Biological Information and Intelligent Design: Signature in the Ribosome

We have vastly different definitions of evidence, I guess. Cornelius referenced papers, yes, but he did nothing at all to address the evidence in them. If you disagree, why don't you offer an example?

Cornelius’s claim is that there is lots of evidence against the Universal Common Descent hypothesis. I agree with this claim. The papers he cited backed up the claim. If you go to the arguments that he linked I believe those are his arguments and the papers are references to those arguments. I only looked at one paper but it solidly supported his claim.

I apologize for the equivocation between evidence information and argument. I need a more careful choice of words.

Or, you could just roll your eyes and ignore benkirk when he goes off on a nitpicking spree. We all have to do it from time to time. :smile_cat:

Hi Bill, welcome to the Forum!

It’s difficult to go all “empirical” when you’re studying a series of events that occurred a few billion years ago. But there certainly are remarkable indications regarding the evolutionary origin of the first eukaryotic cell. See what I wrote earlier in this thread:

Evolutionary theory explains why certain types of organelles integrated in eukaryotic cells appear to have a common ancestor with bacteria (prokaryotic cells). If we discount “miraculous intervention”, there does not seem to be any other explanation for this correspondence than a common origin. Even if an appeal to miraculous intervention would be deemed palatable here, it would imply that God made things with the false appearance of a common origin. That does not fit with God’s character as revealed in the Scriptures.

One side note on assessing the scientific merit of evolutionary theory. I see you’re mostly asking questions about certain key transitions. Those questions are valid and worthwhile and researchers are breaking their heads on them as we speak. However, they do not make or break the current foundation of evolutionary theory. Elsewhere, I wrote the following:

[Evolutionary theory] is a powerful explanatory tool for understanding how present-day species emerged from past populations. It already integrates the findings of diverse fields such as paleontology and genetics in an elegant manner. The scientific merit of evolutionary theory is derived from its ability to do exactly that. It does not hinge on theories concerning the development of the first life-form (abiogenesis) [or other key transitions, which are] still largely beyond the reach of empirical research. - See more at: http://biologos.org/blogs/deborah-haarsma-the-presidents-notebook/light-matters-does-the-big-bang-have-a-big-problem#sthash.kkAMA6sQ.dpuf

Greetings,
Casper

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Hi Casper
Thank you for the kind note. I understand that universal common descent is an a priori assumption based on no other competing detailed explanation. The interesting claims that occurred in the discussion are between Cornelius and Joshua.

Joshua: There is a vast amount of evidence supporting common descent.
Cornelius: There is a vast amount of evidence against common descent.

I agree with both of them, which if true, leaves us with an interesting dilemma.

Should we continue with common descent as an a priori assumption or should we engage other hypothesis such as multiple origins of life?

Hi Christy
Thank you for your advise. I took Ben’s comments in the spirit of trying to push for honest and clear communication.

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[quote=“Billcole, post:61, topic:5974”]
Cornelius’s claim is that there is lots of evidence against the Universal Common Descent hypothesis. I agree with this claim. The papers he cited backed up the claim.[/quote]
Papers plural? Below, you say you only looked at one.

I wouldn’t describe it that way.

[quote]I only looked at one paper but it solidly supported his claim.
[/quote]You only looked at one paper? Which one?

And that is the spirit in which I offered them.

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I think that your understanding is incorrect.

One can posit multiple origins of life (or different replicating components) followed by horizontal transfer (or merger) and then common descent. This is a hypothesis of a coalescence period in the history of life. In any case, the Eukarya, Archaea and Bacteria exhibit a great deal of similar biology and so likely emerged after any “period of multiple origins”. I think they would be from late- or post-coalescence eras.

Hi Argon
Eukarya looks like a unique origin to me. Although I agree with you that there is similar biology, it carries with it significant complex origins.
-the spliceosome
-the nuclear pore complex
-chromosomes

It is not clear at all how the DNA of Archaea and Bacteria become the DNA of Eukarya. There are millions of nucleotides that need to get organized to make two large de novo protein complexes.

The idea that novel species DNA A arose from novel species DNA B may not be right.

Agreed that it’s not clear how the Eukarya emerged. Yet the basic biochemistry, metabolism and sequences/structures of most components are shared across all the kingdoms. The steps leading to the acquisition of the nucleus and formation of chromosomes remains unknown but the origins of many of the genes appear well shared outside the Eukarya. Convergence, rather than divergence from shared ancestry, is not a terribly parsimonious explanation for most cell components. The spliceosome appears to be ancestral in all eukaryotes but the other RNA-splicing types are shared among the bacteria.

About the generation of ‘de novo protein complexes’: I’m not sure the generation of de novo protein complexes would necessarily be unlikely over the course of eukaryotic emergence. We probably also shouldn’t discount the possibility of discovering structurally similar proteins in other domains that may have been recruited. The ‘signals’ indicative of common origin do decay over time.

Their model allows for all kinds of mutations to occur, but also includes a large (and unspecified) contribution to genetic diversity that does not come from mutations. I would expect that contribution, which should be a different frequencies than the contribution from mutations, to look different. But the entire frequency range of genetic variants looks like it’s been produced by the same processes.

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Since others are addressing the first eukaryotic cell, I am curious what your specific problems are with some of these other transitions. One of the defining features of a transitional species is that it is difficult to categorize with certainty because it straddles the boundaries of a group, with some characteristics of that group present and some lacking, or rudimentary.

So, for example:

…is a vertebrate so early that it is uncertain whether it should even be called a vertebrate. It clearly shows a step in evolution, right where you said you had never seen a reasonable explanation. Can you clarify your problem with this transition?

I’m even more puzzled as to what you find unconvincing about the evolution of multicellular organisms:

It seems a pretty straightforward proposition to me, that colonies of single-celled organisms (like stromatolites) become more and more interdependent on each other, until you end up with something which can no longer survive in a non-colonial form (like sponges). Very curious to hear what, specifically, is troubling to explain here, especially since this transition has occurred in separate lineages so many times.

The evolution of mammals is so extensively documented, with such a vast diversity of lineages, that I’m afraid I really couldn’t even begin to guess where to start to address any specific questions you might have about it, much less the obsessively-catalogued family tree of humanity itself. Please do let me know what further details are troubling you!

Nice to see you @billcole!

Yes @Cornelius_Hunter claims this all the time.

I’ve been at this at length with him in the past. He has yet to produce any actual evidence of this. I’ve ready his blog extensively and have yet to see any actual evidence against common descent. I think part of the reason he is so convinced is that he uses an entirely different type of thinking, logic, and methodology as we do in mainstream science. Using his idiosyncratic methodology it is not surprising he comes to different conclusions.

@vjtorley took @Cornelius_Hunter to task on his logic here Baker’s dozen: Thirteen questions for Dr. Hunter | Uncommon Descent, and he has yet to respond to these questions. In particular, @Cornelius_Hunter really needs to answer question #4 before any rational conversation is possible:

Do you accept that if hypothesis A readily explains an empirical fact F and hypothesis B does not, then F (taken by itself) constitutes scientific evidence for A over B? Or putting it another way, if a fact F is predicted by hypothesis A, and compatible with hypothesis B but not predicted by B, then do you agree that F constitutes scientific evidence for A over B? If not, why not?

In all cases by him and others I have seen, the “evidence” that they thinks counts against common descent only works this is way if we adopt an incorrect understanding of evolution. So, they are really just arguments against strawmen understandings of common descent. For example, the recognition horizontal gene transfer complicates the simplified “Tree of Life” is not the evidence against common descent that Hunter thinks it is: Darwin's God: The Evolutionary Tree Continues to Fall: Falsified Predictions, Backpedaling, HGTs and Serendipity Squared. Biology is just a much complicated than our simple models. We can explain somethings with a simple model, but we have to move more complicated models to explain other more things. And in some cases, we do not yet know the complexities necessary to explain what we see. This ignorance though, does not proof that it is impossible to have evolved, just that we have reached the limits of our current understanding.

Alongside these really flawed arguments is a resolute refusal to provide alternate explanations for the wide range of patterns we see that are explained by common descent, but not common design. If we are to reject common descent we need to (1) explain all the patterns explained by common descent AND (2) explain more than common descent can. Just pointing to something that is not fully explained by common descent (which is not even what is happening here) is not enough to reject common descent. We need a more powerful alternate theory.

I do grant that some patterns are explained by common design too (without contradicting common descent), however a larger number of patterns are only explained by common descent. For example, no known design principle explains why human/chimps have one tenth the differences than those between mice/rats. Why are we more similar to chimps than rats are to mice? Common descent explains this quantitatively, theoretically, and_experimentally_, but no design principle does. Likewise, why does synonymous divergence approximately equal intron substitution divergence, and are greater than nonsynonymous divergence? Why does this same pattern (synonymous vs. nonsynonymous, vs. intron) appear in variation and mutation rates too? Why does species divergence closely correlate with mutation rates across the genome? I could go on and on.

Common descent + neutral theory explains and predicts all these patterns and many many more with a solid quantitative framework. There is just so many different and independent patterns that are clearly modeled by neutral theory and common descent that it is impossible to even summarize them here. I could go on and on.

This gets to question #4 above. Common descent predicts so much that common design alone does not. This is certainly not an argument against design, but is a very strong argument for common descent. I’ve asked @Cornelius_Hunter and other anti-common-descent “theorists” to explain these patterns with design principles. There are no takers. I think the reason is obvious; there is no known design explanation for these patterns but common descent. This is why common descent is nearly universally accepted in biology.

There is no debate in mainstream science now, and one has to change the rules entirely (as does @Cornelius_Hunter) to make even a weak case against it.

@Billcole, if not common descent, what do you think explains these patterns?

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Case in point, none of this is evidence against common descent. It is just a laundry list of things that have happened. Some of these things we have some understanding of the evolutionary process behind it. Some parts we do not fully understanding. Human ignorance, however, is not disprove evolution or common descent. Sorry.

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Hi Joshua
Good to hear from you and thanks for your detailed thoughts. Our common ground is the belief that some common descent has occurred. The question is, is it universal. How solid is the claim that all life shares a common ancestor? This claim looks very unlikely to me.

Common descent does explain similarities between species well but does not explain the differences and that is the point CH is making. Especially when a new species has several de novo proteins. Where did these new complex DNA sequences come from? Mutations, HGT, gene duplication etc. When we see unique sequences none of these mechanisms look like the right answer. It is simply too hard to find function in the almost infinite world of DNA sequence space.

The critical area is how new DNA sequences are generated. The transitions I mentioned are areas where significant new sequences are required for new body plans or new protein complexes.

How can we explain these complex sequences appearing through neutral mutations that occur in isolated populations? The math simply does not work.

I think the evidence is pointing to multiple origins of life as an alternative hypothesis
to universal common descent, or multiple origins of life in combination with common descent.

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Hi Lynn
Thanks for reaching out.

I have expressed most of my concerns with these transitions in my answer to Dr Swamidass above.

Thanks for clarifying your concerns! It looks like you’ve hit on a rapidly developing area of scientific investigation for your questions. I wonder if you’re familiar with this article?

http://rstb.royalsocietypublishing.org/content/370/1678/20140332

To sum up, in the past ten years scientists have discovered that de novo genes are significantly more commonplace than previously thought, and working out the pathways by which they evolve (some examples are explored) is a fascinating current area of study.

I would be quite cautious of resting much weight on your assertion that “It is simply too hard to find function in the almost infinite world of DNA sequence space.” Is that just an assumption, or can you back it up?

Hi Lynn
Thanks for your thoughts.

The sequential space problem of the genome is a subject I have discussed extensively. How familiar are you with this topic? It would be helpful to get your views on this. I do believe that this problem is one of the reason for the meeting you cited to update the modern synthesis. A key question is, what are the change mechanisms that are responsible for the generation of de novo genes.

I’m learning as I go! I found the review article I cited very informative; specifically, sections five and six discuss at least two separate pathways for change mechanisms to develop de novo genes. It gets technical so I’m not sure I’d do it justice to summarize, but here’s a very rough, imprecise outline: sometimes a point mutation creates a new stop or start codon, and sometimes existing ‘regulatory’ DNA gets associated with genetic material that wasn’t previously expressed (‘junk’ DNA). New genes are typically expressed at low levels at first so that typically nothing too drastic happens to the organism until deleterious effects can be weeded out and inefficient proto-genes can be tinkered with/improved. A lot of these proto-genes just come and go without anything much happening in terms of phenotype.

I don’t believe I’ve seen anything about the sequential space problem of the genome. I’m falling asleep currently but will look into it tomorrow if you like!

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