Did We Have "Reptilian" Ancestors?

Science

(Bill Cole) #221

Should say not matching. I agree with your comment.


#222

What is or isn’t matching, and what is it being matched to? This is confusing.


(Blogging Graduate Student) #223

And when you do look at sequence data, for example the 3rd base in each codon, there is a clear signal of independent convergence, as expected.

EDIT: (to clarify in case the point was lost in the last few replies - I’m referring to the grouping of bats and whales by echolocation-related genes like Prestin).


#224

For the purposes of Ewert’s paper, Prestin wouldn’t even be considered since even humans have a Prestin gene. According to Homologene, even C. elegans has a Prestin gene. Ewert looked at the distribution of genes, not at their actual sequence.


(Bill Cole) #225

Real biology to me is molecular biologists trying to understand how cells, tissues and organs work. There are millions of experiments here utilizing the scientific method. The id/creationsits and evolutionists are playing a game of who can argue for the consensus ideology.


#226

Where do we find ID/creationists doing this research?

Evolutionists are doing actual research and publishing their work.


(Blogging Graduate Student) #227

Good point. Where does Ewert’s dependency graph group bats and whales together then?


(Bill Cole) #228

The quality of their work will surface over time. I will let you have the last word.


(Timothy Horton) #229

“The check is in the mail”
“I’m from the IRS and I’m here to help you”
“ID scientists will publish their positive evidence any day now, any day”

:smile:


(John Harshman) #230

Look at the diagram Bill posted:

Now think of an unrooted tree representing the 4 taxa in the figure. For convenience, consider an unrooted tree. There are 5 branches, and thus 5 patterns of gene presence/absence that would fit the tree perfectly, one change on one branch, either gain or loss. Together, those five patterns account for 18,199 of the genes in the diagram. There are 4 patterns that would not fit the tree, i.e. they would require changes on two branches. Together, these four patterns account for 221 of the genes in the diagram. (The 10,660 genes shared by all are not relevant.) Anyway, it should be clear to everyone that because 221 genes don’t fit the tree while only 18,199 do fit it, the tree must be wrong.


(Bill Cole) #231

The problem is there are 11000 plus genes here that common descent does not explain with this diagram. I understand that is not your claim as you admit common descent does not explain emergence of novelty. To explain the diversity of life you need to explain the emergence of novelty not just isolated similarities and differences between organisms.


(Mikkel R.) #232

Common descent does not explain the existence of genes, it only explains their distribution into nesting hiearchies.

To explain the diversity of life you need to explain the emergence of novelty not just isolated similarities and differences between organisms.

Yes, I agree. But there’s a difference between explaining all aspects of the diversity of life, and being able to infer that all known life shares common descent. Nobody is saying that common descent is itself the explanation for why different species have different attributes. We agree that it isn’t.

One can infer a common genalogical relationship despite the fact that the members might not share all their attributes. I am not identical to my siblings, each of us have obvious differences or novelties from each other. There is an explanation for why that is, but even if we didn’t know what that explanation was it wouldn’t mean we would be forced to conclude we don’t share common descent.

There are perfectly good explanations for taxonomically restricted genes however. They evolve from non-coding DNA, and then subsequently expand in that clade (mostly by duplication). I have given you plenty of references on that in the past. Less than 2 weeks ago, between Christmas and New year, I showed you examples of genes having evolved de novo from non coding DNA on TSZ.

So subsequently to the split of the mouse and human lineage for example, 2963 genes have evolved in the human lineage (almost all of these would be shared among all primates), and 2596 have evolved in the mouse lineage (most of which would be shared among rodents). And so on and so forth.
The reason the Zebrafish lineage seems to have so many unique genes is, as is explained in the paper, partly because the teleostei clade underwent whole genome duplication some time after they split from the rest of the species in the diagram. So however many genes had evovled in that clade following the split were effectively doubled when that whole genome duplication happened.

What can be immediately inferred is that if more species are included in the figure a clearer picture of gradual accumulation of genes over time would stand out. If we include more fish-species more closely related to zebrafish for example, the number of zebrafish-unique genes would decrease, and provide even more evidence for common descent by how they are distributed into nesting clades.


(John Harshman) #233

If you understand that, why is it a problem? If common descent doesn’t explain what it isn’t meant to explain, how is that an argument against common descent?


#234

In Fig 3 of this paper:

http://bio-complexity.org/ojs/index.php/main/article/download/BIO-C.2018.3/BIO-C.2018.3


#235

That is explained by mutation and selection, as we have noted before.


(Blogging Graduate Student) #236

That’s just a “postulated module” though, not based on any data as of yet.


#237

as in biology we can find many creatures with traits that can be found in other far lineages.


(Timothy Horton) #238

The traits caused by things such as HGT and convergent evolution only produce a tiny bit of noise on the objectively determined overwhelmingly strong branching nested hierarchical signal for common descent. Any tree you make from human-designed objects will be subjective and arbitrary because human designed articles don’t receive heritable traits from their “parents”. Every generation has traits which are strictly at the whim of the designer.


#239

Examples?


#240

the distribution of the alx3 gene for instance:

(https://www.researchgate.net/publication/51478159_Evolution_of_the_Alx_homeobox_gene_family_Parallel_retention_and_independent_loss_of_the_vertebrate_Alx3_gene)