although the prototypic motor protein cannot be traced from their extant structures, it should be emphasized that a number of nonmotor proteins in their class, including translation elongation factors, helicases, proteasomes, are known to generate force. These proteins may be related to the conventional motor protein at the root of cellular evolution (Iyer, Leipe, Koonin, & Aravind, 2004; Kull, Vale, & Fletterick, 1998; Leipe, Wolf, Koonin, & Aravind, 2002; Vale & Milligan, 2000). The class II myosin that forms bipolar filaments emerged after the unconventional myosin had evolved as a transporter. Interaction of bipolar myosin II filaments and actin filaments enabled a new mode of motility; contraction. Contraction drives muscle force generation (Figure 1; type 10b) as well as contributing to amoeboid movement that is also dependent on the contraction of actin and myosin II underneath the cell membrane (Figure 1; type 10a) (Paluch & Raz, 2013; Wessels et al., 1988). Contraction also enabled efficient cytokinesis in cells by forming contractile rings (Uyeda & Nagasaki, 2004), aiding the development of multicellular organisms. In the similar way, the interactions of dynein with microtubules drive movements of eukaryotic flagella for swimming (Figure 1; type 12b) (Gibbons, 1963).
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For more, see this and this and this.

I must also mention that I often collaborate with Jackson Wheat with his videos by helping with his scripts. With the video on Cell cycles from 2 years ago, I added mentioning of some of these papers as well.

So regarding the list of paradoxes Ahmed gives at the end
#1 He says randomness or design. Evolution isn’t synonymous with randomness, so that is already a problem. Even if you say “evolution or design” then in order to argue that one is more reasonable to believe than the other, we must ask which one gives better explanations for the things being discussed. I have provide several papers discussing the evolutionary origins of these systems. So far Ahmed, nor any other ID/creationist, has given us any explanation for how any potential designer designed any of this. Even if you have refuted the evolutionary explanation, that won’t automatically give credence for design. Each explanation must stand on its own merits. You can’t just say that design wins by default. That would again be the old appeal to incredulity.
Evolution cannot explain [insert complex structure here] therefore design wins by default.
So number 1 isn’t a paradox, it’s a bad argument.

#2 Not a paradox. A question with an answer. See all of the above.

#3 Again, not a paradox. There are motor proteins in prokaryotes (homologous to eukaryotic cytoskeletal proteins). The eukaryotic specific motor proteins could have evolved during or just before the evolution of the first eukaryotes. And again, see all of the above for more.

.Fin.

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Fantastic voyage?

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This.

Those animations are grossly misleading on the biophysical level, but we can depend on creationists to pretend that cartoons are the evidence instead of the real evidence that shows them moving stochastically.

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There is a more realistic video, somewhere.

I just found this excellent lecture by Julie Theriot that points the same things out that I did and more.

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