James, Onsi, Stadler and Truman- comedy of errors-part 2
Hello everyone,we are covering James Tour's video titled - Evolution vs design
In last part , I covered on the topic signal network and how they were whining that such a complicated system of embryo formation in fruitfly couldn't have evolved naturally .
In second part , I am going to talk about their second point, TADs ( Topologically Associated Domains)
Here are the exact points regarding TADs (Topologically Associating Domains) they talk about
TADs refer to groupings of chromatin—the complex of DNA and protein—that are bunched together and closer in three-dimensional space,in compact shape.
Transcription factors need to find specific DNA sequences to regulate genes. TADs help solve this search problem by organizing the genome, preventing the "tangled mess" that would otherwise hinder the movement of biological machinery like RNA polymerase.
Research, such as the paper by Dota et al., suggests that "intersegmental jumping" across 3D-proximal segments within TADs significantly speeds up the search process for transcription factors compared to simple diffusion.
Optimal Compaction: Theoretical models suggest an optimal compaction parameter (gamma) for these domains, around 0.7. Empirical measurements of approximately 8,000 human TADs show that they align closely with this theoretical optimum, rather than being too collapsed or too open.
5)Evolutionary Dilemma: The panel noted that the formation of TADs requires specific code (a 19-nucleotide sequence), the CTCF protein, and cohesin rings driven by ATP hydrolysis. They argue that this system presents a challenge for undirected evolutionary theories because intermediate, less-optimized states might have been energetically costly or non-functional, offering no survival advantage until the system is nearly perfect. The speakers suggested that TADs are a hallmark of eukaryotic genomes and were likely a necessary evolutionary or design solution to manage the vastly larger genomes of eukaryotic cells.
My argument -
I found it strange. They are looking at complex TADs of mammals which require cohesin and ctcf proteins interaction. They said ( mainly Truman) that this system is irreducibly complex.
The things in actuality , are much different from what they are saying. Many eukaryotes lack the ctcf - cohesin based TADs. So it's reducible . Like nematodes completely deleted their ctcf gene ,they rely on different mechanism of tad formation. Only basal nematodes like Trichinella spiralis have ctcf.
Insects also lack cohesin- ctcf based TADs network as in higher vetebrates. Platyhelminthes also completely lack the ctcf gene ,like more derived nematodes. They are still surviving . Yeasts completely lacks TADs . Plants have TADs but not like that in higher vetebrates. Jellyfish and sponges also lack the vetebrates level cohesin -ctcf mediated TADs organisation.
They are shocked . Why? Bcoz how is it possible for TADs to spread throughout the genome ?
Well it's easy . Start from simple- cohesin is much older than ctcf. Ctcf gene evolved in common ancestor of bilateria. Over time it acquired mutations in its n terminal region ( front part) which acted as binding site for cohesin,hence helping in formation of TADs.
Ctcf binding sites in genome mainly exist in non coding regions of dna . In few exceptions,they can exist in coding regions. Initially in primitive genome only few such binding sites for ctcf protein could have existed. Then n terminal mutations in the gene made the affinity for this protein increase towards cohesin and form partial tad networks ( not complete) But the most important events in the evolution of so many binding sites for ctcf occured due to retrotransposons which carried ctcf binding sites by copy and paste mechanisms. Those organisms in which ctcf disrupted genes by copy and paste mechanisms were removed from the gene pool. Only those survived whose genes and regulatory elements weren't affected by this retrotranspositions. Also they spread by wgd events. Hence more cohesin ctcf interaction leading to more TADs formation.
Here are links of retrotransposition part
https://www.sciencedirect.com/science/article/pii/S0092867411015078
https://www.nature.com/articles/s41467-020-15520-5
Now creationist might ask ,how did not fully cohesin -ctcf tad genome could exist ? At one time in the past there weren't enough ctcf binding sites ,hence limited compaction of dna.
Nope ,other mechanisms of compaction of dna existed. It's just another extra mechanism that organisms benefitted from.
Finally , Truman says evolutionary novelty is a story . You require lots of energy ,dna ,proteins and finally a long time after over generations mutations fine tune a protein .Intermediate steps are detrimental.
This is laughable. Each step will be beneficial. If a gene gets duplicated,let's suppose ,how much energy is required to maintain it? Negligible. A huge amount of atp is required to maintain membrane transporters and other things. Am I correct ?
And James Tour as usual says that junk dna have functions
What do you all think of Truman ? Any more extra information on TADs ??
Btw ,can someone pls tell me that whether primitive systems require the same compaction parameters value as talked about here?
Waiting for all of your response.